Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 96 of 228
Found at i:28002608 original size:157 final size:154
Alignment explanation
Indices: 28002263--28002609 Score: 333
Period size: 157 Copynumber: 2.2 Consensus size: 154
28002253 AAATTTTAAT
* *
28002263 AAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATCAAATATATT
1 AAGATAATTAATAT-AATAAT-AATATTTTAATCATATTTAAACATAATTATTATCAAATATATT
* * * * * ** *
28002328 TTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTAT
64 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAA
* * * * * * * *
28002393 TATTGTTATTGTTATTTAAATTTTAAT
129 TATTGATACTATAAATGAAAATTT-AG
* * *
28002420 AAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATT
1 AAGATAATTAATAT-AATAAT-AATATTTTAATCATATTTAAACATAATTATTATCAAATATATT
* **
28002485 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
64 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-AAA
28002550 TCATAATATATGATACTATAAATGAAAATTT-G
125 T--TAATAT-TGATACTATAAATGAAAATTTAG
*
28002582 AA-ATAATTAATAT-ATCAT-ATATTTTAAT
1 AAGATAATTAATATAATAATAATATTTTAAT
28002610 TAAAATATAT
Statistics
Matches: 158, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
157 111 0.70
159 8 0.05
160 4 0.03
161 14 0.09
162 2 0.01
163 5 0.03
164 14 0.09
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (154 bp):
AAGATAATTAATATAATAATAATATTTTAATCATATTTAAACATAATTATTATCAAATATATTAT
AATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAATA
TTGATACTATAAATGAAAATTTAG
Found at i:28002725 original size:92 final size:91
Alignment explanation
Indices: 28002621--28002857 Score: 225
Period size: 92 Copynumber: 2.6 Consensus size: 91
28002611 AAAATATATG
* * *
28002621 ATTTAATAAAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAA
1 ATTTAATAAAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAA
*
28002684 AATAA-TAATTATTACATATAATTTAATA
64 AATAATTAA-TATTAAATATAATTTAATA
* * * * * *
28002712 ATTTAAATTAAATTTCATAAAATTCTTGATAATATATTATCTTATATGAATTTATACAATTTAAA
1 ATTT-AATAAAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAA
28002777 ATAATTAATATTAAATATAATTTAAT-
65 ATAATTAATATTAAATATAATTTAATA
* * * * *
28002803 AGTGATATATAATTTCATAAAATT-ATTAATAATAAAATGT-TCTTATATGAATTTA
1 ATTTA-ATAAAATTTCAAAAAATTCA-TAATAAT-AAAT-TATATTATATGAATTTA
28002858 CTAAAATCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
90 1 0.01
91 28 0.23
92 83 0.69
93 9 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (91 bp):
ATTTAATAAAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAA
TAATTAATATTAAATATAATTTAATA
Found at i:28005797 original size:25 final size:25
Alignment explanation
Indices: 28005776--28005825 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
28005766 TTACACATTA
28005776 TCAAATAAAAATAAACAGCACAAAAT
1 TCAAATAAAAATAAACA-CACAAAAT
*
28005802 TTAAATAAAAATAAACACACAAAA
1 TCAAATAAAAATAAACACACAAAA
28005826 CTTTTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (25 bp):
TCAAATAAAAATAAACACACAAAAT
Found at i:28009037 original size:6 final size:7
Alignment explanation
Indices: 28009017--28009043 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28009007 TAACCAAACC
28009017 AACAAAA
1 AACAAAA
28009024 AACAAAA
1 AACAAAA
28009031 AACAAAA
1 AACAAAA
28009038 AACAAA
1 AACAAA
28009044 GAACCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:28015820 original size:10 final size:10
Alignment explanation
Indices: 28015807--28015847 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
28015797 AAAATTAGCC
28015807 TAATTAACTA
1 TAATTAACTA
28015817 TAATTAACTA
1 TAATTAACTA
*
28015827 -AACTTAATTA
1 TAA-TTAACTA
28015837 TAATTAA-TA
1 TAATTAACTA
28015846 TA
1 TA
28015848 GTTGGTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.21
10 20 0.71
11 2 0.07
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAACTA
Found at i:28018444 original size:22 final size:22
Alignment explanation
Indices: 28018419--28018470 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
28018409 TCAATGTCAC
* **
28018419 GACATCCAGAAGCCAATGTTGT
1 GACATCCAGAAGCAAACATTGT
**
28018441 GACATCCCTAAGCAAACATTGT
1 GACATCCAGAAGCAAACATTGT
28018463 GACATCCA
1 GACATCCA
28018471 ACTTTGAGTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (22 bp):
GACATCCAGAAGCAAACATTGT
Found at i:28022227 original size:14 final size:15
Alignment explanation
Indices: 28022208--28022236 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28022198 TCACCTGGGT
28022208 TTAGTTTTTT-TTAA
1 TTAGTTTTTTCTTAA
28022222 TTAGTTTTTTCTTAA
1 TTAGTTTTTTCTTAA
28022237 ATCAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (15 bp):
TTAGTTTTTTCTTAA
Found at i:28034226 original size:42 final size:42
Alignment explanation
Indices: 28034158--28034339 Score: 178
Period size: 42 Copynumber: 4.3 Consensus size: 42
28034148 CGGTGGATTT
28034158 AGCACTTAGCAACCACC-TTAAATTCAGTGATACGGTGAATC
1 AGCACTTAGCAACCACCTTTAAATTCAGTGATACGGTGAATC
** * *
28034199 AATACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATC
1 AGCACTTAGCAACCACCTTTAAATTCAGTGATACGGTGAATC
* * *
28034241 GGCACATAGCAACC-CCTTTCACAA-TCAAATG-TACGGTGGAATC
1 AGCACTTAGCAACCACCTTT-A-AATTC-AGTGATACGGT-GAATC
* * *
28034284 AGCACTTAGCAACCACCTTTAGAA-TCAATAATTCGAG-GAATC
1 AGCACTTAGCAACCACCTTTA-AATTCAGTGATACG-GTGAATC
28034326 AGCACTTAGCAACC
1 AGCACTTAGCAACC
28034340 CCTCGGGGAA
Statistics
Matches: 117, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
41 20 0.17
42 62 0.53
43 29 0.25
44 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (42 bp):
AGCACTTAGCAACCACCTTTAAATTCAGTGATACGGTGAATC
Found at i:28034291 original size:85 final size:84
Alignment explanation
Indices: 28034188--28034342 Score: 211
Period size: 85 Copynumber: 1.8 Consensus size: 84
28034178 AATTCAGTGA
* * * * * * *
28034188 TACGGTGAATCAATACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCGGCACATAGCAA
1 TACGGTGAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGAGGAATCAGCACATAGCAA
28034253 CCCCTTTCACAATCAAATG
66 CCCCTTTCACAATCAAATG
* * *
28034272 TACGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGAGGAATCAGCACTTAGCA
1 TACGGT-GAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGAGGAATCAGCACATAGCA
28034337 ACCCCT
65 ACCCCT
28034343 CGGGGAATCT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 6 0.10
85 54 0.90
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (84 bp):
TACGGTGAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGAGGAATCAGCACATAGCAA
CCCCTTTCACAATCAAATG
Found at i:28052645 original size:40 final size:40
Alignment explanation
Indices: 28052563--28052645 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
28052553 TTCTTCCCAC
* *
28052563 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAATAGGGCA
1 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
* * * *
28052603 ATGGCCATAGGGTTATAAATATAGTTTAAGATACAAGTCA
1 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
28052643 ATG
1 ATG
28052646 AGATGGAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (40 bp):
ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
Found at i:28055217 original size:14 final size:14
Alignment explanation
Indices: 28055194--28055228 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28055184 TAAAACTTTT
28055194 CTTT-AAAACATAA
1 CTTTAAAAACATAA
28055207 CTTTAAAAACATAA
1 CTTTAAAAACATAA
*
28055221 CTTGAAAA
1 CTTTAAAA
28055229 CTTATCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (14 bp):
CTTTAAAAACATAA
Found at i:28067281 original size:82 final size:82
Alignment explanation
Indices: 28067144--28067302 Score: 273
Period size: 82 Copynumber: 1.9 Consensus size: 82
28067134 AACATATCGA
* * * * *
28067144 CTATCGGCTTAATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCGCATAAGTTACGTACG
1 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
28067209 CATGGTCAGTGACTAAG
66 CATGGTCAGTGACTAAG
28067226 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
1 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
28067291 CATGGTCAGTGA
66 CATGGTCAGTGA
28067303 TTAACTCAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (82 bp):
CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
CATGGTCAGTGACTAAG
Found at i:28068791 original size:17 final size:17
Alignment explanation
Indices: 28068769--28068806 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28068759 TAGATTTGGG
28068769 TTAAGAAAATTA-TTTAA
1 TTAAG-AAATTAGTTTAA
*
28068786 TTAAGAAATTAGTTTAT
1 TTAAGAAATTAGTTTAA
28068803 TTAA
1 TTAA
28068807 ATTAATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TTAAGAAATTAGTTTAA
Found at i:28076084 original size:29 final size:29
Alignment explanation
Indices: 28076038--28076098 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
28076028 TACTGGTTGT
*
28076038 ACCTATTCATTACAACCAATTTCGATTGC
1 ACCTATTCATTACAACCAATTTCAATTGC
* * *
28076067 ACCTATTCATTGCGACCAATTTTAATTGC
1 ACCTATTCATTACAACCAATTTCAATTGC
28076096 ACC
1 ACC
28076099 AGTCGATGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (29 bp):
ACCTATTCATTACAACCAATTTCAATTGC
Found at i:28076606 original size:16 final size:17
Alignment explanation
Indices: 28076574--28076614 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
28076564 AATCTAATTC
*
28076574 ATTTGATATATTTAAAT
1 ATTTTATATATTTAAAT
28076591 ATTTTATATA-TTAAAT
1 ATTTTATATATTTAAAT
28076607 ATTTTATA
1 ATTTTATA
28076615 AAAACATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATATATTTAAAT
Found at i:28081924 original size:4 final size:4
Alignment explanation
Indices: 28081915--28081957 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
28081905 GAAAATAGAT
28081915 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
28081958 AATGAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:28083952 original size:100 final size:100
Alignment explanation
Indices: 28083705--28083964 Score: 349
Period size: 100 Copynumber: 2.6 Consensus size: 100
28083695 GTCCAATTTA
* * ** * *
28083705 TTTAACTACAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATATGTTCCACTGCACCGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCACCGCC
* * *
28083770 TGAGAAGTAAGATTCGCTATTGTAGCTTCAATCTT
66 TGAAAAGTAAGATTCGCTACTCTAGCTTCAATCTT
* * * * *
28083805 TTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTGCATCGTC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCACCGCC
* *
28083870 TGAAAAGTAAGATTCGCTGCTCTAGCTTTAATCTT
66 TGAAAAGTAAGATTCGCTACTCTAGCTTCAATCTT
* * *
28083905 TTTAACTGTAATGTCGAGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCATTGCA
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCA
28083965 ATGTCAGGGA
Statistics
Matches: 139, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 139 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (100 bp):
TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCACCGCC
TGAAAAGTAAGATTCGCTACTCTAGCTTCAATCTT
Found at i:28083968 original size:50 final size:50
Alignment explanation
Indices: 28083713--28084011 Score: 201
Period size: 50 Copynumber: 6.0 Consensus size: 50
28083703 TATTTAACTA
* * ** * * *
28083713 CAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATATGTTCCACTG
1 CAATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
** * * * * **
28083763 CACCGCCTGA-GAAGTAAGATTCGCTATTGTAGCTTCAATCTTTTTAACTG
1 CAATGTC-GAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
* *
28083813 CAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTG
1 CAATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
* * * * * * **
28083863 C-ATCGTCTGA-AAAGTAAGATTCGCTGCTCTAGCTTTAATCTTTTTAACTG
1 CAAT-GTC-GAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
* * * * * *
28083913 TAATGTCGAGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCATTG
1 CAATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
** * * * *
28083963 CAATGTC-AGGGAAATAAGATTAGCCGTCGTAGCTTCACTCTGTTCCACT
1 CAATGTCGA-GGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACT
28084012 ACTGCTTAGG
Statistics
Matches: 185, Mismatches: 57, Indels: 14
0.72 0.22 0.05
Matches are distributed among these distances:
49 6 0.03
50 175 0.95
51 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
CAATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG
Found at i:28083996 original size:100 final size:99
Alignment explanation
Indices: 28083705--28083999 Score: 315
Period size: 100 Copynumber: 2.9 Consensus size: 99
28083695 GTCCAATTTA
* * ** * * ** *
28083705 TTTAACTACAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATATGTTCCACTGCACCGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCAATGTC
* * * *
28083770 TGAGAAGTAAGATTCGCTATTGTAGCTTCAATCTT
66 -GGGAAATAAGATTCGCTGTCGTAGCTTCAATCTT
* * *
28083805 TTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTGC-ATCGT
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCAAT-GT
* * *
28083869 CTGAAAAGTAAGATTCGCTGCTC-TAGCTTTAATCTT
65 CGGGAAA-TAAGATTCGCTG-TCGTAGCTTCAATCTT
* * *
28083905 TTTAACTGTAATGTCGAGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCATTGCAATGTC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCAATGTC
* *
28083970 AGGGAAATAAGATTAGCCGTCGTAGCTTCA
66 -GGGAAATAAGATTCGCTGTCGTAGCTTCA
28084000 CTCTGTTCCA
Statistics
Matches: 160, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
99 4 0.03
100 149 0.93
101 7 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (99 bp):
TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCATTGCAATGTC
GGGAAATAAGATTCGCTGTCGTAGCTTCAATCTT
Found at i:28084127 original size:45 final size:43
Alignment explanation
Indices: 28084005--28084164 Score: 162
Period size: 44 Copynumber: 3.6 Consensus size: 43
28083995 CTTCACTCTG
* * * * *
28084005 TTCCACTACTG-CTTAGGGAGATAAGATCTATAATTTTCAGCCTA
1 TTCCACTACTGAC-CAGGGAGATAGGAT-TACAATCTTCAACCTA
* * *
28084049 CTCCACTACTG-CTTAGGGAGATAAGGCTTACAATCTTCAACCTA
1 TTCCACTACTGAC-CAGGGAGAT-AGGATTACAATCTTCAACCTA
28084093 TTCCTACTACTGACCAGGGAGATAGGATTCACAATCTTCAACCTA
1 TTCC-ACTACTGACCAGGGAGATAGGATT-ACAATCTTCAACCTA
* *
28084138 TTCCACTGCTGACCAGAGAGATAGGAT
1 TTCCACTACTGACCAGGGAGATAGGAT
28084165 CAGTGGCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
44 63 0.62
45 37 0.37
46 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
TTCCACTACTGACCAGGGAGATAGGATTACAATCTTCAACCTA
Found at i:28086317 original size:6 final size:6
Alignment explanation
Indices: 28086306--28086358 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
28086296 TGTCCTCTCC
* *
28086306 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCC TTTTCT TTTT-T TTCT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
28086352 TTTTCT T
1 TTTTCT T
28086359 CTTATCATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 8 0.19
6 34 0.81
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:28086410 original size:23 final size:22
Alignment explanation
Indices: 28086377--28086425 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
28086367 TTTCATATTT
*
28086377 TTTTTTTATTTTGACTTTGATCA
1 TTTTTTAATTTTGACTTT-ATCA
* *
28086400 TTTTTTAATTTTTACTTTTTCA
1 TTTTTTAATTTTGACTTTATCA
28086422 TTTT
1 TTTT
28086426 GATTTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTTGACTTTATCA
Found at i:28087584 original size:24 final size:24
Alignment explanation
Indices: 28087526--28087586 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
28087516 GAAGAAAATC
* *
28087526 CAAAATAATGAAAGAATAATTATT
1 CAAAAAAATGAAAGAATAATTACT
* *
28087550 CGAAAAGAATGAAAGAAT-ATTGGCT
1 C-AAAAAAATGAAAGAATAATT-ACT
28087575 CAAAAAAATGAA
1 CAAAAAAATGAA
28087587 TGCAAAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (24 bp):
CAAAAAAATGAAAGAATAATTACT
Found at i:28089389 original size:40 final size:41
Alignment explanation
Indices: 28089293--28089404 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 41
28089283 AGGGTTTAGA
* *
28089293 TGTTACTTAATATTATTGTTAGTAAAAAACTAGTATTATTAT
1 TGTTAGTTAATATTATTTTTAGTAAAAAACTAG-ATTATTAT
* * * **
28089335 T-ATGGTTAGTTATTATTTTTAGTAAAACCCTA-ATTATTAT
1 TGTTAGTTA-ATATTATTTTTAGTAAAAAACTAGATTATTAT
*
28089375 TGTTAGTTAATATTATTTTGAGTATAAAAA
1 TGTTAGTTAATATTATTTTTAGTA-AAAAA
28089405 TATTATTATT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
40 22 0.41
41 12 0.22
42 20 0.37
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (41 bp):
TGTTAGTTAATATTATTTTTAGTAAAAAACTAGATTATTAT
Found at i:28092155 original size:295 final size:295
Alignment explanation
Indices: 28091625--28092214 Score: 1029
Period size: 295 Copynumber: 2.0 Consensus size: 295
28091615 TTCTACAGGC
*
28091625 TGGCTACCTTGATGCCAAGAATGGGTCAGCAACAAGCCGAGCAGATGGAGGCGGGACACGTGTTT
1 TGGCTACCTTGATGCCAAGAATGGGTCAGCAACAAGCCGAGCAGACGGAGGCGGGACACGTGTTT
* * *
28091690 GTCGAACATGTCAAGGATGCAATGGTTGCAAACCGTTGGTTGGCGAGGTTAATAAATGTAGAAAT
66 GTCGAACATGTCAAGGATGCAATGGTTGCAAACCGTCGGTTGGCAAGGTCAATAAATGTAGAAAT
*
28091755 ATATTCACGACTACTAGAAACGTTTCGAATTACTGAGACGATCAGTCGTCGACCTAGTATACCAA
131 ATATTCACGACGACTAGAAACGTTTCGAATTACTGAGACGATCAGTCGTCGACCTAGTATACCAA
*
28091820 CTAGGTCCTATAGAGTTGATCTCCGGAACAGACGGTGCGAGTGCAGGAGGTTCGAAACGCTTCAT
196 CTAGGTCCTATAGAGTTGATCTCCGGAACAGACGGTGCGAGTGCAAGAGGTTCGAAACGCTTCAT
* *
28091885 TATCCATGTGTGCATGTCGTGGCAGCGTGTGCTAA
261 TATCCATGTGCGCATGTCGTGGCAGCGTGTACTAA
*
28091920 TGGCTACCTTGATGCCAAGAATGGGTCAGCAACAA-CTCGAGTAGACGGAGGCGGGACACGTGTT
1 TGGCTACCTTGATGCCAAGAATGGGTCAGCAACAAGC-CGAGCAGACGGAGGCGGGACACGTGTT
* *
28091984 TGTCGAACATGTCAGGGATGCCATGGTTGCAAACCGTCGGTTGGCAAGGTCAATAAATGTAGAAA
65 TGTCGAACATGTCAAGGATGCAATGGTTGCAAACCGTCGGTTGGCAAGGTCAATAAATGTAGAAA
* *
28092049 TATATTCATGACGACTAGAAACGTTTCGAGTTACTGAGACGATCAGTCGTCGACCTAGTATACCA
130 TATATTCACGACGACTAGAAACGTTTCGAATTACTGAGACGATCAGTCGTCGACCTAGTATACCA
* *
28092114 ACTAGGTTCTATGGAGTTGATCTCCGGAACAGACGGTGCGAGTGCAAGAGGTTCGAAACGCTTCA
195 ACTAGGTCCTATAGAGTTGATCTCCGGAACAGACGGTGCGAGTGCAAGAGGTTCGAAACGCTTCA
28092179 TTATCCATGTGCGCATGTCGTGGCAGCGTGTACTAA
260 TTATCCATGTGCGCATGTCGTGGCAGCGTGTACTAA
28092215 AGTGAAAGTT
Statistics
Matches: 279, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
294 1 0.00
295 278 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (295 bp):
TGGCTACCTTGATGCCAAGAATGGGTCAGCAACAAGCCGAGCAGACGGAGGCGGGACACGTGTTT
GTCGAACATGTCAAGGATGCAATGGTTGCAAACCGTCGGTTGGCAAGGTCAATAAATGTAGAAAT
ATATTCACGACGACTAGAAACGTTTCGAATTACTGAGACGATCAGTCGTCGACCTAGTATACCAA
CTAGGTCCTATAGAGTTGATCTCCGGAACAGACGGTGCGAGTGCAAGAGGTTCGAAACGCTTCAT
TATCCATGTGCGCATGTCGTGGCAGCGTGTACTAA
Found at i:28095251 original size:159 final size:155
Alignment explanation
Indices: 28094849--28095260 Score: 394
Period size: 159 Copynumber: 2.6 Consensus size: 155
28094839 GAAAAAAAGC
* * *
28094849 TAGTAAAACACTCTTACTTCGGCCATTTCTTCGTA-TTTTTCCTCAGCATTTTATTA-TTTTAAA
1 TAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
*
28094912 AAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTGCATTATATTTGAAATTTATTA
66 AAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATATTTGAAATTTATTA
* * *
28094977 ATTTAGTGTGTTTTTTAAATTAATT
131 ATTTAGTCTGATTTTTAAATAAATT
* * * * * *
28095002 TAGTGTCAAAAAAACCCTTA-TTCCTGCCCTTTGC-TCGTATTGTTTTCT-CGAATTTTATTACT
1 TA--GT--AAAACACTCTTACTT-CGGCCATTT-CTTCGTATTTTTTTCTCCGCATTTTATTACT
* * * * * * *
28095064 TTCAATAAAAA-AT-ATTATTTTTGTATTTTATTATTTT-CTATTATTTCAGTACATTTTGTTTG
60 TT-AA-AAAAATATCATAATTTCT-AATTTTATAATTTTAC-ATTATTTAAGTACATTATATTTG
*
28095126 AAATATTTGTATTAA-TTATTTCTGAATTTTTAAA-AAATT
121 -AA-A-TT-TATTAATTTA-GTCTG-ATTTTTAAATAAATT
* *
28095165 TAGTAAAACGCTCTTACTTCGGTCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
1 TAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
*
28095230 AAATATCATAATTTCTAATTTTATAAATTTA
66 AAATATCATAATTTCTAATTTTATAATTTTA
28095261 TTAATTTAGT
Statistics
Matches: 201, Mismatches: 34, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
153 2 0.01
155 2 0.01
156 2 0.01
157 32 0.16
158 24 0.12
159 77 0.38
160 31 0.15
161 3 0.01
162 5 0.02
163 15 0.07
164 8 0.04
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (155 bp):
TAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
AAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATATTTGAAATTTATTA
ATTTAGTCTGATTTTTAAATAAATT
Found at i:28095466 original size:264 final size:262
Alignment explanation
Indices: 28094995--28095521 Score: 932
Period size: 264 Copynumber: 2.0 Consensus size: 262
28094985 TGTTTTTTAA
*
28094995 ATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTGTTTTCTCGAATTTTAT
1 ATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTAT
* *
28095060 TACTTTCAATAAAAAATATTATTTTTGTATTTTATTATTTTCTATTATTTCAGTACATTTTGTTT
66 TACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTT
*
28095125 GAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACGCTCTTACTTCGGTCA
131 GAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCGGTCA
28095190 TTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAAAATATCATAATTTCTAATTTTATA
196 TTTCTTCGTA-TTTTTT-TCCGCATTTTATTACTTT-AAAAAATATCATAATTTCTAATTTTATA
28095255 AATTT
258 AATTT
* *
28095260 ATTAATTTAGTGTCAAAAAAACCCTTATTCTTGCCCTTTGCTCGTATTATTTTC-CTGAATTTTG
1 ATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCTC-GAATTTTA
*
28095324 TTACTTTCAA-AAAAAATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTATATTTTGTT
65 TTACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTT
28095388 TGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCGGTC
130 TGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCGGTC
*
28095453 ATTTCTTCGTATTTTTTTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAT
195 ATTTCTTCGTATTTTTTTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAA
28095518 TTT
260 TTT
28095521 A
1 A
28095522 CTTTATTTCA
Statistics
Matches: 253, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
261 33 0.13
262 18 0.07
263 6 0.02
264 127 0.50
265 69 0.27
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (262 bp):
ATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTAT
TACTTTCAATAAAAAATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTT
GAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCGGTCA
TTTCTTCGTATTTTTTTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAAAT
TT
Found at i:28095962 original size:10 final size:10
Alignment explanation
Indices: 28095947--28096072 Score: 81
Period size: 10 Copynumber: 12.6 Consensus size: 10
28095937 TTCTCTTCTC
28095947 CTTTCCTTTT
1 CTTTCCTTTT
28095957 CTTTCCTTCTT
1 CTTTCCTT-TT
28095968 -TTT-CTTTCT
1 CTTTCCTTT-T
*
28095977 TTTTGCTTCTTCTT
1 CTTT-C--CTT-TT
28095991 CTTTCCTTTT
1 CTTTCCTTTT
28096001 CTTTCCTTCTT
1 CTTTCCTT-TT
28096012 -TTT-C-TTT
1 CTTTCCTTTT
*
28096019 CTTTCC-TCT
1 CTTTCCTTTT
28096028 CATTTCCTTTT
1 C-TTTCCTTTT
*
28096039 CTTTCTTTTT
1 CTTTCCTTTT
28096049 CTTT-C-TTT
1 CTTTCCTTTT
28096057 CTTT-CTTCTT
1 CTTTCCTT-TT
28096067 CTTTCC
1 CTTTCC
28096073 CTCTCCTTCT
