Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, whole genome shotgun sequence
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: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:1662378 original size:31 final size:29
Alignment explanation
Indices: 1662311--1662367 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1662301 AAATATTTAT
*
1662311 AATATCGACAATAGTTAAACAAGATATAC
1 AATATCCACAATAGTTAAACAAGATATAC
*
1662340 AATATCCACAATAGTTAAGCAAGATATA
1 AATATCCACAATAGTTAAACAAGATATA
1662368 TTGAATATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (29 bp):
AATATCCACAATAGTTAAACAAGATATAC
Found at i:1665626 original size:623 final size:624
Alignment explanation
Indices: 1664411--1665654 Score: 1985
Period size: 623 Copynumber: 2.0 Consensus size: 624
1664401 TAAGTTTAAG
* *
1664411 AGCTTAAGGGGTAGGCTTATGTCCGTAGAGCAATGAATATGATATATGAGCTTGTGAAGGCTCAA
1 AGCTTAAGGGGTAGGCTTATGTCCATAGAGCAAGGAATATGATATATGAGCTTGTGAAGGCTCAA
*
1664476 AATAATGTTATGCATATGCTTGATACATGAATGATATAGTAAATATGTTTGGCACTAAGATGAGT
66 AATAATGTTATGCATATGCTTGATACATGAATGATATAATAAATATGTTTGGCACTAAGATGAGT
*
1664541 ATGATATGTATGCAAATTATGCAATGTTAATTGATAGGCTATGTGACATAGAGCATGAATGAGAA
131 ATGATATGTATGCAAATTATGCAATGTTAATTGATAGACTATGTGACATAGAGCATGAATGAGAA
* * *
1664606 TTGGTGTGCATTATGGACTTGTGTGTTGATTTTAAGTGAAATATGAATGATTGGAGGTTGTTGAG
196 TTGGTGTGCATGATGGACTTGTGTGTTGATTTTAAGTGAAATATGAATGATTAGAGGTTGTCGAG
* *
1664671 AAGATTTAGAATGAGTTTAGACTTCAAAGAGATCAATTTTTATGAATTTGGACTTATGGATTCGA
261 AAGATTTAGAATGAGTTTAGACTTCAAAGAGACCAATTTTTATGAATTTGGACTTATGGATTCAA
**
1664736 TCCTTGTGCATGGAGGATCAGATCTATGAAGCAAAGGGCTAGAAGAGTGAGTGCACTAGCCTAAG
326 TCCTTGTGCATAAAGGATCAGATCTATGAAGCAAAGGGCTAGAAGAGTGAGTGCACTAGCCTAAG
* * * *
1664801 ATCAAGTACAGACCCTTTGTAGTTGATCTTAAGGTAGGAAATGGAAGCAAGGGTAAACAATCTGG
391 ACCAAGTACAGACCCTTTATAGTCGATCTTAAGGTAGGAAATGGAAGCAAGGGTAAACAATCTAG
* * *
1664866 TCCAAGATCAAGTACCAAGTTCCCATAGTCAATCCTAAAGTGCTAAATTAGCAAAAATCAGGCTT
456 TCCAAGATCAAGTACCAAGCTCCCATAGTCAATCCTAAAGTGCCAAATTAGCAAAAATCAAGCTT
* ** * * * * *
1664931 AAAGCCTTAAACCAAAAAATCCTTCATTTTCTTTTATTTCTTCATTCTTTCATTTGATTTTTGTC
521 AAAGCCTAAAACCAAAAAATCCTTCATTTTCTCCTAATTCTTCATTCTCTCATTCGATTTCTATC
* * * *
1664996 AAATTTCATCCCTCTCCAAACCTTCACACTTTAATGCTA
586 AAATTTCAACCCTCTCAAAACATTCACACTCTAATGCTA
* *
1665035 AGCTTAA-GGGTAGGTTTATGTCTATAGAGCAAGGAATATGATATATGAGCTTGTGAAGGCTCAA
1 AGCTTAAGGGGTAGGCTTATGTCCATAGAGCAAGGAATATGATATATGAGCTTGTGAAGGCTCAA
* ** *
1665099 AATAATGTTATGCATATGCTTGGTACATGAATGATATAATGCATATGTTTGGGACTAAGATGAGT
66 AATAATGTTATGCATATGCTTGATACATGAATGATATAATAAATATGTTTGGCACTAAGATGAGT
*
1665164 ATGATATGTATGCAAATTATGCCATGTTAATTGATAGACTATGTGACATAGAGCATGAATGAGAA
131 ATGATATGTATGCAAATTATGCAATGTTAATTGATAGACTATGTGACATAGAGCATGAATGAGAA
*
1665229 TTGGTGTGCATGATGGACTTGTGTGTTGATTTTAAGTGAAATATGAATGATTAGAGGTTGTCGGG
196 TTGGTGTGCATGATGGACTTGTGTGTTGATTTTAAGTGAAATATGAATGATTAGAGGTTGTCGAG
*
1665294 AAGATTTAGAATGAGTTTAGACTTCAAAGTGACCAATTTTTATGAATTTGGACTTATGGATTCAA
261 AAGATTTAGAATGAGTTTAGACTTCAAAGAGACCAATTTTTATGAATTTGGACTTATGGATTCAA
* *
1665359 T-CTTAGTGCATAAAGGATCAGATCTGTGAAGCAAAAGGG-T-GAAAGAGTGAGTGCACTGGCCT
326 TCCTT-GTGCATAAAGGATCAGATCTATGAAGC-AAAGGGCTAG-AAGAGTGAGTGCACTAGCCT
*
1665421 AAGACCAAGTACAGACCCTTTATAGTCGATCTTAAGGTAGGAAATGGGAGCAAGGGTAAACAATC
388 AAGACCAAGTACAGACCCTTTATAGTCGATCTTAAGGTAGGAAATGGAAGCAAGGGTAAACAATC
* *
1665486 TAGTCCAAGATCAAGTACCAAGCTCCCATAGTCAATCCTAAGGTGCCAGATTAGCAAAAATCAAG
453 TAGTCCAAGATCAAGTACCAAGCTCCCATAGTCAATCCTAAAGTGCCAAATTAGCAAAAATCAAG
*
1665551 TTTAAAGCCCTAAAACC-AAAAATCCTTCATTTTCTCCTAATTCTTCATTCTCTCATTCGATTTC
518 CTTAAAG-CCTAAAACCAAAAAATCCTTCATTTTCTCCTAATTCTTCATTCTCTCATTCGATTTC
** *
1665615 TATTGAATTTCAACCCTTTCAAAACATTCACACTCTAATG
582 TATCAAATTTCAACCCTCTCAAAACATTCACACTCTAATG
1665655 GTAAATCTTG
Statistics
Matches: 568, Mismatches: 48, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
622 4 0.01
623 543 0.96
624 21 0.04
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (624 bp):
AGCTTAAGGGGTAGGCTTATGTCCATAGAGCAAGGAATATGATATATGAGCTTGTGAAGGCTCAA
AATAATGTTATGCATATGCTTGATACATGAATGATATAATAAATATGTTTGGCACTAAGATGAGT
ATGATATGTATGCAAATTATGCAATGTTAATTGATAGACTATGTGACATAGAGCATGAATGAGAA
TTGGTGTGCATGATGGACTTGTGTGTTGATTTTAAGTGAAATATGAATGATTAGAGGTTGTCGAG
AAGATTTAGAATGAGTTTAGACTTCAAAGAGACCAATTTTTATGAATTTGGACTTATGGATTCAA
TCCTTGTGCATAAAGGATCAGATCTATGAAGCAAAGGGCTAGAAGAGTGAGTGCACTAGCCTAAG
ACCAAGTACAGACCCTTTATAGTCGATCTTAAGGTAGGAAATGGAAGCAAGGGTAAACAATCTAG
TCCAAGATCAAGTACCAAGCTCCCATAGTCAATCCTAAAGTGCCAAATTAGCAAAAATCAAGCTT
AAAGCCTAAAACCAAAAAATCCTTCATTTTCTCCTAATTCTTCATTCTCTCATTCGATTTCTATC
AAATTTCAACCCTCTCAAAACATTCACACTCTAATGCTA
Found at i:1668668 original size:17 final size:17
Alignment explanation
Indices: 1668648--1668682 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1668638 AACCTTAAAT
1668648 TTTAATAAATTAACTAA
1 TTTAATAAATTAACTAA
* *
1668665 TTTAATTAATTAATTAA
1 TTTAATAAATTAACTAA
1668682 T
1 T
1668683 AACCAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATAAATTAACTAA
Found at i:1668967 original size:59 final size:59
Alignment explanation
Indices: 1668898--1669015 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
1668888 TAATCTCTAT
* *
1668898 CAACAACTAAATAACCCAATAGATTTTCAAAAAATTAAGTTGTTCAAAAATTGTTCAAG
1 CAACAACTAAATAACCCAATAGATTTTCAAAAAACTAAGTTATTCAAAAATTGTTCAAG
* * ** * * * *
1668957 CAACAGCTAAATTACGTAGTAGATTTTCATAAGACTAAGTTATTTAAAAATTGTTCAAG
1 CAACAACTAAATAACCCAATAGATTTTCAAAAAACTAAGTTATTCAAAAATTGTTCAAG
1669016 AAAATAACTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (59 bp):
CAACAACTAAATAACCCAATAGATTTTCAAAAAACTAAGTTATTCAAAAATTGTTCAAG
Found at i:1670497 original size:21 final size:21
Alignment explanation
Indices: 1670470--1670528 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1670460 CATTAGGAAG
*
1670470 CAAAAGTCTAGAGACATTTCA
1 CAAAAGTATAGAGACATTTCA
* * *
1670491 CATAAGTATTGAGACATTTCT
1 CAAAAGTATAGAGACATTTCA
*
1670512 CAAAAGTATCGAGACAT
1 CAAAAGTATAGAGACAT
1670529 CACCTCTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (21 bp):
CAAAAGTATAGAGACATTTCA
Found at i:1671615 original size:26 final size:26
Alignment explanation
Indices: 1671579--1671635 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1671569 AATTTCTACA
1671579 ATTTTAGTTCATTTTTTTTAAATAAG
1 ATTTTAGTTCATTTTTTTTAAATAAG
1671605 ATTTTAGTTCATTTTTTTTAAATAAG
1 ATTTTAGTTCATTTTTTTTAAATAAG
*
1671631 CTTTT
1 ATTTT
1671636 GCAGTCTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (26 bp):
ATTTTAGTTCATTTTTTTTAAATAAG
Found at i:1680429 original size:2 final size:2
Alignment explanation
Indices: 1680422--1680451 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1680412 TCAAATACAA
1680422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680452 TCTTCTCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1680763 original size:33 final size:33
Alignment explanation
Indices: 1680723--1680805 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1680713 ATCATGCTAA
* * *
1680723 ATTAACATGTCACGTCATTATCAATTATGACAT
1 ATTAACATGTCACATCATCATCAATTAAGACAT
* * *
1680756 GTTAACATGTCACATTATCATCAATTAAGATAT
1 ATTAACATGTCACATCATCATCAATTAAGACAT
**
1680789 ATTAACATACCACATCA
1 ATTAACATGTCACATCA
1680806 GTCGTAAGCT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (33 bp):
ATTAACATGTCACATCATCATCAATTAAGACAT
Found at i:1684473 original size:3 final size:3
Alignment explanation
Indices: 1684467--1684499 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1684457 TGATGATGAT
1684467 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1684500 AATGCAGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1702962 original size:2 final size:2
Alignment explanation
Indices: 1702955--1702988 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1702945 TTAAGGTACC
*
1702955 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1702989 TCAAACAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1710476 original size:54 final size:55
Alignment explanation
Indices: 1710391--1710509 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 55
1710381 ATAATAATAT
* * * * * *
1710391 AAAGTTTTTTTTTCAGAATTTCTTGATTTTTTTCAGCACGTTG-GGAAACTCAAGA
1 AAAG-TTTTCTTTCAAAATTTCTTGATTTTTTCCAGAACGTTGAGAAAACTCAAAA
*
1710446 AGAGTTTTCTTTCAAAATTT-TTGAGTTTTTTCCAGAACGTTGAGAAAACTCAAAA
1 AAAGTTTTCTTTCAAAATTTCTTGA-TTTTTTCCAGAACGTTGAGAAAACTCAAAA
1710501 AAAGTTTTC
1 AAAGTTTTC
1710510 ATAAAAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 4 0.07
54 29 0.54
55 21 0.39
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (55 bp):
AAAGTTTTCTTTCAAAATTTCTTGATTTTTTCCAGAACGTTGAGAAAACTCAAAA
Found at i:1710518 original size:55 final size:54
Alignment explanation
Indices: 1710407--1710519 Score: 129
Period size: 55 Copynumber: 2.1 Consensus size: 54
1710397 TTTTTTTCAG
* * * * * * **
1710407 AATTTCTTGATTTTTTTCAGCACGTTGGGAAACTCAAGAAGAGTTTTCTTTCAA
1 AATTTCTTGATTTTTTCCAGAACGTTGGAAAACTCAAAAAAAGTTTTCATAAAA
1710461 AATTT-TTGAGTTTTTTCCAGAACGTTGAGAAAACTCAAAAAAAGTTTTCATAAAA
1 AATTTCTTGA-TTTTTTCCAGAACGTTG-GAAAACTCAAAAAAAGTTTTCATAAAA
1710516 AATT
1 AATT
1710520 CTCAATTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 4 0.08
