Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 113 of 120
Found at i:33660487 original size:2 final size:2
Alignment explanation
Indices: 33660480--33660514 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33660470 GGAAATTCCA
33660480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33660515 ATCATTTCTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33676690 original size:19 final size:19
Alignment explanation
Indices: 33676666--33676704 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
33676656 ATGGAACGGG
*
33676666 ACGAGGACAAATGTTGTTA
1 ACGAGGACAAATATTGTTA
33676685 ACGAGGACAAATATTGTTA
1 ACGAGGACAAATATTGTTA
33676704 A
1 A
33676705 ATCCATTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (19 bp):
ACGAGGACAAATATTGTTA
Found at i:33677080 original size:17 final size:17
Alignment explanation
Indices: 33677055--33677093 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
33677045 TTGATAAAAT
*
33677055 TTGAATCGGAGTTCGAA
1 TTGATTCGGAGTTCGAA
33677072 TTGATTCGGAGTTCGAA
1 TTGATTCGGAGTTCGAA
33677089 TTGAT
1 TTGAT
33677094 ATGTGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (17 bp):
TTGATTCGGAGTTCGAA
Found at i:33682258 original size:17 final size:17
Alignment explanation
Indices: 33682238--33682275 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
33682228 TAATATCACT
33682238 AAATATTAAAAA-TTCAA
1 AAATATTAAAAAGTT-AA
33682255 AAATATTAAAAAGTTAA
1 AAATATTAAAAAGTTAA
33682272 AAAT
1 AAAT
33682276 TTGTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATATTAAAAAGTTAA
Found at i:33686639 original size:8 final size:8
Alignment explanation
Indices: 33686628--33686669 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
33686618 AAAAATTTAA
33686628 AAAATATT
1 AAAATATT
33686636 AAAATATT
1 AAAATATT
*
33686644 AAAATAAT
1 AAAATATT
*
33686652 ATAATA-T
1 AAAATATT
33686659 -AAATATT
1 AAAATATT
33686666 AAAA
1 AAAA
33686670 AAATTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 4 0.14
7 2 0.07
8 23 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:33686672 original size:25 final size:24
Alignment explanation
Indices: 33686644--33686691 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
33686634 TTAAAATATT
*
33686644 AAAATAATATAATATAAATATTAAA
1 AAAATAATATAAAAT-AATATTAAA
**
33686669 AAAATTTTATAAAATAATATTAA
1 AAAATAATATAAAATAATATTAA
33686692 TGGACCTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAATATAAAATAATATTAAA
Found at i:33686673 original size:11 final size:11
Alignment explanation
Indices: 33686617--33686691 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
33686607 TTAATTATAT
33686617 AAAAAAT-TT-
1 AAAAAATATTA
33686626 AAAAAATATT-
1 AAAAAATATTA
33686636 --AAAATATTA
1 AAAAAATATTA
*
33686645 AAATAATA-TA
1 AAAAAATATTA
*
33686655 ATATAAATATTA
1 A-AAAAATATTA
*
33686667 AAAAAATTTTA
1 AAAAAATATTA
33686678 TAAAATAATATTA
1 -AAAA-AATATTA
33686691 A
1 A
33686692 TGGACCTACA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
8 8 0.15
9 7 0.13
10 5 0.10
11 18 0.35
12 8 0.15
13 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAAATATTA
Found at i:33691126 original size:15 final size:16
Alignment explanation
Indices: 33691106--33691141 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
33691096 TATAAAAGAC
33691106 AATTTAAATT-AAATA
1 AATTTAAATTAAAATA
*
33691121 AATTTAACTTAAAATA
1 AATTTAAATTAAAATA
33691137 AATTT
1 AATTT
33691142 TTGTTTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAATTAAAATA
Found at i:33692477 original size:28 final size:29
Alignment explanation
Indices: 33692446--33692509 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
33692436 AATAATTTTT
33692446 AAATTT-TGAAATATTTAT-AAAAATTCCA
1 AAATTTAT-AAATATTTATAAAAAATTCCA
* * *
33692474 AAATTTATATATATTTTTAAAAAATTCTA
1 AAATTTATAAATATTTATAAAAAATTCCA
33692503 AAATTTA
1 AAATTTA
33692510 AAAAATTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
AAATTTATAAATATTTATAAAAAATTCCA
Found at i:33692514 original size:46 final size:47
Alignment explanation
Indices: 33692458--33692551 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
33692448 ATTTTGAAAT
* *
33692458 ATTTATAAAAATTC-CAA-AATTTATATATATTTTTAAAAAATTCTAAA
1 ATTTATAAAAATTCTAAATAATTTATAAAT-TTTTTAAAAAATT-TAAA
*
33692505 ATTTA-AAAAATTCTAAATAATTTATAAATTTTTTTAAAAATTTAAA
1 ATTTATAAAAATTCTAAATAATTTATAAATTTTTTAAAAAATTTAAA
33692551 A
1 A
33692552 ATATTCTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 13 0.31
47 19 0.45
48 10 0.24
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (47 bp):
ATTTATAAAAATTCTAAATAATTTATAAATTTTTTAAAAAATTTAAA
Found at i:33692752 original size:19 final size:20
Alignment explanation
Indices: 33692728--33692765 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
33692718 TTAATTTTTA
33692728 ATTTAATTCAAAT-AAATTT
1 ATTTAATTCAAATCAAATTT
*
33692747 ATTTAATTTAAATCAAATT
1 ATTTAATTCAAATCAAATT
33692766 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATTCAAATCAAATTT
Found at i:33694552 original size:32 final size:31
Alignment explanation
Indices: 33694478--33694552 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 31
33694468 TAAATTGTAG
*
33694478 TCAA-TTTTTAGGGGAACCAAATAGCATTTTA
1 TCAATTTTTTAGGGG-ACCAAATAACATTTTA
*
33694509 TCAATAATTTTAGGGG-CCTAAATAACAATTTTA
1 TCAAT-TTTTTAGGGGACC-AAATAAC-ATTTTA
33694542 TCAATTTTTTA
1 TCAATTTTTTA
33694553 TGCAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 6 0.16
32 11 0.30
33 20 0.54
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (31 bp):
TCAATTTTTTAGGGGACCAAATAACATTTTA
Found at i:33695787 original size:26 final size:26
Alignment explanation
Indices: 33695758--33695809 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
33695748 ACCCGATCAA
33695758 GTATTTTCTCTTTGTTTGATTTGATT
1 GTATTTTCTCTTTGTTTGATTTGATT
33695784 GTATTTTCTCTTTGTTTGATTTGATT
1 GTATTTTCTCTTTGTTTGATTTGATT
33695810 TAGAGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (26 bp):
GTATTTTCTCTTTGTTTGATTTGATT
Found at i:33706252 original size:2 final size:2
Alignment explanation
Indices: 33706245--33706277 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33706235 TTTGCTTTGA
33706245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33706278 CTTGCAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33727151 original size:16 final size:16
Alignment explanation
Indices: 33727132--33727164 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33727122 ATTTAGTTTT
33727132 AATATAATTTTT-TATA
1 AATAT-ATTTTTATATA
33727148 AATATATTTTTATATA
1 AATATATTTTTATATA
33727164 A
1 A
33727165 GTTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATATTTTTATATA
Found at i:33756431 original size:21 final size:21
Alignment explanation
Indices: 33756405--33756450 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
33756395 TCATGTTTCC
* *
33756405 TGAAGACCCCAATGAGCCTTT
1 TGAAGACACCAATGACCCTTT
* *
33756426 TGAAGATATCAATGACCCTTT
1 TGAAGACACCAATGACCCTTT
33756447 TGAA
1 TGAA
33756451 TCAGGATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (21 bp):
TGAAGACACCAATGACCCTTT
Found at i:33777875 original size:22 final size:22
Alignment explanation