Statistics
Matches: 95, Mismatches: 5, Indels: 31
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.02
8 13 0.14
9 10 0.11
10 50 0.53
11 11 0.12
13 1 0.01
14 7 0.07
15 1 0.01
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:28095966 original size:38 final size:39
Alignment explanation
Indices: 28095924--28096072 Score: 164
Period size: 38 Copynumber: 3.8 Consensus size: 39
28095914 CCTTCTTCTT
28095924 CTTCTTCTTT-TTT-TTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTCTT-TCTTCTCCTTTCCTTTTCTTTC
28095962 CTTCTT-TTTCTTTCTTTTTGCTTCTTCTTCTTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTC--TTT-CTTC-TC--CTTTCCTTTTCTTTC
* *
28096006 CTTCTT-TTTCTTTCTTTCCTCTCATTTCCTTTTCTTT-
1 CTTCTTCTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTC
* *
28096043 CTTTTTCTTTCTTTCTTTCTTCTTCTTTCC
1 CTTCTTCTTTCTTTCTTTCTTCTCCTTTCC
28096073 CTCTCCTTCT
Statistics
Matches: 96, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
37 8 0.08
38 42 0.44
40 3 0.03
41 9 0.09
42 5 0.05
44 29 0.30
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.69
Consensus pattern (39 bp):
CTTCTTCTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:28095973 original size:44 final size:44
Alignment explanation
Indices: 28095918--28096070 Score: 159
Period size: 44 Copynumber: 3.4 Consensus size: 44
28095908 CTCCCCCCTT
* *
28095918 CTTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTCTTTTTTTTCTCTTCTTCTTTCCTTTTCTTTC
* *
28095962 CTTCTTTTTCTT-TCTTTTTGCTTCTTCTTCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTCTTTTTTTTC-TCTTCTTCTTTCCTTTTCTTTC
*
28096006 CTTCTTTTTCTTTCTTTCCTCTCATTTC-CTT-TTCTTTCTTTTTCTTTC
1 CTTCTTTTTC-TTCTTT--T-T--TTTCTCTTCTTCTTTCCTTTTCTTTC
*
28096054 TTTCTTTCTTCTTCTTT
1 CTTCTTT-TTCTTCTTT
28096071 CCCTCTCCTT
Statistics
Matches: 92, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
43 7 0.08
44 42 0.46
45 2 0.02
46 2 0.02
48 29 0.32
49 7 0.08
51 3 0.03
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (44 bp):
CTTCTTTTTCTTCTTTTTTTTCTCTTCTTCTTTCCTTTTCTTTC
Found at i:28096033 original size:28 final size:28
Alignment explanation
Indices: 28095936--28096071 Score: 85
Period size: 28 Copynumber: 4.9 Consensus size: 28
28095926 TCTTCTTTTT
*
28095936 TTTCTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTTC-CTTCT-CTTTCCTTTTCTTTCTTTC
*
28095966 -TT--TT-TCTTTCTTTTTGC-TTCTTCTTC
1 TTTCCTTCTCTTTCCTTTT-CTTTC-T-TTC
*
28095992 TTTCCTTTTCTTTCCTTCTT-TTTCTTTC
1 TTTCCTTCTCTTTCCTT-TTCTTTCTTTC
28096020 TTTCC-TCTCATTTCCTTTTCTTTCTTTTTC
1 TTTCCTTCTC-TTTCCTTTTCTTTC--TTTC
28096050 TTT-CTT-TCTTT-CTTCTTCTTTC
1 TTTCCTTCTCTTTCCTT-TTCTTTC
28096072 CCTCTCCTTC
Statistics
Matches: 87, Mismatches: 4, Indels: 32
0.71 0.03 0.26
Matches are distributed among these distances:
24 12 0.14
25 2 0.02
26 5 0.06
27 10 0.11
28 29 0.33
29 8 0.09
30 19 0.22
31 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (28 bp):
TTTCCTTCTCTTTCCTTTTCTTTCTTTC
Found at i:28096080 original size:82 final size:80
Alignment explanation
Indices: 28095885--28096086 Score: 220
Period size: 82 Copynumber: 2.5 Consensus size: 80
28095875 AAAAATTACC
* *
28095885 TTTTCTTTCTTTCTTTTTCCTTCCTCCC-C-CCTTCTTCTTCTTCTTCTTTTTTTTCTCTTCTCC
1 TTTTCTTTCTTTCTTTTTCCTTCTTCCCTCTCCTT-TTCTTCTCCTTCTTTTTTTTCTCTTCTCC
28095948 TTTCCTTTTCTTTCCT
65 TTTCCTTTTCTTTCCT
* * * *
28095964 TCTT-TTTCTTTCTTTTTGCTTCTTCTTCTTTCCTTTTCTT-TCCTTCTTTTTCTTTCT-TTCCT
1 TTTTCTTTCTTTCTTTTTCCTTCTTC-CCTCTCCTTTTCTTCTCCTTCTTTTT-TTTCTCTT-CT
28096026 CTCATTTCCTTTTCTTT-CT
63 C-C-TTTCCTTTTCTTTCCT
*
28096045 TTTTCTTTCTTTCTTTCTT-CTTCTTTCCCTCTCCTTCTCTTC
1 TTTTCTTTCTTTCTTT-TTCCTTC-TTCCCTCTCCTTTTCTTC
28096087 CCCCCACCCA
Statistics
Matches: 102, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
78 19 0.19
79 16 0.16
80 13 0.13
81 10 0.10
82 39 0.38
83 5 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.66
Consensus pattern (80 bp):
TTTTCTTTCTTTCTTTTTCCTTCTTCCCTCTCCTTTTCTTCTCCTTCTTTTTTTTCTCTTCTCCT
TTCCTTTTCTTTCCT
Found at i:28103135 original size:171 final size:173
Alignment explanation
Indices: 28102850--28103193 Score: 541
Period size: 171 Copynumber: 2.0 Consensus size: 173
28102840 GCTAGGAAGG
* ** *
28102850 TATTTGCGTGAGGAATATCATCGTTTACACAAACAGCAGAACAGTTTTGGGACATCACGTCTATT
1 TATTTGCGTGAGGAATATCATCGTTTACACAAACAGCAAAACAGTTTAAGGACATCACGTCTACT
* *
28102915 GGTCAGCTAGTAAAATAAATATACTTTCACAATGGAAGGTTCAAGGGTTGATG-CCTA-CCTATG
66 GGTCAGCTAGTAAAATAAATATACTTTCACAAAGGAAAGTTCAAGGGTTGATGTCCTATCCTATG
28102978 CAAATATCGAACATAGAATCTATCACCTCTTTGAGTCTTTAAC
131 CAAATATCGAACATAGAATCTATCACCTCTTTGAGTCTTTAAC
* * *
28103021 TATTTGCGTGAGGAATATTATCGTTTACATAAAC-GACAAAACAGTTTAAGGACATCGCGTCTAC
1 TATTTGCGTGAGGAATATCATCGTTTACACAAACAG-CAAAACAGTTTAAGGACATCACGTCTAC
*
28103085 TGGTCAGCTAGTAAAGTAAATATACTTTCACAAAGGAAAGTTCAAGGGTTGATGTCTACCTATCC
65 TGGTCAGCTAGTAAAATAAATATACTTTCACAAAGGAAAGTTCAAGGGTTGATG--T-CCTATCC
28103150 TATGCAAATATCGAACATAGAATCTATCACCTCTTTGAGTCTTT
127 TATGCAAATATCGAACATAGAATCTATCACCTCTTTGAGTCTTT
28103194 TAAGTCTCAT
Statistics
Matches: 157, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
170 1 0.01
171 106 0.68
175 4 0.03
176 46 0.29
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (173 bp):
TATTTGCGTGAGGAATATCATCGTTTACACAAACAGCAAAACAGTTTAAGGACATCACGTCTACT
GGTCAGCTAGTAAAATAAATATACTTTCACAAAGGAAAGTTCAAGGGTTGATGTCCTATCCTATG
CAAATATCGAACATAGAATCTATCACCTCTTTGAGTCTTTAAC
Found at i:28103383 original size:20 final size:20
Alignment explanation
Indices: 28103338--28103376 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28103328 TCTCTTGGTT
28103338 TAATA-TTGAATTTTTTTTC
1 TAATATTTGAATTTTTTTTC
28103357 TAATATTTGAATTTTTTTTC
1 TAATATTTGAATTTTTTTTC
28103377 ATTTATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TAATATTTGAATTTTTTTTC
Found at i:28111893 original size:23 final size:24
Alignment explanation
Indices: 28111841--28111887 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
28111831 TTAGCTCTCA
*
28111841 TGAGCTTCCCGTTATATGGTTCTTG
1 TGAGCTTCCCGTTATA-GGCTCTTG
28111866 TGAGCTTCCCGTTATA-GCTCTT
1 TGAGCTTCCCGTTATAGGCTCTT
28111888 CGGAGCATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (24 bp):
TGAGCTTCCCGTTATAGGCTCTTG
Found at i:28123089 original size:16 final size:17
Alignment explanation
Indices: 28123063--28123098 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28123053 ATTTAACTAT
*
28123063 TATCTTATAATAGTTTA
1 TATCTTATAATAGTATA
28123080 TATC-TATAATAGTATA
1 TATCTTATAATAGTATA
28123096 TAT
1 TAT
28123099 ACATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
TATCTTATAATAGTATA
Found at i:28125509 original size:17 final size:18
Alignment explanation
Indices: 28125487--28125528 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
28125477 ATAAATAAGA
*
28125487 ATTTAATTTATTAAA-AT
1 ATTTAATTAATTAAATAT
*
28125504 ATTTAATTAATTAAATTT
1 ATTTAATTAATTAAATAT
28125522 ATTTAAT
1 ATTTAAT
28125529 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAATTAATTAAATAT
Found at i:28127968 original size:21 final size:21
Alignment explanation
Indices: 28127942--28127982 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28127932 GTGCACTTGC
28127942 TTTAGTCAAATTTTTAATTAG
1 TTTAGTCAAATTTTTAATTAG
28127963 TTTAGTCAAATTTTTAATTA
1 TTTAGTCAAATTTTTAATTA
28127983 ATTTTGCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTAGTCAAATTTTTAATTAG
Found at i:28133616 original size:21 final size:21
Alignment explanation
Indices: 28133587--28133633 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
28133577 ATGCTAGCAA
*
28133587 ATAAAAACATCCAAAATACAT
1 ATAACAACATCCAAAATACAT
28133608 ATAACAACATCCAAAATACAT
1 ATAACAACATCCAAAATACAT
28133629 ATAAC
1 ATAAC
28133634 CACAAGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAACAACATCCAAAATACAT
Found at i:28134573 original size:21 final size:20
Alignment explanation
Indices: 28134527--28134575 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
28134517 TTTAAAAAAA
28134527 AAATAATTTTAACACTTTTT
1 AAATAATTTTAACACTTTTT
28134547 --ATAATTCTTAATCA-TTTTT
1 AAATAATT-TTAA-CACTTTTT
28134566 AAATAATTTT
1 AAATAATTTT
28134576 TTTATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 4 0.16
21 6 0.24
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATAATTTTAACACTTTTT
Found at i:28136132 original size:20 final size:19
Alignment explanation
Indices: 28136109--28136149 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28136099 ATTTAATTTA
28136109 ATAATAAATAAAATATTTTT
1 ATAATAAAT-AAATATTTTT
* *
28136129 ATAATTAATTAATATTTTT
1 ATAATAAATAAATATTTTT
28136148 AT
1 AT
28136150 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATAAATAAATATTTTT
Found at i:28136142 original size:19 final size:19
Alignment explanation
Indices: 28136120--28136159 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28136110 TAATAAATAA
28136120 AATATTTTTATAATTAATT
1 AATATTTTTATAATTAATT
**
28136139 AATATTTTTATTTTTAATT
1 AATATTTTTATAATTAATT
28136158 AA
1 AA
28136160 AAATTATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATATTTTTATAATTAATT
Found at i:28137672 original size:31 final size:31
Alignment explanation
Indices: 28137637--28137710 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
28137627 AGGGAATATG
* *
28137637 GTGGGTGGTTAATTGTGGGATTTAGTGGGGT
1 GTGGGTGGTTAATTATGGGATTTAGTGGGAT
*
28137668 GTGGGTGATTAATTATGGGATTTAGTGGGAT
1 GTGGGTGGTTAATTATGGGATTTAGTGGGAT
* *
28137699 ATGGGTCGTTAA
1 GTGGGTGGTTAA
28137711 GAAATTATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.19, C:0.01, G:0.42, T:0.38
Consensus pattern (31 bp):
GTGGGTGGTTAATTATGGGATTTAGTGGGAT
Found at i:28138576 original size:85 final size:85
Alignment explanation
Indices: 28138461--28138633 Score: 256
Period size: 85 Copynumber: 2.0 Consensus size: 85
28138451 GGGTAGACTG
* * * * * * * *
28138461 TGTATGGCATACGACCGTGTGAAACTATGCAGGCTGTGTGGGGCACATGGCTGCGTGAAATCGTG
1 TGTAGGGCAAACGACCATGTGAAACCATGCAGGCCGTGTGGGGCAAATGGCCGCGTGAAATCATG
*
28138526 CAGCCCGTGAGGTTTGACCA
66 CAGCCCGTGAGGCTTGACCA
28138546 TGTAGGGCAAACGACCATGTGAAACCATGCAGGCCGTGTGGGGCAAATGGCCGCGTGAAATCATG
1 TGTAGGGCAAACGACCATGTGAAACCATGCAGGCCGTGTGGGGCAAATGGCCGCGTGAAATCATG
*
28138611 CAGCCCGTGTGGCTTGACCA
66 CAGCCCGTGAGGCTTGACCA
28138631 TGT
1 TGT
28138634 GAGATTTTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.21
Consensus pattern (85 bp):
TGTAGGGCAAACGACCATGTGAAACCATGCAGGCCGTGTGGGGCAAATGGCCGCGTGAAATCATG
CAGCCCGTGAGGCTTGACCA
Found at i:28139284 original size:5 final size:5
Alignment explanation
Indices: 28139274--28139324 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
28139264 TAGGACTTTG
*** *
28139274 TATGA TATGA TCCAA TATGA TATGA TATGA TATGA -ATCGA TATGT TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TAT-GA TATGA TATGA
28139324 T
1 T
28139325 TTATGATTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 2 0.06
5 32 0.89
6 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (5 bp):
TATGA
Found at i:28164711 original size:22 final size:22
Alignment explanation
Indices: 28164665--28164706 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28164655 AACATAAACC
*
28164665 AATAGAATTGTTATTTTTAGAA
1 AATAGAATTGTTATTTTTAAAA
28164687 AATAGAA-T-TTATTTTTAAAA
1 AATAGAATTGTTATTTTTAAAA
28164707 TAAATTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
AATAGAATTGTTATTTTTAAAA
Found at i:28165293 original size:4 final size:4