54 20 0.41
55 25 0.51
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (54 bp):
AATTTCTTGATTTTTTCCAGAACGTTGGAAAACTCAAAAAAAGTTTTCATAAAA
Found at i:1710656 original size:55 final size:56
Alignment explanation
Indices: 1710581--1710723 Score: 150
Period size: 55 Copynumber: 2.6 Consensus size: 56
1710571 AATTTTTGAC
* *
1710581 TTTTCACTAACATGTTGAGAAAAACTCAGAAATAAAAT-T-TCATAAAACTTTTTGGG
1 TTTTTACTAACATATTGAG-AAAACTCAGAAA-AAAATGTCTCATAAAACTTTTTGGG
*** *
1710637 TTTTTAC-AACATATTGAGAAAA-TCGAGAAAAGGTTGTCTCTTAAAACTTTTTGGG
1 TTTTTACTAACATATTGAGAAAACTC-AGAAAAAAATGTCTCATAAAACTTTTTGGG
* * *
1710692 TTTTTACTAGCACATTGAGAAAACTTAGAAAA
1 TTTTTACTAACATATTGAGAAAACTCAGAAAA
1710724 TGTTTTCATA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
53 4 0.05
54 10 0.14
55 33 0.45
56 25 0.34
57 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (56 bp):
TTTTTACTAACATATTGAGAAAACTCAGAAAAAAATGTCTCATAAAACTTTTTGGG
Found at i:1714329 original size:22 final size:23
Alignment explanation
Indices: 1714304--1714350 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1714294 ATTTCTATGC
1714304 ATTACTA-CAAGAATTAAGCT-AA
1 ATTACTATCAA-AATTAAGCTCAA
1714326 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAATTAAGCTCAA
1714349 AT
1 AT
1714351 AACTCTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (23 bp):
ATTACTATCAAAATTAAGCTCAA
Found at i:1714780 original size:71 final size:71
Alignment explanation
Indices: 1714672--1714813 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
1714662 TCAGGTATGG
** * * *
1714672 TGGTATAGAAATAAGGTTGGTGTCTTGCATCAAGTTTACATAAAATTCTATTTTTCGTTATGGAG
1 TGGTATAGAAATAAGACTGGTGTCTTGCACCAAGTTTACATAAAATTCCATTTTTCGCTATGGAG
1714737 GTAATT
66 GTAATT
* *
1714743 TGGTATAGAAATTAGACTGGTGTCTTGCACCAAGTTTACATAAAATTCCATTTTTTGCTATGGAG
1 TGGTATAGAAATAAGACTGGTGTCTTGCACCAAGTTTACATAAAATTCCATTTTTCGCTATGGAG
1714808 GTAATT
66 GTAATT
1714814 CAACTAACTC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (71 bp):
TGGTATAGAAATAAGACTGGTGTCTTGCACCAAGTTTACATAAAATTCCATTTTTCGCTATGGAG
GTAATT
Found at i:1717288 original size:20 final size:20
Alignment explanation
Indices: 1717242--1717288 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1717232 ATATTTTACT
*
1717242 AATGTATCGATAAATGTATG
1 AATGTATCGATAAATGTAAG
* *
1717262 AAAGTATCGATACAT-TCAAG
1 AATGTATCGATAAATGT-AAG
1717282 AATGTAT
1 AATGTAT
1717289 TGACAGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (20 bp):
AATGTATCGATAAATGTAAG
Found at i:1723239 original size:29 final size:28
Alignment explanation
Indices: 1723159--1723241 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 28
1723149 TGATAGCTTT
*
1723159 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGATAAGAA
1723187 AACATGTTTGGTCTTAATTTAGATAAGAA
1 AACATGTTT-GTCTTAATTTAGATAAGAA
*
1723216 AATATGTTTGTCTTAATTTAAGATAA
1 AACATGTTTGTCTTAATTT-AGATAA
1723242 AATTTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
28 19 0.37
29 32 0.63
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGATAAGAA
Found at i:1723446 original size:18 final size:17
Alignment explanation
Indices: 1723411--1723444 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1723401 ATAATAATAA
1723411 AATAAGAGTTATTATTT
1 AATAAGAGTTATTATTT
1723428 AATAAGGAGTT-TTATTT
1 AATAA-GAGTTATTATTT
1723445 TATCAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (17 bp):
AATAAGAGTTATTATTT
Found at i:1724886 original size:17 final size:17
Alignment explanation
Indices: 1724864--1724896 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1724854 CTTGCAATCC
1724864 TTAGGTTAATATAGACT
1 TTAGGTTAATATAGACT
1724881 TTAGGTTAATATAGAC
1 TTAGGTTAATATAGAC
1724897 ATTTTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (17 bp):
TTAGGTTAATATAGACT
Found at i:1735911 original size:2 final size:2
Alignment explanation
Indices: 1735904--1735938 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1735894 TCTTTGTATG
1735904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1735939 CATAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1737468 original size:27 final size:29
Alignment explanation
Indices: 1737419--1737483 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
1737409 CCAACTAGCT
* * *
1737419 TTTCATTTTCTTTTTTTGTTCTCTTTTTTC
1 TTTCA-TTTCTTTTATTGTTCTCATTTTTA
1737449 TTT-ATTTCTTTTATT-TTCTCATTTTTA
1 TTTCATTTCTTTTATTGTTCTCATTTTTA
1737476 TTTCATTT
1 TTTCATTT
1737484 TCTAGAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 13 0.42
28 14 0.45
29 1 0.03
30 3 0.10
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTCATTTCTTTTATTGTTCTCATTTTTA
Found at i:1739185 original size:36 final size:36
Alignment explanation
Indices: 1739137--1739207 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1739127 GATATGTTGA
* *
1739137 GACTCGATAGAGAGATTTTAGATTGGACTAAGATTG
1 GACTCGACAGAGAGATTTTAGATTGAACTAAGATTG
1739173 GACTCGACAGAGAGATTTTAGATTGAACTAAGATT
1 GACTCGACAGAGAGATTTTAGATTGAACTAAGATT
1739208 TAAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (36 bp):
GACTCGACAGAGAGATTTTAGATTGAACTAAGATTG
Found at i:1742666 original size:23 final size:23
Alignment explanation
Indices: 1742625--1742675 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1742615 TTGAGTTGCT
*
1742625 CAAGGTTGCAGTGAGGAGGA-AG
1 CAAGGTTGCAGTAAGGAGGAGAG
* *
1742647 CCAAGGTTGTAGTAATGAGGAGAG
1 -CAAGGTTGCAGTAAGGAGGAGAG
1742671 CAAGG
1 CAAGG
1742676 CCGCAGCAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.33, C:0.10, G:0.41, T:0.16
Consensus pattern (23 bp):
CAAGGTTGCAGTAAGGAGGAGAG
Found at i:1743993 original size:10 final size:10
Alignment explanation
Indices: 1743978--1744022 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1743968 ACATATTGTA
1743978 TAATTTTTTT
1 TAATTTTTTT
*
1743988 TAATTTCTTT
1 TAATTTTTTT
1743998 TAATTTTTTT
1 TAATTTTTTT
* *
1744008 ATAAATTTTCT
1 -TAATTTTTTT
1744019 TAAT
1 TAAT
1744023 GGCACCCCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:1749157 original size:18 final size:19
Alignment explanation
Indices: 1749118--1749160 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1749108 TTAATATTTT
1749118 AATATTATTGTATTAATAA
1 AATATTATTGTATTAATAA
* *
1749137 AATATTATTTTATT-CTAA
1 AATATTATTGTATTAATAA
1749155 AATATT
1 AATATT
1749161 TCTTTCGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATTATTGTATTAATAA
Found at i:1773977 original size:29 final size:30
Alignment explanation
Indices: 1773936--1774038 Score: 84
Period size: 29 Copynumber: 3.7 Consensus size: 30
1773926 ATAATTGTTA
1773936 TTGT-GTATATATAATTGTTTGTGTTAATT
1 TTGTGGTATATATAATTGTTTGTGTTAATT
1773965 TTGTGGTAT-TATAA-----T-TGTT-ATT
1 TTGTGGTATATATAATTGTTTGTGTTAATT
*
1773987 GTGTGTGTATATATATATATGTTTGTGTTAATT
1 TTGTG-GTATATATA-AT-TGTTTGTGTTAATT
1774020 TTGTGGTCAT-T-TAATTGTT
1 TTGTGGT-ATATATAATTGTT
1774039 ATTGTGTATA
Statistics
Matches: 59, Mismatches: 2, Indels: 26
0.68 0.02 0.30
Matches are distributed among these distances:
22 7 0.12
23 8 0.14
24 5 0.08
25 1 0.02
29 13 0.22
30 6 0.10
31 3 0.05
32 7 0.12
33 9 0.15
ACGTcount: A:0.22, C:0.01, G:0.19, T:0.57
Consensus pattern (30 bp):
TTGTGGTATATATAATTGTTTGTGTTAATT
Found at i:1773999 original size:22 final size:23
Alignment explanation
Indices: 1773957--1774001 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1773947 TAATTGTTTG
*
1773957 TGTTAATTTTGTGGTATTATAAT
1 TGTTAATTGTGTGGTATTATAAT
1773980 TGTT-ATTGTGTGTGTATATATA
1 TGTTAATTGTGTG-GTAT-TATA
1774002 TATATGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (23 bp):
TGTTAATTGTGTGGTATTATAAT
Found at i:1774013 original size:55 final size:50
Alignment explanation
Indices: 1773797--1774154 Score: 356
Period size: 49 Copynumber: 7.1 Consensus size: 50
1773787 TGATATTGTG
* * * * *
1773797 TATATATTTTTTGTATTAATTTTGTTGTAATATAATTGATT-CTGTGTATA
1 TATATATTGTTTGTGTTAATTTTGTGGTATTATAATTG-TTATTGTGTATA
* * * *
1773847 TATAT-TTGGTTGTGTTAATTTTGTAGTATTATAATTTTTATTATGTATA
1 TATATATTGTTTGTGTTAATTTTGTGGTATTATAATTGTTATTGTGTATA
* *** *
1773896 -A-AT-TTGCATTTCTGTTAATTCAATGGTAATATAATTGTTATTGTGTATA
1 TATATATTG--TTTGTGTTAATTTTGTGGTATTATAATTGTTATTGTGTATA
1773945 TATA-ATTGTTTGTGTTAATTTTGTGGTATTATAATTGTTATTGTGTGTGTATA
1 TATATATTGTTTGTGTTAATTTTGTGGTATTATAATTGTTA---T-TGTGTATA
1773998 TATATATATGTTTGTGTTAATTTTGTGGTCATT-TAATTGTTATTGTGTATA
1 TATATAT-TGTTTGTGTTAATTTTGTGGT-ATTATAATTGTTATTGTGTATA
* **
1774049 TATAT-TT-TTGTGTGTTAATTTTGTGGTATTTTAATTGTTATTACGTATA
1 TATATATTGTT-TGTGTTAATTTTGTGGTATTATAATTGTTATTGTGTATA
* **
1774098 TATATGTTTGTTTGTGTTAATTTTGTGGTAAAATAATTTTGTTATTGTGTATA
1 TATAT-ATTGTTTGTGTTAATTTTGTGGTATTATAA--TTGTTATTGTGTATA
1774151 TATA
1 TATA
1774155 AATTAGTAAA
Statistics
Matches: 259, Mismatches: 29, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
47 5 0.02
48 8 0.03
49 131 0.51
50 7 0.03
51 40 0.15
52 4 0.02
53 29 0.11
54 2 0.01
55 30 0.12
56 3 0.01
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (50 bp):
TATATATTGTTTGTGTTAATTTTGTGGTATTATAATTGTTATTGTGTATA
Found at i:1774041 original size:153 final size:147
Alignment explanation
Indices: 1773754--1774154 Score: 408
Period size: 153 Copynumber: 2.7 Consensus size: 147
