Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold118
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1286304
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:190245 original size:52 final size:52
Alignment explanation
Indices: 190167--190294 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
190157 CGAAATATGA
*
190167 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
190219 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
190271 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
190295 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:190321 original size:13 final size:13
Alignment explanation
Indices: 190303--190327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190293 CAAAGATCAG
190303 TGTATCGATACAA
1 TGTATCGATACAA
190316 TGTATCGATACA
1 TGTATCGATACA
190328 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:190407 original size:13 final size:13
Alignment explanation
Indices: 190389--190413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190379 ACAAAAAATA
190389 TGTATCGATACAT
1 TGTATCGATACAT
190402 TGTATCGATACA
1 TGTATCGATACA
190414 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:190409 original size:32 final size:33
Alignment explanation
Indices: 190368--190433 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
190358 AGTAGCTTAA
190368 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
190400 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
190433 A
1 A
190434 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:191163 original size:20 final size:21
Alignment explanation
Indices: 191114--191168 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
191104 AAAAAGACAG
*
191114 AATGTATCGATACATTCATAC
1 AATGTATCGATACATTCATAA
* *
191135 AA-GTCTCGATACATTGA-AA
1 AATGTATCGATACATTCATAA
191154 AATGTATCGATACAT
1 AATGTATCGATACAT
191169 CTAGGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATTCATAA
Found at i:194351 original size:91 final size:91
Alignment explanation
Indices: 194208--194389 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
194198 AAATCTATTT
194208 GCAAGTATGCAAATGCTAATTGTACACATATTAATCCCCAATGGAGTAAATCTCAATCTTTTAAA
1 GCAAGTATGCAAATGCTAATTGTACACATATTAATCCCCAATGGAGTAAATCTCAATCTTTTAAA
194273 TCTTTTTCCCAAAAGTCCACACAAGC
66 TCTTTTTCCCAAAAGTCCACACAAGC
194299 GCAAGTATGCAAATGCTAATTGTACACATATTAATCCCCAATGGAGTAAATCTCAATCTTTTAAA
1 GCAAGTATGCAAATGCTAATTGTACACATATTAATCCCCAATGGAGTAAATCTCAATCTTTTAAA
*
194364 TCTTTTTCCCAAAAGTCCGCACAAGC
66 TCTTTTTCCCAAAAGTCCACACAAGC
194390 TAGTGGCACC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (91 bp):
GCAAGTATGCAAATGCTAATTGTACACATATTAATCCCCAATGGAGTAAATCTCAATCTTTTAAA
TCTTTTTCCCAAAAGTCCACACAAGC
Found at i:194550 original size:30 final size:30
Alignment explanation
Indices: 194511--194585 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
194501 GTAGAGTACC
* *
194511 TTTTCAAAGTCCATAGCTATGTGACACCTCA
1 TTTT-AAAGTCCACAGCTATATGACACCTCA
*
194542 TTTTAAAGTCCACAGCTCTATGACACCTCA
1 TTTTAAAGTCCACAGCTATATGACACCTCA
194572 TTTTAAAGTCCACA
1 TTTTAAAGTCCACA
194586 ACTCTGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 37 0.90
31 4 0.10
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.32
Consensus pattern (30 bp):
TTTTAAAGTCCACAGCTATATGACACCTCA
Found at i:194610 original size:30 final size:29
Alignment explanation
Indices: 194546--195097 Score: 321
Period size: 30 Copynumber: 18.5 Consensus size: 29
194536 ACCTCATTTT
* * *
194546 AAAGTCCACAGCTCTATGACACCTCATT-TT
1 AAAGTCCACAACTCTATGGCACC-C-TTCTC
* *
194576 AAAGTCCACAACTCTGTGGTACCTCTTCTC
1 AAAGTCCACAACTCTATGGCACC-CTTCTC
** * * * *
194606 AAAGTTTAACACCCCTAGTAGAGTA-CCTTTTC
1 AAAG-TCCACAACTCTA-T-G-GCACCCTTCTC
* * * *
194638 AAAGTCCATAAATCTGTGGTACCTCTTCTC
1 AAAGTCCACAACTCTATGGCACC-CTTCTC
*
194668 AAAGTCCACAACTC-ATGGCACCACTTTTC
1 AAAGTCCACAACTCTATGGCACC-CTTCTC
194697 AAAAGTCCACAACT-TAGTGGCA-CCTTCTC
1 -AAAGTCCACAACTCTA-TGGCACCCTTCTC
* ** * *
194726 AAAGTCCACAACTCAATGAAACCCCTTTTT
1 AAAGTCCACAACTCTATGGCA-CCCTTCTC
** * * *
194756 AAAGTCCATGACTCTGTAGCACCCTTTCTT
1 AAAGTCCACAACTCTATGGCACCC-TTCTC
* * * *
194786 AAATTCTACAACTCTTTGGCACCCCTTCTA
1 AAAGTCCACAACTCTATGGCA-CCCTTCTC
* * * *
194816 AAAGTCCATAACT-TCGTGGCATCCCTCCTT
1 AAAGTCCACAACTCT-ATGGCA-CCCTTCTC
* * **
194846 AAAGTCCATAACT-TAATGGTACATTTTCTC
1 AAAGTCCACAACTCT-ATGGCAC-CCTTCTC
* *
194876 AAAGTCCACGACTCAATGGCACCCTTTCTC
1 AAAGTCCACAACTCTATGGCACCC-TTCTC
*
194906 AAAGTCCACAACT-TAGTGGCACCCCTTTTC
1 AAAGTCCACAACTCTA-TGGCA-CCCTTCTC
* * * * *
194936 AAAGCCCATAACTCAATGGCACCCTTTTT
1 AAAGTCCACAACTCTATGGCACCCTTCTC
* * *
194965 AAAATCCACGACTCAATGGCACCCTTCTC
1 AAAGTCCACAACTCTATGGCACCCTTCTC
*
194994 AAAGTCCACAACTCTATGGCACCTCTTCTT
1 AAAGTCCACAACTCTATGGCACC-CTTCTC
* *
195024 AAAGTCTATAACTCTATGGCACCCTTTCTC
1 AAAGTCCACAACTCTATGGCACCC-TTCTC
* *
195054 AAAGTCCATAACT-TCATGGCACCCCTTTTC
1 AAAGTCCACAACTCT-ATGGCA-CCCTTCTC
*
195084 AAAGTCTACAACTC
1 AAAGTCCACAACTC
195098 AGTGGCATCC
Statistics
Matches: 405, Mismatches: 90, Indels: 53
0.74 0.16 0.10
Matches are distributed among these distances:
28 19 0.05
29 79 0.20
30 265 0.65
31 27 0.07
32 10 0.02
33 2 0.00
34 3 0.01
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (29 bp):
AAAGTCCACAACTCTATGGCACCCTTCTC
Found at i:194654 original size:62 final size:62
Alignment explanation
Indices: 194488--194672 Score: 191
Period size: 62 Copynumber: 3.0 Consensus size: 62
194478 CCCCAAGAAA
* * ** *
194488 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAGCTATGTGACACCTCATT-TTAAAG
1 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAACTCTGTGGTACCTC-TTCTCAAAG
** * * * * *
194550 -TCCACAGCTCTA-T-GA-CACCTCATTTTAAAGTCCACAACTCTGTGGTACCTCTTCTCAAAG
1 TTTAACACCCCTAGTAGAGTACCT--TTTCAAAGTCCATAACTCTGTGGTACCTCTTCTCAAAG
*
194610 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAAATCTGTGGTACCTCTTCTCAAAG
1 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAACTCTGTGGTACCTCTTCTCAAAG
194672 T
1 T
194673 CCACAACTCA
Statistics
Matches: 96, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
58 4 0.04
59 4 0.04
60 29 0.30
61 16 0.17
62 37 0.39
63 2 0.02
64 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (62 bp):
TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAACTCTGTGGTACCTCTTCTCAAAG
Found at i:194705 original size:122 final size:120
Alignment explanation
Indices: 194488--194730 Score: 314
Period size: 122 Copynumber: 2.0 Consensus size: 120
194478 CCCCAAGAAA
** *
194488 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAGCTATGTGACACCTCATTTTAAAGTCC
1 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAAATATGTGACACCTCATTTCAAAGTCC
* * *
194553 ACAGCTCTATGACACCTCATTTTAAAGTCCACAACTCT-GTGGTACCTCTTCTCAAAG
66 ACAACTCTATGACACCACATTTTAAAGTCCACAACT-TAGTGGCA-C-CTTCTCAAAG
* **
194610 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAAATCTGTGGTACCTC-TTCTCAAAGTC
1 TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAAATATGTGACACCTCATT-TCAAAGTC
*
194674 CACAACTC-ATGGCACCAC-TTTTCAAAAGTCCACAACTTAGTGGCACCTTCTCAAAG
65 CACAACTCTATGACACCACATTTT--AAAGTCCACAACTTAGTGGCACCTTCTCAAAG
194730 T
1 T
194731 CCACAACTCA
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
120 15 0.14
121 12 0.11
122 80 0.75
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (120 bp):
TTTAACACCCCTAGTAGAGTACCTTTTCAAAGTCCATAAATATGTGACACCTCATTTCAAAGTCC
ACAACTCTATGACACCACATTTTAAAGTCCACAACTTAGTGGCACCTTCTCAAAG
Found at i:194811 original size:60 final size:59
Alignment explanation
Indices: 194509--195138 Score: 373
Period size: 60 Copynumber: 10.6 Consensus size: 59
194499 TAGTAGAGTA
* * * * * *
194509 CCTTTTCAAAGTCCATAGCTATGTGACACCTCATT-TTAAAGTCCACAGCTCTATGACAC
1 CCTTTTCAAAGTCCATAACTCTGTGGCACC-CTTTCTTAAAGTCCACAACTCTATGGCAC
* * * ** * * *
194568 CTCATTTT-AAAGTCCACAACTCTGTGGTA-CCTCTTCTCAAAGTTTAACACCCCTAGTAGAGTA
1 C-C-TTTTCAAAGTCCATAACTCTGTGGCACCCT-TTCTTAAAG-TCCACAACTCTA-T-G-GCA
194631 -
59 C
* * *
194631 CCTTTTCAAAGTCCATAAATCTGTGGTA-CCTCTTCTCAAAGTCCACAACTC-ATGGCAC
1 CCTTTTCAAAGTCCATAACTCTGTGGCACCCT-TTCTTAAAGTCCACAACTCTATGGCAC
* * * **
194689 CACTTTTCAAAAGTCCACAACT-TAGTGGCA-CC-TTCTCAAAGTCCACAACTCAATGAAACC
1 C-CTTTTC-AAAGTCCATAACTCT-GTGGCACCCTTTCTTAAAGTCCACAACTCTATGGCA-C
* * * * * *
194749 CCTTTTTAAAGTCCATGACTCTGTAGCACCCTTTCTTAAATTCTACAACTCTTTGGCACC
1 CCTTTTCAAAGTCCATAACTCTGTGGCACCCTTTCTTAAAGTCCACAACTCTATGGCA-C
* * * * *
194809 CCTTCTAAAAGTCCATAACT-TCGTGGCATCCC-TCCTTAAAGTCCATAACT-TAATGGTAC
1 CCTTTTCAAAGTCCATAACTCT-GTGGCA-CCCTTTCTTAAAGTCCACAACTCT-ATGGCAC
** ** ** *
194868 ATTTTCTCAAAGTCCACGACTCAATGGCACCCTTTCTCAAAGTCCACAACT-TAGTGGCACC
1 CCTTT-TCAAAGTCCATAACTCTGTGGCACCCTTTCTTAAAGTCCACAACTCTA-TGGCA-C
* ** * * *
194929 CCTTTTCAAAGCCCATAACTCAATGGCACCCTTT-TTAAAATCCACGACTCAATGGCAC
1 CCTTTTCAAAGTCCATAACTCTGTGGCACCCTTTCTTAAAGTCCACAACTCTATGGCAC
* * * * *
194987 CCTTCTCAAAGTCCACAACTCTATGGCA-CCTCTTCTTAAAGTCTATAACTCTATGGCAC
1 CCTTTTCAAAGTCCATAACTCTGTGGCACCCT-TTCTTAAAGTCCACAACTCTATGGCAC
* * *
195046 CCTTTCTCAAAGTCCATAACT-TCATGGCACCCCTTT-TCAAAGTCTACAACTC-AGTGGCATC
1 CCTTT-TCAAAGTCCATAACTCT-GTGGCA-CCCTTTCTTAAAGTCCACAACTCTA-TGGCA-C
* * *
195107 CATTTT-AAAGTCCGTGACTC-GTGGCACCCTTT
1 CCTTTTCAAAGTCCATAACTCTGTGGCACCCTTT
195139 TCAAAATCCC
Statistics
Matches: 451, Mismatches: 84, Indels: 74
0.74 0.14 0.12
Matches are distributed among these distances:
57 11 0.02
58 70 0.16
59 86 0.19
60 208 0.46
61 36 0.08
62 37 0.08
63 2 0.00
64 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.30
Consensus pattern (59 bp):
CCTTTTCAAAGTCCATAACTCTGTGGCACCCTTTCTTAAAGTCCACAACTCTATGGCAC
Found at i:194912 original size:208 final size:207
Alignment explanation
Indices: 194636--195119 Score: 536
Period size: 208 Copynumber: 2.3 Consensus size: 207
194626 GAGTACCTTT
* * *
194636 TCAAAGTCCATAAATCT-GTGGTACCTCTTCTCAAAGTCCACAACTCATGGCACCACTTTTCAAA
1 TCAAAGTCCATAACT-TAATGGTACATCTTCTCAAAGTCCACAACTCATGGCACCACTTTTCAAA
* *
194700 AGTCCACAACTTAGTGGCA-CCTTCTCAAAGTCCACAACTCAATGAAACCCCTTTTTAAAGTCCA
65 AGTCCACAACTTAGTGGCACCCTTCTCAAAGCCCACAACTCAATGAAA-CCCTTTTTAAAATCCA
* ** * * * *
194764 TGACTCTGTAGCACCCTTTCTTAAATTCTACAACTCTTTGGCACCCCTTCTAAAAGTCCATAACT
129 CGACTCAATAGCACCC-TTCTCAAAGTCCACAACTCTATGGCACCCCTTCTAAAAGTCCATAACT
*
194829 -TCGTGGCATCCC-TCC
193 CT-ATGGCA-CCCTTCC
* * *
194844 TTAAAGTCCATAACTTAATGGTACATTTTCTCAAAGTCCACGACTCAATGGCACC-CTTTCTC-A
1 TCAAAGTCCATAACTTAATGGTACATCTTCTCAAAGTCCACAACTC-ATGGCACCACTTT-TCAA
* * **
194907 AAGTCCACAACTTAGTGGCACCCCTTTTCAAAGCCCATAACTCAATGGCACCCTTTTTAAAATCC
64 AAGTCCACAACTTAGTGGCA-CCCTTCTCAAAGCCCACAACTCAATGAAACCCTTTTTAAAATCC
* * * *
194972 ACGACTCAATGGCACCCTTCTCAAAGTCCACAACTCTATGGCACCTCTTCTTAAAGTCTATAACT
128 ACGACTCAATAGCACCCTTCTCAAAGTCCACAACTCTATGGCACCCCTTCTAAAAGTCCATAACT
*
195037 CTATGGCACCCTTTC
193 CTATGGCACCCTTCC
* * ** * *
195052 TCAAAGTCCATAACTTCATGGCACCCCTTTTCAAAGTCTACAACTCAGTGGCATCCA-TTTT--A
1 TCAAAGTCCATAACTTAATGGTACATCTTCTCAAAGTCCACAACTCA-TGGCA-CCACTTTTCAA
195114 AAGTCC
64 AAGTCC
195120 GTGACTCGTG
Statistics
Matches: 232, Mismatches: 34, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
207 12 0.05
208 154 0.66
209 43 0.19
210 23 0.10
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (207 bp):
TCAAAGTCCATAACTTAATGGTACATCTTCTCAAAGTCCACAACTCATGGCACCACTTTTCAAAA
GTCCACAACTTAGTGGCACCCTTCTCAAAGCCCACAACTCAATGAAACCCTTTTTAAAATCCACG
ACTCAATAGCACCCTTCTCAAAGTCCACAACTCTATGGCACCCCTTCTAAAAGTCCATAACTCTA
TGGCACCCTTCC
Found at i:195056 original size:148 final size:148
Alignment explanation
Indices: 194886--195152 Score: 376
Period size: 148 Copynumber: 1.8 Consensus size: 148
194876 AAAGTCCACG
*
194886 ACTCAATGGCACCCTTTCTCAAAGTCCACAACTT-AGTGGCACCCCTTTTCAAAGCCCATAACTC
1 ACTCAATGGCACCCTTTCTCAAAGTCCACAACTTCA-TGGCACCCCTTTTCAAAGCCCACAACTC
* *
194950 AATGGCACCCTTTTTAAAATCCACGACTCAATGGCACCCTTCTCAAAGT-CCACAACTCTATGGC
65 AATGGCACCCATTTTAAAATCCACGACTC-ATGGCACCCTTCTCAAAATCCCACAACTCTATGGC
195014 ACCTCTTCTTAAAGTCTATA
129 ACCTCTTCTTAAAGTCTATA
* * * *
195034 ACTCTATGGCACCCTTTCTCAAAGTCCATAACTTCATGGCACCCCTTTTCAAAGTCTACAACTCA
1 ACTCAATGGCACCCTTTCTCAAAGTCCACAACTTCATGGCACCCCTTTTCAAAGCCCACAACTCA
* * * ** * *
195099 GTGGCATCCATTTTAAAGTCCGTGACTCGTGGCACCCTTTTCAAAATCCCACAA
66 ATGGCACCCATTTTAAAATCCACGACTCATGGCACCCTTCTCAAAATCCCACAA
195153 AAGTTAGTGA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
147 16 0.16
148 86 0.83
149 1 0.01
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28
Consensus pattern (148 bp):
ACTCAATGGCACCCTTTCTCAAAGTCCACAACTTCATGGCACCCCTTTTCAAAGCCCACAACTCA
ATGGCACCCATTTTAAAATCCACGACTCATGGCACCCTTCTCAAAATCCCACAACTCTATGGCAC
CTCTTCTTAAAGTCTATA
Found at i:195104 original size:30 final size:29
Alignment explanation
Indices: 194631--195152 Score: 335
Period size: 30 Copynumber: 17.6 Consensus size: 29
194621 TAGTAGAGTA
* * * *
194631 CCTTTTCAAAGTCCATAAATCTGTGGTAC
1 CCTTTTCAAAGTCCACAACTCAGTGGCAC
*
194660 CTCTTCTCAAAGTCCACAACTCA-TGGCAC
1 C-CTTTTCAAAGTCCACAACTCAGTGGCAC
*
194689 CACTTTTCAAAAGTCCACAACTTAGTGGCA-
1 C-CTTTTC-AAAGTCCACAACTCAGTGGCAC
* * **
194719 CCTTCTCAAAGTCCACAACTCAATGAAACC
1 CCTTTTCAAAGTCCACAACTCAGTGGCA-C
* ** * *
194749 CCTTTTTAAAGTCCATGACTCTGTAGCAC
1 CCTTTTCAAAGTCCACAACTCAGTGGCAC
* * * **
194778 CCTTTCTTAAATTCTACAACTCTTTGGCACC
1 CCTTT-TCAAAGTCCACAACTCAGTGGCA-C
* * *
194809 CCTTCTAAAAGTCCATAACTTC-GTGGCATC
1 CCTTTTCAAAGTCCACAAC-TCAGTGGCA-C
* * * * *
194839 CCTCCTT-AAAGTCCATAACTTAATGGTAC
1 CCT-TTTCAAAGTCCACAACTCAGTGGCAC
** * *
194868 ATTTTCTCAAAGTCCACGACTCAATGGCAC
1 CCTTT-TCAAAGTCCACAACTCAGTGGCAC
*
194898 CCTTTCTCAAAGTCCACAACTTAGTGGCACC
1 CCTTT-TCAAAGTCCACAACTCAGTGGCA-C
* * *
194929 CCTTTTCAAAGCCCATAACTCAATGGCAC
1 CCTTTTCAAAGTCCACAACTCAGTGGCAC
* * * *
194958 CCTTTTTAAAATCCACGACTCAATGGCAC
1 CCTTTTCAAAGTCCACAACTCAGTGGCAC
*
194987 CCTTCTCAAAGTCCACAACTCTA-TGGCAC
1 CCTTTTCAAAGTCCACAACTC-AGTGGCAC
* *
195016 CTCTTCTT-AAAGTCTATAACTCTA-TGGCAC
1 C-CTT-TTCAAAGTCCACAACTC-AGTGGCAC
*
195046 CCTTTCTCAAAGTCCATAACTTCA-TGGCACC
1 CCTTT-TCAAAGTCCACAAC-TCAGTGGCA-C
*
195077 CCTTTTCAAAGTCTACAACTCAGTGGCATC
1 CCTTTTCAAAGTCCACAACTCAGTGGCA-C
* ***
195107 CATTTT-AAAGTCCGTGACTC-GTGGCAC
1 CCTTTTCAAAGTCCACAACTCAGTGGCAC
*
195134 CCTTTTCAAAATCCCACAA
1 CCTTTTCAAAGT-CCACAA
195153 AAGTTAGTGA
Statistics
Matches: 388, Mismatches: 82, Indels: 46
0.75 0.16 0.09
Matches are distributed among these distances:
27 6 0.02
28 29 0.07
29 96 0.25
30 229 0.59
31 28 0.07
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.29
Consensus pattern (29 bp):
CCTTTTCAAAGTCCACAACTCAGTGGCAC
Found at i:195512 original size:52 final size:52
Alignment explanation
Indices: 195246--196056 Score: 292
Period size: 52 Copynumber: 15.5 Consensus size: 52
195236 CCTAAAGTCA
* * ** * * * *
195246 CTGGCCTTGAATTAGCATATTAGCA-CCTTTATTTTCTTCAAGTCTAATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCC-TTATCATCTTTAAATCCAATGTCG