Alignment explanation
Indices: 28165276--28165310 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
28165266 TTTGAATTTG
*
28165276 AATT AATC AATT AATT AATT AATT AATT AA-T AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT
28165311 TGAAAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:28178145 original size:11 final size:11
Alignment explanation
Indices: 28178129--28178154 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28178119 ACTCAGCTAT
28178129 TACTTAATACA
1 TACTTAATACA
28178140 TACTTAATACA
1 TACTTAATACA
28178151 TACT
1 TACT
28178155 AAAATAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
TACTTAATACA
Found at i:28179421 original size:13 final size:13
Alignment explanation
Indices: 28179403--28179427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28179393 TACTAATGTA
28179403 ATTAATGAAAGTG
1 ATTAATGAAAGTG
28179416 ATTAATGAAAGT
1 ATTAATGAAAGT
28179428 AATGAGAAGC
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATTAATGAAAGTG
Found at i:28179725 original size:27 final size:27
Alignment explanation
Indices: 28179673--28179725 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28179663 TTCAATAATT
* * *
28179673 ATATAAGTTATTAAAAAATTTCAAAAA
1 ATATAAATTATTAAAAAATATAAAAAA
28179700 ATATAAATTATT-AAAAATAATAAAAA
1 ATATAAATTATTAAAAAAT-ATAAAAA
28179726 TGAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
ATATAAATTATTAAAAAATATAAAAAA
Found at i:28186302 original size:21 final size:21
Alignment explanation
Indices: 28186251--28186303 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
28186241 TTTTTTAAAA
28186251 ATTTT-AAAT-ATATTTTATG
1 ATTTTCAAATAATATTTTATG
*
28186270 A-TTTCTAGATAATATTTTATG
1 ATTTTC-AAATAATATTTTATG
28186291 ATTTTCAAATAAT
1 ATTTTCAAATAAT
28186304 CATATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 3 0.11
21 17 0.61
22 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (21 bp):
ATTTTCAAATAATATTTTATG
Found at i:28187832 original size:12 final size:12
Alignment explanation
Indices: 28187809--28187846 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
28187799 ACATGCACAG
*
28187809 TCAGATTCAGAT
1 TCAGATTTAGAT
*
28187821 TTAGATTTAGAT
1 TCAGATTTAGAT
28187833 TCAGATTTAGAT
1 TCAGATTTAGAT
28187845 TC
1 TC
28187847 GGACTCATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (12 bp):
TCAGATTTAGAT
Found at i:28187834 original size:18 final size:18
Alignment explanation
Indices: 28187811--28187845 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28187801 ATGCACAGTC
28187811 AGATTCAGATTTAGATTT
1 AGATTCAGATTTAGATTT
28187829 AGATTCAGATTTAGATT
1 AGATTCAGATTTAGATT
28187846 CGGACTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (18 bp):
AGATTCAGATTTAGATTT
Found at i:28190913 original size:17 final size:18
Alignment explanation
Indices: 28190891--28190929 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28190881 TGGTGAGCTT
*
28190891 TGGAAA-ACAAGACATTG
1 TGGAAATACAAGACAATG
*
28190908 TGGAAATACAAGTCAATG
1 TGGAAATACAAGACAATG
28190926 TGGA
1 TGGA
28190930 GATTCGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (18 bp):
TGGAAATACAAGACAATG
Found at i:28191605 original size:29 final size:29
Alignment explanation
Indices: 28191561--28191633 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
28191551 GCCTTAATTA
* * * *
28191561 AATTTAAATAATAAAATTATTTGTAATTTT
1 AATTTAAATAA-AAAAGTATATATAATATT
*
28191591 AATTTAAATGAAAAAGTATATATAATATT
1 AATTTAAATAAAAAAGTATATATAATATT
* *
28191620 AATTAAAATTAAAA
1 AATTTAAATAAAAA
28191634 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
AATTTAAATAAAAAAGTATATATAATATT
Found at i:28195993 original size:17 final size:17
Alignment explanation
Indices: 28195971--28196044 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 17
28195961 TTATGATGGA
*
28195971 GCATGAACTGTTATTTT
1 GCATGAACTATTATTTT
* * **
28195988 GCATGAATTGTTATTCA
1 GCATGAACTATTATTTT
* * *
28196005 GTATGAACTAATATTTC
1 GCATGAACTATTATTTT
**
28196022 AAATGAACTATTATTTT
1 GCATGAACTATTATTTT
28196039 GCATGA
1 GCATGA
28196045 GCTTTCATTT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (17 bp):
GCATGAACTATTATTTT
Found at i:28196897 original size:2 final size:2
Alignment explanation
Indices: 28196890--28196930 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28196880 GAATTTACAA
28196890 AG AG AG AG AG 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 AG AG AG AG AG A
28196931 AAATAATGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28197102 original size:17 final size:16
Alignment explanation
Indices: 28197076--28197108 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
28197066 TAAATCTCAG
28197076 ATTTTGATACCCATAT
1 ATTTTGATACCCATAT
28197092 ATTTCTGATACCCATAT
1 ATTT-TGATACCCATAT
28197109 CTTTGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTTGATACCCATAT
Found at i:28203434 original size:49 final size:50
Alignment explanation
Indices: 28203336--28203432 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 50
28203326 CATTTTATCT
* * *
28203336 TTCTATTAACATTCTTCAATTTTTTTATCTAAATTTTTTTGTCCAAAAGA
1 TTCTACTAACATTCTTAAATTTTTTTATCAAAATTTTTTTGTCCAAAAGA
*
28203386 TTCTACTAACGTTCTTAAATTTTTTATAT-AAATATTTTTTTG-CCAAA
1 TTCTACTAACATTCTTAAATTTTTT-TATCAAA-ATTTTTTTGTCCAAA
28203433 GAATTATACC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 29 0.71
51 12 0.29
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (50 bp):
TTCTACTAACATTCTTAAATTTTTTTATCAAAATTTTTTTGTCCAAAAGA
Found at i:28204186 original size:47 final size:47
Alignment explanation
Indices: 28204114--28204204 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
28204104 ATACATTGAG
*
28204114 TTTCATTTAGGCTTCCTTTGAATGCAATTGGACTTCAATAAGTTAGT
1 TTTCATTTAGGCTTCCCTTGAATGCAATTGGACTTCAATAAGTTAGT
* * *
28204161 TTTCATTTAGGCTTCCCTTGGATGCAATTGGACTTTAGTAAGTT
1 TTTCATTTAGGCTTCCCTTGAATGCAATTGGACTTCAATAAGTT
28204205 GGCTCTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (47 bp):
TTTCATTTAGGCTTCCCTTGAATGCAATTGGACTTCAATAAGTTAGT
Found at i:28214167 original size:15 final size:15
Alignment explanation
Indices: 28214143--28214180 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
28214133 TTATAAGTAT
28214143 GTAAAAAAAATAAAA
1 GTAAAAAAAATAAAA
*
28214158 GTAAATAAAATAAAA
1 GTAAAAAAAATAAAA
*
28214173 TTAAAAAA
1 GTAAAAAA
28214181 CTGTAAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
GTAAAAAAAATAAAA
Found at i:28214849 original size:45 final size:44
Alignment explanation
Indices: 28214800--28214922 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 44
28214790 AGTGCTTCAA
* *
28214800 TCTACTCCACTGTAATGTCAGGGAGGTAGGATTTGATTTCTTGGG
1 TCTACTCCACTGCAAT-TCAGGGAGGTAGGATTTGATTTCTTGAG
* * * *
28214845 TCTACCCCACTGCAATTTCAGGG-GGATAAGACTTGCTTTCTTGAG
1 TCTACTCCACTGCAA-TTCAGGGAGG-TAGGATTTGATTTCTTGAG
* *
28214890 TCTGCTCCACTGCAACTTCAGGGAGATAGGATT
1 TCTACTCCACTGCAA-TTCAGGGAGGTAGGATT
28214923 ATTGGCTTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
44 2 0.03
45 59 0.94
46 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (44 bp):
TCTACTCCACTGCAATTCAGGGAGGTAGGATTTGATTTCTTGAG
Found at i:28215324 original size:44 final size:45
Alignment explanation
Indices: 28215276--28215671 Score: 400
Period size: 44 Copynumber: 9.0 Consensus size: 45
28215266 AAGGCTGGTG
* * * *
28215276 TCTTCGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATCTGCT-
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* *
28215320 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * * *
28215364 TCTTCGATCTACTTCAC-ACCAATACATGAAGACAAGATCTACTT
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * * **
28215408 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGC-A
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * * *
28215452 TCTTCGATCCATTTC-CTACCAATATAGGAAGACAGGATCTGCTA
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * * * *
28215496 TCTTCGATCTACTTCAC-GCCAATACATGAAGAAAAGATCTGCTT
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * **
28215540 TCTTTGATCTACTTCGCCACCAATATGGGAAGACAAGA--T-CTA
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * *
28215582 GTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTA
1 -TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
* * *
28215627 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
28215671 T
1 T
28215672 TTTTTAGCCT
Statistics
Matches: 289, Mismatches: 52, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
42 21 0.07
43 61 0.21
44 166 0.57
45 41 0.14
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
Found at i:28215462 original size:132 final size:132
Alignment explanation
Indices: 28215276--28215666 Score: 615
Period size: 132 Copynumber: 3.0 Consensus size: 132
28215266 AAGGCTGGTG
* * * *** * *
28215276 TCTTCGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATCTGCTTCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
* *
28215341 ATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTAC
66 ATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTAC
28215406 TT
131 TT
* * *
28215408 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCATTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
* *
28215473 ATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATCTGC
66 ATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTAC
28215538 TT
131 TT
*
28215540 TCTTTGATCTACTTCGCCACCAATATGGGAAGACAAGATCT--AGTCTTCGATCCACTTCCTACC
1 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA-TCTTCGATCCACTTCCTACC
28215603 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
65 AATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
28215667 GCTATTTTTT
Statistics
Matches: 238, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
130 1 0.00
131 82 0.34
132 155 0.65
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTAC
TT
Found at i:28215589 original size:87 final size:86
Alignment explanation
Indices: 28215302--28215669 Score: 393
Period size: 87 Copynumber: 4.2 Consensus size: 86
28215292 CTATCAATGC
*
28215302 AGGAAGGCAAGATCTGCTTCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
1 AGGAAGACAAGATCTGC-TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
* *
28215367 TCGATCTACTTCACACCAATAC
65 TCGATCTACTTCCCACCAATAT
* * * * *
28215389 ATGAAGACAAGATCTACTTTCTTCGATCTACTTTGCC-ACCAGTATGGGAAGACAAGATCTGC-A
1 AGGAAGACAAGATCTGC--TCTTCGATCCAC-TT-CCTACCAATATAGGAAGACAAGATCTGCTA
* * *
28215452 TCTTCGATCCATTTCCTACCAATAT
62 TCTTCGATCTACTTCCCACCAATAT
* * * * * * *
28215477 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAAAAGATCTGCTTT
1 AGGAAGACAAGATCTGC--TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTAT
*
28215541 CTTTGATCTACTTCGCCACCAATAT
63 CTTCGATCTACTTC-CCACCAATAT
* *
28215566 GGGAAGACAAGATCTAG-TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCT
1 AGGAAGACAAGATCT-GCTCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCT
* * *
28215630 TCGATCTACTTCACGCCAATAC
65 TCGATCTACTTCCCACCAATAT
*
28215652 ATGAAGACAAGATCTGCT
1 AGGAAGACAAGATCTGCT
28215670 ATTTTTTAGC
Statistics
Matches: 231, Mismatches: 41, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
85 1 0.00
86 23 0.10
87 85 0.37
88 72 0.31
89 47 0.20
90 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (86 bp):
AGGAAGACAAGATCTGCTCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTATCTT
CGATCTACTTCCCACCAATAT
Found at i:28218387 original size:40 final size:40
