Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold352
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: 630196
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 4
Found at i:208728 original size:34 final size:34
Alignment explanation
Indices: 208689--208756 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
208679 TACCTAAGTA
208689 AATCCTTATATTTTTATCATACTGAAATAAATTC
1 AATCCTTATATTTTTATCATACTGAAATAAATTC
*
208723 AATCCTTATATTTTTATCATAGTGAAATAAATTC
1 AATCCTTATATTTTTATCATACTGAAATAAATTC
208757 TTACTCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (34 bp):
AATCCTTATATTTTTATCATACTGAAATAAATTC
Found at i:211822 original size:10 final size:9
Alignment explanation
Indices: 211801--211874 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
211791 TATTCGATAT
211801 AAAATCAAA
1 AAAATCAAA
*
211810 AAAGTCAAA
1 AAAATCAAA
211819 AAAATCAAA
1 AAAATCAAA
*
211828 AAGAA-AAAA
1 AA-AATCAAA
211837 AAAATCAAA
1 AAAATCAAA
*
211846 AATCATCAAA
1 AA-AATCAAA
*
211856 AAGA--AAA
1 AAAATCAAA
*
211863 AAATTCAAA
1 AAAATCAAA
211872 AAA
1 AAA
211875 TAAGAAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 35 0.67
10 10 0.19
ACGTcount: A:0.76, C:0.09, G:0.04, T:0.11
Consensus pattern (9 bp):
AAAATCAAA
Found at i:211873 original size:27 final size:27
Alignment explanation
Indices: 211807--211876 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
211797 ATATAAAATC
*
211807 AAAAAAGTCAAAAAA-ATCAAAAAGAAA
1 AAAAAAATCAAAAAATATCAAAAAG-AA
211834 AAAAAAATC-AAAAATCATCAAAAAG-A
1 AAAAAAATCAAAAAAT-ATCAAAAAGAA
*
211860 AAAAAATTCAAAAAATA
1 AAAAAAATCAAAAAATA
211877 AGAAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 15 0.39
27 14 0.37
28 9 0.24
ACGTcount: A:0.76, C:0.09, G:0.04, T:0.11
Consensus pattern (27 bp):
AAAAAAATCAAAAAATATCAAAAAGAA
Found at i:211874 original size:28 final size:27
Alignment explanation
Indices: 211807--211865 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
211797 ATATAAAATC
*
211807 AAAAAAGTCAAAAAAATCAAAAAGAAA
1 AAAAAAATCAAAAAAATCAAAAAGAAA
*
211834 AAAAAAATCAAAAATCATCAAAAAGAAA
1 AAAAAAATCAAAAA-AATCAAAAAGAAA
211862 AAAA
1 AAAA
211866 TTCAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.78, C:0.08, G:0.05, T:0.08
Consensus pattern (27 bp):
AAAAAAATCAAAAAAATCAAAAAGAAA
Found at i:214051 original size:96 final size:97
Alignment explanation
Indices: 213939--214127 Score: 238
Period size: 99 Copynumber: 1.9 Consensus size: 97
213929 GTTCATCAGG
* * **
213939 GATACACTAACACCATTTCTT-TGAGGGGATACTCCAACCCC-GTTTTTTAAACTCCTCGCAATT
1 GATACACCAACACCA-TTCTTCTGAGGGGATACTCCAACCCCTGTTTTTTAAACTCATCAAAATT
** *
214002 TATGTCTCATTTTGTCCAAATTGTCATCATTGA
65 TAAATCTCATTTTGTCCAAATTATCATCATTGA
* * *
214035 GATACACCAACCCCATTCTTCTGAGGGGATACTCCGACCCCTATTTTTTTTAAACTCATCAAAAT
1 GATACACCAACACCATTCTTCTGAGGGGATACTCCAACCCC--TGTTTTTTAAACTCATCAAAAT
*
214100 TTAAATCTTATTTTGTCCAAATTATCAT
64 TTAAATCTCATTTTGTCCAAATTATCAT
214128 TGTCGAGGGA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
95 5 0.06
96 32 0.41
99 41 0.53
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.37
Consensus pattern (97 bp):
GATACACCAACACCATTCTTCTGAGGGGATACTCCAACCCCTGTTTTTTAAACTCATCAAAATTT
AAATCTCATTTTGTCCAAATTATCATCATTGA
Found at i:214209 original size:70 final size:70
Alignment explanation
Indices: 214081--214217 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
214071 ACCCCTATTT
* *
214081 TTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGTCGAGGGATACTCCAA
1 TTTTTAAACTCATCAAAATTTAAATCTTATTTCGACCAAATTATCATTGTCGAGGGATACTCCAA
214146 CCTCG
66 CCTCG
*
214151 TTTTTAAACTCATCGAAATTTAAAGTCTTATTTCGACCAAATTATCATTGTCGA-GGATACTCCA
1 TTTTTAAACTCATCAAAATTTAAA-TCTTATTTCGACCAAATTATCATTGTCGAGGGATACTCCA
214215 ACC
65 ACC
214218 CCATTCTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 36 0.57
71 27 0.43
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (70 bp):
TTTTTAAACTCATCAAAATTTAAATCTTATTTCGACCAAATTATCATTGTCGAGGGATACTCCAA
CCTCG
Found at i:216252 original size:98 final size:98
Alignment explanation
Indices: 216083--216300 Score: 400
Period size: 98 Copynumber: 2.2 Consensus size: 98
216073 TTTTTAATTG
* *
216083 AAAAACGGGGTTGGAGTATCTCCTCGGAGGAATGGGGTTAGAGTGTCCCTGATAATGATAATTTA
1 AAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTCCCTGATAATGATAATTTA
*
216148 GGCAAGAATAAGTTTCAAATCTTGACAAGTTTT
66 GGCAAGAATAAGTTTCAAATCTTGACAACTTTT
*
216181 AAAAACGGAGTTAGAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTCCCTGATAATGATAATTTA
1 AAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTCCCTGATAATGATAATTTA
216246 GGCAAGAATAAGTTTCAAATCTTGACAACTTTT
66 GGCAAGAATAAGTTTCAAATCTTGACAACTTTT
216279 AAAAACGGAGTTGGAGTATCCC
1 AAAAACGGAGTTGGAGTATCCC
216301 TTCAGAGAAA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 115 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (98 bp):
AAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTCCCTGATAATGATAATTTA
GGCAAGAATAAGTTTCAAATCTTGACAACTTTT
Found at i:218523 original size:51 final size:51
Alignment explanation
Indices: 218447--218543 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
218437 ATTTTAACTA
** *
218447 AATGTATCGATACATTTTTCAATGTATCGATACATCTGGGTAAAAAGACAG
1 AATGTATCGATACATTCATCAATGTATCGATACATCTAGGTAAAAAGACAG
218498 AATGTATCGATACATTCAT-ATATGTATCGATACATCTAGGTAAAAA
1 AATGTATCGATACATTCATCA-ATGTATCGATACATCTAGGTAAAAA
218544 TGTGACTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGTATCGATACATTCATCAATGTATCGATACATCTAGGTAAAAAGACAG
Found at i:219587 original size:28 final size:28
Alignment explanation
Indices: 219524--220076 Score: 526
Period size: 28 Copynumber: 19.5 Consensus size: 28
219514 TGCTAACTTG
* **
219524 TGTGGGCTTTAGAGAAGGTTGCCACCAACT
1 TGTGGGCTTT-GA-AAGGATGCCACTGACT
* * * * *
219554 TATGGGCTTTAAAAAGATGCCATTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
219582 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
219610 TGTGGGC-TTCAAAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * ** *
219638 TGAGGGCATCAAAATGG-TGCCACTAACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
*
219666 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
219694 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
219722 TGTGGGCTTTGAGAGAGGTTGCCAAC-GACTT
1 TGTGGGCTTTGA-A-AGGATGCC-ACTGAC-T
219753 GTGTGGGC-TT-AAAGAGATGCCACTGACT
1 -TGTGGGCTTTGAAAG-GATGCCACTGACT
*
219781 TGCGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* *
219810 TATGGGCTTTGAGAAGG-TGCCATTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* * * *
219838 TATGGACTTTTAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
219866 TGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
219894 TGTGGGCTTTGAAAGGATACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
219922 TGTGAGCTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
219950 TGTGGGTTTTCAAAAGATGCCACTGACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
219978 TGTGGGCTTTGAAAGGATGCCACTAACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
220006 TGTGGGTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
220034 TGTGAGCTTTGAGAAGGATGCCACTGACA
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* *
220063 TATGGACTTTGAAA
1 TGTGGGCTTTGAAA
220077 AAGGTCGTAT
Statistics
Matches: 433, Mismatches: 73, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
27 20 0.05
28 307 0.71
29 70 0.16
30 24 0.06
31 5 0.01
32 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:235284 original size:20 final size:20
Alignment explanation
Indices: 235259--235310 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
235249 AAAAGGACAG
* *
235259 AATGTATCGATGCATTGAAA
1 AATGTATCGATACATTAAAA
235279 AATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
235299 AATGTATCGATA
1 AATGTATCGATA
235311 TGTCTGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:239648 original size:19 final size:19
Alignment explanation
Indices: 239626--239670 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
239616 GCAAAAGTAC
239626 AAAAAA-TGAAAAAAACAAA
1 AAAAAAGTG-AAAAAACAAA
*
239645 AAAAAAGTGCAAAAACAAA
1 AAAAAAGTGAAAAAACAAA
239664 ATAAAAA
1 A-AAAAA
239671 AAGGAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAAGTGAAAAAACAAA
Found at i:239693 original size:22 final size:22
Alignment explanation
Indices: 239603--239673 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
239593 CAAAAATGAC
*
239603 AAAAAAGT-CAAAAGCAAAAGTA
1 AAAAAAGTGCAAAAACAAAA-TA
239625 CAAAAAA-TG-AAAAA-AACAA-A
1 -AAAAAAGTGCAAAAACAA-AATA
239645 AAAAAAGTGCAAAAACAAAATA
1 AAAAAAGTGCAAAAACAAAATA
239667 AAAAAAG
1 AAAAAAG
239674 GAACAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
19 6 0.15
20 3 0.07
21 9 0.22
22 17 0.41
23 6 0.15
ACGTcount: A:0.75, C:0.08, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAAAAGTGCAAAAACAAAATA
Found at i:240971 original size:63 final size:63
Alignment explanation
Indices: 240896--242394 Score: 1547
Period size: 63 Copynumber: 24.0 Consensus size: 63
240886 ACATCTTCAT
* ** * *
240896 CCTTTAGTCCTCAAAGAGTAGGATACATTTTTCTATTCAAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
** * * * * * * * **
240959 TTTTTAGTCCTCAAAGTGAAGGACGTTTTTTTCTTTTTAAAGCCTACACTAGTTGGTAGCATT
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
**
241022 TTTTTAGTCCTCAAAGAGCAGGACGC-TTTTTCATTTTCAAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * * *
241085 CCTTTAGTCCTCAAAGAGCAAGATGCCTTTCTCTTTTCAAAGCCCACATGAGTTTGTGGCA--
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * *
241146 CTTTGCTAGTCCTCAAGGAGCAGGACGCCTTTTTTCTTTT-AAAGCTCACACAAGTTGGTGGTAC