Indices: 33777862--33777902 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33777852 TTTATATGAA
33777862 TTTTTA-TTTATTTTTA-AAAC
1 TTTTTATTTTATTTTTATAAAC
33777882 TTTTTTATTTTATTTTTATAA
1 -TTTTTATTTTATTTTTATAA
33777903 TTATTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.33
22 10 0.56
23 2 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTATTTTATTTTTATAAAC
Found at i:33779972 original size:41 final size:41
Alignment explanation
Indices: 33779915--33780027 Score: 172
Period size: 41 Copynumber: 2.8 Consensus size: 41
33779905 TTGTATAAAT
*
33779915 GGAAGACTCATGTCTCGAGATGAGAATGTGACTATGAATAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
* * * * *
33779956 GGAAGACTCATGTCTCGAAATGAAAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
33779997 GGAAGACTCATGTCTCGAGATGAGAATGAGA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGA
33780028 ATAGGGTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
Found at i:33790532 original size:17 final size:18
Alignment explanation
Indices: 33790502--33790536 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33790492 AATTTATATT
*
33790502 TTTTAAATGTATATATAA
1 TTTTAAATGAATATATAA
33790520 TTTTAAA-GAATATATAA
1 TTTTAAATGAATATATAA
33790537 AGAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTAAATGAATATATAA
Found at i:33795161 original size:16 final size:15
Alignment explanation
Indices: 33795132--33795160 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33795122 GGGTATAATA
33795132 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
33795147 AAATATTTAAAAAA
1 AAATATTTAAAAAA
33795161 AGACACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:33809636 original size:19 final size:19
Alignment explanation
Indices: 33809614--33809651 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
33809604 CAAAGGTTGG
33809614 ATGTTTTGGGAGTGAATTC
1 ATGTTTTGGGAGTGAATTC
33809633 ATGTTTTGGGAGTGAATTC
1 ATGTTTTGGGAGTGAATTC
33809652 TTACTTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42
Consensus pattern (19 bp):
ATGTTTTGGGAGTGAATTC
Found at i:33814546 original size:23 final size:21
Alignment explanation
Indices: 33814503--33814550 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
33814493 CTTTTAAACC
33814503 ATTTTTAGTTTTAGAATTTTA
1 ATTTTTAGTTTTAGAATTTTA
*
33814524 TATTTTATAGTTTTCATAA-TTTA
1 -ATTTT-TAGTTTT-AGAATTTTA
33814547 ATTT
1 ATTT
33814551 AATTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTTTAGTTTTAGAATTTTA
Found at i:33818895 original size:15 final size:16
Alignment explanation
Indices: 33818856--33818896 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
33818846 CATTTATCTA
33818856 TTTTATCACTTTGATC
1 TTTTATCACTTTGATC
*
33818872 -TTTAT-ACTTT-TTC
1 TTTTATCACTTTGATC
33818885 TTTTATCACTTT
1 TTTTATCACTTT
33818897 AGCGGCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 2 0.09
14 10 0.45
15 10 0.45
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTATCACTTTGATC
Found at i:33820931 original size:218 final size:218
Alignment explanation
Indices: 33820546--33820982 Score: 847
Period size: 218 Copynumber: 2.0 Consensus size: 218
33820536 ATTATATCTT
*
33820546 TTGTTGGTAAGGATACATTGCAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
1 TTGTTGATAAGGATACATTGCAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
33820611 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
66 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
*
33820676 AACAGAAAAGAAGGTGGACGCTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
131 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
33820741 ATTCAGGTAGTATTCTTTTACTC
196 ATTCAGGTAGTATTCTTTTACTC
*
33820764 TTGTTGATAAGGATACATTGTAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
1 TTGTTGATAAGGATACATTGCAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
33820829 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
66 CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
33820894 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
131 AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
33820959 ATTCAGGTAGTATTCTTTTACTC
196 ATTCAGGTAGTATTCTTTTACTC
33820982 T
1 T
33820983 CAGTTTGATG
Statistics
Matches: 216, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 216 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (218 bp):
TTGTTGATAAGGATACATTGCAATCCGAGTCTAATGGAAAGCTGCCTACTTCTCAAAAAGATTCA
CTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTCAGAATCATTGTCTAGACC
AACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCATCTAAGAACAATTCAGTTG
ATTCAGGTAGTATTCTTTTACTC
Found at i:33822448 original size:200 final size:203
Alignment explanation
Indices: 33822084--33822494 Score: 702
Period size: 200 Copynumber: 2.0 Consensus size: 203
33822074 TCAAAATATT
*
33822084 AGAAAAATGGTAAGCTTTGTGAAAGGCTCTTGTGGCTTTTAGAGGTTTCATATATTATTAGCATT
1 AGAAAAACGGTAAGCTTTGTGAAAGGCTCTTGTGGC-TTTAGAGGTTTCATATATTATTAGCATT
* * *
33822149 AGTAAAAAAAAATTAGTAATTTTCTATCACTCTGTATTTTTCAAGTGTGAGAAACTAGATATGTA
65 AGTAAAAAAAAATAAGTAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTA
*
33822214 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTGTACCTTAATACCGGTT
130 CTGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAATACCGGTT
33822279 TCTCATGAA
195 TCTCATGAA
* *
33822288 AGAAAAACGGT-AGCTTTGTGATAGGCTCTTGTGGC-TTAGAGGTTTCATATATTATTAGCATTT
1 AGAAAAACGGTAAGCTTTGTGAAAGGCTCTTGTGGCTTTAGAGGTTTCATATATTATTAGCATTA
33822351 GTAAAAAAAAA-AAGTAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTAC
66 GTAAAAAAAAATAAGTAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTAC
* * *
33822415 TGTGTGCACCTATTTTCATAATATAGGTTGATCTTTTGGACTCTTTTCTACCTTAGTACTGGTTT
131 TGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAATACCGGTTT
33822480 CTCATGAA
196 CTCATGAA
33822488 AGAAAAA
1 AGAAAAA
33822495 TTAGGGATAA
Statistics
Matches: 197, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
200 126 0.64
201 38 0.19
203 23 0.12
204 10 0.05
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (203 bp):
AGAAAAACGGTAAGCTTTGTGAAAGGCTCTTGTGGCTTTAGAGGTTTCATATATTATTAGCATTA
GTAAAAAAAAATAAGTAATTTTCTATCACTCTATATTCTTCAAGTGTGAGAAACTAGATATGTAC
TGTGTGCACCTATTTTCATAATATAGATTGATCTTTTGGACTCTTTTCTACCTTAATACCGGTTT
CTCATGAA
Found at i:33823658 original size:25 final size:22
Alignment explanation
Indices: 33823630--33823676 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
33823620 CATATCTTAG
33823630 AATATGTTACATTATCTTGTTTGAT
1 AATAT-TT-CATTAT-TTGTTTGAT
*
33823655 AATATTTTATTATTTGTTTGAT
1 AATATTTCATTATTTGTTTGAT
33823677 GGGATGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 5 0.24
24 2 0.10
25 5 0.24
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (22 bp):
AATATTTCATTATTTGTTTGAT
Found at i:33828218 original size:22 final size:21
Alignment explanation
Indices: 33828190--33828230 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
33828180 TCTAATACTT
33828190 GATATACATATATATAGTATTA
1 GATATACATATATAT-GTATTA
*
33828212 GATATACATGTATATGTAT
1 GATATACATATATATGTAT
33828231 ATATATTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (21 bp):
GATATACATATATATGTATTA
Found at i:33832349 original size:14 final size:14