1773744 TATATGTTGT
* * * * *
1773754 TATATTTTT-TTTGTT-ATTTAATTGTAATTTAATTGATATTGTGTATATATTT-TTTGTATTAA
1 TATATTTTTGTCTGTTAATTCAATGGTAATTTAATTGTTATTGTGTATATATTTGTTTGTGTTAA
* *
1773816 TTTTGTTGTAATATAATTG--ATTCTGTGTATATATATTTGGTTGTGTTAATTTTGTAGTATTAT
66 TTTTGTGGTAATATAATTGTTATTTTGTGTATATATATTTGGTTGTGTTAATTTTGTAGTATTAT
*
1773879 AATTTTTATTATGTATA
131 AATTGTTATTATGTATA
*
1773896 -A-ATTTGCATT-TCTGTTAATTCAATGGTAATATAATTGTTATTGTGTATATATAATTGTTTGT
1 TATATTT---TTGTCTGTTAATTCAATGGTAATTTAATTGTTATTGTGTATATAT--TTGTTTGT
* *
1773958 GTTAATTTTGTGGTATTATAATTGTTATTGTGTGTGTATATATATATATGTTTGTGTTAATTTTG
61 GTTAATTTTGTGGTAATATAATTGTTATT-T-TGTGTATATATAT-T-TGGTTGTGTTAATTTTG
* *
1774023 TGGTCATT-TAATTGTTATTGTGTATA
122 TAGT-ATTATAATTGTTATTATGTATA
* *** * *
1774049 TATATTTTTGTGTGTTAATTTTGTGGTATTTTAATTGTTATTACGTATATATATGTTTGTTTGTG
1 TATATTTTTGTCTGTTAATTCAATGGTAATTTAATTGTTATT--GTGTATATA--TTTGTTTGTG
* *
1774114 TTAATTTTGTGGTAAAATAATT-TTGTTATTGTGTATATATA
62 TTAATTTTGTGGTAATATAATTGTTATT-TTGTGTATATATA
1774155 AATTAGTAAA
Statistics
Matches: 214, Mismatches: 24, Indels: 31
0.80 0.09 0.12
Matches are distributed among these distances:
140 4 0.02
141 1 0.00
143 7 0.03
144 31 0.14
146 2 0.01
147 26 0.12
149 3 0.01
151 13 0.06
152 3 0.01
153 73 0.34
154 9 0.04
155 41 0.19
157 1 0.00
ACGTcount: A:0.26, C:0.01, G:0.16, T:0.57
Consensus pattern (147 bp):
TATATTTTTGTCTGTTAATTCAATGGTAATTTAATTGTTATTGTGTATATATTTGTTTGTGTTAA
TTTTGTGGTAATATAATTGTTATTTTGTGTATATATATTTGGTTGTGTTAATTTTGTAGTATTAT
AATTGTTATTATGTATA
Found at i:1774064 original size:104 final size:99
Alignment explanation
Indices: 1773797--1774154 Score: 359
Period size: 104 Copynumber: 3.6 Consensus size: 99
1773787 TGATATTGTG
* * * * * *
1773797 TATATAT-TTTTTGTATTAATTTTGTTGTAATATAATTGATT-CTGTGTATATATATTTGGTTGT
1 TATATATATGTTTGTGTTAATTTTGTGGTAAAATAATTG-TTATTGTGTATATATA-TTGTTTGT
* * *
1773860 GTTAATTTTGTAGTATTATAATTTTTATTATGTATA
64 GTTAATTTTGTGGTATTATAATTGTTATTACGTATA
* *** *
1773896 -A-AT-T-TGCATTTCTGTTAATTCAATGGTAATATAATTGTTATTGTGTATATATAATTGTTTG
1 TATATATATG--TTTGTGTTAATTTTGTGGTAAAATAATTGTTATTGTGTATATAT-ATTGTTTG
**
1773957 TGTTAATTTTGTGGTATTATAATTGTTATTGTGTGTGTATA
63 TGTTAATTTTGTGGTATTATAATTGTTA---T-TACGTATA
* ** *
1773998 TATATATATGTTTGTGTTAATTTTGTGGTCATTTAATTGTTATTGTGTATATATATTTTTGTGTG
1 TATATATATGTTTGTGTTAATTTTGTGGTAAAATAATTGTTATTGTGTATATATATTGTT-TGTG
*
1774063 TTAATTTTGTGGTATTTTAATTGTTATTACGTATA
65 TTAATTTTGTGGTATTATAATTGTTATTACGTATA
* *
1774098 TATATGTTTGTTTGTGTTAATTTTGTGGTAAAATAATTTTGTTATTGTGTATATATA
1 TATATATATGTTTGTGTTAATTTTGTGGTAAAATAA--TTGTTATTGTGTATATATA
1774155 AATTAGTAAA
Statistics
Matches: 217, Mismatches: 27, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
96 2 0.01
97 4 0.02
98 67 0.31
99 1 0.00
100 37 0.17
101 2 0.01
102 26 0.12
103 6 0.03
104 69 0.32
105 1 0.00
106 2 0.01
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (99 bp):
TATATATATGTTTGTGTTAATTTTGTGGTAAAATAATTGTTATTGTGTATATATATTGTTTGTGT
TAATTTTGTGGTATTATAATTGTTATTACGTATA
Found at i:1774535 original size:31 final size:31
Alignment explanation
Indices: 1774487--1774546 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1774477 TTTTAAGTTG
*
1774487 TATAATTTAATATTATTAAAGTGTAAAATGC
1 TATAATTTAATATTATTAAAATGTAAAATGC
* *
1774518 TATAATTTATTCA-TATTAAAATGTTAAAT
1 TATAATTTAAT-ATTATTAAAATGTAAAAT
1774547 TTGTTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (31 bp):
TATAATTTAATATTATTAAAATGTAAAATGC
Found at i:1779991 original size:40 final size:42
Alignment explanation
Indices: 1779936--1780088 Score: 175
Period size: 46 Copynumber: 3.5 Consensus size: 42
1779926 AAATTGAACT
1779936 TCAACTTTGTGAAGCTTGA-G-GGTGAGAGATTATAAGATCG
1 TCAACTTTGTGAAGCTTGAGGAGGTGAGAGATTATAAGATCG
*
1779976 TCAACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCA
1 TCAACTTTGTGAAGCTTGA--G-G-AGGTGAGAGATTATAAGATCG
* * *
1780022 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAGGATTG
1 TCAACTTTGTGAAGCTTGA--G-G-AGGTGAGAGATTATAAGATCG
*
1780068 TCGACTTTGTGAAGCTTGAGG
1 TCAACTTTGTGAAGCTTGAGG
1780089 GTGAAGGTGA
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
40 19 0.19
43 1 0.01
44 2 0.02
46 80 0.78
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (42 bp):
TCAACTTTGTGAAGCTTGAGGAGGTGAGAGATTATAAGATCG
Found at i:1780009 original size:46 final size:46
Alignment explanation
Indices: 1779956--1780099 Score: 252
Period size: 46 Copynumber: 3.1 Consensus size: 46
1779946 GAAGCTTGAG
*
1779956 GGTGAGAGATTATAAGATCGTCAACTTTGTGAAGCTTGAGGGTGAA
1 GGTGAGAGATTATAAGATCGTCGACTTTGTGAAGCTTGAGGGTGAA
*
1780002 GGTGAGAGATTATAAGATCATCGACTTTGTGAAGCTTGAGGGTGAA
1 GGTGAGAGATTATAAGATCGTCGACTTTGTGAAGCTTGAGGGTGAA
* *
1780048 GGTGAGAGATTATAGGATTGTCGACTTTGTGAAGCTTGAGGGTGAA
1 GGTGAGAGATTATAAGATCGTCGACTTTGTGAAGCTTGAGGGTGAA
1780094 GGTGAG
1 GGTGAG
1780100 GGTGACAGAT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 93 1.00
ACGTcount: A:0.28, C:0.08, G:0.35, T:0.28
Consensus pattern (46 bp):
GGTGAGAGATTATAAGATCGTCGACTTTGTGAAGCTTGAGGGTGAA
Found at i:1780449 original size:23 final size:22
Alignment explanation
Indices: 1780407--1780462 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
1780397 ACAAAATTAT
* *
1780407 ATAATTATGTAATTATTATTGTTG
1 ATAATTA-ATAATTAATATT-TTG
*
1780431 ATAATTAATAATTAATATTTTT
1 ATAATTAATAATTAATATTTTG
1780453 AGTAATTAAT
1 A-TAATTAAT
1780463 GTCATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 18 0.64
24 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATAATTAATAATTAATATTTTG
Found at i:1780567 original size:13 final size:13
Alignment explanation
Indices: 1780525--1780570 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1780515 GTTAATTATA
1780525 TAAATTAATATTG
1 TAAATTAATATTG
* *
1780538 TAGATAACATATTG
1 TAAATTA-ATATTG
*
1780552 TAAATTAATTTTG
1 TAAATTAATATTG
1780565 TAAATT
1 TAAATT
1780571 TCATACTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (13 bp):
TAAATTAATATTG
Found at i:1786771 original size:16 final size:17
Alignment explanation
Indices: 1786752--1786796 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1786742 AAAATTATTT
1786752 TTATATCAAA-TAATAA
1 TTATATCAAATTAATAA
*
1786768 TTAT-TAAAATTAATAA
1 TTATATCAAATTAATAA
*
1786784 TTAGATC-AATTAA
1 TTATATCAAATTAA
1786797 AAATCAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
TTATATCAAATTAATAA
Found at i:1786880 original size:2 final size:2
Alignment explanation
Indices: 1786847--1786903 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
1786837 TGTTAGAATA
* * * * *
1786847 AT AT AA AT AT TT AT AT -T AT AT AT GT GT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1786888 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1786904 TAAAACATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1787995 original size:17 final size:17
Alignment explanation
Indices: 1787973--1788005 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1787963 GGTTTGATTG
1787973 TTGTATTTAATTATTTA
1 TTGTATTTAATTATTTA
1787990 TTGTATTTAATTATTT
1 TTGTATTTAATTATTT
1788006 TCATTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTGTATTTAATTATTTA
Found at i:1792229 original size:2 final size:2
Alignment explanation
Indices: 1792224--1792252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1792214 TGTGTGTGTG
1792224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1792253 TCCTGTAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1799581 original size:14 final size:15
Alignment explanation
Indices: 1799562--1799594 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1799552 TAATTATTAT
*
1799562 TATATATATTTTAA-
1 TATATATACTTTAAG
1799576 TATATATACTTTAAG
1 TATATATACTTTAAG
1799591 TATA
1 TATA
1799595 AACATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
TATATATACTTTAAG
Found at i:1807577 original size:35 final size:35
Alignment explanation
Indices: 1807531--1807601 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1807521 GGAACTAAAA
* *
1807531 GAAAGAAAAACTTAAATTTAAATGTTCAATTGATT
1 GAAAGAAAAACTCAAATGTAAATGTTCAATTGATT
*
1807566 GAAAGAAAAACTCAAATGTAAATGTTCGATTGATT
1 GAAAGAAAAACTCAAATGTAAATGTTCAATTGATT
1807601 G
1 G
1807602 CTCAACATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (35 bp):
GAAAGAAAAACTCAAATGTAAATGTTCAATTGATT
Found at i:1812710 original size:3 final size:3
Alignment explanation
Indices: 1812704--1812746 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1812694 TCTTCTAATT
1812704 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1812747 CATCATCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1818322 original size:35 final size:35
Alignment explanation
Indices: 1818239--1818324 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
1818229 AAAGGTAATG
* * *
1818239 TCTTGATAGAGGTTACGCTTGATGTTGCAAAAGTTA
1 TCTTG-TAGAGGTTACGCCTGATCTTGCAAAAGTCA
* *
1818275 TGTTGCAGAGGTTACGCCTGATCTTGCAAAA-TGCA
1 TCTTGTAGAGGTTACGCCTGATCTTGCAAAAGT-CA
*
1818310 TCTTGTAAAGGTTAC
1 TCTTGTAGAGGTTAC
1818325 ACTTAACCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
34 1 0.02
35 36 0.88
36 4 0.10
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (35 bp):
TCTTGTAGAGGTTACGCCTGATCTTGCAAAAGTCA
