Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 20 of 770
Found at i:5422791 original size:23 final size:22
Alignment explanation
Indices: 5422761--5422804 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5422751 TCTCAATTCA
*
5422761 TAAATAAATTCATACCAAAACT
1 TAAATAAAATCATACCAAAACT
*
5422783 TAAACTAAAATCATACCTAAAC
1 TAAA-TAAAATCATACCAAAAC
5422805 ATACGACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAATCATACCAAAACT
Found at i:5423468 original size:43 final size:42
Alignment explanation
Indices: 5423420--5423526 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
5423410 CAATATCAAC
* *
5423420 GTCCCAGACGTGGTCTTACATGTAA-TCAAACATCGATGCCACT
1 GTCCCAGACGTGGTCTTACACG-AAGTCAAACA-CGATGCCAAT
* *
5423463 GTCCCAGACAG-GGTCTTACACGAAGTCAGATACGATGCCAAT
1 GTCCCAGAC-GTGGTCTTACACGAAGTCAAACACGATGCCAAT
* *
5423505 GTCTCAGACATGGTCTTACACG
1 GTCCCAGACGTGGTCTTACACG
5423527 CAAAACAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 30 0.55
43 24 0.44
44 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (42 bp):
GTCCCAGACGTGGTCTTACACGAAGTCAAACACGATGCCAAT
Found at i:5430968 original size:23 final size:22
Alignment explanation
Indices: 5430942--5430997 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
5430932 TCACAATTGG
5430942 GCATTCAAACTCATACCAAATAT
1 GCATTCAAACTCATACCAAA-AT
* * *
5430965 GCATCCAAAGT-ATACCTAAAT
1 GCATTCAAACTCATACCAAAAT
5430986 G-A-TCAAACTCAT
1 GCATTCAAACTCAT
5430998 TTAATAGACT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.19
20 3 0.11
21 3 0.11
22 7 0.26
23 9 0.33
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (22 bp):
GCATTCAAACTCATACCAAAAT
Found at i:5431872 original size:71 final size:71
Alignment explanation
Indices: 5431792--5431935 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
5431782 CTGACGGTCA
5431792 AGACTTAGCTACACGATGCTGCTCACATAAGCTCACGATAATTGCAACACATGACAGAAAACTCA
1 AGACTTAGCTACACGATGCTGCTCACATAAGCTCACGATAATTGCAACACATGACAGAAAACTCA
5431857 GCCACC
66 GCCACC
5431863 AGACTTAGCTACACGATGCTGCTCACATAAGCTCACGATAATTGCAACACATGACAGAAAACTCA
1 AGACTTAGCTACACGATGCTGCTCACATAAGCTCACGATAATTGCAACACATGACAGAAAACTCA
5431928 GCCACC
66 GCCACC
5431934 AG
1 AG
5431936 TAGAACGTAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (71 bp):
AGACTTAGCTACACGATGCTGCTCACATAAGCTCACGATAATTGCAACACATGACAGAAAACTCA
GCCACC
Found at i:5434213 original size:13 final size:13
Alignment explanation
Indices: 5434197--5434238 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5434187 AGGTTTGCAT
*
5434197 ATAGTGTTCACAC
1 ATAGGGTTCACAC
*
5434210 ATAGGGTCCAC-C
1 ATAGGGTTCACAC
5434222 TATAGGGTTCACAC
1 -ATAGGGTTCACAC
5434236 ATA
1 ATA
5434239 CAGGGTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (13 bp):
ATAGGGTTCACAC
Found at i:5434504 original size:45 final size:44
Alignment explanation
Indices: 5434398--5434512 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 44
5434388 TAAAGTCTGA
* *
5434398 CACTAGACTGTGGATACACAACAAAAATTCGCAGATGAAACCTGC
1 CACTAGACTGTGG-TACACAACAAAAATTCACAGATAAAACCTGC
* * **
5434443 CACTGGATTGTGGGTACACAAC-AAAATATCACAGATAAAATTTGC
1 CACTAGACTGT-GGTACACAACAAAAAT-TCACAGATAAAACCTGC
* *
5434488 CACTAGACTATAGGTACACTACAAA
1 CACTAGACTGT-GGTACACAACAAA
5434513 CTATTGCAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
44 5 0.09
45 47 0.84
46 4 0.07
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (44 bp):
CACTAGACTGTGGTACACAACAAAAATTCACAGATAAAACCTGC
Found at i:5434526 original size:45 final size:43
Alignment explanation
Indices: 5434477--5434575 Score: 101
Period size: 45 Copynumber: 2.3 Consensus size: 43
5434467 AATATCACAG
* *
5434477 ATAAAATTTGCCACT-AGACTATAGGTACACTACAAACTATTGCAA
1 ATAAAATTTGCCACTGAG-CTATAGATACACAACAAA-T-TTGCAA
* * * *
5434522 ATAAAATCTGTCACTGAGCTATAGATGCACAACATATTTGCAA
1 ATAAAATTTGCCACTGAGCTATAGATACACAACAAATTTGCAA
*
5434565 ATAAAAGTTGC
1 ATAAAATTTGC
5434576 TCATGAGTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
43 14 0.32
44 1 0.02
45 27 0.61
46 2 0.05
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (43 bp):
ATAAAATTTGCCACTGAGCTATAGATACACAACAAATTTGCAA
Found at i:5435572 original size:28 final size:28
Alignment explanation
Indices: 5435129--5435603 Score: 342
Period size: 28 Copynumber: 17.0 Consensus size: 28
5435119 TTGGTAAAGC
*
5435129 AGGGGACAAAA-TAGTAAAATCT-AAAAAA
1 AGGGG-CAAAACTA-TAAAATCTGAAAAAT
* *
5435157 ATGGGACAAAACTATAAAATCTAAAAAAAT
1 A-GGGGCAAAACTATAAAATCT-GAAAAAT
* * *
5435187 A-GGGAAAAATTGTAAAAT-TGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* ** *
5435213 ATGGGCAAAGTTATAAAA-CATAAAAAAT
1 AGGGGCAAAACTATAAAATC-TGAAAAAT
* * * *
5435241 A-AGGCTAAGCTGTAAAATCTGAAAACAT
1 AGGGGCAAAACTATAAAATCTGAAAA-AT
*
5435269 AGGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
5435297 AGTGGAAAAACTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * *
5435325 AGGAGACAAAATTATAAAATTTGACAAAT
1 AGG-GGCAAAACTATAAAATCTGAAAAAT
* *
5435354 -GGGGCTAAACTATAAAATATGAAAAAAT
1 AGGGGCAAAACTATAAAATCTG-AAAAAT
*
5435382 AGGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
5435410 AAGGGCTAAATTATAAAATCT-AAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
5435437 AAGGG-AAAATTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * **
5435464 ATGTGCAAAACTATAAAATCTTTAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * * *
5435492 AGAGGAAAAATTGTAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* *
5435520 A-GGGCAAAAGTGTAAAATCT-AGAAAAT
1 AGGGGCAAAACTATAAAATCTGA-AAAAT
* * * *
5435547 AGGGGCAAAAGTGTAAAATATGGAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * *
5435575 ATGGGAAAAATTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
5435603 A
1 A
5435604 AGGGACACAA
Statistics
Matches: 361, Mismatches: 68, Indels: 36
0.78 0.15 0.08
Matches are distributed among these distances:
26 21 0.06
27 88 0.24
28 183 0.51
29 63 0.17
30 6 0.02
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.22
Consensus pattern (28 bp):
AGGGGCAAAACTATAAAATCTGAAAAAT
Found at i:5437419 original size:25 final size:23
Alignment explanation
Indices: 5437391--5437456 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 23
5437381 TTGAATTGTG
5437391 TTATTAATTATAAAAATAAAATGAA
1 TTATTAATT-TAAAAATAAAAT-AA
* *
5437416 TTATTACATTTAAAATTAAAAATAT
1 TTATTA-ATTTAAAAAT-AAAATAA
5437441 TTA-TAATTTAAAAATA
1 TTATTAATTTAAAAATA
5437457 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.25
24 2 0.06
25 16 0.44
26 8 0.22
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTATTAATTTAAAAATAAAATAA
Found at i:5437448 original size:16 final size:17
Alignment explanation
Indices: 5437423--5437464 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
5437413 GAATTATTAC
5437423 ATTTAAAA-TTAAAAAT
1 ATTTAAAATTTAAAAAT
*
5437439 ATTTATAATTTAAAAAT
1 ATTTAAAATTTAAAAAT
5437456 A-TTAAAATT
1 ATTTAAAATT
5437465 ATTTGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATTTAAAAAT
Found at i:5449423 original size:178 final size:177
Alignment explanation
Indices: 5449123--5449856 Score: 915
Period size: 176 Copynumber: 4.1 Consensus size: 177
5449113 AGTGACATTG
* * * *
5449123 GACTGAGAATTAAAGATCTTATCTCCCTGA-AGTTGCAGCGGAGCAGATCTTCGCAGATGGTGAA
1 GACTGAGATTTGAAGATCTTATTTCACTGAGA-TTGCAGCGGAGCAGATC-TCG-AGATGGTGAA
5449187 TCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAA
63 TCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAA
* * * *
5449252 GAAAGCAGGTTGAAGAATGAGTCTTATCTTCCTAAGGTAGTAAGGAAGTA
128 GAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
* * **
5449302 GACTGAGATTTGAAGATCTTATTTCTCTGTG-TTGCAGCAAAGCAGATCTTCGCAGATGGTGAAT
1 GACTGAGATTTGAAGATCTTATTTCACTGAGATTGCAGCGGAGCAGATC-TCG-AGATGGTGAAT
* * *
5449366 CTTATCTTCATGTATCGATAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGGAAG
64 CTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAAG
* *
5449431 AGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGTA
129 AGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
* * * *
5449480 GACTGAGATTTAAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGA--TCGAGAATGGTGGATA
1 GACTGAGATTTGAAGATCTTATTTCACTGAGATTGCAGCGGAGCAGATCTCGAG-ATGGTGAATC
* * * * ** *
5449543 TTATCTTCATGTATTGGCAATGGAGCAGATTTTATCACCAGCCTCATCCCTCTGATATAGTAAGA
65 TTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAAGA
* * *
5449608 GAGCAGGTTGAATAATAAATCTTATCTTCCTGAGGTAGCAAGGAAGCA
130 GAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
* * * * ** *
5449656 GATTGAGTTTTGAATATCTTATTTCACTGAGATTGCAGTGGAGCAGATCAAGA-ATGGTGAATCC
1 GACTGAGATTTGAAGATCTTATTTCACTGAGATTGCAGCGGAGCAGATCTCGAGATGGTGAATCT
* * * * * * *
5449720 TATCTCCATGTATCGGCAATGGAGTAGATTTTACCACTAGCCTTATTTCTCTGAGGTGGCAAGAG
66 TATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAAGAG
* *
5449785 AGCGGGTTAAAG-ATGGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
131 AGCAGGTTGAAGAAT-GAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
*
5449832 GACTGAAGA-CTGAAGATCTTATTTC
1 GACTG-AGATTTGAAGATCTTATTTC
5449857 CTCAAGTAAT
Statistics
Matches: 484, Mismatches: 64, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
175 4 0.01
176 273 0.56
177 2 0.00
178 168 0.35
179 37 0.08
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (177 bp):
GACTGAGATTTGAAGATCTTATTTCACTGAGATTGCAGCGGAGCAGATCTCGAGATGGTGAATCT
TATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGAGGTAGCAAGAG
AGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCA
Found at i:5449951 original size:30 final size:30
Alignment explanation
Indices: 5449917--5449976 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5449907 AGTTAACCTA
*
5449917 TCCTATGTCTTTAAGAGCACAGTCAAGATT
1 TCCTATGTCCTTAAGAGCACAGTCAAGATT
5449947 TCCTATGTCCTTAAGAGCACAGTCAAGATT
1 TCCTATGTCCTTAAGAGCACAGTCAAGATT
5449977 CAACAGAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (30 bp):
TCCTATGTCCTTAAGAGCACAGTCAAGATT
Found at i:5451601 original size:18 final size:18
Alignment explanation
Indices: 5451553--5451602 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5451543 ATTTTTATTA
*
5451553 TATCATTTATATTATTTG
1 TATCATTTATATTAATTG
*
5451571 TAAT-GTTTATATTAATTG
1 T-ATCATTTATATTAATTG
*
5451589 TATCATTTGTATTA
1 TATCATTTATATTA
5451603 TTGGTTTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (18 bp):
TATCATTTATATTAATTG
Found at i:5451901 original size:2 final size:2
Alignment explanation
Indices: 5451894--5451925 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5451884 AAATTTAATC
5451894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5451926 AATCCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5456509 original size:130 final size:132
Alignment explanation
Indices: 5456368--5456670 Score: 353
Period size: 130 Copynumber: 2.3 Consensus size: 132
5456358 ATGATTCTCG
* * * * *
5456368 AATTGTCAAATACCGAATATTGCCTTCGTTTTAAATAATTTTTAGAAGATATGAATGAAATCTTG
1 AATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATCTTG
* * *
5456433 AAGGGATATTTGATTATTTTAAAC-AA-TCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