1 CCTT--TAGTCCTCAAAGAGCAGGACG-CTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
241210 C
63 C
* * * * * * *
241211 CCTTTTTAGTCTTTAAAAAACAGGACGTTTTTTTCTTATT-AAAGCGCACACAAGTTGGTGGCA-
1 CC--TTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTT-TTCAAAGCCCACACGAGTTGGTGGCAC
241274 -
63 C
* * * * * * *
241274 CCTTTCAGTCCTCAAAGAGCAGGATG-TCTTTTCCTTTTTAAAGCCCACACAAATTGGCGGTA--
1 CCTTT-AGTCCTCAAAGAGCAGGACGCT-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * * * *
241336 CCTTTCAATCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA-G
1 CCTTT-AGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * **
241399 CTTTTGGTCCTCAAAGAGCAGGACGCTTTTCTC-TTTCAAAGCCCACATGAGTTGGTGGCATT
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
*
241461 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGC-TTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * *
241525 CCTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCGAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * * *
241588 CCTTCAGTCTTCAAAGAACAGGACG-TCTTTTTCTCTTCAAAGCCCACATGAGTTGGTGGCATC
1 CCTTTAGTCCTCAAAGAGCAGGACGCT-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * ** * *
241651 CCTTCAGTCCTCAAAGAGCAAGACATTTTTTTCTTTTCAAAGCCCACACGAGTTAGCGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * *
241714 CCTTTAGTCCTCAAAGACCAGGACCCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * ** *
241777 CATTTTGTCCTCAAAGAGGAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * *
241840 TCTTTAGTCCTCAAAGAGCAGGACGTTTTTTTCTTTTTAAAGCCCACACGAGCTGGTGGCACA
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * * * *
241903 CTTTTAGTCCTTAAAAAGCAGAACGCCTTTTTCTTTTCAAAGCCCATACGATTTGGTGGCA-C
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * ** * *
241965 CTTTTCAGTTCTCAAAGTGCACTATGCTTTTTTCTCTTCAAAGCCCACACGAGTTGGTGGCACC
1 CCTTT-AGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * *
242029 CCTTTAGTCTTCAAAGAGCAGGACG-TCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGTACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCT-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * *
242092 CCTTTAGTCCTCAAAGAGCAGGAC-ATCTTTT-TTTT-AAAGCACACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * *
242152 CCTTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTCGAAGCCCACACGAGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * * * *
242215 CCTTTCGTCCTTAAAGAACATGACGTTTTTTTCTTTTTAAAGCCCACACGAGTTAGTGGCA-C
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * * *
242277 CCTTTAGTCTTCAAAGAGCAAGACG-TATTTTC---T--AAGCCCATACGTGTTGGTGGCACC
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * *
242334 CCTTTAGTCCTCAAAGAGTAGGAC-ATCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCT-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
242395 ACTCTTCTAA
Statistics
Matches: 1198, Mismatches: 203, Indels: 70
0.81 0.14 0.05
Matches are distributed among these distances:
56 19 0.02
57 23 0.02
58 6 0.01
60 45 0.04
61 48 0.04
62 184 0.15
63 752 0.63
64 79 0.07
65 40 0.03
67 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (63 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
Found at i:242568 original size:62 final size:60
Alignment explanation
Indices: 242421--242580 Score: 148
Period size: 62 Copynumber: 2.6 Consensus size: 60
242411 TGCCGTTGGC
* * *
242421 CTTGAATCAACATATTGGCAC--TTGTCATTCTCCTCATCTTCAAGCCTCATATTGCTAG
1 CTTGAATCAACATATTGGCACTTTTATCATTCTCCTCATCTTCAAGCCTAATATCGCTAG
* * * * * * *
242479 CTGTGAATCAGCATATCGACA-TCTTTATC-TTTTCTTTGCATCTTTAAGTCTAATATCGCTAG
1 CT-TGAATCAACATATTGGCACT-TTTATCATTCTC-CT-CATCTTCAAGCCTAATATCGCTAG
*
242541 TCTTGAATCAACATATTGGCACTTTTATCATTCTTCTCAT
1 -CTTGAATCAACATATTGGCACTTTTATCATTCTCCTCAT
242581 TTTTAAGTTC
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
58 2 0.03
59 15 0.19
60 4 0.05
61 8 0.10
62 42 0.55
63 6 0.08
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (60 bp):
CTTGAATCAACATATTGGCACTTTTATCATTCTCCTCATCTTCAAGCCTAATATCGCTAG
Found at i:243517 original size:26 final size:25
Alignment explanation
Indices: 243478--243536 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
243468 ATATAAAATC
* *
243478 AAAAAAATCAAAAATCATTAAAAAG
1 AAAAAAATCAAAAATAATAAAAAAG
* *
243503 AAAAAATTCAAAAAATAATAAAAAAAT
1 AAAAAAATC-AAAAATAAT-AAAAAAG
243530 AAAAAAA
1 AAAAAAA
243537 AACATGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 8 0.30
26 8 0.30
27 11 0.41
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAAAAATCAAAAATAATAAAAAAG
Found at i:243524 original size:25 final size:25
Alignment explanation
Indices: 243478--243535 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
243468 ATATAAAATC
*
243478 AAAAAAATCAAAAATCATTAAAAAG
1 AAAAAAATCAAAAATCAATAAAAAG
* *
243503 AAAAAATTCAAAAAAT-AATAAAAAA
1 AAAAAAATC-AAAAATCAATAAAAAG
243528 ATAAAAAA
1 A-AAAAAA
243536 AAACATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAAAAATCAAAAATCAATAAAAAG
Found at i:243844 original size:27 final size:30
Alignment explanation
Indices: 243770--243849 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 30
243760 AAACGCGTGA
*
243770 AACATGCAGCACGTGAAGAAAGCATGAGGC
1 AACATGCAGCACATGAAGAAAGCATGAGGC
**
243800 AAC-TGCAAAACATGGAAG-AAG-ATG-GGC
1 AACATGCAGCACAT-GAAGAAAGCATGAGGC
*
243827 AACATGCAGCACATGAAGCAAGC
1 AACATGCAGCACATGAAGAAAGC
243850 GTTGCTAGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 10 0.24
28 14 0.34
29 10 0.24
30 7 0.17
ACGTcount: A:0.42, C:0.20, G:0.28, T:0.10
Consensus pattern (30 bp):
AACATGCAGCACATGAAGAAAGCATGAGGC
Found at i:244205 original size:91 final size:91
Alignment explanation
Indices: 244050--244262 Score: 399
Period size: 91 Copynumber: 2.3 Consensus size: 91
244040 TGCAGCAAAC
244050 AAAATGCAATGGGAGACAAAACATGTAACAAGCAACGTGCAAAGCAAGAAAAAATGTGCAGCACG
1 AAAATGCAATGGGAGACAAAACATGTAACAAGCAACGTGCAAAGCAAGAAAAAATGTGCAGCACG
244115 TGGACAACATGGAGAGGGTGATTAAA
66 TGGACAACATGGAGAGGGTGATTAAA
* *
244141 AAAATGCAATGGGAGACAAAACATGTAACAAGGAACGTGCAAAGCAAGAAGAAATGTGCAGCACG
1 AAAATGCAATGGGAGACAAAACATGTAACAAGCAACGTGCAAAGCAAGAAAAAATGTGCAGCACG
*
244206 TGGACAGCATGGAGAGGGTGATTAAA
66 TGGACAACATGGAGAGGGTGATTAAA
244232 AAAATGCAATGGGAGACAAAACATGTAACAA
1 AAAATGCAATGGGAGACAAAACATGTAACAA
244263 AGCATAGAGA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 119 1.00
ACGTcount: A:0.46, C:0.14, G:0.27, T:0.13
Consensus pattern (91 bp):
AAAATGCAATGGGAGACAAAACATGTAACAAGCAACGTGCAAAGCAAGAAAAAATGTGCAGCACG
TGGACAACATGGAGAGGGTGATTAAA
Found at i:245711 original size:97 final size:100
Alignment explanation
Indices: 245608--245794 Score: 263
Period size: 100 Copynumber: 1.9 Consensus size: 100
245598 TATCAGGGAA
* * **
245608 ACACCAACACCATTCCTCTAAGGGGATACTCT-AACTCC-GTTTTT-TAAACTCATCGTAATTTA
1 ACACCAACACCATTCCTCCAAGGGGATACTCTGAACCCCTGTTTTTATAAACTCATCAAAATTTA
*
245670 AGTCTTATTTTGTCCAAATTATCATCATCGGAGAT
66 AATCTTATTTTGTCCAAATTATCATCATCGGAGAT
* * * *
245705 ACACCAACCCCATTCTTCCAAGGGGATACTCTGACCCCCTTTTTTTATAAACTCATCAAAATTTA
1 ACACCAACACCATTCCTCCAAGGGGATACTCTGAACCCCTGTTTTTATAAACTCATCAAAATTTA
*
245770 AATCTTTTTTTGTCCAAATTATCAT
66 AATCTTATTTTGTCCAAATTATCAT
245795 TGTTGGGGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
97 29 0.38
98 4 0.05
99 5 0.06
100 39 0.51
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (100 bp):
ACACCAACACCATTCCTCCAAGGGGATACTCTGAACCCCTGTTTTTATAAACTCATCAAAATTTA
AATCTTATTTTGTCCAAATTATCATCATCGGAGAT
Found at i:245875 original size:70 final size:71
Alignment explanation
Indices: 245747--245882 Score: 177
Period size: 70 Copynumber: 1.9 Consensus size: 71
245737 GACCCCCTTT
* * * * * * **
245747 TTTTATAAACTCATCAAAATTTAAATCTTTTTTTGTCCAAATTATCATTGTTGGGGGATACTCCA
1 TTTTATAAACTAATCAAAATATAAATCTTATTTCGACCAAATAATCATTGTTCAGGGATACTCCA
245812 ACCCTG
66 ACCCTG
245818 TTTT-TAAACTAATCAAAATATAAAGTCTTATTTCGACCAAATAATCATTG-TCAGGGATACTCC
1 TTTTATAAACTAATCAAAATATAAA-TCTTATTTCGACCAAATAATCATTGTTCAGGGATACTCC
245881 AA
65 AA
245883 TCCCATTCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
70 31 0.55
71 25 0.45
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.38
Consensus pattern (71 bp):
TTTTATAAACTAATCAAAATATAAATCTTATTTCGACCAAATAATCATTGTTCAGGGATACTCCA
ACCCTG
Found at i:245943 original size:27 final size:27
Alignment explanation
Indices: 245871--245936 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
245861 ATCATTGTCA
245871 GGGATACTCCAATCCCATTCTTCTGAG
1 GGGATACTCCAATCCCATTCTTCTGAG
* *
245898 AGGATACTCCAATCCCATTCTTTTGAG
1 GGGATACTCCAATCCCATTCTTCTGAG
245925 GGGATACTCCAA
1 GGGATACTCCAA
245937 CCTCATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (27 bp):
GGGATACTCCAATCCCATTCTTCTGAG
Found at i:247161 original size:15 final size:16
Alignment explanation
Indices: 247132--247161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
247122 AATCTTAGTC
247132 TTTTATTAAATAATAT
1 TTTTATTAAATAATAT
247148 TTTTATTAAA-AATA
1 TTTTATTAAATAATA
247162 ATATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTATTAAATAATAT
Found at i:247189 original size:20 final size:20
Alignment explanation
Indices: 247153--247225 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 20
247143 AATATTTTTA
247153 TTAAAA-ATAATATTATATATT
1 TTAAAATATAA-A-TATATATT
247174 TTAAAATATAAATATATATGT
1 TTAAAATATAAATATATAT-T
* *
247195 TTAATAATTTAAAAATTATATT
1 TTAA-AATATAAATA-TATATT
247217 ATTAAAATA
1 -TTAAAATA
247226 ATTTTTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 7 0.16
21 12 0.27
22 16 0.36
23 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
TTAAAATATAAATATATATT
