Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 128 of 222
Found at i:41406713 original size:24 final size:25
Alignment explanation
Indices: 41406672--41406718 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
41406662 AAATTTCGGA
*
41406672 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
41406696 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
41406719 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:41411355 original size:51 final size:49
Alignment explanation
Indices: 41411275--41411462 Score: 200
Period size: 51 Copynumber: 3.7 Consensus size: 49
41411265 TGCCTATAAA
*
41411275 CACGTGTGTAGTACTAA-GTGCAGGCTACTACGTGTA-TCGATAGATAATGGT
1 CACGTGTGTAGTAC-AATGTGCAGGCTACTACGTGTACTCGA-AG-T-TTGGT
* * *
41411326 CACATGTGTAGTACAATGTGCAGGCTACTATGTGTACTGGAAGGCTTTGGT
1 CACGTGTGTAGTACAATGTGCAGGCTACTACGTGTACTCGAA-G-TTTGGT
* * * * *
41411377 CATGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTAGAAAGTTTGAT
1 CACGTGTGTAGTACAATGTGCAGGCTACTACGTGTACTCG-AAGTTTGGT
* *
41411427 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACAATGTGCAGGCTACTACGTGTA
41411463 TCAAAAGATG
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
50 40 0.34
51 71 0.60
52 7 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (49 bp):
CACGTGTGTAGTACAATGTGCAGGCTACTACGTGTACTCGAAGTTTGGT
Found at i:41419137 original size:5 final size:5
Alignment explanation
Indices: 41419127--41419173 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
41419117 AAAACAAAGT
41419127 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
41419174 GTTTTAATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:41420810 original size:20 final size:18
Alignment explanation
Indices: 41420772--41420807 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41420762 TTAATACAAT
41420772 TTAATTATTTTATAAAAA
1 TTAATTATTTTATAAAAA
41420790 TTAATTATTTTATAAAAA
1 TTAATTATTTTATAAAAA
41420808 AATCTTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTATTTTATAAAAA
Found at i:41422201 original size:18 final size:17
Alignment explanation
Indices: 41422174--41422209 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
41422164 GGTTTTGAGT
*
41422174 TGGAATCTAAGTTTAAA
1 TGGAATCTAAGCTTAAA
41422191 TGGATATCTAAGCTTAAA
1 TGGA-ATCTAAGCTTAAA
41422209 T
1 T
41422210 CATGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (17 bp):
TGGAATCTAAGCTTAAA
Found at i:41430037 original size:47 final size:47
Alignment explanation
Indices: 41429966--41430736 Score: 1317
Period size: 47 Copynumber: 16.3 Consensus size: 47
41429956 CCCTTCGGGA
* * * * * *
41429966 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41430013 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430060 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430107 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
41430154 CTTATCACATATATACACTTTCACATTCATCACATCGGTTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430201 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430250 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430297 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430344 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430391 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430438 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430485 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430532 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430579 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430628 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41430675 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41430724 CTTATCACATATA
1 CTTATCACATATA
41430737 CTATCATGTA
Statistics
Matches: 693, Mismatches: 25, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
47 556 0.80
49 137 0.20
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41430044 original size:25 final size:25
Alignment explanation
Indices: 41430016--41430094 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
41430006 ACTCGGCCCT
41430016 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
41430041 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
41430063 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
41430088 ATCACAT
1 ATCACAT
41430095 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41437623 original size:157 final size:157
Alignment explanation
Indices: 41437337--41437656 Score: 577
Period size: 157 Copynumber: 2.0 Consensus size: 157
41437327 TCTCGTGAAC
* * *
41437337 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGTACGACATTCTTCATTATCATTAGCGCATTA
1 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCGTCATTATCATTAGCGCATTA
41437402 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
66 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
41437467 TAAACTCCTATCTGTAGCAAGAAAAGG
131 TAAACTCCTATCTGTAGCAAGAAAAGG
*
41437494 TCTTCCTCCACTGCTACTCCTCTCAAGTCAATGGCACAACATTCGTCATTATCATTAGCGCATTA
1 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCGTCATTATCATTAGCGCATTA
*
41437559 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATGGTCAGTTCACCTTTCTGCACATCAAT
66 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
* *
41437624 TAAAGTCCTGTCTGTAGCAAGAAAAGG
131 TAAACTCCTATCTGTAGCAAGAAAAGG
41437651 TCTTCC
1 TCTTCC
41437657 AAGAATAATT
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (157 bp):
TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCGTCATTATCATTAGCGCATTA
AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
TAAACTCCTATCTGTAGCAAGAAAAGG
Found at i:41453407 original size:18 final size:18
Alignment explanation
Indices: 41453384--41453418 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41453374 CCGATCCTTT
*
41453384 TGTTGCCTCCATTGGAGG
1 TGTTGCCGCCATTGGAGG
*
41453402 TGTTGCCGCCCTTGGAG
1 TGTTGCCGCCATTGGAG
41453419 CACCATTGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.34, T:0.31
Consensus pattern (18 bp):
TGTTGCCGCCATTGGAGG
Found at i:41457072 original size:18 final size:18
Alignment explanation
Indices: 41457049--41457108 Score: 97
Period size: 17 Copynumber: 3.4 Consensus size: 18
41457039 TGAAAAAGAA
41457049 GAAAAAGAGAAAGAAATT
1 GAAAAAGAGAAAGAAATT
41457067 GAAAAAGAGAAA-AAATT
1 GAAAAAGAGAAAGAAATT
*
41457084 GAAAAAGA-AAAGAAATC
1 GAAAAAGAGAAAGAAATT
41457101 GAAAAAGA
1 GAAAAAGA
41457109 ATTTGAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
16 3 0.08
17 25 0.62
18 12 0.30
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (18 bp):
GAAAAAGAGAAAGAAATT
Found at i:41466929 original size:47 final size:47
Alignment explanation
Indices: 41466872--41467175 Score: 398
Period size: 47 Copynumber: 6.4 Consensus size: 47
41466862 ATTGATGTAC
* * *
41466872 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
41466919 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
41466968 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
41467015 ACA-TGTGTATGTGTGATAAGGCTGAATGACCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
41467062 ACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
41467109 AAGTGTATATATGTGATAAGGCCAAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
41467156 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
41467176 TCCCGAAGGG
Statistics
Matches: 234, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 192 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:41470466 original size:40 final size:39
Alignment explanation
Indices: 41470422--41470526 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
41470412 AGTGACCATA
*
41470422 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
41470462 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
41470500 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
41470527 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41470483 original size:39 final size:40
Alignment explanation
Indices: 41470385--41470526 Score: 150
Period size: 40 Copynumber: 3.6 Consensus size: 40
41470375 AATGATGTCT
* * *
41470385 GGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAACC
* *
41470425 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-ACC
*
41470465 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACC
*
41470504 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
41470527 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACC
Found at i:41470545 original size:79 final size:80
Alignment explanation
Indices: 41470385--41470532 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 80
41470375 AATGATGTCT
* **
41470385 GGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAA
41470450 CGAGATACTAATTCC
66 CGAGATACTAATTCC
* * * * *
41470465 GGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTG
41470527 AACGAG
64 AACGAG
41470533 TAGCTATATC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.72
80 15 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAA
CGAGATACTAATTCC
Found at i:41470820 original size:47 final size:47
Alignment explanation
Indices: 41470751--41470918 Score: 336
Period size: 47 Copynumber: 3.6 Consensus size: 47
41470741 AAGGGTTGGT
41470751 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41470798 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41470845 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41470892 AATGTGAAAGTGTATATATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
41470919 TCCCGAAGGG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 121 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:41477504 original size:2 final size:2
Alignment explanation
Indices: 41477499--41477536 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41477489 TGTGTATATA
41477499 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41477537 CATTTGTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41478936 original size:35 final size:35
Alignment explanation
Indices: 41478897--41478971 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
41478887 ATTTATTTAT