** * *** * * * * *
195298 CTTACCTTGAATCAGTATATCAACATCCTTGTCATTTTTAAGTCCAATATCA
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAATCCAATGTCG
* * * * * * * * * *
195350 CTAGCCTTGAATTAGCAGATTAGAACCCTTACCATC-TTAAAGCCCAAAGTCA
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAA-TCCAATGTCG
* * * * * * *
195402 CTAGCCTTGGATC-CCTATATTGGCATCTTTATTATC-TTAAAGT-TAGATATC-
1 CTGGCCTTGAATCAGC-ATATTGGCATCCTTATCATCTTTAAA-TCCA-ATGTCG
* * * *
195453 CTGGCCTTGAATCAGCGTATTAGCATCCTTGTCATCTTTAAATCCATTGTCG
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAATCCAATGTCG
* * *
195505 CTGGCCTTGAATTAGCATATTGGCACCCTTATCATC-TTAAAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAA-TCCAATGTCG
* * * * * * * * **
195557 TTGGCCTTAAATCAGCATATTGGCA-CCTTTATTATCTTTTAGTTCGATATTA
1 CTGGCCTTGAATCAGCATATTGGCATCC-TTATCATCTTTAAATCCAATGTCG
* *
195609 CTGGCCTTGAATCAGCATATTGGCATCCTTACCATCTTTAAATCCAATGTCC
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAATCCAATGTCG
* * * *
195661 CTGGCCTTGAATCAGCACATTGGCA--CTTATCAAAACCTTATTTCCAAAGCCTAATGTCA
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATC---A---TCTTT--AAATCC-AATGTCG
* * * *
195720 CTGGCCTTGAATCAGCACATTGGCACTCTCGTTATC-TC---AAAGTCCGATATTG
1 CTGGCCTTGAATCAGCATATTGGCA-TC-C-TTATCATCTTTAAA-TCCAATGTCG
* * * ** * * *
195772 CTGGCCTCGAATCAACATACTATCA-CCTTTATTATCTTTAACTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCATCC-TTATCATCTTTAAATCCAATGTCG
* * * * * * * * *
195824 CTAGCCTTGAATTAGTATATTGGCATCTTTGTCATCTTTAACTCTAACGTTG
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAATCCAATGTCG
* * * * * * **
195876 CTTGCCTTGAATCAACACATTGGCACCCTTATCATC-TTAAAGTTCAATATTA
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAA-TCCAATGTCG
* * ** *** * * *
195928 CCGACCTTGAATCAATATACAAGCA-CCTTTATTC-TCTTTAAATCCGATATCA
1 CTGGCCTTGAATCAGCATATTGGCATCC-TTA-TCATCTTTAAATCCAATGTCG
* * * * * * *
195980 CTAGCTTTGAATCAACATATTGGCACCCTTA-CTATCTTGAAGTCCAATGTCA
1 CTGGCCTTGAATCAGCATATTGGCATCCTTATC-ATCTTTAAATCCAATGTCG
* * *
196032 CTGGCTTTGAATTAGCACATTGGCA
1 CTGGCCTTGAATCAGCATATTGGCA
196057 CTTGTCAAAA
Statistics
Matches: 560, Mismatches: 160, Indels: 78
0.70 0.20 0.10
Matches are distributed among these distances:
49 5 0.01
50 9 0.02
51 49 0.09
52 428 0.76
53 22 0.04
56 4 0.01
57 1 0.00
58 5 0.01
59 31 0.06
63 1 0.00
64 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (52 bp):
CTGGCCTTGAATCAGCATATTGGCATCCTTATCATCTTTAAATCCAATGTCG
Found at i:195516 original size:155 final size:155
Alignment explanation
Indices: 195243--195677 Score: 444
Period size: 155 Copynumber: 2.8 Consensus size: 155
195233 AAGCCTAAAG
* * * * * * * **
195243 TCACTGGCCTTGAATTAGCATATTAGCACCTTTATTTTCTTCAAGTCTA-ATATCGCTTACCTTG
1 TCACTAGCCTTAAATCACCATATTGGCACCTTTATTATCTTAAAGT-TAGATATC-CTGGCCTTG
* * * * * * *
195307 AATCAGTATATCAACATCCTTGTCATTTTTAAGTCCAATATCACTAGCCTTGAATTAGCAGATTA
64 AATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAATGTCACTGGCCTTGAATTAGCAGATTA
195372 GAACCCTTACCATCTTAAAGCCCAA-A
129 GAACCCTTACCATCTTAAAGCCCAATA
** *
195398 GTCACTAGCCTTGGATC-CCTATATTGGCATCTTTATTATCTTAAAGTTAGATATCCTGGCCTTG
1 -TCACTAGCCTTAAATCACC-ATATTGGCACCTTTATTATCTTAAAGTTAGATATCCTGGCCTTG
* * * * *
195462 AATCAGCGTATTAGCATCCTTGTCATCTTTAAATCCATTGTCGCTGGCCTTGAATTAGCATATTG
64 AATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAATGTCACTGGCCTTGAATTAGCAGATTA
* * *
195527 GCACCCTTATCATCTTAAAGTCCAATA
129 GAACCCTTACCATCTTAAAGCCCAATA
** * * ** * *
195554 TCGTTGGCCTTAAATCAGCATATTGGCACCTTTATTATCTTTTAGTTCGATATTACTGGCCTTGA
1 TCACTAGCCTTAAATCACCATATTGGCACCTTTATTATCTTAAAGTTAGATA-TCCTGGCCTTGA
* ** * *
195619 ATCAGCATATTGGCATCCTTACCATCTTTAAATCCAATGTCCCTGGCCTTGAATCAGCA
65 ATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAATGTCACTGGCCTTGAATTAGCA
195678 CATTGGCACT
Statistics
Matches: 231, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
155 125 0.54
156 106 0.46
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (155 bp):
TCACTAGCCTTAAATCACCATATTGGCACCTTTATTATCTTAAAGTTAGATATCCTGGCCTTGAA
TCAGCATATTAGCATCCTTGTCATCTTTAAATCCAATGTCACTGGCCTTGAATTAGCAGATTAGA
ACCCTTACCATCTTAAAGCCCAATA
Found at i:195801 original size:215 final size:215
Alignment explanation
Indices: 195500--195901 Score: 480
Period size: 215 Copynumber: 1.9 Consensus size: 215
195490 TTAAATCCAT
* * * * * * *
195500 TGTCGCTGGCCTTGAATTAGCATATTGGCACCCTTATCATCTTAAAGTCCAATATCGTTGGCCTT
1 TGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATCGCTGGCCTC
* * * * * * * * *
195565 AAATCAGCATATTGGCACCTTTATTATCTTTTAGTTCGATATTACTGGCCTTGAATCAGCATATT
66 AAATCAACATACTAGCACCTTTATTATCTTTAACTCCAATATCACTAGCCTTGAATCAGCATATT
* *
195630 GGCATCCTTACCATCTTTAAATCCAATGTCCCTGGCCTTGAATCAGCACATTGGCACTTATCAAA
131 GGCATCCTTACCATCTTTAAATCCAACGTCCCTGGCCTTGAATCAACACATTGGCACTTATCAAA
195695 ACCTTATTTCCAAAGCCTAA
196 ACCTTATTTCCAAAGCCTAA
* * * * *
195715 TGTCACTGGCCTTGAATCAGCACATTGGCACTCTCGTTATCTCAAAGTCCGATATTGCTGGCCTC
1 TGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATCGCTGGCCTC
* * * * *
195780 GAATCAACATACTATCACCTTTATTATCTTTAACTCCAATATCGCTAGCCTTGAATTAGTATATT
66 AAATCAACATACTAGCACCTTTATTATCTTTAACTCCAATATCACTAGCCTTGAATCAGCATATT
* ** * * ** *
195845 GGCATCTTTGTCATCTTTAACTCTAACGTTGCTTGCCTTGAATCAACACATTGGCAC
131 GGCATCCTTACCATCTTTAAATCCAACGTCCCTGGCCTTGAATCAACACATTGGCAC
195902 CCTTATCATC
Statistics
Matches: 151, Mismatches: 36, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
215 151 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (215 bp):
TGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATCGCTGGCCTC
AAATCAACATACTAGCACCTTTATTATCTTTAACTCCAATATCACTAGCCTTGAATCAGCATATT
GGCATCCTTACCATCTTTAAATCCAACGTCCCTGGCCTTGAATCAACACATTGGCACTTATCAAA
ACCTTATTTCCAAAGCCTAA
Found at i:195956 original size:371 final size:370
Alignment explanation
Indices: 195448--196115 Score: 879
Period size: 371 Copynumber: 1.8 Consensus size: 370
195438 TTAAAGTTAG
* * **
195448 ATATCCTGGCCTTGAATCAGCGTATTAGCATCCTTGTCATCTTTAAATCCATTGTCGCTGGCCTT
1 ATATCCTAGCCTTGAATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAACGTCGCTGGCCTT
* * * *** * * **
195513 GAATTAGCATATTGGCACCCTTATCATCTTAAAGTCCAATATCGTTGGCCTTAAATCAGCATATT
66 GAATCAACACATTGGCACCCTTATCATCTTAAAGTCCAATATCACCGACCTTAAATCAACATACA
* * * * * * * *
195578 GGCACCTTTATTATCTTTTAGTTCGATATTACTGGCCTTGAATCAGCATATTGGCATCCTTACCA
131 AGCACCTTTATTATCTTTAAATCCGATATCACTAGCCTTGAATCAACATATTGGCACCCTTACCA
* *
195643 TCTTTAAATCCAATGTCCCTGGCCTTGAATCAGCACATTGGCACTTATCAAAACCTTATTTCCAA
196 TCTTGAAATCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTATCAAAACCTTATTTCCAA
*
195708 AG-CCTAATGTCACTGGCCTTGAATCAGCACATTGGCACTCTCGTTATCTCAAAGTCCGATATTG
261 AGTCC-AATGTCACTGGCCTTGAATCAACACATTGGCACTCTCGTTATCTCAAAGTCCGATATTG
195772 CTGGCCTCGAATCAACATACTATCACCTTTATTATCTTTAACTCCA
325 CTGGCCTCGAATCAACATACTATCACCTTTATTATCTTTAACTCCA
* * * * * * * *
195818 ATATCGCTAGCCTTGAATTAGTATATTGGCATCTTTGTCATCTTTAACTCTAACGTTGCTTGCCT
1 ATATC-CTAGCCTTGAATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAACGTCGCTGGCCT
* * * *
195883 TGAATCAACACATTGGCACCCTTATCATCTTAAAGTTCAATATTACCGACCTTGAATCAATATAC
65 TGAATCAACACATTGGCACCCTTATCATCTTAAAGTCCAATATCACCGACCTTAAATCAACATAC
* * *
195948 AAGCACCTTTATTCTCTTTAAATCCGATATCACTAGCTTTGAATCAACATATTGGCACCCTTACT
130 AAGCACCTTTATTATCTTTAAATCCGATATCACTAGCCTTGAATCAACATATTGGCACCCTTACC
* * * * *
196013 ATCTTGAAGTCCAATGTCACTGGCTTTGAATTAGCACATTGGCACTTGTCAAAACCTTTTTTCCA
195 ATCTTGAAATCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTATCAAAACCTTATTTCCA
** *
196078 AAGTCCAATGTCGTTGGCCTTGAATCAATACATTGGCA
260 AAGTCCAATGTCACTGGCCTTGAATCAACACATTGGCA
196116 GTCTTATCAT
Statistics
Matches: 248, Mismatches: 48, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
370 5 0.02
371 241 0.97
372 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (370 bp):
ATATCCTAGCCTTGAATCAGCATATTAGCATCCTTGTCATCTTTAAATCCAACGTCGCTGGCCTT
GAATCAACACATTGGCACCCTTATCATCTTAAAGTCCAATATCACCGACCTTAAATCAACATACA
AGCACCTTTATTATCTTTAAATCCGATATCACTAGCCTTGAATCAACATATTGGCACCCTTACCA
TCTTGAAATCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTATCAAAACCTTATTTCCAA
AGTCCAATGTCACTGGCCTTGAATCAACACATTGGCACTCTCGTTATCTCAAAGTCCGATATTGC
TGGCCTCGAATCAACATACTATCACCTTTATTATCTTTAACTCCA
Found at i:196042 original size:156 final size:156
Alignment explanation
Indices: 195713--196057 Score: 359
Period size: 156 Copynumber: 2.2 Consensus size: 156
195703 TCCAAAGCCT
* * * * * * *
195713 AATGTCACTGGCCTTGAATCAGCACATTGGCACTCTCGTTATCTCAAAGTCCGATATTGCTGGCC
1 AATGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATTACCGACC
* * * * * **
195778 TCGAATCAACATACTATCACCTTTATTATCTTTAACTCCAATATCGCTAGCCTTGAATTAGTATA
66 TCGAATCAACATACAAGCACCTTTATTATCTTTAAATCCAATATCACTAGCCTTGAATCAACATA
* ** * *
195843 TTGGCATCTTTGTCATCTTTAACTCT
131 TTGGCACCTTACTCATCTTGAACTCC
* ** * * * * *
195869 AACGTTGCTTGCCTTGAATCAACACATTGGCACCCTTATCATCTTAAAGTTCAATATTACCGACC
1 AATGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATTACCGACC
* * * * *
195934 TTGAATCAATATACAAGCACCTTTATTCTCTTTAAATCCGATATCACTAGCTTTGAATCAACATA
66 TCGAATCAACATACAAGCACCTTTATTATCTTTAAATCCAATATCACTAGCCTTGAATCAACATA
*
195999 TTGGCACCCTTACT-ATCTTGAAGTCC
131 TTGGCA-CCTTACTCATCTTGAACTCC
* *
196025 AATGTCACTGGCTTTGAATTAGCACATTGGCAC
1 AATGTCACTGGCCTTGAATCAGCACATTGGCAC
196058 TTGTCAAAAC
Statistics
Matches: 148, Mismatches: 40, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
156 144 0.97
157 4 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (156 bp):
AATGTCACTGGCCTTGAATCAGCACATTGGCACCCTCATCATCTCAAAGTCCAATATTACCGACC
TCGAATCAACATACAAGCACCTTTATTATCTTTAAATCCAATATCACTAGCCTTGAATCAACATA
TTGGCACCTTACTCATCTTGAACTCC
Found at i:197691 original size:12 final size:12
Alignment explanation
Indices: 197675--197717 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
197665 CAGCAAGTGG
*
197675 AGAAAAAAAGAG
1 AGAAAAAAAGAA
197687 AGAAAAAAAGAA
1 AGAAAAAAAGAA
197699 AGAAAAAAAGAA
1 AGAAAAAAAGAA
197711 AGAAAAA
1 AGAAAAA
197718 GGGAGAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:198894 original size:143 final size:141
Alignment explanation
Indices: 198663--199153 Score: 670
Period size: 142 Copynumber: 3.5 Consensus size: 141
198653 ATTTGTAGAG
*
198663 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAG-TTTCCATTATGGTACGAAATGAATTTTC
1 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTTTCCATTAAGGTACGAAATGAATTTT-
*
198727 TTAAAAATTAAAAATCAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCATATGG
65 TTAAAAATTAAAAATCAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGG
198792 TTTT-TCATAGGA
130 TTTTCT-ATAGGA
* ** *
198804 GTATAGAAATCTTCAAAA-TATTGCGTATCTTTTTGGTTTTCCATTAAGGTATGAAATGAATTTT
1 GTATAGAAATCTTCAAAACT-TTTCGTATCTTTTCAGTTTTCCATTAAGGTACGAAATGAATTTT
*
198868 GTTAAAAAATTAAAAATCAAATAAAAATTATTATCTTAGTTTTTCAAGATTTCTAATATTCCTAT
65 -TT-AAAAATTAAAAATCAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTAT
*
198933 -GTTTTCTATAAGA
128 GGTTTTCTATAGGA
* * * *
198946 GTATAGAAATCTTCAAAACTTTTTGTATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTT
1 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTTTCCATTAAGGTACGAAATGAATTTTT
* *
199011 TAGAAATTAAAAAAATTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCT-ATATTCCTATG
66 TAAAAATT--AAAAATCAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATG
*
199075 GTCTTCTATAAGGA
129 GTTTTCTAT-AGGA
* * * * * *
199089 -TATAGAAATTTTTAAAACTTTTCGTATCTTTTTAGTATTCAATTAAGGTACAAAATGAGATTTT
1 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTTTCCATTAAGGTACGAAATGA-ATTTT
199153 T
65 T
199154 AAATTTACAA
Statistics
Matches: 312, Mismatches: 28, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
140 7 0.02
141 43 0.14
142 192 0.62
143 70 0.22
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (141 bp):
GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTTTCCATTAAGGTACGAAATGAATTTTT
TAAAAATTAAAAATCAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGT
TTTCTATAGGA
Found at i:200272 original size:16 final size:17
Alignment explanation
Indices: 200245--200278 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
200235 TTTGACATAG
*
200245 AATAATAAATTTATTTT
1 AATAATAAATTTAGTTT
200262 AATAA-AAATTTAGTTT
1 AATAATAAATTTAGTTT
200278 A
1 A
200279 GAAATGCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATAATAAATTTAGTTT
Found at i:207764 original size:13 final size:13
Alignment explanation
Indices: 207746--207770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207736 ATTACTCAAA
207746 TGTATCGATACAT
1 TGTATCGATACAT
207759 TGTATCGATACA
1 TGTATCGATACA
207771 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:207835 original size:52 final size:52
Alignment explanation
Indices: 207779--207903 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
207769 CACTGATCTT
*
207779 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
207831 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
207883 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
207904 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:210036 original size:24 final size:26
Alignment explanation
Indices: 210009--210059 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
209999 TCAAAAATTT
210009 ATTCAT-C-GGAGACACTCCAACCCC
1 ATTCATCCAGGAGACACTCCAACCCC
* *
210033 ATTCCTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGAGACACTCCAACCCC
210060 GTTTTCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 1 0.05
27 16 0.73
ACGTcount: A:0.25, C:0.43, G:0.16, T:0.16
Consensus pattern (26 bp):
ATTCATCCAGGAGACACTCCAACCCC
Found at i:215452 original size:18 final size:18
Alignment explanation
Indices: 215410--215459 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
215400 TCCATCTTCT
215410 TCTCTCCTTCTCTTGTCA
1 TCTCTCCTTCTCTTGTCA
*
215428 TCCCTCCTCTCTCTAT-T-A
1 TCTCTCCT-TCTCT-TGTCA
215446 TCTCTCCTGTCTCT
1 TCTCTCCT-TCTCT
215460 CCTCCTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 20 0.74
19 6 0.22
20 1 0.04
ACGTcount: A:0.06, C:0.42, G:0.04, T:0.48
Consensus pattern (18 bp):
TCTCTCCTTCTCTTGTCA
Found at i:215474 original size:42 final size:42
Alignment explanation
Indices: 215425--215534 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
215415 CCTTCTCTTG
* * *
215425 TCATCCCTCCTCTCTCTATTATCTCTCCTGTCTCTCCTCCTA
1 TCATCCCTCCTCTCTCTACTATCTCTCCGGCCTCTCCTCCTA
*
215467 TCATCCCTCCTATCTCTACTATCTCTCCGGCCTCTCCTCCTA
1 TCATCCCTCCTCTCTCTACTATCTCTCCGGCCTCTCCTCCTA
* *
215509 TCATCCCTCCTCTCTCTTCTTTCTCT
1 TCATCCCTCCTCTCTCTACTATCTCT
215535 TTGAGGGCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.09, C:0.46, G:0.03, T:0.42
Consensus pattern (42 bp):
TCATCCCTCCTCTCTCTACTATCTCTCCGGCCTCTCCTCCTA
Found at i:221170 original size:50 final size:50
Alignment explanation
Indices: 221115--221234 Score: 177
Period size: 50 Copynumber: 2.4 Consensus size: 50
221105 TGATACATCC
*
221115 TTCATTGTATCGATACATTCTGGGTTTTACCCACATGTATCGATAAATTT
