Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 102 of 132
Found at i:31237038 original size:40 final size:41
Alignment explanation
Indices: 31236983--31237059 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
31236973 TTTAGAAAAA
**
31236983 GAAAAAAAATTGAAAAAAAAAAGAAAAAAAAA-AGAAAATT
1 GAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAGAAAATT
***
31237023 GAAAAAAAAAAGAAAAAATTGAGAAAAAAAAAGAGAA
1 GAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAGAA
31237060 GAAAAAGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 27 0.87
41 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (41 bp):
GAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAGAAAATT
Found at i:31237049 original size:29 final size:29
Alignment explanation
Indices: 31236976--31237040 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
31236966 TTTATTATTT
*
31236976 AGAAAAAGAAAA-AAAATTGAAAAAAAAA
1 AGAAAAAAAAAAGAAAATTGAAAAAAAAA
31237004 AGAAAAAAAAAAGAAAATTGAAAAAAAAA
1 AGAAAAAAAAAAGAAAATTGAAAAAAAAA
31237033 AGAAAAAA
1 AGAAAAAA
31237041 TTGAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (29 bp):
AGAAAAAAAAAAGAAAATTGAAAAAAAAA
Found at i:31237073 original size:6 final size:6
Alignment explanation
Indices: 31236976--31237039 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
31236966 TTTATTATTT
* *
31236976 AGAAAA AGAAAA A-AAAT TGAAAA A-AAAA AGAAAA A-AAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
*
31237021 TTGAAAA A-AAAA AGAAAA A
1 -AGAAAA AGAAAA AGAAAA A
31237040 ATTGAGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 18 0.38
6 24 0.51
7 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (6 bp):
AGAAAA
Found at i:31243997 original size:18 final size:18
Alignment explanation
Indices: 31243970--31244016 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 18
31243960 ACTTAAAACA
31243970 TTTA-ATATTATTTAAAT
1 TTTATATATTATTTAAAT
*
31243987 TTTATATATTA---ATAT
1 TTTATATATTATTTAAAT
31244002 TTTAT-TATTATTTAA
1 TTTATATATTATTTAA
31244017 TGGTTCGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
17 5 0.21
18 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATATTATTTAAAT
Found at i:31244017 original size:18 final size:17
Alignment explanation
Indices: 31243969--31244017 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
31243959 GACTTAAAAC
*
31243969 ATTTAATATTATTTAA-
1 ATTTTATATTATTTAAT
31243985 ATTTTATA-TA-TTAAT
1 ATTTTATATTATTTAAT
31244000 ATTTTATTATTATTTAAT
1 ATTTTA-TATTATTTAAT
31244018 GGTTCGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 9 0.32
17 2 0.07
18 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATTATTTAAT
Found at i:31257558 original size:20 final size:19
Alignment explanation
Indices: 31257526--31257571 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
31257516 GCAACCCAAA
31257526 TTAATTTTTATTTT-AAGTT
1 TTAATTTTTATTTTCAAG-T
31257545 TTAATTTTTAATTTTCAAGT
1 TTAATTTTT-ATTTTCAAGT
31257565 TTAATTT
1 TTAATTT
31257572 CAGTTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 13 0.52
21 3 0.12
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTAATTTTTATTTTCAAGT
Found at i:31261420 original size:20 final size:20
Alignment explanation
Indices: 31261395--31261434 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31261385 CATAAATGTG
31261395 TTGGATTAATTGTATTATTT
1 TTGGATTAATTGTATTATTT
31261415 TTGGATTAATTGTATTATTT
1 TTGGATTAATTGTATTATTT
31261435 AACTTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGGATTAATTGTATTATTT
Found at i:31262240 original size:15 final size:16
Alignment explanation
Indices: 31262220--31262252 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31262210 AAGAGAGAAA
31262220 ATATGTG-AGAGAGGG
1 ATATGTGAAGAGAGGG
*
31262235 ATATGTGAAGTGAGGG
1 ATATGTGAAGAGAGGG
31262251 AT
1 AT
31262253 GAGAAATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.24
Consensus pattern (16 bp):
ATATGTGAAGAGAGGG
Found at i:31263409 original size:53 final size:54
Alignment explanation
Indices: 31263343--31263469 Score: 141
Period size: 53 Copynumber: 2.4 Consensus size: 54
31263333 AAAAGTTTTT
* * * *
31263343 GGGGTTTATGAGGAAATAAAAGTTTTG-AAGGAAAACAAAAGGAAAAAAAAATTG
1 GGGGTTT-GGAGGAAGTAAAAATTTTGAAAGGAAAACAAAAAGAAAAAAAAATTG
** *
31263397 GGGGTTTGGAGG-AGTAAAAATTTTGAAAGGAAAGTAAAAAGAAAAAAAATTTG
1 GGGGTTTGGAGGAAGTAAAAATTTTGAAAGGAAAACAAAAAGAAAAAAAAATTG
** *
31263450 GAAGTTTGGCGGAAGTAAAA
1 GGGGTTTGGAGGAAGTAAAA
31263470 TTTGTTTGGG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
52 11 0.18
53 36 0.59
54 14 0.23
ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21
Consensus pattern (54 bp):
GGGGTTTGGAGGAAGTAAAAATTTTGAAAGGAAAACAAAAAGAAAAAAAAATTG
Found at i:31263478 original size:20 final size:20
Alignment explanation
Indices: 31263453--31263511 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
31263443 AAATTTGGAA
* *
31263453 GTTTGGCGGAAGTAAAATTT
1 GTTTGGCGGAAATAAAATTG
*
31263473 GTTTGG-GGAACAAAAAAATTG
1 GTTTGGCGG-A-AATAAAATTG
31263494 GTTTGGCGGAAATAAAAT
1 GTTTGGCGGAAATAAAAT
31263512 CAACTATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.06
20 14 0.44
21 14 0.44
22 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTTGGCGGAAATAAAATTG
Found at i:31263510 original size:21 final size:21
Alignment explanation
Indices: 31263453--31263510 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
31263443 AAATTTGGAA
* *
31263453 GTTTGGCGGAAGT-AAAATTT
1 GTTTGGCGGAAATAAAAATTG
*
31263473 GTTTGG-GGAACAAAAAAATTG
1 GTTTGGCGGAA-ATAAAAATTG
31263494 GTTTGGCGGAAATAAAA
1 GTTTGGCGGAAATAAAA
31263511 TCAACTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 4 0.13
20 6 0.19
21 17 0.55
22 4 0.13
ACGTcount: A:0.38, C:0.05, G:0.29, T:0.28
Consensus pattern (21 bp):
GTTTGGCGGAAATAAAAATTG
Found at i:31265686 original size:79 final size:79
Alignment explanation
Indices: 31265530--31265686 Score: 314
Period size: 79 Copynumber: 2.0 Consensus size: 79
31265520 TATTAAAAAC
31265530 AAACTTGCATATATATTGGTATAACAAGATGTAGGTTCTAAGATTAATCTTTTCTAAACTAAAAT
1 AAACTTGCATATATATTGGTATAACAAGATGTAGGTTCTAAGATTAATCTTTTCTAAACTAAAAT
31265595 AGTATAGTAAAATG
66 AGTATAGTAAAATG
31265609 AAACTTGCATATATATTGGTATAACAAGATGTAGGTTCTAAGATTAATCTTTTCTAAACTAAAAT
1 AAACTTGCATATATATTGGTATAACAAGATGTAGGTTCTAAGATTAATCTTTTCTAAACTAAAAT
31265674 AGTATAGTAAAAT
66 AGTATAGTAAAAT
31265687 CCTATTAAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (79 bp):
AAACTTGCATATATATTGGTATAACAAGATGTAGGTTCTAAGATTAATCTTTTCTAAACTAAAAT
AGTATAGTAAAATG
Found at i:31268375 original size:23 final size:24
Alignment explanation
Indices: 31268334--31268380 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31268324 TTTTTTCAAA
* *
31268334 TTTTGAGTTCGAGTCAATTTGAAT
1 TTTTGAGTTCGAATCAATTCGAAT
*
31268358 TTTTGAGTTTGAAT-AATTCGAAT
1 TTTTGAGTTCGAATCAATTCGAAT
31268381 AAATCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (24 bp):
TTTTGAGTTCGAATCAATTCGAAT
Found at i:31269842 original size:24 final size:24
Alignment explanation
Indices: 31269810--31269856 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31269800 GAAATGGTAA
31269810 TGCTTGGATGAATGGTTAAGTTAG
1 TGCTTGGATGAATGGTTAAGTTAG
*
31269834 TGCTTGGATGAATGGTTGAGTTA
1 TGCTTGGATGAATGGTTAAGTTA
31269857 TACATGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.04, G:0.34, T:0.38
Consensus pattern (24 bp):
TGCTTGGATGAATGGTTAAGTTAG
Found at i:31272387 original size:17 final size:18
Alignment explanation
Indices: 31272367--31272405 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
31272357 CTACTTCTTG
31272367 TTTAGATTAATT-AGAGT
1 TTTAGATTAATTAAGAGT
* *
31272384 TTTAGTTTATTTAAGAGT
1 TTTAGATTAATTAAGAGT
31272402 TTTA
1 TTTA
31272406 TTTATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTAGATTAATTAAGAGT
Found at i:31276581 original size:43 final size:43
Alignment explanation
Indices: 31276528--31276748 Score: 184
Period size: 43 Copynumber: 5.1 Consensus size: 43
31276518 AAAATACCAT
*
31276528 TAAAGAACATGGACTTTAGCGACGCTTTTTGCATAAATGCCGC
1 TAAAGAACATGGACTTTAGCGACGCTTTTTGCACAAATGCCGC
* * *
31276571 TAAAGAACATGGCCTTTAGCTG-CGCTTTTTGCACAAACGTCGC
1 TAAAGAACATGGACTTTAGC-GACGCTTTTTGCACAAATGCCGC
* * * * *
31276614 TAAAAAACATGGTA-TTTAGTGGCGCTTTTAGCACAAACT-CCAC
1 TAAAGAACATGG-ACTTTAGCGACGCTTTTTGCACAAA-TGCCGC
* * **
31276657 TAAAGAACATGGTCTTTAGCGACACTTTTCT-CACAAATGTTGC
1 TAAAGAACATGGACTTTAGCGACGCTTTT-TGCACAAATGCCGC
* * ** *
31276700 TAAAGAACACTGTA-TTTAGCGGCAATTTTCT-CACAAACGCCGC
1 TAAAGAACA-TGGACTTTAGCGACGCTTTT-TGCACAAATGCCGC
31276743 TAAAGA
1 TAAAGA
31276749 CTTTAGTAGC
Statistics
Matches: 143, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
42 2 0.01
43 138 0.97
44 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
TAAAGAACATGGACTTTAGCGACGCTTTTTGCACAAATGCCGC
Found at i:31276825 original size:43 final size:43
Alignment explanation
Indices: 31276778--31276868 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
31276768 AAAAAAGGCT
*
31276778 CTAAAGAACATGGTCTGTAGCAGCGCTTTTACCACAAACGCCG
1 CTAAAGAACATGGTCTGTAGCAGCACTTTTACCACAAACGCCG
* * * *
31276821 CTAAAGAACATGGTCTTTAGCGGCATTTTTCCCACAAACGCCG
1 CTAAAGAACATGGTCTGTAGCAGCACTTTTACCACAAACGCCG
31276864 CTAAA
1 CTAAA
31276869 ATTAACAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
CTAAAGAACATGGTCTGTAGCAGCACTTTTACCACAAACGCCG
Found at i:31277275 original size:66 final size:66
Alignment explanation
Indices: 31277133--31277276 Score: 146
Period size: 66 Copynumber: 2.2 Consensus size: 66
31277123 TTTTCATCAT
* * * * *
31277133 ATTTTGAAGCTGTAGCTGCAATTCGTCATACTTTCTTTGAGATTCTGCTTCCCTCGTTGCTGCCT
1 ATTTT-AAGTTGTAGCTGCAATTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTACCT
**
31277198 TG
65 CC
** * * * *
31277200 GCTTCAAGTTGTAGCTG-AAGTTCATCATATTTTCTTTGAGCCTCTGCTTCTCTCGCTGCTACCT
1 ATTTTAAGTTGTAGCTGCAA-TTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTACCT
31277264 CC
65 CC
31277266 ATTTTAAGTTG
1 ATTTTAAGTTG
31277277 AGCAATTTGC
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
65 2 0.03
66 56 0.93
67 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (66 bp):
ATTTTAAGTTGTAGCTGCAATTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTACCTC
C
Found at i:31280356 original size:41 final size:41
Alignment explanation
Indices: 31280229--31280451 Score: 313
Period size: 41 Copynumber: 5.4 Consensus size: 41
31280219 TTACACTCTA
* * * * *
31280229 TCGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTATTCATAATCTCATTCTAATC
* ** * *
31280271 TGGAGACATGAGTCTTCCTTAACCA-AATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
*
31280311 TTGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
*
31280352 TTGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
*
31280393 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTTATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
31280434 TCGAGACATGAGTCTTCC
1 TCGAGACATGAGTCTTCC
31280452 ATTTATACAA
Statistics
Matches: 167, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 35 0.21
41 117 0.70
42 15 0.09
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTAATC
Found at i:31287608 original size:41 final size:41
Alignment explanation
Indices: 31287441--31287621 Score: 240
Period size: 40 Copynumber: 4.4 Consensus size: 41
31287431 TTATGCTCTA
* * *
31287441 TCGAGCCATAAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTAATCATAATCTCATTCTCATC
* * *
31287483 TGGAGACATGAGTCTTCCTTAACCA-AATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* * *
31287523 TCGAGACATGAGTCTTCCTT-TTCATAATCTCATTCTAATT
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* *
31287563 TCGAGATATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
31287604 TCGAGACATGAGTCTTCC
1 TCGAGACATGAGTCTTCC
31287622 ATTTATACAA
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.02
40 65 0.53
41 41 0.33
42 15 0.12
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
Found at i:31292437 original size:6 final size:6
Alignment explanation
Indices: 31292426--31292457 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31292416 TTGTTATATG