Alignment explanation
Indices: 33832332--33832360 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33832322 TCAAGTTCGT
33832332 AATGTGAAGTTGAC
1 AATGTGAAGTTGAC
33832346 AATGTGAAGTTGAC
1 AATGTGAAGTTGAC
33832360 A
1 A
33832361 TTCTCAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
AATGTGAAGTTGAC
Found at i:33836508 original size:30 final size:27
Alignment explanation
Indices: 33836447--33836510 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 27
33836437 ACTAGTTGAG
* *
33836447 TGACCAATTTAAAAAATCATAGTTGGG
1 TGACCAATTTAAAAAATCATAATTGGA
33836474 TGACCAATTTAAAAAAACTTCATAATTGGA
1 TGACCAATTT-AAAAAA--TCATAATTGGA
33836504 TGACCAA
1 TGACCAA
33836511 AAAAGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 10 0.31
28 6 0.19
30 16 0.50
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (27 bp):
TGACCAATTTAAAAAATCATAATTGGA
Found at i:33846429 original size:63 final size:63
Alignment explanation
Indices: 33846322--33846510 Score: 306
Period size: 63 Copynumber: 3.0 Consensus size: 63
33846312 GAAAGAATAG
* * **
33846322 AAAGAGACAAAGGGACCGTATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACAATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
*
33846385 AATGAGAGAAAGGAACAATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACAATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
* * *
33846448 AAAGAGAGAAAGGAACCATATGCACAGTAAGAGGTCATCAAATAAACGAGAAGGTTCTGTATT
1 AAAGAGAGAAAGGAACAATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
33846511 TGCTATTTGC
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 117 1.00
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (63 bp):
AAAGAGAGAAAGGAACAATATGCACAGTAAGAGGTCATCAAACAAACCAGAAGGTTCTGTATT
Found at i:33848438 original size:2 final size:2
Alignment explanation
Indices: 33848431--33848462 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33848421 CATTCGGTTC
33848431 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33848463 TTATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33857709 original size:7 final size:7
Alignment explanation
Indices: 33857697--33857732 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
33857687 AAAACCATAT
33857697 ATATTAA
1 ATATTAA
33857704 ATATTAA
1 ATATTAA
33857711 ATATTAA
1 ATATTAA
33857718 ATATTAA
1 ATATTAA
33857725 ATA-TAA
1 ATATTAA
33857731 AT
1 AT
33857733 TAATTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATTAA
Found at i:33882064 original size:188 final size:187
Alignment explanation
Indices: 33881734--33882080 Score: 511
Period size: 188 Copynumber: 1.9 Consensus size: 187
33881724 TTCCAGCCTA
* * *
33881734 CATGTGAGACTTCTGCATAAATTAGGTTAATTGCCTCTGTATGCTGTCTGGACTTTTAGCTTTTT
1 CATGTGAGACTTCTGCATAAATTAGGTTAATTGCCTCTATATGCTGTCTAGACTTCTAGCTTTTT
* * * * *
33881799 TCCTTACCTTGAGATGTTTCTTGTATGCACCGGTACTTTAGCTTGGGTTGCTAAATTTATAACTG
66 TCCTTACCTTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAACTG
33881864 AAATGTAGTTTGTGGGAGTTCCTTGAACCCAAGATAGCAACACTGGTATCTCTGTCTT
131 AAATGTAGTTTGTGGGAGTTCCTT-AACCCAAGATAGCAACACTGGTATCTCTGTCTT
* *
33881922 CATGTG-GTACTTTTGCATAAATTAGGTTAGTTGCCTCTATATGCTGT-TCAGACTTCTAGCTTT
1 CATGTGAG-ACTTCTGCATAAATTAGGTTAATTGCCTCTATATGCTGTCT-AGACTTCTAGCTTT
* **
33881985 TTTCTTTACCTTGAGATGCTTCTTGCATGCATTGGTACTTAAGCCTGAGTTGCTAAATTTATAAC
64 TTTCCTTACCTTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAAC
*
33882050 TTG-AATGTAGTTTGTGGGTGTTCCTTAACCC
129 -TGAAATGTAGTTTGTGGGAGTTCCTTAACCC
33882081 TTCTTCATTT
Statistics
Matches: 142, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
187 7 0.05
188 133 0.94
189 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (187 bp):
CATGTGAGACTTCTGCATAAATTAGGTTAATTGCCTCTATATGCTGTCTAGACTTCTAGCTTTTT
TCCTTACCTTGAGATGCTTCTTGCATGCACCGGTACTTAAGCCTGAGTTGCTAAATTTATAACTG
AAATGTAGTTTGTGGGAGTTCCTTAACCCAAGATAGCAACACTGGTATCTCTGTCTT
Found at i:33895400 original size:54 final size:54
Alignment explanation
Indices: 33895337--33895448 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 54
33895327 TAATATTTTC
33895337 TATTTTGATTCTTAGACATTGATAGGAAGGAAA-AAAATTAGAAAGATAAAAAAA
1 TATTTTGATTCTTAGACATTGATAGGAAGGAAAGAAAATTAGAAAGAT-AAAAAA
* *
33895391 TATTTTGATTCTTAGACTTTGATAGGATGGAAAGAAAATTAGAAAGATAAAAAA
1 TATTTTGATTCTTAGACATTGATAGGAAGGAAAGAAAATTAGAAAGATAAAAAA
33895445 TATT
1 TATT
33895449 GAAGGGATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 41 0.75
55 14 0.25
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (54 bp):
TATTTTGATTCTTAGACATTGATAGGAAGGAAAGAAAATTAGAAAGATAAAAAA
Found at i:33895477 original size:17 final size:17
Alignment explanation
Indices: 33895423--33895482 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
33895413 TAGGATGGAA
*
33895423 AGAAAAT-TAGAAAGAT
1 AGAAAATATAGAAGGAT
* *
33895439 AAAAAATATTGAAGGGAT
1 AGAAAATATAGAA-GGAT
33895457 -GAAAATATAGAAGGAT
1 AGAAAATATAGAAGGAT
*
33895473 AGAAATTATA
1 AGAAAATATA
33895483 ATTTTTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 10 0.29
17 22 0.63
18 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (17 bp):
AGAAAATATAGAAGGAT
Found at i:33912217 original size:15 final size:16
Alignment explanation
Indices: 33912197--33912230 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33912187 TTACTATATA
33912197 ATTACA-AAAAAAAAT
1 ATTACACAAAAAAAAT
*
33912212 ATTACACCAAAAAAAT
1 ATTACACAAAAAAAAT
33912228 ATT
1 ATT
33912231 TTTTGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
ATTACACAAAAAAAAT
Found at i:33913281 original size:15 final size:15
Alignment explanation
Indices: 33913261--33913314 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
33913251 ATACTACAAA
33913261 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
33913276 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
33913293 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
33913310 ATATT
1 ATATT
33913315 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:33913421 original size:16 final size:19
Alignment explanation
Indices: 33913396--33913451 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
33913386 TAAAATTGAA
33913396 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
33913415 A-A-TAATAAATTATATTAATT
1 ATATTAAT-AATT-TATTAA-T
33913435 ATATTAATAATTTATTA
1 ATATTAATAATTTATTA
33913452 TATGACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 1 0.03
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:33915218 original size:23 final size:23
Alignment explanation
Indices: 33915192--33915357 Score: 159
Period size: 23 Copynumber: 7.4 Consensus size: 23
33915182 AGTGCTGGGC
33915192 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
33915215 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
33915234 -AC--CGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
33915254 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
33915277 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
33915301 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
33915325 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
33915348 ATCAGAGAGC
1 AACAGAGAGC
33915358 GCGCTAGTGT
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 79 0.68