1 TTCATTGTATCGATACATTCTGGGTTCTACCCACATGTATCGATAAATTT
* * * *
221165 TTCATTATATCGAAACATTCTGGGTTCTACCCATATGTATCGATACATTT
1 TTCATTGTATCGATACATTCTGGGTTCTACCCACATGTATCGATAAATTT
* *
221215 CTCACTGTATCGATACATTC
1 TTCATTGTATCGATACATTC
221235 AGGCATTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (50 bp):
TTCATTGTATCGATACATTCTGGGTTCTACCCACATGTATCGATAAATTT
Found at i:222460 original size:78 final size:78
Alignment explanation
Indices: 222325--222550 Score: 249
Period size: 79 Copynumber: 2.9 Consensus size: 78
222315 TGGGGATAAC
* * * * * * *
222325 AACGGGGCTGGAGTATCCCCGATTCTAGAAAA-TAAGTGTTTTGAAAATAAAATCGGGGTTGGAG
1 AACGGGGATGGAGTATCCCCGATTGTGGAAAATTGA-TGTTTAG-AAATAAAACCGGGGTTAGAG
*
222389 TATCC-CTCGAAAAT
64 TATCCTCGCGAAAAT
**
222403 AACGGGGATGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGCCGGGGTTAGAGT
1 AACGGGGATGGAGTATCCCCGATTGTGGAAAATTGATG-TTTAGAAATAAAACCGGGGTTAGAGT
222468 ATCCTCGCGAAAAT
65 ATCCTCGCGAAAAT
* ** * * **
222482 AACGGGGTTGGAGTATCTTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATAGGGGTTAGAGT
1 AACGGGGATGGAGTATCCCCGATTGTGGAAAATTGATG-TTTAGAAATAAAACCGGGGTTAGAGT
222547 ATCC
65 ATCC
222551 CCGATTGTGA
Statistics
Matches: 125, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
78 52 0.42
79 73 0.58
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (78 bp):
AACGGGGATGGAGTATCCCCGATTGTGGAAAATTGATGTTTAGAAATAAAACCGGGGTTAGAGTA
TCCTCGCGAAAAT
Found at i:222556 original size:51 final size:51
Alignment explanation
Indices: 222485--222583 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
222475 CGAAAATAAC
* ** * ** *
222485 GGGGTTGGAGTATCTTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATA
1 GGGGTTAGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAATA
222536 GGGGTTAGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAA
1 GGGGTTAGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAA
222584 GCCGAGGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (51 bp):
GGGGTTAGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAATA
Found at i:222598 original size:51 final size:51
Alignment explanation
Indices: 222487--222602 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
222477 AAAATAACGG
** * ** * * *
222487 GGTTGGAGTATCTTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATAGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAACAGA
* * *
222538 GGTTAGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAGCCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAACAGA
222589 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
222603 TTCGAAAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAGAAATAAAACAGA
Found at i:222705 original size:131 final size:129
Alignment explanation
Indices: 222406--222860 Score: 495
Period size: 131 Copynumber: 3.5 Consensus size: 129
222396 CGAAAATAAC
* * ** ** * *
222406 GGGGATGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGCCGGGGTTAGAGTAT-
1 GGGGTTGGAGTAT-CCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
* * *
222470 CCTCGCGAAAATAACGGGGTTGGAGTATCTTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAAT
65 CCT-TCGAAAATAACGGGATTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAAT
222535 A
129 A
* *
222536 GGGGTTAGAGTATCCCCGATTGTGAAAAAAT-AATATTTTAGAAATAAAGCCGAGGTTGGAGTAT
1 GGGGTTGGAGTAT-CCCGATTGTG-AAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
*
222600 CCCTTCGAAAATAACGGGATTGGAGTATCCTCGCTTGTGAAAAGATTGGTGTTTTAGAAATAAAA
64 CCCTTCGAAAATAACGGGATTGGAGTATCCTCGATTGTGAAAA-ATTGGTGTTTTAGAAATAAAA
*
222665 TT
128 TA
* * * *
222667 GGGGTTGGAGTATCTCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTTGAGAATC
1 GGGGTTGGAGTATC-CCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
* * * * ** * * * *
222732 CCCTCGAAAATAGA-GGGTTTGGAGTATCCCCAATCATG-AAAATTGATATTTTGGAAATAAAAC
65 CCTTCGAAAATA-ACGGGATTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAAT
*
222795 C
129 A
* *** * *
222796 GGGGTTGGAGTATCCCCAAAATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGCAGTATCC
1 GGGGTTGGAGTATCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCC
222861 ACGAGATGAA
Statistics
Matches: 277, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
128 41 0.15
129 32 0.12
130 93 0.34
131 110 0.40
132 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (129 bp):
GGGGTTGGAGTATCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCC
CTTCGAAAATAACGGGATTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATA
Found at i:222811 original size:50 final size:50
Alignment explanation
Indices: 222750--222875 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 50
222740 AATAGAGGGT
* ** *
222750 TTGGAGTATCCCCAATCATG-AAAATTGATATTTTGGAAATAAAACCGGGG
1 TTGGAGTATCCCCAA-AATGAAAAATCAATATTTTAGAAATAAAACCGGGG
222800 TTGGAGTATCCCCAAAATGAAAAATCAATATTTTAGAAATAAAACCGGGG
1 TTGGAGTATCCCCAAAATGAAAAATCAATATTTTAGAAATAAAACCGGGG
* * * *
222850 TTGCAGTATCCACGAGATGAAAAATC
1 TTGGAGTATCCCCAAAATGAAAAATC
222876 TAGAAATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 3 0.04
50 64 0.96
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (50 bp):
TTGGAGTATCCCCAAAATGAAAAATCAATATTTTAGAAATAAAACCGGGG
Found at i:225181 original size:20 final size:21
Alignment explanation
Indices: 225156--225228 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
225146 AATGCCTGGA
*
225156 TGTATCGATACATTGAA-AAT
1 TGTATCGATACAATGAACAAT
225176 TGTATCGATACAATGAACAA-
1 TGTATCGATACAATGAACAAT
* *
225196 TGTATCGATTCAATGAATAAT
1 TGTATCGATACAATGAACAAT
225217 T-TATCGATACAA
1 TGTATCGATACAA
225229 ATTGTTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 44 0.94
21 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATGAACAAT
Found at i:230435 original size:19 final size:19
Alignment explanation
Indices: 230402--230449 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
230392 AATAAAACAA
230402 AAGAAAAAA-ACAAAAAAG
1 AAGAAAAAAGACAAAAAAG
* *
230420 AAGAAAAAAGAGAAAAGAG
1 AAGAAAAAAGACAAAAAAG
230439 AA-AAGAAAAGA
1 AAGAA-AAAAGA
230450 ACCTACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGACAAAAAAG
Found at i:230450 original size:17 final size:16
Alignment explanation
Indices: 230390--230450 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
230380 TTTTTTTTGC
*
230390 AAAATAAAACAAAAGA-
1 AAAA-AAAAGAAAAGAG
230406 AAAAAACAA-AAAAGAAG
1 AAAAAA-AAGAAAAG-AG
*
230423 AAAAAAGAGAAAAGAG
1 AAAAAAAAGAAAAGAG
230439 AAAAGAAAAGAA
1 AAAA-AAAAGAA
230451 CCTACTTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 7 0.18
16 14 0.37
17 17 0.45
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAAAAGAAAAGAG
Found at i:231505 original size:61 final size:61
Alignment explanation
Indices: 231410--232022 Score: 725
Period size: 61 Copynumber: 10.0 Consensus size: 61
231400 CTATCATTTC
** *
231410 AGTCCTCAAAGAGTAGGATGCCTTCTCCATTTAAATCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * *
231471 AGTCCTCAAAGAGTAAGATGCCTTCTTTTTTTAAAGCCCACACAAGTTGGTAGCATCTTTT
1 AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * ** *
231532 AGTCCTTAAAGAATAGGACACCTT-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGTAGGATGCCTTCTCT-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
** *
231593 AGTCCTCAAAGAGTAGGACACCTTCTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
231653 AGTCCTCAAAGAGCAGGATGCTTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * * **
231714 GAGTCCTTAAAGAGTAGGATACTTTCTCCTTTTAAAGCCCACACAAGTTGATGGCATATTTT
1 -AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * * *
231776 AGTCCTCAAAGAGCATGAGGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
231837 AGTCCTCAAAGAGCAGGATGCCATTC-CTTTTTAAAGCCCACACAAGTGGGTGGCACCTTTT
1 AGTCCTCAAAGAGTAGGATGCC-TTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * *
231898 AGTCCCCAAAGAGCAGGA--CACTTCT-TTTTTAAAGCCTACACAAGCTGGTGGCACCTTCT
1 AGTCCTCAAAGAGTAGGATGC-CTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
231957 AGTCCTCAAAGAGTAAGATGCCTCTCTTCTTTTTCATCTTAAAGGCCACACAAGTTGGTGGCACC
1 AGTCCTCAAAGAGTAGGATGCCT-TC-TC---TT--T-TTAAAGCCCACACAAGTTGGTGGCACC
232022 T
58 T
232023 ATCTACTTCA
Statistics
Matches: 476, Mismatches: 58, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
59 49 0.10
60 61 0.13
61 279 0.59
62 59 0.12
66 2 0.00
68 1 0.00
69 25 0.05
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (61 bp):
AGTCCTCAAAGAGTAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
Found at i:232546 original size:30 final size:30
Alignment explanation
Indices: 232510--232583 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
232500 TTCCATAATT
**
232510 TGTATCGATACATTCTGGGTTCTACCCAGA
1 TGTATCGATACATTCTAAGTTCTACCCAGA
* *
232540 TGTATCGATACATTCTAAGTTTTACCTAGA
1 TGTATCGATACATTCTAAGTTCTACCCAGA
**
232570 TGTATTAATACATT
1 TGTATCGATACATT
232584 TCTCAATGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (30 bp):
TGTATCGATACATTCTAAGTTCTACCCAGA
Found at i:235215 original size:80 final size:79
Alignment explanation
Indices: 235120--235347 Score: 237
Period size: 79 Copynumber: 2.9 Consensus size: 79
235110 TTTCACCATC
* *
235120 GGGGATATTCCAACCCCGATTTTATTTTCAAAACATCGATTTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGA-TTTTTCACAATCGGGGATACTCCAA
235185 CCCTGTTATTTTCGA-
65 CCCTGTTA-TTTCGAT
* * * * * * **
235200 GGGGATACTCTAACCCCGATTTTA-TTTCTAAAATACCAATTTTTCACTATTGAAGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACATCGATTTTTCACAATCGGGGATACTCCAA
*
235264 -CCTCGTTATTTCTAT
65 CCCT-GTTATTTCGAT
* * * * * * *
235279 GGGGATAGTCCAACCCTGATTTTATTTCCAAAACACCGATCTTCCACAATCGGGAATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
235344 CCTG
66 CCTG
235348 GCTTTATTTC
Statistics
Matches: 119, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
78 8 0.07
79 76 0.64
80 35 0.29
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAAC
CCTGTTATTTCGAT
Found at i:235347 original size:51 final size:51
Alignment explanation
Indices: 235287--235393 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
235277 ATGGGGATAG
* * *
235287 TCCAACCCTGATTTTATTTCCAAAACACCGATCTTCCACAATCGGGAATAC
1 TCCAACCCTGACTTTATTTCCAAAACACCGATCTTCCACAATCAGAAATAC
* * * *
235338 TCCAACCCTGGCTTTATTTCCAAAACATCGATTTTCCATAATCAGAAATAC
1 TCCAACCCTGACTTTATTTCCAAAACACCGATCTTCCACAATCAGAAATAC
235389 TCCAA
1 TCCAA
235394 TCCCGTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.29
Consensus pattern (51 bp):
TCCAACCCTGACTTTATTTCCAAAACACCGATCTTCCACAATCAGAAATAC
Found at i:235468 original size:79 final size:79
Alignment explanation
Indices: 235350--235502 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
235340 CAACCCTGGC
* *
235350 TTTATTTCCAAAACATCGATTTTCCATAATCAGAAATACTCCAATCCC-GTTATTTCTGAGCAGA
1 TTTATTTCCAAAACATCGATTTTCCACAATCAGAAATACTCCAA-CCCTGTTATTTCCGAGCAGA
235414 TACTCTAACCTCAGT
65 TACTCTAACCTCAGT
* * * * ** **
235429 TTTATTTCCAAAACATCTATTTTCCACCATCGGAGATACTTTAACCCTGTTATTTCCGAGGGGAT
1 TTTATTTCCAAAACATCGATTTTCCACAATCAGAAATACTCCAACCCTGTTATTTCCGAGCAGAT
235494 ACTCTAACC
66 ACTCTAACC
235503 CTAATTTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.05
79 60 0.95
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
TTTATTTCCAAAACATCGATTTTCCACAATCAGAAATACTCCAACCCTGTTATTTCCGAGCAGAT
ACTCTAACCTCAGT
Found at i:235483 original size:209 final size:210
Alignment explanation
Indices: 235093--235510 Score: 443
Period size: 209 Copynumber: 2.0 Consensus size: 210
235083 GAGAGAATAC
* * * * * * * *
235093 TTTCTAAAACACCAATTTTTCACCATCGGGGATATTCCAACCCCGATTTTATTTTCAAAACATCG
1 TTTCCAAAACACCAATCTTCCACAATCGGGAATACTCCAACCCCGACTTTATTTCCAAAACATCG
* * ** * ** *
235158 ATTTTTTCACAATCGGGGATACTCTAACCCTGTTATTTTCGAGGGGATACTCTAACCCCGATTTT
66 ATTTTTCCACAATCAGAAATACTCCAACCCTGTTATTTTCGAGCAGATACTCTAACCCAGATTTT
* * * * * * *
235223 ATTTCTAAAATACCAATTTTTCACTATTGAAGATACTCCAACCTCGTTATTT-CTATGGGGATAG
131 ATTTCCAAAACACCAATTTTCCACCATCGAAGATACTCCAACCTCGTTATTTCCGA-GGGGATAC
*
235287 TCCAACCCTGATTTTA
195 TCCAACCCTAATTTTA
* * *
235303 TTTCCAAAACACCGATCTTCCACAATCGGGAATACTCCAACCCTGGCTTTATTTCCAAAACATCG
1 TTTCCAAAACACCAATCTTCCACAATCGGGAATACTCCAACCCCGACTTTATTTCCAAAACATCG
*
235368 A-TTTTCCATAATCAGAAATACTCCAATCCC-GTTA-TTTCTGAGCAGATACTCTAACCTCAG-T
66 ATTTTTCCACAATCAGAAATACTCCAA-CCCTGTTATTTTC-GAGCAGATACTCTAACC-CAGAT
* * * **
235429 TTTATTTCCAAAACATCTATTTTCCACCATCGGAGATACTTTAACC-CTGTTATTTCCGAGGGGA
128 TTTATTTCCAAAACACCAATTTTCCACCATCGAAGATACTCCAACCTC-GTTATTTCCGAGGGGA
*
235493 TACTCTAACCCTAATTTT
192 TACTCCAACCCTAATTTT
235511 TATCTCTAAA
Statistics
Matches: 169, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
208 5 0.03
209 102 0.60
210 62 0.37
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (210 bp):
TTTCCAAAACACCAATCTTCCACAATCGGGAATACTCCAACCCCGACTTTATTTCCAAAACATCG
ATTTTTCCACAATCAGAAATACTCCAACCCTGTTATTTTCGAGCAGATACTCTAACCCAGATTTT
ATTTCCAAAACACCAATTTTCCACCATCGAAGATACTCCAACCTCGTTATTTCCGAGGGGATACT
CCAACCCTAATTTTA
Found at i:240031 original size:8 final size:8
Alignment explanation
Indices: 240009--240069 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
239999 GTTTATCCCA
*
240009 AAAAAAAA
1 AAAAAAAC
240017 AACAAAAAC
1 AA-AAAAAC
240026 AAAAAAA-
1 AAAAAAAC
** *
240033 GGAAAAAT
1 AAAAAAAC
240041 AAAAAAAC
1 AAAAAAAC
*
240049 AAAAAACC
1 AAAAAAAC
240057 AAAAAAAC
1 AAAAAAAC
240065 AAAAA
1 AAAAA
240070 CTAAAAATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 5 0.12
8 31 0.72
9 7 0.16
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:240082 original size:15 final size:15
Alignment explanation
Indices: 240012--240076 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
240002 TATCCCAAAA
240012 AAAAAAACAAAAA-C
1 AAAAAAACAAAAACC
* *
240026 AAAAAAAGGAAAAA-T
1 AAAAAAA-CAAAAACC
240041 AAAAAAACAAAAAACC
1 AAAAAAAC-AAAAACC
*
240057 AAAAAAACAAAAACT
1 AAAAAAACAAAAACC
240072 AAAAA
1 AAAAA
240077 TTCAAATGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.16
15 28 0.65
16 8 0.19
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAAAACAAAAACC
Found at i:244498 original size:49 final size:49
Alignment explanation
Indices: 244433--245012 Score: 563
Period size: 49 Copynumber: 11.9 Consensus size: 49
244423 ATGTTACAGA
* * * ** *
244433 TGCCAATATGCTGATTTAAGGCCAGTGATTTTGGACTTAAAGGTGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* *
244482 TGCTAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGG
* * * *
244534 TGTCGATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* *
244583 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * *
244632 TGCCAATGTGTTGATTCAAGGCCAGCGACATTAGACTTAATGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGG
* * * * * *
244684 CGCCAATATGTTGATTCAAGGCCAACTATATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * *
244733 TGCCAATGTGCTGATTCAAGGCAAGCAACATTGGACTTAAAGGTGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * * * *
244782 TGCTAATGTACTGATTCAAGGCTAGTGACATTAGACTTAAAGATGAAAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGG
* * * * * *
244834 CGCCATTATGCTGATTCAAGGCTAGCGATATTGGACTCAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * *
244883 TGCCAATGTGCTGATTCAAAGCTAGCAACATTGGACTT--A-A--AA-G
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * * *
244926 TGCCAATGTGCTAATTCAAAGCCAACAACATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
* * *
244969 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
245013 AGATGCCACC
Statistics
Matches: 447, Mismatches: 69, Indels: 31
0.82 0.13 0.06
Matches are distributed among these distances:
42 3 0.01
43 70 0.16
44 2 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 244 0.55
52 125 0.28
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
Found at i:244556 original size:101 final size:98
Alignment explanation
Indices: 244433--245012 Score: 572
Period size: 101 Copynumber: 5.9 Consensus size: 98
244423 ATGTTACAGA
* * * * *
244433 TGCCAATATGCTGATTTAAGGCCAGTGATTTTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
244498 TAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGATG---AAGG
* *
244534 TGTCGATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
*
244599 CAAGGCCAGCAACATTGGACTTAAAGGTGAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGATGAAGG
* * * * * * * *
244632 TGCCAATGTGTTGATTCAAGGCCAGCGACATTAGACTTAATGATGACAAAGGCGCCAATATGTTG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTG
* * *
244697 ATTCAAGGCCAACTATATTGGACTTAAAGATGAAGG
63 ATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGG
* * * * * * *
244733 TGCCAATGTGCTGATTCAAGGCAAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTACTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* ** *
244798 CAAGGCTAGTGACATTAGACTTAAAGATGAAAAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGATG---AAGG
* * * *
244834 CGCCATTATGCTGATTCAAGGCTAGCGATATTGGACTCAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
244899 CAAAGCTAGCAACATTGGACTT--A-A--AA-G
66 CAAGGCCAGCAACATTGGACTTAAAGATGAAGG
* * * * * * *
244926 TGCCAATGTGCTAATTCAAAGCCAACAACATTGGACTT----A--AAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
*
244985 CAAGGCCAGCAATATTGGACTTAGAAGA
66 CAAGGCCAGCAACATTGGACTTA-AAGA
245013 AGATGCCACC
Statistics
Matches: 400, Mismatches: 69, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
86 38 0.09
88 1 0.00
89 1 0.00
90 1 0.00
92 29 0.07
93 2 0.00
98 81 0.20
99 1 0.00
101 246 0.62
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (98 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
CAAGGCCAGCAACATTGGACTTAAAGATGAAGG
Found at i:244628 original size:150 final size:149
Alignment explanation
Indices: 244433--244923 Score: 721
Period size: 150 Copynumber: 3.3 Consensus size: 149
244423 ATGTTACAGA
* * ** **
244433 TGCCAATATGCTGATTTAAGGCCAGTGATTTTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
* * * *
244498 TAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGTCGATATGCTGATTCAAGGCCAGCGAT
66 CAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCG-CAATATGCTGATTCAAGGCCAGCGAT
244563 ATTGGACTTAAAGATGAAGG
130 ATTGGACTTAAAGATGAAGG
* *
244583 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGTTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
* * * *
244648 CAAGGCCAGCGACATTAGACTTAATGATGACAAAGGCGCCAATATGTTGATTCAAGGCCAACTAT
66 CAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCG-CAATATGCTGATTCAAGGCCAGCGAT
244713 ATTGGACTTAAAGATGAAGG
130 ATTGGACTTAAAGATGAAGG
* *
244733 TGCCAATGTGCTGATTCAAGGCAAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTACTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
* * * * *
244798 CAAGGCTAGTGACATTAGACTTAAAGATGAAAAAGGCGCCATTATGCTGATTCAAGGCTAGCGAT
66 CAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCG-CAATATGCTGATTCAAGGCCAGCGAT
*
244863 ATTGGACTCAAAGATGAAGG
130 ATTGGACTTAAAGATGAAGG
* *
244883 TGCCAATGTGCTGATTCAAAGCTAGCAACATTGGACTTAAA
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAA
244924 AGTGCCAATG
Statistics
Matches: 308, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
150 308 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (149 bp):
TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATGTGCTGATT
CAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCGCAATATGCTGATTCAAGGCCAGCGATA
TTGGACTTAAAGATGAAGG
Found at i:244943 original size:43 final size:43
Alignment explanation
Indices: 244882--245007 Score: 189
Period size: 43 Copynumber: 2.9 Consensus size: 43
244872 AAAGATGAAG
*
244882 GTGCCAATGTGCTGATTCAAAGCTAGCAACATTGGACTTAAAA
1 GTGCCAATGTGCTGATTCAAAGCCAGCAACATTGGACTTAAAA
* * *
244925 GTGCCAATGTGCTAATTCAAAGCCAACAACATTGGACTTAAAG
1 GTGCCAATGTGCTGATTCAAAGCCAGCAACATTGGACTTAAAA
* * *
244968 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTA
1 GTGCCAATGTGCTGATTCAAAGCCAGCAACATTGGACTTA
245008 GAAGAAGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (43 bp):
GTGCCAATGTGCTGATTCAAAGCCAGCAACATTGGACTTAAAA
Found at i:245056 original size:28 final size:26
Alignment explanation
Indices: 245016--245239 Score: 133
Period size: 27 Copynumber: 8.0 Consensus size: 26
245006 TAGAAGAAGA
* *
245016 TGCCACCAACTTGTGTGCTTTTGCAGGT
1 TGCCACTAACTTGTG-GC-TTTGAAGGT
*
245044 TGCCACTACCTTGTAGGCTTTGAAGGT
1 TGCCACTAACTTGT-GGCTTTGAAGGT
*
245071 TGCCACTAACATGTGGGCTTTGAAGGT
1 TGCCACTAACTTGT-GGCTTTGAAGGT
* * * * **
245098 TGCCATTGACTTGTGGGATTGGAAAAT
1 TGCCACTAACTTGT-GGCTTTGAAGGT
* *
245125 GTGCCACTAACTTGTGGGCTTTTGAAAAGA
1 -TGCCACTAACTTGT-GGC-TTTG-AAGGT
* *
245155 TGCCATTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTAACTTGT-GGC-TTTGAAGGT
* * *
245183 TGCCATTGACTTGTGGGCTTTGAAAGGGG
1 TGCCACTAACTTGT-GGCTTTG-AA-GGT
* *
245212 TGCCATTGACTTGTGGGCTTTGGAAGGT
1 TGCCACTAACTTGT-GGCTTT-GAAGGT
245240 GAGGAATGTC
Statistics
Matches: 164, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
27 56 0.34
28 54 0.33
29 50 0.30
30 4 0.02
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.33
Consensus pattern (26 bp):
TGCCACTAACTTGTGGCTTTGAAGGT
Found at i:245187 original size:57 final size:56
Alignment explanation
Indices: 245053--245239 Score: 227
Period size: 57 Copynumber: 3.3 Consensus size: 56
245043 TTGCCACTAC
* * *
245053 CTTGTAGGCTTT-GAAGGTTGCCACTAACATGTGGGCTTTG-AAGGTTGCCATTGA
1 CTTGTGGGCTTTGGAAGGTTGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGA
* ** *
245107 CTTGTGGG-ATTGGAAAATGTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCATTGA
1 CTTGTGGGCTTTGGAAGGT-TGCCACTAACTTGTGGGC-TTTGAAAGGATGCCATTGA
* * * *
245164 CTTGTGGGCTTTTGAAGGTTGCCATTGACTTGTGGGCTTTGAAAGGGGTGCCATTGA
1 CTTGTGGGCTTTGGAAGGTTGCCACTAACTTGTGGGCTTTGAAA-GGATGCCATTGA
245221 CTTGTGGGCTTTGGAAGGT
1 CTTGTGGGCTTTGGAAGGT
245240 GAGGAATGTC
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
53 2 0.02
54 11 0.10
55 17 0.15
56 11 0.10
57 64 0.58
58 6 0.05
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (56 bp):
CTTGTGGGCTTTGGAAGGTTGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGA
Found at i:245233 original size:29 final size:28
Alignment explanation
Indices: 245053--245238 Score: 180
Period size: 29 Copynumber: 6.6 Consensus size: 28
245043 TTGCCACTAC
* * * *
245053 CTTGTAGGCTTTG-AAGGTTGCCACTAA
1 CTTGTGGGCTTTGAAAGGGTGCCATTGA
* *
245080 CATGTGGGCTTTG-AAGGTTGCCATTGA
1 CTTGTGGGCTTTGAAAGGGTGCCATTGA
* * ** * *
245107 CTTGTGGGATTGGAAAATGTGCCACTAA
1 CTTGTGGGCTTTGAAAGGGTGCCATTGA
* *
245135 CTTGTGGGCTTTTGAAAAGATGCCATTGA
1 CTTGTGGGC-TTTGAAAGGGTGCCATTGA
*
245164 CTTGTGGGCTTTTG-AAGGTTGCCATTGA
1 CTTGTGGGC-TTTGAAAGGGTGCCATTGA
245192 CTTGTGGGCTTTGAAAGGGGTGCCATTGA
1 CTTGTGGGCTTTGAAA-GGGTGCCATTGA
*
245221 CTTGTGGGCTTTGGAAGG
1 CTTGTGGGCTTTGAAAGG
245239 TGAGGAATGT
Statistics
Matches: 133, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
27 37 0.28
28 42 0.32
29 54 0.41
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (28 bp):
CTTGTGGGCTTTGAAAGGGTGCCATTGA
Found at i:246697 original size:14 final size:14
Alignment explanation
Indices: 246669--246714 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
246659 ATCTGAACCC
*
246669 TTTTTGTTGTT-TT
1 TTTTTCTTGTTGTT
*
246682 TTTTTCTTTTTGTT
1 TTTTTCTTGTTGTT
*
246696 TTTTTGTTGTTGTT
1 TTTTTCTTGTTGTT
246710 TTTTT
1 TTTTT
246715 TGCGGAGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (14 bp):
TTTTTCTTGTTGTT
Found at i:259439 original size:13 final size:13
Alignment explanation
Indices: 259421--259446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
259411 CAAGGTAGCT
259421 TTGTATCGATACA
1 TTGTATCGATACA
259434 TTGTATCGATACA
1 TTGTATCGATACA
259447 ATACATTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:265015 original size:52 final size:52
Alignment explanation
Indices: 264868--264994 Score: 227
Period size: 52 Copynumber: 2.4 Consensus size: 52
264858 GAATATGAAG
* *
264868 ATTTGCCTGCATGTATTGATACATTTCATAGTGTATCGATACATCTAGGCAA
1 ATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAA
*
264920 ATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAA
1 ATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAA
264972 ATTTGCCTGCATGTATCGATACA
1 ATTTGCCTGCATGTATCGATACA
264995 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
ATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAA
Found at i:265077 original size:13 final size:13
Alignment explanation
Indices: 265059--265136 Score: 75
Period size: 13 Copynumber: 5.5 Consensus size: 13
265049 AGCTTCGTAG
265059 CGATACATTGTAT
1 CGATACATTGTAT
** *
265072 CGATACAAAGCAT
1 CGATACATTGTAT
265085 CGATACATTGTAT
1 CGATACATTGTAT
265098 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
265117 CGATACATTGTAT
1 CGATACATTGTAT
265130 CGATACA
1 CGATACA
265137 ACACTTTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
13 36 0.68
14 1 0.02
16 6 0.11
18 1 0.02
19 9 0.17
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:265124 original size:32 final size:33
Alignment explanation
Indices: 265083--265152 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 33
265073 GATACAAAGC
265083 ATCGATACATTGTATCGATACAACAC-TTATGT
1 ATCGATACATTGTATCGATACAACACTTTATGT
265115 ATCGATACATTGTATCGATACAACACTTTATGT
1 ATCGATACATTGTATCGATACAACACTTTATGT
265148 ATCGA
1 ATCGA
265153 AACAAATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 26 0.70
33 11 0.30
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (33 bp):
ATCGATACATTGTATCGATACAACACTTTATGT
Found at i:266131 original size:49 final size:49
Alignment explanation
Indices: 265976--266457 Score: 505
Period size: 49 Copynumber: 10.1 Consensus size: 49
265966 TTTAGGAATG
* *
265976 TTAAAGATGAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
266025 TTAAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGTAC
1 TT-AAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * **
266078 TTAAAGATGAAGGTGCCAATGTGTTGATTCAAGGCCAACAACATTGGGT
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
266127 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
266177 TT---G--G-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
266220 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
266269 TT----A--AAGGTGCTAATGTGCTAATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
266312 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
266361 TT---G--G-AGGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
266404 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGTGATATTGAAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
266453 TTAAA
1 TTAAA
266458 AGAAGATGCC
Statistics
Matches: 354, Mismatches: 56, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
43 109 0.31
44 1 0.00
45 1 0.00
46 4 0.01
47 1 0.00
48 1 0.00
49 146 0.41
50 47 0.13
52 7 0.02
53 37 0.10
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:266200 original size:43 final size:43
Alignment explanation
Indices: 266139--266441 Score: 282
Period size: 43 Copynumber: 6.6 Consensus size: 43
266129 AAAAGATGAG
* * *
266139 GGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGAA
* *
266182 GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT---G---AA
* *
266231 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGAA
* * * *
266274 GGTGCTAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT---G---AA
* * *
266323 GGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGAA
* * *
266366 GGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----TGAA
*
266415 GATGCCAATATGCTGATTCAAGGCCAG
1 GGTGCCAATATGCTGATTCAAGGCCAG
266442 TGATATTGAA
Statistics
Matches: 211, Mismatches: 31, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
43 107 0.51
44 1 0.00
46 2 0.01
49 101 0.48
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (43 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGAA
Found at i:266263 original size:92 final size:92
Alignment explanation
Indices: 265986--266454 Score: 641
Period size: 92 Copynumber: 5.0 Consensus size: 92
265976 TTAAAGATGA
* * *
265986 AGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAAGATGACAAAGGCGCCAATAT
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGAT---AAAGGTGCCAATAT
*
266051 GCTGATTCAAGGCCAGCGATATTGTACTTAAAGATG
62 GCTGATTCAAGGCCAGCGATATTGGACTT---G--G
* * * ** * *
266087 AAGGTGCCAATGTGTTGATTCAAGGCCAACAACATTGGGTTTAAAAGATGAGGGTGCCAATATGC
1 -AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATAAAGGTGCCAATATGC
*
266152 TGATTCAAGGCTAGCGATATTGGACTTGG
64 TGATTCAAGGCCAGCGATATTGGACTTGG
266181 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
**
266246 ATTCAAGGCCAGCGATATTGGACTTAA
66 ATTCAAGGCCAGCGATATTGGACTTGG
* *
266273 AGGTGCTAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
*
266338 ATTCAAGGCTAGCGATATTGGACTTGG
66 ATTCAAGGCCAGCGATATTGGACTTGG
* * *
266365 AGGTGCGAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
* *
266430 ATTCAAGGCCAGTGATATTGAACTT
66 ATTCAAGGCCAGCGATATTGGACTT
266455 AAAAGAAGAT
Statistics
Matches: 334, Mismatches: 33, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
92 216 0.65
93 36 0.11
94 1 0.00
96 1 0.00
99 38 0.11
102 42 0.13
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (92 bp):
AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTGG
Found at i:266502 original size:33 final size:33
Alignment explanation
Indices: 266464--266686 Score: 312
Period size: 33 Copynumber: 6.9 Consensus size: 33
266454 TAAAAGAAGA
* * * *
266464 TGCCACCAACTTGTATGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
* **
266497 TGCCACCGACTTGTGTGGGCTTT--AGAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGG-T
*
266529 TGCCACCGACTTATGTGGGCTTTGGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
* *
266562 TGCCA-CGACTTGTGTGGGCTTT-GAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
266593 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
266626 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
266659 TGCCACCGACTTGTGTGGGCTTT-GAAAA