Found at i:247250 original size:27 final size:25
Alignment explanation
Indices: 247197--247284 Score: 63
Period size: 25 Copynumber: 3.4 Consensus size: 25
247187 ATATATGTTT
** *
247197 AATAATTTAAAAATTATATTATT-AA
1 AATAATTTTTAAA-TATTTTATTAAA
*
247222 AATAATTTTTAAATTTTTTAAATTAAA
1 AATAATTTTTAAATATTTT--ATTAAA
* *
247249 AATTAA-TATTAAATATTTTATTAAT
1 AA-TAATTTTTAAATATTTTATTAAA
*
247274 AATAATATTTA
1 AATAATTTTTA
247285 CCTCGAGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
24 7 0.14
25 21 0.43
26 3 0.06
27 15 0.31
28 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATAATTTTTAAATATTTTATTAAA
Found at i:247271 original size:18 final size:17
Alignment explanation
Indices: 247250--247283 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
247240 TAAATTAAAA
*
247250 ATTAATATTAAATATTTT
1 ATTAATAAT-AATATTTT
247268 ATTAATAATAATATTT
1 ATTAATAATAATATTT
247284 ACCTCGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAATAATAATATTTT
Found at i:249022 original size:2 final size:2
Alignment explanation
Indices: 249015--249047 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
249005 GTTTTTGAAT
249015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
249048 TTGCAGAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:250194 original size:30 final size:30
Alignment explanation
Indices: 250160--250221 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
250150 TAATATTAAT
*
250160 ATTGTGTTAATATAAAGTTAACCCCATAAC
1 ATTGTGTTAATATAAAGTCAACCCCATAAC
*
250190 ATTGTGTTAATATAAAGTCGACCCCATAAC
1 ATTGTGTTAATATAAAGTCAACCCCATAAC
250220 AT
1 AT
250222 GTTGTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (30 bp):
ATTGTGTTAATATAAAGTCAACCCCATAAC
Found at i:250730 original size:2 final size:2
Alignment explanation
Indices: 250723--250750 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
250713 GTTTTGTAAT
250723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250751 AAAGAGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:252899 original size:2 final size:2
Alignment explanation
Indices: 252892--252920 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
252882 TTTTCTTTAC
252892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
252921 AGTAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:254179 original size:1 final size:1
Alignment explanation
Indices: 254173--254199 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
254163 AAGGATTATT
254173 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
254200 CCTTGATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:257816 original size:17 final size:16
Alignment explanation
Indices: 257774--257817 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
257764 TTTAGTAGTA
*
257774 AATAAGTATTAAATAT
1 AATAAGTATTTAATAT
*
257790 AATAAATATTTAATAAT
1 AATAAGTATTTAAT-AT
*
257807 AATATGTATTT
1 AATAAGTATTT
257818 GATTAAGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
AATAAGTATTTAATAT
Found at i:258536 original size:2 final size:2
Alignment explanation
Indices: 258529--258561 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
258519 TTCTCTAACT
258529 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
258562 ATTTACCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:264961 original size:64 final size:64
Alignment explanation
Indices: 264888--265017 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
264878 CATGAGAAAC
264888 AAACAAGTTTGTGCGAGTAAGCATGAAAATATAACTACTTGATATTTAACTGCAACAATCAAAT
1 AAACAAGTTTGTGCGAGTAAGCATGAAAATATAACTACTTGATATTTAACTGCAACAATCAAAT
264952 AAACAAGTTTGTGCGAGTAAGCATGAAAATATAACTACTTGATATTTAACTGCAACAATCAAAT
1 AAACAAGTTTGTGCGAGTAAGCATGAAAATATAACTACTTGATATTTAACTGCAACAATCAAAT
265016 AA
1 AA
265018 GGCAGAACAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (64 bp):
AAACAAGTTTGTGCGAGTAAGCATGAAAATATAACTACTTGATATTTAACTGCAACAATCAAAT
Found at i:267774 original size:18 final size:20
Alignment explanation
Indices: 267753--267791 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
267743 TGGGATAAAT
267753 AAAAAAA-GCTTAAA-TATA
1 AAAAAAACGCTTAAACTATA
*
267771 AAAAAAACGTTTAAACTATA
1 AAAAAAACGCTTAAACTATA
267791 A
1 A
267792 TACATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAAACGCTTAAACTATA
Found at i:267777 original size:19 final size:20
Alignment explanation
Indices: 267753--267791 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
267743 TGGGATAAAT
267753 AAAAAAAGCTTAAA-TATAA
1 AAAAAAAGCTTAAACTATAA
* *
267772 AAAAAACGTTTAAACTATAA
1 AAAAAAAGCTTAAACTATAA
267792 TACATAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAAAGCTTAAACTATAA
Found at i:268807 original size:26 final size:26
Alignment explanation
Indices: 268755--268808 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
268745 ATGGGATTAT
* *
268755 GGATAGATTTGAGGTAGATTTTGATA
1 GGATAGATTTGAGGTAGATCTTAATA
*
268781 GGATAGATTTGAGGTGGATCTTAATA
1 GGATAGATTTGAGGTAGATCTTAATA
268807 GG
1 GG
268809 CTATCTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (26 bp):
GGATAGATTTGAGGTAGATCTTAATA
Found at i:269056 original size:18 final size:18
Alignment explanation
Indices: 269015--269057 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
269005 GATGTATCTT
269015 AAATTGAAAATAATTTAG
1 AAATTGAAAATAATTTAG
** * *
269033 TTATTGATAGTAATTTAG
1 AAATTGAAAATAATTTAG
269051 AAATTGA
1 AAATTGA
269058 GAAAACCATA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
AAATTGAAAATAATTTAG
Found at i:271365 original size:18 final size:18
Alignment explanation
Indices: 271344--271385 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
271334 TAGCAAACCT
271344 TAAAAAAAGAGC-AACAGA
1 TAAAAAAAGAGCTAA-AGA
*
271362 TAAAAAATGAGCTAAAGA
1 TAAAAAAAGAGCTAAAGA
271380 -AAAAAA
1 TAAAAAA
271386 TTTGGATCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (18 bp):
TAAAAAAAGAGCTAAAGA
Found at i:271368 original size:17 final size:17
Alignment explanation
Indices: 271345--271386 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
271335 AGCAAACCTT
271345 AAAAAAA-GAGC-AACAG
1 AAAAAAATGAGCTAA-AG
271361 ATAAAAAATGAGCTAAAG
1 A-AAAAAATGAGCTAAAG
271379 AAAAAAAT
1 AAAAAAAT
271387 TTGGATCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 13 0.57
18 7 0.30
19 2 0.09
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAATGAGCTAAAG
Found at i:274169 original size:16 final size:17
Alignment explanation
Indices: 274143--274175 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
274133 CATCAATAAA
274143 CATATTTATTTTGAAAT
1 CATATTTATTTTGAAAT
*
274160 CATA-TTATTTTTAAAT
1 CATATTTATTTTGAAAT
274176 TCACATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (17 bp):
CATATTTATTTTGAAAT
Found at i:275261 original size:2 final size:2
Alignment explanation
Indices: 275256--275295 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
275246 TATATAGCCA
275256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275296 CTCAATTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277898 original size:31 final size:33
Alignment explanation
Indices: 277839--277910 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
277829 TAGTTTAGGC
*
277839 ATTAAAAATTATAAATAAAATTATTAATT-TTT
1 ATTAAAAAGTATAAATAAAATTATTAATTATTT
* *
277871 ATTAAAAAGTATATATAATA-TATTAATTATTT
1 ATTAAAAAGTATAAATAAAATTATTAATTATTT
*
277903 TTTAAAAA
1 ATTAAAAA
277911 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATTAAAAAGTATAAATAAAATTATTAATTATTT
Found at i:280276 original size:17 final size:18
Alignment explanation
Indices: 280238--280279 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
280228 CTAAGTTCAT
280238 TTTAAAGTTAATAAAAAA
1 TTTAAAGTTAATAAAAAA
280256 -TTAAA-TTAA-AAATAAA
1 TTTAAAGTTAATAAA-AAA
280272 TTTAAAGT
1 TTTAAAGT
280280 ATATAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.14
16 7 0.33
17 10 0.48
18 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
TTTAAAGTTAATAAAAAA
Found at i:281629 original size:21 final size:22
Alignment explanation
Indices: 281556--281622 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
281546 TTTTTTAATT
*
281556 TATTAAAT-TTATAATAAATATTA
1 TATTAAATATTAT-ATATAT-TTA
** *
281579 TATTATTTAATTATATATATTTT
1 TATTAAAT-ATTATATATATTTA
281602 TATTAAATATTAT-TATATTTA
1 TATTAAATATTATATATATTTA
281623 ATATAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.20
22 5 0.14
23 14 0.40
24 5 0.14
25 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAAATATTATATATATTTA
Found at i:281731 original size:18 final size:20
Alignment explanation
Indices: 281708--281745 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
281698 CATCAAACCA
281708 TTAATC-TAATTT-AATTTT
1 TTAATCTTAATTTAAATTTT
281726 TTAATCTTAATTTAAATTTT
1 TTAATCTTAATTTAAATTTT
281746 AAGGGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATCTTAATTTAAATTTT
Found at i:282003 original size:16 final size:16
Alignment explanation
Indices: 281969--282006 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
281959 TTTTAATTTA
*
281969 TTTTTTAAAATATAAT
1 TTTTTTAAAATAAAAT
*
281985 TTTTTTAAAA-AAAAG
1 TTTTTTAAAATAAAAT
282000 TTTTTTA
1 TTTTTTA
282007 TCCGTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTTAAAATAAAAT
Found at i:286341 original size:64 final size:64
Alignment explanation
Indices: 286250--286379 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 64
286240 ATATTGGTAT
* *
286250 GTAAAATTGGCCTCTCAATAATGTGAAAGCAAACTCTAGAACATACATTTGGTATGTAAAACTG
1 GTAAAACTGGCCTCTCAATAATGTGAAAGCAAACTCTAGAACATACAATTGGTATGTAAAACTG
* * * * *
286314 GTAAAACTGGTCTCTCAATTATTTGAAATCAAACTGTAGAACATACAATTGGTATGTAAAACTG