24 2 0.02
25 16 0.14
26 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:33915223 original size:48 final size:44
Alignment explanation
Indices: 33915167--33915357 Score: 167
Period size: 48 Copynumber: 4.2 Consensus size: 44
33915157 CGAAGTATTG
*
33915167 AACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACAGAAGTGCT----AACAGAGAGCACACAAAGTGCTA
* * * *
33915215 AACAGAGAGTACACAA-AG-T-AC--CGAGCACACAAAGTGCTA
1 AACAGAGAGCACAGAAGTGCTAACAGAGAGCACACAAAGTGCTA
* *
33915254 ATCAGAGAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACA-GAAGTGCTAA-CAGAGAGCACACAAAGTGCT-A
* *
33915301 TAACAGAGAGCACGAGACGTGCTAAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCAC-AGAAGTGCT-AACAGAGAGCACACAAAGTGCTA
*
33915348 ATCAGAGAGC
1 AACAGAGAGC
33915358 GCGCTAGTGT
Statistics
Matches: 119, Mismatches: 13, Indels: 24
0.76 0.08 0.15
Matches are distributed among these distances:
39 28 0.24
40 2 0.02
41 3 0.03
42 1 0.01
43 1 0.01
44 1 0.01
46 25 0.21
47 3 0.03
48 52 0.44
49 3 0.03
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (44 bp):
AACAGAGAGCACAGAAGTGCTAACAGAGAGCACACAAAGTGCTA
Found at i:33915252 original size:39 final size:39
Alignment explanation
Indices: 33915198--33915272 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
33915188 GGGCAACAGA
*
33915198 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACC
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACC
* *
33915237 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
33915273 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACC
Found at i:33918228 original size:25 final size:25
Alignment explanation
Indices: 33918181--33918228 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
33918171 TTTAATTATT
*
33918181 AAATTTCATAGTAAAACATAATATA
1 AAATTTCATAGTAAAACACAATATA
*
33918206 AAATTTCATATTAAATA-ACAATA
1 AAATTTCATAGTAAA-ACACAATA
33918229 CATGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATTTCATAGTAAAACACAATATA
Found at i:33920943 original size:17 final size:17
Alignment explanation
Indices: 33920921--33920981 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
33920911 AATAGGGTTC
33920921 CTAATACTTATTTACTA
1 CTAATACTTATTTACTA
* * *
33920938 CTAATATTGTATATCTATGTC
1 CTAATACT-TAT-T-TA-CTA
*
33920959 CTAATACTCATTTACTA
1 CTAATACTTATTTACTA
33920976 CTAATA
1 CTAATA
33920982 TCGTATATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
17 14 0.42
18 5 0.15
19 2 0.06
20 4 0.12
21 8 0.24
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.44
Consensus pattern (17 bp):
CTAATACTTATTTACTA
Found at i:33921316 original size:3 final size:3
Alignment explanation
Indices: 33921310--33921363 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
33921300 TATCATCATC
33921310 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33921358 ATT ATT
1 ATT ATT
33921364 GTAAAGCTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33928792 original size:59 final size:58
Alignment explanation
Indices: 33928655--33928974 Score: 432
Period size: 59 Copynumber: 5.4 Consensus size: 58
33928645 AATTTTTGAC
* * *
33928655 TTTCGGGGGTAAAATGGTAATTTTTTGTGAAATCTGGGTT-AAAATGGGATTTTGGAAAG
1 TTTC-GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAATTTTGGAAAG
* *
33928714 -TTCGGGGGCAAAATGGTAATTTTTGGTGAAAAT-GGGGTTAAAAATAGAATTTAGGAAAG
1 TTTC-GGGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAAT-GAATTTTGGAAAG
* * * **
33928773 TTTAGGGGTAAAACGGTAATTTTTGGTAAAATTAGGGTTAAAAATGAGATTTTGGAAAG
1 TTTCGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGA-ATTTTGGAAAG
*
33928832 TTT-GGGGCTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATGAAATTTTGGAAAG
1 TTTCGGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATG-AATTTTGGAAAG
33928891 TTTCGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
1 TTTCGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAATTTTGGAAAG
33928950 TTTCGGGGTAAAATGGTAATTTTTG
1 TTTCGGGGTAAAATGGTAATTTTTG
33928975 AATAGTTTAG
Statistics
Matches: 235, Mismatches: 17, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
58 41 0.17
59 186 0.79
60 8 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
TTTCGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAATTTTGGAAAG
Found at i:33930045 original size:3 final size:3
Alignment explanation
Indices: 33930039--33930121 Score: 60
Period size: 3 Copynumber: 27.0 Consensus size: 3
33930029 ATTTAAAAAA
* * * **
33930039 ATT ATT ATT AATT ATT A-T ATTT ATT ACT ATC ATT AAT ATT ATT GGT
1 ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
33930085 ATT ATTT ATT ATT ATA ATT ATT AAT AAT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33930122 GGTAGCATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
2 2 0.03
3 52 0.84
4 8 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:33930119 original size:31 final size:31
Alignment explanation
Indices: 33930038--33930121 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
33930028 AATTTAAAAA
33930038 AATTATTATTAATTATTA-TATTTATTACTAT
1 AATTATTATTAA-TATTATTATTTATTACTAT
* * * ** *
33930069 CATTAATATTATTGGTATTATTTATTATTAT
1 AATTATTATTAATATTATTATTTATTACTAT
*
33930100 AATTATTAATAATATTATTATT
1 AATTATTATTAATATTATTATT
33930122 GGTAGCATTT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
30 3 0.08
31 37 0.93
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
AATTATTATTAATATTATTATTTATTACTAT
Found at i:33931176 original size:19 final size:19
Alignment explanation
Indices: 33931154--33931203 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
33931144 TTTTTATAGC
*
33931154 AATTAATATTTTTAAA-TTA
1 AATTAATA-ATTTAAATTTA
33931173 AATTAATAATTTAAATTTA
1 AATTAATAATTTAAATTTA
33931192 AATTATATAATT
1 AATTA-ATAATT
33931204 GTGTAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAATAATTTAAATTTA
Found at i:33936653 original size:20 final size:18
Alignment explanation
Indices: 33936611--33936658 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
33936601 TGTTTACATT
33936611 TTTTAAAATTTTTAAAAA
1 TTTTAAAATTTTTAAAAA
* *
33936629 ATTTAAAATTGCTTTCAAAA
1 TTTTAAAATT--TTTAAAAA
33936649 TTTTAAAATT
1 TTTTAAAATT
33936659 ATTTTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTAAAATTTTTAAAAA
Found at i:33936842 original size:13 final size:13
Alignment explanation
Indices: 33936824--33936848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33936814 TAGCATATTA
33936824 AAAAAATAATTTT
1 AAAAAATAATTTT
33936837 AAAAAATAATTT
1 AAAAAATAATTT
33936849 CAAAGTTTTG
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:33944158 original size:36 final size:36
Alignment explanation
Indices: 33944118--33944201 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
33944108 ATGTGGTCAT
*
33944118 AGCCGTAGCCCAAGTCGAAGTCGAACCTCTATTCGC
1 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
33944154 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
1 AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
*
33944190 AGCCATAGCCCA
1 AGCCGTAGCCCA
33944202 GTTGATTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (36 bp):
AGCCGTAGCCCAAGTCGAAGTCGAACCCCTATTCGC
Found at i:33949084 original size:84 final size:84