31292426 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TT
31292458 CTATCATCCT
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:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:31292562 original size:8 final size:8
Alignment explanation
Indices: 31292547--31292582 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
31292537 GATTGTTTTT
31292547 AATAATTA
1 AATAATTA
*
31292555 ACTAATTA
1 AATAATTA
*
31292563 AATATTTA
1 AATAATTA
31292571 AATAATTA
1 AATAATTA
31292579 AATA
1 AATA
31292583 TTTGGATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (8 bp):
AATAATTA
Found at i:31292571 original size:16 final size:16
Alignment explanation
Indices: 31292547--31292585 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31292537 GATTGTTTTT
* *
31292547 AATAATTAACTAATTA
1 AATATTTAAATAATTA
31292563 AATATTTAAATAATTA
1 AATATTTAAATAATTA
31292579 AATATTT
1 AATATTT
31292586 GGATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTTAAATAATTA
Found at i:31292685 original size:36 final size:36
Alignment explanation
Indices: 31292644--31292765 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
31292634 AAATATTTTG
31292644 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATT
1 AATTAAATATTTGGGTTTAGGGTTTAATAAATAAC----T
** * *
31292684 AAATAATAAATATTTGGG-TT-GTTTTTAATAATTAAAT
1 -AAT--TAAATATTTGGGTTTAGGGTTTAATAAATAACT
* *
31292721 AATTAAATATTTGAGTTTAGGGTTGAATAAATAACT
1 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACT
31292757 AATTAAATA
1 AATTAAATA
31292766 ATAAATATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
34 11 0.16
35 2 0.03
36 24 0.36
37 1 0.01
41 15 0.22
42 2 0.03
43 12 0.18
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (36 bp):
AATTAAATATTTGGGTTTAGGGTTTAATAAATAACT
Found at i:31292724 original size:41 final size:41
Alignment explanation
Indices: 31292647--31292817 Score: 156
Period size: 41 Copynumber: 4.2 Consensus size: 41
31292637 TATTTTGAAT
** *
31292647 TAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAA
1 TAAATATTTGGG-TT-GTTTTTAATAAATAAATAATTAAATAA
* *
31292690 TAAATATTTGGGTTGTTTTTAATAATTAAATAATTAAATATT
1 TAAATATTTGGGTTGTTTTTAATAAATAAATAATTAAATA-A
* * * *
31292732 TGAGT-TTAGGGTTG-----AATAAATAACTAATTAAATAA
1 TAAATATTTGGGTTGTTTTTAATAAATAAATAATTAAATAA
* * *
31292767 TAAATATTTAGATTGTTTTTAATAATTAAATAATTAAATAA
1 TAAATATTTGGGTTGTTTTTAATAAATAAATAATTAAATAA
31292808 TTAAATATTT
1 -TAAATATTT
31292818 TAAATTAAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
35 3 0.03
36 24 0.24
41 49 0.48
42 14 0.14
43 12 0.12
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (41 bp):
TAAATATTTGGGTTGTTTTTAATAAATAAATAATTAAATAA
Found at i:31292739 original size:77 final size:77
Alignment explanation
Indices: 31292644--31292806 Score: 290
Period size: 77 Copynumber: 2.1 Consensus size: 77
31292634 AAATATTTTG
* * * *
31292644 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATAAATATTTGGGTTGTTTT
1 AATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATAAATATTTAGATTGTTTT
31292709 TAATAATTAAAT
66 TAATAATTAAAT
31292721 AATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATAAATATTTAGATTGTTTT
1 AATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATAAATATTTAGATTGTTTT
31292786 TAATAATTAAAT
66 TAATAATTAAAT
31292798 AATTAAATA
1 AATTAAATA
31292807 ATTAAATATT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (77 bp):
AATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATAAATATTTAGATTGTTTT
TAATAATTAAAT
Found at i:31292800 original size:8 final size:8
Alignment explanation
Indices: 31292787--31292814 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31292777 GATTGTTTTT
31292787 AATAATTA
1 AATAATTA
31292795 AATAATTA
1 AATAATTA
31292803 AATAATTA
1 AATAATTA
31292811 AATA
1 AATA
31292815 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATTA
Found at i:31292824 original size:99 final size:95
Alignment explanation
Indices: 31292713--31292956 Score: 289
Period size: 92 Copynumber: 2.6 Consensus size: 95
31292703 TGTTTTTAAT
*
31292713 AATTAAATAATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATAAATATTTAG
1 AATTAAATAATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAAT--AT-TTGA-
* * *
31292778 ATTGTTTTTAATAATTAAATAATTAAATAATTAA
62 ATTATTTTCAATAATTAAATAATTAAATAAATAA
** *
31292812 ATATTTTA-AATTAAATATTTGAGTTTAGGATTGAATAAATAACTAATT--A-AATATTTGAATT
1 A-ATTAAATAATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATATTTGAATT
* ** *
31292873 ATTTTCAATAATTAAATATTTATTTAAATAT
65 ATTTTCAATAATTAAATAATTAAATAAATAA
* * *
31292904 AATTAAATAATTAAATATTTGGGTTTAGGGTTTAATAAATAACTGATTAAATA
1 AATTAAATAATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATA
31292957 TCTAGGACTT
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
91 4 0.03
92 64 0.52
93 3 0.02
94 3 0.02
95 1 0.01
96 3 0.02
97 1 0.01
99 40 0.33
100 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (95 bp):
AATTAAATAATTAAATATTTGAGTTTAGGGTTGAATAAATAACTAATTAAATAATATTTGAATTA
TTTTCAATAATTAAATAATTAAATAAATAA
Found at i:31293629 original size:13 final size:13
Alignment explanation
Indices: 31293611--31293635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31293601 ATTCAATGTC
31293611 AACTACCATTTTG
1 AACTACCATTTTG
31293624 AACTACCATTTT
1 AACTACCATTTT
31293636 CATCAAACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (13 bp):
AACTACCATTTTG
Found at i:31295244 original size:17 final size:17
Alignment explanation
Indices: 31295218--31295317 Score: 55
Period size: 17 Copynumber: 5.9 Consensus size: 17
31295208 ACGAGGTTCA
*
31295218 GGCGTAAAGAAGAGAAT
1 GGCGTGAAGAAGAGAAT
* **
31295235 GGCGTGAAGAATA-TTT
1 GGCGTGAAGAAGAGAAT
* ****
31295251 CGACGTGAAGAAGATTCC
1 -GGCGTGAAGAAGAGAAT
*
31295269 GGCGTGAAGAAGAGAAG
1 GGCGTGAAGAAGAGAAT
31295286 GGCGTG-AG--GAGAAT
1 GGCGTGAAGAAGAGAAT
31295300 CGGGCGTGAAGAAGAGAA
1 --GGCGTGAAGAAGAGAA
31295318 GGGTGAGAGT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.08
16 9 0.15
17 42 0.68
18 1 0.02
19 5 0.08
ACGTcount: A:0.37, C:0.10, G:0.39, T:0.14
Consensus pattern (17 bp):
GGCGTGAAGAAGAGAAT
Found at i:31295557 original size:42 final size:43
Alignment explanation
Indices: 31295472--31295565 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
31295462 GTTATTACAT
* *
31295472 ACCTTTAGCGGCGTTTTTCCCATAAACGCCGCTAATGACCTGG
1 ACCTTTTGCGGCGTTTTTCCAATAAACGCCGCTAATGACCTGG
* * *
31295515 ACCTTTTGCGGCG-TTTTCCAATAAATGCTGCTATTG-CTCTGG
1 ACCTTTTGCGGCGTTTTTCCAATAAACGCCGCTAATGAC-CTGG
31295557 ACCTTTTGC
1 ACCTTTTGC
31295566 ATGTTATTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 1 0.02
42 32 0.71
43 12 0.27
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (43 bp):
ACCTTTTGCGGCGTTTTTCCAATAAACGCCGCTAATGACCTGG
Found at i:31297189 original size:41 final size:41
Alignment explanation
Indices: 31297113--31297335 Score: 302
Period size: 41 Copynumber: 5.4 Consensus size: 41
31297103 CTATTGCTTA
* * *
31297113 ACCTTTAGCGGCGTTTTTCCCATAAACGCCACTAATGCTCTT
1 ACCTTTAGCGGCG-TTTTCTCATAAACGCCGCTAATGCTCTG
* * *
31297155 ACCTTTAGCGGCGTTTTCTAATAAACACCGCTAATCCTCTG
1 ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
*
31297196 ACCTTTAGTGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
*
31297237 ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTA
1 ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
* ** * *
31297278 ACCTTTAACGATGTTTTCACATAAACGCCGCTAATGCTCAG
1 ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
* *
31297319 ACATTTGGCGGCGTTTT
1 ACCTTTAGCGGCGTTTT
31297336 TCCTATAAGC
Statistics
Matches: 158, Mismatches: 23, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
41 145 0.92
42 13 0.08
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTG
Found at i:31297364 original size:123 final size:122
Alignment explanation
Indices: 31297103--31297375 Score: 307
Period size: 123 Copynumber: 2.2 Consensus size: 122
31297093 GAAAATGTCG
* * * *
31297103 CTATTGCTTAACCTTTAGCGGCGTTTTTCCCATAAACGCCACTAATGCTCTTACCTTTAGCGGCG
1 CTATTGTTTAACCTTTAGCGGCG-TTTTCCCATAAACGCCACTAATGCTCTAACCTTTAACGACG
* * * *
31297168 TTTTCTAATAAACACCGCTAATCCTCTGACCTTTAGTGGCGTTTTCTCATAAACGCCG
65 TTTTCTAATAAACACCGCTAATCCTCAGACATTTAGCGGCGTTTTCTCATAAACGCCA
* * * * * *
31297226 CTAATGCTCTGACCTTTAGCGGCGTTTTCTCATAAACGCCGCTAATGCTCTAACCTTTAACGATG
1 CTATTG-TTTAACCTTTAGCGGCGTTTTCCCATAAACGCCACTAATGCTCTAACCTTTAACGACG
* * * *
31297291 TTTTC-ACATAAACGCCGCTAATGCTCAGACATTTGGCGGCGTTTT-TCCTATAAGCGCCA
65 TTTTCTA-ATAAACACCGCTAATCCTCAGACATTTAGCGGCGTTTTCT-C-ATAAACGCCA
* *
31297350 CTATTGTTTTACCTTTTGCGGCGTTT
1 CTATTGTTTAACCTTTAGCGGCGTTT
31297376 ATGGGAAAAC
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
122 2 0.02
123 95 0.77
124 27 0.22
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (122 bp):
CTATTGTTTAACCTTTAGCGGCGTTTTCCCATAAACGCCACTAATGCTCTAACCTTTAACGACGT
TTTCTAATAAACACCGCTAATCCTCAGACATTTAGCGGCGTTTTCTCATAAACGCCA
Found at i:31297371 original size:41 final size:40
Alignment explanation
Indices: 31297326--31297416 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
31297316 CAGACATTTG
* * *
31297326 GCGGCGTTTTTCCTATAAGCGCCACTATTGTTTTACCTTTT
1 GCGGCGTTTTTCCGA-AAACGCCACTATTGCTTTACCTTTT
* ** * *
31297367 GCGGCGTTTATGGGAAAACGCCGCTATTGCTTTATCTTTT
1 GCGGCGTTTTTCCGAAAACGCCACTATTGCTTTACCTTTT
31297407 GCGGCGTTTT
1 GCGGCGTTTT
31297417 CTGTCCAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 30 0.73
41 11 0.27
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (40 bp):
GCGGCGTTTTTCCGAAAACGCCACTATTGCTTTACCTTTT
Found at i:31299115 original size:12 final size:13
Alignment explanation
Indices: 31299093--31299121 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31299083 TCTATTATAC
31299093 ATTTAAAAAAATT
1 ATTTAAAAAAATT
31299106 ATTT-AAAAAATT
1 ATTTAAAAAAATT
31299118 ATTT
1 ATTT
31299122 TTATACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAAAAAAATT
Found at i:31302071 original size:20 final size:20
Alignment explanation
Indices: 31302041--31302091 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
31302031 CGAAAAATAA
*
31302041 TTTCTGAAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
* *
31302061 TTTCTTGAAAATGATTTATT
1 TTTCTGGAAAATGATTTACT
31302081 TTTCTGGAAAA
1 TTTCTGGAAAA
31302092 GCTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31303315 original size:17 final size:17
Alignment explanation
Indices: 31303267--31303318 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 17
31303257 ATATATGAAA
* *
31303267 TATAAATTTTAAATATT
1 TATAAAATTTAATTATT
*
31303284 TTTAATAAATATTAATTATT
1 TAT-A-AAAT-TTAATTATT
31303304 TATAAAATTTAATTA
1 TATAAAATTTAATTA
31303319 GAATATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 9 0.32
18 5 0.18
19 4 0.14
20 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAAATTTAATTATT
Found at i:31304271 original size:29 final size:30
Alignment explanation
Indices: 31304217--31304275 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
31304207 GAATTGGATC
* *
31304217 AAATCAAAATTTCTTGTATAAAATTGCACA
1 AAATCAAAATTTCATGCATAAAATTGCACA
*
31304247 AAATCAAAA-TTCATGCATATAATTGCACA
1 AAATCAAAATTTCATGCATAAAATTGCACA
31304276 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGCATAAAATTGCACA
Found at i:31305936 original size:34 final size:34
Alignment explanation
Indices: 31305893--31305973 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
31305883 AAAGTCCAAG
*
31305893 TAAACAATATTTGGGTAAGGTAAAAGATAAAAAAT
1 TAAA-AATATTTGGGTAAGATAAAAGATAAAAAAT
*
31305928 TAAAAATATTTGGGTAAGATAAAAGGTAAAAAAT
1 TAAAAATATTTGGGTAAGATAAAAGATAAAAAAT
31305962 TAAAAATATTTG
1 TAAAAATATTTG
31305974 AGTTAAGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 40 0.91
35 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.16, T:0.28
Consensus pattern (34 bp):
TAAAAATATTTGGGTAAGATAAAAGATAAAAAAT
Found at i:31308379 original size:21 final size:21
Alignment explanation
Indices: 31308355--31308408 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
31308345 ATTTTTTAAT
31308355 AAAAATAAATA-AAAATTTATA