Found at i:1818820 original size:24 final size:25
Alignment explanation
Indices: 1818792--1818853 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1818782 TTACTTAATC
*
1818792 TATTGAT-CTAGATCTTTAGGATTT
1 TATTGATAATAGATCTTTAGGATTT
* *
1818816 TATTGTTAATAGATCTTTATGATTT
1 TATTGATAATAGATCTTTAGGATTT
* *
1818841 AATTGTTAATAGA
1 TATTGATAATAGA
1818854 CCTCACACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 6 0.18
25 27 0.82
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.50
Consensus pattern (25 bp):
TATTGATAATAGATCTTTAGGATTT
Found at i:1818828 original size:25 final size:25
Alignment explanation
Indices: 1818800--1818853 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1818790 TCTATTGATC
*
1818800 TAGATCTTTAGGATTTTATTGTTAA
1 TAGATCTTTAGGATTTAATTGTTAA
*
1818825 TAGATCTTTATGATTTAATTGTTAA
1 TAGATCTTTAGGATTTAATTGTTAA
1818850 TAGA
1 TAGA
1818854 CCTCACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (25 bp):
TAGATCTTTAGGATTTAATTGTTAA
Found at i:1827726 original size:2 final size:2
Alignment explanation
Indices: 1827719--1827749 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1827709 ATGTGATGGA
1827719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1827750 GACATCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1843091 original size:72 final size:71
Alignment explanation
Indices: 1842971--1843156 Score: 178
Period size: 72 Copynumber: 2.6 Consensus size: 71
1842961 TAGAAGAGAT
* * * * * *
1842971 TGAGCCAACGAGCATATTGTTGGAAATATCCAGAGAAGTCAACTTGGTCAA-CCGACCCAAGGTG
1 TGAGCCAACAAGCTTATTGTTGGACAGATCCAGAGTAGTCAACTTGGTCAATCCG-CCCAAAGTG
1843035 GAAGGGAA
65 GAA-GGAA
* * **
1843043 TGAGCCAACAAGCTTATTGTTGGACAGATCAAGAGTGGTCATA-TTGGTCAATTTGCCCAAAGTG
1 TGAGCCAACAAGCTTATTGTTGGACAGATCCAGAGTAGTCA-ACTTGGTCAATCCGCCCAAAGTG
1843107 GAAGGAA
65 GAAGGAA
* * * * * *
1843114 TTACACCAACTAGCTTGTTGTTAGACAGATCCAGAGTAATCAA
1 TGA-GCCAACAAGCTTATTGTTGGACAGATCCAGAGTAGTCAA
1843157 GTTCTTCAGT
Statistics
Matches: 93, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
71 7 0.08
72 84 0.90
73 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (71 bp):
TGAGCCAACAAGCTTATTGTTGGACAGATCCAGAGTAGTCAACTTGGTCAATCCGCCCAAAGTGG
AAGGAA
Found at i:1848721 original size:2 final size:2
Alignment explanation
Indices: 1848709--1848745 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1848699 AAGAGCCCTA
*
1848709 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1848746 AGCCCAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1849093 original size:2 final size:2
Alignment explanation
Indices: 1849086--1849111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1849076 ACTTTTACGG
1849086 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
1849112 GTACACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1883818 original size:18 final size:18
Alignment explanation
Indices: 1883780--1883831 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
1883770 ATAGAGACAC
* *
1883780 CCATACATGCACACATA-
1 CCATACATACTCACATAG
1883797 -CATACATACTCACATAG
1 CCATACATACTCACATAG
*
1883814 CCATATATACTCACATAG
1 CCATACATACTCACATAG
1883832 ATAATGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.47
18 16 0.53
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (18 bp):
CCATACATACTCACATAG
Found at i:1892551 original size:73 final size:73
Alignment explanation
Indices: 1892440--1892579 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 73
1892430 AAACCTATAT
* *
1892440 TTATAAAAATGTATTCATTAATGACGATCATTGAAATATTTTTT-CTATTATTATTAGTAAGATT
1 TTATAAAAATGTATTCATAAATGACGATCATTGAAATATTTTTTACTATAATTATTAGTAAGATT
1892504 TATACCCA
66 TATACCCA
* * *
1892512 TTATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAAAATGTATTCAT-AAATGACGATCATTGAAATATTTTTTACTATAATTATTAGTAAGAT
1892577 TTA
65 TTA
1892580 CTCCATTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 17 0.28
73 24 0.39
74 20 0.33
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (73 bp):
TTATAAAAATGTATTCATAAATGACGATCATTGAAATATTTTTTACTATAATTATTAGTAAGATT
TATACCCA
Found at i:1892592 original size:74 final size:72
Alignment explanation
Indices: 1892438--1892594 Score: 219
Period size: 74 Copynumber: 2.2 Consensus size: 72
1892428 CAAAACCTAT
* * *
1892438 ATTTATAAAAATGTATTCATTAATGACGATCATTGAAATATTTTTTCTATTATTATTAGTAAGAT
1 ATTTATAAATATGTATTCATAAATGACGATCATTGAAATATTTTTTCTATAATTATTAGTAAGAT
1892503 TTATACCC
66 TTATA-CC
* *
1892511 A-TTATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAG
1 ATTTATAAATATGTATTCAT-AAATGACGATCATTGAAATATTTTTT-CTATAATTATTAGTAAG
1892575 ATTTACT-CC
64 ATTTA-TACC
1892584 ATTTATAAATA
1 ATTTATAAATA
1892595 AAAAATTTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
72 17 0.23
73 28 0.37
74 29 0.39
75 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (72 bp):
ATTTATAAATATGTATTCATAAATGACGATCATTGAAATATTTTTTCTATAATTATTAGTAAGAT
TTATACC
Found at i:1898896 original size:32 final size:32
Alignment explanation
Indices: 1898860--1898961 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
1898850 TGAGGGATTG
1898860 GCGCTGCAGGTGCTGGAGGGGAAGTTTTGGCA
1 GCGCTGCAGGTGCTGGAGGGGAAGTTTTGGCA
** *
1898892 GCGCTGCA-GCCCT-G-GGGG-A-TTGGTGCTGCA
1 GCGCTGCAGGTGCTGGAGGGGAAGTT-TTG--GCA
*
1898922 GCGTTGCAGGTGCTGGAGGGGAAGTTTTGGCA
1 GCGCTGCAGGTGCTGGAGGGGAAGTTTTGGCA
*
1898954 ACGCTGCA
1 GCGCTGCA
1898962 ACGTTGGGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 4 0.08
30 11 0.21
31 6 0.11
32 18 0.34
33 4 0.08
34 3 0.06
35 2 0.04
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.22
Consensus pattern (32 bp):
GCGCTGCAGGTGCTGGAGGGGAAGTTTTGGCA
Found at i:1898911 original size:54 final size:54
Alignment explanation
Indices: 1898824--1898983 Score: 176
Period size: 62 Copynumber: 2.8 Consensus size: 54
1898814 CTCCAGCAGA
* * *
1898824 GGGAAGTTTTGGCAGGGCCGCAGCGCTGAGGGATTGGCGCTGCAGGTGCTGGAG
1 GGGAAGTTTTGGCAGCGCTGCAGCGCTGGGGGATTGGCGCTGCAGGTGCTGGAG
*
1898878 GGGAAGTTTTGGCAGCGCTGCAGCCCTGGGGGATTGGTGCTGCAGCGTTGCAGGTGCTGGAG
1 GGGAAGTTTTGGCAGCGCTGCAGCGCTGGGGGA-T--TG--GC-GC--TGCAGGTGCTGGAG
* * * *
1898940 GGGAAGTTTTGGCAACGCTGCAACGTTGGGGGATTGGCCCTGCA
1 GGGAAGTTTTGGCAGCGCTGCAGCGCTGGGGGATTGGCGCTGCA
1898984 ACGCTGCAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
54 33 0.37
55 1 0.01
56 1 0.01
57 4 0.04
59 4 0.04
60 2 0.02
61 1 0.01
62 43 0.48
ACGTcount: A:0.15, C:0.19, G:0.44, T:0.21
Consensus pattern (54 bp):
GGGAAGTTTTGGCAGCGCTGCAGCGCTGGGGGATTGGCGCTGCAGGTGCTGGAG
Found at i:1898961 original size:62 final size:62
Alignment explanation
Indices: 1898861--1899023 Score: 213
Period size: 62 Copynumber: 2.6 Consensus size: 62
1898851 GAGGGATTGG
** *
1898861 CGCTGCAGGTGCTGGAGGGGAAGTTTTGGCAGCGCTGCAGCCCTGGGGGATTGGTGCTGCAG
1 CGCTGCAGGTGCTGGAGGGGAAGTTTTGGCAGCGCTGCAGCCCTGGGGGATTGGCCCTGCAA
* * * **
1898923 CGTTGCAGGTGCTGGAGGGGAAGTTTTGGCAACGCTGCAACGTTGGGGGATTGGCCCTGCAA
1 CGCTGCAGGTGCTGGAGGGGAAGTTTTGGCAGCGCTGCAGCCCTGGGGGATTGGCCCTGCAA
* *
1898985 CGCTGCAGTTGCTAGGATGGG-AG-TTTGGCAGCGCTGCAG
1 CGCTGCAGGTGCT-GGAGGGGAAGTTTTGGCAGCGCTGCAG
1899024 GTGCTGGAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
61 14 0.16
62 67 0.77
63 6 0.07
ACGTcount: A:0.15, C:0.20, G:0.42, T:0.22
Consensus pattern (62 bp):
CGCTGCAGGTGCTGGAGGGGAAGTTTTGGCAGCGCTGCAGCCCTGGGGGATTGGCCCTGCAA
Found at i:1900902 original size:25 final size:25
Alignment explanation
Indices: 1900840--1900903 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1900830 AAAAAATGAA
1900840 AATAT-AATACAAATGTAAACACCT
1 AATATAAATACAAATGTAAACACCT
* *
1900864 AATA-ATAGTCCAAATGTAAACATCC-
1 AATATA-AATACAAATGTAAACA-CCT
1900889 AATATAAATACAAAT
1 AATATAAATACAAAT
1900904 CTTAGTGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 4 0.12
25 25 0.78
26 3 0.09
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (25 bp):
AATATAAATACAAATGTAAACACCT
Found at i:1901491 original size:22 final size:22
Alignment explanation
Indices: 1901463--1901514 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1901453 AAATGTGTGT
1901463 ATATATATACAAACATAAATAC
1 ATATATATACAAACATAAATAC
*
1901485 ATATATATACAAACATATATAC
1 ATATATATACAAACATAAATAC
1901507 ATATATAT
1 ATATATAT
1901515 GTATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATATATACAAACATAAATAC
Found at i:1901502 original size:12 final size:12
Alignment explanation
Indices: 1901465--1901507 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1901455 ATGTGTGTAT
1901465 ATATATACAAAC
1 ATATATACAAAC
* *
1901477 ATAAATAC--AT
1 ATATATACAAAC
1901487 ATATATACAAAC
1 ATATATACAAAC
1901499 ATATATACA
1 ATATATACA
1901508 TATATATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.32
12 17 0.68
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (12 bp):
ATATATACAAAC
Found at i:1906836 original size:16 final size:16
Alignment explanation
Indices: 1906817--1906858 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1906807 TAATATGTTA
1906817 AATTACTAATTTAATT
1 AATTACTAATTTAATT
* *
1906833 AATTGATTCA-TTAATT
1 AATT-ACTAATTTAATT
1906849 AATTACTAAT
1 AATTACTAAT
1906859 ACATGATTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 4
0.71 0.14 0.14