Alignment explanation
Indices: 33948956--33949119 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
33948946 TGAGTCGGTG
* * * *
33948956 CAAGATTCTCCTTTCTTTTAATATTTTAAAATTCAATTATTTCATGGTAATGATTTAAACAG-TG
1 CAAGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAAC-GTTG
33949020 TACTATTTGTGTTATGGGTA
65 TACTATTTGTGTTATGGGTA
* *
33949040 CAAGATTCTCCTTTCTTTTGATATATTAAAATTCAATCAATTCATGGAAATGTTTTAAACGTTGT
1 CAAGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAACGTTGT
33949105 ACTATTTGTGTTATG
66 ACTATTTGTGTTATG
33949120 CACATGCTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 1 0.01
84 72 0.99
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (84 bp):
CAAGATTCTCCTTTCTTTTAATATATTAAAATTCAATCAATTCATGGAAATGATTTAAACGTTGT
ACTATTTGTGTTATGGGTA
Found at i:33961722 original size:33 final size:33
Alignment explanation
Indices: 33961685--33961782 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
33961675 AAGCACAAGT
*
33961685 AGAAGTCCTGCAAGATCTCGGAGAAGCATTAGC
1 AGAAGTCCTGTAAGATCTCGGAGAAGCATTAGC
* ** * *
33961718 AGAAGCCCCATAAGATCTAGGAGAAGCAATAGC
1 AGAAGTCCTGTAAGATCTCGGAGAAGCATTAGC
33961751 AGAAGTCCTGTAAGATCTTCTAGGAGAAGCAT
1 AGAAGTCCTGTAAGATC-TC--GGAGAAGCAT
33961783 GAGTAGGAGC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
33 41 0.80
34 1 0.02
36 9 0.18
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (33 bp):
AGAAGTCCTGTAAGATCTCGGAGAAGCATTAGC
Found at i:33972884 original size:12 final size:13
Alignment explanation
Indices: 33972838--33972879 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
33972828 AATTCTAAGA
33972838 TTATTGAAAAGTATT
1 TTATT-AAAA-TATT
33972853 ATTATT-AAATATT
1 -TTATTAAAATATT
33972866 TTATTAAAATATT
1 TTATTAAAATATT
33972879 T
1 T
33972880 GTTAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 12 0.48
14 3 0.12
16 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (13 bp):
TTATTAAAATATT
Found at i:33997260 original size:18 final size:18
Alignment explanation
Indices: 33997214--33997268 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
33997204 TCTTTTATTG
* *
33997214 AGAAAA-AAATAAAATTA
1 AGAAAATAAAAAAAATAA
*
33997231 ATAAAATGAAAAAAAATAA
1 AGAAAAT-AAAAAAAATAA
*
33997250 AGAAAATAAAAAAGATAA
1 AGAAAATAAAAAAAATAA
33997268 A
1 A
33997269 ATAAATTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 15 0.48
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AGAAAATAAAAAAAATAA
Found at i:34007311 original size:14 final size:15
Alignment explanation
Indices: 34007275--34007314 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
34007265 CGAAATTAAA
34007275 TTATAATTTTATTATT
1 TTATAA-TTTATTATT
34007291 TTAATAATTTA-TATT
1 TT-ATAATTTATTATT
34007306 TTATAATTT
1 TTATAATTT
34007315 TTAAAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 6 0.26
16 6 0.26
17 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATAATTTATTATT
Found at i:34007343 original size:29 final size:31
Alignment explanation
Indices: 34007303--34007370 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
34007293 AATAATTTAT
* *
34007303 ATTTTATAATTTTT-AAAGAATTAAA-TCA-A
1 ATTTTATTATTTTTAAAAAAATTAAAGT-ATA
34007332 ATTTTATTATTTTTAAAAAAATTAAAGTATA
1 ATTTTATTATTTTTAAAAAAATTAAAGTATA
34007363 ATTTTATT
1 ATTTTATT
34007371 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.38
30 11 0.32
31 10 0.29
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (31 bp):
ATTTTATTATTTTTAAAAAAATTAAAGTATA
Found at i:34007953 original size:19 final size:19
Alignment explanation
Indices: 34007929--34007967 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34007919 TATAAATTGA
* *
34007929 AAATAAATTTTACCATTAT
1 AAATAAATGTTACAATTAT
*
34007948 AAATAAGTGTTACAATTAT
1 AAATAAATGTTACAATTAT
34007967 A
1 A
34007968 TATCATTCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATAAATGTTACAATTAT
Found at i:34009923 original size:20 final size:21
Alignment explanation
Indices: 34009888--34009926 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34009878 TTTTTTTAAA
*
34009888 AATATTTATATTATTTTATTT
1 AATATTTATATAATTTTATTT
34009909 AATATTTA-ATAATTTTAT
1 AATATTTATATAATTTTAT
34009927 ACATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATATTTATATAATTTTATTT
Found at i:34010442 original size:6 final size:6
Alignment explanation
Indices: 34010428--34010461 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
34010418 AGCTAAGCCC
* *
34010428 CTCAAG CTCAGG CTCAGG CTCAGG CTCACG CTCA
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCA
34010462 TCTACTCGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.18
Consensus pattern (6 bp):
CTCAGG
Found at i:34018948 original size:28 final size:29
Alignment explanation
Indices: 34018895--34018950 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
34018885 TAACATTTTA
34018895 AAATATAATATATTTAATTTTCTAATATC
1 AAATATAATATATTTAATTTTCTAATATC
* *
34018924 AAATA-AATA-ATTATATTTTTTTAATAT
1 AAATATAATATATT-TAATTTTCTAATAT
34018951 ATTGCATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.12
28 16 0.67
29 5 0.21
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATATAATATATTTAATTTTCTAATATC
Found at i:34026785 original size:2 final size:2
Alignment explanation
Indices: 34026778--34026807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34026768 AAGAGATTAT
34026778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34026808 GGAAAGGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34029519 original size:2 final size:2
Alignment explanation
Indices: 34029512--34029546 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34029502 AAACAAACAA
34029512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34029547 AACTTAAGAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34030157 original size:17 final size:17
Alignment explanation
Indices: 34030135--34030178 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
34030125 TCAAATTATT
34030135 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
34030152 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAA
34030169 TTAAATTTAT
1 TTAAATTTAT
34030179 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:34030171 original size:6 final size:6
Alignment explanation
Indices: 34030134--34030210 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
34030124 ATCAAATTAT
* * *
34030134 TTTAAA TTT-AT TTTAAA ATTAAA TTT-AT TTTAAA TTTAAA TTTATAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TT-T-AAA
* *
34030183 TTTAAA TTTAGA TTT-AA TATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
34030211 TTAAATGAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
5 11 0.20
6 35 0.64
7 3 0.05
8 3 0.05
9 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:34030185 original size:15 final size:15
Alignment explanation
Indices: 34030143--34030192 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
34030133 TTTTAAATTT
34030143 ATTT-TAAAA-TTAA
1 ATTTATAAAATTTAA
*
34030156 ATTTATTTTAAATTTAA
1 ATTTA--TAAAATTTAA
34030173 ATTTATAAAATTTAA
1 ATTTATAAAATTTAA
34030188 ATTTA
1 ATTTA
34030193 GATTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
15 14 0.45
16 4 0.13