66 AAAGGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
5456496 CA
131 CA
* ** * * * * * *
5456498 AATTGCCAAATATCGTGTATCACCTTCG-TTCAAGGGA-TTTTAAAAGACATGAGTGAAATTTTG
1 AATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATCTTG
* * * *
5456561 AAATGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
66 AAAGGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
*
5456626 CG
131 CA
* * *
5456628 AATTGTCAAATATCAAATCTCGTCTTCGTTTTAAAGAATTTTT
1 AATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTT
5456671 GAATGAATGA
Statistics
Matches: 137, Mismatches: 32, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
128 41 0.30
129 7 0.05
130 79 0.58
131 6 0.04
132 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (132 bp):
AATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATCTTG
AAAGGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
CA
Found at i:5457712 original size:2 final size:2
Alignment explanation
Indices: 5457705--5457729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5457695 TAATGTATTA
5457705 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5457730 AATTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5457884 original size:5 final size:5
Alignment explanation
Indices: 5457874--5457905 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5457864 CATTATGTGA
5457874 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
5457906 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5457899 original size:9 final size:9
Alignment explanation
Indices: 5457875--5457905 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5457865 ATTATGTGAA
5457875 AAATAAAAT
1 AAATAAAAT
5457884 AAAATAAAAT
1 -AAATAAAAT
5457894 AAATAAAAT
1 AAATAAAAT
5457903 AAA
1 AAA
5457906 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5462907 original size:152 final size:152
Alignment explanation
Indices: 5462737--5463025 Score: 352
Period size: 151 Copynumber: 1.9 Consensus size: 152
5462727 GATAAAATAC
* *
5462737 ATATAATAATAAACTAAAAGATATGTTATATAAGATTATAT-ATTTAAAAGACGAGAATAAATTT
1 ATATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGA--AGAATAAATTT
* *
5462801 AAAAGAAACTATATGCGTAAAATAATAT-AGAATTAATAATATGCAT-AGAATAAAA-TAATATT
64 AAAAGAAACTACATGCATAAAATAATATAAG-ATTAATAATATGCATGA-AATAAAATTAATATT
5462863 ACTATAAAGTACGTATATATATATAT
127 ACTATAAAGTACGTATATATATATAT
** * * * * * *
5462889 ATATAATAATAATTTAAAAGATGTATTATGTAGGATTATGTAATATAATATAAGAATAAATTTAA
1 ATATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGAAGAATAAATTTAA
* * * * * *
5462954 AGGGAATTACATGTATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATTTTATTA
66 AAGAAACTACATGCATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATATTACTA
5463019 TAAAGTA
131 TAAAGTA
5463026 TATGTATATA
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
151 55 0.48
152 53 0.46
153 7 0.06
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (152 bp):
ATATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGAAGAATAAATTTAA
AAGAAACTACATGCATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATATTACTA
TAAAGTACGTATATATATATAT
Found at i:5466823 original size:20 final size:20
Alignment explanation
Indices: 5466798--5466837 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5466788 TTGTCAAATC
5466798 CCTACTGAAGCAACTTGGCT
1 CCTACTGAAGCAACTTGGCT
5466818 CCTACTGAAGCAACTTGGCT
1 CCTACTGAAGCAACTTGGCT
5466838 AAGAGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
CCTACTGAAGCAACTTGGCT
Found at i:5467707 original size:18 final size:18
Alignment explanation
Indices: 5467683--5467722 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
5467673 ATCTCTCTCA
5467683 ATAAAAATTCAAAACATTT
1 ATAAAAATTCAAAA-ATTT
*
5467702 ATAAAAATTCTAAAATTT
1 ATAAAAATTCAAAAATTT
5467720 ATA
1 ATA
5467723 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTCAAAAATTT
Found at i:5471284 original size:74 final size:75
Alignment explanation
Indices: 5471204--5471350 Score: 269
Period size: 75 Copynumber: 2.0 Consensus size: 75
5471194 TATTTTATAT
5471204 ATAAAAATAAATTT-AAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCA
1 ATAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCA
5471268 AAAAAATTGA
66 AAAAAATTGA
*
5471278 ATAAAAATAAATTTAAAAAATATAATATATCAAATACAGTAAAAATATTAAAATAAATGTTTCCA
1 ATAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCA
*
5471343 AATAAATT
66 AAAAAATT
5471351 AAAAATACAT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 14 0.20
75 56 0.80
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (75 bp):
ATAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCA
AAAAAATTGA
Found at i:5476704 original size:2 final size:2
Alignment explanation
Indices: 5476697--5476729 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5476687 TTAAAAATAA
5476697 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5476730 GAAAATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5485542 original size:17 final size:17
Alignment explanation
Indices: 5485520--5485581 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
5485510 ATATTGAACT
5485520 ATTCAAACTCAATGAGA
1 ATTCAAACTCAATGAGA
*
5485537 ATTCAAA-TATATATTGA-A
1 ATTCAAACT-CA-A-TGAGA
5485555 CTATTCAAACTCAATGAGA
1 --ATTCAAACTCAATGAGA
5485574 ATTCAAAC
1 ATTCAAAC
5485582 ATTCACTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 1 0.03
17 16 0.44
18 5 0.14
19 5 0.14
20 8 0.22
21 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (17 bp):
ATTCAAACTCAATGAGA
Found at i:5485556 original size:37 final size:37
Alignment explanation
Indices: 5485506--5485580 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
5485496 ATATTAATTT
5485506 ATATATATTGAACTATTCAAACTCAATGAGAATTCAA
1 ATATATATTGAACTATTCAAACTCAATGAGAATTCAA
5485543 ATATATATTGAACTATTCAAACTCAATGAGAATTCAA
1 ATATATATTGAACTATTCAAACTCAATGAGAATTCAA
5485580 A
1 A
5485581 CATTCACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (37 bp):
ATATATATTGAACTATTCAAACTCAATGAGAATTCAA
Found at i:5485729 original size:18 final size:18
Alignment explanation
Indices: 5485677--5485936 Score: 100
Period size: 18 Copynumber: 14.1 Consensus size: 18
5485667 TCATTAACAC
*
5485677 TCAG-AACAATTATTTAT
1 TCAGTAACAATTAATTAT
* * *
5485694 TCAGTAACAGTCAGTTAT
1 TCAGTAACAATTAATTAT
*
5485712 TCGGTAACAATTAATTAT
1 TCAGTAACAATTAATTAT
* * * *
5485730 TCAATAATAACTAGTTAT
1 TCAGTAACAATTAATTAT
* *
5485748 TTAGTATCGATCAATTGATCGGT-T
1 TCAGTA---A-CAATTAAT---TAT
* *
5485772 ATCTAGTAACAGTCAATTAT
1 -TC-AGTAACAATTAATTAT
*
5485792 TCAGTAA-AATCAGA-TAT
1 TCAGTAACAATTA-ATTAT
*
5485809 TCAGTAAAAATTAAGTTAT
1 TCAGTAACAATTAA-TTAT
* *
5485828 TCAGTAAC-AGTCATTCAT
1 TCAGTAACAATTAATT-AT
* **
5485846 TCAGTGACAATCCATTAT
1 TCAGTAACAATTAATTAT
* ** *
5485864 TCAATAATGATCAATTAT
1 TCAGTAACAATTAATTAT
* *
5485882 TCAGTAA-TATTCAGTTAT
1 TCAGTAACAATT-AATTAT
*
5485900 TCAGTAACAGTTAATTAT
1 TCAGTAACAATTAATTAT
* *
5485918 TCAGTAATAATCAATTAT
1 TCAGTAACAATTAATTAT
5485936 T
1 T
5485937 TTATAATTTT
Statistics
Matches: 179, Mismatches: 45, Indels: 37
0.69 0.17 0.14
Matches are distributed among these distances:
17 23 0.13
18 117 0.65
19 20 0.11
20 1 0.01
21 1 0.01
22 9 0.05
23 1 0.01
24 1 0.01
25 2 0.01
26 4 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (18 bp):
TCAGTAACAATTAATTAT
Found at i:5485830 original size:19 final size:18
Alignment explanation
Indices: 5485788--5485834 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
5485778 TAACAGTCAA
*
5485788 TTATTCAGT-AAAATCAG
1 TTATTCAGTAAAAATAAG
*
5485805 ATATTCAGTAAAAATTAAG
1 TTATTCAGTAAAAA-TAAG
5485824 TTATTCAGTAA
1 TTATTCAGTAA
5485835 CAGTCATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAAAAATAAG
Found at i:5485882 original size:54 final size:54
Alignment explanation
Indices: 5485776--5485936 Score: 166
Period size: 54 Copynumber: 3.0 Consensus size: 54
5485766 TCGGTTATCT
* * * *
5485776 AGTAACAGTCAATTATTCAGTAA-AATCAGA-TATTCAGTAAAAATTAAGTTATTC
1 AGTAACAGTCAGTTATTCAGTAACAATCA-ATTATTCAATAATAATCAA-TTATTC
* * *
5485830 AGTAACAGTCA-TTCATTCAGTGACAATCCATTATTCAATAATGATCAATTATTC
1 AGTAACAGTCAGTT-ATTCAGTAACAATCAATTATTCAATAATAATCAATTATTC
* * * * *
5485884 AGTAATATTCAGTTATTCAGTAACAGTTAATTATTCAGTAATAATCAATTATT
1 AGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAATAATAATCAATTATT
5485937 TTATAATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 2 0.02
54 68 0.76
55 19 0.21
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (54 bp):
AGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAATAATAATCAATTATTC
Found at i:5485900 original size:36 final size:36
Alignment explanation
Indices: 5485784--5485936 Score: 125
Period size: 36 Copynumber: 4.2 Consensus size: 36
5485774 CTAGTAACAG
* * *
5485784 TCAATTATTCAGTAA-AATCAGA-TATTCAGTAAAAA
1 TCAATTATTCAATAACAGTCA-ATTATTCAGTAATAA
* * * *
5485819 TTAAGTTATTCAGTAACAGTC-ATTCATTCAGTGACAA
1 TCAA-TTATTCAATAACAGTCAATT-ATTCAGTAATAA
* * *
5485856 TCCATTATTCAATAA-TGATCAATTATTCAGTAATAT
1 TCAATTATTCAATAACAG-TCAATTATTCAGTAATAA
* * *
5485892 TCAGTTATTCAGTAACAGTTAATTATTCAGTAATAA
1 TCAATTATTCAATAACAGTCAATTATTCAGTAATAA
5485928 TCAATTATT
1 TCAATTATT
5485937 TTATAATTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
35 5 0.05
36 69 0.74
37 19 0.20
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (36 bp):
TCAATTATTCAATAACAGTCAATTATTCAGTAATAA
Found at i:5486561 original size:9 final size:9
Alignment explanation
Indices: 5486547--5486571 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5486537 ATAAATCAAT
5486547 TCAATATAA
1 TCAATATAA
5486556 TCAATATAA
1 TCAATATAA
5486565 TCAATAT
1 TCAATAT
5486572 TCAATCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (9 bp):
TCAATATAA
Found at i:5486567 original size:23 final size:22
Alignment explanation
Indices: 5486523--5486569 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5486513 CAATTCAAAC
*
5486523 ATTCACATATATTCATAAATCA
1 ATTCACATATAATCATAAATCA
5486545 ATTCA-ATATAATCAATATAATCA
1 ATTCACATATAATC-ATA-AATCA
5486568 AT
1 AT
5486570 ATTCAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTCACATATAATCATAAATCA
Found at i:5491626 original size:33 final size:33
Alignment explanation
Indices: 5491562--5491625 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
5491552 AAAAGGTAAA
5491562 ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
1 ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
5491595 ATTTAGAAAATTTTA-AAATTAATTA-TAAAAA
1 ATTTA-AAAATTTTATAAA--AATTAGTAAAAA
5491626 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 8 0.29
34 15 0.54
35 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
Found at i:5491968 original size:19 final size:20
Alignment explanation
Indices: 5491944--5491993 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5491934 AAATATTATG
* *
5491944 ATTTTTACAATT-TATAATT
1 ATTTTTAAAATTGCATAATT
5491963 ATTTTTTAAAATTGCATAATT
1 A-TTTTTAAAATTGCATAATT
*
5491984 ATTTTCAAAA
1 ATTTTTAAAA
5491994 GAATTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTAAAATTGCATAATT
Found at i:5492088 original size:19 final size:18
Alignment explanation
Indices: 5492031--5492106 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
5492021 ATTTTAAAAA
5492031 TACAATTTTT-ATACTTTTT
1 TACAATTTTTAATA--TTTT
* *
5492050 TACAATTTTTAAGAACTTT
1 TACAATTTTTAA-TATTTT
5492069 TACAACTTTTTAATATTTT
1 TACAA-TTTTTAATATTTT
*
5492088 TA-AATTATTTTATATTTT
1 TACAATT-TTTAATATTTT
5492106 T
1 T
5492107 TAAAATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.04
18 13 0.27
19 24 0.50
20 8 0.17
21 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (18 bp):
TACAATTTTTAATATTTT
Found at i:5492199 original size:21 final size:22
Alignment explanation
Indices: 5492175--5492220 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5492165 GTTTATTAAG
5492175 TTTTTT-C-ATTTTAAAATATT
1 TTTTTTACAATTTTAAAATATT
*
5492195 TTTTTTACAATTTTTAAATATT
1 TTTTTTACAATTTTAAAATATT
5492217 TTTT
1 TTTT
5492221 AATGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTTACAATTTTAAAATATT
Found at i:5494439 original size:2 final size:2
Alignment explanation
Indices: 5494434--5494461 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5494424 TTTAGGGATA
5494434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5494462 TTCCCTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5499747 original size:40 final size:40
Alignment explanation
Indices: 5499703--5499840 Score: 100
Period size: 46 Copynumber: 3.1 Consensus size: 40
5499693 TATCAACTTT
5499703 TTTTTAGATTAACATAATAAATATGATGATTTGATTTTAA
1 TTTTTAGATTAACATAATAAATATGATGATTTGATTTTAA
* * * *
5499743 TTTTTATTACTTTTTTAAAATAATTATAATATG-TGA-TAGTATTATCAA
1 TTTTTA-GA-----TTAACATAA-TA-AATATGATGATTTG-ATT-TTAA
5499791 CTTTTTTTTAGATTAACATAATAAATATGATGATTTGATTTTAA
1 ----TTTTTAGATTAACATAATAAATATGATGATTTGATTTTAA
5499835 TTTTTA
1 TTTTTA
5499841 TTACTTTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 32
0.65 0.07 0.28
Matches are distributed among these distances:
40 12 0.16
41 1 0.01
44 9 0.12
45 8 0.11
46 20 0.27
47 8 0.11
48 9 0.12
51 1 0.01
52 6 0.08
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (40 bp):
TTTTTAGATTAACATAATAAATATGATGATTTGATTTTAA
Found at i:5499800 original size:92 final size:92
Alignment explanation
Indices: 5499670--5499849 Score: 360
Period size: 92 Copynumber: 2.0 Consensus size: 92
5499660 ATGTAACCGT
5499670 ATAATTATAATATGTGATAGTATTATCAACTTTTTTTTAGATTAACATAATAAATATGATGATTT
1 ATAATTATAATATGTGATAGTATTATCAACTTTTTTTTAGATTAACATAATAAATATGATGATTT
5499735 GATTTTAATTTTTATTACTTTTTTAAA
66 GATTTTAATTTTTATTACTTTTTTAAA
5499762 ATAATTATAATATGTGATAGTATTATCAACTTTTTTTTAGATTAACATAATAAATATGATGATTT
1 ATAATTATAATATGTGATAGTATTATCAACTTTTTTTTAGATTAACATAATAAATATGATGATTT
5499827 GATTTTAATTTTTATTACTTTTT
66 GATTTTAATTTTTATTACTTTTT
5499850 ACATAATTAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (92 bp):
ATAATTATAATATGTGATAGTATTATCAACTTTTTTTTAGATTAACATAATAAATATGATGATTT
GATTTTAATTTTTATTACTTTTTTAAA
Found at i:5501823 original size:25 final size:24
Alignment explanation
Indices: 5501769--5501830 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
5501759 TTTACTCTAC
*
5501769 TTTAAAAAT-TGAATGTAATTAAT
1 TTTAAAAATATAAATGTAATTAAT
* *
5501792 TTGAAAAATATAAATTTAATTTAAT
1 TTTAAAAATATAAATGTAA-TTAAT
*
5501817 TTTAAAATTATAAA
1 TTTAAAAATATAAA
5501831 CTATTGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTAAAAATATAAATGTAATTAAT
Found at i:5507329 original size:31 final size:30
Alignment explanation
Indices: 5507285--5507385 Score: 98
Period size: 36 Copynumber: 3.2 Consensus size: 30
5507275 GGTGGCTAGG
5507285 TTTTTT-TATTTTTTTTTGGTTAGGTTTTTC
1 TTTTTTCT-TTTTTTTTTGGTTAGGTTTTTC
5507315 TTTTTTCTTCTTTTTTTTAGGGGGGTTAGGTTTTTC
1 TTTTTTCTT-TTTTTTTT-----GGTTAGGTTTTTC
* *
5507351 TTTTTTCTTTTTTTTTAGGGTTAGGGTTTT-
1 TTTTTTCTTTTTTTTT-TGGTTAGGTTTTTC
5507381 TTTTT
1 TTTTT
5507386 AGAGAAGGCT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
30 12 0.20
31 20 0.33
35 7 0.11
36 22 0.36
ACGTcount: A:0.06, C:0.05, G:0.18, T:0.71
Consensus pattern (30 bp):
TTTTTTCTTTTTTTTTTGGTTAGGTTTTTC
Found at i:5507363 original size:34 final size:36
Alignment explanation
Indices: 5507302--5507370 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
5507292 ATTTTTTTTT
5507302 GGTTAGGTTTTTCTTTTTTCTTCTTTTTTTTAGGGG
1 GGTTAGGTTTTTCTTTTTTCTTCTTTTTTTTAGGGG
5507338 GGTTAGGTTTTTCTTTTTTC-T-TTTTTTTTAGGG
1 GGTTAGGTTTTTCTTTTTTCTTCTTTTTTTTAGGG
5507371 TTAGGGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 12 0.36
35 1 0.03
36 20 0.61
ACGTcount: A:0.06, C:0.07, G:0.22, T:0.65
Consensus pattern (36 bp):
GGTTAGGTTTTTCTTTTTTCTTCTTTTTTTTAGGGG
Found at i:5507385 original size:36 final size:35
Alignment explanation
Indices: 5507285--5507385 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 35
5507275 GGTGGCTAGG
* *
5507285 TTTTTTTATTTTTTTTT--GGTTA-GGTTTTTCTT
1 TTTTTTTCTTTTTTTTTAGGGTTAGGGTTTTTTTT
* *
5507317 TTTTCTTC-TTTTTTTTAGGG---GGGTTAGGTTTTT
1 TTTTTTTCTTTTTTTTTAGGGTTAGGGTT--TTTTTT
*
5507350 CTTTTTTCTTTTTTTTTAGGGTTAGGGTTTTTTTT
1 TTTTTTTCTTTTTTTTTAGGGTTAGGGTTTTTTTT
5507385 T
1 T
5507386 AGAGAAGGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
31 12 0.23
32 6 0.12
33 12 0.23
34 12 0.23
35 5 0.10
37 5 0.10
ACGTcount: A:0.06, C:0.05, G:0.18, T:0.71
Consensus pattern (35 bp):
TTTTTTTCTTTTTTTTTAGGGTTAGGGTTTTTTTT
Found at i:5508105 original size:17 final size:18
Alignment explanation
Indices: 5508085--5508118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5508075 AAAAATTTTA
5508085 AAATT-TTAAAAATAAAT
1 AAATTCTTAAAAATAAAT
5508102 AAATTCTTAAAAATAAA
1 AAATTCTTAAAAATAAA
5508119 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTCTTAAAAATAAAT
Found at i:5508786 original size:32 final size:31
Alignment explanation
Indices: 5508742--5508840 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 31
5508732 GGTGGCTAGG
*
5508742 TTTTTTT-ATTTTTTTTTGGTTAGGTTTTTC
1 TTTTTTTCTTTTTTTTTTGGTTAGGTTTTTC
**
5508772 TTTTTCTTCTTTTTTTTGGGGGTTAGGTTTTTC
1 TTTTT-TTCTTTTTTTT-TTGGTTAGGTTTTTC
*
5508805 -TTTTTTCTTTTTTTTTTAGGGTTAGGGTTTT-
1 TTTTTTTCTTTTTTTTTT--GGTTAGGTTTTTC
5508836 TTTTT
1 TTTTT
5508841 GAGAAGGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 5 0.09
31 13 0.23
32 26 0.46
33 13 0.23
ACGTcount: A:0.05, C:0.05, G:0.17, T:0.73
Consensus pattern (31 bp):
TTTTTTTCTTTTTTTTTTGGTTAGGTTTTTC
Found at i:5508796 original size:33 final size:31
Alignment explanation
Indices: 5508750--5508840 Score: 116
Period size: 33 Copynumber: 2.9 Consensus size: 31
5508740 GGTTTTTTTA
5508750 TTTTTTTTT--GGTTAGGTTTTTCTTTTTCT
1 TTTTTTTTTAGGGTTAGGTTTTTCTTTTTCT
*
5508779 TCTTTTTTTTGGGGGTTAGGTTTTTCTTTTTTCT
1 T-TTTTTTTT-AGGGTTAGGTTTTTC-TTTTTCT
*
5508813 TTTTTTTTTAGGGTTAGGGTTTT-TTTTT
1 TTTTTTTTTAGGGTTAGGTTTTTCTTTTT
5508841 GAGAAGGCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
29 1 0.02
30 13 0.24
32 12 0.22
33 21 0.38
34 8 0.15
ACGTcount: A:0.04, C:0.05, G:0.19, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTAGGGTTAGGTTTTTCTTTTTCT
Found at i:5509676 original size:88 final size:87
Alignment explanation
Indices: 5509532--5510146 Score: 376
Period size: 88 Copynumber: 7.3 Consensus size: 87
5509522 CACGTGAGCC
** *
5509532 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--AAACTTAACTTGAAAAGTAGATT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATT-AAAAG-AGA-T
*
5509595 TTGAAAATACCTCGATATGTGACTG
63 TTGAAAATACCTCGACATGTGACTG
* *
5509620 AAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATT-AAA-AGA-CT-
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAGAGATTTG
* * ***
5509680 CAACTCAACTCTCG-CA---GAAAA
66 AAAAT--AC-CTCGACATGTGACTG
* * *
5509701 AAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAA-A-AAA--AACAGA-AAT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTGAAAAACAGAAATTAAAAGAGATT
* * *
5509761 TGAAAATAGCTC-AGCACGTGAGC-C
64 TGAAAATACCTCGA-CATGTGA-CTG
** *
5509785 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--AAACTTAACTTGAAAAGTAGATT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATT-AAAAG-AGA-T
*
5509848 TTGAAAATACCTCGATATGTGACTG
63 TTGAAAATACCTCGACATGTGACTG
* * *
5509873 AAGGTTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTGAAAAACAGAAATT-AAA-AGA-CT-
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAGAGATTTG
* * ***
5509933 CAACTCAACTCTCG-CA---GAAAA
66 AAAAT--AC-CTCGACATGTGACTG
* * *
5509954 AAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG-AAAA-A-AAA--AACAGA-AAT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTGAAAAACAGAAATTAAAAGAGATT
* * *
5510013 TGAAAATAGCTCAG-CACGTGAGC-C
64 TGAAAATACCTC-GACATGTGA-CTG
* *
5510037 AAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTG-AAAACA-AAATCTGAAAAACAGAT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAAT-T--AAAAGAGA-
*
5510099 TTTGAAAATACCTCGACATGTGACCCG
62 TTTGAAAATACCTCGACATGTGA-CTG
5510126 -AGGCTCAACTCACCTCTCGCA
1 AAGGCTCAACTCACCTCTCGCA
5510147 GAAATTACAA
Statistics
Matches: 411, Mismatches: 61, Indels: 110
0.71 0.10 0.19
Matches are distributed among these distances:
79 3 0.01
80 23 0.06
81 78 0.19
82 27 0.07
83 43 0.10
84 56 0.14
85 18 0.04
86 5 0.01
87 22 0.05
88 119 0.29
89 17 0.04
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (87 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAGAGATTTG
AAAATACCTCGACATGTGACTG
Found at i:5509725 original size:81 final size:77
Alignment explanation
Indices: 5509625--5510079 Score: 258
Period size: 81 Copynumber: 5.5 Consensus size: 77
5509615 GACTGAAGGT
5509625 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAA-ACT-AACTCAACT
5509690 CTCGCAGAAAAAAAGC
64 CT-G-AGAAAAAAAGC
* *
5509706 TCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAAAAAAAACAGAAATTGAAAA-TAG
1 TCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTG------AAAAACAGAAATTAAAAACTAA
* * ** *
5509770 CTCAGCACGTGAG--CCAAGGC
57 CTCAACTC-TGAGAAAAAAAGC
* * *
5509790 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA---AAC-AG-AAATTA-A-----AAAC
* * * * *** * *
5509855 TACCTCGA-TATGTGACTGAAGGT
54 TAACTCAACTCTGAGAAAAAAAGC
*
5509878 TCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAA-ACT-AACTCAACT
5509943 CTCGCAGAAAAAAAGC
64 CT-G-AGAAAAAAAGC
* *
5509959 TCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAAAAAAACAGAAATTGAAAA-TAGC
1 TCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTG-----AAAAACAGAAATTAAAAACTAAC
* * ** *
5510023 TCAGCACGTGAG--CCAAGGC
58 TCAACTC-TGAGAAAAAAAGC
*
5510042 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
5510080 CAAAATCTGA
Statistics
Matches: 295, Mismatches: 41, Indels: 82
0.71 0.10 0.20
Matches are distributed among these distances:
75 4 0.01
76 5 0.02
77 2 0.01
78 5 0.02
79 5 0.02
80 8 0.03
81 63 0.21
82 16 0.05
83 32 0.11
84 46 0.16
85 2 0.01
86 13 0.04
87 22 0.07
88 39 0.13
89 17 0.06
90 16 0.05
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (77 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAACTAACTCAACTCT
GAGAAAAAAAGC
Found at i:5509944 original size:253 final size:252