Alignment explanation
Indices: 28218289--28218458 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
28218279 TCCTCGTTCA
* * * *
28218289 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
28218328 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
28218368 AATGCCTTTGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
28218408 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
28218448 AAGGCCTTCGG
1 AATGCCTTCGG
28218459 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 34 0.29
40 83 0.71
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:28218471 original size:40 final size:40
Alignment explanation
Indices: 28218287--28218511 Score: 204
Period size: 40 Copynumber: 5.7 Consensus size: 40
28218277 GCTCCTCGTT
* * * * * *
28218287 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
28218327 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
28218366 CGAATGCCTTTGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
28218406 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
** * * * *
28218446 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
28218487 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
28218512 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 112 0.70
41 11 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:28218520 original size:41 final size:41
Alignment explanation
Indices: 28218443--28218520 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28218433 TTAGTATCTC
* * *
28218443 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28218484 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28218521 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28221067 original size:42 final size:42
Alignment explanation
Indices: 28221017--28221099 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
28221007 ATTCACGATT
**
28221017 CTTCGCATATAGTAATATATATTGGTACCAGGGACGATTATG
1 CTTCGCATATAACAATATATATTGGTACCAGGGACGATTATG
* *
28221059 CTTCGCATATAACAATATATCTTGGTACTAGGGACGATTAT
1 CTTCGCATATAACAATATATATTGGTACCAGGGACGATTAT
28221100 TATTCTCCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (42 bp):
CTTCGCATATAACAATATATATTGGTACCAGGGACGATTATG
Found at i:28233275 original size:18 final size:18
Alignment explanation
Indices: 28233223--28233276 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
28233213 TGTATTATAA
* *
28233223 TATTAATTAATAAAACAT
1 TATTACTTAATAAAATAT
*
28233241 TATTACTTATTAAAATAT
1 TATTACTTAATAAAATAT
*
28233259 TATTACTTAATATAATAT
1 TATTACTTAATAAAATAT
28233277 AATTTAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTACTTAATAAAATAT
Found at i:28238615 original size:16 final size:16
Alignment explanation
Indices: 28238594--28238626 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28238584 ACACTTACGC
28238594 TTCCCAAATTGTCAGA
1 TTCCCAAATTGTCAGA
28238610 TTCCCAAATTGTCAGA
1 TTCCCAAATTGTCAGA
28238626 T
1 T
28238627 CTGAGTCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (16 bp):
TTCCCAAATTGTCAGA
Found at i:28244568 original size:14 final size:14
Alignment explanation
Indices: 28244545--28244575 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28244535 AATAATTACT
*
28244545 AAATATAATAAATA
1 AAATAAAATAAATA
28244559 AAATAAAATAAATA
1 AAATAAAATAAATA
28244573 AAA
1 AAA
28244576 AGAAAAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:28249996 original size:17 final size:17
Alignment explanation
Indices: 28249958--28249996 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28249948 ATTAAAATCT
*
28249958 AAAAATTAAATTAAAAC
1 AAAAATTAAATAAAAAC
28249975 AAAAATTAAA-AAAAAC
1 AAAAATTAAATAAAAAC
28249991 ATAAAA
1 A-AAAA
28249997 ATGGCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATTAAATAAAAAC
Found at i:28253521 original size:29 final size:31
Alignment explanation
Indices: 28253461--28253525 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
28253451 AACAGATATC
28253461 AATCATGCAGTGAACAATATGAAATATCATT
1 AATCATGCAGTGAACAATATGAAATATCATT
28253492 AATCGATGCAGT-AACAATA-GAAA-ATCATT
1 AATC-ATGCAGTGAACAATATGAAATATCATT
28253521 AATCA
1 AATCA
28253526 GTGTAGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.03
29 10 0.30
30 4 0.12
31 11 0.33
32 7 0.21
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (31 bp):
AATCATGCAGTGAACAATATGAAATATCATT
Found at i:28253944 original size:27 final size:27
Alignment explanation
Indices: 28253925--28254602 Score: 770
Period size: 27 Copynumber: 25.3 Consensus size: 27
28253915 GGGTATAACA
*
28253925 GTCATTTTAACCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28253952 ATTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28253979 ATCATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254006 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28254033 GTTATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28254060 GTTATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28254087 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254114 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
28254141 GTCATTTTACCCTATAGGGGTATTTTT
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
28254168 ATCATTCTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28254195 GTTATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
** *
28254222 GTCATTTTACCC--TGTAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** ** *
28254247 GTTATTTTACCCGGTGGGGACATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28254274 GTCATTTTACCCTATGAGGGTATTCCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
28254301 GTCATTCTACCCTATGCAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254328 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254355 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254382 GTCATTTTACCCTAT-GAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
28254408 ATCATTCTACCCTAT-AGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28254434 GTTATTTTACCCTATGGGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28254461 ATCATTTTACCTTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28254488 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
28254515 ATCACTTTATCCTATAGGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28254542 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28254569 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
28254596 GTCATTT
1 GTCATTT
28254603 ATTGACCTCT
Statistics
Matches: 552, Mismatches: 96, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
25 22 0.04
26 43 0.08
27 487 0.88
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:28254868 original size:20 final size:20
Alignment explanation
Indices: 28254835--28254872 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28254825 TGAGCCCACA
*
28254835 TGGCCCATTTCGGCCCAACG
1 TGGCCCATTACGGCCCAACG
*
28254855 TGGCCTATTACGGCCCAA
1 TGGCCCATTACGGCCCAA
28254873 GACCATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.21
Consensus pattern (20 bp):
TGGCCCATTACGGCCCAACG
Found at i:28257960 original size:25 final size:25
Alignment explanation
Indices: 28257918--28257971 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
28257908 AAATGGATGC
*
28257918 GTTTGGAGGGTATATTTGGTTGTGT
1 GTTTGGAGGCTATATTTGGTTGTGT
*
28257943 GTTTGGAGGCTATGTTTGGTTGTGT
1 GTTTGGAGGCTATATTTGGTTGTGT
28257968 -TTTG
1 GTTTG
28257972 TGAGTGATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.09, C:0.02, G:0.39, T:0.50
Consensus pattern (25 bp):
GTTTGGAGGCTATATTTGGTTGTGT
Found at i:28262191 original size:30 final size:27
Alignment explanation
Indices: 28262126--28262205 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 27
28262116 ATCCATATTT
28262126 ATGGAAAGTCAAAGATATGGGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATCAA
28262153 AT--AAAGTCAAAGATATGGGTATCAAA
1 ATGGAAAGTCAAAGATATGGGTATC-AA
28262179 TATTGGAAAGTCAAAGATATGGGTATC
1 -A-TGGAAAGTCAAAGATATGGGTATC
28262206 GCGATATTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
25 21 0.44
26 2 0.04
27 3 0.06
28 1 0.02
30 21 0.44
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.25
Consensus pattern (27 bp):
ATGGAAAGTCAAAGATATGGGTATCAA
Found at i:28262367 original size:2 final size:2
Alignment explanation
Indices: 28262360--28262422 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
28262350 AAGGTATTGT
28262360 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28262402 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
28262423 TTGTAAATTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28266784 original size:25 final size:25
Alignment explanation
Indices: 28266750--28266827 Score: 93
Period size: 25 Copynumber: 2.9 Consensus size: 25
28266740 ATATTTATGG
*
28266750 AAAGTCAAAGTTATGGGTATCAAAT
1 AAAGTCAAAGATATGGGTATCAAAT
28266775 AAAGTCAAAGATATGGGTATCAAATATT
1 AAAGTCAAAGATATGGGTATC-AA-A-T
*
28266803 GGAAAGTCAAATATATGGGTATCAA
1 --AAAGTCAAAGATATGGGTATCAA
28266828 GATATTGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 20 0.43
26 2 0.04
27 1 0.02
28 1 0.02
29 2 0.04
30 20 0.43
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAGTCAAAGATATGGGTATCAAAT
Found at i:28266811 original size:30 final size:30
Alignment explanation
Indices: 28266747--28266835 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
28266737 TCCATATTTA
*
28266747 TGGAAAGTCAAAGTTATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
28266774 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
28266802 TGGAAAGTCAAATATATGGGTATCAAGATAT
1 TGGAAAGTCAAAGATATGGGTATCAA-ATAT
28266833 TGG
1 TGG
28266836 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 22 0.41
31 7 0.13
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.28
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:28266827 original size:15 final size:15
Alignment explanation
Indices: 28266779--28266832 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
28266769 TCAAATAAAG
*
28266779 TCAAAGATATGGGTA
1 TCAAATATATGGGTA
**
28266794 TCAAATAT-TGGAAA
1 TCAAATATATGGGTA
28266808 GTCAAATATATGGGTA
1 -TCAAATATATGGGTA
28266824 TCAAGATAT
1 TCAA-ATAT
28266833 TGGCATAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.13
15 19 0.61
16 8 0.26
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
TCAAATATATGGGTA
Found at i:28275489 original size:22 final size:23
Alignment explanation
Indices: 28275464--28275517 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
28275454 TTATAAATTC
28275464 AATTTAA-ATGATATAAT-ATAAT
1 AATTTAACAT-ATATAATAATAAT
*
28275486 AATTTCAAGCATATTTAATAATAAT
1 AATTT-AA-CATATATAATAATAAT
28275511 AATTTAA
1 AATTTAA
28275518 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 8 0.30
25 12 0.44
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
AATTTAACATATATAATAATAAT
Found at i:28277396 original size:18 final size:17
Alignment explanation
Indices: 28277373--28277415 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
28277363 ATTTAGTTAT
28277373 TATTATATCTATTATTAC
1 TATTATATCT-TTATTAC
*
28277391 TATTATCATCTTTATTAT
1 TATTAT-ATCTTTATTAC
28277409 TATTATA
1 TATTATA
28277416 GTTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATCTTTATTAC
Found at i:28277411 original size:6 final size:6
Alignment explanation
Indices: 28277358--28277451 Score: 52
Period size: 6 Copynumber: 15.3 Consensus size: 6
28277348 TTTAGCAATT
* *