17 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATAAAATTTAA
Found at i:34030188 original size:21 final size:23
Alignment explanation
Indices: 34030162--34030210 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
34030152 TTAAATTTAT
34030162 TTTAAATTTAAATTT-ATA-AAA
1 TTTAAATTTAAATTTAATATAAA
*
34030183 TTTAAATTTAGATTTAATATAAA
1 TTTAAATTTAAATTTAATATAAA
34030206 TTTAA
1 TTTAA
34030211 TTAAATGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.56
22 3 0.12
23 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATATAAA
Found at i:34030206 original size:32 final size:31
Alignment explanation
Indices: 34030143--34030209 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
34030133 TTTTAAATTT
* *
34030143 ATTT-TAAAATTAAATTTATTTTAAATTTAA
1 ATTTATAAAATTAAATTTAATTTAAATATAA
34030173 ATTTATAAAATTTAAATTTAGATTT-AATATAA
1 ATTTATAAAA-TTAAATTTA-ATTTAAATATAA
34030205 ATTTA
1 ATTTA
34030210 ATTAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.12
31 5 0.16
32 20 0.62
33 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
ATTTATAAAATTAAATTTAATTTAAATATAA
Found at i:34030974 original size:3 final size:3
Alignment explanation
Indices: 34030896--34030962 Score: 80
Period size: 3 Copynumber: 21.3 Consensus size: 3
34030886 GCATTAATTT
**
34030896 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GCA ATA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
34030945 AGTTA TTA ATA ATA ATA A
1 A--TA ATA ATA ATA ATA A
34030963 ATAACATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 51 0.93
4 2 0.04
5 1 0.02
6 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34031264 original size:15 final size:16
Alignment explanation
Indices: 34031237--34031266 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34031227 TTCTTTTAAA
34031237 ATTTTCACAGATCTGG
1 ATTTTCACAGATCTGG
34031253 ATTTTC-CAGATCTG
1 ATTTTCACAGATCTG
34031267 TAATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (16 bp):
ATTTTCACAGATCTGG
Found at i:34032052 original size:30 final size:29
Alignment explanation
Indices: 34032016--34032210 Score: 130
Period size: 30 Copynumber: 6.6 Consensus size: 29
34032006 GAACTATCCA
*
34032016 AAAATTATATTTTGACCCCAAAACTTTTGG
1 AAAATTATATTTTGACCCCAAAACTTTT-C
* ** ** *
34032046 AAAATTACATCCTGACCCTTAAACGTTTCC
1 AAAATTATATTTTGACCCCAAAAC-TTTTC
* *
34032076 AAAATTATATTTTAACCCTAAAA-TTTTC
1 AAAATTATATTTTGACCCCAAAACTTTTC
34032104 TAAAAATTATATTTTGACCCC-AAACTTTTC
1 --AAAATTATATTTTGACCCCAAAACTTTTC
**** *
34032134 AAAATTATA-TTTGATATGAAAACTTTCTA
1 AAAATTATATTTTGACCCCAAAACTTT-TC
* * *
34032163 AAAATTACCATTTT-ACCCCCAAACTTTCC
1 AAAATTA-TATTTTGACCCCAAAACTTTTC
34032192 AAAATT-TCATTTTTGACCC
1 AAAATTAT-A-TTTTGACCC
34032211 AAATTTCACC
Statistics
Matches: 125, Mismatches: 29, Indels: 22
0.71 0.16 0.12
Matches are distributed among these distances:
27 5 0.04
28 21 0.17
29 21 0.17
30 72 0.58
31 6 0.05
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCAAAACTTTTC
Found at i:34032082 original size:60 final size:58
Alignment explanation
Indices: 34032007--34032145 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 58
34031997 GAAGTCCCTG
* * * *
34032007 AACTATCCAAAAATTATATTTTGACCCCAAAACTTTT-GGAAAATTACATCCTGACCCTTA
1 AACTTTCC-AAAATTATATTTTAACCCCAAAA-TTTTCGAAAAATTACATCCTGACCC-CA
* * * **
34032067 AACGTTTCCAAAATTATATTTTAACCCTAAAATTTTCTAAAAATTATATTTTGACCCCA
1 AAC-TTTCCAAAATTATATTTTAACCCCAAAATTTTCGAAAAATTACATCCTGACCCCA
*
34032126 AACTTTTCAAAATTATATTT
1 AACTTTCCAAAATTATATTT
34032146 GATATGAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 16 0.24
59 8 0.12
60 39 0.58
61 4 0.06
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.37
Consensus pattern (58 bp):
AACTTTCCAAAATTATATTTTAACCCCAAAATTTTCGAAAAATTACATCCTGACCCCA
Found at i:34032235 original size:117 final size:115
Alignment explanation
Indices: 34032105--34032416 Score: 307
Period size: 117 Copynumber: 2.7 Consensus size: 115
34032095 AAAATTTTCT
* ** *
34032105 AAAAATTA-TATTTTGACCCCAAACTTTTCAAAATTAT-ATTTGATATGAAAACTTT-CTAAAAA
1 AAAAATTACCATTTT-ACCCCAAACTTTTCAAAATT-TCATTTGA-ACCAAAA-TTTACCAAAAA
*
34032167 TTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTGACC-CAAATTTCACC
62 TTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTC-AATTTCACC
* * ***
34032221 AAGAATTACCATTTTACCCCTAAA-TTTTCCAAAATTTCATTTTAACCCTGATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCC-AAACTTTT-CAAAATTTCATTTGAACCAAAATTT-ACCAAAAAT
* *
34032285 TACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACC
63 TACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
* * *
34032338 AAAAATTACCATTTTACGCCCGAACTTTTCAAAATTCTCGTTTTG-ACC-CAATTTCAACC-AAA
1 AAAAATTACCATTTTAC-CCCAAACTTTTCAAAATT-TC-ATTTGAACCAAAATTT--ACCAAAA
*
34032400 ATTACCATTTTGCCCCC
61 ATTACCATTTTACCCCC
34032417 GGGTATCCAA
Statistics
Matches: 163, Mismatches: 21, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
115 3 0.02
116 19 0.12
117 122 0.75
118 16 0.10
119 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (115 bp):
AAAAATTACCATTTTACCCCAAACTTTTCAAAATTTCATTTGAACCAAAATTTACCAAAAATTAC
CATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACC
Found at i:34032250 original size:59 final size:58
Alignment explanation
Indices: 34032162--34032415 Score: 327
Period size: 59 Copynumber: 4.3 Consensus size: 58
34032152 AAAACTTTCT
*
34032162 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTGACCCAAATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACCC-AATTTCACC
* * * *
34032221 AAGAATTACCATTTTACCCCTAAATTTTCCAAAATTTCA-TTTTAACCCTGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACCC-AATTTCACC
* *
34032279 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACC-CAATTTCACC
* * *
34032338 AAAAATTACCATTTTACGCCC-GAACTTTTCAAAATTCTC-GTTTTGACCCAATTTCAACC
1 AAAAATTACCATTTTAC-CCCTAAACTTTCCAAAATT-TCATTTTTGACCCAATTTC-ACC
*
34032397 -AAAATTACCATTTTGCCCC
1 AAAAATTACCATTTTACCCC
34032416 CGGGTATCCA
Statistics
Matches: 174, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
57 3 0.02
58 73 0.42
59 93 0.53
60 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACCCAATTTCACC
Found at i:34032269 original size:28 final size:28
Alignment explanation
Indices: 34032163--34032321 Score: 135
Period size: 29 Copynumber: 5.5 Consensus size: 28
34032153 AAACTTTCTA
* *
34032163 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATT-CCATTTTACCCCTAAATTTTCC
* *
34032192 AAAATTTCATTTTTGA-CCC-AAATTTCACC
1 AAAATTCCA-TTTT-ACCCCTAAATTT-TCC
34032221 AAGAATTACCATTTTACCCCTAAATTTTCC
1 AA-AATT-CCATTTTACCCCTAAATTTTCC
* * * *
34032251 AAAATTTCATTTTAACCCT-GATTTCACC
1 AAAATTCCATTTTACCCCTAAATTT-TCC
*
34032279 AAAAATTACCATTTTACCCCTAAACTTTCC
1 -AAAATT-CCATTTTACCCCTAAATTTTCC
34032309 AAAATTCCATTTT
1 AAAATTCCATTTT
34032322 TGACCTCGAT
Statistics
Matches: 105, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
27 4 0.04
28 27 0.26
29 34 0.32
30 29 0.28
31 11 0.10
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTAAATTTTCC
Found at i:34032294 original size:30 final size:31
Alignment explanation
Indices: 34032162--34032353 Score: 133
Period size: 29 Copynumber: 6.5 Consensus size: 31
34032152 AAAACTTTCT
* *