Matches are distributed among these distances:
15 3 0.15
16 14 0.70
17 3 0.15
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTACTAATTTAATT
Found at i:1907004 original size:17 final size:18
Alignment explanation
Indices: 1906979--1907013 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1906969 CTTCTAATAC
1906979 ATTACATTACTTAATTAA
1 ATTACATTACTTAATTAA
*
1906997 ATTA-ATTATTTAATTAA
1 ATTACATTACTTAATTAA
1907014 CTCATTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTACATTACTTAATTAA
Found at i:1908520 original size:21 final size:21
Alignment explanation
Indices: 1908496--1908535 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1908486 CCTAAATTTT
1908496 TTTTAAGAAA-CCCAAAAACTC
1 TTTT-AGAAAGCCCAAAAACTC
*
1908517 TTTTAGAAAGCCTAAAAAC
1 TTTTAGAAAGCCCAAAAAC
1908536 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (21 bp):
TTTTAGAAAGCCCAAAAACTC
Found at i:1908605 original size:13 final size:13
Alignment explanation
Indices: 1908589--1908628 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1908579 ACCATAATCC
*
1908589 ACAAAAAAAAGAA
1 ACAAAAAAAACAA
1908602 ACAAAAAAAACAA
1 ACAAAAAAAACAA
* *
1908615 ATAAAAAACACAA
1 ACAAAAAAAACAA
1908628 A
1 A
1908629 ATGCAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (13 bp):
ACAAAAAAAACAA
Found at i:1910787 original size:20 final size:20
Alignment explanation
Indices: 1910762--1910811 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1910752 TAACATAAAA
*
1910762 TTAAATTAAAACAATTTGAT
1 TTAAATTAAAACAATATGAT
* **
1910782 TTAAATTGACTCAATATGAT
1 TTAAATTAAAACAATATGAT
*
1910802 TTAAACTAAA
1 TTAAATTAAA
1910812 TTACGAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (20 bp):
TTAAATTAAAACAATATGAT
Found at i:1912274 original size:33 final size:34
Alignment explanation
Indices: 1912193--1912283 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
1912183 AGCCTCGTAA
* *
1912193 TGTTTTTTACAGGATCAAGTGAAACCTTTACAAG
1 TGTTTTTTACAAGATCAAGTGAAACCCTTACAAG
* * *
1912227 -GTTTCTTACGAGATCAAGTGAAACCCTTGC-AG
1 TGTTTTTTACAAGATCAAGTGAAACCCTTACAAG
* *
1912259 TGTTTTTTTCAAGATCAAGCGAAAC
1 TGTTTTTTACAAGATCAAGTGAAAC
1912284 TCTTCAACAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (34 bp):
TGTTTTTTACAAGATCAAGTGAAACCCTTACAAG
Found at i:1918594 original size:25 final size:26
Alignment explanation
Indices: 1918547--1918597 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1918537 AAATAACTTC
*
1918547 TTTTTATCTCAAATTAATGTAATTAA
1 TTTTTATCTCAAATTAATATAATTAA
1918573 TTTTTAT-TCAAATATAA-ATAATTAA
1 TTTTTATCTCAAAT-TAATATAATTAA
1918598 AATGTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTATCTCAAATTAATATAATTAA
Found at i:1919531 original size:15 final size:16
Alignment explanation
Indices: 1919495--1919529 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1919485 TTATTCAAAC
*
1919495 TTTTATTATTTGGATT
1 TTTTATTATTTCGATT
*
1919511 TTTTATTATTTCTATT
1 TTTTATTATTTCGATT
1919527 TTT
1 TTT
1919530 ATAATGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTATTATTTCGATT
Found at i:1922348 original size:11 final size:11
Alignment explanation
Indices: 1922334--1922440 Score: 83
Period size: 11 Copynumber: 9.4 Consensus size: 11
1922324 TTCTTTTTGG
1922334 TTTTTTTTCTT
1 TTTTTTTTCTT
1922345 TTTTTTTTCTT
1 TTTTTTTTCTT
* *
1922356 TTTGTTGTC-T
1 TTTTTTTTCTT
*
1922366 TTTTTTTCCTT
1 TTTTTTTTCTT
* *
1922377 TCTTTATTCTT
1 TTTTTTTTCTT
*
1922388 TTCTTTCTTCTTT
1 TT-TTTTTTC-TT
1922401 TGTCCTTTTTTCCTT
1 T-T--TTTTTT-CTT
*
1922416 TTTTCTTTC-T
1 TTTTTTTTCTT
1922426 TTTTTTTTCTT
1 TTTTTTTTCTT
1922437 TTTT
1 TTTT
1922441 AATTCCCTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
10 16 0.21
11 34 0.45
12 11 0.14
13 3 0.04
14 2 0.03
15 9 0.12
16 1 0.01
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:1922357 original size:32 final size:34
Alignment explanation
Indices: 1922315--1922440 Score: 86
Period size: 32 Copynumber: 3.8 Consensus size: 34
1922305 AAATCATTCA
* * *
1922315 TTTTTCCTTTTCTTTTTG-GTTTTTTTT-CTTTT
1 TTTTTTCTTTTCTTTTTGTCTTTTTTTTCCTTTC
*
1922347 TTTTTTC-TTT-TTGTTGTCTTTTTTTTCCTTTC
1 TTTTTTCTTTTCTTTTTGTCTTTTTTTTCCTTTC
* *
1922379 TTTATTCTTTTCTTTCT-TCTTTTGTCCTTT--TTTCC
1 TTTTTTCTTTTCTTTTTGTCTTTT-T--TTTCCTTT-C
* *
1922414 TTTTTTCTTTCTTTTTTTTTCTTTTTT
1 TTTTTTCTTT-TCTTTTTGTCTTTTTT
1922441 AATTCCCTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
30 5 0.07
31 11 0.15
32 16 0.22
33 9 0.12
34 8 0.11
35 10 0.14
36 9 0.12
37 6 0.08
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (34 bp):
TTTTTTCTTTTCTTTTTGTCTTTTTTTTCCTTTC
Found at i:1922373 original size:20 final size:20
Alignment explanation
Indices: 1922345--1922441 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
1922335 TTTTTTTCTT
1922345 TTTTTTTTCTTTTTGT-TGTC
1 TTTTTTTTCTTTTT-TATGTC
1922365 TTTTTTTTCCTTTCTTTAT-TC
1 TTTTTTTT-CTTT-TTTATGTC
* *
1922386 TTTTCTTTCTTCTTT-TGTC
1 TTTTTTTTCTTTTTTATGTC
* * * *
1922405 CTTTTTTCCTTTTTTCTTTC
1 TTTTTTTTCTTTTTTATGTC
1922425 TTTTTTTTTCTTTTTTA
1 -TTTTTTTTCTTTTTTA
1922442 ATTCCCTAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
18 1 0.02
19 16 0.26
20 14 0.23
21 27 0.44
22 3 0.05
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTATGTC
Found at i:1923428 original size:2 final size:2
Alignment explanation
Indices: 1923421--1923453 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1923411 TTTTGCTATG
1923421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1923454 TAAGTCAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1933909 original size:21 final size:19
Alignment explanation
Indices: 1933874--1933916 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1933864 TTTTCATTTA
1933874 ATTTTTTATTAAATTTTATTC
1 ATTTTTTATTAAA--TTATTC
1933895 ATTTTTTA-TACAATTATTC
1 ATTTTTTATTA-AATTATTC
1933914 ATT
1 ATT
1933917 AAATTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 10 0.48
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTATTAAATTATTC
Found at i:1936934 original size:15 final size:15
Alignment explanation
Indices: 1936897--1936935 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1936887 ACAATTTATC
1936897 TATAATTTATTTTGA
1 TATAATTTATTTTGA
* **
1936912 TATTATTTATTTTTT
1 TATAATTTATTTTGA
1936927 TATAATTTA
1 TATAATTTA
1936936 CTGTTAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TATAATTTATTTTGA
Found at i:1936956 original size:2 final size:2
Alignment explanation
Indices: 1936949--1936973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1936939 TTAACAATTC
1936949 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
1936974 ATGGTTCGAA
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:1938006 original size:111 final size:111
Alignment explanation
Indices: 1937793--1938015 Score: 250
Period size: 111 Copynumber: 2.0 Consensus size: 111
1937783 AGCATGTGAT
* * * * *
1937793 TTATAAACTTATTTAAATTTTATTTTGAGAGTTTAAGACCTTACAAGGTTGGGCTTAAGTTTTAG
1 TTATAAACTTACTTAAATTATATTTTCAGAGTTTAAGACCTCACAAGGTTGGGCTTAAGTTTCAG
** *
1937858 TCCATGATATAGATTGAGTCATGCGATGCATATGGATGAATGCATG
66 TCCATGATATAGATTGAGTCATGCGACCCATAAGGATGAATGCATG
* *** *
1937904 TTATAGACTTACTTAAATTATATTTTCAGAGTTTAAGACCTCATGTGGTTGGGGTTAAGTTTCAG
1 TTATAAACTTACTTAAATTATATTTTCAGAGTTTAAGACCTCACAAGGTTGGGCTTAAGTTTCAG
* * * * * * *
1937969 -CTCGTGATATAGGTTGGGTCGTGTGACCCCTAAGGATGGATGCATG
66 TC-CATGATATAGATTGAGTCATGCGACCCATAAGGATGAATGCATG
1938015 T
1 T
1938016 AGACTGAATT
Statistics
Matches: 91, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
110 1 0.01
111 90 0.99
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (111 bp):
TTATAAACTTACTTAAATTATATTTTCAGAGTTTAAGACCTCACAAGGTTGGGCTTAAGTTTCAG
TCCATGATATAGATTGAGTCATGCGACCCATAAGGATGAATGCATG
Found at i:1945166 original size:18 final size:16
Alignment explanation
Indices: 1945135--1945176 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
1945125 GAACAAATAG
1945135 TATAAAAAAATATAAA
1 TATAAAAAAATATAAA
1945151 TATAAATAATAATATAAA
1 TATAAA-AA-AATATAAA
1945169 TA-AAAAAA
1 TATAAAAAA
1945177 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 8 0.33
17 5 0.21
18 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TATAAAAAAATATAAA
Found at i:1946460 original size:7 final size:7
Alignment explanation
Indices: 1946448--1946473 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1946438 TAAGGATCTG
1946448 CTGCCAT
1 CTGCCAT
1946455 CTGCCAT
1 CTGCCAT
1946462 CTGCCAT
1 CTGCCAT
1946469 CTGCC
1 CTGCC
1946474 TTGAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.46, G:0.15, T:0.27
Consensus pattern (7 bp):
CTGCCAT
Found at i:1952828 original size:1 final size:1
Alignment explanation
Indices: 1952822--1952848 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1952812 TAAGTTTGGT
1952822 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1952849 TGGAGTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1983280 original size:52 final size:52
Alignment explanation
Indices: 1983200--1983310 Score: 195
Period size: 52 Copynumber: 2.1 Consensus size: 52
1983190 TGAAGTTCTA
*
1983200 GTCATTATCCACGGATGAGTTTTGCTGGATTGAACAATTGCTGTAGGTCCTT
1 GTCATTATCCACGGATGAGTTTTGCTGGACTGAACAATTGCTGTAGGTCCTT
* *