28277358 TTATTA TTTAGTTA TTATTA -TATCTA TTATTA CTATTA TCATCT- TTATTA
1 TTATTA -TTA-TTA TTATTA TTAT-TA TTATTA TTATTA TTAT-TA TTATTA
* * * *
28277408 TTATTA -TAGTTA TTTTTA -TAGTTA TTTTTA TTTTTA TTTTTA TT
1 TTATTA TTA-TTA TTATTA TTA-TTA TTATTA TTATTA TTATTA TT
28277452 TACTTATGTA
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
5 7 0.10
6 49 0.69
7 12 0.17
8 3 0.04
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (6 bp):
TTATTA
Found at i:28277420 original size:12 final size:11
Alignment explanation
Indices: 28277358--28277438 Score: 65
Period size: 12 Copynumber: 6.9 Consensus size: 11
28277348 TTTAGCAATT
28277358 TTATTATT-TA
1 TTATTATTATA
28277368 GTTATTATTATA
1 -TTATTATTATA
28277380 TCTATTATTACTA
1 T-TATTATTA-TA
* *
28277393 TTATCATCTTTA
1 TTATTAT-TATA
28277405 TTATTATTATA
1 TTATTATTATA
*
28277416 GTTATTTTTATA
1 -TTATTATTATA
*
28277428 GTTATTTTTAT
1 -TTATTATTAT
28277439 TTTTATTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
11 12 0.20
12 44 0.73
13 4 0.07
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (11 bp):
TTATTATTATA
Found at i:28277452 original size:6 final size:6
Alignment explanation
Indices: 28277417--28277452 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
28277407 ATTATTATAG
**
28277417 TTATTT TTATAG TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
28277453 ACTTATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:28282579 original size:7 final size:7
Alignment explanation
Indices: 28282569--28282601 Score: 52
Period size: 6 Copynumber: 5.0 Consensus size: 7
28282559 AAAAAAACAA
28282569 AAAAATG
1 AAAAATG
28282576 -AAAATG
1 AAAAATG
28282582 AAAAATG
1 AAAAATG
28282589 -AAAATG
1 AAAAATG
28282595 AAAAATG
1 AAAAATG
28282602 GAAAGGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:28282587 original size:13 final size:13
Alignment explanation
Indices: 28282569--28282601 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28282559 AAAAAAACAA
28282569 AAAAATGAAAATG
1 AAAAATGAAAATG
28282582 AAAAATGAAAATG
1 AAAAATGAAAATG
28282595 AAAAATG
1 AAAAATG
28282602 GAAAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:28284083 original size:44 final size:44
Alignment explanation
Indices: 28283976--28284937 Score: 582
Period size: 44 Copynumber: 22.3 Consensus size: 44
28283966 TCACACCAGG
* * * * *
28283976 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAAAATTA-CAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCG-AAGA-TAGTA-A
* * *
28284022 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * *
28284066 TCCTATCTCCCTGAGATTACAGTGGAGCGGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * * ** *
28284105 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGATAGTAA
* * * **
28284146 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATAGTA-A
* * *
28284192 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * *
28284236 TCCTATCTCCCTGAGATTACAGTGGAGCAGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * * ** *
28284275 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGATAGTAA
* * * **
28284316 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATAGTA-A
* * *
28284362 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * * **
28284406 TCCTATCTCTCTGAGATTACAGTGGAGCGGAT--TA-A-AG-GG
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * ** * ** *
28284445 TCTTATCTCTCTGA-AGTTACAATAGAATAGATCGCA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGATAGTAA
* * * *
28284486 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATA-GT-A-A
** * *
28284532 TCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * *
28284576 TCCTATCTCCCTGAGATTACAGTGGAGCGGAT--TA-A-AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * ** * *
28284615 TCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCG--TATCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGAT-AGTAA
* * *
28284656 TCTTATCTCCTTGAGATTACAGTGGAGCAGACCGAAGAATTA-CAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-A-TAGTA-A
* *
28284702 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * *
28284746 TCTTATCTCCCTAAGATTACAGTGGAGCAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG-ATAGTA-A
* * *
28284792 TCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
** *
28284836 TCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
* * * *
28284880 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
*
28284924 TCCTATCTCCCTGA
1 TCTTATCTCCCTGA
28284938 AGTTGCAGCG
Statistics
Matches: 717, Mismatches: 149, Indels: 102
0.74 0.15 0.11
Matches are distributed among these distances:
38 4 0.01
39 104 0.15
40 9 0.01
41 114 0.16
42 16 0.02
44 254 0.35
45 22 0.03
46 193 0.27
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGATAGTAA
Found at i:28284092 original size:170 final size:170
Alignment explanation
Indices: 28283806--28285001 Score: 1664
Period size: 170 Copynumber: 7.0 Consensus size: 170
28283796 ATTATACACA
* *
28283806 TCTTATTTCCCTGAGATTACGGTGGAACAGACCGAAAAATTACAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
* ** * * *
28283871 CAGTGGAGCAGATTGAATATAGTAATCCTATCTCCCTAAGATTAGAGTGGAGCGAATTAAAGGAT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
* *
28283936 CTTATCTCTTTGAAGTTACAGTAGAGTAGATCACACCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
*
28283976 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAAAATTACAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
**
28284041 CAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
28284106 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
**
28284146 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
*
28284211 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGGAT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
*
28284276 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTACCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
**
28284316 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
* *
28284381 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCTCTGAGATTACAGTGGAGCGGATTAAAGGGT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
* *
28284446 CTTATCTCTCTGAAGTTACAATAGAATAGATCGCACCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
*
28284486 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
*
28284551 CAACGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
* * *
28284616 CTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
* * *
28284656 TCTTATCTCCTTGAGATTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
** * * * **
28284721 CAGCGGAGCAGATCAAAGATAGTAATCTTATCTCCCTAAGATTACAGTGGAGCAGACCGAAGAAT
66 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGC-G---GATTAA-
* * ** * ** ** *
28284786 TGCAGATCTTATCTCCCT-AAGATTACAGCGGAGCAGATCAAAGATAGTAA
126 AG--GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCGCA-CCAG--G
* ** * ** *
28284836 TCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAG-A-TAGTA-ATCTTATCTCCCTGAGATT
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTA-CAGATCTTATCTCCCTGAGATT
* * *
28284898 ACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGA-AGTTGCAGCGGAGCGGATTAAAGC
65 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAG-
*
28284962 CACAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCG
128 ----GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
28285002 TATCAGGCCT
Statistics
Matches: 934, Mismatches: 75, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
170 759 0.81
171 1 0.00
173 1 0.00
174 8 0.01
175 1 0.00
176 31 0.03
177 32 0.03
178 67 0.07
179 2 0.00
180 32 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (170 bp):
TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGAT
CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
Found at i:28284169 original size:80 final size:80
Alignment explanation
Indices: 28284069--28284683 Score: 450
Period size: 87 Copynumber: 7.3 Consensus size: 80
28284059 ATAGTAATCC
28284069 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
*
28284134 GATCGCACCAGGTCT
66 GATCGAACCAGGTCT
* ** *
28284149 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTA-GATCTTATCTCCCTG-AGATTAC
1 TATCTCCCTGAGATTACAGTGG---AG--CG--G-ATTAAAGGATCTTATCTCTCTGAAG-TTAC
** * * * * *
28284212 AGCGGAGCAGATTGAAGCTAGTAATCC
57 AGTAGAGTAGATCGAA-CCAG--GTCT
*
28284239 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
*
28284304 GATCGTACCAGGTCT
66 GATCGAACCAGGTCT
* ** *
28284319 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTTA-GATCTTATCTCCCTG-AGATTAC
1 TATCTCCCTGAGATTACAGTGG---AG--CG--G-ATTAAAGGATCTTATCTCTCTGAAG-TTAC
** * * * * *
28284382 AGCGGAGCAGATTGAAGCTAGTAATCC
57 AGTAGAGTAGATCGAA-CCAG--GTCT
* * * *
28284409 TATCTCTCTGAGATTACAGTGGAGCGGATTAAAGGGTCTTATCTCTCTGAAGTTACAATAGAATA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
*
28284474 GATCGCACCAGGTCT
66 GATCGAACCAGGTCT
* ** *
28284489 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCA-GATCTTATCTCCCTG-AGATTAC
1 TATCTCCCTGAGATTACAGTGG---AG--CG--G-ATTAAAGGATCTTATCTCTCTGAAG-TTAC
*** * * * * *
28284552 AACGGAGCAGATTGAAGCTAGTAATCC
57 AGTAGAGTAGATCGAA-CCAG--GTCT
*
28284579 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTG
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
* *
28284644 GATCGTATCAGGTCT
66 GATCGAACCAGGTCT
*
28284659 TATCTCCTTGAGATTACAGTGGAGC
1 TATCTCCCTGAGATTACAGTGGAGC
28284684 AGACCGAAGA
Statistics
Matches: 408, Mismatches: 85, Indels: 84
0.71 0.15 0.15
Matches are distributed among these distances:
80 92 0.23
82 20 0.05
83 91 0.22
84 6 0.01
85 10 0.02
86 6 0.01
87 94 0.23
88 21 0.05
90 68 0.17
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (80 bp):
TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
GATCGAACCAGGTCT
Found at i:28284676 original size:41 final size:39
Alignment explanation
Indices: 28284579--28284683 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 39
28284569 CTAGTAATCC
* *
28284579 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCT
1 TATCTCCTTGAGATTACAGTAGAGCGGATTAAAGGATCT
* *
28284618 TATCT-CTCTGA-AGTTACAGTAGAGTGGATCGTATCAGG-TCT
1 TATCTCCT-TGAGA-TTACAGTAGAGCGGAT--TA-AAGGATCT
*
28284659 TATCTCCTTGAGATTACAGTGGAGC
1 TATCTCCTTGAGATTACAGTAGAGC
28284684 AGACCGAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
38 2 0.04
39 22 0.42
41 23 0.43
42 6 0.11
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (39 bp):
TATCTCCTTGAGATTACAGTAGAGCGGATTAAAGGATCT
Found at i:28284971 original size:88 final size:86
Alignment explanation
Indices: 28283847--28284989 Score: 717
Period size: 90 Copynumber: 13.3 Consensus size: 86
28283837 CCGAAAAATT
* * ** * *
28283847 ACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAATATAGTAATCCTATCTCCCTAAGA
1 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAGA
*
28283912 TTAGAGTGGAGC-GAATTAAAG
66 TTACAGTGGAGCAG-ATTAAAG
** ** * * * *
28283933 ---GATCTTATCTCTTTGA-AGTTACAGTAGAGTAGATC-ACA-CCAG--GTCTTATTTCCCTGA
1 ACAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGA-AGCTAGTAATCTTATCTCCCTGA
* ** *
28283990 GATTACAGTGGAACAGACCGAAAAATT
64 GATTACAGTGGAGCAGA---TTAAA-G
* ** *
28284017 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGA
1 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAGA
*
28284082 TTACAGTGGAGCGGATTAAAG
66 TTACAGTGGAGCAGATTAAAG
* ** * * * * *
28284103 ---GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-CCAG--GTCTTATTTCCCTGAG