41478897 TTATTTCT-TATCTATTATT-TTTATTATTAGTTAG-A
1 TTATTT-TATATCT-TTATTGTTTATTATTA-TTAGTA
* *
41478932 TTATTTTATTTCTTTATTGTTTGTTATTATTAGTA
1 TTATTTTATATCTTTATTGTTTATTATTATTAGTA
41478967 TTATT
1 TTATT
41478972 ATTTGTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.67
Consensus pattern (35 bp):
TTATTTTATATCTTTATTGTTTATTATTATTAGTA
Found at i:41480598 original size:6 final size:6
Alignment explanation
Indices: 41480577--41480619 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
41480567 AGTCCATTTG
* *
41480577 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
41480620 CTTAGACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:41480611 original size:18 final size:17
Alignment explanation
Indices: 41480577--41480619 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
41480567 AGTCCATTTG
41480577 TTTTA-TTTTATTTTAT
1 TTTTATTTTTATTTTAT
41480593 TTTTATTTTTATGTTTAT
1 TTTTATTTTTAT-TTTAT
*
41480611 TGTTATTTT
1 TTTTATTTT
41480620 CTTAGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 6 0.25
18 13 0.54
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:41488971 original size:39 final size:41
Alignment explanation
Indices: 41488912--41489010 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 41
41488902 ATCACTATAA
41488912 ATATTTTATTGTTAATAATA-TT-CTTAATATAAAATTTT-G
1 ATATTTTATTGTTAATAATATTTACTTAAT-TAAAATTTTCG
* *
41488951 ATATTTTATTGTTACA-AATATTTATTTAATTTAAATTTTCG
1 ATATTTTATTGTTA-ATAATATTTACTTAATTAAAATTTTCG
*
41488992 ATATTGTTATTGTCAATAA
1 ATATT-TTATTGTTAATAA
41489011 CGTTATCTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
39 18 0.35
40 11 0.22
41 12 0.24
42 10 0.20
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (41 bp):
ATATTTTATTGTTAATAATATTTACTTAATTAAAATTTTCG
Found at i:41489931 original size:21 final size:20
Alignment explanation
Indices: 41489901--41489983 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
41489891 TTTAAATATA
*
41489901 AAATTCATAAAATATTATTAG
1 AAATTTATAAAATATT-TTAG
*
41489922 AAATTTAT-AAATAATTATAG
1 AAATTTATAAAAT-ATTTTAG
*
41489942 AAA-TTATAGAAA-ATTTT-T
1 AAATTTATA-AAATATTTTAG
*
41489960 AAATGTTATAAAAAATTTTAG
1 AAAT-TTATAAAATATTTTAG
41489981 AAA
1 AAA
41489984 AATATAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
18 3 0.06
19 11 0.22
20 20 0.40
21 16 0.32
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATTTATAAAATATTTTAG
Found at i:41489955 original size:10 final size:10
Alignment explanation
Indices: 41489900--41489994 Score: 54
Period size: 10 Copynumber: 9.4 Consensus size: 10
41489890 TTTTAAATAT
41489900 AAAATTCATA-
1 AAAATT-ATAG
41489910 AAATATTATTAG
1 AAA-ATTA-TAG
*
41489922 AAATTTATA-
1 AAAATTATAG
41489931 AATAATTATAG
1 AA-AATTATAG
41489942 -AAATTATAG
1 AAAATTATAG
*
41489951 AAAATTTTTA-
1 AAAA-TTATAG
** *
41489961 AATGTTATAA
1 AAAATTATAG
*
41489971 AAAATTTTAG
1 AAAATTATAG
*
41489981 AAAAATATAG
1 AAAATTATAG
41489991 AAAA
1 AAAA
41489995 AATATAAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
9 14 0.22
10 36 0.55
11 12 0.18
12 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AAAATTATAG
Found at i:41489976 original size:30 final size:31
Alignment explanation
Indices: 41489902--41490015 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 31
41489892 TTAAATATAA
*
41489902 AATTCATAAAATATTATTAG-AAATTTATAAAT
1 AATT-ATAAAAAATTA-TAGAAAATTTATAAAT
* *
41489934 AATTAT-AGAAATTATAGAAAATTTTTAAAT
1 AATTATAAAAAATTATAGAAAATTTATAAAT
* * * *
41489964 -GTTATAAAAAATTTTAGAAAA-ATATAGAAA
1 AATTATAAAAAATTATAGAAAATTTATA-AAT
* * *
41489994 AAATATAAAAAAATATAAAAAA
1 AATTATAAAAAATTATAGAAAA
41490016 AGGTATAGAA
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
29 10 0.16
30 32 0.50
31 18 0.28
32 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (31 bp):
AATTATAAAAAATTATAGAAAATTTATAAAT
Found at i:41490022 original size:12 final size:10
Alignment explanation
Indices: 41489966--41490016 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
41489956 TTTTAAATGT
*
41489966 TATAAAAAAT
1 TATAAAAAAA
* *
41489976 TTTAGAAAAA
1 TATAAAAAAA
41489986 TATAGAAAAAA
1 TATA-AAAAAA
41489997 TATAAAAAAA
1 TATAAAAAAA
41490007 TATAAAAAAA
1 TATAAAAAAA
41490017 GGTATAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:41490027 original size:12 final size:11
Alignment explanation
Indices: 41489981--41490028 Score: 64
Period size: 10 Copynumber: 4.4 Consensus size: 11
41489971 AAAATTTTAG
41489981 AAAAATATAGA
1 AAAAATATAGA
41489992 AAAAATATA-A
1 AAAAATATAGA
41490002 AAAAATATA-A
1 AAAAATATAGA
41490012 AAAAAGGTATAGA
1 AAAAA--TATAGA
41490025 AAAA
1 AAAA
41490029 TCTTAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 16 0.47
11 9 0.26
12 4 0.12
13 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (11 bp):
AAAAATATAGA
Found at i:41490799 original size:23 final size:23
Alignment explanation
Indices: 41490755--41490800 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
41490745 ATATTTTTCC
*
41490755 ATATTTTTCTAAAATATATTATA
1 ATATTTTTCTAAAACATATTATA
41490778 ATATTTTTCTAAAAACAT-TTATA
1 ATATTTTTCT-AAAACATATTATA
41490801 GCATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTTTTCTAAAACATATTATA
Found at i:41490806 original size:23 final size:23
Alignment explanation
Indices: 41490757--41490806 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
41490747 ATTTTTCCAT
* *
41490757 ATTTTTCTAAAATATATTATAAT
1 ATTTTTCTAAAACATATTATAAC
*
41490780 ATTTTTCTAAAAACAT-TTATAGC
1 ATTTTTCT-AAAACATATTATAAC
41490803 ATTT
1 ATTT
41490807 AAAATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTTCTAAAACATATTATAAC
Found at i:41490953 original size:28 final size:29
Alignment explanation
Indices: 41490921--41490979 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
41490911 TTACTTAAGT
41490921 AATCAATTAAGCCCTCGTAAAATAA-AAA
1 AATCAATTAAGCCCTCGTAAAATAATAAA
** *
41490949 AATCAATTAAGTTCTTGTAAAATAATAAA
1 AATCAATTAAGCCCTCGTAAAATAATAAA
41490978 AA
1 AA
41490980 ATCGTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (29 bp):
AATCAATTAAGCCCTCGTAAAATAATAAA
Found at i:41492101 original size:4 final size:4
Alignment explanation
Indices: 41492094--41492119 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41492084 TATAGATAGG
41492094 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
41492120 ATTCCATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:41496255 original size:89 final size:88
Alignment explanation
Indices: 41496162--41496714 Score: 312
Period size: 89 Copynumber: 6.3 Consensus size: 88
41496152 CGGCTTTAAC
*
41496162 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT-CACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-TTCAGTCT-CCTCCACTGCAACTTCA
41496226 GGAGGATAAGACTTGCTTACTTAGT
64 GGAGGATAAGACTTGCTTACTTAGT
* * * * * *
41496251 CTGCTCCACTGCAACTTTAGGGAGATAAGACTAG--A-TGC-GATCTTCT-CTCTGCAACTTCA-
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATTTCAG-TCTCCTCCACTGCAACTTCAG
** * *
41496310 GAGAGATAAGATCCAAGGTT--TTAAT
65 GAG-GATAAGA--CTTGCTTACTTAGT
** ** * * ** * *
41496335 CCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGC-TTT-AACCTACTCCACTACAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATTTCAGTCTCCTCCACTGCAACTTCA
* *
41496398 GG-GAGATAAGATTTGC-CATCTTCAGT
64 GGAG-GATAAGACTTGCTTA-CTT-AGT
* * * * *
41496424 CTGCTTCACTGTAACTTCA-GGAGGATAAGATTTGCTTACTT-AGTCTGCTCCACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGATTTGC-CATTTCAGTCTCCTCCACTGCAACTTCA
* * * * *
41496487 GGAAGATAAGACTAG-ATGC-GA-T
64 GGAGGATAAGACTTGCTTACTTAGT
* * * *
41496509 CTGCT-CTCTGCAACTTCAGAGAGATAAGA--T-CCAAGGTTTTAATC-CACTCCACTGCAACTT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCC-A--TTTCAGTCTC-CTCCACTGCAACTT
** * * * * **
41496569 CAAAAAGATAGGA-TT-ATCAGCTTTAAC
62 CAGGAGGATAAGACTTGCTTA-C-TTAGT
41496596 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCT-CACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-TTCAGTCT-CCTCCACTGCAACTTCA
*
41496660 AGAGGATAAGACTTGCTTACTTAGT
64 GGAGGATAAGACTTGCTTACTTAGT
*
41496685 CTGCTCCACTGCAACTTCAGGGAGAGAAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA
41496715 CTAGATGCGA
Statistics
Matches: 344, Mismatches: 79, Indels: 82
0.68 0.16 0.16
Matches are distributed among these distances:
81 2 0.01
82 1 0.00
83 6 0.02
84 97 0.28
85 13 0.04
86 8 0.02
87 11 0.03
88 49 0.14
89 145 0.42
90 7 0.02
91 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (88 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATTTCAGTCTCCTCCACTGCAACTTCAGG
AGGATAAGACTTGCTTACTTAGT
Found at i:41496266 original size:44 final size:45
Alignment explanation
Indices: 41496162--41496716 Score: 253
Period size: 44 Copynumber: 12.7 Consensus size: 45
41496152 CGGCTTTAAC
* * *
41496162 CTGCTCCACTACAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGT
41496207 CTGC-CTCACTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAGT
1 CTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
* * * * *
41496251 CTGCTCCACTGCAACTTTAGG-GAGATAAGACTAG-ATGC-GA-T
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
* * ** * *
41496292 CTTCT-CTCTGCAACTTCA-GAGAGATAAGATCCAAGGTT--TTAAT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTTAGT
** * * * **
41496335 CCACTCCACTGCAACTTCA-GAAAGATAGGATTATCGGC-T--TTAAC
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACT-T--GCTTACTTAGT
* * * *
41496379 CTACTCCACTACAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGT
* * *
41496424 CTGCTTCACTGTAACTTCAGGAG-GATAAGATTTGCTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
* * * *
41496468 CTGCTCCACTGCAACTTCAGGA-AGATAAGACTAG-ATGC-GA-T
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
* ** * *
41496509 CTGCT-CTCTGCAACTTCA-GAGAGATAAGATCCAAGGTT--TTAAT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTTAGT
** * * * * * **
41496552 CCACTCCACTGCAACTTCA-AAAAGATAGGA-TT-ATCAGCTTTAAC
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-C-TTAGT
* *
41496596 CTGCTCCACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGT
* *