1983252 GTCATTATCCATGGATGAGTTTTTCTGGACTGAACAATTGCTGTAGGTCCTT
1 GTCATTATCCACGGATGAGTTTTGCTGGACTGAACAATTGCTGTAGGTCCTT
1983304 GTCATTA
1 GTCATTA
1983311 ATAGTTTTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (52 bp):
GTCATTATCCACGGATGAGTTTTGCTGGACTGAACAATTGCTGTAGGTCCTT
Found at i:1992979 original size:2 final size:2
Alignment explanation
Indices: 1992974--1993005 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1992964 ATTAACAATC
1992974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1993006 GGGTGAAGTA
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):
AT
Found at i:2000012 original size:22 final size:22
Alignment explanation
Indices: 1999984--2000028 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1999974 ATAATCCAAC
*
1999984 ATGATGATT-GTCATGGAAATGA
1 ATGATGATTGGT-AAGGAAATGA
2000006 ATGATGATTGGTAAGGAAATGA
1 ATGATGATTGGTAAGGAAATGA
2000028 A
1 A
2000029 CTAATTAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (22 bp):
ATGATGATTGGTAAGGAAATGA
Found at i:2000581 original size:59 final size:58
Alignment explanation
Indices: 2000472--2001043 Score: 560
Period size: 59 Copynumber: 9.7 Consensus size: 58
2000462 CATTGGGGAA
* * *
2000472 TTAAATCGAACCTG-TTTGAGATA-GTCGAGCCTAGATTAAGTTTAGAAATTTGAATTTT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTAG-AATTTCAA-TTT
* * * * *
2000530 TTAAATCGAACCTATTGTG-GATAGGTCGAGCCTATATCAAGTTTACGAATTTCAATCT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTA-GAATTTCAATTT
* * * * * *
2000588 TTAAATCAAACCTATTTTGATATAGGTCGAGCCTAGATTAAGTTTAAAATTTTCAATTTT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGAA-TTTCAA-TTT
* * * * * * *
2000648 TTAAGTTGAACTTGTTGTGAGATAGGTTGAGCCTATATCAAGTCTAAGAATTTCAATCT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCT-AGAATTTCAATTT
* * *
2000707 TTAAGTTGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAATCT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTA-GAATTTCAATTT
* * * * *
2000766 TTAAATCGAACTTGTTTTGAGATAGGCCGAGCCTAGGTTAAGTATAGGAATTTCAATTTTTT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTA-GAATTTCAA---TTT
* * * * * * *
2000828 TTAAATCGAACCT-ATTTGAGATAGGTCCAACCTAGATTAAGTTTACGAATTTTAATCT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTA-GAATTTCAATTT
*
2000886 TTAAATCAAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTCAATTT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTAG-AATTTCAATTT
** * * * *
2000945 TTAAATTAAACCTGTTTTGAGATAGATCGAGCCTAGATTAAATCTAAGAATTTTAA-TT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCT-AGAATTTCAATTT
* * * *
2001003 TTAAATCAAACCTATTTAGAGATAGGTCAAGCCTAGATCAA
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAA
2001044 ATAGCTTAAG
Statistics
Matches: 432, Mismatches: 68, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
58 91 0.21
59 245 0.57
60 45 0.10
61 37 0.09
62 14 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (58 bp):
TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTAGAATTTCAATTT
Found at i:2000924 original size:179 final size:175
Alignment explanation
Indices: 2000472--2001040 Score: 637
Period size: 179 Copynumber: 3.2 Consensus size: 175
2000462 CATTGGGGAA
* * * * *
2000472 TTAAATCGAACCTGTTTGAGATA-GTCGAGCCTAGATTAAGTTTAGAAATTTGAATTTTTTAAAT
1 TTAAATCGAACCTATTTGAGATAGGTCCAACCTAGATTAAGTTTAG-AATTTCAA-TCTTTAAAT
* * * *
2000536 CGAACCTATTGTG-GATAGGTCGAGCCTATATCAAGTTTACGAATTTCAATCTTTAAATCAAACC
64 CGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAATCTTTAAATCAAACC
* * * *
2000600 TATTTTGATATAGGTCGAGCCTAGATTAAGTTTAAAATTTTCAATTTT
129 TGTTTTGAGATAGGTCGAGCCTAGATTAAGTATAGAA-TTTCAATTTT
* * * * ** * * * * *
2000648 TTAAGTTGAACTTGTTGTGAGATAGGTTGAGCCTATATCAAGTCTAAGAATTTCAATCTTTAAGT
1 TTAAATCGAACCTATT-TGAGATAGGTCCAACCTAGATTAAGT-TTAGAATTTCAATCTTTAAAT
* * *
2000713 TGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAATCTTTAAATCGAACT
64 CGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAATCTTTAAATCAAACC
* *
2000778 TGTTTTGAGATAGGCCGAGCCTAGGTTAAGTATAGGAATTTCAATTTTTT
129 TGTTTTGAGATAGGTCGAGCCTAGATTAAGTATA-GAATTTCAA--TTTT
*
2000828 TTAAATCGAACCTATTTGAGATAGGTCCAACCTAGATTAAGTTTACGAATTTTAATCTTTAAATC
1 TTAAATCGAACCTATTTGAGATAGGTCCAACCTAGATTAAGTTTA-GAATTTCAATCTTTAAATC
* * *
2000893 AAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTA-GAAATTTCAATTTTTAAATTAAACC
65 GAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACG-AATTTCAATCTTTAAATCAAACC
* * * *
2000957 TGTTTTGAGATAGATCGAGCCTAGATTAAATCTAAGAATTTTAA--TT
129 TGTTTTGAGATAGGTCGAGCCTAGATTAAGTAT-AGAATTTCAATTTT
*
2001003 TTAAATCAAACCTATTTAGAGATAGGT-CAAGCCTAGAT
1 TTAAATCGAACCTATTT-GAGATAGGTCCAA-CCTAGAT
2001041 CAAATAGCTT
Statistics
Matches: 333, Mismatches: 48, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
175 21 0.06
176 29 0.09
177 24 0.07
178 107 0.32
179 135 0.41
180 17 0.05
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (175 bp):
TTAAATCGAACCTATTTGAGATAGGTCCAACCTAGATTAAGTTTAGAATTTCAATCTTTAAATCG
AACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTCTACGAATTTCAATCTTTAAATCAAACCTG
TTTTGAGATAGGTCGAGCCTAGATTAAGTATAGAATTTCAATTTT
Found at i:2005055 original size:16 final size:16
Alignment explanation
Indices: 2005034--2005069 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2005024 TCATTAGAAA
2005034 TAGTTATATAAACCAC
1 TAGTTATATAAACCAC
2005050 TAGTTATATAAACCAC
1 TAGTTATATAAACCAC
2005066 TAGT
1 TAGT
2005070 GGGTTAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (16 bp):
TAGTTATATAAACCAC
Found at i:2007123 original size:74 final size:74
Alignment explanation
Indices: 2007033--2007231 Score: 249
Period size: 74 Copynumber: 2.7 Consensus size: 74
2007023 AGCCAGTTCA
* *
2007033 AAGACAGAGAAGACTTAGTCGACTAAGAAGCATGGTTAGTCAACTATGAGCTTACTACCA-AAGA
1 AAGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCTTACTACCAGAAGA
2007097 CTTCAATTAC
66 -TTCAATTAC
* * * * * * * *
2007107 AAGACAGAG-AGAACTTAATCGACTAAGAAGCTTGGCTAGTCAATTAAAAGTTTACTGCTAGAGG
1 AAGACAGAGAAG-ACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCTTACTACCAGAAG
*
2007171 ATTCAATTAT
65 ATTCAATTAC
* *
2007181 AAGACAGAGAAGACTTAATCAACTAAGAAGCATGGTTAGTCATCTAAGAGC
1 AAGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGC
2007232 ACTTTGACTA
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
73 2 0.02
74 97 0.93
75 5 0.05
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (74 bp):
AAGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCTTACTACCAGAAGA
TTCAATTAC
Found at i:2014235 original size:2 final size:2
Alignment explanation
Indices: 2014228--2014263 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2014218 GAAAAAGAGA
*
2014228 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2014264 CCTCAGGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2029118 original size:21 final size:22
Alignment explanation
Indices: 2029083--2029126 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2029073 CTCTTAAAGT
2029083 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
2029105 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
2029126 A
1 A
2029127 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:2033691 original size:27 final size:29
Alignment explanation
Indices: 2033654--2033715 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
2033644 ATCAACATAG
*
2033654 CAGAATGTCATAAATAAC-TAAACATCAT
1 CAGAATGTCATAAACAACTTAAACATCAT
*
2033682 TAGAAT-TCATAAACAACTTAAACATCAT
1 CAGAATGTCATAAACAACTTAAACATCAT
2033710 CAGAAT
1 CAGAAT
2033716 CAGACTCTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (29 bp):
CAGAATGTCATAAACAACTTAAACATCAT
Found at i:2042932 original size:29 final size:30
Alignment explanation
Indices: 2042887--2042994 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 30
2042877 ATTACCTTAT
*
2042887 TAAAAATATTTATAATTATATAAATAAAATA
1 TAAAAATA-TTAAAATTATATAAATAAAATA
*
2042918 -AAAAATATTAAAATTA-A-AATTAAAATA
1 TAAAAATATTAAAATTATATAAATAAAATA
* *
2042945 TAAGAATA--AAAATTAAAATAAA-ATAAATA
1 TAAAAATATTAAAATT-ATATAAATA-AAATA
*
2042974 TAAAAA-ATTAAATTTATATAA
1 TAAAAATATTAAAATTATATAA
2042995 TAATAGGTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.10
27 10 0.16
28 10 0.16
29 25 0.40
30 12 0.19
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (30 bp):
TAAAAATATTAAAATTATATAAATAAAATA
Found at i:2042942 original size:20 final size:20
Alignment explanation
Indices: 2042919--2042964 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2042909 AATAAAATAA
*
2042919 AAAATATTAA-AATTAAAATT
1 AAAATA-TAAGAATAAAAATT
2042939 AAAATATAAGAATAAAAATT
1 AAAATATAAGAATAAAAATT
2042959 AAAATA
1 AAAATA
2042965 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAATATAAGAATAAAAATT
Found at i:2043084 original size:32 final size:32
Alignment explanation
Indices: 2043047--2043160 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 32
2043037 TATGTTAAAG
2043047 AAATGAAAATAAATATATATAGACATAATAAT
1 AAATGAAAATAAATATATATAGACATAATAAT
*
2043079 AAATG-AAATAAATA-ATAT-GTCATTAA-AAT
1 AAATGAAAATAAATATATATAGACA-TAATAAT
* * * *
2043108 ATAATTTAAAATATATATTATATA-ATAAAATAAT
1 A-AA-TGAAAATAAATA-TATATAGACATAATAAT
*
2043142 -AATAAAAATAAA-ATATATA