1 GTAAAACTGGCCTCTCAATAATGTGAAAGCAAACTCTAGAACATACAATTGGTATGTAAAACTG
286378 GT
1 GT
286380 CTCTTAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (64 bp):
GTAAAACTGGCCTCTCAATAATGTGAAAGCAAACTCTAGAACATACAATTGGTATGTAAAACTG
Found at i:286925 original size:20 final size:20
Alignment explanation
Indices: 286888--286926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
286878 ATTTTTCAAG
* * *
286888 TATATAATTTTTTTATATAT
1 TATATAATTATATCATATAT
286908 TATATAATTATATCATATA
1 TATATAATTATATCATATA
286927 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATAATTATATCATATAT
Found at i:287245 original size:25 final size:25
Alignment explanation
Indices: 287196--287245 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
287186 TTGAACTTTA
* *
287196 AACTTAGTTTTAGCTTTTTTTTTTT
1 AACTTAGTTTTAGCTTTCTTATTTT
* *
287221 AACTTATTTTTATCTTTCTTATTTT
1 AACTTAGTTTTAGCTTTCTTATTTT
287246 GCTTATAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.68
Consensus pattern (25 bp):
AACTTAGTTTTAGCTTTCTTATTTT
Found at i:287492 original size:2 final size:2
Alignment explanation
Indices: 287487--287517 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
287477 ATATATATAT
287487 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
287518 AGATAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:288377 original size:19 final size:19
Alignment explanation
Indices: 288342--288379 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
288332 CTCTTTTTCT
*
288342 TATCTTCTAAAGTTTCTTC
1 TATCTTCTAAAGATTCTTC
288361 TATCTTCTACAA-ATTCTTC
1 TATCTTCTA-AAGATTCTTC
288380 CCTATCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.50
Consensus pattern (19 bp):
TATCTTCTAAAGATTCTTC
Found at i:289160 original size:44 final size:44
Alignment explanation
Indices: 289097--289231 Score: 243
Period size: 44 Copynumber: 3.1 Consensus size: 44
289087 TTGGTAATGG
*
289097 GAAGATTGAGTTGCTGTAAGCGTATTCATTGGAGGATACTAGGT
1 GAAGATTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTAGGT
*
289141 GAAGATTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTCGGT
1 GAAGATTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTAGGT
*
289185 GAAGTTTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTAGGT
1 GAAGATTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTAGGT
289229 GAA
1 GAA
289232 CAAGCTACTT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 87 1.00
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.33
Consensus pattern (44 bp):
GAAGATTGAGTTGTTGTAAGCGTATTCATTGGAGGATACTAGGT
Found at i:290600 original size:28 final size:28
Alignment explanation
Indices: 290540--290594 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
290530 CATTTAAAAG
290540 AATTAAAATATTAAAAAATATATTTTAT
1 AATTAAAATATTAAAAAATATATTTTAT
290568 AATTAAAAT-TTAAATAAA-ATATTTTAT
1 AATTAAAATATTAAA-AAATATATTTTAT
290595 TTATTATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTAAAATATTAAAAAATATATTTTAT
Found at i:290948 original size:18 final size:19
Alignment explanation
Indices: 290927--290965 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
290917 TTATAATTTG
*
290927 AATTAATTTATGAA-AAAT
1 AATTAATTTATAAACAAAT
290945 AATTAATTTATAAACAAAT
1 AATTAATTTATAAACAAAT
290964 AA
1 AA
290966 AAAGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTAATTTATAAACAAAT
Found at i:291194 original size:26 final size:25
Alignment explanation
Indices: 291165--291219 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
291155 TTTTAAAATA
*
291165 ATATAATTGTAATTAATATATATTTT-
1 ATATAATT-TAAATAATATA-ATTTTC
*
291191 ATATAATTTAAATGATATAATTTTC
1 ATATAATTTAAATAATATAATTTTC
291216 ATAT
1 ATAT
291220 GTTTTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 13 0.50
26 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
ATATAATTTAAATAATATAATTTTC
Found at i:291504 original size:18 final size:19
Alignment explanation
Indices: 291457--291511 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
291447 TATTAAGGAA
*
291457 ATAATATTACTTAAATAAT
1 ATAATATTATTTAAATAAT
*
291476 ATAAT-TATATTTATA-AAT
1 ATAATAT-TATTTAAATAAT
*
291494 ATAATATTATTTTAATAA
1 ATAATATTATTTAAATAA
291512 AAATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATTATTTAAATAAT
Found at i:292087 original size:32 final size:32
Alignment explanation
Indices: 292024--292085 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
292014 GTTACACAAA
*
292024 ATAATATAAATATATGAATTATTAAATTTTAT
1 ATAATATAAATATATGAATTATCAAATTTTAT
*
292056 ATAATATAAAT-TATTAATATATCATAATTT
1 ATAATATAAATATATGAAT-TATCA-AATTT
292086 ATGTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 15 0.58
33 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (32 bp):
ATAATATAAATATATGAATTATCAAATTTTAT
Found at i:293966 original size:2 final size:2
Alignment explanation
Indices: 293959--293996 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
293949 TGGACCAAGC
293959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293997 TACCTGCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294835 original size:20 final size:20
Alignment explanation
Indices: 294797--294837 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
294787 AATTCATTAA
294797 AAAATTAAATATTTTATAAAT
1 AAAATTAAATA-TTTATAAAT
294818 AAAATTATAATA-TTATAAAT
1 AAAATTA-AATATTTATAAAT
294838 GTATTTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTAAATATTTATAAAT
Found at i:295838 original size:44 final size:45
Alignment explanation
Indices: 295711--295870 Score: 182
Period size: 44 Copynumber: 3.5 Consensus size: 45
295701 TACTTATCTT
* *
295711 TTAAGTAATTTAATTTAATTAAAAATAATATTTTTTTTTCATATATCTC
1 TTAATTAATTTAATTTAATTAAAAATAA-ATTTTTTATT-AT-T-TCTC
* * **
295760 TCAATTAAATTAATTTAATTAAAGCTAAATTTTTTATT-TTTCTC
1 TTAATTAATTTAATTTAATTAAAAATAAATTTTTTATTATTTCTC
295804 TTAATTAATTTAATTTAATTAAAAATAAATTTTTTTGATTCATTT-T-
1 TTAATTAATTTAATTTAATTAAAAATAAA-TTTTTT-ATT-ATTTCTC
295850 TTAATTAATTTAATTTAATTA
1 TTAATTAATTTAATTTAATTA
295871 GATATAAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
44 29 0.30
45 7 0.07
46 25 0.26
47 1 0.01
48 12 0.12
49 23 0.24
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (45 bp):
TTAATTAATTTAATTTAATTAAAAATAAATTTTTTATTATTTCTC
Found at i:297647 original size:6 final size:6
Alignment explanation
Indices: 297636--297678 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
297626 AAGCGACGAG
* *
297636 GAAGGA GAAGGA GAAGGA GAAGCA GAAGGA GAAGGA GCAGGA G
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA G
297679 GAGCCACGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:301841 original size:22 final size:24
Alignment explanation
Indices: 301789--301843 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
301779 ATATTTAAAA
301789 TATTT-TATATTTATATATGATTT
1 TATTTATATATTTATATATGATTT
* **
301812 AAAATATATATTTATAT-T-ATTT
1 TATTTATATATTTATATATGATTT
301834 TATTTATATA
1 TATTTATATA
301844 ATCGTATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 11 0.44
23 3 0.12
24 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTTATATATTTATATATGATTT
Found at i:303849 original size:22 final size:22
Alignment explanation
Indices: 303817--303864 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
303807 ATTGCAGAGG
*
303817 TGCAAAGGTGTAGAATTTTTAT
1 TGCAAACGTGTAGAATTTTTAT
303839 TGCAAACGTGTAGAATTTTTAT
1 TGCAAACGTGTAGAATTTTTAT
303861 TGCA
1 TGCA
303865 TGTCAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (22 bp):
TGCAAACGTGTAGAATTTTTAT
Found at i:308336 original size:20 final size:20
Alignment explanation
Indices: 308308--308345 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
308298 CTTCCCACCC
308308 TTTCCTTCT-TTCTCCTCTTT
1 TTTCCTTCTCTT-TCCTCTTT
*
308328 TTTCTTTCTCTTTCCTCT
1 TTTCCTTCTCTTTCCTCT
308346 ATTCCTCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTCCTTCTCTTTCCTCTTT
Found at i:310895 original size:14 final size:15
Alignment explanation
Indices: 310878--310914 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
310868 TGATTAATTT
310878 AAAATATTTAAAT-A
1 AAAATATTTAAATCA
*
310892 AAAATAATTAAATCA
1 AAAATATTTAAATCA
310907 AAAA-ATTT
1 AAAATATTT
310915 CAACATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATATTTAAATCA
Found at i:312479 original size:14 final size:15
Alignment explanation
Indices: 312453--312489 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
312443 GAAAAATAAA
312453 AAAATTATAAATTTT
1 AAAATTATAAATTTT
312468 AAAATT-TAAA-TTT
1 AAAATTATAAATTTT
*
312481 CAAATTATA
1 AAAATTATA
312490 TGTTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 8 0.40
14 6 0.30
15 6 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:313885 original size:28 final size:28
Alignment explanation
Indices: 313848--313918 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
313838 TCAATTTTTA
313848 TTATTTTTTAATT-TTTTTAA-AAGTTAT
1 TTATTTTTTAATTATTTTTAATAA-TTAT
*
313875 GTTATTTTTTATTTTATTTTTAATAATTAT
1 -TTATTTTTTA-ATTATTTTTAATAATTAT
313905 TTATTTTTTAATTA
1 TTATTTTTTAATTA
313919 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 13 0.34
29 12 0.32
30 11 0.29
31 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TTATTTTTTAATTATTTTTAATAATTAT
Found at i:313894 original size:29 final size:28
Alignment explanation
Indices: 313848--313917 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
313838 TCAATTTTTA
313848 TTATTTTTTAA-TTTTTTTAA-AAGTTAT
1 TTATTTTTTAATTTTTTTTAATAA-TTAT
*
313875 GTTATTTTTTATTTTATTTTTAATAATTAT
1 -TTATTTTTTAATTT-TTTTTAATAATTAT
313905 TTATTTTTTAATT
1 TTATTTTTTAATT