41496641 CTAC-CTCACTGCAACTTCAAGAG-GATAAGACTTGCTTACTTAGT
1 CTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
*
41496685 CTGCTCCACTGCAACTTCAGG-GAGAGAAGACT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACT
41496717 AGATGCGATC
Statistics
Matches: 393, Mismatches: 74, Indels: 87
0.71 0.13 0.16
Matches are distributed among these distances:
39 3 0.01
40 41 0.10
41 13 0.03
42 10 0.03
43 17 0.04
44 197 0.50
45 106 0.27
46 6 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGT
Found at i:41496410 original size:217 final size:217
Alignment explanation
Indices: 41496035--41496740 Score: 1268
Period size: 217 Copynumber: 3.3 Consensus size: 217
41496025 AGATAATACT
*
41496035 TGCTCCACTGCAACTTCAGGGAAATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
* *
41496100 AAGATCCAATGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTG
66 AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTG
41496165 CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
131 CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
41496230 GATAAGACTTGCTTACTTAGTC
196 GATAAGACTTGCTTACTTAGTC
* *
41496252 TGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTTCTCTCTGCAACTTCAGAGAGAT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
*
41496317 AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTA
66 AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTG
* *
41496382 CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTTCACTGTAACTTCAGGAG
131 CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
*
41496447 GATAAGATTTGCTTACTTAGTC
196 GATAAGACTTGCTTACTTAGTC
*
41496469 TGCTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
* *
41496534 AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAAAAAGATAGGATTATCAGCTTTAACCTG
66 AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTG
* * *
41496599 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAAGAG
131 CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
41496664 GATAAGACTTGCTTACTTAGTC
196 GATAAGACTTGCTTACTTAGTC
*
41496686 TGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGATCTGCTCTCTGCAACT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
41496741 GCTCCACTAT
Statistics
Matches: 466, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 466 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (217 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGAT
AAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTG
CTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAG
GATAAGACTTGCTTACTTAGTC
Found at i:41496855 original size:44 final size:45
Alignment explanation
Indices: 41496739--41496859 Score: 135
Period size: 44 Copynumber: 2.7 Consensus size: 45
41496729 CTCTCTGCAA
*
41496739 CTGCTCCACT-ATAACTTCAGGGAGATAAGATTTGCCATCTTCAGT
1 CTGCTCCACTGA-AACTTCAGGGAGATAAGACTTGCCATCTTCAGT
* *
41496784 CTGC-CTCACTGAAACTTCA-GGAGGATAATACTTG-CTTACTT-AGT
1 CTGCTC-CACTGAAACTTCAGGGA-GATAAGACTTGCCAT-CTTCAGT
*
41496828 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGAAACTTCAGGGAGATAAGACT
41496860 AGATGCGATC
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
44 33 0.51
45 31 0.48
46 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (45 bp):
CTGCTCCACTGAAACTTCAGGGAGATAAGACTTGCCATCTTCAGT
Found at i:41496858 original size:143 final size:143
Alignment explanation
Indices: 41496596--41496883 Score: 513
Period size: 143 Copynumber: 2.0 Consensus size: 143
41496586 CAGCTTTAAC
* *
41496596 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAA
1 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGAAACTTCAA
41496661 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
66 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
41496726 CTGCTCTCTGCAA
131 CTGCTCTCTGCAA
* * *
41496739 CTGCTCCACTATAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGAAACTTCAG
1 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGAAACTTCAA
* *
41496804 GAGGATAATACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGAT
66 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
41496869 CTGCTCTCTGCAA
131 CTGCTCTCTGCAA
41496882 CT
1 CT
41496884 TCAGAGAGAT
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (143 bp):
CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGAAACTTCAA
GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
CTGCTCTCTGCAA
Found at i:41508745 original size:15 final size:15
Alignment explanation
Indices: 41508709--41508747 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
41508699 GTAAATATCG
41508709 TGATAATAAATACAA
1 TGATAATAAATACAA
41508724 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
41508739 TGATAATAA
1 TGATAATAA
41508748 TTTTAACGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:41511941 original size:30 final size:30
Alignment explanation
Indices: 41511905--41511964 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41511895 GTGGACCAAG
41511905 TTGGGTTTTGGTTGCATGAATTTGAGGGTT
1 TTGGGTTTTGGTTGCATGAATTTGAGGGTT
41511935 TTGGGTTTTGGTTGCATGAATTTGAGGGTT
1 TTGGGTTTTGGTTGCATGAATTTGAGGGTT
41511965 AAAATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.03, G:0.37, T:0.47
Consensus pattern (30 bp):
TTGGGTTTTGGTTGCATGAATTTGAGGGTT
Found at i:41513259 original size:20 final size:20
Alignment explanation
Indices: 41513231--41513279 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
41513221 ATATATCCTG
*
41513231 ATTTTATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
*
41513251 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTCTAATCA
*
41513271 AATTGATTT
1 ATTTGATTT
41513280 AATTGCCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTCTAATCA
Found at i:41523802 original size:23 final size:23
Alignment explanation
Indices: 41523767--41523888 Score: 192
Period size: 23 Copynumber: 5.3 Consensus size: 23
41523757 AGTGTTATTG
*
41523767 ATCAATGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
*
41523789 ATTCAGTGGTAGCTACGGCTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
41523813 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
41523836 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41523859 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41523882 ATCAGTG
1 ATCAGTG
41523889 TGGATTTATG
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
22 1 0.01
23 89 0.98
24 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:41524137 original size:23 final size:25
Alignment explanation
Indices: 41524091--41524138 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
41524081 GAAATTGCTA
* *
41524091 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
41524116 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
41524139 TATTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:41525749 original size:19 final size:18
Alignment explanation
Indices: 41525725--41525767 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
41525715 TGGGCCTCAA
41525725 TGGGCCAAAATGGGCTGTG
1 TGGGCCAAAATGGGCT-TG
* *
41525744 TGGGCC-CAGTGGGCTTG
1 TGGGCCAAAATGGGCTTG
41525761 TGGGCCA
1 TGGGCCA
41525768 CACGGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.14, C:0.21, G:0.44, T:0.21
Consensus pattern (18 bp):
TGGGCCAAAATGGGCTTG
Found at i:41526103 original size:27 final size:27
Alignment explanation
Indices: 41526047--41526160 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
41526037 CCAAAATTTA
*
41526047 TAAAATGATCGTAATG-CCCTGTAGGT
1 TAAAATGATCGTAATGCCCCTGTAGGG
*
41526073 TAAAATGATCGTAATACCCCTGTAGGG
1 TAAAATGATCGTAATGCCCCTGTAGGG
* * *
41526100 TAAAATAACCATAATGCCCCTGTAGGG
1 TAAAATGATCGTAATGCCCCTGTAGGG
41526127 TAAAATGA-CTGTAATGCCCCTGTA-GG
1 TAAAATGATC-GTAATGCCCCTGTAGGG
41526153 TAAAATGA
1 TAAAATGA
41526161 CTATAATACC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
26 26 0.33
27 52 0.67
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TAAAATGATCGTAATGCCCCTGTAGGG
Found at i:41526266 original size:24 final size:24
Alignment explanation
Indices: 41526234--41526328 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
41526224 CCCTCGAGGT
* *
41526234 TAAATGATTGATTTGTTTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* * * *
41526258 TAAGTGATTGATTAGTCTGAGATG
1 TAAATGACTGATTTGTCTGTGATG
*
41526282 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
41526306 TAAATGACTGATTTGTCTGTGAT
1 TAAATGACTGATTTGTCTGTGAT
41526329 TGGTATAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:41526343 original size:24 final size:23
Alignment explanation
Indices: 41526292--41526362 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
41526282 TAAATGACTG
* *
41526292 ATTTGTCTGTGATT-TAAATGACTG
1 ATTTGTCTGTGATTGT--ATAACTA
41526316 ATTTGTCTGTGATTGGTATAACTA
1 ATTTGTCTGTGATT-GTATAACTA
*
41526340 ATTTGTCTATGAATTGTATAACT
1 ATTTGTCTGTG-ATTGTATAACT
41526363 GATTCTGAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 37 0.90
25 3 0.07
26 1 0.02
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.46
Consensus pattern (23 bp):
ATTTGTCTGTGATTGTATAACTA
Found at i:41526469 original size:27 final size:27
Alignment explanation
Indices: 41526429--41526493 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
41526419 ATAGAGGAAG
*
41526429 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTAGTGGCT-TGGCCACATA
41526454 TCACTGTTACTAGTGGCTTGGCCACATA
1 T-ACTGTTACTAGTGGCTTGGCCACATA
41526482 TACTGTTACTAG
1 TACTGTTACTAG
41526494 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (27 bp):
TACTGTTACTAGTGGCTTGGCCACATA
Found at i:41526499 original size:27 final size:27
Alignment explanation
Indices: 41526447--41526499 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41526437 TGGTGGCTCT
**
41526447 GCCACAATCACTGTTACTAGTGGCTTG
1 GCCACAATCACTGTTACTAGCAGCTTG
41526474 GCCACATAT-ACTGTTACTAGCAGCTT
1 GCCACA-ATCACTGTTACTAGCAGCTT
41526500 TGCTACGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTAGCAGCTTG
Found at i:41526561 original size:32 final size:32
Alignment explanation
Indices: 41526523--41526730 Score: 215