Alignment explanation
Indices: 5509496--5510146 Score: 1164
Period size: 253 Copynumber: 2.6 Consensus size: 252
5509486 AACAGACATT
5509496 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5509561 TTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
66 TTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
5509626 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
131 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
5509691 TCGCAGAAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAAA
196 TCGCAGAAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG-AAAAA
5509749 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
5509814 TTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
66 TTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
*
5509879 CAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
131 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
5509944 TCGCAGAAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAA
196 TCGCAGAAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAA
*
5510001 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * ** * *
5510066 TTGA-TTTTTGAAAAC-AAAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCG-AG
66 TTGATTTTTTG-AAACTTAACT-TGAAAAGTAGATTTTGAAAATACCTCGATATGTGA-CTGAAG
*
5510128 GCTCAACTCACCTCTCGCA
128 GTTCAACTCACCTCTCGCA
5510147 GAAATTACAA
Statistics
Matches: 385, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
251 9 0.02
252 128 0.33
253 248 0.64
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (252 bp):
AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAACTTAACTTGAAAAGTAGATTTTGAAAATACCTCGATATGTGACTGAAGGTT
CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
TCGCAGAAAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAA
Found at i:5510345 original size:72 final size:72
Alignment explanation
Indices: 5510255--5510703 Score: 374
Period size: 72 Copynumber: 6.3 Consensus size: 72
5510245 TTTTTTTTTG
* **
5510255 TTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
5510320 AGTTGAA
66 AGTTGAA
* **
5510327 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
*
5510392 AGTTGATT
66 AGTTGA-A
* *
5510400 TTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATAT
1 TTTTGAAA-ACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
*
5510465 GAGCTG-A
65 GAGTTGAA
* * * *** * ** * * *
5510472 TTTTGAAAAAGTAGAAATT-AAAAGGTTCAACC-CA-C--CTCTCGCAATATGAGTTGA-TTCTT
1 TTTTG-AAAA-CAGAAATTGAAAA---T--ACCTCAGCGTGTCTTG-AGGCTCAACTCACCTCTC
*
5510531 G-AACA--ACG-T-AA
58 GCAATATGA-GTTGAA
* * *
5510542 -ATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
5510606 AGTTGAA
66 AGTTGAA
* * * ** *
5510613 -ATT-AAAACACAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATAT
1 TTTTGAAAACA-GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT
5510676 GAGTTG-A
65 GAGTTGAA
*
5510683 TTTTGAAAACAAAAATT-AAAA
1 TTTTGAAAACAGAAATTGAAAA
5510704 GGCTTAACTC
Statistics
Matches: 302, Mismatches: 49, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
63 3 0.01
64 2 0.01
65 2 0.01
66 5 0.02
67 13 0.04
68 11 0.04
69 4 0.01
70 16 0.05
71 69 0.23
72 84 0.28
73 25 0.08
74 61 0.20
75 2 0.01
76 2 0.01
77 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (72 bp):
TTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGAA
Found at i:5510544 original size:54 final size:54
Alignment explanation
Indices: 5510444--5510549 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5510434 GTCTTGAGGC
*
5510444 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5510498 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5510550 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5510656 original size:71 final size:71
Alignment explanation
Indices: 5510543--5510703 Score: 236
Period size: 71 Copynumber: 2.3 Consensus size: 71
5510533 ACAACGTAAA
* * *
5510543 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
*
5510608 TTGAAA
66 TTGAAT
* *
5510614 TT-AAAACACAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAAAACA-AAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
5510678 GTTGATT
65 GTTGAAT
5510685 TTGAAAACAAAAATT-AAAA
1 TTGAAAACAAAAATTGAAAA
5510704 GGCTTAACTC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
70 10 0.12
71 66 0.80
72 6 0.07
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (71 bp):
TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGAAT
Found at i:5510851 original size:71 final size:71
Alignment explanation
Indices: 5510703--5510965 Score: 347
Period size: 70 Copynumber: 3.7 Consensus size: 71
5510693 AAAAATTAAA
* * * * *
5510703 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACT-AAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
5510765 GCCCCG
66 GCCCCG
* *
5510771 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
* **
5510836 GTCTTG
66 GCCCCG
* * *
5510842 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
5510905 TGCCCCG
65 TGCCCCG
*
5510912 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
5510966 GGCTTAACTC
Statistics
Matches: 166, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
68 26 0.16
69 10 0.06
70 66 0.40
71 47 0.28
72 14 0.08
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GCCCCG
Found at i:5511113 original size:70 final size:70
Alignment explanation
Indices: 5511000--5511430 Score: 306
Period size: 72 Copynumber: 6.1 Consensus size: 70
5510990 GAGTCAACTA
**
5511000 AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
1 AAAATACCTCAACGTGTCTTGAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTGAAAACAA
*
5511065 CAATT-
65 AAATTG
5511070 AAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTTGAAAGA
1 AAAATACCTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTG-A-TTTTGAAA-A
5511135 CAAAAATTG
62 CAAAAATTG
* * *
5511144 AAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAA-AG
1 AAAATACCTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTGAAAACA-
5511208 TAGAAATT-
64 -A-AAATTG
*** *** * *** * ** * * * * **
5511216 AAAA-GGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTG-AACA--ACG-T-AAATTGAAAA
1 AAAATACCTCAA--CGTGTCTTG-AGGCTCAACTCACTCTCGCAATATGA-GTTGATTTTGAAAA
*
5511275 CAGAAATTG
62 CAAAAATTG
* * * ** *
5511284 AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACA
1 AAAATACCTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTGAAA-ACA
5511349 AAAATTG
64 AAAATTG
* * ** *
5511356 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
1 AAAATACCTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTG-AAAACA
5511421 AAAATT-
64 AAAATTG
5511427 AAAA
1 AAAA
5511431 GGCTTAACTC
Statistics
Matches: 283, Mismatches: 55, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
66 5 0.02
67 12 0.04
68 7 0.02
69 12 0.04
70 54 0.19
71 19 0.07
72 94 0.33
73 27 0.10
74 53 0.19
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (70 bp):
AAAATACCTCAACGTGTCTTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTGAAAACAAA
AATTG
Found at i:5511119 original size:179 final size:182
Alignment explanation
Indices: 5510819--5511147 Score: 490
Period size: 179 Copynumber: 1.8 Consensus size: 182
5510809 AAACAAAAAT
**
5510819 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACA
1 TAAAAATACCTCAACGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACA
*
5510884 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG-A-TTT
66 AAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAATTTT
5510947 TGAAAAACAAAAATT-AAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAC
131 TGAAAAACAAAAATTGAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAC
*
5510998 TAAAAATACCTCAACGTGTCCCGAGGCTCAACTCA-CTTCTCGCAATATGAGTTGATTTTGAAA-
1 TAAAAATACCTCAACGTGTCCCGAGGCTCAACTCATC-TCTCGCAATATGAGTTGA--TTAAAAC
* * ** * *
5511061 ACAACAATT-AAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAAT
63 ACAAAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAT
*
5511125 TTTTGAAAGACAAAAATTGAAAA
128 TTTTGAAAAACAAAAATTGAAAA
5511148 TACCTCAGCA
Statistics
Matches: 133, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
178 1 0.01
179 97 0.73
180 9 0.07
181 22 0.17
182 4 0.03
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (182 bp):
TAAAAATACCTCAACGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACA
AAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAATTTT
TGAAAAACAAAAATTGAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAC
Found at i:5511179 original size:725 final size:728
Alignment explanation
Indices: 5510273--5511854 Score: 2924
Period size: 725 Copynumber: 2.2 Consensus size: 728
5510263 ACAGAAATTG
** *
5510273 AAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA
1 AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG-ATTTTGAAAACA
* * * ** * *
5510338 GA-AATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
65 -ACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTT
5510402 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
129 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
5510467 GCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTG
194 GCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTG
5510532 AACAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCT
259 AACAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCT
5510597 CGCAATATGAGTTGAAATTAAAACAC-AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACT
324 CGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACT
5510661 CACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAA
389 CACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAA
5510725 TATGAGTCAATTTAAAACATAAACT-AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTC
454 TATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTC
5510789 GCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCA
519 GCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCA
5510854 TCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCA
584 TCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCA
5510919 ACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCG
649 ACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAC-AAAATTAAAAGGCTTAACTCACCTCTCG
5510984 CAATATGAGTCAACTA
713 CAATATGAGTCAACTA
5511000 AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
1 AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
5511065 CAATT-AAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTT
66 CAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTT
5511129 GAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGC
131 GAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGC
5511194 TGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAA
196 TGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAA
5511259 CAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCG
261 CAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCG
5511324 CAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCA
326 CAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCA
5511389 CCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATA
391 CCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATA
* * * *
5511454 TGAGTCAATTTAAAACATAGACTAAAAATACCTTAGCGTGTCCCGAGGCTCAACTCACTTTTCGC
456 TGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGC
5511519 AATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATC
521 AATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATC
*
5511584 TCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
586 TCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAAC
* *
5511649 TCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAGGCTTAACTCACTTCTTGCAA
651 TCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAA
5511714 TATGAGTCAACTA
716 TATGAGTCAACTA
*
5511727 AAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
1 AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
*
5511792 CAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCACAATATGAGTTG-ATTTT
66 CAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTT
5511855 CCTTGAAAAG
Statistics
Matches: 832, Mismatches: 18, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
725 273 0.33
726 81 0.10
727 226 0.27
728 252 0.30
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (728 bp):
AAAATACCTCAACGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAA
CAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTT
GAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGC
TGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAA
CAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCA
CCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATA
TGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGC
AATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATC
TCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAAC
TCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAA
TATGAGTCAACTA
Found at i:5511269 original size:54 final size:54
Alignment explanation
Indices: 5511169--5511274 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5511159 GTCTTGAGGC
*
5511169 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5511223 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5511275 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5511525 original size:122 final size:124
Alignment explanation
Indices: 5511305--5511800 Score: 402
Period size: 108 Copynumber: 4.0 Consensus size: 124
5511295 GCGTGACCTG
* *
5511305 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
5511370 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * * * *
5511430 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAGACTAAAAATACCTTAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * * *
5511492 TGTCCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATT-AAA
** * * * * * * * *
5511552 ATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAAT
1 A-GGCTCAAC---TC---A-CCTC-TCGCA-ATAT-G-AGT-TGA---AATTAAAACACAAAAAC
* *
5511617 TGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-
50 TAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAC
5511681 ACAAAATTAAA
115 A-AAAATTAAA
* * *
5511692 AGGCTTAACTCACTTCTTGCAATATGA---G----T------C---AACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * * *
5511741 TGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAACAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
5511800 A
1 A
5511801 ATACCTCAAC
Statistics
Matches: 298, Mismatches: 51, Indels: 61
0.73 0.12 0.15
Matches are distributed among these distances:
108 70 0.23
109 1 0.00
111 1 0.00
117 1 0.00
121 12 0.04
122 63 0.21
123 12 0.04
124 2 0.01
125 27 0.09
126 2 0.01
128 1 0.00
129 2 0.01
130 5 0.02
131 5 0.02
132 4 0.01
133 2 0.01
134 1 0.00
136 3 0.01
139 5 0.02
140 11 0.04
141 68 0.23
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:5511573 original size:71 final size:71
Alignment explanation
Indices: 5511430--5511692 Score: 320
Period size: 71 Copynumber: 3.7 Consensus size: 71
5511420 AAAAATTAAA
* * * * * * *
5511430 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAGACTAAAAATACCTTAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
*
5511493 GTCCCG
66 GTCCTG
* * *
5511499 AGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
*
5511564 GTCTTG
66 GTCCTG
* * *
5511570 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
*
5511633 TGCCCTG
65 TGTCCTG
*
5511640 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-ACAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACA-AAAATTAAAA
5511693 GGCTTAACTC
Statistics
Matches: 164, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
69 30 0.18
70 63 0.38
71 66 0.40
72 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GTCCTG
Found at i:5511662 original size:141 final size:140
Alignment explanation
Indices: 5511430--5511692 Score: 368
Period size: 141 Copynumber: 1.9 Consensus size: 140
5511420 AAAAATTAAA
* * * * *
5511430 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAGACTAAAAATACCTTAGCGTGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAGCGTGT
* * *
5511495 CCCGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAAATACCTC
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAC-AAAATTAAAAATACCTC
5511559 AACGTGTCTTG
130 AACGTGTCTTG
* ** * *
5511570 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAA-ACAAAAACTAAAAATACCTCAGCGTG
5511635 -CCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAA
65 TCCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAA
5511693 GGCTTAACTC
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
140 36 0.34
141 66 0.62
142 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (140 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTAAAAACAAAAACTAAAAATACCTCAGCGTGT
CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAATACCTCA
ACGTGTCTTG
Found at i:5516863 original size:12 final size:12
Alignment explanation
Indices: 5516843--5516878 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5516833 TGGGATATGC
*
5516843 AATGTATGAATG
1 AATGCATGAATG
5516855 AATGCATGAATG
1 AATGCATGAATG
5516867 AATGCATGAATG
1 AATGCATGAATG
5516879 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5519489 original size:34 final size:32
Alignment explanation
Indices: 5519394--5519492 Score: 118
Period size: 34 Copynumber: 3.1 Consensus size: 32
5519384 GGTGGCTAGG
*
5519394 TTTTTT-TATTTTTTTT-GGTTA-GGTTTTTC
1 TTTTTTCTTTTTTTTTTGGGTTAGGGTTTTTC
5519423 TTTTTTCTTTTTTTTTTTGGGGGTTA-GGTTTTTC
1 TTTTTTC-TTTTTTTTTT--GGGTTAGGGTTTTTC
5519457 TTTTTTCTTTTTTTTTTAGGGTTAGGGTTTTT-
1 TTTTTTCTTTTTTTTTT-GGGTTAGGGTTTTTC
5519489 TTTT
1 TTTT
5519493 GAGAAGGCTT
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
29 6 0.10
31 9 0.15
32 10 0.16
33 17 0.27
34 20 0.32
ACGTcount: A:0.05, C:0.04, G:0.17, T:0.74
Consensus pattern (32 bp):
TTTTTTCTTTTTTTTTTGGGTTAGGGTTTTTC
Found at i:5520211 original size:17 final size:18
Alignment explanation
Indices: 5520191--5520224 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5520181 AAAAATTTTA
5520191 AAATT-TTAAAAATAAAT
1 AAATTCTTAAAAATAAAT
5520208 AAATTCTTAAAAATAAA
1 AAATTCTTAAAAATAAA
5520225 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTCTTAAAAATAAAT
Found at i:5521617 original size:22 final size:22
Alignment explanation
Indices: 5521589--5521638 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
5521579 CTCAGGTTAC
5521589 ATGTTAGTCACTTATGTTTGAA
1 ATGTTAGTCACTTATGTTTGAA
5521611 ATGTTAGTCACTTATGTTTGAA
1 ATGTTAGTCACTTATGTTTGAA
5521633 ATGTTA
1 ATGTTA
5521639 CGTTTTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (22 bp):
ATGTTAGTCACTTATGTTTGAA
Found at i:5524403 original size:27 final size:27
Alignment explanation
Indices: 5524343--5524429 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
5524333 GTAATGCAAA
* *
5524343 AATCTAACCGTTACAATATGGTCGTTGG
1 AATCTGACCGTTACAATATGCT-GTTGG
* *
5524371 GATCTGACCATTACAATATGCTGTTGG
1 AATCTGACCGTTACAATATGCTGTTGG
**
5524398 AATCTGACCGTTACAATATGCCATTGG
1 AATCTGACCGTTACAATATGCTGTTGG
5524425 AATCT
1 AATCT
5524430 AGTCGTTGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 33 0.65
28 18 0.35
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (27 bp):
AATCTGACCGTTACAATATGCTGTTGG
Found at i:5537210 original size:49 final size:49
Alignment explanation
Indices: 5537105--5537210 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 49
5537095 GGGGAGCATG
* * * *
5537105 AGCGTGTGCGATTACACGGGTAAATTAGGTAGGCCGTGTGGAGCACACG
1 AGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGTGGAGCACACA
* * *
5537154 GGTGTGTGCAATTACACGGGCAAATCAGGTAGGTCGTGTGG-GACACACA
1 AGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGTGGAG-CACACA
5537203 AGCGTGTG
1 AGCGTGTG
5537211 AAATCACATA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 1 0.02
49 46 0.98
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.21
Consensus pattern (49 bp):
AGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGTGGAGCACACA
Found at i:5538610 original size:31 final size:31
Alignment explanation
Indices: 5538569--5538627 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5538559 AAGGTCACTA
*
5538569 AACTATTTGAAAGTTTTCATTTAAGTCATTG
1 AACTAGTTGAAAGTTTTCATTTAAGTCATTG
*
5538600 AACTAGTTGAAAGTTTTTATTTAAGTCA
1 AACTAGTTGAAAGTTTTCATTTAAGTCA
5538628 CTGGACTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (31 bp):
AACTAGTTGAAAGTTTTCATTTAAGTCATTG
Found at i:5540336 original size:243 final size:243
Alignment explanation
Indices: 5539904--5540395 Score: 894
Period size: 243 Copynumber: 2.0 Consensus size: 243
5539894 TTCCTCATCC
5539904 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
* *
5539969 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTATCATTCTCCTTGTAGGTGCGTCGGA
* * *
5540034 AAGGATCTCCCCGAAACATTTTATTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
131 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
*
5540099 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCTCCATCCACT
196 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
*
5540147 GGAATGTCCAAATCCCATACCCTGAAGATATCCGCTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
5540212 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTATCATTCTCCTTGTAGGTGCGTCGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTATCATTCTCCTTGTAGGTGCGTCGGA
* *
5540277 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCTGCTGGGTACCAGTCCTC
131 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
*
5540342 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTTTCTCCATCCACT
196 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
5540390 GGAATG
1 GGAATG
5540396 ACAAGAAGAT
Statistics
Matches: 239, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 239 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (243 bp):
GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTATCATTCTCCTTGTAGGTGCGTCGGA
AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
Found at i:5544540 original size:31 final size:31
Alignment explanation