313918 AAAATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 10 0.27
29 14 0.38
30 11 0.30
31 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (28 bp):
TTATTTTTTAATTTTTTTTAATAATTAT
Found at i:313926 original size:30 final size:30
Alignment explanation
Indices: 313862--313928 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
313852 TTTTTAATTT
** *
313862 TTTTAAAAGTTATGTTATTTTTTATTTTAT
1 TTTTAAAAGTTATGTTATTTTTTATTAAAA
313892 TTTTAATAA-TTAT-TTATTTTTTAATTAAAA
1 TTTTAA-AAGTTATGTTATTTTTT-ATTAAAA
313922 TTTTAAA
1 TTTTAAA
313929 TATCTACAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 10 0.31
30 20 0.62
31 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTAAAAGTTATGTTATTTTTTATTAAAA
Found at i:314030 original size:29 final size:28
Alignment explanation
Indices: 313993--314054 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
313983 TAATTTTTAT
* *
313993 ATAATATAAATTA-TATTATATTTATAAAA
1 ATAAAATAAATTATTA-TATAATTA-AAAA
*
314022 ATAAAATAACTTATTATATAATTAAAAA
1 ATAAAATAAATTATTATATAATTAAAAA
314050 ATAAA
1 ATAAA
314055 TAAGTGACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.31
29 18 0.62
30 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAAAATAAATTATTATATAATTAAAAA
Found at i:324067 original size:23 final size:24
Alignment explanation
Indices: 324035--324083 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
324025 AAATTCCACT
* *
324035 AAGAATGAAAGAGAAAAAA-AAGA
1 AAGAAAGAAAGAAAAAAAAGAAGA
324058 AAGAAAGAAAGAAAAAAAAGAAGA
1 AAGAAAGAAAGAAAAAAAAGAAGA
324082 AA
1 AA
324084 CTTTAGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAAAAAGAAGA
Found at i:328271 original size:101 final size:102
Alignment explanation
Indices: 328075--328357 Score: 295
Period size: 103 Copynumber: 2.8 Consensus size: 102
328065 CAACTTATTT
* * * * * **
328075 AAAAGGATTAACTAGGATGAAACCGATAAGTCGATAAGTTTAAAAGGGGTTGACGAGGATGAAAT
1 AAAAGG-TTAACTAGGGTGAAACTGATAAGTCAATAAGTTT--AAGAGGTTGACCAGGACAAAAT
* ** *
328140 TAACAAGTCAGTAAAGGGTGACCAGGATAAAACCTAAGT-
63 TGACAAGTCAACAAAGGCTGACCAGGATAAAACCTAAGTG
* * *
328179 CAAAGGTTGACTAGGGTGAAAATGATAAGTCAATAAGTTTAAGAGGTTGACCAGGACAAAATTGA
1 AAAAGGTTAACTAGGGTGAAACTGATAAGTCAATAAGTTTAAGAGGTTGACCAGGACAAAATTGA
* *
328244 CAAGTCAACAAAGGCTGACTAGTATAAAACCTAAGTG
66 CAAGTCAACAAAGGCTGACCAGGATAAAACCTAAGTG
* * * *
328281 AAAAGGGTTAACTAGGGTGAAACTGACAAGT-AACCAAGTTTAAGA-GTTGATC-GAGACAAAAC
1 AAAA-GGTTAACTAGGGTGAAACTGATAAGTCAA-TAAGTTTAAGAGGTTGACCAG-GACAAAAT
*
328343 TGACAAGTTAACAAA
63 TGACAAGTCAACAAA
328358 TGAGAAAGGG
Statistics
Matches: 151, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
101 52 0.34
102 32 0.21
103 62 0.41
104 5 0.03
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (102 bp):
AAAAGGTTAACTAGGGTGAAACTGATAAGTCAATAAGTTTAAGAGGTTGACCAGGACAAAATTGA
CAAGTCAACAAAGGCTGACCAGGATAAAACCTAAGTG
Found at i:328571 original size:78 final size:78
Alignment explanation
Indices: 328437--328582 Score: 188
Period size: 78 Copynumber: 1.9 Consensus size: 78
328427 ATAAGTCAAC
* *
328437 AGATGAGAAAGGTTAAGTGAGAAAAAACCTACAAGTCAATTAAAAATGAAAGGTTGACCGAGACA
1 AGATGAGAAAGGTTAACTGAGAAAAAACCTACAAGTCAATGAAAAA-GAAAGGTTGACCGAGACA
328502 AAATCCATGAGTCA
65 AAATCCATGAGTCA
* * * * *
328516 AGATGAGAAGGGTTGACTGCGACAAAA-CTACAAGTCAATGAATAAA-AAAGAGTTGATCGAGAC
1 AGATGAGAAAGGTTAACTGAGAAAAAACCTACAAGTCAATGAA-AAAGAAAG-GTTGACCGAGAC
328579 AAAA
64 AAAA
328583 CTTACAAGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
77 4 0.07
78 29 0.50
79 25 0.43
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (78 bp):
AGATGAGAAAGGTTAACTGAGAAAAAACCTACAAGTCAATGAAAAAGAAAGGTTGACCGAGACAA
AATCCATGAGTCA
Found at i:328611 original size:40 final size:39
Alignment explanation
Indices: 328439--328611 Score: 129
Period size: 41 Copynumber: 4.4 Consensus size: 39
328429 AAGTCAACAG
* * * * *
328439 ATGAGAAAGGTTAAGTGAGAAAAAACCTACAAGTCAATTA
1 ATGAGAAGGGTTGACTGAGACAAAA-CTACAAGTCAATGA
** * * *
328479 AAAATGAAAGGTTGACCGAGACAAAA-TCCATGAGTCAA-G-
1 ATGA-GAAGGGTTGACTGAGACAAAACTACA--AGTCAATGA
*
328518 ATGAGAAGGGTTGACTGCGACAAAACTACAAGTCAATGA
1 ATGAGAAGGGTTGACTGAGACAAAACTACAAGTCAATGA
* * *
328557 ATAAAAAAGAGTTGA-TCGAGACAAAACTTACAAGTCAATGA
1 AT-GAGAAGGGTTGACT-GAGACAAAAC-TACAAGTCAATGA
328598 ATGAGAAGGGTTGA
1 ATGAGAAGGGTTGA
328612 GTGGCATTTG
Statistics
Matches: 103, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
37 6 0.06
38 19 0.18
39 11 0.11
40 29 0.28
41 38 0.37
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.18
Consensus pattern (39 bp):
ATGAGAAGGGTTGACTGAGACAAAACTACAAGTCAATGA
Found at i:329313 original size:77 final size:76
Alignment explanation
Indices: 329067--329303 Score: 287
Period size: 76 Copynumber: 3.1 Consensus size: 76
329057 TTCCACCAAC
* * * *
329067 AGTCGAAACAAACTT-ATAATAAGTTAAAGTAGAAGATCATAATAGGGAATATGTGATTCTACAA
1 AGTCAAAACAAA-TTGATAACAAGCTAAAGTAGAAGATCATAATAGGGAATATGTGGTTCTACAA
* *
329131 TTTCCTATCAAC
65 TTTCCCATCAAT
* * * * * * *
329143 ATTCGAAACAAATTGATAACAAGCTAGAGTAGATGATCATGATAGGAAATATGTGGTTCTATAAT
1 AGTCAAAACAAATTGATAACAAGCTAAAGTAGAAGATCATAATAGGGAATATGTGGTTCTACAAT
* *
329208 TTCCCGTTAAT
66 TTCCCATCAAT
* * *
329219 AGTCAAAACAAATTGATAACAGGCTAAAGTTAGAAGATCATAATGGGGAATATGTGGTTTTACAA
1 AGTCAAAACAAATTGATAACAAGCTAAAG-TAGAAGATCATAATAGGGAATATGTGGTTCTACAA
329284 TTTCCCATCAAT
65 TTTCCCATCAAT
329296 AGTCAAAA
1 AGTCAAAA
329304 TGAACTGATA
Statistics
Matches: 134, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
75 2 0.01
76 85 0.63
77 47 0.35
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (76 bp):
AGTCAAAACAAATTGATAACAAGCTAAAGTAGAAGATCATAATAGGGAATATGTGGTTCTACAAT
TTCCCATCAAT
Found at i:333893 original size:8 final size:8
Alignment explanation
Indices: 333882--333913 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
333872 GTATGTATAT
333882 ATGTATGC
1 ATGTATGC
333890 ATGTATGC
1 ATGTATGC
333898 ATGTATGC
1 ATGTATGC
333906 ATGATATG
1 ATG-TATG
333914 AGCATGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:333893 original size:16 final size:16
Alignment explanation
Indices: 333874--333912 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
333864 TAATGTTTGT
333874 ATGTATATATGTATGC
1 ATGTATATATGTATGC
**
333890 ATGTATGCATGTATGC
1 ATGTATATATGTATGC
333906 ATG-ATAT
1 ATGTATAT
333913 GAGCATGTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.41
Consensus pattern (16 bp):
ATGTATATATGTATGC
Found at i:338252 original size:148 final size:148
Alignment explanation
Indices: 337980--338253 Score: 343
Period size: 148 Copynumber: 1.9 Consensus size: 148
337970 TGGCTCTAAT
* * * * *
337980 AAAATTATCAAAATGCTCTTTGGTATACCTTTGACGTGAAAATATCCTAGTAAACCTAAAAGATA
1 AAAATTATCAAAATACCCTTAGGTATACCTTTGACGTGAAAATATCCTAGTAAACCCAAAAGACA
** * ** * * **
338045 TGAAAAGATTGTAAAAATTCAAACCTATCCTAAATGTATACCTTTTGGGTAAAAACAACCCAGCC
66 CCAAAAGATCGTAAAAATTCAAACCTATCCTAAACATAGACCTTTAGCATAAAAACAACCCAGCC
338110 TAGGACTCGATTTCTAGG
131 TAGGACTCGATTTCTAGG
* * * *
338128 AAAATTATCAAAGTACCCTTAGGTATACCTTTGATGTGAAAATATCCTGGTAATCCCAAAAGACA
1 AAAATTATCAAAATACCCTTAGGTATACCTTTGACGTGAAAATATCCTAGTAAACCCAAAAGACA
* * *
338193 CCAAAGGATCGTAAAAAGTT-GAACCTATCCTAAACATAGACCTTTAGCATAAAAGCAACCC
66 CCAAAAGATCGTAAAAA-TTCAAACCTATCCTAAACATAGACCTTTAGCATAAAAACAACCC
338254 GGTGACTACC
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
148 102 0.98
149 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (148 bp):
AAAATTATCAAAATACCCTTAGGTATACCTTTGACGTGAAAATATCCTAGTAAACCCAAAAGACA
CCAAAAGATCGTAAAAATTCAAACCTATCCTAAACATAGACCTTTAGCATAAAAACAACCCAGCC
TAGGACTCGATTTCTAGG
Found at i:345796 original size:12 final size:12
Alignment explanation
Indices: 345779--345807 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
345769 AGAATGAAAG
345779 AGAAAAAAAGAA
1 AGAAAAAAAGAA
345791 AGAAAAAAAGAA
1 AGAAAAAAAGAA
345803 A-AAAA
1 AGAAAA
345808 CTCCAGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:349646 original size:41 final size:41
Alignment explanation
Indices: 349573--349676 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
349563 CAAAATCCAT
*
349573 AAGTCAACG-ATGAGAAAG-GTTGACTGGGACAAAA-TCTAC
1 AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACT-TAC
* *
349612 GAGTCAATGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
1 AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
*
349653 AAGTCAACGAATGAGAAA-AGTTGA
1 AAGTCAACGAATAAGAAAGAGTTGA
349677 GTGGCATTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.12
40 14 0.25
41 34 0.61
42 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.18
Consensus pattern (41 bp):
AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
Found at i:350320 original size:13 final size:13
Alignment explanation
Indices: 350302--350326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350292 CATAAAATGT
350302 TGTATCGATACAA
1 TGTATCGATACAA
350315 TGTATCGATACA
1 TGTATCGATACA
350327 TACTTTTTGT
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:350342 original size:32 final size:33
Alignment explanation
Indices: 350282--350347 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
350272 TTCAACGATT
350282 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
350315 TGTATCGATACAT-ACTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
350347 T
1 T
350348 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:350408 original size:13 final size:13
Alignment explanation
Indices: 350390--350414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350380 ATTACTCACA
350390 TGTATCGATACAT
1 TGTATCGATACAT
350403 TGTATCGATACA
1 TGTATCGATACA
350415 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:350479 original size:52 final size:52