1 AAAAATAAATACAAAA-TTATA
*
31308376 AAAAATACATACAAAATTATA
1 AAAAATAAATACAAAATTATA
*
31308397 AATAAATGAATA
1 AA-AAATAAATA
31308409 TCATTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAATAAATACAAAATTATA
Found at i:31308964 original size:20 final size:20
Alignment explanation
Indices: 31308939--31308982 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
31308929 CTTAAATTGA
*
31308939 TTTATTTATAATATTATTAT
1 TTTATTTATAAAATTATTAT
*
31308959 TTTATTTTTAAAATTATTAT
1 TTTATTTATAAAATTATTAT
31308979 TTTA
1 TTTA
31308983 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTTATAAAATTATTAT
Found at i:31321327 original size:42 final size:42
Alignment explanation
Indices: 31321267--31321354 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
31321257 GTCACAAACT
*
31321267 GTGTATCAAGCCGTGTAACTCTCTAACTTGGGCCATACGACC
1 GTGTATCAAGCCGTGTAACTCTCTAACTTAGGCCATACGACC
* * *
31321309 GTGTGTCAGGCCGTGTAACTCTCTAACTTAGGCCATACGATC
1 GTGTATCAAGCCGTGTAACTCTCTAACTTAGGCCATACGACC
31321351 GTGT
1 GTGT
31321355 CCCAACCTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (42 bp):
GTGTATCAAGCCGTGTAACTCTCTAACTTAGGCCATACGACC
Found at i:31322289 original size:62 final size:62
Alignment explanation
Indices: 31322184--31322302 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
31322174 TTATACAACA
*
31322184 TCTTATCTCAATAAGTTACCACAAACTTACTGAATAAAGTGAATGTTAGGGGCACCCGATAC
1 TCTTATCTCAATAAGTTACCACAAACTTACTGAATAAACTGAATGTTAGGGGCACCCGATAC
* * * *
31322246 TCTTATCTCAATAAGTTACCTCAACCTTACTTAATGAACTGAATGTTAGGGGCACCC
1 TCTTATCTCAATAAGTTACCACAAACTTACTGAATAAACTGAATGTTAGGGGCACCC
31322303 TGTACTTAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (62 bp):
TCTTATCTCAATAAGTTACCACAAACTTACTGAATAAACTGAATGTTAGGGGCACCCGATAC
Found at i:31322501 original size:68 final size:70
Alignment explanation
Indices: 31322420--31322578 Score: 205
Period size: 68 Copynumber: 2.3 Consensus size: 70
31322410 GCACCTAGCA
* * *
31322420 CTAGTCGAATAAACCGAGGATTTGTGTGCCCAACACTAGTCAGAAAAACTGACGAAGG-T-TGCC
1 CTAGTCGGATAAACCGACGATTTGTGTGCCCAACACTAGTCAGAAAAACTGACAAAGGTTGTGCC
*
31322483 CATCG
66 CAGCG
* * * ** *
31322488 CTAGTCGGATAAACTGACGATTTGTGTGCCCAGCACTAGTCATATGAACTGACAAAGGTTGTGTC
1 CTAGTCGGATAAACCGACGATTTGTGTGCCCAACACTAGTCAGAAAAACTGACAAAGGTTGTGCC
31322553 CAGCG
66 CAGCG
*
31322558 CTAGTCGGATAGACCGACGAT
1 CTAGTCGGATAAACCGACGAT
31322579 GTAAATAGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
68 50 0.65
69 1 0.01
70 26 0.34
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (70 bp):
CTAGTCGGATAAACCGACGATTTGTGTGCCCAACACTAGTCAGAAAAACTGACAAAGGTTGTGCC
CAGCG
Found at i:31322538 original size:35 final size:35
Alignment explanation
Indices: 31322416--31322540 Score: 121
Period size: 35 Copynumber: 3.6 Consensus size: 35
31322406 GTTTGCACCT
* *
31322416 AGCACTAGTC-GAATAAACCGAGGATTTGTGTGCCC
1 AGCACTAGTCAG-ATAAACTGACGATTTGTGTGCCC
* * **
31322451 AACACTAGTCAGAAAAACTGACGA-AGGT-TGCCC
1 AGCACTAGTCAGATAAACTGACGATTTGTGTGCCC
* * *
31322484 ATCGCTAGTCGGATAAACTGACGATTTGTGTGCCC
1 AGCACTAGTCAGATAAACTGACGATTTGTGTGCCC
* *
31322519 AGCACTAGTCATATGAACTGAC
1 AGCACTAGTCAGATAAACTGAC
31322541 AAAGGTTGTG
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
33 25 0.36
34 4 0.06
35 40 0.57
36 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (35 bp):
AGCACTAGTCAGATAAACTGACGATTTGTGTGCCC
Found at i:31323912 original size:15 final size:15
Alignment explanation
Indices: 31323892--31323924 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
31323882 GAAAACTCGA
31323892 AAATAAAGAACCCTC
1 AAATAAAGAACCCTC
31323907 AAATAAAGAACCCTC
1 AAATAAAGAACCCTC
31323922 AAA
1 AAA
31323925 ACGTAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.24, G:0.06, T:0.12
Consensus pattern (15 bp):
AAATAAAGAACCCTC
Found at i:31324084 original size:24 final size:24
Alignment explanation
Indices: 31324056--31324114 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
31324046 TAGACTAATA
*
31324056 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
31324080 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
31324104 AGAGTTTAACT
1 AGAGTTTAACT
31324115 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:31333914 original size:22 final size:21
Alignment explanation
Indices: 31333889--31333939 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
31333879 ATGTTATTAA
31333889 TTATTTTTAAA-AAATATTTAT
1 TTATTTTTAAATAAATATTT-T
31333910 GTTA-TTTTAAATTAAATATTTT
1 -TTATTTTTAAA-TAAATATTTT
31333932 TTATTTTT
1 TTATTTTT
31333940 TATTTGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.38
22 8 0.31
23 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTTTTAAATAAATATTTT
Found at i:31336431 original size:334 final size:335
Alignment explanation
Indices: 31335537--31338869 Score: 5048
Period size: 334 Copynumber: 10.0 Consensus size: 335
31335527 CGTCTGTTTT
* * * *
31335537 GTATCGTCGTTA-TTCC-CTCTCTTTTTTTATGCATTTTGCTTCCCTGAAAATTCCCTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* *
31335600 GCGAAAT-ACATGTCATTCGTTGCAACACCTT-GGTGTCATCTTTGAT--AAAAAAA-AATACCA
66 GCGAAATCAC-TGTCATACGTTGCAACA-CTTCGGTGTCATCTTTGATAAAAAAAAACAACACCA
* * *
31335660 AAAGGATCTCCTCTTCTCCTTCTTCAACTCTGTCCAATTAGATTTCCCTAGAAAACAACCAAACT
129 AAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACT
*
31335725 CTCCAAAAATCCATGCAAATGTTTGAATGTATCACTCCTAAAATTGTTATACCATAAAATCAGTA
194 CTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTA
31335790 ATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAA
259 ATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAA
*
31335855 AGAGAAGGTTAA
324 AGAGAAGGTTGA
*
31335867 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCTTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * * *
31335932 GCGAAATCACTGTCATACGTTACAAGACTTGGGTGTCATCTTTGATAATAATAAAAA-AAAACCA
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAA-AA-AAAAACAACACCA
* *
31335996 AAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAAAAAACAACCAAACT
129 AAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACT
* *
31336061 CTCCAAAAATCCATGCAAAAGTTTGAATGTATCACCCCTAAAATTATTATACCATAAAATCAGTA
194 CTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTA
* **
31336126 ATAAATCGAGAATGTATATGATTGATTTCTTGATAAAGTGAAATACA-GAAAATAAAAGTGATAA
259 ATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATA-AGGAAAATAAAAGTGATAA
31336190 AAGAGAAGGTTGA
323 AAGAGAAGGTTGA
* * * * *
31336203 GTATCGACGTTA-TTCC-CTCTCTTTTTTTACGCTTTTTGCTTCCCCGAAAATTCCCTAGTTCAC
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * * *
31336266 GTGAAATTATTGTCATACGTTGCAACACTTCAGTGTCATCTTTGATAAAAAAACAACAACACCAA
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAAA-AACAACACCAA
* * * * * * *
31336331 AAGGCTCTCCTCGTCTTCGTCTTTAACTCTATCTGAATAGATTTCCCTAGAAAATAACCAAACTC
130 AAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTC
31336396 TCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAA
195 TCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAA
* *
31336461 TAAATCGAGAATGTATATGATTGA-TT-TC--T--AGCTAAAATAAGGAAAATAAAAGTGATAAA
260 TAAATCAAGAATGTATATGATTGATTTCTCAATAAAG-TGAAATAAGGAAAATAAAAGTGATAAA
31336520 AGAGAAGGTTGA
324 AGAGAAGGTTGA
* * *
31336532 GTATCGTCGTTATTCCCTCTCTCT-TTTTTATGCTTTTTGCTTCCTCGAAAATTCCCTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* *
31336596 GTGAAATCACTGTCATACATTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAAAAAACACAAC
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGAT-----AAAAAAAA-ACAAC
* *
31336661 ACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAAATTTCCTTAGAAAACAACCA
125 ACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCA
31336726 AACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATC
190 AACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATC
*
31336791 AGTAATAAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGA
255 AGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGA
31336856 TAAAAGAGAAGGTTGA
320 TAAAAGAGAAGGTTGA
*
31336872 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCTTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * *
31336937 GCGAAATCACTGTCATACGTTACAAGACTTGGGTGTCATCTTTGATAATAATAATAAA-AA-ACC
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAA-AA-AA-AAACAACACC
* *
31337000 AAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAAAAAACAACCAAAC
128 AAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAAC
* *
31337065 TCTCCAAAAATCCATGCAAAAGTTTGAATGTATCACCCCTAAAATTATTATACCATAAAATC-GA
193 TCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAG-
* * *
31337129 TAATAAATCGAGAATGTATATGATTGATTTCTCGATAAAGTGAAATACGGAAAATAAAAGTGATA
257 TAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATA
31337194 AAAGAGAAGGTTGA
322 AAAGAGAAGGTTGA
* * * *
31337208 GTATCGTCGTTA-TTCC-CTCTCTTTTTTTACGCTTTTTGCTTCCCCGAAAATTCCCTAGTTCAC
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * * * *
31337271 GTGAAATTATTGACATACGTTGCAACACTTCAGTGTCATCTTTGATAAAAAAAAACAACAACACC
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGAT--AAAAAAA-AACAACACC
* * * * *
31337336 AAAAGGCTTTCCTCTTCTCCGTCTTCAACTCTATCTGAATAGATTTCCCTAGAAAATAACCAAAC
128 AAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAAC
*
31337401 TCTCCAAAAATCCATGAAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGT
193 TCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGT
* *
31337466 AATAAATCGAGAATGTATATGATTGA-TT-TC--T--AGCTAAAATAAGGAAAATAAAAGTGATA
258 AATAAATCAAGAATGTATATGATTGATTTCTCAATAAAG-TGAAATAAGGAAAATAAAAGTGATA
31337525 AAAGAGAAGGTTGA
322 AAAGAGAAGGTTGA
* *
31337539 GTATCGTCGTTA-TTCC-CTCTCTCTTTTTAATGCTTTTTGCTTCCTCGAAAATTCCCTAGTTGA
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTT-AGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGA
* *
31337602 TGTGAAATCACTGTCATACATTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAAACACAACAC
65 TGCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGAT--AAAAAAAA-ACAACAC
* *
31337667 CAAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATTCGATTAAATTTCCCTAGAAAACAACCAAA
127 CAAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAA
* *
31337732 CTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTAATGCCATAAAATCAG
192 CTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAG
*
31337797 TAATAAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATA
257 TAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATA
31337862 AAAGAGAAGGTTGA
322 AAAGAGAAGGTTGA
31337876 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
*
31337941 GCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGAT-AAAAAAAACAACACCAAA
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAACAACACCAAA
* * *
31338005 AGGCTCTCCTCTTCTCCTTCTTCAACTTTATCCAATTAAATTTCCCTAGAAAACAACCAAACTCT
131 AGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCT
31338070 CCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAAT
196 CCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAAT
31338135 AAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
261 AAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
*
31338200 ATAAGGTTGA
326 AGAAGGTTGA
* * *
31338210 GTATCGTTGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTTCCTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * * *
31338275 GCAAAATCACTGTTATACGTTGCAACACTTCGATGTCATCTTTGATAAAAAACAACAACACCAAA
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAACAACACCAAA
* *
31338340 ATG--CT-CTCTTCTCCTTCTTCAACTCTATCCGATTAAATTTCCCTAGAAAACAACCAAACTCT
131 AGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCT
* *
31338402 CCAAAAATCCATGCAAATATTTGAATGTATCATCCCTAAAATTGTTATACCATAAAATCAGTAAT
196 CCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAAT
* *
31338467 AAATTAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAAGAAAATAAAAGTGATAAAAG
261 AAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
31338532 AGAAGGTTGA
326 AGAAGGTTGA
* *
31338542 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCAAAAATTTCCTAGTTGAT
1 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