34032162 AAAAATTACCATTTTACCCCCAAACTTT--CC
1 AAAAATTACCATTTTAACCCTAAA-TTTCACC
* *
34032192 -AAAATT-TCATTTTTGACCC-AAATTTCACC
1 AAAAATTACCA-TTTTAACCCTAAATTTCACC
* * *
34032221 AAGAATTACCATTTTACCCCTAAATTT-TCC
1 AAAAATTACCATTTTAACCCTAAATTTCACC
* *
34032251 -AAAATT-TCATTTTAACCCT-GATTTCACC
1 AAAAATTACCATTTTAACCCTAAATTTCACC
*
34032279 AAAAATTACCATTTTACCCCTAAACTTT--CC
1 AAAAATTACCATTTTAACCCTAAA-TTTCACC
* **
34032309 -AAAATT-CCATTTTTGA-CCTCGATTTCACC
1 AAAAATTACCA-TTTTAACCCTAAATTTCACC
34032338 AAAAATTACCATTTTA
1 AAAAATTACCATTTTA
34032354 CGCCCGAACT
Statistics
Matches: 125, Mismatches: 21, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
27 10 0.08
28 25 0.20
29 38 0.30
30 37 0.30
31 12 0.10
32 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATTACCATTTTAACCCTAAATTTCACC
Found at i:34034703 original size:13 final size:13
Alignment explanation
Indices: 34034685--34034709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34034675 AGTTCTAAAC
34034685 TCTAATAAGTGTA
1 TCTAATAAGTGTA
34034698 TCTAATAAGTGT
1 TCTAATAAGTGT
34034710 TCTTTCTAAG
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TCTAATAAGTGTA
Found at i:34034849 original size:24 final size:24
Alignment explanation
Indices: 34034788--34034850 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
34034778 TAGACTAATA
* *
34034788 AGAGTTTAACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
34034812 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
34034836 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
34034851 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:34035107 original size:15 final size:15
Alignment explanation
Indices: 34035087--34035126 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
34035077 TAAACCCGAA
34035087 AACCCGAAAACAAAG
1 AACCCGAAAACAAAG
34035102 AACCCGAAAACAAAG
1 AACCCGAAAACAAAG
34035117 AACCCGAAAA
1 AACCCGAAAA
34035127 ACGTAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.60, C:0.28, G:0.12, T:0.00
Consensus pattern (15 bp):
AACCCGAAAACAAAG
Found at i:34035187 original size:13 final size:13
Alignment explanation
Indices: 34035169--34035193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34035159 AGTTCTAAAC
34035169 TCTAATGAGTGTA
1 TCTAATGAGTGTA
34035182 TCTAATGAGTGT
1 TCTAATGAGTGT
34035194 TCTTTCTAAG
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:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (13 bp):
TCTAATGAGTGTA
Found at i:34035333 original size:24 final size:24
Alignment explanation
Indices: 34035272--34035334 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
34035262 TAGACTAATA
* * *
34035272 AGAGATTAACTCAAAAAAATAAAT
1 AGAGTTTAACTGAAAAAAATAAAC
* * *
34035296 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAAAAAATAAAC
34035320 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
34035335 GATTATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAAAAAATAAAC
Found at i:34037308 original size:24 final size:24
Alignment explanation
Indices: 34037262--34037323 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
34037252 TAGACTAATA
* * *
34037262 AGAGTTTAACTCAAATAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
34037286 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
34037310 AGAATTTAACTGAA
1 AGAGTTTAACTGAA
34037324 TGCTTATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:34048466 original size:19 final size:19
Alignment explanation
Indices: 34048429--34048476 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
34048419 AGTTATTAAT
* *
34048429 TAAATTTAACTAAATAATAA
1 TAAAATTAACTAAAAAAT-A
34048449 TAAAATTAA-TAAAAAATA
1 TAAAATTAACTAAAAAATA
34048467 TAAATATTAA
1 TAAA-ATTAA
34048477 AGGTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTAACTAAAAAATA
Found at i:34052550 original size:23 final size:23
Alignment explanation
Indices: 34052524--34052569 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
34052514 AATTTCGAAT
**
34052524 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
34052547 TTCGAGTTAAACGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
34052570 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:34052638 original size:9 final size:9
Alignment explanation
Indices: 34052614--34052660 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
34052604 TTAATTTTCA
34052614 AATTCGAAT
1 AATTCGAAT
* *
34052623 TACTCGAAT
1 AATTCGAAT
34052632 AATTCGAAT
1 AATTCGAAT
34052641 AATTCGAAT
1 AATTCGAAT
*
34052650 AAATCGAAT
1 AATTCGAAT
34052659 AA
1 AA
34052661 AGTTATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34052877 original size:42 final size:42
Alignment explanation
Indices: 34052818--34052901 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
34052808 CAAATATATT
* *
34052818 TAAACTCAAATATAATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
*
34052860 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
34052902 AACTCCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:34068295 original size:36 final size:36
Alignment explanation
Indices: 34068248--34068321 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
34068238 GTGCCCACCC
34068248 ATGTATGATTAATTAGGTTGCCATTTCTCAAAAACA
1 ATGTATGATTAATTAGGTTGCCATTTCTCAAAAACA
34068284 ATGTATGATTAATTAGGTTGCCATTTCTCAAAAACA
1 ATGTATGATTAATTAGGTTGCCATTTCTCAAAAACA
34068320 AT
1 AT
34068322 ATCGCTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (36 bp):
ATGTATGATTAATTAGGTTGCCATTTCTCAAAAACA
Found at i:34084680 original size:29 final size:29
Alignment explanation
Indices: 34084648--34084711 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
34084638 TAATGTGTAT
*
34084648 AATTACATTAAGTAAAAAATAATATATAA
1 AATTACATTAAATAAAAAATAATATATAA
* * *
34084677 AATTATACGTTAAATAAAAATTTATATATAA
1 AA-T-TACATTAAATAAAAAATAATATATAA
34084708 AATT
1 AATT
34084712 GATATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.10
30 2 0.07
31 24 0.83
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTACATTAAATAAAAAATAATATATAA
Found at i:34086829 original size:2 final size:2
Alignment explanation
Indices: 34086822--34086846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34086812 AAGCCACTAC
34086822 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34086847 ATGAGAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34092466 original size:23 final size:23
Alignment explanation
Indices: 34092438--34092493 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
34092428 CAAAATAGTG
*
34092438 AGAAAACAACAAAAAAAATAG-A
1 AGAAAACAACAAAAAAAAGAGCA
**
34092460 AGCAAAACAGTAAAAAAAAGAGCA
1 AG-AAAACAACAAAAAAAAGAGCA
34092484 AGAAAACAAC
1 AGAAAACAAC
34092494 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (23 bp):
AGAAAACAACAAAAAAAAGAGCA
Found at i:34109012 original size:17 final size:17
Alignment explanation
Indices: 34108990--34109028 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
34108980 CTCCACATTG
*
34108990 ACAAGAATTCTCAACGA
1 ACAAGAACTCTCAACGA
34109007 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
34109024 ACAAG
1 ACAAG
34109029 TTCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:34115126 original size:2 final size:2