1 TGCCACCGACTTGTGTGGGCTTTGGAAAA
266687 GAAAAAGGTG
Statistics
Matches: 170, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
31 15 0.09
32 61 0.36
33 90 0.53
34 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
Found at i:266687 original size:64 final size:65
Alignment explanation
Indices: 266464--266686 Score: 335
Period size: 65 Copynumber: 3.4 Consensus size: 65
266454 TAAAAGAAGA
* * * * *
266464 TGCCACCAACTTGTATGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT-AGAGGGGA
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGG-
266528 T
65 T
*
266529 TGCCACCGACTTATGTGGGCTTTGGAAAAAGGTTGCCA-CGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
* *
266593 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAAGG
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGG
266658 T
65 T
266659 TGCCACCGACTTGTGTGGGCTTT-GAAAA
1 TGCCACCGACTTGTGTGGGCTTTGGAAAA
266687 GAAAAAGGTG
Statistics
Matches: 146, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
64 55 0.38
65 61 0.42
66 30 0.21
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (65 bp):
TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
Found at i:266760 original size:27 final size:27
Alignment explanation
Indices: 266722--267130 Score: 332
Period size: 27 Copynumber: 13.9 Consensus size: 27
266712 CTTAGAAGGA
*
266722 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
* *
266749 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266776 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266810 AAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGGCTT
*
266844 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266871 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGGGTGCCACGGAGTTGTGGGCTT
** * *
266905 AAAAGGGTGCCACATAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266932 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266966 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
266993 AGAAGGAAAAATAGTGCCACGGAGTTGTGGGCTT
1 AAAAGG-------GTGCCACGGAGTTGTGGGCTT
*
267027 AAAAGGGTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
267054 AAAAGGGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
* *
267081 AAAAGGGTGCCACTGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
267108 AAAAGGGTGCCACAGAGTTGTGG
1 AAAAGGGTGCCACGGAGTTGTGG
267131 ACTTTGGAGA
Statistics
Matches: 314, Mismatches: 33, Indels: 70
0.75 0.08 0.17
Matches are distributed among these distances:
27 191 0.61
28 2 0.01
33 1 0.00
34 120 0.38
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:266788 original size:61 final size:61
Alignment explanation
Indices: 266688--266815 Score: 229
Period size: 61 Copynumber: 2.1 Consensus size: 61
266678 CTTTGAAAAG
*
266688 AAAAAGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
266749 AAAAGGGTGCCATGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
266810 AAAAGG
1 AAAAGG
266816 AAAAAGAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.33, C:0.12, G:0.36, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:266802 original size:95 final size:95
Alignment explanation
Indices: 266687--267059 Score: 416
Period size: 95 Copynumber: 4.0 Consensus size: 95
266677 GCTTTGAAAA
*
266687 GAAAAAG-GTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
266751 AAGGGTGCCATGGAGTTGTGGACTTAGAAG
66 AAGGGTGCCACGGAGTTGTGGACTTAGAAG
* * *
266781 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAA
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
266846 AAGGGTGCCACGGAGTTGTGGACTTAGAAG
66 AAGGGTGCCACGGAGTTGTGGACTTAGAAG
* * ** * *
266876 GAAAAAGAGTGCCACGGAGTTGTGGGCTT-------AAAAGGGTGCCACATAGTTATGGACTTAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT--
* *
266934 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-----
64 -----AAAAGGGTGCCACGGAGTTGTGGACTTAGAAG
* *
266966 --AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAATAGTGCCACGGAGTTGTGGGCTTAA
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
* * *
267029 AAGGGTGCCATGGAGTTGTGGGCTTAAAAG
66 AAGGGTGCCACGGAGTTGTGGACTTAGAAG
267059 G
1 G
267060 GTGCCACAGA
Statistics
Matches: 235, Mismatches: 23, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
88 71 0.30
94 7 0.03
95 157 0.67
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (95 bp):
GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
AAGGGTGCCACGGAGTTGTGGACTTAGAAG
Found at i:266848 original size:61 final size:61
Alignment explanation
Indices: 266783--267113 Score: 487
Period size: 61 Copynumber: 5.5 Consensus size: 61
266773 CTTAGAAGGA
* * *
266783 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
266844 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
** * *
266905 AAAAGGGTGCCACATAGTTATGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
266966 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAATAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
267027 AAAAGGGTGCCATGGAGTTGTGGGCTTAAAA-G-----G-GTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
267081 AAAAGGGTGCCACTGAGTTGTGGACTTAAAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
267114 GTGCCACAGA
Statistics
Matches: 250, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
54 48 0.19
55 1 0.00
60 1 0.00
61 200 0.80
ACGTcount: A:0.30, C:0.13, G:0.36, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:266988 original size:88 final size:89
Alignment explanation
Indices: 266878--267113 Score: 241
Period size: 88 Copynumber: 2.7 Consensus size: 89
266868 CTTAGAAGGA
*
266878 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACATAGTTATGGACTTAGAAGG-AAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACATAGTTATGGACTTAGAAGGCAAAA
266942 AGAGTGCCACGGAGTTGTGGGCTT
66 AGAGTGCCACGGAGTTGTGGGCTT
* * ** * * * * ** *
266966 AAAAGGGTGCCACGGAGTTGTGGACTTAGAA--G-GAAAAATAGTGCCACGGAGTT-GTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACATAGT--TATGGACTTAGAAGGC-A
* *
267027 AAAAGGGTGCCATGGAGTTGTGGGCTT
63 AAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
267054 AAAAGGGTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCAC-TGAGTTGTGGACTTAAAAGG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAT-AGTTATGGACTTAGAAGG
267114 GTGCCACAGA
Statistics
Matches: 112, Mismatches: 27, Indels: 16
0.72 0.17 0.10
Matches are distributed among these distances:
85 7 0.06
86 4 0.04
87 6 0.05
88 81 0.72
89 5 0.04
90 4 0.04
91 5 0.04
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (89 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACATAGTTATGGACTTAGAAGGCAAAA
AGAGTGCCACGGAGTTGTGGGCTT
Found at i:267218 original size:30 final size:30
Alignment explanation
Indices: 267115--267219 Score: 156
Period size: 30 Copynumber: 3.5 Consensus size: 30
267105 CTTAAAAGGG
* * *
267115 TGCCACAGAGTTGTGGACTTTGGAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTGG-GATAAAA
*
267146 TGCCACTGAGTCCTGGACTTTGGGATAAAA
1 TGCCACTGAGTCGTGGACTTTGGGATAAAA
267176 TGCCACTGAGTCGTGGACTTTGGGATAAAA
1 TGCCACTGAGTCGTGGACTTTGGGATAAAA
*
267206 TGCCACTAAGTCGT
1 TGCCACTGAGTCGT
267220 CCCCACATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 48 0.71
31 20 0.29
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGGGATAAAA
Found at i:278359 original size:42 final size:42
Alignment explanation
Indices: 278246--278362 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 42
278236 ATCATTCCAA
* * * * * * *
278246 TCTTCATCTTTCGTTTGCTCGTTGGCTTAAACCTAGGAGAGT
1 TCTTCATCATTCATCTGCCCGTTGGCTTAGACCTAGAAGACT
* * ** *
278288 TCTTCATCATTCGTCTGGCCGACGACTTAGACCTAGAAGACT
1 TCTTCATCATTCATCTGCCCGTTGGCTTAGACCTAGAAGACT
*
278330 TCTTTATCATTCATCTGCCCGTTGGCTTAGACC
1 TCTTCATCATTCATCTGCCCGTTGGCTTAGACC
278363 CGGGGGACTT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (42 bp):
TCTTCATCATTCATCTGCCCGTTGGCTTAGACCTAGAAGACT
Found at i:278918 original size:43 final size:43
Alignment explanation
Indices: 278785--278987 Score: 128
Period size: 44 Copynumber: 4.7 Consensus size: 43
278775 TAAGACTCGA
** * *
278785 GAGAC-TCCTTTATCAATTGTCTACCTATCAGCTTAGACCAGG
1 GAGACTTCCTTTATCAATTGTCTACCCGTCAGCTTATACCTGG
* ** ** * * *
278827 GAGACTTCCATTCATCTTTTGTCTACTTGTCAGCTCA-ATCCCGA
1 GAGACTTCC-TTTATCAATTGTCTACCCGTCAGCTTATA-CCTGG
*
278871 GAGACTTCCTTTATCAATTGTCTACCCGTTAGCTTATACCTGG
1 GAGACTTCCTTTATCAATTGTCTACCCGTCAGCTTATACCTGG
* * ** *
278914 GAGAC-TCCTCTTCATC-ATTCATATACCCGTTGGCTTAGT-CTTGG
1 GAGACTTCCT-TT-ATCAATT-GTCTACCCGTCAGCTTA-TACCTGG
* * *
278958 GAGACTTTCTTTATCAATCGTCTGCCCGTC
1 GAGACTTCCTTTATCAATTGTCTACCCGTC
278988 GGTTTAAACC
Statistics
Matches: 124, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
42 9 0.07
43 47 0.38
44 64 0.52
45 4 0.03
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (43 bp):
GAGACTTCCTTTATCAATTGTCTACCCGTCAGCTTATACCTGG
Found at i:280194 original size:168 final size:165
Alignment explanation
Indices: 279961--280872 Score: 853
Period size: 167 Copynumber: 5.5 Consensus size: 165
279951 ATTCTTCTTA
* * * * * * ** *
279961 TTTTTC-AAATTACGAGGTTTTCTTCTTCATAAATTTTTTTG-GGAGGATTTCTCTTAATGTTTA
1 TTTTTCGAAA-TACGATGTTTTCTACTCCGTAAATTTTTTAGAGG-GGATTTTTCTTGGTTTTTA
* * * *
280024 ATTTTTAAAATTCATCAAATATTTTTATTTATTTCAAATTAATTCAGTTTTCAAAAATTCATTTA
64 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCACTCA
* * *
280089 TGTTCATGAGCTTTTGATTTTTTTCTTCAAAATTCCCAT
129 TTTTCATGAG-TTTTGATTTTTTTCTT-GAAACTCCCAT
** * * * *
280128 TTTCCCAAAATACGGTAGTTTTCTATTCCGTAAATTTTTCTAGA-AGGATTTTTCTTGGTTTTTA
1 TTTTTCGAAATACGAT-GTTTTCTACTCCGTAAATTTTT-TAGAGGGGATTTTTCTTGGTTTTTA
* *
280192 ATTTTTAAAATTCATAAAATATTATTATTTATTTCACATTAATTCAGTTTTCAAAAATTCACTCA
64 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCACTCA
280257 TTTTCATGAGTTTTTGATTTTGTTTCTTGAAACT-CC-T
129 TTTTCATGAG-TTTTGATTTT-TTTCTTGAAACTCCCAT
** * * *
280294 TTTTTTTACATACGATTTTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTT-TTAGGTTTTTAA
1 TTTTTCGAAATACGATGTTTTCTACTCCGTAAATTTTTTAGAGGGGATTTTTCTT-GGTTTTTAA
** * * * *
280358 TTTTTAAAATTCATCAAATATCCTTATCTGA-TTCATGTTAATTTACTTTTCAAAAATTCACTCA
65 TTTTTAAAATTCATCAAATATTATTAT-TTATTTCATATTAATTCAGTTTTCAAAAATTCACTCA
* * * *
280422 TTTTCATGAGTTTTCAATTTTTTCCTTGAAATTCCCTT
129 TTTTCATGAGTTTT-GATTTTTTTCTTGAAACTCCCAT
* * ** * * *
280460 TTTTTTGAAATATGACATTTTCTACTCCATAAATTTTTTTTA-AGCGGATTTTTCTTGGTTTTGA
1 TTTTTCGAAATACGATGTTTTCTACTCCGTAAA--TTTTTTAGAGGGGATTTTTCTTGGTTTTTA
* * *
280524 ATTTTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCTGTTTTCAAAAATTCACTTA
64 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCACTCA
*
280589 TTTTCATGAGTTTTTGATTTTTTTCCTTCAAACTCCCAT
129 TTTTCATGAG-TTTTGATTTTTTT-CTTGAAACTCCCAT
* * * ** * *
280628 TTTTTCGAAATATGGTGTTTTCAACTATGTAAATTTTTTA-AGGGGGATTTTTCTTAGTTTTAAA
1 TTTTTCGAAATACGATGTTTTCTACTCCGTAAATTTTTTAGA-GGGGATTTTTCTTGGTTTTTAA
* * * *
280692 TTTTTAAAATTCATCAAATATCATTATTTGA-TTCATATTAATTTAGTTTT-AAAAATTTAATTC
65 TTTTTAAAATTCATCAAATATTATTATTT-ATTTCATATTAATTCAGTTTTCAAAAA-TTCACTC
** *
280755 ATTTTCATGAGTTTTGGA-TTTTTTGATGAAATTCTCC-T
128 ATTTTCATGAGTTTT-GATTTTTTTCTTGAAACTC-CCAT
* * * * * * * * **
280793 TTTTTCCGAGAA-ACTAAGTTTTTTTCTCCGTAAAATTTTTCGAGGGGCTTTTTCTTAGTTTAGA
1 TTTTT-CGA-AATACGATGTTTTCTACTCCGTAAATTTTTTAGAGGGGATTTTTCTTGGTTTTTA
*
280857 ATTTTTAAAACTCATC
64 ATTTTTAAAATTCATC
280873 TAATGTTGTT
Statistics
Matches: 616, Mismatches: 104, Indels: 51
0.80 0.13 0.07
Matches are distributed among these distances:
164 19 0.03
165 119 0.19
166 122 0.20
167 180 0.29
168 168 0.27
169 8 0.01
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (165 bp):
TTTTTCGAAATACGATGTTTTCTACTCCGTAAATTTTTTAGAGGGGATTTTTCTTGGTTTTTAAT
TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCACTCATT
TTCATGAGTTTTGATTTTTTTCTTGAAACTCCCAT
Found at i:280597 original size:332 final size:330
Alignment explanation
Indices: 279990--280871 Score: 976
Period size: 332 Copynumber: 2.6 Consensus size: 330
279980 TTCTTCTTCA
* * * ** *
279990 TAAATTTTTTTG-GGAGGATTTCTCTTAATGTTTAATTTTTAAAATTCATCAAATATTTTTATTT
1 TAAATTTTTTTGAGG-GGATTT-TTTTAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTG
* * * * *
280054 ATTTCAAATTAATTCAGTTTTCAAAAATTCATTTATGTTCATGAGCTTTTGATTTTTTTCTTCAA
64 A-TTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATGAG-TTTTGA-TTTTTTCTT-GA
* * ** * *
280119 AATTCCCATTTTCCCAAAATACGGTAGTTTTCTATTCCGTAAATTTTTCTAGAAGGATTTTTCTT
125 AATTCCCTTTTTTCCAAAATACGACAGTTTTCTACTCCATAAATTTTTCTAGAAGGATTTTTCTT
*
280184 GGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTCACATTAATTCAGTTTTCAAAAA
190 GGTTTTGAATTTTTAAAATTCATAAAATATTATTATTTATTTCACATTAATTCAGTTTTCAAAAA
* ** * *
280249 TTCACTCATTTTCATGAGTTTTTGATTTTGTTT-CTTGAAACT-CC-TTTTTTTTACATACGATT
255 TTCACTCATTTTCATGAGTTTTTGATTTT-TTTCCTTCAAACTCCCATTTTTTCGAAATACGATG
* *
280311 TTTTCTACTCCG
319 TTTTCAACTACG
*
280323 TAAATTTTTTTGAGGGGATTTTTTTAGGTTTTTAATTTTTAAAATTCATCAAATATCCTTATCTG
1 TAAATTTTTTTGAGGGGATTTTTTTA-GTTTTTAATTTTTAAAATTCATCAAATATCATTAT-TG
* * * *
280388 ATTCATGTTAATTTACTTTTCAAAAATTCACTCATTTTCATGAGTTTTCAATTTTTTCCTTGAAA
64 ATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTT-GATTTTTT-CTTGAAA
*** * * *
280453 TTCCCTTTTTTTTGAAATATGACA-TTTTCTACTCCATAAATTTTTTTTA-AGCGGATTTTTCTT
127 TTCCCTTTTTTCCAAAATACGACAGTTTTCTACTCCATAAA-TTTTTCTAGA-AGGATTTTTCTT
* *
280516 GGTTTTGAATTTTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCTGTTTTCAAAAA
190 GGTTTTGAATTTTTAAAATTCATAAAATATTATTATTTATTTCACATTAATTCAGTTTTCAAAAA
* * *
280581 TTCACTTATTTTCATGAGTTTTTGATTTTTTTCCTTCAAACTCCCATTTTTTCGAAATATGGTGT
255 TTCACTCATTTTCATGAGTTTTTGATTTTTTTCCTTCAAACTCCCATTTTTTCGAAATACGATGT
*
280646 TTTCAACTATG
320 TTTCAACTACG
* *
280657 TAAA-TTTTTTAAGGGGGATTTTTCTTAGTTTTAAATTTTTAAAATTCATCAAATATCATTATTT
1 TAAATTTTTTTGA-GGGGATTTTT-TTAGTTTTTAATTTTTAAAATTCATCAAATATCATTA-TT
* **
280721 GATTCATATTAATTTAGTTTT-AAAAATTTAATTCATTTTCATGAGTTTTGGATTTTTTGATGAA
63 GATTCATATTAATTTAGTTTTCAAAAA-TTCATTCATTTTCATGAGTTTT-GATTTTTTCTTGAA
* * * * * * * *
280785 ATTCTCCTTTTTTCCGAGAA-ACTA-AGTTTTTTTCTCCGTAAAATTTTTCGAG-GGGCTTTTTC
126 ATTC-CCTTTTTTCC-AAAATACGACAGTTTTCTACTCCAT-AAATTTTTCTAGAAGGATTTTTC
* * *
280847 TTAGTTTAGAATTTTTAAAACTCAT
188 TTGGTTTTGAATTTTTAAAATTCAT
280872 CTAATGTTGT
Statistics
Matches: 462, Mismatches: 68, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
331 18 0.04
332 149 0.32
333 142 0.31
334 144 0.31
335 9 0.02
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (330 bp):
TAAATTTTTTTGAGGGGATTTTTTTAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTGAT
TCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTGATTTTTTCTTGAAATTCC
CTTTTTTCCAAAATACGACAGTTTTCTACTCCATAAATTTTTCTAGAAGGATTTTTCTTGGTTTT
GAATTTTTAAAATTCATAAAATATTATTATTTATTTCACATTAATTCAGTTTTCAAAAATTCACT
CATTTTCATGAGTTTTTGATTTTTTTCCTTCAAACTCCCATTTTTTCGAAATACGATGTTTTCAA
CTACG
Found at i:281449 original size:13 final size:13
Alignment explanation
Indices: 281431--281458 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