Period size: 32 Copynumber: 6.5 Consensus size: 32
41526513 CTAATGGCTT
*
41526523 TGTGCCGGTCATATTACCGTTACTGATGGTTG
1 TGTGCCGATCATATTACCGTTACTGATGGTTG
* * * *
41526555 TGTGCCGATCATATCACTGCTACTAATGGCTT-
1 TGTGCCGATCATATTACCGTTACTGATGG-TTG
*
41526587 TGTGCCGATCATATTACCGTTATTGATGGTTG
1 TGTGCCGATCATATTACCGTTACTGATGGTTG
* * * *
41526619 TGTACCGATCATATCACTGCTACTGATGGCTT-
1 TGTGCCGATCATATTACCGTTACTGATGG-TTG
*
41526651 TGTGCCGATCATATTACCGTTACTGATGGCTG
1 TGTGCCGATCATATTACCGTTACTGATGGTTG
* * ** *
41526683 TGTGCCGGTCATATCATTGCTACTGATGGCTT-
1 TGTGCCGATCATATTACCGTTACTGATGG-TTG
*
41526715 TGTGCCAATCATATTA
1 TGTGCCGATCATATTA
41526731 GTTTACTTAT
Statistics
Matches: 142, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
31 3 0.02
32 134 0.94
33 5 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (32 bp):
TGTGCCGATCATATTACCGTTACTGATGGTTG
Found at i:41526587 original size:64 final size:64
Alignment explanation
Indices: 41526508--41526730 Score: 365
Period size: 64 Copynumber: 3.5 Consensus size: 64
41526498 TTTGCTACGA
*
41526508 TGCTACTAATGGCTTTGTGCCGGTCATATTACCGTTACTGATGGTTGTGTGCCGATCATATCAC
1 TGCTACTAATGGCTTTGTGCCGATCATATTACCGTTACTGATGGTTGTGTGCCGATCATATCAC
* *
41526572 TGCTACTAATGGCTTTGTGCCGATCATATTACCGTTATTGATGGTTGTGTACCGATCATATCAC
1 TGCTACTAATGGCTTTGTGCCGATCATATTACCGTTACTGATGGTTGTGTGCCGATCATATCAC
* * * *
41526636 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTGTGTGCCGGTCATATCAT
1 TGCTACTAATGGCTTTGTGCCGATCATATTACCGTTACTGATGGTTGTGTGCCGATCATATCAC
* *
41526700 TGCTACTGATGGCTTTGTGCCAATCATATTA
1 TGCTACTAATGGCTTTGTGCCGATCATATTA
41526731 GTTTACTTAT
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 149 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (64 bp):
TGCTACTAATGGCTTTGTGCCGATCATATTACCGTTACTGATGGTTGTGTGCCGATCATATCAC
Found at i:41527012 original size:34 final size:29
Alignment explanation
Indices: 41526985--41527072 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 29
41526975 CTGTTTCTGC
41526985 ATTGGGCTAAGGCCCACAATGTTACTG-T
1 ATTGGGCTAAGGCCCACAATGTTACTGTT
*
41527013 ATTGGGCTAAGGCCCACATTGTTACTG-T
1 ATTGGGCTAAGGCCCACAATGTTACTGTT
** *
41527041 ATTGGGCTGTGGCCCACACACTGATACTGTT
1 ATTGGGCTAAGGCCCACA-A-TGTTACTGTT
41527072 A
1 A
41527073 CTGTTAATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 43 0.83
30 7 0.13
31 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (29 bp):
ATTGGGCTAAGGCCCACAATGTTACTGTT
Found at i:41527017 original size:28 final size:28
Alignment explanation
Indices: 41526976--41527058 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
41526966 TGACTGACAC
* *
41526976 TGTTTCTGCATTGGGCTAAGGCCCACAA
1 TGTTACTGTATTGGGCTAAGGCCCACAA
*
41527004 TGTTACTGTATTGGGCTAAGGCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAA
**
41527032 TGTTACTGTATTGGGCTGTGGCCCACA
1 TGTTACTGTATTGGGCTAAGGCCCACA
41527059 CACTGATACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAA
Found at i:41528510 original size:15 final size:15
Alignment explanation
Indices: 41528490--41528518 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41528480 TCAAGTCAAT
41528490 AAAGAAAAAGAAAAC
1 AAAGAAAAAGAAAAC
41528505 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
41528519 GAAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAAC
Found at i:41528520 original size:20 final size:21
Alignment explanation
Indices: 41528490--41528528 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41528480 TCAAGTCAAT
41528490 AAAGAAAAAGAAAACAAAGAA
1 AAAGAAAAAGAAAACAAAGAA
*
41528511 AAAG-AAAAGAAAAGAAAG
1 AAAGAAAAAGAAAACAAAG
41528529 GGGAGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAAAACAAAGAA
Found at i:41539274 original size:7 final size:7
Alignment explanation
Indices: 41539262--41539296 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
41539252 GAAACAAAAG
41539262 AATAAAT
1 AATAAAT
41539269 AATAAAT
1 AATAAAT
41539276 AATAAAT
1 AATAAAT
41539283 AAT-AAT
1 AATAAAT
41539289 AATAAAT
1 AATAAAT
41539296 A
1 A
41539297 TTCCCCACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:41542148 original size:5 final size:5
Alignment explanation
Indices: 41542140--41542168 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41542130 AAGAAAAGAA
41542140 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
41542169 AAGTATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:41544300 original size:28 final size:28
Alignment explanation
Indices: 41544260--41544407 Score: 154
Period size: 28 Copynumber: 5.3 Consensus size: 28
41544250 TATTCCATGT
*
41544260 AAGAGTTCACATGGACTATCATTCAAGC
1 AAGAGTCCACATGGACTATCATTCAAGC
** * *
41544288 AAGAGTCTGCATGGACTATTC-TTCATGT
1 AAGAGTCCACATGGACTA-TCATTCAAGC
*
41544316 AAGAGTCCACATGGACTATCATTCCAGC
1 AAGAGTCCACATGGACTATCATTCAAGC
* * ** * *
41544344 CAGAGTCCCCATAAACTATCCTTTAAGC
1 AAGAGTCCACATGGACTATCATTCAAGC
* *
41544372 AAGAGTCTACATGGACTATCTTTCAAGC
1 AAGAGTCCACATGGACTATCATTCAAGC
41544400 AAGAGTCC
1 AAGAGTCC
41544408 TCAGGAACTA
Statistics
Matches: 93, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
27 2 0.02
28 89 0.96
29 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (28 bp):
AAGAGTCCACATGGACTATCATTCAAGC
Found at i:41544327 original size:56 final size:56
Alignment explanation
Indices: 41544236--41544406 Score: 193
Period size: 56 Copynumber: 3.1 Consensus size: 56
41544226 ATTTAGGTAT
* *
41544236 GAGTCTACAAGGACTATTC--CATGTAAGAGTTCACATGGACTATCATTCAAGCAA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
* * *
41544290 GAGTCTGCATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCCAGCCA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
** ** * * * * * *
41544346 GAGTCCCCATAAACTATCCTTTAAGCAAGAGTCTACATGGACTATCTTTCAAGCAA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
41544402 GAGTC
1 GAGTC
41544407 CTCAGGAACT
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
54 17 0.17
56 81 0.83
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (56 bp):
GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
Found at i:41547654 original size:45 final size:47
Alignment explanation
Indices: 41547603--41547694 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 47
41547593 ATATAGAACC
* * * *
41547603 ACACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTTAACCTTATT
1 ACACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTATT
41547648 ACACTTCATCTATTTGATATTGATTAGAATAAGGTGTTTCAACCTTA
1 ACACTTCATCTATTT-ATATT-ATTAGAATAAGGTGTTTCAACCTTA
41547695 CTGTAAGAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 13 0.33
47 4 0.10
49 22 0.56
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (47 bp):
ACACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTATT
Found at i:41547740 original size:13 final size:13
Alignment explanation
Indices: 41547722--41547751 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41547712 TGCCCGGCCC
*
41547722 ATAAACCAACAAA
1 ATAAACCAAAAAA
41547735 ATAAACCAAAAAA
1 ATAAACCAAAAAA
41547748 ATAA
1 ATAA
41547752 TAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.17, G:0.00, T:0.10
Consensus pattern (13 bp):
ATAAACCAAAAAA
Found at i:41548030 original size:19 final size:18
Alignment explanation
Indices: 41548008--41548053 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
41547998 GCACATGTAG
41548008 CGCCTCCGCGCCAAAGCCA
1 CGCCTCCGCGCC-AAGCCA
* *
41548027 CGCCTCCGAGCCGAGCCA
1 CGCCTCCGCGCCAAGCCA
*
41548045 CGCCACCGC
1 CGCCTCCGC
41548054 CAGGGACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.17, C:0.54, G:0.24, T:0.04
Consensus pattern (18 bp):
CGCCTCCGCGCCAAGCCA
Found at i:41548045 original size:18 final size:19
Alignment explanation
Indices: 41548008--41548048 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41547998 GCACATGTAG
*
41548008 CGCCTCCGCGCCAAAGCCA
1 CGCCTCCGAGCCAAAGCCA
*
41548027 CGCCTCCGAGCC-GAGCCA
1 CGCCTCCGAGCCAAAGCCA
41548045 CGCC
1 CGCC
41548049 ACCGCCAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.17, C:0.54, G:0.24, T:0.05
Consensus pattern (19 bp):
CGCCTCCGAGCCAAAGCCA
Found at i:41549017 original size:3 final size:3
Alignment explanation
Indices: 41549002--41549040 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
41548992 ATTGTTCTGT
*
41549002 TTA TTA TCT- TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41549041 GTAGTAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41549126 original size:23 final size:22
Alignment explanation
Indices: 41549086--41549128 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
41549076 TTTCCTAACC
41549086 TTTTTTATATACGTTTATTTTA
1 TTTTTTATATACGTTTATTTTA
41549108 TTTTATTATATA-GTATTATTT
1 TTTT-TTATATACGT-TTATTT
41549129 GGCGTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTTTATATACGTTTATTTTA
Found at i:41559930 original size:15 final size:15
Alignment explanation
Indices: 41559910--41559962 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
41559900 GGTGAAAAAG
*
41559910 ATAATATCTTTTAAA
1 ATAATATATTTTAAA
41559925 ATAATAATATTATTAAAA
1 ATAAT-ATATT-TT-AAA
*
41559943 ATAATTGTATTTTAAA
1 ATAA-TATATTTTAAA
41559959 ATAA
1 ATAA
41559963 AGATAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 11 0.34
17 4 0.12
18 11 0.34
19 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATAATATATTTTAAA
Found at i:41559953 original size:18 final size:17
Alignment explanation
Indices: 41559910--41559959 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
41559900 GGTGAAAAAG
*
41559910 ATAATATCTTTTAAAATA
1 ATAATAT-TTTAAAAATA
41559928 ATAATATTATTAAAAATA
1 ATAATATT-TTAAAAATA
**
41559946 ATTGTATTTTAAAA
1 ATAATATTTTAAAA
41559960 TAAAGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAATATTTTAAAAATA
Found at i:41560407 original size:8 final size:8
Alignment explanation
Indices: 41560394--41560425 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
41560384 ATTATTGAAC
41560394 TTATAAAT
1 TTATAAAT
41560402 TTATAAAT
1 TTATAAAT
41560410 TTATAAAT
1 TTATAAAT
41560418 TTATAAAT
1 TTATAAAT
41560426 ATGTTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTATAAAT
Found at i:41562981 original size:21 final size:21
Alignment explanation
Indices: 41562943--41562983 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41562933 CAAACCCTAA
*
41562943 TAAGTATCAATACCTTTTGAT
1 TAAGTATCAATAACTTTTGAT
* *
41562964 TAAGTATCGATAATTTTTGA
1 TAAGTATCAATAACTTTTGA
41562984 AATATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (21 bp):
TAAGTATCAATAACTTTTGAT
Found at i:41562995 original size:100 final size:101
Alignment explanation
Indices: 41562865--41563051 Score: 236
Period size: 100 Copynumber: 1.9 Consensus size: 101
41562855 CTTTTTGGCC
* * * * * *
41562865 AAGTATTGATATTTTTTGAATTATCGATA-CCCTCTCTT-AAA-CAATACCAAAGTGGCATTCTA
1 AAGTATCGATAATTTTTGAAATATCAATACCCCT-TCTTAAAAGCAATACCAAAATGACATTCTA
41562927 TTTTCACAAACCCTAATAAGTATCAATACCTTTTGATT
65 TTTT-ACAAACCCTAATAAGTATCAATACCTTTTGATT
* * * *
41562965 AAGTATCGATAATTTTTGAAATATTAATACCCCTTCTTAAAAGCGATACCAAAATGACATTTTGT
1 AAGTATCGATAATTTTTGAAATATCAATACCCCTTCTTAAAAGCAATACCAAAATGACATTCTAT
*
41563030 TTTTCAAACCCTAATAAGTATC
66 TTTACAAACCCTAATAAGTATC
41563052 GATATTTTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
100 28 0.38
101 25 0.34
102 20 0.27
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (101 bp):
AAGTATCGATAATTTTTGAAATATCAATACCCCTTCTTAAAAGCAATACCAAAATGACATTCTAT
TTTACAAACCCTAATAAGTATCAATACCTTTTGATT
Found at i:41563076 original size:80 final size:81
Alignment explanation
Indices: 41562964--41563139 Score: 221
Period size: 80 Copynumber: 2.2 Consensus size: 81
41562954 ACCTTTTGAT
* * * *
41562964 TAAGTATCGATAATTTTTGAAATATTAATACCCCTTCTTAAAAGCGATAC-CAAAATGACATTTT
1 TAAGTATCGATAATTTTTGAAATATTAATACCCCTTCTTAAAAACGATACTAAAAATAACATTAT
41563028 GTTTTTCAAACCCTAA
66 GTTTTTCAAACCCTAA
* *
41563044 TAAGTATCGAT-ATTTTCTGAATTATTGATACCCCTTCTTAAAAACGATACTAAAAATAACATTA
1 TAAGTATCGATAATTTT-TGAAATATTAATACCCCTTCTTAAAAACGATACTAAAAATAACATTA
* ** *
41563108 TGTTTCTCACAAAACTTA
65 TGTTTTTCA-AACCCTAA
41563126 TAAAGTATCGATAA
1 T-AAGTATCGATAA
41563140 AATTGTTTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 5 0.06
80 41 0.51
81 18 0.22
82 6 0.07
83 10 0.12
84 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (81 bp):
TAAGTATCGATAATTTTTGAAATATTAATACCCCTTCTTAAAAACGATACTAAAAATAACATTAT
GTTTTTCAAACCCTAA
Found at i:41563813 original size:6 final size:6
Alignment explanation
Indices: 41563802--41563833 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
41563792 GAGCTAACAA
41563802 ATAATT ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT ATAATT AT
41563834 TTTATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:41564257 original size:21 final size:19
Alignment explanation
Indices: 41564215--41564260 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
41564205 TATTTAAAAT
* *
41564215 AAAATCATATTTATATTTA
1 AAAATTATATTTATAATTA
41564234 AAAATTATATTTATTTAATTA
1 AAAATTATATTTA--TAATTA
41564255 AAAATT
1 AAAATT
41564261 TGAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 12 0.52
21 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTATATTTATAATTA
Found at i:41564526 original size:11 final size:11
Alignment explanation
Indices: 41564510--41564576 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
41564500 CTTTTATAGA
41564510 ATTATAAATAT
1 ATTATAAATAT
41564521 ATTATAAATAT
1 ATTATAAATAT
41564532 AGATTATAAAT-T
1 --ATTATAAATAT
*
41564544 ATAGATAAATACT
1 AT-TATAAATA-T
*
41564557 ATTATAAAAAT
1 ATTATAAATAT
41564568 A-TATAAATA
1 ATTATAAATA
41564577 GCAAAATTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 9 0.19
11 19 0.40
12 7 0.15
13 12 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
ATTATAAATAT
Found at i:41564537 original size:24 final size:24
Alignment explanation
Indices: 41564504--41564576 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
41564494 GTGGTGCTTT
41564504 TATAGAATTATAAATATATTATAAA
1 TATAG-ATTATAAATATATTATAAA
*
41564529 TATAGATTATAAAT-TATAGATAAA
1 TATAGATTATAAATATAT-TATAAA
*
41564553 TACT--ATTATAAAAATA-TATAAA
1 TA-TAGATTATAAATATATTATAAA
41564575 TA
1 TA
41564577 GCAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 7 0.17
23 11 0.26
24 18 0.43
25 6 0.14
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (24 bp):
TATAGATTATAAATATATTATAAA
Found at i:41564931 original size:19 final size:19
Alignment explanation
Indices: 41564903--41564945 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41564893 TTATTTTTAA
41564903 TTTA-ATATTTAAT-AATT
1 TTTATATATTTAATAAATT
*
41564920 TTATATATATTTATTAAATT
1 TT-TATATATTTAATAAATT
41564940 TTTATA
1 TTTATA
41564946 GTTAGTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 12 0.55
20 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATATTTAATAAATT
Found at i:41564934 original size:23 final size:23
Alignment explanation
Indices: 41564908--41564967 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
41564898 TTTAATTTAA
* *
41564908 TATTTAATAATTTTATA-TATATT
1 TATTTAATATTTTTATAGT-TAGT
41564931 TA-TTAA-ATTTTTATAGTTAGT
1 TATTTAATATTTTTATAGTTAGT
41564952 TATCTTAATATTTTTA
1 TAT-TTAATATTTTTA
41564968 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 13 0.42
22 5 0.16
23 6 0.19
24 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (23 bp):
TATTTAATATTTTTATAGTTAGT
Found at i:41564992 original size:31 final size:32
Alignment explanation
Indices: 41564921--41564993 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 32
41564911 TTAATAATTT
*
41564921 TATATATATTTATTAAATTTTTATAGTTAGTTA
1 TATA-ATATTTATTAAATTTTTATAGTTAGTAA
* *
41564954 TCTTAATATTT-TT-AATTTTTATATTATAGTAA
1 T-ATAATATTTATTAAATTTTTATAGT-TAGTAA
41564986 TATAATAT
1 TATAATAT
41564994 AAAACATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
31 17 0.50
32 8 0.24
33 7 0.21
34 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (32 bp):
TATAATATTTATTAAATTTTTATAGTTAGTAA
Found at i:41569611 original size:33 final size:33
Alignment explanation
Indices: 41569573--41569640 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
41569563 GTATCATTAC
*
41569573 TTAGTATTGTCATATGCATGAGCAAACAGTCAT
1 TTAGTATTGTCAAATGCATGAGCAAACAGTCAT
41569606 TTAGTATTGTCAAATGCATGAGCAAACAGTCAT
1 TTAGTATTGTCAAATGCATGAGCAAACAGTCAT
41569639 TT
1 TT
41569641 GCTCTATGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (33 bp):
TTAGTATTGTCAAATGCATGAGCAAACAGTCAT
Found at i:41573001 original size:24 final size:24
Alignment explanation
Indices: 41572974--41573020 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
41572964 ATATCATCTT
41572974 TGATATATTAATAATTCATGTAGA
1 TGATATATTAATAATTCATGTAGA
41572998 TGATATATTAATAATTCATGTAG
1 TGATATATTAATAATTCATGTAG
41573021 TTTATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (24 bp):
TGATATATTAATAATTCATGTAGA
Found at i:41578755 original size:47 final size:46
Alignment explanation
Indices: 41578677--41578967 Score: 339
Period size: 47 Copynumber: 6.2 Consensus size: 46
41578667 CTTATACATA
* *** *
41578677 AAATTGGACAGCATTTATACATCCCGTTTGGACAGCATATAAACACC
1 AAATTGGACAGCATATATACA-CCAAATTGGACAGCATATATACACC
* * *
41578724 AAATTGAATAGCATTTATACACCAAAATTGGACAGCATATATACACC
1 AAATTGGACAGCATATATACACC-AAATTGGACAGCATATATACACC
* * * *
41578771 AAATTGGGCAGCATATATATACCAAATTGGACAGCATTTTTACACC
1 AAATTGGACAGCATATATACACCAAATTGGACAGCATATATACACC
* * * *
41578817 AAAATTGGACAGCATATATATACCAAATTGGACAACATTTTTACACC
1 -AAATTGGACAGCATATATACACCAAATTGGACAGCATATATACACC
* * *
41578864 AAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACC
1 -AAATTGGACAGCATATATACACCAAATTGGACAGCATATATACACC
* * *
41578911 AAATTGGACAACATTTTTACACCAAAATTGGACAGCATATATACACC
1 AAATTGGACAGCATATATACACC-AAATTGGACAGCATATATACACC
41578958 AAATTGGACA
1 AAATTGGACA
41578968 TGAATCGAAT
Statistics
Matches: 213, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
46 42 0.20
47 171 0.80
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (46 bp):
AAATTGGACAGCATATATACACCAAATTGGACAGCATATATACACC
Found at i:41578787 original size:70 final size:71
Alignment explanation
Indices: 41578668--41578967 Score: 349
Period size: 70 Copynumber: 4.3 Consensus size: 71
41578658 TAGATAGCTC
* * *** * * *
41578668 TTATACA-TAAAATTGGACAGCATTTATACATCCCGTTTGGACAGCATATAAACACC-AAATTGA
1 TTATACACCAAAATTGGACAGCATATATACA-CCAAATTGGACAACATATATACACCAAAATTGG
*
41578731 ATAGCAT
65 ACAGCAT
* * *
41578738 TTATACACCAAAATTGGACAGCATATATACACCAAATTGGGCAGCATATATATACC-AAATTGGA
1 TTATACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATATATACACCAAAATTGGA
41578802 CAGCAT
66 CAGCAT
* * * *
41578808 TTTTACACCAAAATTGGACAGCATATATATACCAAATTGGACAACATTTTTACACCAAAATTGGA
1 TTATACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATATATACACCAAAATTGGA
41578873 CAGCAT
66 CAGCAT
* * * * * *
41578879 ATAGACACC-AAATTGGGCAGCATATATATACCAAATTGGACAACATTTTTACACCAAAATTGGA
1 TTATACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATATATACACCAAAATTGGA
41578943 CAGCAT
66 CAGCAT
*
41578949 ATATACACC-AAATTGGACA
1 TTATACACCAAAATTGGACA
41578968 TGAATCGAAT
Statistics
Matches: 205, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 164 0.80
71 41 0.20
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (71 bp):
TTATACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATATATACACCAAAATTGGA
CAGCAT
Found at i:41578887 original size:117 final size:117
Alignment explanation
Indices: 41578677--41578967 Score: 458
Period size: 117 Copynumber: 2.5 Consensus size: 117
41578667 CTTATACATA
* *** * * * *
41578677 AAATTGGACAGCATTTATACATCC-CGTTTGGACAGCATATAAACACCAAATTGAATAGCATTTA
1 AAATTGGACAGCATTTTTACA-CCAAAATTGGACAGCATATATACACCAAATTGGACAACATTTA
*
41578741 TACACCAAAATTGGACAGCATATATACACCAAATTGGGCAGCATATATATACC
65 TACACCAAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACC
* *
41578794 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATATATACCAAATTGGACAACATTTTT
1 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATTTAT
41578859 ACACCAAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACC
66 ACACCAAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACC
*