1 ACAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAG
* ***
28284161 ATTACAGTGGAACAGACCGAAG
65 ATTACAGTGGAGCAGATTAAAG
* * *
28284183 AATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT
1 -A---CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCT
28284248 GAGATTACAGTGGAGCAGATTAAAG
62 GAGATTACAGTGGAGCAGATTAAAG
* ** * * * * *
28284273 ---GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTA-CCAG--GTCTTATTTCCCTGAG
1 ACAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAG
* ***
28284331 ATTACAGTGGAACAGACCGAAG
65 ATTACAGTGGAGCAGATTAAAG
* * * *
28284353 AATTTTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCTCT
1 -A---CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCT
*
28284418 GAGATTACAGTGGAGCGGATTAAAG
62 GAGATTACAGTGGAGCAGATTAAAG
* * *** ** * * * *
28284443 ---GGTCTTATCTCTCTGA-AGTTACAATAGAATAGATCGCA-CCAG--GTCTTATTTCCCTGAG
1 ACAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAG
* ***
28284501 ATTACAGTGGAACAGACCGAAG
65 ATTACAGTGGAGCAGATTAAAG
* * *
28284523 AATTTCAGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT
1 -A---CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCT
*
28284588 GAGATTACAGTGGAGCGGATTAAAG
62 GAGATTACAGTGGAGCAGATTAAAG
* ** ** * * * *
28284613 ---GATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCGTATC-AG--GTCTTATCTCCTTGAG
1 ACAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAG
** *
28284671 ATTACAGTGGAGCAGACCGAAGAATT
65 ATTACAGTGGAGCAGA--TTA-AA-G
* * *
28284697 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCTTATCTCCCTAAGA
1 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAGA
***
28284762 TTACAGTGGAGCAGACCGAAG
66 TTACAGTGGAGCAGATTAAAG
* * *
28284783 AATTGCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATCAAAGATAGTAATCTTATCTCCCT
1 -A---CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCT
** *
28284848 GAGATTACAGCAGAGCAGATTGAAG
62 GAGATTACAGTGGAGCAGATTAAAG
* * * *
28284873 ATAGTAATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGA
1 ACAG--ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGA
* * *
28284938 -AGTTGCAGCGGAGCGGATTAAAG
64 GA-TTACAGTGGAGCAGATTAAAG
*
28284961 CCACAGATCTTATCTCTCTGA-AGTTACAG
1 --ACAGATCTTATCTCCCTGAGA-TTACAG
28284990 TAGAGTGGAT
Statistics
Matches: 805, Mismatches: 179, Indels: 144
0.71 0.16 0.13
Matches are distributed among these distances:
80 142 0.18
81 1 0.00
82 19 0.02
83 150 0.19
86 2 0.00
87 153 0.19
88 109 0.14
89 1 0.00
90 228 0.28
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (86 bp):
ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGCTAGTAATCTTATCTCCCTGAGA
TTACAGTGGAGCAGATTAAAG
Found at i:28284975 original size:44 final size:43
Alignment explanation
Indices: 28283849--28284989 Score: 411
Period size: 44 Copynumber: 26.6 Consensus size: 43
28283839 GAAAAATTAC
* * *
28283849 AGATCTTATCTCCCTG-AGATTACAGTGGAGCAGATTGAATAT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * *
28283891 AGTAATCCTATCTCCCT-AAGATTAGAGTGGAGC-GAATTAAAG--
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAG-ATTAAAGAT
** ** * * * **
28283933 -GATCTTATCTCTTTGAAG-TTACAGTAGAGTAGATCACA-CC
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * * ** *
28283973 AGGTCTTATTTCCCTG-AGATTACAGTGGAACAGACCGAAAAATT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGA-TTAAAGA-T
* *
28284017 ACAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAATAT
1 --AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * *
28284061 AGTAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAG--
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* ** * *** **
28284103 -GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCGCA-CC
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * * ***
28284143 AGGTCTTATTTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTTT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-A---T
* *
28284189 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* *
28284231 AGTAATCCTATCTCCCTG-AGATTACAGTGGAGCAGATTAAAG--
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* ** * *** **
28284273 -GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCGTA-CC
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * * ***
28284313 AGGTCTTATTTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTTT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-A---T
* *
28284359 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGCT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * *
28284401 AGTAATCCTATCTCTCTG-AGATTACAGTGGAGCGGATTAAAG--
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * *** ** *** **
28284443 -GGTCTTATCTCTCTGAAG-TTACAATAGAATAGATCGCA-CC
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * * ***
28284483 AGGTCTTATTTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-A--T
* * *
28284528 CAGATCTTATCTCCCTG-AGATTACAACGGAGCAGATTGAAGCT
1 -AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * *
28284571 AGTAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAG--
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* ** ** *
28284613 -GATCTTATCTCTCTGAAG-TTACAGTAGAGTGGA-T--CGTAT
1 AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-AT
* * * ***
28284652 CAGGTCTTATCTCCTTG-AGATTACAGTGGAGCAGACCGAAGAATT
1 -AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-A-T
*
28284697 ACAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGAT
1 --AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* ***
28284741 AGTAATCTTATCTCCCT-AAGATTACAGTGGAGCAGACCGAAGAATT
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG-A-T
*
28284787 GCAGATCTTATCTCCCT-AAGATTACAGCGGAGCAGATCAAAGAT
1 --AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* *
28284831 AGTAATCTTATCTCCCTG-AGATTACAGCAGAGCAGATTGAAGAT
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * *
28284875 AGTAATCTTATCTCCCTG-AGATTACAGCGGAGTAGATTGAAGCT
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
* * * *
28284919 AGTAATCCTATCTCCCTGAAG-TTGCAGCGGAGCGGATTAAAGCCAC
1 AG--ATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAG--AT
*
28284965 AGATCTTATCTCTCTGAAG-TTACAG
1 AGATCTTATCTCCCTGAAGATTACAG
28284990 TAGAGTGGAT
Statistics
Matches: 854, Mismatches: 167, Indels: 154
0.73 0.14 0.13
Matches are distributed among these distances:
36 1 0.00
38 1 0.00
39 125 0.15
40 22 0.03
41 134 0.16
42 18 0.02
43 2 0.00
44 335 0.39
45 9 0.01
46 205 0.24
48 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (43 bp):
AGATCTTATCTCCCTGAAGATTACAGCGGAGCAGATTAAAGAT
Found at i:28286569 original size:3 final size:3
Alignment explanation
Indices: 28286552--28286642 Score: 55
Period size: 3 Copynumber: 29.7 Consensus size: 3
28286542 TTTAGCAATT
* *
28286552 TTA TTA TTTA GTTA TTA TTA TTA -TA TCTA TTA TTA CTA TTA TCA -TA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
28286598 TTTA CTA TTA TTA -TA GTTA TTA TTA -TA GTTA TTT TTA TTT TTA TT
1 -TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
28286643 TACTTATGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
2 7 0.10
3 46 0.68
4 15 0.22
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28286584 original size:12 final size:11
Alignment explanation
Indices: 28286564--28286635 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 11
28286554 ATTATTTAGT
28286564 TATTATTATTA
1 TATTATTATTA
28286575 TATCTATTATTA
1 TAT-TATTATTA
28286587 CTATTATCATATT-
1 -TATTAT--TATTA
*
28286600 TACTATTATTA
1 TATTATTATTA
28286611 TAGTTATTATTA
1 TA-TTATTATTA
*
28286623 TAGTTATTTTTA
1 TA-TTATTATTA
28286635 T
1 T
28286636 TTTTATTTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
10 4 0.08
11 5 0.10
12 36 0.69
13 3 0.06
14 4 0.08
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.60
Consensus pattern (11 bp):
TATTATTATTA
Found at i:28286982 original size:16 final size:16
Alignment explanation
Indices: 28286945--28286982 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
28286935 TTTGAATGAA
28286945 TGTTTTTAATTTTTAT
1 TGTTTTTAATTTTTAT
28286961 TCGTTTTT-ATATTTTAT
1 T-GTTTTTAAT-TTTTAT
28286978 TGTTT
1 TGTTT
28286983 GTATGTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (16 bp):
TGTTTTTAATTTTTAT
Found at i:28288035 original size:3 final size:3
Alignment explanation
Indices: 28288027--28288051 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28288017 ATAACAAATG
28288027 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
28288052 ACCATCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28289888 original size:27 final size:26
Alignment explanation
Indices: 28289831--28289900 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 26
28289821 TTGTTGCACC
*
28289831 AGAATGAGAGGCTGAGATTGGAGTTAA
1 AGAATGAGAAGCTGAGATTGGAG-TAA
28289858 AGAATGAGAAGCTGAGATT-G-G---
1 AGAATGAGAAGCTGAGATTGGAGTAA
28289879 AGAATGAGAAGCTGAGATTGGA
1 AGAATGAGAAGCTGAGATTGGA
28289901 ATTAGAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 19 0.47
22 1 0.03
25 1 0.03
26 1 0.03
27 18 0.45
ACGTcount: A:0.39, C:0.04, G:0.37, T:0.20
Consensus pattern (26 bp):
AGAATGAGAAGCTGAGATTGGAGTAA
Found at i:28289908 original size:27 final size:26
Alignment explanation
Indices: 28289831--28289909 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 26
28289821 TTGTTGCACC
* *
28289831 AGAATGAGAGGCTGAGATTGGAGTTAA
1 AGAATGAGAAGCTGAGATTGGA-TTAG
28289858 AGAATGAGAAGCTGAGATT-G----G
1 AGAATGAGAAGCTGAGATTGGATTAG
28289879 AGAATGAGAAGCTGAGATTGGAATTAG
1 AGAATGAGAAGCTGAGATTGG-ATTAG
28289906 AGAA
1 AGAA
28289910 GCTCAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
21 19 0.43
22 1 0.02
26 1 0.02
27 23 0.52
ACGTcount: A:0.41, C:0.04, G:0.35, T:0.20
Consensus pattern (26 bp):
AGAATGAGAAGCTGAGATTGGATTAG
Found at i:28290384 original size:12 final size:12
Alignment explanation
Indices: 28290367--28290391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28290357 CCACTCAACA
28290367 ACCTATCTCATT
1 ACCTATCTCATT
28290379 ACCTATCTCATT
1 ACCTATCTCATT
28290391 A
1 A
28290392 GGTACGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (12 bp):
ACCTATCTCATT
Found at i:28292322 original size:16 final size:16
Alignment explanation
Indices: 28292301--28292368 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
28292291 TTTGGTTCGT
28292301 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28292317 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
28292333 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
28292349 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28292365 TGTA
1 TGTA
28292369 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28292623 original size:16 final size:16
Alignment explanation
Indices: 28292586--28292627 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28292576 TTAATCATAT
*
28292586 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28292602 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28292617 TTAAAATATAT
1 TTAAAATATAT
28292628 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28292634 original size:14 final size:15
Alignment explanation
Indices: 28292595--28292636 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28292585 TTTAAACATA
*
28292595 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28292610 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28292624 A-TATAATTTAATA
1 ATTATAATTAAATA