1 AAATGAAAATAAATATATATA
2043161 AAAATAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
29 13 0.20
30 10 0.15
31 18 0.27
32 15 0.23
33 2 0.03
34 8 0.12
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (32 bp):
AAATGAAAATAAATATATATAGACATAATAAT
Found at i:2043158 original size:27 final size:26
Alignment explanation
Indices: 2043127--2043205 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 26
2043117 AATATATATT
2043127 ATATAATAAAATAATAATAAAAATAAA
1 ATAT-ATAAAATAATAATAAAAATAAA
2043154 ATATAT-AAA-AAT-A-AAAAATAAA
1 ATATATAAAATAATAATAAAAATAAA
* *
2043176 ATAT-TATAATTA-AATAAAAATAAA
1 ATATATAAAATAATAATAAAAATAAA
2043200 ATATAT
1 ATATAT
2043206 GACATTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
21 1 0.02
22 15 0.33
23 3 0.07
24 16 0.36
25 4 0.09
26 2 0.04
27 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
ATATATAAAATAATAATAAAAATAAA
Found at i:2043212 original size:25 final size:23
Alignment explanation
Indices: 2043142--2043214 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
2043132 ATAAAATAAT
2043142 AATAAAAATAAAATATATAA--A
1 AATAAAAATAAAATATATAATTA
2043163 AATAAAAAATAAAATATTATAATTA
1 AAT-AAAAATAAAATA-TATAATTA
2043188 AATAAAAATAAAATATATGACATTA
1 AATAAAAATAAAATATAT-A-ATTA
2043213 AA
1 AA
2043215 ATTATATAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.07
22 12 0.26
23 8 0.17
24 13 0.28
25 10 0.22
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (23 bp):
AATAAAAATAAAATATATAATTA
Found at i:2043218 original size:31 final size:31
Alignment explanation
Indices: 2043124--2043228 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
2043114 TAAAATATAT
*
2043124 ATTATATAATAAA-ATAATAATAAAA-A-TAAA
1 ATTATATAA-AAATA-AAAAATAAAACATTAAA
* *
2043154 A-TATATAAAAATAAAAAATAAAATATTATA
1 ATTATATAAAAATAAAAAATAAAACATTAAA
* * **
2043184 ATTAAATAAAAATAAAATATATGACATTAAA
1 ATTATATAAAAATAAAAAATAAAACATTAAA
2043215 ATTATATAAGAAAT
1 ATTATATAA-AAAT
2043229 GATATATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
28 12 0.20
29 9 0.15
30 5 0.08
31 31 0.51
32 4 0.07
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (31 bp):
ATTATATAAAAATAAAAAATAAAACATTAAA
Found at i:2043223 original size:25 final size:25
Alignment explanation
Indices: 2043126--2043257 Score: 94
Period size: 26 Copynumber: 5.2 Consensus size: 25
2043116 AAATATATAT
2043126 TATATAA-TAAAA-TAATAATAAAAA
1 TATATAATTAAAATTAATAAT-AAAA
* * * *
2043150 TAAAATATATAAAAATAAAAAATAAAA
1 T-ATATA-ATTAAAATTAATAATAAAA
*
2043177 TATTATAATT-AAA-TAAAAATAAAA
1 TA-TATAATTAAAATTAATAATAAAA
*
2043201 TATATGACATTAAAATTATATAA-GAAA
1 TATAT-A-ATTAAAATTA-ATAATAAAA
*
2043228 TGATATATTTAAAATTAATAATAAAA
1 T-ATATAATTAAAATTAATAATAAAA
2043254 TATA
1 TATA
2043258 AATATATTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
23 3 0.04
24 14 0.16
25 17 0.20
26 20 0.24
27 19 0.22
28 12 0.14
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (25 bp):
TATATAATTAAAATTAATAATAAAA
Found at i:2043434 original size:15 final size:15
Alignment explanation
Indices: 2043414--2043467 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
2043404 TTTTCCCTGT
2043414 AATCACATTACTTGC
1 AATCACATTACTTGC
2043429 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
2043444 AATCACATTACCTGT
1 AATCACATTACTTGC
2043459 AATCACATT
1 AATCACATT
2043468 GCATTATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:2045279 original size:18 final size:18
Alignment explanation
Indices: 2045256--2045300 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2045246 CATACTTTTT
2045256 AGTCTTCTTAGTCGACTA
1 AGTCTTCTTAGTCGACTA
2045274 AGTCTTCTTAGTCGACTA
1 AGTCTTCTTAGTCGACTA
2045292 AGTCTTCTT
1 AGTCTTCTT
2045301 TATCTCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (18 bp):
AGTCTTCTTAGTCGACTA
Found at i:2045861 original size:35 final size:35
Alignment explanation
Indices: 2045821--2045973 Score: 153
Period size: 36 Copynumber: 4.3 Consensus size: 35
2045811 NNNNNNNNNN
* * *
2045821 CTTAATTAAATAATTTAATTAATTAAGCTCAATAA
1 CTTAATTAAATAATTTAATCAATTAGGCCCAATAA
* * *
2045856 TTTAATTAAATAATTTTAATCAATTAGGCCCCATGA
1 CTTAATTAAATAA-TTTAATCAATTAGGCCCAATAA
* * * *
2045892 CTTTATTAAACAAATTTAATCAATTACGCTCAATAA
1 CTTAATTAAA-TAATTTAATCAATTAGGCCCAATAA
*** * *
2045928 CTTAATTGTTTAATTTAATTAATTAGGCCCAATGA
1 CTTAATTAAATAATTTAATCAATTAGGCCCAATAA
2045963 CTTAATTAAAT
1 CTTAATTAAAT
2045974 TGTTTATTCA
Statistics
Matches: 91, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
35 40 0.44
36 49 0.54
37 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (35 bp):
CTTAATTAAATAATTTAATCAATTAGGCCCAATAA
Found at i:2045881 original size:36 final size:35
Alignment explanation
Indices: 2045822--2045973 Score: 126
Period size: 35 Copynumber: 4.3 Consensus size: 35
2045812 NNNNNNNNNC
*
2045822 TTAATTAAATAATTTAATTAATTAAGCTCAATAAT
1 TTAATTAAATAATTTAATCAATTAAGCTCAATAAT
* * * *
2045857 TTAATTAAATAATTTTAATCAATTAGGCCCCATGACT
1 TTAATTAAATAA-TTTAATCAATTAAGCTCAAT-AAT
* * *
2045894 TT-ATTAAACAAATTTAATCAATTACGCTCAATAAC
1 TTAATTAAA-TAATTTAATCAATTAAGCTCAATAAT
*** * * * * *
2045929 TTAATTGTTTAATTTAATTAATTAGGCCCAATGAC
1 TTAATTAAATAATTTAATCAATTAAGCTCAATAAT
2045964 TTAATTAAAT
1 TTAATTAAAT
2045974 TGTTTATTCA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
35 43 0.47
36 42 0.46
37 6 0.07
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (35 bp):
TTAATTAAATAATTTAATCAATTAAGCTCAATAAT
Found at i:2045988 original size:71 final size:72
Alignment explanation
Indices: 2045821--2045972 Score: 200
Period size: 71 Copynumber: 2.1 Consensus size: 72
2045811 NNNNNNNNNN
* * *
2045821 CTTAATTAAA-TAATTTAATTAATTAAGCTCAATAATTTAATTAAATAATTTTAATCAATTAGGC
1 CTTAATTAAACAAATTTAATCAATTAAGCTCAATAACTTAATTAAATAATTTTAATCAATTAGGC
*
2045885 CCCATGA
66 CCAATGA
* * *** *
2045892 CTTTATTAAACAAATTTAATCAATTACGCTCAATAACTTAATTGTTTAA-TTTAATTAATTAGGC
1 CTTAATTAAACAAATTTAATCAATTAAGCTCAATAACTTAATTAAATAATTTTAATCAATTAGGC
2045956 CCAATGA
66 CCAATGA
2045963 CTTAATTAAA
1 CTTAATTAAA
2045973 TTGTTTATTC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
71 38 0.55
72 31 0.45
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (72 bp):
CTTAATTAAACAAATTTAATCAATTAAGCTCAATAACTTAATTAAATAATTTTAATCAATTAGGC
CCAATGA
Found at i:2051237 original size:33 final size:33
Alignment explanation
Indices: 2051199--2051264 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2051189 GCTTCAACAT
2051199 TACAATTAACGCTAGCACAAACTTACAAACACA
1 TACAATTAACGCTAGCACAAACTTACAAACACA
2051232 TACAATTAACGCTAGCACAAACTTACAAACACA
1 TACAATTAACGCTAGCACAAACTTACAAACACA
2051265 CTAAACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (33 bp):
TACAATTAACGCTAGCACAAACTTACAAACACA
Found at i:2055914 original size:17 final size:17
Alignment explanation
Indices: 2055894--2055928 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2055884 AAAAATTTTA
*
2055894 TTAATAAAATATTAATT
1 TTAATAAAATATAAATT
*
2055911 TTAATAAATTATAAATT
1 TTAATAAAATATAAATT
2055928 T
1 T
2055929 AATTAGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATAAAATATAAATT
Found at i:2056952 original size:35 final size:35
Alignment explanation
Indices: 2056911--2057141 Score: 259
Period size: 35 Copynumber: 6.5 Consensus size: 35
2056901 TACTTGATTA
* *
2056911 AAATTATTTACTTAAGTTGTTGGGCTTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTAATT
* * *
2056946 AAATTATTTAATTAA-TTCATTGAGCCTAATTGATT
1 AAATTATTTAATTAAGTT-ATTGGGCTTAATTAATT
* * * *
2056981 AAAATTGTTTATTTAAGTTACTGGACTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCTTAATTAATT
* * *
2057017 AAATTATTTAATTAAGTCATTGGGCCTAATTTATT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTAATT
* *
2057052 AAAATTATTTAATTAAGTTGTTGGACTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCTTAATTAATT
*
2057088 AAATTATTTAATTAAGTTATTGGG-TCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCT-TAATTAATT
**
2057123 AAATTAAATAATTAAGTTA
1 AAATTATTTAATTAAGTTA
2057142 ATTGAGTTTC
Statistics
Matches: 162, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
34 3 0.02
35 102 0.63
36 55 0.34
37 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.46
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCTTAATTAATT
Found at i:2056979 original size:71 final size:71
Alignment explanation
Indices: 2056904--2057140 Score: 343
Period size: 71 Copynumber: 3.4 Consensus size: 71
2056894 TCTCAAGTAC
* * *
2056904 TTGATTAAAATTATTTACTTAAGTTGTTGGGCTTAATTAATTAAATTATTTAATTAATTCATTGA
1 TTGATTAAAATTATTTAATTAAGTTGTTGGACTTAATTAATTAAATTATTTAATTAATTCATTGG
2056969 GCCTAA
66 GCCTAA
* * ** *
2056975 TTGATTAAAATTGTTTATTTAAGTTACTGGACTTAATTAATTAAATTATTTAATTAAGTCATTGG
1 TTGATTAAAATTATTTAATTAAGTTGTTGGACTTAATTAATTAAATTATTTAATTAATTCATTGG
2057040 GCCTAA
66 GCCTAA
*
2057046 TTTATTAAAATTATTTAATTAAGTTGTTGGACTTAATTAATTAAATTATTTAATTAAGTT-ATTG
1 TTGATTAAAATTATTTAATTAAGTTGTTGGACTTAATTAATTAAATTATTTAATTAA-TTCATTG
*
2057110 GGTCTAA
65 GGCCTAA
**
2057117 TTGATT-AAATTAAATAATTAAGTT
1 TTGATTAAAATTATTTAATTAAGTT
2057141 AATTGAGTTT
Statistics
Matches: 148, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
70 16 0.11
71 131 0.89
72 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (71 bp):