Alignment explanation
Indices: 350423--350543 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
350413 CACTGATCTT
*
350423 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
350475 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
350527 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
350544 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:358823 original size:31 final size:32
Alignment explanation
Indices: 358785--358868 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 32
358775 ATACCTTTTT
358785 AAAGTCCACGACTCAGTGGCAATCTCTTC-TC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTC
* * *
358816 AAAGTCCACGACTCAGTGGCATTTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTC
* * *
358848 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
358869 CCTTTTTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 26 0.57
32 20 0.43
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (32 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTTC
Found at i:358982 original size:33 final size:33
Alignment explanation
Indices: 358849--359150 Score: 349
Period size: 33 Copynumber: 8.8 Consensus size: 33
358839 TTTTTCTTCA
*
358849 AAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTC-TTTTCCTTTT
358882 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTT
1 -AAGCCCACAACTCCGTGGCACTC-TTTT-CC-TTTT
358919 AAAGCCCACAACTCCGTGGCACACTCTTTTCCTTTT
1 -AAGCCCACAACTCCGTGG--CACTCTTTTCCTTTT
* * *
358955 AAGTCCACGACTCCGTGGCACTCTTTTCCTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTTT
* *
358988 AAGCCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTTT
*
359021 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTC-TTTTCCTTTT
359055 AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACTC---TTTTCC-TTTT
* *
359092 AAAGCCCACAACTCTGTGGCAC-CTTGTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACTCTT-TTCCTTTT
* *
359126 AAGTCCACAACTTCGTGGCA-TCTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
359151 CACCCTTTCT
Statistics
Matches: 240, Mismatches: 16, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.00
33 84 0.35
34 60 0.25
35 25 0.10
36 12 0.05
37 29 0.12
38 24 0.10
39 5 0.02
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.34
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACTCTTTTCCTTTT
Found at i:359025 original size:138 final size:139
Alignment explanation
Indices: 358816--359170 Score: 420
Period size: 138 Copynumber: 2.6 Consensus size: 139
358806 ATCTCTTCTC
* * * * *
358816 AAAGTCCACGACTCAGTGGCA-TTTTTTTCTTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
1 AAAGTCCACGACTCAGTGGCACTCTTTTCCTTTAAAGCCCACAACTACGTGGCACTC-TTTTCCT
* *
358879 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACAC-
65 TCTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCT-AAGCCCACAACTCCGTGGCACACT
358943 TCTTTTCC-TTTT
127 TCTTTTCCTTTTT
*
358955 -AAGTCCACGACTCCGTGGCACTCTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCTT
1 AAAGTCCACGACTCAGTGGCACTCTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCTT
* *
359019 CT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
66 CTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACACTTCTT
359083 TTCCTTTTT
131 TTCCTTTTT
* * * * * * * *
359092 AAAGCCCACAACTCTGTGGCAC-CTTGTTCTTTTTAAGTCCACAACTTCGTGGCA-TCTTTCACC
1 AAAGTCCACGACTCAGTGGCACTCTT-TTCCTTTAAAGCCCACAACTACGTGGCACTCTTT--TC
359155 CTTTCTAAAGCCCACA
63 C-TTCTAAAGCCCACA
359171 CAAGTCGGTG
Statistics
Matches: 188, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
135 22 0.12
136 10 0.05
137 14 0.07
138 89 0.47
139 39 0.21
140 5 0.03
141 9 0.05
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.34
Consensus pattern (139 bp):
AAAGTCCACGACTCAGTGGCACTCTTTTCCTTTAAAGCCCACAACTACGTGGCACTCTTTTCCTT
CTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACACTTCTT
TTCCTTTTT
Found at i:359198 original size:33 final size:34
Alignment explanation
Indices: 359161--359224 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
359151 CACCCTTTCT
359161 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
359194 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
359225 AAGCCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (34 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
Found at i:359231 original size:30 final size:30
Alignment explanation
Indices: 359152--359231 Score: 106
Period size: 33 Copynumber: 2.5 Consensus size: 30
359142 GGCATCTTTC
359152 ACCCTTTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCC-TTCT-AAGCCCACACAAGTCGGTGGCA
*
359184 ACCTTCTTCCAAAGCCCACACAAGTCGGTGGCA
1 ACC--CTT-CTAAGCCCACACAAGTCGGTGGCA
359217 ACCCTTCTAAGCCCA
1 ACCCTTCTAAGCCCA
359232 ATATAGCTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 8 0.19
31 3 0.07
32 3 0.07
33 27 0.63
34 2 0.05
ACGTcount: A:0.28, C:0.38, G:0.16, T:0.19
Consensus pattern (30 bp):
ACCCTTCTAAGCCCACACAAGTCGGTGGCA
Found at i:359288 original size:49 final size:49
Alignment explanation
Indices: 359224--360128 Score: 1089
Period size: 49 Copynumber: 18.7 Consensus size: 49
359214 GCAACCCTTC
* * * *
359224 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
359273 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359316 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
359368 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
359417 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * **
359460 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
359509 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
359552 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359601 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359650 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359699 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* * * * *
359748 TAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359796 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359845 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
359894 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* * * *
359943 TAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
359991 TAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
360040 TAAGTCCAATATAGCTTGGCCTTGAATCAGCATATCGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGC-TGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
*
360093 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
360129 ACATCCTTTT
Statistics
Matches: 728, Mismatches: 97, Indels: 59
0.82 0.11 0.07
Matches are distributed among these distances:
43 115 0.16
45 2 0.00
47 2 0.00
48 81 0.11
49 424 0.58
50 24 0.03
52 61 0.08
53 19 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:359841 original size:195 final size:196
Alignment explanation
Indices: 359224--360128 Score: 1229
Period size: 195 Copynumber: 4.7 Consensus size: 196
359214 GCAACCCTTC
* * * * * * * *
359224 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
* * * * *
359289 GGCCTTGACTCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* * * * * * * *
359348 ATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTA
131 ATTGGCA-C--TTGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATCA
359413 TCTT
193 TCTT
* *
359417 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-----TTAAGTCCAATATCGCT
1 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
** *
359476 GGCCTTGAATCAGCATATTGGCGTCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
66 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* * *
359541 ATT-G-----GCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCT
131 ATTGGCACTTGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATCATCT
359600 T
196 T
359601 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
*
359666 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* *
359731 ATTGGCACTTGCACCATTAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATCT
131 ATTGGCACTTGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATCATCT
359795 T
196 T
359796 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
*
359861 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* * *
359926 ATTGGCACTTGCACCATTAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCT
131 ATTGGCACTTGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATCATCT
359990 T
196 T
* * *
359991 TAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGC-
* * *
360056 TGGCCTTGAATCAGCATATCGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCA
65 TGGCCTTGAATCAGCATATTGGCAC-CTTT--ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCA
360121 GCACATTG
127 GCACATTG
360129 ACATCCTTTT
Statistics
Matches: 650, Mismatches: 40, Indels: 38
0.89 0.05 0.05
Matches are distributed among these distances:
184 87 0.13
185 1 0.00
187 35 0.05
188 1 0.00
190 80 0.12
191 1 0.00
192 2 0.00
193 72 0.11
195 295 0.45
196 34 0.05
197 3 0.00
199 39 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (196 bp):
TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
ATTGGCACTTGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATCATCT
T
Found at i:360250 original size:67 final size:68
Alignment explanation
Indices: 360142--360268 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
360132 TCCTTTTTCA
* * *
360142 TCATCTTCAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
360206 TCT
66 TCT
* * * * *
360209 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
360269 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (68 bp):
TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:364563 original size:12 final size:12
Alignment explanation
Indices: 364546--364574 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
364536 AGAATGAAAG
364546 AGAAAAAAAGAA
1 AGAAAAAAAGAA
364558 AGAAAAAAAGAA
1 AGAAAAAAAGAA
364570 A-AAAA
1 AGAAAA
364575 CTCCAGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:368413 original size:41 final size:41
Alignment explanation
Indices: 368340--368443 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
368330 CAAAATCCAT
*
368340 AAGTCAACG-ATGAGAAAG-GTTGACTGGGACAAAA-TCTAC
1 AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACT-TAC
* *
368379 GAGTCAATGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
1 AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
*
368420 AAGTCAACGAATGAGAAA-AGTTGA
1 AAGTCAACGAATAAGAAAGAGTTGA
368444 GTGGCATTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.12
40 14 0.25
41 34 0.61
42 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.18
Consensus pattern (41 bp):
AAGTCAACGAATAAGAAAGAGTTGACTGGGACAAAACTTAC
Found at i:369087 original size:13 final size:13
Alignment explanation
Indices: 369069--369093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369059 CATAAAATGT
369069 TGTATCGATACAA
1 TGTATCGATACAA
369082 TGTATCGATACA
1 TGTATCGATACA
369094 TACTTTTTGT
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:369109 original size:32 final size:33
Alignment explanation
Indices: 369049--369114 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
369039 TTCAACGATT
369049 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
369082 TGTATCGATACAT-ACTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
369114 T
1 T
369115 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:369174 original size:13 final size:13
Alignment explanation
Indices: 369156--369180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369146 ATTACTCACA
369156 TGTATCGATACAT
1 TGTATCGATACAT
369169 TGTATCGATACA
1 TGTATCGATACA
369181 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:369245 original size:52 final size:52
Alignment explanation
Indices: 369189--369309 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
369179 CACTGATCTT
*
369189 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
369241 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
369293 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
369310 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:372652 original size:76 final size:76
Alignment explanation
Indices: 372563--372798 Score: 224
Period size: 76 Copynumber: 3.0 Consensus size: 76
372553 CCAACACCTT
* * * *
372563 AAACAAATTGATAATAAGTTAAAGTGGAAGATTATAATGTGGAATATATGATTCTATAATTTCCC
1 AAACAAATTGATAATAAGCTAAAGTGGAAGATCATAATGAGGAATATATGATTCTACAATTTCCC
372628 ATCAACAGTCA
66 ATCAACAGTCA
* * * * * * *
372639 AAACAAACTGATAACAAGCTAGAGTAGATGATCATGAT-AGGAA-ATAAGTAGTTCTACAATTTC
1 AAACAAATTGATAATAAGCTAAAGTGGAAGATCATAATGAGGAATATATG-A-TTCTACAATTTC
*
372702 CCATCAACAGTCG
64 CCATCAACAGTCA
* * * * * *
372715 AAACAAATTAATGATAAGCTAAAGTTAGAAGAAGATCATAATGGGGAATATGTGGTTTTTACAAT
1 AAACAAATTGATAATAAGCTAAAG-T-G--GAAGATCATAATGAGGAATATAT-GATTCTACAAT
*
372780 TTCCCATCAATAGTCA
61 TTCCCATCAACAGTCA
372796 AAA
1 AAA
372799 TGAATTAATA
Statistics
Matches: 124, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
74 4 0.03
75 5 0.04
76 72 0.58
77 1 0.01
80 10 0.08
81 29 0.23
82 2 0.02
83 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (76 bp):
AAACAAATTGATAATAAGCTAAAGTGGAAGATCATAATGAGGAATATATGATTCTACAATTTCCC
ATCAACAGTCA
Found at i:373242 original size:13 final size:13
Alignment explanation
Indices: 373224--373264 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
373214 TATTGCAATG
373224 CAATGTATCGATA
1 CAATGTATCGATA
*
373237 CAATGTATCAATA
1 CAATGTATCGATA
* *
373250 CATTGTATGGATA
1 CAATGTATCGATA
373263 CA
1 CA
373265 CCTTGCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:373354 original size:22 final size:20
Alignment explanation
Indices: 373326--373408 Score: 98
Period size: 20 Copynumber: 4.0 Consensus size: 20
373316 AGTAGCTACC
373326 AAATGTATCGATACATATATAG
1 AAATGTATCGATACA-AT-TAG
373348 AAATGTATCGATACAATTCCAG
1 AAATGTATCGATACAATT--AG
373370 -AATGTATCGATAC-ATCTAG
1 AAATGTATCGATACAAT-TAG
*
373389 AATTGTATCGATACAATTAG
1 AAATGTATCGATACAATTAG
373409 CCCAATGGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
19 2 0.04
20 18 0.33
21 18 0.33
22 17 0.31
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
AAATGTATCGATACAATTAG
Found at i:373401 original size:41 final size:42
Alignment explanation
Indices: 373327--373406 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
373317 GTAGCTACCA
373327 AATGTATCGATACATATATAGAAATGTATCGATACAATTCCAG
1 AATGTATCGATACA-ATATAGAAATGTATCGATACAATTCCAG
* *
373370 AATGTATCGATAC-ATCTAGAATTGTATCGATACAATT
1 AATGTATCGATACAATATAGAAATGTATCGATACAATT
373407 AGCCCAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 22 0.63
43 13 0.37
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (42 bp):
AATGTATCGATACAATATAGAAATGTATCGATACAATTCCAG
Found at i:377682 original size:52 final size:52
Alignment explanation
Indices: 377602--377845 Score: 168
Period size: 52 Copynumber: 4.5 Consensus size: 52
377592 GTTGAAAAAA
* *
377602 AATTCAAGGCCAACGATATTAGACTTAAAGATGACAAAGGTGCCAATGTGCT
1 AATTCAAGGCCAATGACATTAGACTTAAAGATGACAAAGGTGCCAATGTGCT
* * ** *
377654 AATTCAAGGCCAATGACATTAGATTTAAAGATGA-AAAGAATGATAAAGGTGTCGAT
1 AATTCAAGGCCAATGACATTAGACTTAAAGATGACAAAG-GTG-CCAA--TGT-GCT
* * * * ** *
377710 ATACTGATATAAGGCCAATAAAATTGGACTTAAAGATGACAAAGGCACCAATATGCT
1 A-A-T--T-CAAGGCCAATGACATTAGACTTAAAGATGACAAAGGTGCCAATGTGCT
* * * * * *
377767 AATTCAAGGCCAGTGATATTAGA-TTTAAGAAAGAAAAAGGTGCTAATGTGCT
1 AATTCAAGGCCAATGACATTAGACTTAAAG-ATGACAAAGGTGCCAATGTGCT
* * *
377819 GATTCAAGGCCAGTGACATTGGACTTA
1 AATTCAAGGCCAATGACATTAGACTTA
377846 GAAAGAGATG
Statistics
Matches: 144, Mismatches: 35, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
51 9 0.06
52 83 0.58
53 5 0.03
55 4 0.03
56 4 0.03
57 4 0.03
58 3 0.02
60 3 0.02
61 25 0.17
62 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.25
Consensus pattern (52 bp):
AATTCAAGGCCAATGACATTAGACTTAAAGATGACAAAGGTGCCAATGTGCT
Found at i:378003 original size:33 final size:33
Alignment explanation
Indices: 377922--378099 Score: 143
Period size: 33 Copynumber: 5.5 Consensus size: 33
377912 ATGCCACTGT
*
377922 CTTGTGTGGGCTTT--AGAAGGTTTGCCACCAA
1 CTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAA
* * ***
377953 CTTATGTGGGCTATAGAGAAGGGTTGCCATTTA
1 CTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAA
* ** * * *
377986 CTTGTGTAGGCTTTAGAGAAATGTTGCTATCGA
1 CTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAA
* *
378019 CTTGTATGGG-TTT-TAGAAGAGGTTGCCACCAA
1 CTTGTGTGGGCTTTAGAGAAG-GGTTGCCACCAA
* *
378051 CTTGTGTGGGCTTTAGAAGAA--GTTGCTACCAG
1 CTTGTGTGGGCTTTAG-AGAAGGGTTGCCACCAA
*
378083 TTTGTGTGGGCTTTAGA
1 CTTGTGTGGGCTTTAGA
378100 AAATGGTGCC
Statistics
Matches: 114, Mismatches: 27, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
31 17 0.15
32 44 0.39
33 49 0.43
35 4 0.04
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (33 bp):
CTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAA
Found at i:378054 original size:32 final size:32
Alignment explanation
Indices: 377922--378100 Score: 150
Period size: 32 Copynumber: 5.6 Consensus size: 32
377912 ATGCCACTGT
377922 CTTGTGTGGGCTTTAGAAG--GTTTGCCACCAA
1 CTTGTGTGGGCTTTAGAAGAAG-TTGCCACCAA
* * ***
377953 CTTATGTGGGCTATAG-AGAAGGGTTGCCATTTA
1 CTTGTGTGGGCTTTAGAAGAA--GTTGCCACCAA
* * * *
377986 CTTGTGTAGGCTTTAG-AGAAATGTTGCTATCGA
1 CTTGTGTGGGCTTTAGAAG-AA-GTTGCCACCAA
* * *
378019 CTTGTATGGGTTTTAGAAGAGGTTGCCACCAA
1 CTTGTGTGGGCTTTAGAAGAAGTTGCCACCAA
* *
378051 CTTGTGTGGGCTTTAGAAGAAGTTGCTACCAG
1 CTTGTGTGGGCTTTAGAAGAAGTTGCCACCAA
*
378083 TTTGTGTGGGCTTTAGAA
1 CTTGTGTGGGCTTTAGAA
378101 AATGGTGCCC
Statistics
Matches: 117, Mismatches: 25, Indels: 11
0.76 0.16 0.07
Matches are distributed among these distances:
30 2 0.02
31 14 0.12
32 52 0.44
33 44 0.38
34 5 0.04
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (32 bp):
CTTGTGTGGGCTTTAGAAGAAGTTGCCACCAA
Found at i:378157 original size:29 final size:29
Alignment explanation
Indices: 378124--378465 Score: 449
Period size: 29 Copynumber: 11.9 Consensus size: 29
378114 ACGCATGAGC
* *
378124 TTTGAAACGATGCCACTGACTTGTGGACT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
**
378153 TTTGAAAGGATGCCACTGACTCATGGGC-
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
* *
378181 TTTGAAAGGATGCCACTAACTTCTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
*
378210 TTTGAAAAGATGCCACTGACTTGTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
* * *
378239 TTAAGAAAGGATGCCATTGACTTATGGGCT
1 TT-TGAAAGGATGCCACTGACTTGTGGGCT
378269 TTTGAAAGGATGCCACTGACTCT-TGGG-T
1 TTTGAAAGGATGCCACTGACT-TGTGGGCT
*
378297 TTTGAAAGGATGCCACTAACTTGTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
* * * **
378326 TTTGAAAAGATGTCATTGACTCATGGG-T
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
378354 TTTGAAAGGATGCCACTGACTTGTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
* *
378383 TTTGAAATGATGCCATTGACTTGTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
* *
378412 TTTGAAAGGATGCTATTGACTTGTGGGCT
1 TTTGAAAGGATGCCACTGACTTGTGGGCT
*
378441 TTTGAAAGGATACCACTGACTTGTG
1 TTTGAAAGGATGCCACTGACTTGTG
378466 TGGGCTTTAG
Statistics
Matches: 272, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.00