* * * *
31338607 GCGAAATCACTATCATACATTGCAAGACTTGGGTGTCATCTTTGATAATAATAAAAA-AA-ACCA
66 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAA-AA-AAAAACAACACCA
*
31338670 AAAGG-------C-TCTCC-TCTTCAACTATATCCGATTAGATTTCCCTAGAAAACAACCAAACT
129 AAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACT
* * *
31338726 CTCCAAAAATCCATGCAAATGCTTGAATGTATCACCCCTAAAATTATTATACCATAAAATCAATA
194 CTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTA
* * *
31338791 ATAAATCAAGAATATCTATGATTGATTTCTCAATAAAGCGAAATAAGGAAAATAAAAGTGATAAA
259 ATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAA
31338856 AGAGAAGGTTGA
324 AGAGAAGGTTGA
31338868 GT
1 GT
31338870 GATGTCAAAG
Statistics
Matches: 2762, Mismatches: 189, Indels: 108
0.90 0.06 0.04
Matches are distributed among these distances:
326 177 0.06
327 5 0.00
328 4 0.00
329 47 0.02
330 96 0.03
331 78 0.03
332 617 0.22
333 17 0.01
334 639 0.23
335 203 0.07
336 580 0.21
337 58 0.02
338 85 0.03
339 15 0.01
340 61 0.02
341 80 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (335 bp):
GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCTAGTTGAT
GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAACAACACCAAA
AGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCT
CCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAAT
AAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
AGAAGGTTGA
Found at i:31338380 original size:666 final size:666
Alignment explanation
Indices: 31335537--31338869 Score: 4964
Period size: 666 Copynumber: 5.0 Consensus size: 666
31335527 CGTCTGTTTT
* * *
31335537 GTATCGTCGTTATTCCCTCTCTTTTTTTATGCATTTTGCTTCCCTGAAAATTCCCTAGTTGATGC
1 GTATCGTCGTTATTCCCTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTCCCTAGTTGATGC
* *
31335602 GAAAT-ACATGTCATTCGTTGCAACACCTT-GGTGTCATCTTTGAT-AAAAA-AA-AATACCAAA
66 GAAATCAC-TGTCATACGTTGCAACA-CTTCGGTGTCATCTTTGATAAAAAACAACAACACCAAA
* *
31335662 AGGATCTCCTCTTCTCCTTCTTCAACTCTGTCCAATTAGATTTCCCTAGAAAACAACCAAACTCT
129 AGG-TCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCT
*
31335727 CCAAAAATCCATGCAAATGTTTGAATGTATCACTCCTAAAATTGTTATACCATAAAATCAGTAAT
193 CCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAAT
*
31335792 AAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
258 AAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAG
*
31335857 AGAAGGTTAAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTC
323 AGAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTC
* * *
31335922 CTTAGTTGATGCGAAATCACTGTCATACGTTACAA-GACTTGGGTGTCATCTTTGATAATAATAA
388 CCTAGTTGATGCGAAATCACTGTCATACGTTGCAACG-CTTCGGTGTCATCTTTGATAA-AA-AA
* * *
31335986 AAAAAAACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAAAAAA
450 AACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAGAAAA
* *
31336051 CAACCAAACTCTCCAAAAATCCATGCAAAAGTTTGAATGTATCACCCCTAAAATTATTATACCAT
515 CAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCAT
* **
31336116 AAAATCAGTAATAAATCGAGAATGTATATGATTGATTTCTTGATAAAGTGAAATACA-GAAAATA
580 AAAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATA-AGGAAAATA
31336180 AAAGTGATAAAAGAGAAGGTTGA
644 AAAGTGATAAAAGAGAAGGTTGA
* * * * * * *
31336203 GTATCGACGTTATTCCCTCTCTTTTTTTACGCTTTTTGCTTCCCCGAAAATTCCCTAGTTCACGT
1 GTATCGTCGTTATTCCCTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTCCCTAGTTGATGC
* * *
31336268 GAAATTATTGTCATACGTTGCAACACTTCAGTGTCATCTTTGATAAAAAAACAACAACACCAAAA
66 GAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGAT-AAAAAACAACAACACCAAAA
* * * * * * *
31336333 GGCTCTCCTCGTCTTCGTCTTTAACTCTATCTGAATAGATTTCCCTAGAAAATAACCAAACTCTC
130 GG-TCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCTC
31336398 CAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAATA
194 CAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAATA
*
31336463 AATC-GAGAATGTATATGATTGA-TT-TC--T--AGCTAAAATAAGGAAAATAAAAGTGATAAAA
259 AATCAG-GAATGTATATGATTGATTTCTCAATAAAG-TGAAATAAGGAAAATAAAAGTGATAAAA
* * *
31336521 GAGAAGGTTGAGTATCGTCGTTATTCCCTCTCTCT-TTTTTATGCTTTTTGCTTCCTCGAAAATT
322 GAGAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATT
* * *
31336585 CCCTAGTTGATGTGAAATCACTGTCATACATTGCAACACTTCGGTGTCATCTTTGATAAAAAAAA
387 CCCTAGTTGATGCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGAT------AA
* * *
31336650 AAAAACACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAAATTTCCTTA
446 AAAAA-ACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTA
31336715 GAAAACAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTAT
510 GAAAACAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTAT
*
31336780 ACCATAAAATCAGTAATAAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAA
575 ACCATAAAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAA
31336845 AATAAAAGTGATAAAAGAGAAGGTTGA
640 AATAAAAGTGATAAAAGAGAAGGTTGA
* *
31336872 GTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCTTAGTTGAT
1 GTATCGTCGTTA-TTCC-CTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTCCCTAGTTGAT
* * * * *
31336937 GCGAAATCACTGTCATACGTTACAAGACTTGGGTGTCATCTTTGATAATAATAATAA-AAAACCA
64 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAA-AA-AACAACAACACCA
* *
31337001 AAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAAAAAACAACCAAACT
127 AAAGG-TCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACT
* *
31337066 CTCCAAAAATCCATGCAAAAGTTTGAATGTATCACCCCTAAAATTATTATACCATAAAATC-GAT
191 CTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAG-T
* *
31337130 AATAAATC-GAGAATGTATATGATTGATTTCTCGATAAAGTGAAATACGGAAAATAAAAGTGATA
255 AATAAATCAG-GAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATA
* *
31337194 AAAGAGAAGGTTGAGTATCGTCGTTA-TTCC-CTCTCTTTTTTTACGCTTTTTGCTTCCCCGAAA
319 AAAGAGAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAA
* * * * * * * *
31337257 ATTCCCTAGTTCACGTGAAATTATTGACATACGTTGCAACACTTCAGTGTCATCTTTGATAAAAA
384 ATTCCCTAGTTGATGCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGAT---AA
* * * * *
31337322 AAAACAACAACACCAAAAGGCTTTCCTCTTCTCCGTCTTCAACTCTATCTGAATAGATTTCCCTA
446 AAAA-AACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTA
* *
31337387 GAAAATAACCAAACTCTCCAAAAATCCATGAAAATGTTTGAATGTATCACCCCTAAAATTGTTAT
510 GAAAACAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTAT
* *
31337452 ACCATAAAATCAGTAATAAATCGAGAATGTATATGATTGA-TT-TC--T--AGCTAAAATAAGGA
575 ACCATAAAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAG-TGAAATAAGGA
31337511 AAATAAAAGTGATAAAAGAGAAGGTTGA
639 AAATAAAAGTGATAAAAGAGAAGGTTGA
*
31337539 GTATCGTCGTTATTCCCTCTCTCTTTTTAATGCTTTTTGCTT-CCTCGAAAATTCCCTAGTTGAT
1 GTATCGTCGTTATTCCCTCTCTCTTTTT-AGGCTTTTTGCTTCCCT-GAAAATTCCCTAGTTGAT
* * *
31337603 GTGAAATCACTGTCATACATTGCAACACTTCGGTGTCATCTTTGATAAAAAAAAAACACAACACC
64 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGAT--AAAAAACA-ACAACACC
* *
31337668 AAAAGGCTCTCCTCTTCTCCTTCTTCAACTCTATTCGATTAAATTTCCCTAGAAAACAACCAAAC
126 AAAAGG-TCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAAC
* *
31337733 TCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTAATGCCATAAAATCAGT
190 TCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGT
31337798 AATAAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAA
255 AATAAATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAA
31337863 AAGAGAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAA
320 AAGAGAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAA
31337928 TTCCCTAGTTGATGCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGATAAAAAA
385 TTCCCTAGTTGATGCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGATAAAAAA
* * *
31337993 AACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTTTATCCAATTAAATTTCCCTAGAAAA
450 AACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAGAAAA
31338058 CAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCAT
515 CAACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCAT
31338123 AAAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAA
580 AAAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAA
*
31338188 AAGTGATAAAAGATAAGGTTGA
645 AAGTGATAAAAGAGAAGGTTGA
* *
31338210 GTATCGTTGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTTCCTAGTTGAT
1 GTATCGTCGTTA-TTCC-CTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTCCCTAGTTGAT
* * *
31338275 GCAAAATCACTGTTATACGTTGCAACACTTCGATGTCATCTTTGATAAAAAACAACAACACCAAA
64 GCGAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAACAACAACACCAAA
* *
31338340 ATG-CT-CTCTTCTCCTTCTTCAACTCTATCCGATTAAATTTCCCTAGAAAACAACCAAACTCTC
129 AGGTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCTC
* *
31338403 CAAAAATCCATGCAAATATTTGAATGTATCATCCCTAAAATTGTTATACCATAAAATCAGTAATA
194 CAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAATA
* * *
31338468 AATTAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAAGAAAATAAAAGTGATAAAAGA
259 AATCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAGA
* *
31338533 GAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCAAAAATTTC
324 GAAGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCC
* * *
31338598 CTAGTTGATGCGAAATCACTATCATACATTGCAA-GACTTGGGTGTCATCTTTGATAATAATAAA
389 CTAGTTGATGCGAAATCACTGTCATACGTTGCAACG-CTTCGGTGTCATCTTTGATAA-AA-AAA
*
31338662 A-AAAACCAAAAGG-------C-TCTCC-TCTTCAACTATATCCGATTAGATTTCCCTAGAAAAC
451 ACAACACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAGAAAAC
* *
31338717 AACCAAACTCTCCAAAAATCCATGCAAATGCTTGAATGTATCACCCCTAAAATTATTATACCATA
516 AACCAAACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATA
* * * *
31338782 AAATCAATAATAAATCAAGAATATCTATGATTGATTTCTCAATAAAGCGAAATAAGGAAAATAAA
581 AAATCAGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAA
31338847 AGTGATAAAAGAGAAGGTTGA
646 AGTGATAAAAGAGAAGGTTGA
31338868 GT
1 GT
31338870 GATGTCAAAG
Statistics
Matches: 2443, Mismatches: 171, Indels: 114
0.90 0.06 0.04
Matches are distributed among these distances:
658 179 0.07
659 5 0.00
660 1 0.00
664 79 0.03
665 78 0.03
666 623 0.26
667 77 0.03
668 231 0.09
669 238 0.10
670 250 0.10
671 281 0.12
672 245 0.10
673 18 0.01
674 6 0.00
675 81 0.03
676 49 0.02
677 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (666 bp):
GTATCGTCGTTATTCCCTCTCTCTTTTTAGGCTTTTTGCTTCCCTGAAAATTCCCTAGTTGATGC
GAAATCACTGTCATACGTTGCAACACTTCGGTGTCATCTTTGATAAAAAACAACAACACCAAAAG
GTCTCCTCTTCTCCTTCTTCAACTCTATCCGATTAGATTTCCCTAGAAAACAACCAAACTCTCCA
AAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATCAGTAATAAA
TCAGGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGATAAAAGAGA
AGGTTGAGTATCGTCGTTATTTCCTCTCTCTCTTTTTAGGCTTTTTGCTTCCCCGAAAATTCCCT
AGTTGATGCGAAATCACTGTCATACGTTGCAACGCTTCGGTGTCATCTTTGATAAAAAAAACAAC
ACCAAAAGGCTCTCCTCTTCTCCTTCTTCAACTATATCCGATTAGATTTCCCTAGAAAACAACCA
AACTCTCCAAAAATCCATGCAAATGTTTGAATGTATCACCCCTAAAATTGTTATACCATAAAATC
AGTAATAAATCAAGAATGTATATGATTGATTTCTCAATAAAGTGAAATAAGGAAAATAAAAGTGA
TAAAAGAGAAGGTTGA
Found at i:31344859 original size:14 final size:14
Alignment explanation
Indices: 31344827--31344860 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31344817 AATTAAATTA
*
31344827 ATAAATTTCTCAAT
1 ATAATTTTCTCAAT
31344841 ATAATTTTCTCAAT
1 ATAATTTTCTCAAT
*
31344855 CTAATT
1 ATAATT
31344861 CTATTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTTTCTCAAT
Found at i:31345504 original size:28 final size:24
Alignment explanation
Indices: 31345454--31345518 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
31345444 TTTGACTCAG
31345454 ACAGAGTTTAATTGAAACAAATAA
1 ACAGAGTTTAATTGAAACAAATAA
*
31345478 ACAGAGTTTAATTGAAACAATTAA
1 ACAGAGTTTAATTGAAACAAATAA
* *
31345502 ATAGAGTTTAACTGAAA
1 ACAGAGTTTAATTGAAA
31345519 GATTATTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.28
Consensus pattern (24 bp):
ACAGAGTTTAATTGAAACAAATAA
Found at i:31347459 original size:24 final size:24
Alignment explanation
Indices: 31347432--31347496 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
31347422 TTTGACTCAG
31347432 ACAGAGTTTAATTGAAACAAATAA
1 ACAGAGTTTAATTGAAACAAATAA
*
31347456 ACAGAGTTTAATTGAAACAATTAA
1 ACAGAGTTTAATTGAAACAAATAA
* *