TTGATTAAAATTATTTAATTAAGTTGTTGGACTTAATTAATTAAATTATTTAATTAATTCATTGG
GCCTAA
Found at i:2057767 original size:44 final size:44
Alignment explanation
Indices: 2057704--2057787 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
2057694 GTTAGTTTTG
* *
2057704 TTTTTGCTATATTTTTATTTGTATATGATGCATGATTAACTCTA
1 TTTTTGCTACATTTTTATTTGTATATGATGCATAATTAACTCTA
*
2057748 TTTTTGTTACATTTTTATTTGTATATGATGCATAATTAAC
1 TTTTTGCTACATTTTTATTTGTATATGATGCATAATTAAC
2057788 CCTCACGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (44 bp):
TTTTTGCTACATTTTTATTTGTATATGATGCATAATTAACTCTA
Found at i:2061991 original size:2 final size:2
Alignment explanation
Indices: 2061986--2062014 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2061976 TTTGGGTGTG
2061986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2062015 TAATGTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2072229 original size:39 final size:39
Alignment explanation
Indices: 2072186--2072264 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
2072176 AAAAGGAATA
* *
2072186 TCCTTGTTATTTGGGATTAGTTCTTATAATCTTGGAGTC
1 TCCTTGTTATTTGGGAATAATTCTTATAATCTTGGAGTC
*
2072225 TCCTTGTTATTTTGGAATAATTCTTATAATCTTGGAGTC
1 TCCTTGTTATTTGGGAATAATTCTTATAATCTTGGAGTC
2072264 T
1 T
2072265 AAGCTTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (39 bp):
TCCTTGTTATTTGGGAATAATTCTTATAATCTTGGAGTC
Found at i:2072928 original size:18 final size:19
Alignment explanation
Indices: 2072881--2072928 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
2072871 TACGAAAAGG
2072881 AAAAATAAAAAATAAGTAAA
1 AAAAATAAAAAAT-AGTAAA
2072901 AAATAA-AAAAAAT-GTAAA
1 AAA-AATAAAAAATAGTAAA
2072919 AAAAATAAAA
1 AAAAATAAAA
2072929 TTACTAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 12 0.46
20 10 0.38
21 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (19 bp):
AAAAATAAAAAATAGTAAA
Found at i:2072928 original size:20 final size:18
Alignment explanation
Indices: 2072881--2072921 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2072871 TACGAAAAGG
2072881 AAAAATAAAAAATAAGTA
1 AAAAATAAAAAATAAGTA
2072899 AAAAATAAAAAA-AATGTA
1 AAAAATAAAAAATAA-GTA
2072917 AAAAA
1 AAAAA
2072922 AATAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAATAAGTA
Found at i:2084347 original size:29 final size:29
Alignment explanation
Indices: 2084281--2084340 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2084271 ATTTTACGTT
* *
2084281 TAAGACAATGCTGATAGTACGACAAGTAA
1 TAAGACAATGATGATAGTACGACAACTAA
*
2084310 TAAGACAATGATGATAGTATGACAACTAA
1 TAAGACAATGATGATAGTACGACAACTAA
2084339 TA
1 TA
2084341 TTACAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (29 bp):
TAAGACAATGATGATAGTACGACAACTAA
Found at i:2087549 original size:72 final size:69
Alignment explanation
Indices: 2087432--2087631 Score: 238
Period size: 72 Copynumber: 2.8 Consensus size: 69
2087422 CAAAAAGGTG
* *
2087432 AATGTGGATAGTAAAATGCCCACAAACATAGTTATGAGAGTGGATGAGTAAGTCTCCACCGCTTA
1 AATGTGGATAGTAAAATGCCCACAAACAAAGGTATGAGAGTGGATGAGTAAGTCTCCA---CTTA
2087497 ATTAATA
63 ATTAATA
* * * *
2087504 AATGTGGATAGTAAAATGCCTACAAACACAGGTATGAGAGTGGATGAGTAAGTCTCCATTTTATT
1 AATGTGGATAGTAAAATGCCCACAAACAAAGGTATGAGAGTGGATGAGTAAGTCTCCACTTAATT
**
2087569 GTTA
66 AATA
* * * * * *
2087573 AATGTGGATGGTAAAATGCCCACAAATATAAAGTTTGAAAGTAGATGAGTAAGTCTCCA
1 AATGTGGATAGTAAAATGCCCACAAACA-AAGGTATGAGAGTGGATGAGTAAGTCTCCA
2087632 ACACTTGATG
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
69 32 0.29
70 25 0.22
72 55 0.49
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (69 bp):
AATGTGGATAGTAAAATGCCCACAAACAAAGGTATGAGAGTGGATGAGTAAGTCTCCACTTAATT
AATA
Found at i:2087913 original size:71 final size:71
Alignment explanation
Indices: 2087838--2088011 Score: 183
Period size: 71 Copynumber: 2.5 Consensus size: 71
2087828 ATGCGGGGCG
* * *
2087838 TCATACCACATGTGACAAGGGCTAGATGTAGGGTGTTATTCCACACGAACACTT-GGGCTAGATG
1 TCATACCACATATGACAAGGGCTAGATGTAGGGCGCTATTCCACACGAACA-TTCGGGCTAGATG
2087902 TGAGGCA
65 TGAGGCA
* * * **
2087909 TCATACCACACATGACAA-GGTTCAGATGT-GAAGCGCTATTCCACATTAACATTCGGGCTAGAT
1 TCATACCACATATGACAAGGGCT-AGATGTAG-GGCGCTATTCCACACGAACATTCGGGCTAGAT
*
2087972 GTGGGGCA
64 GTGAGGCA
* * **
2087980 TTATACCATATATGATGAGGGCTAGATGTAGG
1 TCATACCACATATGACAAGGGCTAGATGTAGG
2088012 CCATCATACC
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
70 6 0.07
71 72 0.88
72 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (71 bp):
TCATACCACATATGACAAGGGCTAGATGTAGGGCGCTATTCCACACGAACATTCGGGCTAGATGT
GAGGCA
Found at i:2092870 original size:16 final size:17
Alignment explanation
Indices: 2092845--2092876 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2092835 CCATAATATC
2092845 TATTGCCCTAAAACCCT
1 TATTGCCCTAAAACCCT
2092862 TATTG-CCTAAAACCC
1 TATTGCCCTAAAACCC
2092877 ATGGCTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (17 bp):
TATTGCCCTAAAACCCT
Found at i:2107381 original size:6 final size:6
Alignment explanation
Indices: 2107372--2107440 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
2107362 TATTATAATT
* * *
2107372 AAAATAA AAAATA TTAAAATTA AAATTA AAATATA AGAATA AAAATT AAAAT-
1 AAAAT-A AAAATA --AAAA-TA AAAATA AAA-ATA AAAATA AAAATA AAAATA
2107424 AAAATA AAATATA AAAA
1 AAAATA AAA-ATA AAAA
2107441 ATTAACNNNN
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
5 5 0.10
6 22 0.43
7 18 0.35
8 4 0.08
9 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (6 bp):
AAAATA
Found at i:2107386 original size:21 final size:21
Alignment explanation
Indices: 2107360--2107402 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2107350 AATATTTTAT
*
2107360 AATATTATAATTAAAATAAAA
1 AATATTAAAATTAAAATAAAA
*
2107381 AATATTAAAATTAAAATTAAA
1 AATATTAAAATTAAAATAAAA
2107402 A
1 A
2107403 TATAAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATTAAAATTAAAATAAAA
Found at i:2107401 original size:12 final size:12
Alignment explanation
Indices: 2107363--2107439 Score: 65
Period size: 12 Copynumber: 6.6 Consensus size: 12
2107353 ATTTTATAAT
*
2107363 ATTATAATTAAA
1 ATTAAAATTAAA
*
2107375 A-TAAAA--AAT
1 ATTAAAATTAAA
2107384 ATTAAAATTAAA
1 ATTAAAATTAAA
2107396 ATTAAAATATAAGA
1 ATTAAAAT-TAA-A
*
2107410 ATAAAAATTAAA
1 ATTAAAATTAAA
2107422 A-TAAAA-TAAA
1 ATTAAAATTAAA
2107432 ATATAAAA
1 AT-TAAAA
2107440 AATTAACNNN
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
9 3 0.06
10 10 0.19
11 8 0.15
12 18 0.34
13 6 0.11
14 8 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (12 bp):
ATTAAAATTAAA
Found at i:2107404 original size:20 final size:20
Alignment explanation
Indices: 2107360--2107424 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
2107350 AATATTTTAT
* *
2107360 AATATTATAATTAAAATAAAA
1 AATATTAAAATTAAAAT-TAA
2107381 AATATTAAAATTAAAATTAA
1 AATATTAAAATTAAAATTAA
*
2107401 AATA-TAAGAATAAAAATTAA
1 AATATTAA-AATTAAAATTAA
2107421 AATA
1 AATA
2107425 AAATAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.08
20 21 0.52
21 16 0.40
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AATATTAAAATTAAAATTAA
Found at i:2107426 original size:25 final size:26
Alignment explanation
Indices: 2107372--2107445 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 26
2107362 TATTATAATT
* *
2107372 AAAATAAAAAATATTAAAATTAAAATT
1 AAAATAAAATATA-AAAAATTAAAATT
2107399 AAAATATAAGA-AT-AAAAATTAAAA-T
1 AAAATA-AA-ATATAAAAAATTAAAATT
2107424 AAAATAAAATATAAAAAATTAA
1 AAAATAAAATATAAAAAATTAA
2107446 CNNNNNNNNN
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
23 1 0.02
24 4 0.10
25 16 0.38
26 10 0.24
27 6 0.14
28 4 0.10
29 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (26 bp):
AAAATAAAATATAAAAAATTAAAATT
Found at i:2107526 original size:33 final size:33
Alignment explanation
Indices: 2107475--2107559 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 33
2107465 AAACAAATTA
**
2107475 AAAT-AAAATATATAATATAAAAAAT-ATGTTAAAG
1 AAATGAAAATA-A-AATATAAAAAATCATAAT-AAG
* * *
2107509 AAATGAAAATAAAATATATAAGATCATAATAAT
1 AAATGAAAATAAAATATAAAAAATCATAATAAG
2107542 AAATGAAAATAAAATATA
1 AAATGAAAATAAAATATA
2107560 TGTCATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 30 0.68
34 8 0.18
35 6 0.14
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATCATAATAAG
Found at i:2109326 original size:27 final size:25
Alignment explanation
Indices: 2109291--2109341 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2109281 CCTTTTCAAA
*
2109291 ATTTCTAAAATTATTTATTTATTTTAT
1 ATTTCTAAAA-TAATT-TTTATTTTAT
*
2109318 ATTTTTAAAATAATTTTTATTTTA
1 ATTTCTAAAATAATTTTTATTTTA
2109342 ATAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTCTAAAATAATTTTTATTTTAT
Found at i:2109348 original size:27 final size:27
Alignment explanation
Indices: 2109290--2109358 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
2109280 ACCTTTTCAA
* *
2109290 AATTTCTAAAATTATTTATTTATTTTAT
1 AATTTATAAAA-TAATTATTTATTTTAT
*
2109318 -ATTTTTAAAATAATT-TTTATTTTAAT
1 AATTTATAAAATAATTATTTATTTT-AT
2109344 AATTTATATAAATAA
1 AATTTATA-AAATAA
2109359 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 8 0.23
26 6 0.17
27 15 0.43
28 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTATAAAATAATTATTTATTTTAT
Done.