281421 ACTTTTTACC
281431 ATGTATCGATACA
1 ATGTATCGATACA
281444 ATGTATCGATACA
1 ATGTATCGATACA
281457 AT
1 AT
281459 ATCCCACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:281450 original size:33 final size:33
Alignment explanation
Indices: 281408--281480 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
281398 GCTGTTAGGC
** * *
281408 ACAATGTATCAATACTTTTTACCATGTATCGAT
1 ACAATGTATCAATACAATATACCACGTATCGAT
* *
281441 ACAATGTATCGATACAATATCCCACGTATCGAT
1 ACAATGTATCAATACAATATACCACGTATCGAT
281474 ACAATGT
1 ACAATGT
281481 CCCATGTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (33 bp):
ACAATGTATCAATACAATATACCACGTATCGAT
Found at i:281471 original size:20 final size:20
Alignment explanation
Indices: 281446--281496 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
281436 TCGATACAAT
281446 GTATCGATACAATATCCCAC
1 GTATCGATACAATATCCCAC
* *
281466 GTATCGATACAATGTCCCAT
1 GTATCGATACAATATCCCAC
281486 GTATCGATACA
1 GTATCGATACA
281497 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (20 bp):
GTATCGATACAATATCCCAC
Found at i:281550 original size:20 final size:19
Alignment explanation
Indices: 281525--281575 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
281515 CTGCCAGTTT
*
281525 TATGTATCGATATAATTAAG
1 TATGTATCGATAGAA-TAAG
*
281545 TATGTATCGATAGAATGAG
1 TATGTATCGATAGAATAAG
*
281564 CATGTATCGATA
1 TATGTATCGATA
281576 CAAAGCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (19 bp):
TATGTATCGATAGAATAAG
Found at i:298463 original size:31 final size:32
Alignment explanation
Indices: 298395--298472 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
298385 TCAGATTTAA
* *
298395 CTAG-ATGTATCGATATATTTGGCTCAAAAAC
1 CTAGAATGTATCGATATATTTAGATCAAAAAC
*
298426 CCAGAATGTATCGATATATTTAGATC-AAAAC
1 CTAGAATGTATCGATATATTTAGATCAAAAAC
*
298457 CTAGAATGTATTGATA
1 CTAGAATGTATCGATA
298473 CAATGAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 22 0.54
32 19 0.46
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (32 bp):
CTAGAATGTATCGATATATTTAGATCAAAAAC
Found at i:298484 original size:51 final size:50
Alignment explanation
Indices: 298428--298547 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 50
298418 TCAAAAACCC
* * * **
298428 AGAATGTATCGATATATTTAG-ATCAAAACCTAGAATGTATTGATACAATGA
1 AGAATGTATCGATACATTT-GCATCAAAACCCAGAATATATCAATACAAT-A
*
298479 AGAATGTATTGATACATTTGCATCAAAACCCAGAATATATCAATACAATA
1 AGAATGTATCGATACATTTGCATCAAAACCCAGAATATATCAATACAATA
*
298529 AAAATGTATCGATACATTT
1 AGAATGTATCGATACATTT
298548 TCTTTCTAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 19 0.32
51 41 0.68
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (50 bp):
AGAATGTATCGATACATTTGCATCAAAACCCAGAATATATCAATACAATA
Found at i:298610 original size:20 final size:20
Alignment explanation
Indices: 298585--298675 Score: 173
Period size: 20 Copynumber: 4.5 Consensus size: 20
298575 ACAAGGTCTA
298585 GTATTGATACATTCACTAAT
1 GTATTGATACATTCACTAAT
298605 GTATTGATACATTCACTAAT
1 GTATTGATACATTCACTAAT
298625 GTATTGATACATTCACTAAT
1 GTATTGATACATTCACTAAT
*
298645 GTATTGATACATTCACTTAT
1 GTATTGATACATTCACTAAT
298665 GTATTGATACA
1 GTATTGATACA
298676 AATTGTAGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
GTATTGATACATTCACTAAT
Found at i:299402 original size:52 final size:52
Alignment explanation
Indices: 299325--299464 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
299315 TTTGGAATGA
* * *
299325 AAATGTATCGATGCATTTTTCATTGTATCGATACATTTTAGGTTTTGAAC-C
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTGAACTC
* * * * * *
299376 AAATGTATTGGGTACATTCTTCATTGTATTGATACATTCTGGGTTTTGGACTT
1 AAATGTA-TCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTGAACTC
* * *
299429 AAATGTATCGATACATTCTTTAATGTATCAATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
299465 GCAGGCAAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
51 7 0.10
52 58 0.81
53 7 0.10
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTGAACTC
Found at i:301287 original size:13 final size:13
Alignment explanation
Indices: 301269--301293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301259 TACTATGAAC
301269 ATGTATCGATACA
1 ATGTATCGATACA
301282 ATGTATCGATAC
1 ATGTATCGATAC
301294 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:301291 original size:32 final size:33
Alignment explanation
Indices: 301250--301314 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
301240 TGCTAGTTTC
*
301250 ATGTATCGATACTATG-AACATGTATCGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
* *
301282 ATGTATCGATACTAAGCAATATGTATTGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
301315 TTAGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACTAAGCAACATGTATCGATACA
Found at i:302370 original size:12 final size:12
Alignment explanation
Indices: 302350--302380 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
302340 CTAGCATACA
*
302350 ACTACTCCTATG
1 ACTAATCCTATG
302362 ACTAATCCTATG
1 ACTAATCCTATG
302374 ACTAATC
1 ACTAATC
302381 ATTACTCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (12 bp):
ACTAATCCTATG
Found at i:310484 original size:13 final size:13
Alignment explanation
Indices: 310466--310491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310456 CATTATTCAA
310466 TGTATCGATACAT
1 TGTATCGATACAT
310479 TGTATCGATACAT
1 TGTATCGATACAT
310492 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:310555 original size:20 final size:19
Alignment explanation
Indices: 310530--310603 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
310520 TTTACCCAGA
310530 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
310550 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
310570 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
310590 TGTATCGATACATT
1 TGTATCGATACATT
310604 CAGGCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:322193 original size:11 final size:11
Alignment explanation
Indices: 322166--322248 Score: 69
Period size: 12 Copynumber: 6.9 Consensus size: 11
322156 CTCTTCTAAA
322166 AAAAAAAGAAAC
1 AAAAAAA-AAAC
*
322178 AAAAACAAAAAT
1 AAAAA-AAAAAC
322190 AAAAAAAAAAC
1 AAAAAAAAAAC
322201 AAAAAACAAAA-
1 AAAAAA-AAAAC
*
322212 AAAAAACAAAAT
1 AAAAAA-AAAAC
322224 AAAGAAAAAAGAC
1 AAA-AAAAAA-AC
322237 AGAAAAGAAAAA
1 A-AAAA-AAAAA
322249 AACCTGCTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
11 22 0.36
12 23 0.38
13 10 0.16
14 6 0.10
ACGTcount: A:0.84, C:0.07, G:0.06, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:322198 original size:17 final size:17
Alignment explanation
Indices: 322178--322250 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 17
322168 AAAAAGAAAC
322178 AAAAACAAAAATAAAAA
1 AAAAACAAAAATAAAAA
*
322195 AAAAACAAAAAACAAAAA
1 AAAAAC-AAAAATAAAAA
322213 AAAAAC-AAAATAAAGAA
1 AAAAACAAAAATAAA-AA
*
322230 AAAAGACAGAAAAGAAAAA
1 AAAA-ACA-AAAATAAAAA
322249 AA
1 AA
322251 CCTGCTTAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.15
17 12 0.25
18 18 0.38
19 4 0.08
20 7 0.15
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.03
Consensus pattern (17 bp):
AAAAACAAAAATAAAAA
Found at i:322205 original size:24 final size:22
Alignment explanation
Indices: 322163--322222 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
322153 CTTCTCTTCT
*
322163 AAAAAAAAAAGAAACAAAAACA
1 AAAAAAAAAAAAAACAAAAACA
322185 AAAATAAAAAAAAAACAAAAAACA
1 AAAA-AAAAAAAAAAC-AAAAACA
*
322209 AAAAAAAAACAAAA
1 AAAAAAAAAAAAAA
322223 TAAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 4 0.12
23 19 0.56
24 11 0.32
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAAACAAAAACA
Found at i:322206 original size:35 final size:35
Alignment explanation
Indices: 322166--322250 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 35
322156 CTCTTCTAAA
322166 AAAAAAAGAAACAAAAACAAAAATAAA-AAAAAA-AC
1 AAAAAAAGAAA-AAAAAC-AAAATAAAGAAAAAAGAC
*
322201 AAAAAACAAAAAAAAAACAAAATAAAGAAAAAAGAC
1 AAAAAA-AGAAAAAAAACAAAATAAAGAAAAAAGAC
*
322237 -AGAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
322251 CCTGCTTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 16 0.36
35 22 0.50
36 6 0.14
ACGTcount: A:0.85, C:0.07, G:0.06, T:0.02
Consensus pattern (35 bp):
AAAAAAAGAAAAAAAACAAAATAAAGAAAAAAGAC
Found at i:322250 original size:1 final size:1
Alignment explanation
Indices: 322163--322233 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
322153 CTTCTCTTCT
* * * * * * * * *
322163 AAAAAAAAAAGAAACAAAAACAAAAATAAAAAAAAAACAAAAAACAAAAAAAAAACAAAATAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
322228 AAAAAA
1 AAAAAA
322234 GACAGAAAAG
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:326073 original size:13 final size:13
Alignment explanation
Indices: 326055--326079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326045 CAAAGATTAG
326055 TGTATCGATACAA
1 TGTATCGATACAA
326068 TGTATCGATACA
1 TGTATCGATACA
326080 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:326803 original size:55 final size:52
Alignment explanation
Indices: 326742--327491 Score: 204
Period size: 49 Copynumber: 14.7 Consensus size: 52
326732 GGACCAATAC
*
326742 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATG-TCAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAG---AAGAATGCT-AATGT
** * * ** *
326797 GCTGATTCACGGTTAGCGATATTAGACTTGAAGATGAGAAGAATGCTAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * * ** * *
326849 GCTGATTCAAGGCCAACAACATTGAGTTTCAAAGATGACGAAG-GCGCAAATAT
1 GCTGATTCACGGCCAACGATATTGGGTTT-AAAGATGA-GAAGAATGCTAATGT
* * * ** * * *
326902 GCTGATTCAAGGCCAGCAATATTGGACTTAAAGAT--GAAG-GTGCCAAAGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * * * * * ** * *
326951 GCTGATTCAAGGCCTAGCGACATTGGACTTAAAAGTTGACAA-AGGCGCCAATAT
1 GCTGATTCACGGCC-AACGATATTGG-GTTTAAAGATGAGAAGA-ATGCTAATGT
* * ** * *
327005 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAG-GTGCCAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * ** * ** * ** * *
327054 GCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGACAA-AGGCGCCAATAT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGA-ATGCTAATGT
* ** * *
327106 GCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--GAAG-GTGCCAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * ** * * * * *
327155 GCTGATTCAAGGCCAGCGACATTGGACTTAATGATGACAA-AGGTGCCAATAT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGA-ATGCTAATGT
* * ** *
327207 GCTGATTCAAGGCCAGCGATATTGGAATTAAAGAT--GAAG-ATGCCAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * ** * ** * *
327256 GCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAA-AGGCGCCAATAT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGA-ATGCTAATGT
* * ** * *
327308 GTTGATTCTA-GGCCAGCGATATTGGACTTAAAGAT--GAAG-GTGCCAATGT
1 GCTGATTC-ACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * ** * * * * *
327357 GCTGATTCAAGGCCAGCGACATTGGACTTAAACATGACAA-AGGTGCCAATAT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGA-ATGCTAATGT
* * ** *
327409 GCTGATTCAAGGCCAACGGTATTGGACTTAAAGAT-A-AAG-ATGCCAATGT
1 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
* * * *
327458 GATGATTCATGGCCAGCGACATT-GGTCTTAAAGA
1 GCTGATTCACGGCCAACGATATTGGGT-TTAAAGA
327492 CAAGGTGCCA
Statistics
Matches: 559, Mismatches: 103, Indels: 72
0.76 0.14 0.10
Matches are distributed among these distances:
48 2 0.00
49 216 0.39
50 19 0.03
51 15 0.03
52 200 0.36
53 51 0.09
54 25 0.04
55 31 0.06
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAGAATGCTAATGT
Found at i:327130 original size:52 final size:51
Alignment explanation
Indices: 326735--327724 Score: 936
Period size: 52 Copynumber: 19.8 Consensus size: 51
326725 GATAAAGGGA
* * * **
326735 CCAATACGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G-AAAAGG-TG
* * * ** * * * *
326790 TCAATGTGCTGATTCACGGTTAGCGATATTAGACTTGAAGATGAGAAGAATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAG-GTG
* * * * * * * *
326842 CTAATGTGCTGATTCAAGGCCAACAACATT-GAGTTTCAAAGATGACGAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGA-CTT-AAAGATGA-AAAGGTG
* *
326895 CAAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATG--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * *
326944 CCAA-AGTGCTGATTCAAGGCCTAGCGACATTGGACTTAAAAGTTGACAAAGGCG
1 CCAATA-TGCTGATTCAAGGCC-AGCGATATTGGACTT-AAAGATGA-AAAGGTG
326998 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * * * *
327047 CCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
*
327099 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * *
327148 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAATGATGACAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
* *
327200 CCAATATGCTGATTCAAGGCCAGCGATATTGGAATTAAAGATG--AAGATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * *
327249 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
* *
327301 CCAATATGTTGATTCTAGGCCAGCGATATTGGACTTAAAGATG--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * *
327350 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAACATGACAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
* * *
327402 CCAATATGCTGATTCAAGGCCAACGGTATTGGACTTAAAGAT--AAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * * * * *
327451 CCAATGTGATGATTCATGGCCAGCGACATTGGTCTT-AA-A-GACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
*
327499 CCAATATACTGATTCAAGGCCAGCGATATTGGAC-T-----T--AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * * * * * *
327542 CC-A-ATGTTGATTCAAGGCTAGTGACATTGGTCTCAAAGATGATAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
* *
327592 CTAATATGCTGATTCAAGGCCAACGATATTGGAC-T-----T--AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
* * * *
327635 CCAATGTGCTGATTCAAGG-CAGTGACATTGGACTTAAAGATGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AAAGGTG
*
327686 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
327725 AGAAAATGCC
Statistics
Matches: 765, Mismatches: 122, Indels: 99
0.78 0.12 0.10
Matches are distributed among these distances:
41 23 0.03
42 12 0.02
43 32 0.04
46 1 0.00
47 3 0.00
48 37 0.05
49 234 0.31
50 20 0.03
51 33 0.04
52 256 0.33
53 51 0.07
54 30 0.04
55 33 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (51 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAGGTG
Found at i:327131 original size:101 final size:101
Alignment explanation
Indices: 326791--327724 Score: 1233
Period size: 101 Copynumber: 9.4 Consensus size: 101
326781 AAAAGGATGT
* * ** * * * *
326791 CAATGTGCTGATTCACGGTTAGCGATATTAGACTTGAAGATGAGAAGAATGCTAATGTGCTGATT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAG-GTGCCAATGTGCTGATT
* * * *
326856 CAAGGCCAACAACATT-GAGTTTCAAAGATGACGAAGGCGC
63 CAAGGCCAGCGACATTGGA-CTT-AAAGATGACAAAGGCGC
* * *
326896 AAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGCCAAAGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
*
326961 GGCCTAGCGACATTGGACTTAAAAGTTGACAAAGGCGC