Indices: 5544504--5544565 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5544494 ATACATAATT
*
5544504 AAAAATATAT-TAAAATAATTAATTAAAAATA
1 AAAAATATATATAAAAT-ACTAATTAAAAATA
* *
5544535 AAAAATATTTATAAAATACTAATTACAAATA
1 AAAAATATATATAAAATACTAATTAAAAATA
5544566 TTTAATGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAATATATATAAAATACTAATTAAAAATA
Found at i:5545017 original size:16 final size:16
Alignment explanation
Indices: 5544996--5545059 Score: 65
Period size: 16 Copynumber: 3.6 Consensus size: 16
5544986 TTACAAAAAG
5544996 AATACAAGAGAAATAT
1 AATACAAGAGAAATAT
5545012 AATACAAGATACACACGAAATAT
1 AATACAAG------A-GAAATAT
5545035 AATACAAGAGAAATAT
1 AATACAAGAGAAATAT
5545051 AATACAAGA
1 AATACAAGA
5545060 CACACACGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
16 24 0.59
17 1 0.02
22 1 0.02
23 15 0.37
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (16 bp):
AATACAAGAGAAATAT
Found at i:5545050 original size:39 final size:39
Alignment explanation
Indices: 5544996--5545070 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
5544986 TTACAAAAAG
*
5544996 AATACAAGAGAAATATAATACAAGATACACACGAAATAT
1 AATACAAGAGAAATATAATACAAGACACACACGAAATAT
5545035 AATACAAGAGAAATATAATACAAGACACACACGAAA
1 AATACAAGAGAAATATAATACAAGACACACACGAAA
5545071 ATCAGTAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.60, C:0.15, G:0.11, T:0.15
Consensus pattern (39 bp):
AATACAAGAGAAATATAATACAAGACACACACGAAATAT
Found at i:5545070 original size:23 final size:22
Alignment explanation
Indices: 5545005--5545070 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
5544995 GAATACAAGA
5545005 GAAATATAATACAAGATACACAC
1 GAAATATAATACAAGA-ACACAC
5545028 GAAATATAATACAAG-----A-
1 GAAATATAATACAAGAACACAC
5545044 GAAATATAATACAAGACACACAC
1 GAAATATAATACAAGA-ACACAC
5545067 GAAA
1 GAAA
5545071 ATCAGTAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 15 0.42
17 1 0.03
22 1 0.03
23 19 0.53
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (22 bp):
GAAATATAATACAAGAACACAC
Found at i:5545974 original size:37 final size:37
Alignment explanation
Indices: 5545927--5545997 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
5545917 ATATTATCAT
*
5545927 TATTAATATTATTC-TTGCTATTATTGTTACTATTAGA
1 TATTAATATTA-TCATTACTATTATTGTTACTATTAGA
* * *
5545964 TATTATTATTATCATTACTATTTTTGTTATTATT
1 TATTAATATTATCATTACTATTATTGTTACTATT
5545998 TTTATTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 27 0.93
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (37 bp):
TATTAATATTATCATTACTATTATTGTTACTATTAGA
Found at i:5545995 original size:21 final size:21
Alignment explanation
Indices: 5545969--5546044 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 21
5545959 TTAGATATTA
5545969 TTATTATCATTACTATTTTTG
1 TTATTATCATTACTATTTTTG
* *
5545990 TTATTATTTTTATTACTATTTCTG
1 TTATTA---TCATTACTATTTTTG
** *
5546014 TTATTATTTTTACTATTATT-
1 TTATTATCATTACTATTTTTG
*
5546034 TTACTATCATT
1 TTATTATCATT
5546045 TTTTTTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 8 0.18
21 17 0.39
24 19 0.43
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (21 bp):
TTATTATCATTACTATTTTTG
Found at i:5546004 original size:24 final size:24
Alignment explanation
Indices: 5545966--5546035 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
5545956 CTATTAGATA
* *
5545966 TTATTATTATCATTACTATTTTTG
1 TTATTATTTTTATTACTATTTTTG
*
5545990 TTATTATTTTTATTACTATTTCTG
1 TTATTATTTTTATTACTATTTTTG
* *
5546014 TTATTATTTTTACTATTATTTT
1 TTATTATTTTTATTACTATTTT
5546036 ACTATCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (24 bp):
TTATTATTTTTATTACTATTTTTG
Found at i:5546748 original size:35 final size:35
Alignment explanation
Indices: 5546704--5546864 Score: 200
Period size: 35 Copynumber: 4.6 Consensus size: 35
5546694 TCCTTATTGA
*
5546704 AATACCATACCTACATTTCACAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* * **
5546739 AATGCCATACCTAC-GTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* *
5546773 AATATCATACCTACGTTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* *
5546808 GATACCATACCTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* *
5546843 GATACCATACCTACGTTTCACA
1 AATACCATACCTACATTTCACA
5546865 CTTTGCCATG
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
33 3 0.03
34 24 0.22
35 82 0.75
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5546820 original size:69 final size:70
Alignment explanation
Indices: 5546704--5546864 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 70
5546694 TCCTTATTGA
* * * **
5546704 AATACCATACCTACATTTCACAACTCGGTATGGGAAATGCCATACCTAC-GTTCTTAACTCAGTA
1 AATACCATACCTACGTTTCACAACTCAGTATGGGAAATACCATACCTACAGTTCACAACTCAGTA
5546768 TGGAT
66 TGGAT
* * * *
5546773 AATATCATACCTACGTTTCACAACTCAGTAT-GGATGATACCATACCTACATTTCACAACTCGGT
1 AATACCATACCTACGTTTCACAACTCAGTATGGGA-AATACCATACCTACAGTTCACAACTCAGT
5546837 ATGGAT
65 ATGGAT
*
5546843 GATACCATACCTACGTTTCACA
1 AATACCATACCTACGTTTCACA
5546865 CTTTGCCATG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
68 3 0.04
69 40 0.51
70 36 0.46
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (70 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGGAAATACCATACCTACAGTTCACAACTCAGTA
TGGAT
Found at i:5549152 original size:125 final size:126
Alignment explanation
Indices: 5548891--5549177 Score: 310
Period size: 125 Copynumber: 2.3 Consensus size: 126
5548881 TTGGAAGTTT
* * **
5548891 GAGAGATCGTGCCCAATCGTG-TAGGGTTTTGATTTTTTACATTCAACTAAAATATGGAATACCC
1 GAGAAATCGTGCCCAATCGTGCT-GGGTTTCGA-TTTTTACATTCAACTAAAATACAGAATACCC
* * * * ** *
5548955 TTGTGAAATTTCGTCCACGTTTTCTTAAATTAAAACGAGGCAATATTTTGTGTTTGGGAGTTT
64 TTGTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTTGGAAAATC
* * * * *
5549018 GAGAGATCGTGCCCAATCATGCTGGGTTTCGATTTTT-CATTCGAC-AAAAGTACATAATATCCT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTACATTCAACTAAAA-TACAGAATACCCT
* * * * *
5549081 TTTGAAATTTCATCTATGTTTTCTTAAATTAAAATGAGGCAATATTCTGTATTTGTAAAATC
65 TGTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTTGGAAAATC
* * *
5549143 GATAAATCGTGCCCAATCGTGCTAGGTTGCGATTT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
5549178 ATCGTTTGGC
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
124 4 0.03
125 96 0.72
126 5 0.04
127 28 0.21
128 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (126 bp):
GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTACATTCAACTAAAATACAGAATACCCTT
GTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTTGGAAAATC
Found at i:5556667 original size:19 final size:19
Alignment explanation
Indices: 5556612--5556875 Score: 64
Period size: 20 Copynumber: 13.4 Consensus size: 19
5556602 ATATTTTTTC
*
5556612 ATAAAAATATTTTAAAAATT
1 ATAAAAAT-TATTAAAAATT
** ***
5556632 ATAAAAAAAAAGGAAAATT
1 ATAAAAATTATTAAAAATT
5556651 ATAAAAATTATTAAAAATT
1 ATAAAAATTATTAAAAATT
* * *
5556670 A-AAATATTTTTTTAAAATGCT
1 ATAAA-AATTATTAAAAAT--T
* * * *
5556691 ATTAAAATTAATATATACTT
1 ATAAAAATTATTA-AAAATT
* *
5556711 ATAAATATTATTAAAAAAT
1 ATAAAAATTATTAAAAATT
* *
5556730 CTAATAAAAT-TTAATAAATT
1 ATAA-AAATTATTAA-AAATT
5556750 ATAAAAAATTCA-TAAAAA-T
1 AT-AAAAATT-ATTAAAAATT
*
5556769 ATTTAAAATGTCA-TAAAAACTT
1 A-TAAAAAT-T-ATTAAAAA-TT
* *
5556791 -TTAAAATTCTTAAAACAATT
1 ATAAAAATTATT-AAA-AATT
*
5556811 ATAATAAATCATTAAAAA-T
1 ATAA-AAATTATTAAAAATT
*
5556830 ACTTAAAA-TATT-AAAATT
1 A-TAAAAATTATTAAAAATT
5556848 GATATAAACA-TA-TAAAAATT
1 -ATA-AAA-ATTATTAAAAATT
5556868 ATCAAAAA
1 AT-AAAAA
5556876 AATCATCAAA
Statistics
Matches: 177, Mismatches: 41, Indels: 54
0.65 0.15 0.20
Matches are distributed among these distances:
17 4 0.02
18 9 0.05
19 65 0.37
20 69 0.39
21 18 0.10
22 12 0.07
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATTAAAAATT
Found at i:5556686 original size:29 final size:29
Alignment explanation
Indices: 5556649--5556727 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
5556639 AAAAGGAAAA
**
5556649 TTATAAAAATTATTAAAAATTAAAATATTT
1 TTAT-AAAATTATTAAAAATTAAAATATAC
* *
5556679 TTTTAAAATGCTATT-AAAATTAATATATAC
1 TTATAAAAT--TATTAAAAATTAAAATATAC
5556709 TTATAAATATTATTAAAAA
1 TTATAAA-ATTATTAAAAA
5556728 ATCTAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
29 9 0.22
30 25 0.62
31 6 0.15
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (29 bp):
TTATAAAATTATTAAAAATTAAAATATAC
Found at i:5556757 original size:30 final size:31
Alignment explanation
Indices: 5556717--5556774 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
5556707 ACTTATAAAT
*
5556717 ATTATTAAAAAATC-TAATAAA-ATTTAATAA
1 ATTATAAAAAAATCATAA-AAATATTTAATAA
*
5556747 ATTATAAAAAATTCATAAAAATATTTAA
1 ATTATAAAAAAATCATAAAAATATTTAA
5556775 AATGTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTATAAAAAAATCATAAAAATATTTAATAA
Found at i:5557620 original size:19 final size:18
Alignment explanation
Indices: 5557560--5557656 Score: 67
Period size: 19 Copynumber: 5.2 Consensus size: 18
5557550 TTTAAATACG
* *
5557560 TTTTATTAATTTTATAAAA
1 TTTTA-TAATATTATTAAA
5557579 TTTTATAAT-TTATTAACA
1 TTTTATAATATTATTAA-A
*
5557597 TTTTTATAATATTATATTAA
1 -TTTTATAATATTAT-TAAA
5557617 TTTTAATAATATT-TTAATA
1 TTTT-ATAATATTATTAA-A
*
5557636 TTTAATAAT-TT-TTATAA
1 TTTTATAATATTATTA-AA
5557653 TTTT
1 TTTT
5557657 GTCCTGATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
17 15 0.23
18 13 0.20
19 23 0.35
20 13 0.20
21 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAATATTATTAAA
Found at i:5557623 original size:17 final size:18
Alignment explanation
Indices: 5557603--5557644 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5557593 AACATTTTTA
*
5557603 TAATATTATATTAAT-TT
1 TAATAATATATTAATATT
*
5557620 TAATAATATTTTAATATT
1 TAATAATATATTAATATT
5557638 TAATAAT
1 TAATAAT
5557645 TTTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATAATATATTAATATT
Found at i:5557639 original size:49 final size:46
Alignment explanation
Indices: 5557563--5557653 Score: 121
Period size: 49 Copynumber: 1.9 Consensus size: 46
5557553 AAATACGTTT
*
5557563 TATTAATTTTATAAAATTTTATAATTTATTAACATTTTTATAATATTA
1 TATTAATTTTATAAAATTTTATAATTTAAT-A-ATTTTTATAATATTA
*
5557611 TATTAATTTTAATAATATTTTA-ATATTTAATAATTTTTATAAT
1 TATTAATTTT-ATAAAATTTTATA-ATTTAATAATTTTTATAAT
5557654 TTTGTCCTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 11 0.28
48 12 0.31
49 16 0.41
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (46 bp):
TATTAATTTTATAAAATTTTATAATTTAATAATTTTTATAATATTA
Found at i:5557648 original size:17 final size:17
Alignment explanation
Indices: 5557603--5557656 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
5557593 AACATTTTTA
* *
5557603 TAATATTATATTAATTT
1 TAATAATATTTTAATTT
5557620 TAATAATATTTTAATATT
1 TAATAATATTTTAAT-TT
*
5557638 TAATAATTTTTATAATTT
1 TAATAATATTT-TAATTT
5557656 T
1 T
5557657 GTCCTGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.41
18 15 0.47
19 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATAATATTTTAATTT
Found at i:5557649 original size:10 final size:10
Alignment explanation
Indices: 5557459--5557656 Score: 84