28292637 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28292733 original size:15 final size:15
Alignment explanation
Indices: 28292705--28292763 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
28292695 ATAAAATATA
28292705 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28292720 TATTAAATATATTAT
1 AATTAAATATATTAT
28292735 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28292748 AATTTAATAATATTAT
1 AATTAAAT-ATATTAT
28292764 TAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 19 0.51
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28292734 original size:120 final size:120
Alignment explanation
Indices: 28292584--28293049 Score: 738
Period size: 120 Copynumber: 3.9 Consensus size: 120
28292574 ATTTAATCAT
*
28292584 ATTTAAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 ATTT-AACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAAT
* * *
28292648 AATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
64 AATAAATATTCTTATATGAATTTAATAAAATCATAATATATGATACTATAAAATATA
* * * *
28292705 AATTAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAATATTATTAATA
1 ATTTAACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAATA
* * *
28292769 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATAAATATTCTTATATGAATTTAATAAAATCATAATATATGATACTATAAAATATA
*
28292825 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAA
* *
28292890 TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
66 TAAATATTCTTATATGAATTTAATAAAATCATAATATATGATACTATAAAATATA
* *
28292945 ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAG
1 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAA
28293010 TAAATATTCTTATATGAATTTAATAAAATCATAAGTATAT
66 TAAATATTCTTATATGAATTTAATAAAATCATAA-TATAT
28293050 AATATAGATT
Statistics
Matches: 328, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
120 317 0.97
121 11 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAA
TAAATATTCTTATATGAATTTAATAAAATCATAATATATGATACTATAAAATATA
Found at i:28292764 original size:44 final size:43
Alignment explanation
Indices: 28292682--28292766 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
28292672 CTCAAATCAT
* *
28292682 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
* *
28292725 AATATATTATAAT-TAAAATATATAATT-TAATAA-TATTATTA
1 AATATATGATAATATAAAATATA-AATTAAAATAATTATTATTA
28292766 A
1 A
28292767 TAATCAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 13 0.35
43 15 0.41
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
Found at i:28292910 original size:38 final size:37
Alignment explanation
Indices: 28292863--28293038 Score: 131
Period size: 38 Copynumber: 4.5 Consensus size: 37
28292853 TTAATAAAAA
*
28292863 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAATTCTTAATATTAAATATTAT
*
28292900 TATATGAATTTAATAAAA-TCATAATA-TATAATACTATAT
1 TATAT-AATTTAATAAAATTCTTAATATTA-AATA-T-TAT
* * * * ** *
28292939 AATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAA
1 TATATAATTT--AATAA-AATTCTT--A-AT-ATTAAATATTAT
* *
28292983 TATATAATTTAATAAAATTCTTAATAGTAAATATTCT
1 TATATAATTTAATAAAATTCTTAATATTAAATATTAT
28293020 TATATGAATTTAATAAAAT
1 TATAT-AATTTAATAAAAT
28293039 CATAAGTATA
Statistics
Matches: 106, Mismatches: 19, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
36 2 0.02
37 27 0.25
38 33 0.31
39 7 0.07
40 5 0.05
41 6 0.06
42 7 0.07
44 11 0.10
45 2 0.02
46 5 0.05
47 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCTTAATATTAAATATTAT
Found at i:28293007 original size:17 final size:18
Alignment explanation
Indices: 28292846--28292999 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
28292836 TTATTATTAA
28292846 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
28292864 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* ****
28292882 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
28292901 ATATGAATTTAAT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
28292919 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* *
28292935 ATATAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
28292954 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
28292966 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
28292984 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
28293000 TTCTTAATAG
Statistics
Matches: 99, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 2 0.02
15 5 0.05
16 8 0.08
17 16 0.16
18 41 0.41
19 15 0.15
20 3 0.03
21 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28306628 original size:41 final size:41
Alignment explanation
Indices: 28306569--28306720 Score: 180
Period size: 41 Copynumber: 3.7 Consensus size: 41
28306559 TTTTGTAAGT
*
28306569 TCAGGCTTTATGCTTAGCAGGCTTTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* *
28306610 TCAGGCTTTATGCCTAGCAGGC-TCAGTGTCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTA-TGCCGGTGAATTATA
* * * * * * *
28306651 TCAGACCTTATGTCTAGCAGGTTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* *
28306692 TCGGGCTTTGTGCCTAGCAGGCTTTATGC
1 TCAGGCTTTATGCCTAGCAGGCTTTATGC
28306721 ACTACACCAA
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
40 2 0.02
41 87 0.97
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
Found at i:28306935 original size:41 final size:41
Alignment explanation
Indices: 28306890--28307450 Score: 735
Period size: 41 Copynumber: 13.7 Consensus size: 41
28306880 GAACTTTCGG
* *
28306890 GGGCTTTAGCGGCATTTTTGAGAAAGCGTCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
28306931 GGGCTTTAGCCGCGTTTTTGAGAAAGCGCTGCTAATGATCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
28306972 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
28307013 GGGCTTTAACGGCGTTTTTGAGAAAGCGCTGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * **
28307054 AGGCTTTAGCGGCATTTTTGAGAAAGCATCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
28307095 TGGCTTTAGCGGCATTTTTTATAAAGCGCCGCTAATGCTAA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
28307136 TGGCATTAGCGGCGTTTTTGAGGAAGCGTCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
28307177 GGGCTTTAACGGTGTTTTTGAGGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
28307218 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTAA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
28307259 AGGCTTTAGCGGTGTTTTTGAGAAAGCACCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * ** *
28307300 TGGCTTTAGCGGCATTTTTTATAAAGCATCGCTAATGCTAA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * **
28307341 TGGCTTTAGCGGCGTTTTTGAGGAAGCGCATCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* **
28307382 GGGCTTTAGCGGTGTTTTTGAGGGAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
28307423 AGGCTTTAGCGGCGTTTTTGAGAAAGCG
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCG
28307451 TCGCGAATTC
Statistics
Matches: 451, Mismatches: 69, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 451 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:28307786 original size:7 final size:7
Alignment explanation
Indices: 28307744--28307797 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
28307734 GTGTTACCAT
*
28307744 TTTAAGG
1 TTTATGG
*
28307751 TTTATGA
1 TTTATGG
*
28307758 ATTATGGG
1 TTTAT-GG
*
28307766 TTTAGGG
1 TTTATGG
*
28307773 GTTATGG
1 TTTATGG
28307780 TTTATGG
1 TTTATGG
28307787 TTTATGG
1 TTTATGG
28307794 TTTA
1 TTTA
28307798 AAGGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 33 0.89
8 4 0.11
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:28307849 original size:14 final size:14
Alignment explanation
Indices: 28307686--28307851 Score: 74
Period size: 14 Copynumber: 11.9 Consensus size: 14
28307676 TATCACTATA
*
28307686 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
28307700 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* * *
28307714 GATTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
28307728 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
28307744 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
** *
28307757 AATTATGGGTTTAGG
1 GTTTA-GGGTTTATG
* *
28307772 GGTTATGGTTTATG
1 GTTTAGGGTTTATG
* *
28307786 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* * *
28307801 G-CTGGGGTTTAAG
1 GTTTAGGGTTTATG
28307814 GTTTA--G-TTATG
1 GTTTAGGGTTTATG
*
28307825 TGTTAAGGGTTTATG
1 -GTTTAGGGTTTATG
28307840 GTTTAGGGTTTA
1 GTTTAGGGTTTA
28307852 GATTAACTAG
Statistics
Matches: 111, Mismatches: 29, Indels: 24
0.68 0.18 0.15
Matches are distributed among these distances:
11 4 0.04
12 7 0.06
13 4 0.04
14 69 0.62
15 26 0.23
17 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28308125 original size:14 final size:15
Alignment explanation
Indices: 28308099--28308136 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
28308089 AATAATTATA
28308099 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
28308114 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
28308128 TATGG-TTTA
1 TATGGATTTA
28308137 AGGGTTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:28308180 original size:22 final size:22
Alignment explanation
Indices: 28308137--28308196 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
28308127 TTATGGTTTA
* * *
28308137 AGGGTTGGGATTTAAGGTTTAG
1 AGGGTTAGGAGTTAAGGGTTAG
*
28308159 AGGGTTAGGAGTTAGGGGTTAG
1 AGGGTTAGGAGTTAAGGGTTAG
*
28308181 -GGGTTAAGAGTTAAGG
1 AGGGTTAGGAGTTAAGG
28308197 ATTTAGGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (22 bp):
AGGGTTAGGAGTTAAGGGTTAG
Found at i:28308209 original size:22 final size:22
Alignment explanation
Indices: 28308148--28308221 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
28308138 GGGTTGGGAT
*
28308148 TTAAGG-TTTAGAGGGTTAGGAG
1 TTAAGGATTTAG-GGGTTAAGAG
**
28308170 TT-AGGGGTTAGGGGTTAAGAG
1 TTAAGGATTTAGGGGTTAAGAG
* *
28308191 TTAAGGATTTAGGGTTTAAGAT
1 TTAAGGATTTAGGGGTTAAGAG
28308213 TTAAGGATT
1 TTAAGGATT
28308222 CAAGGGTTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
21 14 0.32
22 30 0.68
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.35
Consensus pattern (22 bp):
TTAAGGATTTAGGGGTTAAGAG
Found at i:28308619 original size:14 final size:13
Alignment explanation
Indices: 28308594--28308635 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
28308584 AGATAGTACT
28308594 AATTAGTTTTTTA
1 AATTAGTTTTTTA
28308607 AATTAGCTTTTTTA
1 AATTAG-TTTTTTA
* *
28308621 ATTTA-TATTTTA
1 AATTAGTTTTTTA
28308633 AAT
1 AAT
28308636 ATGTTCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 8 0.32
13 6 0.24
14 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (13 bp):
AATTAGTTTTTTA
Found at i:28308715 original size:14 final size:14
Alignment explanation
Indices: 28308696--28308740 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
28308686 TTAATTATGA
28308696 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
*
28308710 TTATAGTTTATGGT
1 TTATAGTTTAGGGT
* * *
28308724 ATATGGTGTAGGGT
1 TTATAGTTTAGGGT
28308738 TTA
1 TTA
28308741 ATGTTTAAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:28308782 original size:15 final size:14
Alignment explanation
Indices: 28308764--28308800 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
28308754 ACTATTTTAA
28308764 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
28308778 GGGTTTAAGGATTAT
1 -GGTTTATGGATTAT
28308793 GGTTTATG
1 GGTTTATG
28308801 ATTTATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (14 bp):
GGTTTATGGATTAT
Done.