66 GGCC-AGCGACATTGGACTT-AAAGATGACAAAGGCGC
326999 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* *
327064 GGCTAGTGACATTGGACTTAAAGATGACAAAGGCGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
*
327100 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* *
327165 GGCCAGCGACATTGGACTTAATGATGACAAAGGTGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
* *
327201 CAATATGCTGATTCAAGGCCAGCGATATTGGAATTAAAGATGAAGATGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
327266 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
* *
327302 CAATATGTTGATTCTAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* *
327367 GGCCAGCGACATTGGACTTAAACATGACAAAGGTGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
* * * * * *
327403 CAATATGCTGATTCAAGGCCAACGGTATTGGACTTAAAGATAAAGATGCCAATGTGATGATTCAT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* *
327468 GGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
*
327500 CAATATACTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT--TGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * * * *
327557 GGCTAGTGACATTGGTCTCAAAGATGATAAAGGCGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
* *
327593 TAATATGCTGATTCAAGGCCAACGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* ** *
327652 GG-CAGTGACATTGGACTTAAAGATGATGAAGGTGC
66 GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
*
327687 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
327725 AGAAAATGCC
Statistics
Matches: 749, Mismatches: 69, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
89 23 0.03
90 2 0.00
91 13 0.02
92 2 0.00
93 53 0.07
94 60 0.08
95 10 0.01
97 39 0.05
98 3 0.00
99 1 0.00
100 2 0.00
101 378 0.50
102 35 0.05
103 93 0.12
104 2 0.00
105 33 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (101 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
GGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
Found at i:327645 original size:43 final size:42
Alignment explanation
Indices: 327584--327673 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
327574 TCAAAGATGA
* *
327584 TAAAGGCGCTAATATGCTGATTCAAGGCCAACGATATTGGACT
1 TAAAGGCGCCAATATGCTGATTCAAGG-CAACGACATTGGACT
* * **
327627 TAAAGGTGCCAATGTGCTGATTCAAGGCAGTGACATTGGACT
1 TAAAGGCGCCAATATGCTGATTCAAGGCAACGACATTGGACT
327669 TAAAG
1 TAAAG
327674 ATGATGAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 17 0.41
43 24 0.59
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (42 bp):
TAAAGGCGCCAATATGCTGATTCAAGGCAACGACATTGGACT
Found at i:327837 original size:35 final size:36
Alignment explanation
Indices: 327792--327996 Score: 207
Period size: 35 Copynumber: 5.9 Consensus size: 36
327782 TGAAAATGAG
327792 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
*
327826 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
* *
327862 AAAGA-TGCCACGGAGTTATGGTCTTTGAAAA--GAA
1 AAAGAGTGCCACGGAGTTGTGGACTTT-AAAAGGGAA
* * *
327896 CAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGGA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
* * * * *
327931 AACGGGTGCCACAGAGTCGTGGACTTT-GAA--G-A
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
*
327963 AAAGAGATGCCATGGAGTTGTGGAC-TTAAAAGGG
1 AAAGAG-TGCCACGGAGTTGTGGACTTTAAAAGGG
327997 TGTTACAGAG
Statistics
Matches: 141, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
32 7 0.05
33 22 0.16
34 30 0.21
35 43 0.30
36 39 0.28
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (36 bp):
AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
Found at i:327910 original size:34 final size:34
Alignment explanation
Indices: 327771--328053 Score: 201
Period size: 36 Copynumber: 8.3 Consensus size: 34
327761 TTCCACTGAT
* *
327771 TTGTGGGCTTTTGAAAATGAGAAAGATGCCACGGAG
1 TTGTGGGC-TTT-AAAAGGAAAAAGATGCCACGGAG
*
327807 TTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTTAAAA-GGAAAAAGA-TGCCACGGAG
327842 TTGTGGGCTTTAAAAGGGAAAAAGATGCCACGGAG
1 TTGTGGGCTTTAAAA-GGAAAAAGATGCCACGGAG
* * * *
327877 TTATGGTCTTTGAAAA-GAACAAGGTGCCACGGAG
1 TTGTGGGCTTT-AAAAGGAAAAAGATGCCACGGAG
** * *
327911 TTGTGGGCTTTAAAAGGGGAAACGGGTGCCACAGAG
1 TTGTGGGCTTTAAAA--GGAAAAAGATGCCACGGAG
* * * *
327947 TCGTGGACTTT-GAA-GAAAAGAGATGCCATGGAG
1 TTGTGGGCTTTAAAAGGAAAA-AGATGCCACGGAG
* ** *
327980 TTGTGGAC-TTAAAAGG-----G-TGTTACAGAG
1 TTGTGGGCTTTAAAAGGAAAAAGATGCCACGGAG
* *
328007 TTGTGGGCTTTGAAAAAAGAAAAAGGTGCCACGGAG
1 TTGTGGGCTTT--AAAAGGAAAAAGATGCCACGGAG
328043 TTGTGGGCTTT
1 TTGTGGGCTTT
328054 GTAGAAAAGA
Statistics
Matches: 195, Mismatches: 33, Indels: 38
0.73 0.12 0.14
Matches are distributed among these distances:
27 13 0.07
28 3 0.02
30 5 0.03
32 6 0.03
33 26 0.13
34 35 0.18
35 39 0.20
36 68 0.35
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.23
Consensus pattern (34 bp):
TTGTGGGCTTTAAAAGGAAAAAGATGCCACGGAG
Found at i:327916 original size:69 final size:69
Alignment explanation
Indices: 327792--327996 Score: 233
Period size: 70 Copynumber: 3.0 Consensus size: 69
327782 TGAAAATGAG
327792 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGATGCCACGGAGTTGTGGACTTTGAAAA--G-AAAAGAGTGCCACGGAGTTGTGGGCTTTAA
327855 AAGGGAA
63 AAGGGAA
* *
327862 AAAGATGCCACGGAGTTATGGTCTTTGAAAAGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGATGCCACGGAGTTGTGGACTTTGAAAAGAA-AAGAGTGCCACGGAGTTGTGGGCTTTAAAA
327926 GGGGAA
65 -GGGAA
** * * * * *
327932 ACGGGTGCCACAGAGTCGTGGACTTTG--AAGAAAAGAGATGCCATGGAGTTGTGGAC-TTAAAA
1 AAAGATGCCACGGAGTTGTGGACTTTGAAAAGAAAAGAG-TGCCACGGAGTTGTGGGCTTTAAAA
327994 GGG
65 GGG
327997 TGTTACAGAG
Statistics
Matches: 118, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
67 6 0.05
68 12 0.10
69 44 0.37
70 50 0.42
71 2 0.02
72 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
AAAGATGCCACGGAGTTGTGGACTTTGAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
GGAA
Found at i:328085 original size:31 final size:30
Alignment explanation
Indices: 328050--328107 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
328040 GAGTTGTGGG
328050 CTTTGTAGA-AAAGATGCCACTAAGTCGTAGA
1 CTTTG-AGACAAA-ATGCCACTAAGTCGTAGA
* *
328081 CTTTGGGACAAAATGCCCCTAAGTCGT
1 CTTTGAGACAAAATGCCACTAAGTCGT
328108 GGGCTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (30 bp):
CTTTGAGACAAAATGCCACTAAGTCGTAGA
Found at i:329379 original size:11 final size:11
Alignment explanation
Indices: 329364--329410 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
329354 GCCTTTGCAC
329364 TTTTTTTGTGT
1 TTTTTTTGTGT
329375 GTTTTTTT-TGT
1 -TTTTTTTGTGT
329386 TTTTTTTG-GT
1 TTTTTTTGTGT
*
329396 TTTTTTTTTGT
1 TTTTTTTGTGT
329407 TTTT
1 TTTT
329411 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.50
11 9 0.28
12 7 0.22
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:329388 original size:21 final size:21
Alignment explanation
Indices: 329364--329410 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
329354 GCCTTTGCAC
329364 TTTTTTTGTGTGTTTTTTTTGT
1 TTTTTTTG-GTGTTTTTTTTGT
*
329386 TTTTTTTGGTTTTTTTTTTGT
1 TTTTTTTGGTGTTTTTTTTGT
329407 TTTT
1 TTTT
329411 ATTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (21 bp):
TTTTTTTGGTGTTTTTTTTGT
Found at i:329415 original size:12 final size:11
Alignment explanation
Indices: 329364--329428 Score: 69
Period size: 11 Copynumber: 5.8 Consensus size: 11
329354 GCCTTTGCAC
*
329364 TTTTTTTGTGT
1 TTTTTTTTTGT
*
329375 GTTTTTTTTG-
1 TTTTTTTTTGT
*
329385 TTTTTTTTGGT
1 TTTTTTTTTGT
329396 TTTTTTTTTGT
1 TTTTTTTTTGT
*
329407 TTTTATTTTTAT
1 TTTT-TTTTTGT
329419 TTTTATTTTT
1 TTTT-TTTTT
329429 TTTAAAAGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
10 8 0.17
11 22 0.48
12 16 0.35
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:336396 original size:13 final size:13
Alignment explanation
Indices: 336378--336402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
336368 CAAAGATTAG
336378 TGTATCGATACAA
1 TGTATCGATACAA
336391 TGTATCGATACA
1 TGTATCGATACA
336403 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:336481 original size:19 final size:19
Alignment explanation
Indices: 336457--336502 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
336447 CGATACATTG
336457 TATCGATACAAAACTTATA
1 TATCGATACAAAACTTATA
* *
336476 TATCGATACAACACTTATG
1 TATCGATACAAAACTTATA
336495 TATCGATA
1 TATCGATA
336503 TATTGTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (19 bp):
TATCGATACAAAACTTATA
Found at i:337169 original size:29 final size:29
Alignment explanation
Indices: 337136--337226 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
337126 GATGCCTTTT
337136 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
337165 CCTTTC--AGTCCTCA-AAG-AGCTGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGG-CA
*
337191 CCTTTCAAAGCCCACACAAGTTGGTAGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
337220 CCTTTCA
1 CCTTTCA
337227 GTCCTCAAAG
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
25 4 0.09
26 10 0.22
27 6 0.13
28 6 0.13
29 17 0.37
30 3 0.07
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (29 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:337197 original size:26 final size:26
Alignment explanation
Indices: 337165--337252 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
337155 GTTGGTGGCA
337165 CCTTTCAGTCCTCAAAGAGCTGGACG
1 CCTTTCAGTCCTCAAAGAGCTGGACG
* * * * *
337191 CCTTTCAAAGCCCACACA-AGTTGGTAGCA
1 CCTTTC--AGTCCTCAAAGAGCTGG-A-CG
* *
337220 CCTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAGTCCTCAAAGAGCTGGACG
337246 CCTTTCA
1 CCTTTCA
337253 AAGCCCACAC
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
26 13 0.29
27 13 0.29
28 12 0.27
29 7 0.16
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCTGGACG
Found at i:337405 original size:61 final size:59
Alignment explanation
Indices: 337109--337431 Score: 360
Period size: 55 Copynumber: 5.5 Consensus size: 59
337099 TTTCACTTTT
* *
337109 CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACGCC-TTTCCTTT-AAAGCCCACACAAGTTGGTGGCACCTTC
* * *
337170 CAGTCCTCAAAGAGCTGGACGCCTTT-C---AAAGCCCACACAAGTTGGTAGCACCTTT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
337225 CAGTCCTCAAAGAGCAGGATGCCTTT-C---AAAGCCCACACAAATTGGT-GCATTTTC
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * **
337279 CAGTCCTCAAACAGTAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTT-AAAGCCCACACAAGTTGGTGGCACCTTC
* *
337339 CAGTCCTCAAAGATCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
1 CAGTCCTCAAAGAGCAGGACGCCTT-TCC-TTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
337399 CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
1 C-AGTCCTCAAAGAGCAGGACGC-CTTTCCTTT
337432 CGCCTTTTTA
Statistics
Matches: 230, Mismatches: 22, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
54 28 0.12
55 71 0.31
59 19 0.08
60 39 0.17
61 68 0.30
62 5 0.02
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (59 bp):
CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:337595 original size:60 final size:59
Alignment explanation
Indices: 337442--337693 Score: 291
Period size: 60 Copynumber: 4.3 Consensus size: 59
337432 CGCCTTTTTA
* *
337442 TCCTCAAAGAGCAGGATG----CCTTTTAAAGCCCACACAAGCTGGTGGCAC-CTTCAG
1 TCCTCAAAGAGCAGGATGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* *
337496 TCCTCAAAGAGCAGGACAAGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAG
1 TCCTCAAAGAGCAGG--ATGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* * *
337557 TCCTCAAAGAGCAGGATGTTTTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTTCCAG
1 TCCTCAAAGAGCAGGATGTTTTCCTTTT--AAAGCCCACACAAGTTGGTGGCACTTTTCAG
* * * * *
337617 TCCTCAAAGGGCAGGACGTCTTTTCTTCTCAAAGCCCACACGAGTTGGTGGCACTTTTCAG
1 TCCTCAAAGAGCAGGATGT-TTTCCTT-TTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
*
337678 TCCTCAAAGAGTAGGA
1 TCCTCAAAGAGCAGGA
337694 CACACTTCCT
Statistics
Matches: 167, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
54 15 0.09
56 2 0.01
59 11 0.07
60 73 0.44
61 65 0.39
62 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (59 bp):
TCCTCAAAGAGCAGGATGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
Found at i:337597 original size:214 final size:213
Alignment explanation
Indices: 337228--337634 Score: 572
Period size: 214 Copynumber: 1.9 Consensus size: 213
337218 CACCTTTCAG
* **
337228 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAATTGGTGCATTTTCCAGTCCTCAAACAG
1 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAACTGGTGCACCTTCCAGTCCTCAAACAG
* ** *
337293 TAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGATCAGGA
66 CAGGACAACTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
337358 TGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
131 TG-CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGACGC
337422 TCTCTCCTTTCGCCTTTTTA
194 TCTCTCCTTTCGCCTTTTTA
* * *
337442 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-CAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAACTGGT-GCACCTTCCAGTCCTCAAACA
* * *
337506 GCAGGACAAGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCA
65 GCAGGACAACTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCA
* * *
337570 GGATG-TTTTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGA
128 GGATGCTTCTCCTTTT--AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
337633 CG
191 CG
337635 TCTTTTCTTC
Statistics
Matches: 171, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
213 8 0.05
214 99 0.58
215 60 0.35
216 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (213 bp):
TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAACTGGTGCACCTTCCAGTCCTCAAACAG
CAGGACAACTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
TGCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTC
TCTCCTTTCGCCTTTTTA
Found at i:337624 original size:275 final size:268
Alignment explanation
Indices: 337173--337694 Score: 669
Period size: 275 Copynumber: 1.9 Consensus size: 268
337163 CACCTTTCAG
* *
337173 TCCTCAAAGAGCTGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCACCTTTCAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTAGCACCTTTCAGTCCTCAAAGA
*
337238 GCAGGATGCCTTTCAAAGCCCACACAAATTGGTGCATTTTCCAGTCCTCAAACAGTAGGACGCCT
66 GCAGGATGCCTTTCAAAGCCCACACAAATTGGTGCATTTTCCAGTCCTCAAACAGCAGGACG-CT
** * *
337303 TTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGATCAGGATGCCTTCTCC
130 TTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTT-TCC
*
337368 TT-TTAAAGCCCACACAAGTTGGTGGCACTTC-CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
194 TTCTCAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCAAAGAGCAGGACGCTCTCTCCTT
337431 TCGCCTTTTTA
258 TCGCCTTTTTA
* * *
337442 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTAGCACCTTTCAGTCCTCAAAGA
* * * * *
337506 GCAGGACAAGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCA
66 GCAGG---A---TGCCTTTCAAAGCCCACACAAATTGGT-GCA-TTTTCCAGTCCTCAAACAGCA