41578911 AAATTGGACAACATTTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACA
1 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACA
41578968 TGAATCGAAT
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
116 2 0.01
117 158 0.99
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (117 bp):
AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACAACATTTAT
ACACCAAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACC
Found at i:41579855 original size:44 final size:43
Alignment explanation
Indices: 41579743--41579857 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
41579733 TTCGTACAAC
* *
41579743 GCCATCGTCCCAGACGTGGTCTTACATGTAATCACATATCGAT
1 GCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGAT
* * *
41579786 -CCCACTGTCCCAAACAG-GGTTTTACACGTAAATCACA-AGTCGAT
1 GCCAAC-GTCCCAGAC-GTGGTCTTACACGT-AATCACATA-TCGAT
*
41579830 GCCAACGTACCAGACGTGGTCTTACACG
1 GCCAACGTCCCAGACGTGGTCTTACACG
41579858 ACAACACATA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
42 3 0.05
43 20 0.35
44 30 0.53
45 4 0.07
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGAT
Found at i:41583522 original size:18 final size:18
Alignment explanation
Indices: 41583499--41583562 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
41583489 GTTGAAAATT
41583499 ATGTTGACAGAGGCACCA
1 ATGTTGACAGAGGCACCA
* ***
41583517 ATGTTGACACA-GCTTGAA
1 ATGTTGACAGAGGC-ACCA
*
41583535 TATGTTGATAGAGGCACCA
1 -ATGTTGACAGAGGCACCA
41583554 ATGTTGACA
1 ATGTTGACA
41583563 CAACTTGAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 10 0.30
20 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
ATGTTGACAGAGGCACCA
Found at i:41583548 original size:37 final size:37
Alignment explanation
Indices: 41583498--41583572 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
41583488 AGTTGAAAAT
*
41583498 TATGTTGACAGAGGCACCAATGTTGACACAGCTTGAA
1 TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
*
41583535 TATGTTGATAGAGGCACCAATGTTGACACAACTTGAA
1 TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
41583572 T
1 T
41583573 CTAGGAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (37 bp):
TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
Found at i:41589614 original size:27 final size:27
Alignment explanation
Indices: 41589565--41589619 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
41589555 AACTTTTCTA
* *
41589565 TTTGTATCTAGTTAGTCCCTAAATTTT
1 TTTGGATCTAGTTAGTCCCTAAACTTT
* * *
41589592 TTTGGATCTAGTTGGTTCTTAAACTTT
1 TTTGGATCTAGTTAGTCCCTAAACTTT
41589619 T
1 T
41589620 ATTCCGTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.53
Consensus pattern (27 bp):
TTTGGATCTAGTTAGTCCCTAAACTTT
Found at i:41589869 original size:3 final size:3
Alignment explanation
Indices: 41589861--41589894 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
41589851 TTAGGGTTAG
* *
41589861 AGA AGA AGA AAA AGA AGA AAA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41589895 TGAGAAGAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41590282 original size:36 final size:36
Alignment explanation
Indices: 41590242--41590380 Score: 136
Period size: 36 Copynumber: 3.9 Consensus size: 36
41590232 CTGAAAACCG
* *
41590242 GCTTATGTTTTGTA-ATATTGTTGTTGGTATATTGTT
1 GCTTATGTTGT-TACATATTGTTGCTGGTATATTGTT
* ** *
41590278 GCTTATGTAGTTACATATTGTTGCTAATATATTGCT
1 GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
* * * *
41590314 GCTTATGTTGTTATACATGGTTACTGGTATATTGTT
1 GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
* * * *
41590350 GCTTATGTTGTTATACATGGCTGCTGGTATA
1 GCTTATGTTGTTACATATTGTTGCTGGTATA
41590381 CATGGCTAAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 2 0.02
36 84 0.98
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.50
Consensus pattern (36 bp):
GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
Found at i:41591088 original size:24 final size:22
Alignment explanation
Indices: 41591061--41591114 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
41591051 AGCTTTTCTC
* *
41591061 TTGGGGCAGCGTCTTTTTGATGAG
1 TTGGGGCAG-G-CTTGTTAATGAG
41591085 TTGGGGCA-GCTTGTTAATGAG
1 TTGGGGCAGGCTTGTTAATGAG
41591106 TTGGGGCAG
1 TTGGGGCAG
41591115 TTTGTAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 18 0.67
22 1 0.04
24 8 0.30
ACGTcount: A:0.15, C:0.11, G:0.41, T:0.33
Consensus pattern (22 bp):
TTGGGGCAGGCTTGTTAATGAG
Found at i:41591106 original size:21 final size:21
Alignment explanation
Indices: 41591080--41591176 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
41591070 CGTCTTTTTG
41591080 ATGAGTTGGGGCAGCTTGTTA
1 ATGAGTTGGGGCAGCTTGTTA
*
41591101 ATGAGTTGGGGCAGTTTG-TA
1 ATGAGTTGGGGCAGCTTGTTA
* * * *
41591121 ACTAAGTTGGGGTA-CTCTCTTG
1 A-TGAGTTGGGGCAGCT-TGTTA
* * *
41591143 CTGATTTGGGGTAGCTTGTTA
1 ATGAGTTGGGGCAGCTTGTTA
* *
41591164 CTGAGTTGAGGCA
1 ATGAGTTGGGGCA
41591177 ACTACTTGGT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.07
21 51 0.88
22 3 0.05
ACGTcount: A:0.19, C:0.11, G:0.35, T:0.35
Consensus pattern (21 bp):
ATGAGTTGGGGCAGCTTGTTA
Found at i:41591883 original size:28 final size:28
Alignment explanation
Indices: 41591841--41591895 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
41591831 ATACACCCCC
** *
41591841 TAAAAAATAGTCACTATATGCATATTAT
1 TAAAAAATACACACTACATGCATATTAT
41591869 TAAAAAATACACACTACATGCATATTA
1 TAAAAAATACACACTACATGCATATTA
41591896 AAAAATAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (28 bp):
TAAAAAATACACACTACATGCATATTAT
Found at i:41592190 original size:205 final size:203
Alignment explanation
Indices: 41591833--41592212 Score: 550
Period size: 205 Copynumber: 1.9 Consensus size: 203
41591823 CAACAACCAT
* * * *
41591833 ACACCCCCTAAAAAATAGTCACTATATGCATATTATTAAAAAATACACACTACATGCATATTAAA
1 ACACCCCCTAAAAAACAGTAACTACATGCATATTATTAAAAAAAACACACTACATGCATATTAAA
* *
41591898 AAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTGCATGCATATTAAAAAAAAATCAT
66 AAATAGTCAACAACATGTGACCATCCCCACCAACAATCACTGCATGCATATTAAAAAAAAATCAC
* * *
41591963 ACACCTACACCCCTCCTAAAAAACA-GTCATTGCATGCATATTAAATAGTCATGCACACCAACAA
131 ACACCTACACCACT-CTAAAAAA-AGGTCACTACATGCATATTAAATAGTCATGCACACCAACAA
41592027 TCATACACAC
194 TCATACACAC
* * *
41592037 ACACACCCCTAAAAAACAGTAACTACATGCATATTATTAAAAAAAACTCATTGCATGCATATTAA
1 ACAC-CCCCTAAAAAACAGTAACTACATGCATATTATTAAAAAAAACACACTACATGCATATTAA
* * *
41592102 AAAATAGTCAACAACATGTGACCATCCCCACCAACAATCATTGTATGCATATTAAAAAAACATTC
65 AAAATAGTCAACAACATGTGACCATCCCCACCAACAATCACTGCATGCATATTAAAAAAA-AATC
41592167 ACACACAC-ACACACACT-TAAAAAAAGGTCACTACATGCATATTAAA
129 ACACAC-CTACAC-CACTCTAAAAAAAGGTCACTACATGCATATTAAA
41592213 AAGTAGTAAA
Statistics
Matches: 156, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
204 5 0.03
205 135 0.87
206 12 0.08
207 4 0.03
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (203 bp):
ACACCCCCTAAAAAACAGTAACTACATGCATATTATTAAAAAAAACACACTACATGCATATTAAA
AAATAGTCAACAACATGTGACCATCCCCACCAACAATCACTGCATGCATATTAAAAAAAAATCAC
ACACCTACACCACTCTAAAAAAAGGTCACTACATGCATATTAAATAGTCATGCACACCAACAATC
ATACACAC
Found at i:41595597 original size:25 final size:25
Alignment explanation
Indices: 41595568--41595630 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
41595558 ATCGCTCTCT
41595568 CGAGCCATATAACGAGAAGCTCATG
1 CGAGCCATATAACGAGAAGCTCATG
* * * *
41595593 TGAGCCATGTAATGGGAAGCTCATG
1 CGAGCCATATAACGAGAAGCTCATG
*
41595618 CGATCCA-ATAACG
1 CGAGCCATATAACG
41595631 GGTAGCTCCG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
CGAGCCATATAACGAGAAGCTCATG
Found at i:41595769 original size:24 final size:26
Alignment explanation
Indices: 41595703--41595762 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
41595693 AGCCTTATCA
*
41595703 GGAAGCTTACAAAGAGCCAATTAATG
1 GGAAGCTCACAAAGAGCCAATTAATG
41595729 GGAAGCTCACAAAGAGCC-A-TAATCG
1 GGAAGCTCACAAAGAGCCAATTAAT-G
41595754 GGAAGCTCA
1 GGAAGCTCA
41595763 TAAGAGCTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 4 0.12
25 11 0.34
26 17 0.53
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCAATTAATG
Found at i:41596232 original size:21 final size:21
Alignment explanation
Indices: 41596208--41596250 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41596198 TAAATTTAAC
41596208 TCAATTTAATACAATTCATAT
1 TCAATTTAATACAATTCATAT
* *
41596229 TCAATTTAATCCAATTCGTAT
1 TCAATTTAATACAATTCATAT
41596250 T
1 T
41596251 TTTGACAAAA
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:0.37, C:0.16, G:0.02, T:0.44
Consensus pattern (21 bp):
TCAATTTAATACAATTCATAT
Found at i:41597486 original size:18 final size:18
Alignment explanation
Indices: 41597463--41597577 Score: 85
Period size: 18 Copynumber: 6.5 Consensus size: 18
41597453 CATTAATAAC
*
41597463 AAAT-AAAACCCAAAATCG
1 AAATCAAAA-CCAAAATCA
*
41597481 AAAT--AACCCAAAATCA
1 AAATCAAAACCAAAATCA
*
41597497 AAATCAAAATCAAAAT-A
1 AAATCAAAACCAAAATCA
*
41597514 GAAATCAAAATCAAAATCA
1 -AAATCAAAACCAAAATCA
*** *
41597533 AAATCAAAATGGAAATCG
1 AAATCAAAACCAAAATCA
* * *
41597551 AAATCGAAATCGAAATCA
1 AAATCAAAACCAAAATCA
41597569 AAATCAAAA
1 AAATCAAAA
41597578 TCGAAATTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.15
17 3 0.04
18 66 0.80
19 1 0.01
ACGTcount: A:0.63, C:0.17, G:0.06, T:0.15
Consensus pattern (18 bp):
AAATCAAAACCAAAATCA
Found at i:41597490 original size:16 final size:16
Alignment explanation
Indices: 41597469--41597500 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41597459 TAACAAATAA
*
41597469 AACCCAAAATCGAAAT
1 AACCCAAAATCAAAAT
41597485 AACCCAAAATCAAAAT
1 AACCCAAAATCAAAAT
41597501 CAAAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.25, G:0.03, T:0.12
Consensus pattern (16 bp):
AACCCAAAATCAAAAT
Found at i:41597498 original size:6 final size:6
Alignment explanation
Indices: 41597489--41597602 Score: 131
Period size: 6 Copynumber: 19.0 Consensus size: 6
41597479 CGAAATAACC
41597489 CAAAAT CAAAAT CAAAAT CAAAAT -AGAAAT CAAAAT CAAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CA-AAAT CAAAAT CAAAAT CAAAAT