31347480 ACAGAATTTAACTGAAA
1 ACAGAGTTTAATTGAAA
31347497 GATTATTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.26
Consensus pattern (24 bp):
ACAGAGTTTAATTGAAACAAATAA
Found at i:31350116 original size:73 final size:74
Alignment explanation
Indices: 31349997--31350148 Score: 279
Period size: 73 Copynumber: 2.1 Consensus size: 74
31349987 CATCCCTTTG
*
31349997 ATGTACTTCTAGATTCTACAAAGCGACAATTACAAGTTTCATCCTTATAGACGTTATTCTTGATA
1 ATGTACTTCTAGATTCTACAAAGCGACAATTACAAGTTTCATCCTTATAGACATTATTCTTGATA
31350062 -AAGAGAGA
66 CAAGAGAGA
*
31350070 ATGTACTTCTAGATTCTACTAAGCGACAATTACAAGTTTCATCCTTATAGACATTATTCTTGATA
1 ATGTACTTCTAGATTCTACAAAGCGACAATTACAAGTTTCATCCTTATAGACATTATTCTTGATA
31350135 CAAGAGAGA
66 CAAGAGAGA
31350144 ATGTA
1 ATGTA
31350149 TCAAAGTAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 63 0.83
74 13 0.17
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (74 bp):
ATGTACTTCTAGATTCTACAAAGCGACAATTACAAGTTTCATCCTTATAGACATTATTCTTGATA
CAAGAGAGA
Found at i:31354072 original size:39 final size:39
Alignment explanation
Indices: 31354008--31354082 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
31353998 TCCGTTTAGC
* *
31354008 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
* *
31354047 ACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTC
31354083 TCTGTTGCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
Found at i:31354083 original size:23 final size:22
Alignment explanation
Indices: 31353934--31354121 Score: 138
Period size: 23 Copynumber: 8.4 Consensus size: 22
31353924 CACTCTCCGA
*
31353934 TTAGCACTGTGTGTGCTCTCCGT
1 TTAGCACT-TGTGTGCTCTCTGT
*
31353957 TTAGCACTTTGTGTGCTCTAC-AT
1 TTAGCAC-TTGTGTGCTCT-CTGT
* * *
31353980 TTAGCACGTCTCGTGCTCTCCGT
1 TTAGCACTTGT-GTGCTCTCTGT
*
31354003 TTAGCACTTCGTGTGCTCTCTGA
1 TTAGCACTT-GTGTGCTCTCTGT
*
31354026 TTAGCACTT-TGTG-TGCTCAG-
1 TTAGCACTTGTGTGCT-CTCTGT
* *
31354046 -TA-C-TTTGTGTACTCTCTGT
1 TTAGCACTTGTGTGCTCTCTGT
31354065 TTAGCACTGTGTGTGCTCTCTGT
1 TTAGCACT-TGTGTGCTCTCTGT
*
31354088 TGCCTAGCACTTATGTGCTCTCTGT
1 T---TAGCACTTGTGTGCTCTCTGT
*
31354113 TTAGTACTT
1 TTAGCACTT
31354122 CGGTACTCTC
Statistics
Matches: 133, Mismatches: 16, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.02
18 8 0.06
19 3 0.02
20 3 0.02
21 9 0.07
22 11 0.08
23 73 0.55
24 3 0.02
25 14 0.11
26 7 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (22 bp):
TTAGCACTTGTGTGCTCTCTGT
Found at i:31359763 original size:4 final size:4
Alignment explanation
Indices: 31359754--31359796 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
31359744 AAAGGGCATT
*
31359754 AATA AATA AATA AATA AATGA AA-A AACA ACATA AATA AATA AA
1 AATA AATA AATA AATA AAT-A AATA AATA A-ATA AATA AATA AA
31359797 AAAGGCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
3 3 0.09
4 26 0.74
5 6 0.17
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:31361242 original size:13 final size:14
Alignment explanation
Indices: 31361224--31361257 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
31361214 AATTTTATAT
31361224 TTTAAAAA-ATAAA
1 TTTAAAAATATAAA
*
31361237 TTTAAAAATATAAT
1 TTTAAAAATATAAA
31361251 TTTAAAA
1 TTTAAAA
31361258 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTAAAAATATAAA
Found at i:31365279 original size:23 final size:23
Alignment explanation
Indices: 31365253--31365297 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31365243 AAGCTTTTCT
*
31365253 ATTAAGTTAATTTTTTTTAAATA
1 ATTAAGTTAATTTTCTTTAAATA
* *
31365276 ATTACGTTTATTTTCTTTAAAT
1 ATTAAGTTAATTTTCTTTAAAT
31365298 TAAGAGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTAAGTTAATTTTCTTTAAATA
Found at i:31367271 original size:15 final size:17
Alignment explanation
Indices: 31367241--31367273 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
31367231 GCTATGAAAC
31367241 AAATATATATTATAATA
1 AAATATATATTATAATA
31367258 AAATA-ATA-TATAATA
1 AAATATATATTATAATA
31367273 A
1 A
31367274 GATCATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATATATTATAATA
Found at i:31371165 original size:35 final size:35
Alignment explanation
Indices: 31371126--31371192 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
31371116 TTCAATCCCC
*
31371126 AATTTCCAATTTT-ATATTTTCAATCTTCAAATTTA
1 AATTTCCAATTTTGA-ATTTTCAATCCTCAAATTTA
* *
31371161 AATTTTCAATTTTGAATTTTCGATCCTCAAAT
1 AATTTCCAATTTTGAATTTTCAATCCTCAAAT
31371193 ATTTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (35 bp):
AATTTCCAATTTTGAATTTTCAATCCTCAAATTTA
Found at i:31371171 original size:7 final size:7
Alignment explanation
Indices: 31371125--31371181 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
31371115 ATTCAATCCC
*
31371125 CAATTTC
1 CAATTTT
31371132 CAATTTT
1 CAATTTT
31371139 -ATATTTT
1 CA-ATTTT
*
31371146 CAATCTT
1 CAATTTT
*
31371153 CAAATTT
1 CAATTTT
*
31371160 AAATTTT
1 CAATTTT
31371167 CAATTTT
1 CAATTTT
*
31371174 GAATTTT
1 CAATTTT
31371181 C
1 C
31371182 GATCCTCAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
6 1 0.03
7 37 0.95
8 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.53
Consensus pattern (7 bp):
CAATTTT
Found at i:31373785 original size:241 final size:240
Alignment explanation
Indices: 31373296--31373876 Score: 1004
Period size: 241 Copynumber: 2.4 Consensus size: 240
31373286 TAGATGTATG
*
31373296 CATCAATGACTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATG
1 CATCAATGATTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATG
* *
31373361 ATAGTTATATATAATAGTAGTACACTATATA--ACATATTGTTATATATTATTGTTTAATATTAT
66 ATAGTTATATATAATAGTAGTACATTATATATTACATATTATTATATATTATTGTTTAATATTAT
31373424 ACTAGTTGAAATATGCTCTAGTCCCTATACTTTTCGACATTTCAAAATTAATCCTCATACTATAT
131 ACTAGTTGAAATATGCTCTAGTCCCTATACTTTTCGACATTTCAAAATTAATCCTCATACTATAT
* *
31373489 TATATAATGTTATATCATATCATATATTAATAGTTTATATATTCA
196 TATATAATGTTATATCATATCATATATTAATAGTTTATAAATACA
* **
31373534 CATAAATGATTAAACATTATAATATCATCCAATATTATATCTTTTATTATAATCTATATATAATG
1 CATCAATGATTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATG
31373599 ATAGTTATATATAATAGTAGTACATTATATATTACATATTATTATATATTATTGTTTAATATTAT
66 ATAGTTATATATAATAGTAGTACATTATATATTACATATTATTATATATTATTGTTTAATATTAT
* * * *
31373664 ACTAGTTGAAATATGCTCTAATTCTCTATACTTTTCGACATTTCAAAATTAGTCCTCCTACTATA
131 ACTAGTTGAAATATGCTCT-AGTCCCTATACTTTTCGACATTTCAAAATTAATCCTCATACTATA
*
31373729 TTATATAATGTTATATCATATTATATATTAATAGTTTATAAATACA
195 TTATATAATGTTATATCATATCATATATTAATAGTTTATAAATACA
*
31373775 CATCAATGATTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATT
1 CATCAATGATTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATG
*
31373840 ATAGTTATATATTATAGTAGTACATTATATATTACAT
66 ATAGTTATATATAATAGTAGTACATTATATATTACAT
31373877 TTAAAAATTA
Statistics
Matches: 322, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
238 91 0.28
240 50 0.16
241 181 0.56
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (240 bp):
CATCAATGATTAAACATTATAATATCATGTAATATTATATCTTTTATTATAATCTATATATAATG
ATAGTTATATATAATAGTAGTACATTATATATTACATATTATTATATATTATTGTTTAATATTAT
ACTAGTTGAAATATGCTCTAGTCCCTATACTTTTCGACATTTCAAAATTAATCCTCATACTATAT
TATATAATGTTATATCATATCATATATTAATAGTTTATAAATACA
Found at i:31376661 original size:20 final size:20
Alignment explanation
Indices: 31376638--31376681 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31376628 TTTTTTTATC
*
31376638 TTATTATTAATATA-TATTTT
1 TTATT-TTAATATATTATATT
*
31376658 TTATTTTATTATATTATATT
1 TTATTTTAATATATTATATT
31376678 TTAT
1 TTAT
31376682 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTAATATATTATATT
Found at i:31387171 original size:17 final size:17
Alignment explanation
Indices: 31387141--31387177 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31387131 AAGTAATTAT
*
31387141 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
*
31387158 AAGAAGATGGAAGGTTA
1 AAGAAGATGAAAGGTTA
31387175 AAG
1 AAG
31387178 GTCAAGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:31388049 original size:18 final size:18
Alignment explanation
Indices: 31388026--31388095 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
31388016 TTGGGATTTA
31388026 TTTTAAATTTAAATGTAT
1 TTTTAAATTTAAATGTAT
* *
31388044 TTTTAAATTTGAATTTGTTAAA
1 TTTTAAATTT-AA-ATG-T-AT
* *
31388066 ATTTAAATTTAAATATAT
1 TTTTAAATTTAAATGTAT
*
31388084 GTTTAAATTTAA
1 TTTTAAATTTAA
31388096 TATTATTCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 22 0.54
19 3 0.07
20 3 0.07
21 3 0.07
22 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTAAATTTAAATGTAT
Found at i:31388086 original size:24 final size:22
Alignment explanation
Indices: 31388045--31388095 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
31388035 TAAATGTATT
*
31388045 TTTAAATTTGAATTTGTTAAAA
1 TTTAAATTTAAATTTGTTAAAA
*
31388067 TTTAAATTTAAATATATGTTTAAA
1 TTTAAATTTAAAT-T-TGTTAAAA
31388091 TTTAA
1 TTTAA
31388096 TATTATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (22 bp):
TTTAAATTTAAATTTGTTAAAA
Found at i:31389619 original size:92 final size:92
Alignment explanation
Indices: 31389462--31389978 Score: 818
Period size: 92 Copynumber: 5.6 Consensus size: 92
31389452 CGTAATGGGT
* * *
31389462 TAAAGCTGAATAGCAAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
*
31389527 TCAATTCTTATCCTCTTGAATTTATAG
66 TCAATTCTTATCCTCTTGAAGTTATAG
* *
31389554 TAAAGCTAGATAACGGACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
31389619 TCAATTCTTATCCTCTTGAAGTTATAG
66 TCAATTCTTATCCTCTTGAAGTTATAG
* * **
31389646 TAAAGCTGGATAACGAACCTTTATCTCTCTTAAGTTATAGTAAAAGCAAGATGAAGCCCCAAACG
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
31389711 TCAATTCTTATCCTCTTGAAGTTATAG
66 TCAATTCTTATCCTCTTGAAGTTATAG
* *
31389738 TAAAACTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTCCAAACG
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
*
31389803 TCAATTCTTATCCGCTTGAAGTTATAG
66 TCAATTCTTATCCTCTTGAAGTTATAG
* *
31389830 TAAAGCTGGATAACGAACCTTTATCTCTTTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
* *
31389895 TCAATTCTTATACTCTTGAAATTATAG
66 TCAATTCTTATCCTCTTGAAGTTATAG
* ** * * * *
31389922 TAAAGTTGGATAATAAACCTTTATCTCTTTGAAGTTGTAGTAAGAGCGAGATAAAGC
1 TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
31389979 CTCGACATCA
Statistics
Matches: 394, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 394 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (92 bp):
TAAAGCTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACG
TCAATTCTTATCCTCTTGAAGTTATAG
Found at i:31389670 original size:40 final size:40
Alignment explanation
Indices: 31389626--31389872 Score: 149
Period size: 40 Copynumber: 5.6 Consensus size: 40
31389616 ACGTCAATTC
31389626 TTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
1 TTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
** *
31389666 TTATCTCTCTT-AAGTTATAGTAAAAGCAAGATGAAGCCCCAAACGTCAATT
1 TTATC-CTCTTGAAGTTATAGT-AAAGCTGGAT-AA----CGAAC--C---T
*
31389717 CTTATCCTCTTGAAGTTATAGTAAAACTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
** *
31389758 TTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTCCAAACGTCAATT
1 TTATCCTCT-TGAAGTTATAGTAA-AGCTGGAT-AA----CGAAC--C---T
*
31389809 CTTATCCGCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
*
31389850 TTAT-CTCTTTAAAGTTATAGTAA
1 TTATCCTC-TTGAAGTTATAGTAA
31389873 GAGCAAGATG
Statistics
Matches: 161, Mismatches: 17, Indels: 58
0.68 0.07 0.25
Matches are distributed among these distances:
39 6 0.04
40 51 0.32
41 20 0.12
42 4 0.02
44 2 0.01
46 16 0.10
48 2 0.01
50 4 0.02
51 20 0.12
52 33 0.20
53 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGCTGGATAACGAACCT
Found at i:31408564 original size:138 final size:138
Alignment explanation
Indices: 31408316--31408599 Score: 532
Period size: 138 Copynumber: 2.1 Consensus size: 138
31408306 AGAGGTCGGT
*
31408316 TGCATTTTTCAATGATAACCAAATAATATATGAGCTCATGTATCACATGTGTGCAACCCGAAGTT
1 TGCATTATTCAATGATAACCAAATAATATATGAGCTCATGTATCACATGTGTGCAACCCGAAGTT
* *
31408381 CGCGATACAATTTCTTGAAATAATTTGATTGTGCACAATCTCTATAGAATTCAATTTGTGCTAAC
66 CGCGATACAATTTCTTGAAATAATTTGATTATGCACAATCTCTATAGAATGCAATTTGTGCTAAC