28 73 0.27
29 172 0.63
30 26 0.10
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (29 bp):
TTTGAAAGGATGCCACTGACTTGTGGGCT
Found at i:378172 original size:57 final size:57
Alignment explanation
Indices: 378087--378461 Score: 455
Period size: 57 Copynumber: 6.5 Consensus size: 57
378077 TACCAGTTTG
* * * * *
378087 TGTGGGCTTTAGAAAATGG-TGCCCCTGACGCATGAGCTTTGAAACGATGCCACTGACT
1 TGTGGGCTTTTG-AAA-GGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACT
* *
378145 TGTGGACTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACT
* * ** *
378202 TCTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAGAAAGGATGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGCTTT--GAAAGGATGCCACTGACT
* * * *
378261 TATGGGCTTTTGAAAGGATGCCACTGACTCTTGGGTTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACT
* * * *
378318 TGTGGGCTTTTGAAAAGATGTCATTGACTCATGGGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACT
* * ** * *
378375 TGTGGGCTTTTGAAATGATGCCATTGACTTGTGGGCTTTTGAAAGGATGCTATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGC-TTTGAAAGGATGCCACTGACT
*
378433 TGTGGGCTTTTGAAAGGATACCACTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
378462 TGTGTGGGCT
Statistics
Matches: 276, Mismatches: 37, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
56 2 0.01
57 169 0.61
58 55 0.20
59 50 0.18
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACT
Found at i:378413 original size:173 final size:172
Alignment explanation
Indices: 378124--378461 Score: 532
Period size: 173 Copynumber: 2.0 Consensus size: 172
378114 ACGCATGAGC
* *
378124 TTTGAAACGATGCCACTGACTTGTGGACTTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAG
1 TTTGAAACGATGCCACTAACTTGTGGACTTTTGAAAAGATGCCACTGACTCATGGGCTTTGAAAG
378189 GATGCCACTAACTTCTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTAAGAAAGGATGCC
66 GATGCCACTAACTTCTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTT-AGAAAGGATGCC
*
378254 ATTGACTTATGGGCTTTTGAAAGGATGCCACTGACTCTTGGGT
130 ATTGACTTATGGGCTTTTGAAAGGATACCACTGACTCTTGGGT
* * * * *
378297 TTTGAAAGGATGCCACTAACTTGTGGGCTTTTGAAAAGATGTCATTGACTCATGGGTTTTGAAAG
1 TTTGAAACGATGCCACTAACTTGTGGACTTTTGAAAAGATGCCACTGACTCATGGGCTTTGAAAG
* * * * * *
378362 GATGCCACTGACTTGTGGGCTTTTGAAATGATGCCATTGACTTGTGGGCTTTTGAAAGGATGCTA
66 GATGCCACTAACTTCTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTAGAAAGGATGCCA
*
378427 TTGACTTGTGGGCTTTTGAAAGGATACCACTGACT
131 TTGACTTATGGGCTTTTGAAAGGATACCACTGACT
378462 TGTGTGGGCT
Statistics
Matches: 150, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
172 44 0.29
173 106 0.71
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (172 bp):
TTTGAAACGATGCCACTAACTTGTGGACTTTTGAAAAGATGCCACTGACTCATGGGCTTTGAAAG
GATGCCACTAACTTCTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTAGAAAGGATGCCA
TTGACTTATGGGCTTTTGAAAGGATACCACTGACTCTTGGGT
Found at i:379564 original size:29 final size:28
Alignment explanation
Indices: 379532--379589 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
379522 TCTCTTTTGA
379532 TTTTGCCATTGCATTTTTTTATGTTTTTTT
1 TTTTG-CATTGCATTTTTTTAT-TTTTTTT
* * *
379562 TTTTGCTTTTCATTTTTTTCTTTTTTTT
1 TTTTGCATTGCATTTTTTTATTTTTTTT
379590 GAAGGGAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 13 0.52
30 5 0.20
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76
Consensus pattern (28 bp):
TTTTGCATTGCATTTTTTTATTTTTTTT
Found at i:386805 original size:20 final size:20
Alignment explanation
Indices: 386780--386830 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
386770 ATTTGCCTGT
386780 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
386800 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
386820 ATGTATCGATA
1 ATGTATCGATA
386831 TATTTGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:386863 original size:22 final size:22
Alignment explanation
Indices: 386835--386879 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
386825 TCGATATATT
*
386835 TGGGTCAAAAACCTAGAATGTA
1 TGGGTCAAAAACCCAGAATGTA
386857 TGGGTCAAAAACCCAGAATGTA
1 TGGGTCAAAAACCCAGAATGTA
386879 T
1 T
386880 CTATACAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (22 bp):
TGGGTCAAAAACCCAGAATGTA
Found at i:386898 original size:20 final size:20
Alignment explanation
Indices: 386873--386927 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
386863 AAAAACCCAG
*
386873 AATGTATCTATACAATGAAT-
1 AATGTATCGATACAAT-AATA
386893 AATGTATCGATACAAATAATA
1 AATGTATCGATAC-AATAATA
386914 AATGTATCGATACA
1 AATGTATCGATACA
386928 TTTATTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAATAATA
Found at i:386919 original size:21 final size:21
Alignment explanation
Indices: 386873--386927 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
386863 AAAAACCCAG
*
386873 AATGTATCTATAC-AATGAAT
1 AATGTATCGATACAAATGAAT
386893 AATGTATCGATACAAAT-AAT
1 AATGTATCGATACAAATGAAT
386913 AAATGTATCGATACA
1 -AATGTATCGATACA
386928 TTTATTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAAATGAAT
Found at i:389548 original size:45 final size:44
Alignment explanation
Indices: 389442--389531 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
389432 CTTTAATTTC
389442 ATAAACATGAATGTTTTTTATTCATATTTATTTTTGTTTGTTGG
1 ATAAACATGAATGTTTTTTATTCATATTTATTTTTGTTTGTTGG
*
389486 ATAAACATGAATGTTTTTTATTCATATTTTTTTTTGTTTGTTGG
1 ATAAACATGAATGTTTTTTATTCATATTTATTTTTGTTTGTTGG
389530 AT
1 AT
389532 TGAATTTGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.58
Consensus pattern (44 bp):
ATAAACATGAATGTTTTTTATTCATATTTATTTTTGTTTGTTGG
Found at i:389642 original size:49 final size:48
Alignment explanation
Indices: 389589--389681 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
389579 TATGTTCAAA
* *
389589 GTATCGATACATCTGGATTTTTCCAGAATGTATCGATACAATGCAACTT
1 GTATCGATACATCTGG-TTTTCCCAGAATATATCGATACAATGCAACTT
* * * *
389638 GTATCTATACATCTGGTTTTCCCAGATTATATTGATATAATGCA
1 GTATCGATACATCTGGTTTTCCCAGAATATATCGATACAATGCA
389682 TGATGTATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 23 0.61
49 15 0.39
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (48 bp):
GTATCGATACATCTGGTTTTCCCAGAATATATCGATACAATGCAACTT
Found at i:389696 original size:48 final size:49
Alignment explanation
Indices: 389589--389697 Score: 114
Period size: 48 Copynumber: 2.2 Consensus size: 49
389579 TATGTTCAAA
* * * *
389589 GTATCGATACATCTGGATTTTTCCAGAATGTATCGATACAATGCAACTT
1 GTATTGATACATCTGGATTTTCCCAGAATATATCGATACAATGCAACAT
* * * **
389638 GTATCT-ATACATCTGG-TTTTCCCAGATTATATTGATATAATGCATGAT
1 GTAT-TGATACATCTGGATTTTCCCAGAATATATCGATACAATGCAACAT
389686 GTATTGATACAT
1 GTATTGATACAT
389698 ATTGTATCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
47 1 0.02
48 34 0.69
49 14 0.29
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (49 bp):
GTATTGATACATCTGGATTTTCCCAGAATATATCGATACAATGCAACAT
Found at i:390824 original size:21 final size:21
Alignment explanation
Indices: 390767--390827 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
390757 GTTACATTTT
* **
390767 TGCCTTTGGTGTATTAATACA
1 TGCCTTTGATGTATCGATACA
*
390788 TGCCTTTAATGTATCGATACA
1 TGCCTTTGATGTATCGATACA
390809 TGCCTTTGATGTATCGATA
1 TGCCTTTGATGTATCGATA
390828 TAAAGTCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (21 bp):
TGCCTTTGATGTATCGATACA
Found at i:393152 original size:78 final size:75
Alignment explanation
Indices: 393062--393212 Score: 196
Period size: 78 Copynumber: 2.0 Consensus size: 75
393052 TTTTCATCTT
* *
393062 AGGGGATACTCCACCCCCACTTTTAATTTT-AAAATATTAAAATTTTCATCTCGGGGATACTCCA
1 AGGGGATACTCCAACCCCA-TTTTAATTTTCAAAATATTAAAATTTTCATCTC-GAGATACTCCA
393126 ACCCGTTATTTTCG
64 A-CC-TTATTTTCG
* * * * *
393140 AGGGGATACTCCAACCCCATTTTTATTTTCAAAATTTTAAATTTTTTATCTCGAGATACTCTAAC
1 AGGGGATACTCCAACCCCATTTTAATTTTCAAAATATTAAAATTTTCATCTCGAGATACTCCAAC
393205 CTTATTTT
66 CTTATTTT
393213 TATTTCCAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
75 7 0.11
76 2 0.03
77 19 0.29
78 37 0.57
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (75 bp):
AGGGGATACTCCAACCCCATTTTAATTTTCAAAATATTAAAATTTTCATCTCGAGATACTCCAAC
CTTATTTTCG
Found at i:399945 original size:51 final size:51
Alignment explanation
Indices: 399866--399968 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
399856 AAACTTTAAA
* * * *
399866 CTCGGTTTTATTTCTAAAATACTGATTTTTCACCT-TTGGGGATACTCTAAC
1 CTCGGTTTTATTTCTAAAACACTAATTTTCCA-CTATCGGGGATACTCTAAC
*
399917 CTCGGTTTTATTTTTAAAACA-TCAATTTTCCACTATCGGGGATACTCTAAC
1 CTCGGTTTTATTTCTAAAACACT-AATTTTCCACTATCGGGGATACTCTAAC
399968 C
1 C
399969 CCGTTATTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
50 3 0.07
51 42 0.93
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (51 bp):
CTCGGTTTTATTTCTAAAACACTAATTTTCCACTATCGGGGATACTCTAAC
Found at i:399990 original size:79 final size:79
Alignment explanation
Indices: 399903--400082 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 79
399893 TTTCACCTTT
* * * * * *
399903 GGGGATACTCTAACCTCGGTTTTATTTTTAAAACA-TCAAT-TTTCCACTATCGGGGATACTCTA
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACT-AATGTTT-CACTATCGAGGATACTCCA
399966 ACCCCGTTATTTCCGA
64 ACCCCGTTATTTCCGA
*
399982 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATGTTTTACTATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATGTTTCACTATCGAGGATACTCCAAC
* **
400047 CCTGTTATTTTTGA
66 CCCGTTATTTCCGA
*
400061 GGGGATACTCCAATCCC-GTTTT
1 GGGGATACTCCAACCCCAGTTTT
400083 TATCTCCAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
78 5 0.06
79 79 0.90
80 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATGTTTCACTATCGAGGATACTCCAAC
CCCGTTATTTCCGA
Done.