* *
337570 GGATG-TTTTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGA
123 GGACGCTTTTC--TTT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
* * * * *
337633 CGTCTTTTCTTCTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGAC
185 CGCCTTTCCTTCTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGAC
337695 ACACTTCCTT
Statistics
Matches: 217, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
268 20 0.09
269 44 0.20
271 1 0.00
273 5 0.02
274 28 0.13
275 109 0.50
276 10 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (268 bp):
TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTAGCACCTTTCAGTCCTCAAAGA
GCAGGATGCCTTTCAAAGCCCACACAAATTGGTGCATTTTCCAGTCCTCAAACAGCAGGACGCTT
TTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCCTT
CTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCG
CCTTTTTA
Found at i:337651 original size:121 final size:114
Alignment explanation
Indices: 337435--337693 Score: 335
Period size: 121 Copynumber: 2.2 Consensus size: 114
337425 CTCCTTTCGC
337435 CTTTTTA-TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCC
1 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCC
*
337499 TCAAAGAGCAGGACAAGTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
66 TCAAAGAGCAGGAC-AGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
337549 CTTTTTAGTCCTCAAAGAGCAGGATGTTTTCTTTTTGCAAAG-CCACACAAGTTGGTGGCACCTT
1 CTTTTTAGTCCTCAAAGAGCAGGATG----CCTTTT--AAAGCCCACACAAGCTGGTGGCACCTT
* * *
337613 CCAGTCCTCAAAGGGCAGGAC-GTCTTTTCTTCTCAAAGCCCACACGAGTTGGTGGCA
60 -CAGTCCTCAAAGAGCAGGACAGT-TTTCCTT-TCAAAGCCCACACAAGTTGGTGGCA
* *
337670 CTTTTCAGTCCTCAAAGAGTAGGA
1 CTTTTTAGTCCTCAAAGAGCAGGA
337694 CACACTTCCT
Statistics
Matches: 127, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
114 7 0.06
115 18 0.14
119 7 0.06
120 27 0.21
121 68 0.54
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (114 bp):
CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCC
TCAAAGAGCAGGACAGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:338672 original size:13 final size:13
Alignment explanation
Indices: 338654--338679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338644 CATTATTCAA
338654 TGTATCGATACAT
1 TGTATCGATACAT
338667 TGTATCGATACAT
1 TGTATCGATACAT
338680 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:338743 original size:20 final size:19
Alignment explanation
Indices: 338718--338788 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
338708 TTTACCCACA
*
338718 TGTATCGATACATTTTGCGT
1 TGTATCGATACATTTT-CAT
**
338738 TGTATCGATACAATGCTCAT
1 TGTATCGATAC-ATTTTCAT
*
338758 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
338778 TGTATCGATAC
1 TGTATCGATAC
338789 CTTCACTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:341131 original size:51 final size:51
Alignment explanation
Indices: 341075--341519 Score: 341
Period size: 51 Copynumber: 8.6 Consensus size: 51
341065 TTAATTTTCT
*
341075 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* * * * *
341126 TAATTTTCCATAATTGGGGATACTCCAACTCCGATTTTATTT-TCGAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACAC
* *
341177 CAATTTTCCACAATCGGGGATACTCCAACCCC-AGTTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGA-TTTTATTTCT-AAAACAC
* * * * * *
341228 CAATTTTCCTTTAATCGGGGATACTCTAACTCTGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACAC
* * * * * * ** * *
341281 CAATTTTTCACAAACGGGGATTCTCCAACCCTG--TTAATCATCGGGGATACTC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC--TAAAACAC
*** ** * *
341333 CAACCCCGTT-ATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACAC
1 CAA--TTTTTCATAATC--GGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* * * * * *
341387 CAATTCTCCATAATCGGGGATACTCCAACTCCAATTTTATTT-T-TAATAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* *
341436 CAATTTTTCAAAATCGGGGATACTCCAACTCCGATTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACAC
* *
341487 CAATTTCTCACAATCGGGGATACTCCAACCCCG
1 CAATTTTTCATAATCGGGGATACTCCAACCCCG
341520 CTATTTTTGC
Statistics
Matches: 309, Mismatches: 67, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
49 43 0.14
50 8 0.03
51 154 0.50
52 52 0.17
53 22 0.07
54 9 0.03
55 15 0.05
56 2 0.01
57 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
Found at i:341558 original size:210 final size:209
Alignment explanation
Indices: 341141--341544 Score: 530
Period size: 210 Copynumber: 1.9 Consensus size: 209
341131 TTCCATAATT
* *
341141 GGGGATACTCCAACTCCGATTTTATTTTCGAAACACCAATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
* ** * *
341206 CCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCTAACTCTGATTTTATTT
66 CCCAATTTTATTTT-AAAACACCAATTTTCCTAAAATCGGGGATACTCCAACTCCGATTTTATTT
* * * *
341271 CCAAAAACACCAATTTTTCACAAACGGGGATTCTCCAACCCTGTTAATCATCGGGGATACTCCAA
130 CCAAAAACACCAATTTCTCACAAACGGGGATACTCCAACCCCGCTAATCATCGGGGATACTCCAA
*
341336 CCCCGTTATTTTCGA
195 CCACGTTATTTTCGA
* *
341351 GGGGATACTCCAAC-CTCGGTTTTA-TTTCTAAAACACCAATTCTCCATAATCGGGGATACTCCA
1 GGGGATACTCCAACTC-CGATTTTATTTTC-AAAACACCAATTCTCCACAATCGGGGATACTCCA
* * * *
341414 ACTCCAATTTTATTTT-TAATACCAATTTTTC-AAAATCGGGGATACTCCAACTCCGATTTTATT
64 ACCCCAATTTTATTTTAAAACACCAATTTTCCTAAAATCGGGGATACTCCAACTCCGATTTTATT
* * * **
341477 TTC-AAAACACCAATTTCTCACAATCGGGGATACTCCAACCCCGCTATTTTTGCGGGGATACTCC
129 TCCAAAAACACCAATTTCTCACAAACGGGGATACTCCAACCCCGCTAATCAT-CGGGGATACTCC
341541 AACC
193 AACC
341545 GTAATTTTAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
206 40 0.24
207 46 0.27
208 12 0.07
209 5 0.03
210 66 0.39
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (209 bp):
GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
CCCAATTTTATTTTAAAACACCAATTTTCCTAAAATCGGGGATACTCCAACTCCGATTTTATTTC
CAAAAACACCAATTTCTCACAAACGGGGATACTCCAACCCCGCTAATCATCGGGGATACTCCAAC
CACGTTATTTTCGA
Found at i:342705 original size:107 final size:108
Alignment explanation
Indices: 342497--342713 Score: 382
Period size: 108 Copynumber: 2.0 Consensus size: 108
342487 AGCAATATGT
* *
342497 ATCGATACTTTCTAGGGTTTTGACCTTTGTAGCTTTAGTCAACCTTTATATATTGATACAAATAC
1 ATCGATACTTTCTAGGATTTTGACCTTTGTAGCTTAAGTCAACCTTTATATATTGATACAAATAC
* *
342562 CTATGTATTGATACTTTCAATTATTTTTACTTGAAAATATTTG
66 CTATGTATCGATACTTTCAATTATTTTTACTTGAAAACATTTG
*
342605 ATCGATACTTTCTAGGATTTTGACCTTTGTAGCTTAAGTCAACCTTTATGTATTGATACAAAT-C
1 ATCGATACTTTCTAGGATTTTGACCTTTGTAGCTTAAGTCAACCTTTATATATTGATACAAATAC
342669 CTATGTATCGATACTTTCAATTATTTTTACTTGAAAACATTTG
66 CTATGTATCGATACTTTCAATTATTTTTACTTGAAAACATTTG
342712 AT
1 AT
342714 TTATTGCTTG
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
107 44 0.42
108 60 0.58
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (108 bp):
ATCGATACTTTCTAGGATTTTGACCTTTGTAGCTTAAGTCAACCTTTATATATTGATACAAATAC
CTATGTATCGATACTTTCAATTATTTTTACTTGAAAACATTTG
Found at i:344228 original size:142 final size:141
Alignment explanation
Indices: 343742--344236 Score: 592
Period size: 142 Copynumber: 3.5 Consensus size: 141
343732 TATAAATTTT
* **
343742 GAAAATCTTATTTTGTACCTTAATAGAGAACCGAAAAGATATAAAAAGTTTTGAAGATTTCTATA
1 GAAAAT-TTATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATA
* *
343807 CTCCTACAGAAAACCATAGGAATA-TAGAAATCTTGAACAATTAAGACAATAATTTTTTTAAATT
65 CTCCTACGGAAAACCATAGGAATATTAGAAATCTTGAA-AATTAAGATAATAATTTTTTT---TT
343871 --TTTTTAATTTTTAA
126 GATTTTTAATTTTTAA
* * * * *
343885 -AAATTTTATTTCATACCTTAATGGAGAACCGAAAAGATATGAAAAGTTTTGAAGATTTTTATAC
1 GAAAATTTATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATAC
* * * * * *
343949 TCTTACGAAAAAGCATATGAATATTAGAAATCTTCAAAAATTAAGATAATAATTTTTATTTGATT
66 TCCTACGGAAAACCATAGGAATATTAGAAATCTT-GAAAATTAAGATAATAATTTTTTTTTGA-T
*
344014 TTTTATTTTTTAA
129 TTTTAATTTTTAA
* * * * * *
344027 GAAAATTCAATTCCTACCTTAAT-GAAAAACTAGAAAGATACGAAAAGTTTTGAAGATTTCTATA
1 GAAAATTTATTTCGTACCTTAATAGAGAACCGA-AAAGATACGAAAAGTTTTGAAGATTTCTATA
*
344091 CTCCTACGGAAAACCATAGGAATATTA-AAATTGTTGAAAGATTAAGATAATAATTTTTTTTTGA
65 CTCCTACGGAAAACCATAGGAATATTAGAAA-TCTTGAAA-ATTAAGATAATAATTTTTTTTTGA
344155 TTTTTAATTTTTAA
128 TTTTTAATTTTTAA
* **
344169 GAAAATTTATTTCGTACCTTATTAGA-AAGTTGAAAAGATACGAAAAGTTTTGAAGATTTCTATA
1 GAAAATTTATTTCGTACCTTAATAGAGAA-CCGAAAAGATACGAAAAGTTTTGAAGATTTCTATA
344233 -TCCT
65 CTCCT
344237 TACATATAAC
Statistics
Matches: 302, Mismatches: 39, Indels: 24
0.83 0.11 0.07
Matches are distributed among these distances:
139 2 0.01
141 76 0.25
142 123 0.41
143 101 0.33
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (141 bp):
GAAAATTTATTTCGTACCTTAATAGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATAC
TCCTACGGAAAACCATAGGAATATTAGAAATCTTGAAAATTAAGATAATAATTTTTTTTTGATTT
TTAATTTTTAA
Found at i:347458 original size:35 final size:36
Alignment explanation
Indices: 347415--347891 Score: 305
Period size: 35 Copynumber: 13.0 Consensus size: 36
347405 CAAGGCGATA
*
347415 ACCA-ATACAGTCAAACGA-GAATGAAAAAG-GTTTG
1 ACCAGATACAGCCAAACGATG-ATGAAAAAGAGTTTG
*
347449 ACCAGATACAACCAAACGATGATG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* *
347484 ACTAGATACAGCAAAACGATGATG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* ** *
347519 ACTAGATGTAGCCAAACGATGATG-AAAAGGGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* * **
347554 ACGAGATGCAGCCAAACGATGATGAAAAGAAAGCAACATGATGTCA
1 ACCAGATACAGCCAAACGATGATG--AA-AAAG----A-G-T-TTG
** *** *
347600 AAAAGAGTTTGGCCAAATACAGCCAAACGATGATGAAAAGAGTTTG
1 ACCAGA-TACAGCC-AA-AC-G----ATGATGA--AAAAGAGTTTG
* * * *
347646 AACAGATAAAGCCAAATGATG-TTAAAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* *
347681 ACCAGATGCAGCCAAACGATGGTG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* *
347716 ACCAAATATAGCCAAACGATGATG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* ** ** *
347751 ACCAAATGTAGGTAAACGATAAT-AAAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* *
347786 ACTAGATGCAGCCAAACGATGATG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* * *
347821 AACAAATGCAGCCAAACGATGATG-AAAAGAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
* * * *
347856 AACAAATGCAGCCAAACGATGATG-AAAATAGTTTG
1 ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
347891 A
1 A
347892 ACAAATATAG
Statistics
Matches: 364, Mismatches: 52, Indels: 53
0.78 0.11 0.11
Matches are distributed among these distances:
34 9 0.02
35 300 0.82
36 2 0.01
37 2 0.01
38 3 0.01
39 4 0.01
42 1 0.00
43 1 0.00
44 3 0.01
45 5 0.01
46 11 0.03
47 5 0.01
48 3 0.01
49 3 0.01
50 1 0.00
52 1 0.00
53 4 0.01
54 6 0.02
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (36 bp):
ACCAGATACAGCCAAACGATGATGAAAAAGAGTTTG
Found at i:347462 original size:44 final size:43
Alignment explanation
Indices: 347343--347463 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 43
347333 GGCTAATCGG
* * *
347343 GAATGAAAACGGTTTGACCATAGTGGTAACCAATACAATAAACGA
1 GAATGAAAAAGGTTTGACCAGA-T-ATAACCAATACAATAAACGA
* * ** *
347388 GAA-CAAAAAGGGTTGACCAAGGCGATAACCAATACAGTCAAACGA
1 GAATGAAAAAGGTTTGACC-A-GATATAACCAATACAAT-AAACGA
*
347433 GAATGAAAAAGGTTTGACCAGATACAACCAA
1 GAATGAAAAAGGTTTGACCAGATATAACCAA
347464 ACGATGATGA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
44 32 0.54
45 14 0.24
46 13 0.22
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (43 bp):
GAATGAAAAAGGTTTGACCAGATATAACCAATACAATAAACGA
Found at i:347534 original size:70 final size:68
Alignment explanation
Indices: 347426--347891 Score: 393
Period size: 70 Copynumber: 6.9 Consensus size: 68
347416 CCAATACAGT
** *
347426 CAAACGA-GAATGAAAA-AGGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGACTAG
1 CAAACGATG-ATGAAAAGA-GTTTGA-CAGATGTAGCCAAACGATGATGAAAAGAGTTTGAC-AG
*
347489 ATACAGC
62 ATGCAGC
* *
347496 AAAACGATGATGAAAAGAGTTTGACTAGATGTAGCCAAACGATGATGAAAAGGGTTTGACGAGAT
1 CAAACGATGATGAAAAGAGTTTGAC-AGATGTAGCCAAACGATGATGAAAAGAGTTTGAC-AGAT
347561 GCAGC
64 GCAGC
***** * * * * *
347566 CAAACGATGATGAAAAGAAAGCAACATGATGT---CAAA--A--A-G---AG-TTTGGCCAAATA
1 CAAACGATGATGAAAAGAGTTTGACA-GATGTAGCCAAACGATGATGAAAAGAGTTTGACAGATG
347619 CAGC
65 CAGC
** * * *
347623 CAAACGATGATGAAAAGAGTTTGAACAGATAAAGCCAAATGATGTTAAAAAGAGTTTGACCAGAT
1 CAAACGATGATGAAAAGAGTTTG-ACAGATGTAGCCAAACGATGATGAAAAGAGTTTGA-CAGAT
347688 GCAGC
64 GCAGC
* * * *
347693 CAAACGATGGTGAAAAGAGTTTGACCAAATATAGCCAAACGATGATGAAAAGAGTTTGACCAAAT
1 CAAACGATGATGAAAAGAGTTTGA-CAGATGTAGCCAAACGATGATGAAAAGAGTTTGA-CAGAT
* *
347758 GTAGG
64 GCAGC
* * * * *
347763 TAAACGATAATAAAAAGAGTTTGACTAGATGCAGCCAAACGATGATGAAAAGAGTTTGAACAAAT
1 CAAACGATGATGAAAAGAGTTTGAC-AGATGTAGCCAAACGATGATGAAAAGAGTTTG-ACAGAT
347828 GCAGC
64 GCAGC
* * *
347833 CAAACGATGATGAAAAGAGTTTGAACAAATGCAGCCAAACGATGATGAAAATAGTTTGA
1 CAAACGATGATGAAAAGAGTTTG-ACAGATGTAGCCAAACGATGATGAAAAGAGTTTGA
347892 ACAAATATAG
Statistics
Matches: 319, Mismatches: 55, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
57 28 0.09
58 7 0.02
59 2 0.01
60 4 0.01
62 2 0.01
63 1 0.00
65 1 0.00
67 4 0.01
68 2 0.01
69 8 0.03
70 255 0.80
71 5 0.02
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.19
Consensus pattern (68 bp):
CAAACGATGATGAAAAGAGTTTGACAGATGTAGCCAAACGATGATGAAAAGAGTTTGACAGATGC
AGC
Found at i:347572 original size:105 final size:104
Alignment explanation
Indices: 347418--347891 Score: 458
Period size: 105 Copynumber: 4.6 Consensus size: 104
347408 GGCGATAACC
* * *
347418 AATACAGTCAAACGA-GAATGAAAA-AGGTTTGACCAGATACAACCAAACGATGATGAAAAGAGT
1 AATACAGCCAAACGATG-ATGAAAAGA-GTTTGA-CAGATGCAGCCAAACGATGATGAAAAGAGT
*
347481 TTGACTAGATACAGCAAAACGATGATGAAAAGAGTTTGACTA
63 TTGACTAGATACAGCAAAACGATGATGAAAAGAGTTTGACCA
* ** *
347523 GATGTAGCCAAACGATGATGAAAAGGGTTTGACGAGATGCAGCCAAACGATGATG---A-A----
1 AATACAGCCAAACGATGATGAAAAGAGTTTGAC-AGATGCAGCCAAACGATGATGAAAAGAGTTT
* * * *
347580 -A--AGA-A-AGCAACATGATG-TCAAAAAGAGTTTGGCCA
65 GACTAGATACAGCAAAACGATGAT-GAAAAGAGTTTGACCA
** * * *
347615 AATACAGCCAAACGATGATGAAAAGAGTTTGAACAGATAAAGCCAAATGATGTTAAAAAGAGTTT
1 AATACAGCCAAACGATGATGAAAAGAGTTTG-ACAGATGCAGCCAAACGATGATGAAAAGAGTTT
* * * *
347680 GACCAGATGCAGCCAAACGATGGTGAAAAGAGTTTGACCA
65 GACTAGATACAGCAAAACGATGATGAAAAGAGTTTGACCA
* * * ** * *
347720 AATATAGCCAAACGATGATGAAAAGAGTTTGACCAAATGTAGGTAAACGATAATAAAAAGAGTTT
1 AATACAGCCAAACGATGATGAAAAGAGTTTGA-CAGATGCAGCCAAACGATGATGAAAAGAGTTT
* * *
347785 GACTAGATGCAGCCAAACGATGATGAAAAGAGTTTGAACA
65 GACTAGATACAGCAAAACGATGATGAAAAGAGTTTGACCA
* * *
347825 AATGCAGCCAAACGATGATGAAAAGAGTTTGAACAAATGCAGCCAAACGATGATGAAAATAGTTT
1 AATACAGCCAAACGATGATGAAAAGAGTTTG-ACAGATGCAGCCAAACGATGATGAAAAGAGTTT
347890 GA
65 GA
347892 ACAAATATAG
Statistics
Matches: 301, Mismatches: 47, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
91 1 0.00
92 66 0.22
93 3 0.01
94 3 0.01
95 1 0.00
96 2 0.01
101 2 0.01
102 1 0.00
103 3 0.01
104 2 0.01
105 214 0.71
106 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (104 bp):
AATACAGCCAAACGATGATGAAAAGAGTTTGACAGATGCAGCCAAACGATGATGAAAAGAGTTTG
ACTAGATACAGCAAAACGATGATGAAAAGAGTTTGACCA
Done.