*
31408446 AACGTTGG
131 AACGCTGG
31408454 TGCATTATTCAATGATAACCAAATAATATATGAGCTCATGTATCACATGTGTGCAACCCGAAGTT
1 TGCATTATTCAATGATAACCAAATAATATATGAGCTCATGTATCACATGTGTGCAACCCGAAGTT
31408519 CGCGATACAATTTCTTGAAATAATTTGATTATGCACAATCTCTATAGAATGCAATTTGTGCTAAC
66 CGCGATACAATTTCTTGAAATAATTTGATTATGCACAATCTCTATAGAATGCAATTTGTGCTAAC
31408584 AACGCTGG
131 AACGCTGG
31408592 TGCATTAT
1 TGCATTAT
31408600 ATCCCTAGCA
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 142 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (138 bp):
TGCATTATTCAATGATAACCAAATAATATATGAGCTCATGTATCACATGTGTGCAACCCGAAGTT
CGCGATACAATTTCTTGAAATAATTTGATTATGCACAATCTCTATAGAATGCAATTTGTGCTAAC
AACGCTGG
Found at i:31411269 original size:10 final size:11
Alignment explanation
Indices: 31411235--31411274 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31411225 ATACTTGAAA
31411235 TTTTAAAATAT
1 TTTTAAAATAT
* *
31411246 ATTAAAAATAT
1 TTTTAAAATAT
31411257 TTTTAAAAT-T
1 TTTTAAAATAT
31411267 TTTTAAAA
1 TTTTAAAA
31411275 AAATAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:31411358 original size:36 final size:34
Alignment explanation
Indices: 31411300--31411371 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 34
31411290 TACTCTTATT
31411300 ATAATTTTTAAAAAATTATAAATAATAATAAAAA
1 ATAATTTTTAAAAAATTATAAATAATAATAAAAA
**
31411334 ATAATTTTTAGAAAAATTATTAAATTTTAATAAAAA
1 ATAATTTTTA-AAAAATTA-TAAATAATAATAAAAA
31411370 AT
1 AT
31411372 TAAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 10 0.29
35 8 0.24
36 16 0.47
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
ATAATTTTTAAAAAATTATAAATAATAATAAAAA
Found at i:31411382 original size:20 final size:21
Alignment explanation
Indices: 31411345--31411383 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
31411335 TAATTTTTAG
* *
31411345 AAAAATTATTAAATTTTAATA
1 AAAAATTATAAAAATTTAATA
31411366 AAAAATTA-AAAAATTTAA
1 AAAAATTATAAAAATTTAA
31411384 AATTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTATAAAAATTTAATA
Found at i:31411735 original size:10 final size:10
Alignment explanation
Indices: 31411722--31411809 Score: 51
Period size: 10 Copynumber: 9.3 Consensus size: 10
31411712 CTATATAAAA
31411722 TTTTATAATT
1 TTTTATAATT
31411732 TTTTAT-A-T
1 TTTTATAATT
* *
31411740 TTCTAT-ATA
1 TTTTATAATT
*
31411749 TTTTATAACT
1 TTTTATAATT
**
31411759 TTTTACGA--
1 TTTTATAATT
**
31411767 TTTTATAAAA
1 TTTTATAATT
*
31411777 TTTTACAATT
1 TTTTATAATT
*
31411787 TTTTATATTT
1 TTTTATAATT
*
31411797 TTTTCTAATT
1 TTTTATAATT
31411807 TTT
1 TTT
31411810 AATATTTATT
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
8 13 0.22
9 6 0.10
10 39 0.67
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:31411756 original size:27 final size:27
Alignment explanation
Indices: 31411715--31411797 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
31411705 CTTACGACTA
31411715 TATAAAATTTTATAATTTTTTATATTT
1 TATAAAATTTTATAATTTTTTATATTT
* * *
31411742 CTAT-ATATTTTATAACTTTTTACGATTT
1 -TATAAAATTTTATAATTTTTTA-TATTT
*
31411770 TATAAAATTTTACAATTTTTTATATTT
1 TATAAAATTTTATAATTTTTTATATTT
31411797 T
1 T
31411798 TTTCTAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (27 bp):
TATAAAATTTTATAATTTTTTATATTT
Found at i:31411775 original size:55 final size:58
Alignment explanation
Indices: 31411675--31411796 Score: 169
Period size: 55 Copynumber: 2.2 Consensus size: 58
31411665 TTTTACGAAA
* * *
31411675 TTTATATTTCTTTACATTTTATATAATTTTCTTACGACTATATAAAATTTTATAATTT
1 TTTATATTTCTATACATTTTATATAACTTTCTTACGACTATATAAAATTTTACAATTT
* * *
31411733 TTTATATTTCTATATA-TTT-TATAACTTT-TTACGATTTTATAAAATTTTACAATTT
1 TTTATATTTCTATACATTTTATATAACTTTCTTACGACTATATAAAATTTTACAATTT
31411788 TTTATATTT
1 TTTATATTT
31411797 TTTTCTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 33 0.57
56 8 0.14
57 3 0.05
58 14 0.24
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTATATAACTTTCTTACGACTATATAAAATTTTACAATTT
Found at i:31411798 original size:18 final size:18
Alignment explanation
Indices: 31411722--31411798 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 18
31411712 CTATATAAAA
*
31411722 TTTTATAATTTTTTATAT
1 TTTTACAATTTTTTATAT
* * *
31411740 TTCTA-TATATTTTATAACT
1 TTTTACAATTTTTTAT-A-T
* * * *
31411759 TTTTACGATTTTATAAAA
1 TTTTACAATTTTTTATAT
31411777 TTTTACAATTTTTTATAT
1 TTTTACAATTTTTTATAT
31411795 TTTT
1 TTTT
31411799 TTCTAATTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
17 8 0.19
18 23 0.53
19 6 0.14
20 6 0.14
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTACAATTTTTTATAT
Found at i:31411800 original size:20 final size:21
Alignment explanation
Indices: 31411783--31411821 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31411773 AAAATTTTAC
*
31411783 AATTTTTTATATTT-TTTTCT
1 AATTTTTAATATTTATTTTCT
31411803 AATTTTTAATATTTATTTT
1 AATTTTTAATATTTATTTT
31411822 TATTAAAATT
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:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
AATTTTTAATATTTATTTTCT
Found at i:31412933 original size:6 final size:6
Alignment explanation
Indices: 31412922--31412977 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
31412912 AATAATATAC
** * *
31412922 TTATTT TTATTT TATATTT TT-TAC ATATTT TTATTT TTATTT TTATAT
1 TTATTT TTATTT T-TATTT TTATTT TTATTT TTATTT TTATTT TTATTT
31412970 TT-TTT TTA
1 TTATTT TTA
31412978 ATTTATTCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
5 6 0.15
6 27 0.69
7 6 0.15
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:31413420 original size:17 final size:17
Alignment explanation
Indices: 31413398--31413433 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
31413388 TTAAGAATTG
31413398 TATTATTTAT-ATATTTT
1 TATTATTTATGAT-TTTT
31413415 TATTATTTATGATTTTT
1 TATTATTTATGATTTTT
31413432 TA
1 TA
31413434 AATCTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTATTTATGATTTTT
Found at i:31416260 original size:4 final size:4
Alignment explanation
Indices: 31416240--31416317 Score: 104
Period size: 4 Copynumber: 19.8 Consensus size: 4
31416230 TTAGAAATCT
* * * * *
31416240 ATAC ATAC CTAC CTAC ATAC ATAC ATAC ATAT ATAC AT-C ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
31416287 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
31416318 TTTGCATGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
3 3 0.04
4 65 0.96
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:31422857 original size:18 final size:17
Alignment explanation
Indices: 31422834--31422883 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
31422824 GGTTGAACCT
31422834 ATTTATAATTTTTTAATA
1 ATTTATAATTTTTTAA-A
*
31422852 ATTTATTATTTTTTTAAA
1 ATTTA-TAATTTTTTAAA
*
31422870 ATTT-TAATTATTTA
1 ATTTATAATTTTTTA
31422884 TTTAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.29
18 10 0.36
19 10 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATAATTTTTTAAA
Found at i:31422879 original size:20 final size:19
Alignment explanation
Indices: 31422842--31422889 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
31422832 CTATTTATAA
31422842 TTTTTTAATAATTTATTAT
1 TTTTTTAATAATTTATTAT
31422861 TTTTTTAA-AATTTTAATTAT
1 TTTTTTAATAA-TTT-ATTAT
*
31422881 TTATTTAAT
1 TTTTTTAAT
31422890 TATTGTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 11 0.44
20 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAATAATTTATTAT
Found at i:31423271 original size:30 final size:29
Alignment explanation
Indices: 31423223--31423289 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
31423213 TTAAAAATCT
*
31423223 TTAAAAATTATAAAAATTTTACAAAAAGA
1 TTAAAAATTATAAAAATTTTACAAAAAAA
*
31423252 TTAAAAGATT-TAAATAATTTTATAAAAAAA
1 TTAAAA-ATTATAAA-AATTTTACAAAAAAA
31423282 TTAAAAAT
1 TTAAAAAT
31423290 ATGTTAGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
TTAAAAATTATAAAAATTTTACAAAAAAA
Found at i:31424269 original size:19 final size:18
Alignment explanation
Indices: 31424245--31424286 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
31424235 AAAACTTAAA
31424245 AAAAAACAAATTTGAAAAT
1 AAAAAACAAATTT-AAAAT
* *
31424264 AAAAAATAAATTTTAAAT
1 AAAAAACAAATTTAAAAT
31424282 AAAAA
1 AAAAA
31424287 TCACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAACAAATTTAAAAT
Found at i:31424294 original size:17 final size:18
Alignment explanation
Indices: 31424240--31424286 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31424230 TCAAAAAAAC
*
31424240 TTAAA-AAAAAACAAATT
1 TTAAATAAAAAATAAATT
*
31424257 TGAAAATAAAAAATAAATT
1 T-TAAATAAAAAATAAATT
31424276 TTAAATAAAAA
1 TTAAATAAAAA
31424287 TCACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 12 0.48
19 12 0.48
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
TTAAATAAAAAATAAATT
Found at i:31424893 original size:60 final size:59
Alignment explanation
Indices: 31424817--31425020 Score: 207
Period size: 60 Copynumber: 3.4 Consensus size: 59
31424807 GTCCCTAAAC
* * *
31424817 TTTTCAAAAATCACATTTTAACCCCTAAACTTTCTAAAAATTCAAATTTAACCCTCATAT
1 TTTTCAAAAATTACATTTTAACCCCTAAACTTTCTAAAAA-TCAAATTTAACCCCCAAAT
* * * * * *
31424877 TTTTCAAAAATTACATTTTAA-ACTTAAACTTTCCAAAAA-AAATATTTTTAACCCCCACAC
1 TTTTCAAAAATTACATTTTAACCCCTAAACTTTCTAAAAATCAA-A--TTTAACCCCCAAAT
* * *
31424937 TATCCAAAAATTACATTTTAACCCCCTAAACTTTCCT-AAAATCACATTTTAACCCCCAAAT
1 TTTTCAAAAATTACATTTTAA-CCCCTAAACTTT-CTAAAAATCA-AATTTAACCCCCAAAT
*
31424998 TTTTAAAAAATTACATTTTAACC
1 TTTTCAAAAATTACATTTTAACC
31425021 TAAATTTTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
57 2 0.02
58 1 0.01
59 15 0.13
60 52 0.45
61 30 0.26
62 13 0.11
63 2 0.02
64 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (59 bp):
TTTTCAAAAATTACATTTTAACCCCTAAACTTTCTAAAAATCAAATTTAACCCCCAAAT
Found at i:31424955 original size:31 final size:30
Alignment explanation
Indices: 31424813--31425020 Score: 177
Period size: 30 Copynumber: 6.9 Consensus size: 30
31424803 GGAGGTCCCT
* * *
31424813 AAACTTTTCAAAAATCACATTTTAACCCCT
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* * *
31424843 AAACTTTCTAAAAATT-CAAATTTAACCCTC
1 AAACTTTCCAAAAATTAC-ATTTTAACCCCC
* * * * **
31424873 ATATTTTTCAAAAATTACATTTTAA-ACTT
1 AAACTTTCCAAAAATTACATTTTAACCCCC
** *
31424902 AAACTTTCCAAAAAAAATATTTTTAACCCCC
1 AAACTTTCCAAAAATTACA-TTTTAACCCCC
* *
31424933 ACACTATCCAAAAATTACATTTTAACCCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
* *
31424963 TAAACTTTCCTAAAATCACATTTTAACCCCC
1 -AAACTTTCCAAAAATTACATTTTAACCCCC
* **
31424994 AAATTTTTAAAAAATTACATTTTAACC
1 AAACTTTCCAAAAATTACATTTTAACC
31425021 TAAATTTTTT
Statistics
Matches: 137, Mismatches: 36, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
29 16 0.12
30 79 0.58
31 42 0.31
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.35
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTAACCCCC
Found at i:31426021 original size:32 final size:32
Alignment explanation
Indices: 31425956--31426021 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
31425946 AAATTGATAT
**
31425956 ATGATCCTTTGCATTTTCTATGAAATATTATG
1 ATGATCCTTTGCATTTTCTATGAAATACCATG
*
31425988 ATGATCTTTTGCATTTTCTATGAAATACCATG
1 ATGATCCTTTGCATTTTCTATGAAATACCATG
31426020 AT
1 AT
31426022 AATATTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (32 bp):
ATGATCCTTTGCATTTTCTATGAAATACCATG
Found at i:31428098 original size:169 final size:169
Alignment explanation
Indices: 31427671--31428170 Score: 934
Period size: 169 Copynumber: 3.0 Consensus size: 169
31427661 GAGCAAAAAA
*
31427671 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTTCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
1 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
31427736 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
66 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
* *
31427801 GATATTGCCAAAGGAAATTGAAAATAAAT---GAATTTT
131 GATATCGCCAAAGGAAATTGGAAATAAATGAGGAATTTT
31427837 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
1 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
* *
31427902 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCATCGAAGTAATTTATGGCTAATTGAAGACAAGAT