Period size: 10 Copynumber: 20.4 Consensus size: 10
5557449 AATTTTAAGT
5557459 TTTTTAATAA
1 TTTTTAATAA
*
5557469 CTTTT-ATAA
1 TTTTTAATAA
*
5557478 TTTTCAATAA
1 TTTTTAATAA
*
5557488 TTTCTT-ATGA
1 TTT-TTAATAA
*
5557498 TTTTTTATAA
1 TTTTTAATAA
*
5557508 GTTTTTAAGAA
1 -TTTTTAATAA
5557519 TTTTT-AT-A
1 TTTTTAATAA
*
5557527 TGTTTTTATAA
1 T-TTTTAATAA
*
5557538 GATTTTAA-ATA
1 -TTTTTAATA-A
* *
5557549 TTTTAAATAC
1 TTTTTAATAA
* *
5557559 GTTTTATTAA
1 TTTTTAATAA
5557569 TTTTATAA-AA
1 TTTT-TAATAA
5557579 -TTTT-ATAA
1 TTTTTAATAA
*
5557587 TTTATTAA-CA
1 TTT-TTAATAA
5557597 TTTTT-ATAA
1 TTTTTAATAA
* *
5557606 TATTATATTAA
1 T-TTTTAATAA
5557617 -TTTTAATAA
1 TTTTTAATAA
5557626 TATTTTAAT-A
1 T-TTTTAATAA
5557636 --TTTAATAA
1 TTTTTAATAA
5557644 TTTTT-ATAA
1 TTTTTAATAA
5557653 TTTT
1 TTTT
5557657 GTCCTGATAT
Statistics
Matches: 139, Mismatches: 26, Indels: 47
0.66 0.12 0.22
Matches are distributed among these distances:
7 7 0.05
8 7 0.05
9 38 0.27
10 57 0.41
11 30 0.22
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:5558823 original size:14 final size:13
Alignment explanation
Indices: 5558797--5558821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5558787 ATGTTTTGGG
5558797 TTTTTTTATTTTA
1 TTTTTTTATTTTA
5558810 TTTTTTTATTTT
1 TTTTTTTATTTT
5558822 TAAAAATTTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:5571105 original size:39 final size:39
Alignment explanation
Indices: 5571057--5571134 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
5571047 TGTGCCTTTT
* *
5571057 ATCCCATTTATATAAGCATTCTCATTACATTAAAGAGGG
1 ATCCCATTTATATAAACATTCTCATTACACTAAAGAGGG
* *
5571096 ATCCTATTTATATAAACATTCTCCTTACACTAAAGAGGG
1 ATCCCATTTATATAAACATTCTCATTACACTAAAGAGGG
5571135 GGATAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (39 bp):
ATCCCATTTATATAAACATTCTCATTACACTAAAGAGGG
Found at i:5571566 original size:21 final size:22
Alignment explanation
Indices: 5571528--5571568 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5571518 GCTAATGTGG
*
5571528 GATTCAAATTTAAGTTTTAACA
1 GATTCAAAATTAAGTTTTAACA
*
5571550 GATT-AAAATTAATTTTTAA
1 GATTCAAAATTAAGTTTTAA
5571569 TAATGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTCAAAATTAAGTTTTAACA
Found at i:5571665 original size:69 final size:69
Alignment explanation
Indices: 5571567--5571715 Score: 194
Period size: 69 Copynumber: 2.2 Consensus size: 69
5571557 ATTAATTTTT
* * * * * *
5571567 AATAATGAA-AAGTGAGT-TATGGGAGTATTCTCTAGTCAATTTGGGATTAAAATTGACTTTTTA
1 AATAATGAAGAAGTTA-TCTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTA
*
5571630 ATGAA
65 ATAAA
* *
5571635 TATAGTGAAGAAGTTATCTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTAA
1 AATAATGAAGAAGTTATCTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTAA
5571700 TAAA
66 TAAA
5571704 AATAATGAAGAA
1 AATAATGAAGAA
5571716 ATTGTCACTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
68 8 0.12
69 60 0.88
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (69 bp):
AATAATGAAGAAGTTATCTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTAA
TAAA
Found at i:5574972 original size:70 final size:68
Alignment explanation
Indices: 5574827--5575033 Score: 229
Period size: 70 Copynumber: 3.0 Consensus size: 68
5574817 TAAGGTAAAT
* * * * * * *
5574827 GTGAGATATTGGAGTGTTGTCTAGCCAATGTAGGATTAAAATTAATTTTTAATGAAAACAGTGAA
1 GTGAGCTATAGGAGTATTCTCTAGTCAATGTGGGATTAAAATTAATTTTTAATGAAAATAGTGAA
* *
5574892 TAC
66 GAA
* *
5574895 GTGAGCTAT-GAGAGTATAT-TTTAGTTAATGTGGGATTAAAATTAACTTTTTTAATGAAAATAG
1 GTGAGCTATAG-GAGTAT-TCTCTAGTCAATGTGGGATTAAAATTAA--TTTTTAATGAAAATAG
*
5574958 TAAAGAA
62 TGAAGAA
* *
5574965 GTTAGCTATAGGAGTATTCTCTAGTCAATGTGGGATTAAAATTAAATTTTTAATAAAAATAGTGA
1 GTGAGCTATAGGAGTATTCTCTAGTCAATGTGGGATTAAAATT-AATTTTTAATGAAAATAGTGA
5575030 AGAA
65 AGAA
5575034 ATTATCATTT
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
67 1 0.01
68 35 0.30
69 23 0.20
70 55 0.47
71 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.35
Consensus pattern (68 bp):
GTGAGCTATAGGAGTATTCTCTAGTCAATGTGGGATTAAAATTAATTTTTAATGAAAATAGTGAA
GAA
Found at i:5578553 original size:11 final size:11
Alignment explanation
Indices: 5578520--5578553 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5578510 GGCAAACAGT
5578520 AAAGAAATTTA
1 AAAGAAATTTA
*
5578531 AAA-AAGTTTA
1 AAAGAAATTTA
5578541 AAAGAAATTTA
1 AAAGAAATTTA
5578552 AA
1 AA
5578554 CATGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (11 bp):
AAAGAAATTTA
Found at i:5580427 original size:28 final size:29
Alignment explanation
Indices: 5580395--5580458 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
5580385 TTTAATTTTG
* *
5580395 TCAATTTTTTCA-ACTAAAATTGA-TAAGA
1 TCAATTTTCTCATACTAAAATCGATTAA-A
*
5580423 TCAATTTTCTCATATTAAAATCGATTAAA
1 TCAATTTTCTCATACTAAAATCGATTAAA
5580452 TCAATTT
1 TCAATTT
5580459 CAAAAACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 11 0.35
29 17 0.55
30 3 0.10
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (29 bp):
TCAATTTTCTCATACTAAAATCGATTAAA
Found at i:5596219 original size:44 final size:43
Alignment explanation
Indices: 5596114--5596228 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 43
5596104 CTGGCATTTC
* * *
5596114 GCCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTATA
1 GCCTGCTAGGCTCGAAGCCCGATATCATTTCACCAGCATTAAA
*
5596157 GCCTGCTAGGCCCGAAGCCCGATAAT-ATTATTCACCAGC-TTAAA
1 GCCTGCTAGGCTCGAAGCCCGAT-ATCA-T-TTCACCAGCATTAAA
* *
5596201 GCTTGCTAGGCTCAAAGCCCGAATATCA
1 GCCTGCTAGGCTCGAAGCCCG-ATATCA
5596229 CCATTATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
43 22 0.37
44 27 0.45
45 11 0.18
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
GCCTGCTAGGCTCGAAGCCCGATATCATTTCACCAGCATTAAA
Found at i:5596378 original size:28 final size:28
Alignment explanation
Indices: 5596347--5596418 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
5596337 TTGATATTTT
* *
5596347 GCACACTATGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
5596375 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
5596403 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
5596419 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:5599441 original size:43 final size:43
Alignment explanation
Indices: 5599393--5599509 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
5599383 GTTATCGATA
* * * *
5599393 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATGGGCATCGTAT
5599436 TGTGATTACGTGTAAGACCATGTCTGGGACATGGGCATCGTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATGGGCATCGTAT
* * *
5599479 TATGATTTCGTGTAAGACCCTGTCTGGGACA
1 TGTGATTACGTGTAAGACCATGTCTGGGACA
5599510 GTGGTATCGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATGTCTGGGACATGGGCATCGTAT
Found at i:5602758 original size:28 final size:27
Alignment explanation
Indices: 5602709--5602762 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5602699 ACATTTCGAA
*
5602709 ATCATTTCATAGCCAACAATCATACATT
1 ATCATATCATAGCCAACAATCA-ACATT
*
5602737 ATCATATCATAGTCAA-ATATCAACAT
1 ATCATATCATAGCCAACA-ATCAACAT
5602763 AAAGTCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (27 bp):
ATCATATCATAGCCAACAATCAACATT
Found at i:5604302 original size:42 final size:41
Alignment explanation
Indices: 5604190--5604307 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 41
5604180 GAAAAGATCG
** * * *
5604190 TACAATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAA
1 TACAATGCC-ATGTCCCAGACATGGTCTTACACGAAATAAAA
* *
5604232 TATCGATGCCATTGTCCCAGACAGGGTCTTACACGAAATAAAA
1 TA-CAATGCCA-TGTCCCAGACATGGTCTTACACGAAATAAAA
*
5604275 TACAATACCGATGTCCCAGACATGGTCTTACAC
1 TACAATGCC-ATGTCCCAGACATGGTCTTACAC
5604308 ATAAATCTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
TACAATGCCATGTCCCAGACATGGTCTTACACGAAATAAAA
Found at i:5605964 original size:125 final size:125
Alignment explanation
Indices: 5605630--5606027 Score: 444
Period size: 128 Copynumber: 3.2 Consensus size: 125
5605620 GGCCAAACAT
* * * * *
5605630 GAACTACCGTAGAAAAAAAGCATCCACGTGGGAGCTTTTTTCATAAATTTTGCTGACAGTGCACC
1 GAACTACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCAT-AATTTTGCTGACAATGCATC
* * * * *
5605695 CTACTTCAAGCGTTTTTGACACCATTTATTCAGAACTGTCTTCTCAAAATTATTTTTTTTTAG
65 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTA--TTTTTTTAG
* * * *
5605758 GAACTACTATAGAAAAATAA-CGTCCACTTAGGAGCTTTTTTCAATATTTTTGCTGACAATGCAT
1 GAACTACTGTAGAAAAA-AAGCGTCCACATGGGAGCTTTTTTC-ATAATTTTGCTGACAATGCAT
* * * * *
5605822 CCTGCATAAAGTGTTTTTGACACTATTTGTTCAAAACCATCTTCTTAAAATTATTTTTTTAG
64 CCTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTTAG
* * *
5605884 GAATTACTGTAGAAGAAGAGCGTCCACATGGGAG-TTTTTTCAGTAATTTTGCTGACAATGCATC
1 GAACTACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCA-TAATTTTGCTGACAATGCATC
* * * *
5605948 ATGCTTGAAGCATTTTTGACATTATCTTGTT-AGAACCGTCTTCTCAAAATTATTTTTTCT-G
65 CTGCTTAAAGCGTTTTTGACACTAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTTT-TAG
* *
5606009 AAACTACTCTAGAAAAAAA
1 GAACTACTGTAGAAAAAAA
5606028 AAGCAAAATC
Statistics
Matches: 225, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
124 1 0.00
125 86 0.38
126 41 0.18
128 93 0.41
129 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCATAATTTTGCTGACAATGCATCC
TGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTTAG
Found at i:5606147 original size:34 final size:35
Alignment explanation
Indices: 5606106--5606205 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 35
5606096 TTTAAAAAAA
* *
5606106 CTAAACCCTAATTTAATTAATTTTCTTTAAAA-CT
1 CTAAACCCTAATTTAATTAATTTTATTTAAAACCC
*
5606140 TTAAACCCTAATTTAACTT-A-TTTATTTAAAACCC
1 CTAAACCCTAATTTAA-TTAATTTTATTTAAAACCC
* *
5606174 CTAAAACCTAATTTAATTAATTTTTTTTAAAA
1 CTAAACCCTAATTTAATTAATTTTATTTAAAA
5606206 AAACTCTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 12 0.21
34 32 0.57
35 12 0.21
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (35 bp):
CTAAACCCTAATTTAATTAATTTTATTTAAAACCC
Found at i:5606285 original size:34 final size:33
Alignment explanation
Indices: 5606240--5606340 Score: 150
Period size: 34 Copynumber: 3.0 Consensus size: 33
5606230 TTAAAATTCT
5606240 ACCCTACACCTAAATTATTTTAACAAAACTTTAA
1 ACCCTA-ACCTAAATTATTTTAACAAAACTTTAA
**
5606274 ACCCTGAACCTAAATTATTTTAACAAAACCCT-A
1 ACCCT-AACCTAAATTATTTTAACAAAACTTTAA
5606307 ACCCTAACCCTAAATTATTTTAACAAAACTTTAA
1 ACCCTAA-CCTAAATTATTTTAACAAAACTTTAA
5606341 TCTTAAACCT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
32 2 0.03
33 28 0.47
34 29 0.48
35 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.31
Consensus pattern (33 bp):
ACCCTAACCTAAATTATTTTAACAAAACTTTAA
Found at i:5606319 original size:33 final size:34
Alignment explanation
Indices: 5606240--5606335 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 34
5606230 TTAAAATTCT
**
5606240 ACCCT-ACACCTAAATTATTTTAACAAAACTTTAA
1 ACCCTAAC-CCTAAATTATTTTAACAAAACCCTAA
5606274 ACCCTGAA-CCTAAATTATTTTAACAAAACCCT-A
1 ACCCT-AACCCTAAATTATTTTAACAAAACCCTAA
5606307 ACCCTAACCCTAAATTATTTTAACAAAAC
1 ACCCTAACCCTAAATTATTTTAACAAAAC