** * * * *
41597537 CAAAAT GGAAAT CGAAAT CGAAAT CGAAAT CAAAAT CAAAAT CGAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
* **
41597585 TAAAAT TGAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT
41597603 AACCCAAAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
5 1 0.01
6 94 0.98
7 1 0.01
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.18
Consensus pattern (6 bp):
CAAAAT
Found at i:41597626 original size:16 final size:16
Alignment explanation
Indices: 41597607--41597644 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
41597597 CAAAATAACC
41597607 CAAAATAACCCTAAAT
1 CAAAATAACCCTAAAT
41597623 CAAAATAACCCTAAAT
1 CAAAATAACCCTAAAT
41597639 CTAAAA
1 C-AAAA
41597645 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (16 bp):
CAAAATAACCCTAAAT
Found at i:41598250 original size:50 final size:50
Alignment explanation
Indices: 41598169--41598304 Score: 218
Period size: 50 Copynumber: 2.7 Consensus size: 50
41598159 TTATAACATT
41598169 AGTGACTGTTTTGTCACTTTTCCAAAGTTGAGTGATTGAAATGAAACCTA
1 AGTGACTGTTTTGTCACTTTTCCAAAGTTGAGTGATTGAAATGAAACCTA
* *
41598219 GGTGATTGTTTTGTCACTTTTCCAAAGTTGAGTGATTGAAATGAAACCTA
1 AGTGACTGTTTTGTCACTTTTCCAAAGTTGAGTGATTGAAATGAAACCTA
***
41598269 AGTGACTGTTTTGTCAGCTAACCCAAAGTTGAGTGA
1 AGTGACTGTTTTGTCA-CTTTTCCAAAGTTGAGTGA
41598305 CTGTTGGTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 62 0.79
51 16 0.21
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (50 bp):
AGTGACTGTTTTGTCACTTTTCCAAAGTTGAGTGATTGAAATGAAACCTA
Found at i:41598506 original size:66 final size:66
Alignment explanation
Indices: 41598439--41598570 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
41598429 TATATAATTT
* * * *
41598439 AATAAAATTTT-TAATATAATTATTTTTATATTAAATTATATTAGAATGTTTAAAATATTGTATT
1 AATAAAATTTTGAAAT-TAAATA-TTTTATATTAAATTATATTAAAATATTTAAAATATTGTATT
41598503 TTA
64 TTA
* * * *
41598506 AATTATATTTTGAAATTAAATATTTTATATTAAATTATATTAAAATATTTCAAATATTTTATTTT
1 AATAAAATTTTGAAATTAAATATTTTATATTAAATTATATTAAAATATTTAAAATATTGTATTTT
41598571 TATATTTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 39 0.70
67 14 0.25
68 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (66 bp):
AATAAAATTTTGAAATTAAATATTTTATATTAAATTATATTAAAATATTTAAAATATTGTATTTT
A
Found at i:41598512 original size:34 final size:32
Alignment explanation
Indices: 41598462--41598570 Score: 112
Period size: 34 Copynumber: 3.3 Consensus size: 32
41598452 ATATAATTAT
*
41598462 TTTTATATTAAATTATATTAGAATGTTTAAAATA
1 TTTTATTTTAAATTATATTAGAAT-TTT-AAATA
* * *
41598496 TTGTATTTTAAATTATATTTTGAA-ATTAAATA
1 TTTTATTTTAAATTATA-TTAGAATTTTAAATA
* *
41598528 TTTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTTATTTTAAATTATATTAGAAT-TTT-AAATA
41598562 TTTTATTTT
1 TTTTATTTT
41598571 TATATTTTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.07
32 20 0.33
33 4 0.07
34 28 0.46
35 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (32 bp):
TTTTATTTTAAATTATATTAGAATTTTAAATA
Found at i:41598539 original size:32 final size:34
Alignment explanation
Indices: 41598462--41598546 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 34
41598452 ATATAATTAT
*
41598462 TTTTATATTAAATTATA-TTAGAATGTTTAAAATA
1 TTTTATATTAAATTATATTTAGAA-GATTAAAATA
* * *
41598496 TTGTATTTTAAATTATATTTTGAA-ATT-AAATA
1 TTTTATATTAAATTATATTTAGAAGATTAAAATA
41598528 TTTTATATTAAATTATATT
1 TTTTATATTAAATTATATT
41598547 AAAATATTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
32 22 0.50
33 2 0.05
34 15 0.34
35 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTTATATTAAATTATATTTAGAAGATTAAAATA
Found at i:41602513 original size:84 final size:85
Alignment explanation
Indices: 41602385--41602554 Score: 272
Period size: 84 Copynumber: 2.0 Consensus size: 85
41602375 ATTTCTGCTA
*
41602385 TTTGAGCTTAGGTTCAACACAAGCTCAACGAATGCAAACCAGCTGACATCAGTATCTAGTGATGT
1 TTTGAGCTTAGGTT-AACACAAGCTCAACGAATGCAAACCAGCTGACATCAATATCTAGTGATGT
41602450 ATACTCATCATGATTTTTCGG
65 ATACTCATCATGATTTTTCGG
* *
41602471 TTTGAGCTTAGG-T-ACACAAGCTCCACGATGTGCAAACCAGCTGACATCAATATCTAGTGATGT
1 TTTGAGCTTAGGTTAACACAAGCTCAACGA-ATGCAAACCAGCTGACATCAATATCTAGTGATGT
*
41602534 ATACTCATCATGGTTTTTCGG
65 ATACTCATCATGATTTTTCGG
41602555 CAATGGGCCA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
83 14 0.18
84 52 0.66
85 1 0.01
86 12 0.15
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (85 bp):
TTTGAGCTTAGGTTAACACAAGCTCAACGAATGCAAACCAGCTGACATCAATATCTAGTGATGTA
TACTCATCATGATTTTTCGG
Found at i:41605637 original size:16 final size:16
Alignment explanation
Indices: 41605616--41605646 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41605606 AATTAATTTA
41605616 AATTAAAAAATTTTCC
1 AATTAAAAAATTTTCC
41605632 AATTAAAAAATTTTC
1 AATTAAAAAATTTTC
41605647 TCAACCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAAAATTTTCC
Found at i:41609042 original size:15 final size:15
Alignment explanation
Indices: 41609004--41609034 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41608994 ATGAGGCCCA
41609004 CATGGCCCAACTCGG
1 CATGGCCCAACTCGG
41609019 CATGGCCCAACTCGG
1 CATGGCCCAACTCGG
41609034 C
1 C
41609035 TCGGCCCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATGGCCCAACTCGG
Found at i:41622832 original size:27 final size:27
Alignment explanation
Indices: 41622775--41622835 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
41622765 GATGGGATGT
**
41622775 TAAACACAAGATAGTCTGTCGAGACTT
1 TAAACACAAGATAGTCTGTCGAGACGA
* * * *
41622802 TAAACACATGATAGTTTGTTGGGACGA
1 TAAACACAAGATAGTCTGTCGAGACGA
41622829 TAAACAC
1 TAAACAC
41622836 GGGGTATATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (27 bp):
TAAACACAAGATAGTCTGTCGAGACGA
Found at i:41629085 original size:32 final size:32
Alignment explanation
Indices: 41629030--41629328 Score: 271
Period size: 32 Copynumber: 9.4 Consensus size: 32
41629020 GAATGGCTAC
* *
41629030 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41629061 AAGCCATCAGTAGCAGTGATATGATCGGCCCA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** * *
41629093 CAGCCATCAGTAATGGTAACATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
41629125 AAGCCATCAGCAGCAGTGATATGATCGGCCCA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** *
41629157 CAGCCATCAGTAATGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
41629189 AAGCCATCAGCAGCAGTGATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
41629221 CATCCATCAGTAACAGTAAAATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41629253 CAA-CCATC-GATAACGGTAACATGATTGGCACA
1 -AAGCCATCAG-TAACAGTAATATGATCGGCACA
* * *
41629285 AAGCCATCAGTAACGGTACTATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
41629317 AAGCCATCAGTA
1 AAGCCATCAGTA
41629329 GCACCGCAGC
Statistics
Matches: 210, Mismatches: 53, Indels: 9
0.77 0.19 0.03
Matches are distributed among these distances:
31 13 0.06
32 195 0.93
33 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:41629131 original size:64 final size:64
Alignment explanation
Indices: 41629031--41629331 Score: 340
Period size: 64 Copynumber: 4.7 Consensus size: 64
41629021 AATGGCTACA
* * * * *
41629031 AGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCCCAC
1 AGCCATCAGTAACGGTAACATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAC
* * * *
41629094 AGCCATCAGTAATGGTAACATGATCGGTACAAAGCCATCAGCAGCAGTGATATGATCGGCCCAC
1 AGCCATCAGTAACGGTAACATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAC
* * *
41629158 AGCCATCAGTAATGGTAACATGATCGGCACAAAGCCATCAGCAGCAGTGATATGATCGGTACAC
1 AGCCATCAGTAACGGTAACATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAC
* * * * * * * * *
41629222 ATCCATCAGTAACAGTAAAATGATCGACACACAA-CCATC-GATAACGGTAACATGATTGGCACA
1 AGCCATCAGTAACGGTAACATGATCGGCACA-AAGCCATCAG-TAGCAGTGATATGATCGGCACA
*
41629285 A
64 C
*
41629286 AGCCATCAGTAACGGT-ACTATGATTGGCACAAAGCCATCAGTAGCA
1 AGCCATCAGTAACGGTAAC-ATGATCGGCACAAAGCCATCAGTAGCA
41629332 CCGCAGCAAA
Statistics
Matches: 202, Mismatches: 30, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
63 13 0.06
64 186 0.92
65 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (64 bp):
AGCCATCAGTAACGGTAACATGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAC
Found at i:41629367 original size:26 final size:26
Alignment explanation
Indices: 41629333--41629384 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
41629323 TCAGTAGCAC
*
41629333 CGCAGCAAAGCTACCAGCAACAGTAT
1 CGCAACAAAGCTACCAGCAACAGTAT
* * *
41629359 CGCAACAAAGCTGCCAGTAATAGTAT
1 CGCAACAAAGCTACCAGCAACAGTAT
41629385 ATGTGGCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (26 bp):
CGCAACAAAGCTACCAGCAACAGTAT
Found at i:41629543 original size:24 final size:25
Alignment explanation
Indices: 41629500--41629557 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
41629490 CCATGCTTAG
*
41629500 AATCAGTCAT-TCAAATCACAGACA
1 AATCAGTCATACCAAATCACAGACA
*
41629524 AATTAGTCATACCAAA-CACAGACA
1 AATCAGTCATACCAAATCACAGACA
41629548 AATCAGTCAT
1 AATCAGTCAT
41629558 TTAACCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.21
Consensus pattern (25 bp):
AATCAGTCATACCAAATCACAGACA
Found at i:41629652 original size:27 final size:27
Alignment explanation
Indices: 41629622--41629963 Score: 366
Period size: 27 Copynumber: 12.7 Consensus size: 27
41629612 CCACCAGGGC
* *
41629622 ATTAAGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41629649 ATTACGAG-CATTTTACCCTACAGGGGA
1 ATTACG-GTCATTTTACCCTACAGGGGT
* * * *
41629676 ATTATGGTTATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41629703 ATTACGATTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41629730 ATTACGGTCATTTTACCCTACAAGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
41629757 ATTACAGTCATTTTACCCTACAAGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41629784 ATTACAGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
41629811 ATTACGATCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41629838 ATTACGATCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
41629865 ATTACGAT-AATTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
41629891 ATTACAGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * *
41629918 ATTTCGGT-ATTCTACCTTACGGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
41629944 ATTTTGGTCATTTTAACCTA
1 ATTACGGTCATTTTACCCTA
41629964 TCGAGGGTAT
Statistics
Matches: 269, Mismatches: 42, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
26 42 0.16
27 226 0.84
28 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:41629690 original size:54 final size:54
Alignment explanation
Indices: 41629618--41629974 Score: 405
Period size: 54 Copynumber: 6.6 Consensus size: 54
41629608 TTACCCACCA
* * *
41629618 GGGCATTAAGGTCATTTTACCCTACAAGGGTATTACGAGCATTTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
* * * * **
41629672 GGGAATTATGGTTATTTTACCCTATAGGGGCATTACGATTATTTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
* * * * *
41629726 GGGTATTACGGTCATTTTACCCTACAAGGGCATTAC-AGTCATTTTACCCTACAA
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAG-CATTTTACCCTACAG
* *
41629780 GGGCATTACAGTCATTTTACCCTATAGGGGTATTACGATCATTTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
* * * *
41629834 GGGTATTACGATCATTTTACCCTATAGGGGTATTACGA-TAATTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
* * * * * *
41629887 GGGCATTACAGTCATTTTACCCTATAGGGGTATTTCG-GTATTCTACCTTACGG
1 GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
** * *
41629940 GGGCATTTTGGTCATTTTAACCTATCGAGGGTATT
1 GGGCATTACGGTCATTTTACCCTATAG-GGGTATT
41629975 TTAGTTCAGA
Statistics
Matches: 258, Mismatches: 41, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
53 80 0.31
54 177 0.69
55 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (54 bp):
GGGCATTACGGTCATTTTACCCTATAGGGGTATTACGAGCATTTTACCCTACAG
Found at i:41630514 original size:63 final size:63
Alignment explanation
Indices: 41630427--41630556 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
41630417 CCCCATTCAG
41630427 AATAAGGAACAAATGAGATGTGATATATATAACTCTCCACAACAACAACCTTCCCCAAATCCC
1 AATAAGGAACAAATGAGATGTGATATATATAACTCTCCACAACAACAACCTTCCCCAAATCCC
41630490 AATAAGGAACAAATGAGATGTGATATATATAACTCTCCACAACAACAACCTTCCCCAAATCCC
1 AATAAGGAACAAATGAGATGTGATATATATAACTCTCCACAACAACAACCTTCCCCAAATCCC
41630553 AATA
1 AATA
41630557 TTCTCTCCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (63 bp):
AATAAGGAACAAATGAGATGTGATATATATAACTCTCCACAACAACAACCTTCCCCAAATCCC
Found at i:41642137 original size:30 final size:31
Alignment explanation
Indices: 41642101--41642161 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
41642091 TGACAGTACA
*
41642101 GTGTGGGCCTTAGCCCATTACAGTAA-CAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
41642131 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
41642162 ACAATGTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (31 bp):
GTGTGGGCCTTAGCCCAATACAGTAATCAGT
Found at i:41642295 original size:26 final size:26
Alignment explanation
Indices: 41642263--41642343 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
41642253 AACACACCAA
* *
41642263 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTACCAGTAACAG
41642289 TGA-CGCAGCAAAGCTACCAGTAACAG
1 T-ATCGCAGCAAAGCTACCAGTAACAG
* *
41642315 TATCACAGAAAAGCTACCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
41642341 TAT
1 TAT
41642344 ACTTCCTCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.02
26 47 0.96
27 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAACAG
Found at i:41642521 original size:27 final size:26
Alignment explanation
Indices: 41642490--41642792 Score: 214
Period size: 27 Copynumber: 11.2 Consensus size: 26
41642480 GGGTATAATA
**
41642490 GTCATTTTACCTTATAAGGGTATTTC
1 GTCATTTTACCTTATGGGGGTATTTC
* * * ** *
41642516 GTTCATTTCATCTAATAAGGGTAATTC
1 G-TCATTTTACCTTATGGGGGTATTTC
* * *
41642543 ATTCATTTTACCATATGGGGGTATTTT
1 -GTCATTTTACCTTATGGGGGTATTTC
**
41642570 GATCATTCCACCCTT-TGGGGGTATTTC
1 G-TCATTTTA-CCTTATGGGGGTATTTC
* * ***
41642597 AGTCATTCTACCATATAAAGGTATTTC
1 -GTCATTTTACCTTATGGGGGTATTTC
*
41642624 GGTCATTTTACCTTATGGGGGTATTTTA
1 -GTCATTTTACCTTATGGGGGTA-TTTC
* *
41642652 GTGATTTTACCTTCTGGGGGTATTTC
1 GTCATTTTACCTTATGGGGGTATTTC
*
41642678 AGTCATTTTACCCTATGGGGGTATTTC
1 -GTCATTTTACCTTATGGGGGTATTTC
* * *
41642705 GGTCATTCTACCCTATGGAGGTATTTC
1 -GTCATTTTACCTTATGGGGGTATTTC
* *
41642732 TATCATTTTA-CTCTGTGGGGGTATTTC
1 -GTCATTTTACCT-TATGGGGGTATTTC
* *
41642759 GGTCATTTTACCTTATGAGGGTAATTTG
1 -GTCATTTTACCTTATGGGGGT-ATTTC
41642787 GTCATT
1 GTCATT
41642793 CTACTATATA
Statistics
Matches: 216, Mismatches: 50, Indels: 21
0.75 0.17 0.07
Matches are distributed among these distances:
26 8 0.04
27 195 0.90
28 13 0.06
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCTTATGGGGGTATTTC
Found at i:41643510 original size:12 final size:12
Alignment explanation
Indices: 41643493--41643534 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
41643483 ATCCCAATAT
41643493 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
41643505 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
*
41643517 TCTCTCCTCAAT
1 TCTCTCCTCAAA
41643529 TCTCTC
1 TCTCTC
41643535 TACGACTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.21, C:0.40, G:0.00, T:0.38
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:41643513 original size:24 final size:24
Alignment explanation
Indices: 41643488--41643534 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
41643478 CCCAAATCCC
41643488 AATATTCTCTCCTCAAATCTCTCCA
1 AATA-TCTCTCCTCAAATCTCTCCA
*
41643513 AATATCTCTCCTCAATTCTCTC
1 AATATCTCTCCTCAAATCTCTC
41643535 TACGACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATCTCTCCTCAAATCTCTCCA
Found at i:41645079 original size:26 final size:26
Alignment explanation
Indices: 41644973--41645079 Score: 144
Period size: 26 Copynumber: 4.1 Consensus size: 26
41644963 AACACACCAA
* *
41644973 TATCGCAACAAAGCTACCAGTAATAG
1 TATCGCAGCAAAGCTACCAGTAACAG
*
41644999 TGA-CGCAGCAAAGCTACCAATAACAG
1 T-ATCGCAGCAAAGCTACCAGTAACAG
*
41645025 TAACGCAGCAAAGCTACCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
* *
41645051 TATCGCAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAACAG
41645077 TAT
1 TAT
41645080 ACTTCCTCCA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 1 0.01
26 70 0.97
27 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAACAG
Found at i:41645239 original size:25 final size:25
Alignment explanation
Indices: 41645197--41645325 Score: 75
Period size: 27 Copynumber: 4.8 Consensus size: 25
41645187 TAAGGCCATA
*
41645197 CAGTCATTTCATCTCCTAGGGGTATAAT
1 CAGTCATTTTA-C-CCTAGGGGTAT-AT
* *
41645225 -AGTCGTTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCC--TAGGGGTATAT
*
41645251 CAGTCATTTTACCCTATAGGGCTA-ATT
1 CAGTCATTTTACCC--TAGGGGTATA-T
*
41645278 CAATCATTTTACCCTATGGGGGTA-ATT
1 CAGTCATTTTACCCTA--GGGGTATA-T
*
41645305 CATTCATTTTACCCTATGGGG
1 CAGTCATTTTACCCTA-GGGG
41645326 GTATTTCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.05
26 6 0.07
27 75 0.88
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (25 bp):
CAGTCATTTTACCCTAGGGGTATAT
Found at i:41645243 original size:27 final size:28
Alignment explanation
Indices: 41645213--41645577 Score: 184
Period size: 27 Copynumber: 13.6 Consensus size: 28
41645203 TTTCATCTCC
* *
41645213 TAGGGGTATAAT-AGTCGTTTTACCCTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
41645240 TAGGGGTAT-TTCAGTCATTTTACCCTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
* *
41645267 TAGGGCTA-ATTCAATCATTTTACCCTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
* *
41645294 TGGGGGTA-ATTCATTCATTTTACCCTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
* *
41645321 TGGGGGTAT-TTC-GATCATTTCACCCGT-
1 TAGGGGTATATTCAG-TCATTTTACCC-TA
* * *
41645348 T-GGGG-ATATTTCGGTCATTCTACCATA
1 TAGGGGTATA-TTCAGTCATTTTACCCTA
* * * *
41645375 T-GAGAGTAT-TTCGGTCATTTTACCTTT
1 TAG-GGGTATATTCAGTCATTTTACCCTA
* * *
41645402 TGGGGGTAT-TTC-GATCATTTTGCCTTA
1 TAGGGGTATATTCAG-TCATTTTACCCTA
* *
41645429 TGGGGGTAT-TTC-GATCATTTTAACCTA
1 TAGGGGTATATTCAG-TCATTTTACCCTA
* * *
41645456 TGGGGGGTAT-TTC-GATTATTCTACCCTA
1 T-AGGGGTATATTCAG-TCATTTTACCCTA
* * *
41645484 TAGAGGTAT-TTCGGTCATTTTACCTTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
** *
41645511 T-GAGGGTAT-TTTGGTCATTTTAACCTA
1 TAG-GGGTATATTCAGTCATTTTACCCTA
* ** *
41645538 TGGGGGT-T-TTTGGTCATTCTACCCTA
1 TAGGGGTATATTCAGTCATTTTACCCTA
41645564 T-GGGGTAT-TTCAGT
1 TAGGGGTATATTCAGT
41645578 GCAGACATTG
Statistics
Matches: 282, Mismatches: 38, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
25 7 0.02
26 31 0.11
27 211 0.75
28 31 0.11
29 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (28 bp):
TAGGGGTATATTCAGTCATTTTACCCTA
Found at i:41645338 original size:54 final size:54
Alignment explanation
Indices: 41645230--41645577 Score: 328
Period size: 54 Copynumber: 6.5 Consensus size: 54
41645220 ATAATAGTCG
* * * * *
41645230 TTTTACCCTATAGGGGTATTTCAGTCATTTTACCCTATAGGGCTAATTCAATCA
1 TTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCA
* *
41645284 TTTTACCCTATGGGGGTAATTCATTCATTTTACCCTATGGGGGTATTTCGATCA
1 TTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCA
* * * * * * * *
41645338 TTTCACCCGT-TGGGGATATTTCGGTCATTCTACCATATGAGAGTATTTCGGTCA
1 TTTTACCC-TATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCA
* * * *
41645392 TTTTACCTTTTGGGGGTATTTC-GATCATTTTGCCTTATGGGGGTATTTCGATCA
1 TTTTACCCTATGGGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCGATCA
* * * * * *
41645446 TTTTAACCTATGGGGGGTATTTC-GATTATTCTACCCTATAGAGGTATTTCGGTCA
1 TTTTACCCTAT-GGGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCGATCA
* * ** * * *
41645501 TTTTACCTTATGAGGGTATTTTGGTCATTTTAACCTATGGGGGT-TTTTGGTCA
1 TTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCA
*
41645554 TTCTACCCTAT-GGGGTATTTCAGT
1 TTTTACCCTATGGGGGTATTTCAGT
41645578 GCAGACATTG
Statistics
Matches: 238, Mismatches: 51, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
52 10 0.04
53 19 0.08
54 162 0.68
55 47 0.20
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (54 bp):
TTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCA
Done.