66 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
31427967 GATATCGCCAAAGGAAATTGGAAATAAATGAGGAATTTT
131 GATATCGCCAAAGGAAATTGGAAATAAATGAGGAATTTT
31428006 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
1 GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
31428071 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
66 CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
31428136 GATATCGCCAAAGGAAATTGGAAATAAATGAGGAA
131 GATATCGCCAAAGGAAATTGGAAATAAATGAGGAA
31428171 GGACTCCAAC
Statistics
Matches: 324, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
166 154 0.48
169 170 0.52
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (169 bp):
GGTGTATTAGTGCATAACTTTTGCTAGTTTAGTTCCGTGGCCATTTTTGGAAAGTCAAAAGGTCT
CTTGTCGAGTATTCTCTAAGGGTTACTCTCCGTCGAAGGAATTTATGGCTAATTGAAGACAAGAT
GATATCGCCAAAGGAAATTGGAAATAAATGAGGAATTTT
Found at i:31429496 original size:15 final size:15
Alignment explanation
Indices: 31429458--31429496 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
31429448 AAACAAAAGG
*
31429458 AAAAGAAAAGAAGAA
1 AAAAGAAAGGAAGAA
31429473 AAGAA-AAAGGAAGAA
1 AA-AAGAAAGGAAGAA
31429488 AAAAGAAAG
1 AAAAGAAAG
31429497 TCAAGATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGGAAGAA
Found at i:31430831 original size:112 final size:110
Alignment explanation
Indices: 31430630--31430941 Score: 373
Period size: 112 Copynumber: 2.8 Consensus size: 110
31430620 TTATATGGGT
* * *
31430630 TATTTTTAATCTTTTCATTCGTGCGAGTTTTACCTCCAATAAAATTTAATTTTGTCCACCTTATG
1 TATTTTTAATCTTTTCATTCATGCGAGTTTTACCTCCAATAAAATTTAATTTTATCCACCTTA-C
* * **
31430695 AACCTGTTCAAGAATTTTTACATTGAAATAATGGTAAGTGGACCAA
65 AACCTGTTCAAGCATTTTTGCATTGAAATAACAGTAAGTGGACCAA
* ** * *
31430741 TGATTTTTAATCTTTTCATTCATTCGACCTTTGCCTCCAATACAATTTAATTTTATCCACCTTAC
1 T-ATTTTTAATCTTTTCATTCATGCGAGTTTTACCTCCAATAAAATTTAATTTTATCCACCTTAC
** * *
31430806 AACCTTGTTCAAGCACGTTTGCATTGAAATAACAGTTAGTGGACTAA
65 AACC-TGTTCAAGCATTTTTGCATTGAAATAACAGTAAGTGGACCAA
* * * *
31430853 TA-----ATTCTTTTCATTCACGCAAGTTTTACCTCCAATAAAATTCAATTTTATCCACCTTACA
1 TATTTTTAATCTTTTCATTCATGCGAGTTTTACCTCCAATAAAATTTAATTTTATCCACCTTACA
31430913 ACCCTGTTCAAGCATTTTTGCATTGAAAT
66 A-CCTGTTCAAGCATTTTTGCATTGAAAT
31430942 GACGATTAAC
Statistics
Matches: 171, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
106 73 0.43
107 2 0.01
111 6 0.04
112 90 0.53
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (110 bp):
TATTTTTAATCTTTTCATTCATGCGAGTTTTACCTCCAATAAAATTTAATTTTATCCACCTTACA
ACCTGTTCAAGCATTTTTGCATTGAAATAACAGTAAGTGGACCAA
Found at i:31431718 original size:39 final size:39
Alignment explanation
Indices: 31431657--31432845 Score: 341
Period size: 39 Copynumber: 30.3 Consensus size: 39
31431647 CCATCAGCCA
*
31431657 ATCTTTTACCCC-A-CGATAGGGGCAAATTACAACCATCAG
1 ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
* * *** *
31431696 ATCTTTTACCCCGATCATGGGGCAAATCACTGTCAGCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCA-TCAG
* * *
31431735 ATCTCTTATCCCGCGA-CA-AGGGCAGATTGCAACCATTC-G
1 ATCTTTTA-CCC-CGATCATGGGGCAGATTACAACCA-TCAG
* * * * *
31431774 ATCTTTTACTCCGATCATGGGGCAGATCACTATCAGCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCA-TCAG
* ** *
31431813 ATCTCTTACCCC-A-CGATAAAGGCAGATTGCAACCATCAG
1 ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
* *
31431852 ATATTTTACCCCGATCATGGGGCAGA-T-C-ACCGTCAG
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCATCAG
* * **
31431888 CCAATCTCTTACCCC-A-CGATAGGGGCAGATTGCAACCATTTG
1 ---ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
* * * * * ***
31431930 ATATTTTACCCTGATCATGGGACAAATCACTGTCATCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCAT-CAG
* * * * * *
31431969 ATCTCTTACCCCGCAACA-AGGGTAAATTGCAACCATCAG
1 ATCTTTTACCCCG-ATCATGGGGCAGATTACAACCATCAG
* * *
31432008 ATCTTTTACCCCGATCATGGGG-AAACT-CACCGTCAATCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAAC--C-ATCAG
* * *
31432047 ATCTCTT-CCCACGA-CA-GGGGCAGATTACAACTATCCG
1 ATCTTTTACCC-CGATCATGGGGCAGATTACAACCATCAG
* * * ** *
31432084 ATCTGTTACCCTGATCATGGGGCAGATCATTATCATCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCAT-CAG
* * *
31432123 ATCTCTTACCCC-A-CGATAAGGGCAGATTGCAACCATCAG
1 ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
** * * * *
31432162 ATCTTTTACCCCGATCATGGGATAGATCACTATCAACCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTAC-AACCATCAG
* **
31432201 ATCTCTTACCCCGCGA-CA-GGGGCAGATTGTAACCATCAG
1 ATCTTTTA-CCC-CGATCATGGGGCAGATTACAACCATCAG
* * * ** * *
31432240 ATCTTTTACCCCTTATCATGGGGTAGATCACTGTCAACCA-
1 ATCTTTTACCCC-GATCATGGGGCAGATTAC-AACCATCAG
* * * *
31432280 ATCTCTTACCCCGCGA-CA-GAGGCAGATTGCAACCATCCG
1 ATCTTTTA-CCC-CGATCATGGGGCAGATTACAACCATCAG
* **** *
31432319 AACTTTTACCCCGATCATGGGGCAGATTAGTGTCAGCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCA-TCAG
* * **
31432358 ATCTCTTATCCCG-TGACA-GGGGCAGATTGTAACCATCAG
1 ATCTTTTACCCCGAT--CATGGGGCAGATTACAACCATCAG
* * * *
31432397 ATCTTTTACCCCGATCATGGGACAGATCACTATCAGTCA-
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCA-TCAG
* * *
31432436 ATCTCTTACCCAGCGAT-A-GGGGCGGATTGCAACCATCAG
1 ATCTTTTACCC--CGATCATGGGGCAGATTACAACCATCAG
* * *
31432475 ATCTTTTACCCCGAT-ATGAGGCA-AAT-C-ACCGTCAG
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCATCAG
* *
31432510 CCAATCTCTTACCCCG--CGATAGGGGCAGATTACAACCATCAA
1 ---ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
* * *
31432552 ATCTTTTATCTCGATCATGGGGCAGA-T-C-ACCGTCAG
1 ATCTTTTACCCCGATCATGGGGCAGATTACAACCATCAG
* *
31432588 CCAATCTCTTACCCCG--CGATAAGGGCAGATTACAACCATCAG
1 ---ATCTTTTACCCCGATC-AT-GGGGCAGATTACAACCATCAG
* * * ** *
31432630 CCAATCTCTTACCTCGATTATAAGGCAGATTGA-TACCATCCA-
1 ---ATCTTTTACCCCGATCATGGGGCAGATT-ACAACCAT-CAG
* * * *
31432672 ATCTCTTACCCCGATCATAGGGTAGATTGA-AACTATCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATT-ACAACCAT-CAG
*
31432711 ATCTCTTACCCCGATCATGGGGCAGATTGA-AGACATCATCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATT-ACA-AC--CAT-CAG
* * *
31432753 ATCTCTTACCCTGATCATAGGGCAGATTGA-AACCATCCA-
1 ATCTTTTACCCCGATCATGGGGCAGATT-ACAACCAT-CAG
* * *
31432792 ATCTCTTACCTCGATCATGGGGCAGATTGAAACAATCATCTA-
1 ATCTTTTACCCCGATCATGGGGCAGATT---ACAACCATC-AG
31432834 ATCTTTTACCCC
1 ATCTTTTACCCC
31432846 TAAATCACGA
Statistics
Matches: 843, Mismatches: 209, Indels: 193
0.68 0.17 0.16
Matches are distributed among these distances:
35 7 0.01
36 17 0.02
37 35 0.04
38 86 0.10
39 495 0.59
40 70 0.08
41 30 0.04
42 98 0.12
43 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTTTTACCCCGATCATGGGGCAGATTACAACCATCAG
Found at i:31431777 original size:78 final size:78
Alignment explanation
Indices: 31431650--31432818 Score: 1212
Period size: 78 Copynumber: 14.9 Consensus size: 78
31431640 TACATCACCA
* * * *
31431650 TCAGCCAATCTTTTACCCCACGATAGGGGCAAATTACAACCATCAGATCTTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
*
31431715 GGGCAAATCACTG
66 GGGCAGATCACTG
* * * *
31431728 TCAGCCAATCTCTTATCCCGCGACAAGGGCAGATTGCAACCATTC-GATCTTTTACTCCGATCAT
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCA-TCAGATCTTTTACCCCGATCAT
*
31431792 GGGGCAGATCACTA
65 GGGGCAGATCACTG
* ** *
31431806 TCAGCCAATCTCTTACCCCACGATAAAGGCAGATTGCAACCATCAGATATTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
*
31431871 GGGCAGATCACCG
66 GGGCAGATCACTG
* ** * *
31431884 TCAGCCAATCTCTTACCCCACGATAGGGGCAGATTGCAACCATTTGATATTTTACCCTGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* *
31431949 GGACAAATCACTG
66 GGGCAGATCACTG
* * * * * *
31431962 TCATCCAATCTCTTACCCCGCAACAAGGGTAAATTGCAACCATCAGATCTTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* *
31432027 GGG-AAACTCACCG
66 GGGCAGA-TCACTG
** * * * * * * *
31432040 TCAATCAATCTCTT--CCCACGACAGGGGCAGATTACAACTATCCGATCTGTTACCCTGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* *
31432103 GGGCAGATCATTA
66 GGGCAGATCACTG
* * *
31432116 TCATCCAATCTCTTACCCCACGATAAGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
** *
31432181 GGATAGATCACTA
66 GGGCAGATCACTG
* * * *
31432194 TCAACCAATCTCTTACCCCGCGACAGGGGCAGATTGTAACCATCAGATCTTTTACCCCTTATCAT
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCC-GATCAT
*
31432259 GGGGTAGATCACTG
65 GGGGCAGATCACTG
* * * * *
31432273 TCAACCAATCTCTTACCCCGCGACAGAGGCAGATTGCAACCATCCGAACTTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* *
31432338 GGGCAGATTAGTG
66 GGGCAGATCACTG
* * * *
31432351 TCAGCCAATCTCTTATCCCGTGACAGGGGCAGATTGTAACCATCAGATCTTTTACCCCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* *
31432416 GGACAGATCACTA
66 GGGCAGATCACTG
* * *
31432429 TCAGTCAATCTCTTACCCAGCGATAGGGGCGGATTGCAACCATCAGATCTTTTACCCCGAT-ATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
* * *
31432493 AGGCAAATCACCG
66 GGGCAGATCACTG
* * * *
31432506 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTACAACCATCAAATCTTTTATCTCGATCATG
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
*
31432571 GGGCAGATCACCG
66 GGGCAGATCACTG
* * * * *
31432584 TCAGCCAATCTCTTACCCCGCGATAAGGGCAGATTACAACCATCAGCCAATCTCTTACCTCGATT
1 TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAG---ATCTTTTACCCCGATC
** * *
31432649 ATAAGGCAGATTGA-TA
63 ATGGGGCAGA-TCACTG
* * * * * *
31432665 CCATCCAATCTCTTACCCCGATC-ATA-GGGTAGATTGAAACTATCCA-ATCTCTTACCCCGATC
1 TCAGCCAATCTCTTACCCCG--CGATAGGGGCAGATTGCAACCAT-CAGATCTTTTACCCCGATC
* *
31432727 ATGGGGCAGATTGAAGAC-A
63 ATGGGGCAGA-T---CACTG
* * * * *
31432746 TCATCCAATCTCTTACCCTGATC-ATA-GGGCAGATTGAAACCATCCA-ATCTCTTACCTCGATC
1 TCAGCCAATCTCTTACCCCG--CGATAGGGGCAGATTGCAACCAT-CAGATCTTTTACCCCGATC
31432808 ATGGGGCAGAT
63 ATGGGGCAGAT
31432819 TGAAACAATC
Statistics
Matches: 932, Mismatches: 140, Indels: 36
0.84 0.13 0.03
Matches are distributed among these distances:
76 57 0.06
77 72 0.08
78 599 0.64
79 73 0.08
80 1 0.00
81 122 0.13
82 7 0.01
83 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (78 bp):
TCAGCCAATCTCTTACCCCGCGATAGGGGCAGATTGCAACCATCAGATCTTTTACCCCGATCATG
GGGCAGATCACTG
Found at i:31432657 original size:120 final size:118
Alignment explanation
Indices: 31432506--31432824 Score: 330
Period size: 120 Copynumber: 2.7 Consensus size: 118
31432496 CAAATCACCG
* * *
31432506 TCAGCCAATCTCTTACCCCG--CGATAGGGGCAGATT-ACAACCATCAAATCTTTTATCTCGATC
1 TCAGCCAATCTCTTA-CCCGATC-ATA-GGGCAGATTGA-AACCATCCAATCTCTTACCTCGATC
* *
31432568 ATGGGGCAGAT-CACCGTCAGCCAATCTCTTACCCCG--CGATAAGGGCAGATT-ACA-ACCA
62 ATGGGGCAGATGAAAC-T-AGCCAATCTCTTACCCCGATC-AT-AGGGCAGATTGA-AGA-CA
* * * * *
31432626 TCAGCCAATCTCTTACCTCGATTATAAGGCAGATTGATACCATCCAATCTCTTACCCCGATCATA
1 TCAGCCAATCTCTTACC-CGATCATAGGGCAGATTGAAACCATCCAATCTCTTACCTCGATCATG
* * *
31432691 GGGTAGATTGAAACTATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
65 GGGCAGA-TGAAACTAGCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACA
*
31432746 TCATCCAATCTCTTACCCTGATCATAGGGCAGATTGAAACCATCCAATCTCTTACCTCGATCATG
1 TCAGCCAATCTCTTACCC-GATCATAGGGCAGATTGAAACCATCCAATCTCTTACCTCGATCATG
31432811 GGGCAGATTGAAAC
65 GGGCAGA-TGAAAC
31432825 AATCATCTAA
Statistics
Matches: 168, Mismatches: 20, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
119 3 0.02
120 152 0.90
121 10 0.06
122 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (118 bp):
TCAGCCAATCTCTTACCCGATCATAGGGCAGATTGAAACCATCCAATCTCTTACCTCGATCATGG
GGCAGATGAAACTAGCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGACA
Found at i:31432699 original size:81 final size:80
Alignment explanation
Indices: 31432510--31432845 Score: 309
Period size: 81 Copynumber: 4.2 Consensus size: 80
31432500 TCACCGTCAG
* * *
31432510 CCAATCTCTTACCCCG--CGATAGGGGCAGATT-ACAACCAT-CAAATCTTTTATCTCGATCATG
1 CCAATCTCTTACCCCGATC-ATA-GGGCAGATTGA-AACCATACCAATCTCTTACCTCGATCATG
* * * *
31432571 GGGCAGA-TCA-CCGTCAG
63 GGGCAGATTGAGAC-ACAT
*
31432588 CCAATCTCTTACCCCG--CGATAAGGGCAGATT-ACAACCATCAGCCAATCTCTTACCTCGATTA
1 CCAATCTCTTACCCCGATC-AT-AGGGCAGATTGA-AACCAT-A-CCAATCTCTTACCTCGATCA
** *
31432650 TAAGGCAGATTGATAC-CAT
61 TGGGGCAGATTGAGACACAT
* * *
31432669 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAACTAT-CCAATCTCTTACCCCGATCATGGGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAACCATACCAATCTCTTACCTCGATCATGGGG