5606336 TTTAATCTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
32 2 0.04
33 27 0.47
34 27 0.47
36 1 0.02
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (34 bp):
ACCCTAACCCTAAATTATTTTAACAAAACCCTAA
Found at i:5614611 original size:17 final size:17
Alignment explanation
Indices: 5614585--5614617 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5614575 AAAGGAAAAA
5614585 AATGAATCTTAAAAACG
1 AATGAATCTTAAAAACG
*
5614602 AATGAGTCTTAAAAAC
1 AATGAATCTTAAAAAC
5614618 TTAATAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
AATGAATCTTAAAAACG
Found at i:5616434 original size:230 final size:230
Alignment explanation
Indices: 5616031--5616494 Score: 811
Period size: 230 Copynumber: 2.0 Consensus size: 230
5616021 GTCAACTGCT
*
5616031 ACTAAGATGTATTTATTCCCAAATGAACTAGGGAATGGGCCCATGAAATCGATACCCCAGACGTC
1 ACTAAGATGTATTTATTCCCAAATGAACTAGGGAATGGGCCCATGAAATCGATACCCCAAACGTC
*
5616096 AAATATTTCACATGAAAGCATATAATTTTGAGGCATTTCATCACGTTTAGATATGTTACCTGTCC
66 AAATATTTCACATGAAAGCATATAATTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
* * *
5616161 GTTGGCATTTGTCACATGAAGTAACACACCTGATAGCGTCTTTGAATAATGAAGGCCAATAAGAA
131 GTTGGCATTTGTCACATGAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
*
5616226 CCTGATTCAAGTACTTTGTGTGTGGTCTTAGTTCC
196 CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
* * *
5616261 ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATGGGCCTATGAAATCGATACCCCAAATGTC
1 ACTAAGATGTATTTATTCCCAAATGAACTAGGGAATGGGCCCATGAAATCGATACCCCAAACGTC
*
5616326 AAATATTTCACATGAAAGCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
66 AAATATTTCACATGAAAGCATATAATTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
* *
5616391 GTTGGCATTTGTCACATGAAGTAATATACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
131 GTTGGCATTTGTCACATGAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
*
5616456 CCTGATTCAAGTATTTTGTGTGCGGTCTTAGTTCC
196 CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
5616491 ACTA
1 ACTA
5616495 TAGTGTCCTC
Statistics
Matches: 221, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
230 221 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (230 bp):
ACTAAGATGTATTTATTCCCAAATGAACTAGGGAATGGGCCCATGAAATCGATACCCCAAACGTC
AAATATTTCACATGAAAGCATATAATTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
GTTGGCATTTGTCACATGAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
Found at i:5623140 original size:46 final size:44
Alignment explanation
Indices: 5623036--5623143 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5623026 TGTCTTTGAC
** * * *
5623036 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5623080 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5623126 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5623144 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5630519 original size:46 final size:44
Alignment explanation
Indices: 5630415--5630522 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5630405 TGTCTTTGAC
** * * *
5630415 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5630459 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5630505 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5630523 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5636287 original size:25 final size:25
Alignment explanation
Indices: 5636253--5636304 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
5636243 TTCTAGAAGA
* *
5636253 TTTAGTATTTATGAGTATAATATAT
1 TTTAGCATTTATGAGCATAATATAT
* *
5636278 TTTAGCATTTGTTAGCATAATATAT
1 TTTAGCATTTATGAGCATAATATAT
5636303 TT
1 TT
5636305 GACTTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTAGCATTTATGAGCATAATATAT
Found at i:5637995 original size:19 final size:19
Alignment explanation
Indices: 5637971--5638024 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
5637961 CAATCAAATT
*
5637971 ATAAAATTTAATATTTTTA
1 ATAAAATATAATATTTTTA
5637990 ATAAAATATAATATTTTTA
1 ATAAAATATAATATTTTTA
* *
5638009 ATTAAATAAAATATTT
1 ATAAAATATAATATTT
5638025 AAAATTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAAATATAATATTTTTA
Found at i:5638030 original size:19 final size:19
Alignment explanation
Indices: 5637993--5638032 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5637983 ATTTTTAATA
* **
5637993 AAATATAATATTTTTAATT
1 AAATAAAATATTTAAAATT
5638012 AAATAAAATATTTAAAATT
1 AAATAAAATATTTAAAATT
5638031 AA
1 AA
5638033 GTTTAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAAAATATTTAAAATT
Found at i:5639248 original size:8 final size:8
Alignment explanation
Indices: 5639237--5639265 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5639227 GATATATATA
5639237 TATATAGT
1 TATATAGT
5639245 TATATAGT
1 TATATAGT
5639253 TATATAGT
1 TATATAGT
5639261 TATAT
1 TATAT
5639266 GGTACATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
TATATAGT
Found at i:5641956 original size:2 final size:2
Alignment explanation
Indices: 5641949--5641976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5641939 ACTCCACTAA
5641949 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
5641977 AGGAGGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5643350 original size:29 final size:29
Alignment explanation
Indices: 5643317--5643404 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
5643307 AATGTATTTC
5643317 AATATTTTCAATAAATTTTATTATTAACA
1 AATATTTTCAATAAATTTTATTATTAACA
* *
5643346 AATA-TTTGAATTAAA---TA-T-TTAA-T
1 AATATTTTCAA-TAAATTTTATTATTAACA
*
5643369 AATATTTTCAA-CAATCTTTATTATTAACA
1 AATATTTTCAATAAAT-TTTATTATTAACA
5643398 AATATTT
1 AATATTT
5643405 GAATTAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 9 0.20
25 1 0.02
26 4 0.09
27 1 0.02
28 9 0.20
29 15 0.33
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (29 bp):
AATATTTTCAATAAATTTTATTATTAACA
Found at i:5643835 original size:19 final size:19
Alignment explanation
Indices: 5643811--5643880 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
5643801 ATTATATTTT
5643811 ATCATAAAAATTGTTAAAA
1 ATCATAAAAATTGTTAAAA
* *
5643830 ATCATAAAAAAATATTAAAA
1 ATCAT-AAAAATTGTTAAAA
* *
5643850 TTGATAAAAATTCG-TAAAA
1 ATCATAAAAATT-GTTAAAA
* *
5643869 CTTATAAAAATT
1 ATCATAAAAATT
5643881 ATAAAATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (19 bp):
ATCATAAAAATTGTTAAAA
Found at i:5643859 original size:10 final size:9
Alignment explanation
Indices: 5643814--5643886 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 9
5643804 ATATTTTATC
5643814 ATAAAAATT
1 ATAAAAATT
* *
5643823 GTTAAAAATC
1 -ATAAAAATT
*
5643833 ATAAAAAAAT
1 AT-AAAAATT
*
5643843 ATTAAAATT
1 ATAAAAATT
5643852 GATAAAAATT
1 -ATAAAAATT
* *
5643862 CGTAAAACTT
1 -ATAAAAATT
5643872 ATAAAAATT
1 ATAAAAATT
5643881 ATAAAA
1 ATAAAA
5643887 TTTCTTATAA
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
9 19 0.40
10 29 0.60
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5643868 original size:29 final size:29
Alignment explanation
Indices: 5643814--5643886 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
5643804 ATATTTTATC
*
5643814 ATAAAAATTGTTAAAAATCATAAAAAAAT
1 ATAAAAATTGATAAAAATCATAAAAAAAT
* * **
5643843 ATTAAAATTGATAAAAATTCGT-AAAACTT
1 ATAAAAATTGATAAAAA-TCATAAAAAAAT
5643872 ATAAAAATT-ATAAAA
1 ATAAAAATTGATAAAA
5643887 TTTCTTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 6 0.16
29 28 0.76
30 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
ATAAAAATTGATAAAAATCATAAAAAAAT
Found at i:5644767 original size:9 final size:9
Alignment explanation
Indices: 5644755--5644971 Score: 57
Period size: 9 Copynumber: 22.3 Consensus size: 9
5644745 TTATTAAAAA
5644755 TTATAATTT
1 TTATAATTT
5644764 TTATAATTT
1 TTATAATTT
*
5644773 ATTACAGCATATT
1 -TTATA--AT-TT
*
5644786 TTGA-ATTTT
1 TT-ATAATTT
*
5644795 TTATAAGTT
1 TTATAATTT
*
5644804 TTATAATTAC
1 TTATAATT-T
* *
5644814 TGAAAATTT
1 TTATAATTT
*
5644823 TTATAAGTT
1 TTATAATTT
*
5644832 TTATAAGTAT
1 TTATAA-TTT
* * *
5644842 TAATCATAT
1 TTATAATTT
*
5644851 TTATACTTT
1 TTATAATTT
*
5644860 TTTTAATGTAT
1 TTATAAT-T-T
5644871 CTTATAACTTTT
1 -TTATAA--TTT
5644883 TTATGAATCTT
1 TTAT-AAT-TT
5644894 TTATAATTT
1 TTATAATTT
*
5644903 TTAAAAGTTT
1 TTATAA-TTT
* *
5644913 ATAGAAAGTTT
1 TTA-TAA-TTT
5644924 TTA-ATATTT
1 TTATA-ATTT
5644933 TT-T-ATTT
1 TTATAATTT
5644940 TTAATATATTT
1 TT-ATA-ATTT
5644951 TT-TAAGTTT
1 TTATAA-TTT
*
5644960 TTATGATTT
1 TTATAATTT
5644969 TTA
1 TTA
5644972 ATTTTTTTAA
Statistics
Matches: 156, Mismatches: 27, Indels: 50
0.67 0.12 0.21
Matches are distributed among these distances:
7 6 0.04
8 2 0.01
9 75 0.48
10 29 0.19
11 26 0.17
12 13 0.08
13 4 0.03
14 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (9 bp):
TTATAATTT
Found at i:5644968 original size:18 final size:18
Alignment explanation
Indices: 5644918--5644991 Score: 66
Period size: 18 Copynumber: 4.1 Consensus size: 18
5644908 AGTTTATAGA
5644918 AAGTTTTTAATATTTTTT
1 AAGTTTTTAATATTTTTT
5644936 -A-TTTTTAATATATTTTTT
1 AAGTTTTT-A-ATATTTTTT
5644954 AAGTTTTT-ATGA-TTTTT
1 AAGTTTTTAAT-ATTTTTT
*
5644971 AATTTTTTTAATAGTTTTTT
1 AA-GTTTTTAATA-TTTTTT
5644991 A
1 A
5644992 TGAGAAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
16 5 0.11
17 11 0.24
18 16 0.35
19 3 0.07
20 11 0.24
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
AAGTTTTTAATATTTTTT
Found at i:5644993 original size:29 final size:30
Alignment explanation
Indices: 5644921--5644994 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
5644911 TTATAGAAAG
5644921 TTTTTAATA-TTTTT-T-ATTTTTAATATA
1 TTTTTAATAGTTTTTATGATTTTTAATATA
*
5644948 TTTTTTA-AGTTTTTATGATTTTTAAT-T-
1 TTTTTAATAGTTTTTATGATTTTTAATATA
5644975 TTTTTAATAGTTTTTTATGA
1 TTTTTAATAG-TTTTTATGA
5644995 GAAATAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 1 0.03
27 17 0.43
28 4 0.10
29 18 0.45
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (30 bp):
TTTTTAATAGTTTTTATGATTTTTAATATA
Found at i:5663504 original size:16 final size:16
Alignment explanation
Indices: 5663480--5663518 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5663470 TTTCATTAAG
*
5663480 AAAACCAGTTAAACCA
1 AAAATCAGTTAAACCA
5663496 AAAATCAGTTAAACCA
1 AAAATCAGTTAAACCA
5663512 AAAATCA
1 AAAATCA
5663519 TGCTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAATCAGTTAAACCA
Found at i:5663525 original size:17 final size:16
Alignment explanation
Indices: 5663489--5663525 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5663479 GAAAACCAGT
*
5663489 TAAACCAAAAATCAGT
1 TAAACCAAAAATCAGC
5663505 TAAACCAAAAATCATGC
1 TAAACCAAAAATCA-GC
5663522 TAAA
1 TAAA
5663526 AAAATCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (16 bp):
TAAACCAAAAATCAGC
Found at i:5666983 original size:18 final size:16
Alignment explanation
Indices: 5666946--5666985 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5666936 CGTACTGAGC
5666946 GAGAGAGGAGAACCGG
1 GAGAGAGGAGAACCGG
5666962 GAGAGAGGAGAACCGG
1 GAGAGAGGAGAACCGG
5666978 GAGAGAGG
1 GAGAGAGG
5666986 TCGGAGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.53, T:0.00
Consensus pattern (16 bp):
GAGAGAGGAGAACCGG
Done.