31432733 CAGATTGAAGACATCAT
66 CAGATTG-AGACA-CAT
*
31432750 CCAATCTCTTACCCTGATCATAGGGCAGATTGAAACCAT-CCAATCTCTTACCTCGATCATGGGG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAACCATACCAATCTCTTACCTCGATCATGGGG
*
31432814 CAGATTGAAACAATCAT
66 CAGATTGAGAC-A-CAT
* *
31432831 CTAATCTTTTACCCC
1 CCAATCTCTTACCCC
31432846 TAAATCACGA
Statistics
Matches: 221, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
78 65 0.29
79 4 0.02
80 3 0.01
81 142 0.64
82 5 0.02
83 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (80 bp):
CCAATCTCTTACCCCGATCATAGGGCAGATTGAAACCATACCAATCTCTTACCTCGATCATGGGG
CAGATTGAGACACAT
Found at i:31434514 original size:30 final size:29
Alignment explanation
Indices: 31434475--31434680 Score: 143
Period size: 30 Copynumber: 6.9 Consensus size: 29
31434465 CCTAGAAGGT
*
31434475 CCCTAAACTTTTCAAAAATCACATTTTAA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
** * *
31434504 CCCTTAAAC-TTTCTAAAAATTTGAATTTGA
1 CCC-TAAACTTTTC-AAAAATTACATTTTAA
*
31434534 CCCTAATACTTTCCAAAAATTACATTTTAA
1 CCCTAA-ACTTTTCAAAAATTACATTTTAA
* ** *
31434564 CCC-AAACTTTCCAAAAAAATT-GGTTTTAGC
1 CCCTAAACTTTTC--AAAAATTACATTTTA-A
* *
31434594 CCCTAAACTTTCCAAAAATTATATTTTAA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
* *
31434623 CCCCT-AACTTTTTAAAAAATATATATTTTAA
1 -CCCTAAAC-TTTTCAAAAAT-TACATTTTAA
* *
31434654 CCCTCAAATTTTTCAAAACTT-CATTTT
1 CCCT-AAACTTTTCAAAAATTACATTTT
31434681 CCGACCCCAT
Statistics
Matches: 141, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
28 7 0.05
29 32 0.23
30 69 0.49
31 31 0.22
32 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCAAAAATTACATTTTAA
Found at i:31434551 original size:60 final size:59
Alignment explanation
Indices: 31434475--31434642 Score: 198
Period size: 59 Copynumber: 2.8 Consensus size: 59
31434465 CCTAGAAGGT
* * *
31434475 CCCTAAACTTTTCAAAAATCACATTTTAACCCTTAAACTTTCTAAAAATTTGAATTT-GA
1 CCCTAAACTTTCCAAAAATTACATTTTAACCC-TAAACTTTCTAAAAAATTGAATTTAGA
* ** *
31434534 CCCTAATACTTTCCAAAAATTACATTTTAACCC-AAACTTTCCAAAAAAATTGGTTTTAGC
1 CCCTAA-ACTTTCCAAAAATTACATTTTAACCCTAAACTTT-CTAAAAAATTGAATTTAGA
* *
31434594 CCCTAAACTTTCCAAAAATTATATTTTAACCCCT-AACTTTTTAAAAAAT
1 CCCTAAACTTTCCAAAAATTACATTTTAA-CCCTAAACTTTCTAAAAAAT
31434643 ATATATTTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
58 7 0.07
59 47 0.50
60 40 0.43
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATTACATTTTAACCCTAAACTTTCTAAAAAATTGAATTTAGA
Found at i:31435913 original size:19 final size:20
Alignment explanation
Indices: 31435891--31435928 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31435881 TATTTTAAAT
31435891 AATTAAAA-AACAATATTTG
1 AATTAAAATAACAATATTTG
*
31435910 AATTAAAATAACATTATTT
1 AATTAAAATAACAATATTT
31435929 TATATATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTAAAATAACAATATTTG
Found at i:31435987 original size:16 final size:17
Alignment explanation
Indices: 31435956--31435989 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31435946 TATTTAAAAT
*
31435956 ATTTTATAATATTTTTA
1 ATTTTATAAGATTTTTA
31435973 ATTTTA-AAGATTTTTA
1 ATTTTATAAGATTTTTA
31435989 A
1 A
31435990 AATTTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTATAAGATTTTTA
Found at i:31441295 original size:27 final size:27
Alignment explanation
Indices: 31441257--31441323 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
31441247 TATATAGACC
*
31441257 GATTATTTAACTAGTAGACAAAGTATA
1 GATTATTTAACTAGTAGACAAAGTAAA
*
31441284 GATTATTTAACTAGTAGACGAAGTAAA
1 GATTATTTAACTAGTAGACAAAGTAAA
31441311 GATTATTTAACTA
1 GATTATTTAACTA
31441324 CATAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (27 bp):
GATTATTTAACTAGTAGACAAAGTAAA
Found at i:31442372 original size:20 final size:18
Alignment explanation
Indices: 31442329--31442384 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
31442319 ACTTTATAAC
*
31442329 CTAAAAAATTATAAAAAGT
1 CTAAAAAA-TATAAAAAAT
*
31442348 CTAAAGATTATATAAAAAAT
1 CTAAA-A-AATATAAAAAAT
*
31442368 TTAAAAAATATAAAAAA
1 CTAAAAAATATAAAAAA
31442385 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 14 0.45
21 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (18 bp):
CTAAAAAATATAAAAAAT
Found at i:31445032 original size:2 final size:2
Alignment explanation
Indices: 31445025--31445059 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31445015 CTTGAAACAA
*
31445025 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31445060 TTACTCTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:31445625 original size:2 final size:2
Alignment explanation
Indices: 31445618--31445652 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31445608 GTTCTTGTAC
31445618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31445653 GTTTGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31445703 original size:2 final size:2
Alignment explanation
Indices: 31445696--31445724 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31445686 TGCATACATC
31445696 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31445725 ATAAACTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31447235 original size:121 final size:121
Alignment explanation
Indices: 31447021--31447265 Score: 463
Period size: 121 Copynumber: 2.0 Consensus size: 121
31447011 GTCATTGATG
31447021 TAACTCGAATCGAGATTATATTTGAGATAGTGAACACCTTAACTATTAGATCAACACACGGGGTT
1 TAACTCGAATCGAGATTATATTTGAGATAGTGAACACCTTAACTATTAGATCAACACACGGGGTT
*
31447086 CTCCAAAATATTTTTCTTATGTTAAAATTACCATCCTTTTAATATCTACATATCAT
66 CTCCAAAATATTTTACTTATGTTAAAATTACCATCCTTTTAATATCTACATATCAT
31447142 TAACTCGAATCGAGATTATATTTGAGATAGTGAACACCTTAACTATTAGATCAACACACGGGGTT
1 TAACTCGAATCGAGATTATATTTGAGATAGTGAACACCTTAACTATTAGATCAACACACGGGGTT
* *
31447207 CTCTAAAATGTTTTACTTATGTTAAAATTACCATCCTTTTAATATCTACATATCAT
66 CTCCAAAATATTTTACTTATGTTAAAATTACCATCCTTTTAATATCTACATATCAT
31447263 TAA
1 TAA
31447266 TAGAATTTGG
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (121 bp):
TAACTCGAATCGAGATTATATTTGAGATAGTGAACACCTTAACTATTAGATCAACACACGGGGTT
CTCCAAAATATTTTACTTATGTTAAAATTACCATCCTTTTAATATCTACATATCAT
Found at i:31448286 original size:21 final size:21
Alignment explanation
Indices: 31448261--31448314 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
31448251 AATACATTAA
*
31448261 ATTAAAAAAATAAATCTTAATT
1 ATTAAAAAAATAAA-CGTAATT
31448283 -TTAAAAAAATAAACGTAATT
1 ATTAAAAAAATAAACGTAATT
31448303 ATCTAAAAAAAT
1 AT-TAAAAAAAT
31448315 TAACTCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 14 0.48
22 9 0.31
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTAAAAAAATAAACGTAATT
Found at i:31451523 original size:33 final size:33
Alignment explanation
Indices: 31451485--31451551 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
31451475 ACAAATGAGG
31451485 TTATTATTTTTTAGCATTGGTATCGAGAAGAGA
1 TTATTATTTTTTAGCATTGGTATCGAGAAGAGA
31451518 TTATTATTTTTTAGCATTGGTATCGAGAAGAGA
1 TTATTATTTTTTAGCATTGGTATCGAGAAGAGA
31451551 T
1 T
31451552 GGAAGAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (33 bp):
TTATTATTTTTTAGCATTGGTATCGAGAAGAGA
Found at i:31455105 original size:5 final size:5
Alignment explanation
Indices: 31455086--31455117 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
31455076 AAAAATGCTA
31455086 AAAAT -AAAT -AAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
31455118 GGACTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:31455132 original size:29 final size:27
Alignment explanation
Indices: 31455094--31455196 Score: 66
Period size: 29 Copynumber: 3.6 Consensus size: 27
31455084 TAAAAATAAA
*
31455094 TAAATAAAATAAAATAAAATAAAAGGAC
1 TAAATTAAATAAAATAAAATAAAAGG-C
** *
31455122 TAAATTGAAATTGTAAT-AAATTAAAGGC
1 TAAATT-AAA-TAAAATAAAATAAAAGGC
* *
31455150 ATAAATTAAA-AAAATTATAATACAAAGGGT
1 -TAAATTAAATAAAA-TAAAATA-AAA-GGC
31455180 TAAATTAAAATAAAATA
1 TAAATT-AAATAAAATA
31455197 GAAAATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 12 0.21
29 27 0.47
30 11 0.19
31 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (27 bp):
TAAATTAAATAAAATAAAATAAAAGGC
Found at i:31456347 original size:13 final size:13
Alignment explanation
Indices: 31456329--31456353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31456319 TTTGTAATGA
31456329 ATTTAAAAATTTT
1 ATTTAAAAATTTT
31456342 ATTTAAAAATTT
1 ATTTAAAAATTT
31456354 CGGATTGGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAAAATTTT
Found at i:31457316 original size:31 final size:31
Alignment explanation
Indices: 31457281--31457343 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
31457271 TTAACAGCCC
31457281 AGTGATTTAAATAAAAACTTTCGAATAGTTT
1 AGTGATTTAAATAAAAACTTTCGAATAGTTT
* * *
31457312 AGTGATTTAAATGAAATCTTTTGAATAGTTT
1 AGTGATTTAAATAAAAACTTTCGAATAGTTT
31457343 A
1 A
31457344 ATAACTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (31 bp):
AGTGATTTAAATAAAAACTTTCGAATAGTTT
Found at i:31460740 original size:2 final size:2
Alignment explanation
Indices: 31460735--31460761 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31460725 TTGAAAAATA
31460735 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31460762 AAGTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31463349 original size:5 final size:5
Alignment explanation
Indices: 31463335--31463371 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
31463325 CCCCCTCTTG
31463335 AATT- AATTA AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
31463372 CAATAATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:31466730 original size:17 final size:17
Alignment explanation
Indices: 31466708--31466746 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
31466698 AGGTGGAGAA
* *
31466708 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
31466725 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
31466742 CTTGT
1 CTTGT
31466747 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:31470248 original size:32 final size:32
Alignment explanation
Indices: 31470212--31470275 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
31470202 CTATGCGTGT
*
31470212 GTTGTCAATTAAGTTTATGTTCTCCAGTTTGA
1 GTTGTCAATTAAGTCTATGTTCTCCAGTTTGA
*
31470244 GTTGTGAATTAAGTCTATGTTCTCCAGTTTGA
1 GTTGTCAATTAAGTCTATGTTCTCCAGTTTGA
31470276 TCATTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.45
Consensus pattern (32 bp):
GTTGTCAATTAAGTCTATGTTCTCCAGTTTGA
Found at i:31475646 original size:23 final size:25
Alignment explanation
Indices: 31475605--31475657 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
31475595 TTTTTGGAAG
31475605 TTTT-GTCTTGTCTTGTACAAAT-A
1 TTTTAGTCTTGTCTTGTACAAATGA
* *
31475628 TTTTAGTCTTGT-TTTTACAAGTGA
1 TTTTAGTCTTGTCTTGTACAAATGA
31475652 TTTTAG
1 TTTTAG
31475658 GGATGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (25 bp):
TTTTAGTCTTGTCTTGTACAAATGA
Found at i:31485640 original size:20 final size:20
Alignment explanation
Indices: 31485603--31485640 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31485593 AGAACAAAGC
*
31485603 TGAAGAAGACTTAGAAGACT
1 TGAAGAAGACTTACAAGACT
31485623 TGAAGAAG-CATTACAAGA
1 TGAAGAAGAC-TTACAAGA
31485641 AACTTCGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (20 bp):
TGAAGAAGACTTACAAGACT
Found at i:31490263 original size:18 final size:18
Alignment explanation
Indices: 31490242--31490281 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31490232 TGAGCCAGTG
*
31490242 TGCTTGAACGAGCCAATA
1 TGCTCGAACGAGCCAATA
*
31490260 TGCTCGAATGAGCCAATA
1 TGCTCGAACGAGCCAATA
31490278 TGCT
1 TGCT
31490282 ATTCCTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (18 bp):
TGCTCGAACGAGCCAATA
Found at i:31492679 original size:24 final size:24
Alignment explanation
Indices: 31492644--31492690 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31492634 GCCTCAGATA
31492644 GATAGATCTGTGGTAGTATTTATT
1 GATAGATCTGTGGTAGTATTTATT
* *
31492668 GATAGATTTGTGGTTGTATTTAT
1 GATAGATCTGTGGTAGTATTTAT
31492691 CGATGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (24 bp):
GATAGATCTGTGGTAGTATTTATT
Done.