Alignment explanation
Indices: 34115119--34115169 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
34115109 CTCCTAAACG
* *
34115119 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC TC AC AC TC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
34115161 AC AC TC AC A
1 AC AC AC AC A
34115170 TTGTCTCTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.49, G:0.00, T:0.06
Consensus pattern (2 bp):
AC
Found at i:34118709 original size:2 final size:2
Alignment explanation
Indices: 34118702--34118749 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
34118692 CTTTTTCCCT
34118702 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34118744 TC TC TC
1 TC TC TC
34118750 GAATAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:34120675 original size:2 final size:2
Alignment explanation
Indices: 34120668--34120700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34120658 TTTTGCTCCT
34120668 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34120701 TACAACATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34121606 original size:2 final size:2
Alignment explanation
Indices: 34121599--34121636 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34121589 AATGAATCCC
34121599 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34121637 GTAGATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:34123469 original size:2 final size:2
Alignment explanation
Indices: 34123462--34123489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34123452 TAGCTTTTCG
34123462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34123490 GATGCATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34124357 original size:15 final size:17
Alignment explanation
Indices: 34124337--34124370 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
34124327 CTATCATTTT
34124337 CCATCCC-CTCCC-CTC
1 CCATCCCTCTCCCTCTC
34124352 CCATCCCTCTCCCTCTC
1 CCATCCCTCTCCCTCTC
34124369 CC
1 CC
34124371 TCTTCCCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.06, C:0.71, G:0.00, T:0.24
Consensus pattern (17 bp):
CCATCCCTCTCCCTCTC
Found at i:34124595 original size:16 final size:16
Alignment explanation
Indices: 34124574--34124604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34124564 ATCACTGTGC
34124574 TATACACATATATACG
1 TATACACATATATACG
*
34124590 TATACATATATATAC
1 TATACACATATATAC
34124605 TTGGAAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (16 bp):
TATACACATATATACG
Found at i:34125126 original size:20 final size:20
Alignment explanation
Indices: 34125103--34125142 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34125093 GAATTGAAAC
34125103 CTGAGTAACTGTTTTGTCAG
1 CTGAGTAACTGTTTTGTCAG
* *
34125123 CTGAGTGATTGTTTTGTCAG
1 CTGAGTAACTGTTTTGTCAG
34125143 TTACCCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.42
Consensus pattern (20 bp):
CTGAGTAACTGTTTTGTCAG
Found at i:34125160 original size:30 final size:31
Alignment explanation
Indices: 34125124--34125182 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
34125114 TTTTGTCAGC
*
34125124 TGAGTGATTG-TTTTGTCAGTTACCCAAAGT
1 TGAGTGATTGTTTTTGTAAGTTACCCAAAGT
*
34125154 TGAGTGATTGTTTTTGTAATTTACCCAAA
1 TGAGTGATTGTTTTTGTAAGTTACCCAAA
34125183 AAAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (31 bp):
TGAGTGATTGTTTTTGTAAGTTACCCAAAGT
Found at i:34128597 original size:3 final size:3
Alignment explanation
Indices: 34128589--34128631 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
34128579 GATGGAAAGA
34128589 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
34128632 TTTTTATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34134440 original size:28 final size:27
Alignment explanation
Indices: 34134369--34134440 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
34134359 ATTTAAAACA
*
34134369 TATTATTT-AATTACTATTTTATATATTT
1 TATTATTTAAATTA--ATTTTAAATATTT
*
34134397 TA-TAATTAAATTTTAATTTTAAATATTTT
1 TATTATTTAAA--TTAATTTTAAATA-TTT
34134426 TATTATTTAAATTAA
1 TATTATTTAAATTAA
34134441 ATTCGGACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
27 4 0.11
28 17 0.47
29 5 0.14
30 10 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTATTTAAATTAATTTTAAATATTT
Found at i:34137538 original size:7 final size:7
Alignment explanation
Indices: 34137526--34137557 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
34137516 TTCTGGTTTT
34137526 GAACAGG
1 GAACAGG
34137533 GAACAGG
1 GAACAGG
34137540 GAACAGG
1 GAACAGG
34137547 GAACAGG
1 GAACAGG
34137554 GAAC
1 GAAC
34137558 GCTTGCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.41, T:0.00
Consensus pattern (7 bp):
GAACAGG
Found at i:34156781 original size:19 final size:20
Alignment explanation
Indices: 34156745--34156792 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
34156735 CAACCATGTA
**
34156745 TGACAAAAATTGGTCATTTC
1 TGACAAAAATTGACCATTTC
34156765 TGACAAAAATT-ACCATTTC
1 TGACAAAAATTGACCATTTC
*
34156784 TCACAAAAA
1 TGACAAAAA
34156793 CTATTATGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (20 bp):
TGACAAAAATTGACCATTTC
Found at i:34160792 original size:6 final size:6
Alignment explanation
Indices: 34160781--34160814 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
34160771 ACACATCTCT
34160781 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTT
34160815 TTTCCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (6 bp):
TCTTCA
Found at i:34185405 original size:15 final size:15
Alignment explanation
Indices: 34185385--34185414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34185375 AAAAACTAGC
34185385 ATTACTTAGGCTTAG
1 ATTACTTAGGCTTAG
34185400 ATTACTTAGGCTTAG
1 ATTACTTAGGCTTAG
34185415 TTTAGCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
ATTACTTAGGCTTAG
Found at i:34187808 original size:177 final size:176
Alignment explanation
Indices: 34187512--34187867 Score: 649
Period size: 177 Copynumber: 2.0 Consensus size: 176
34187502 AGATTATAAA
34187512 AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
1 AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
*
34187577 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATTTGAAGAGTACTAAAAAAAAT
66 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACT-AAAAAAAT
* *
34187642 TTGAAATCAAAACAAAAAATCCAACCAATTAGTACATGGGATGGAAC
130 GTGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
34187689 AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
1 AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
* *
34187754 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTATAAATCTGGAGAGTACTAAAAAAATG
66 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACTAAAAAAATG
*
34187819 TGAAATCAAACCAAAAAATCCAACAAATTAGTACATGGGATGGAAC
131 TGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
34187865 AAT
1 AAT
34187868 ATCTAAAGAA
Statistics
Matches: 173, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
176 55 0.32
177 118 0.68
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (176 bp):
AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACTAAAAAAATG
TGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
Found at i:34194385 original size:50 final size:50
Alignment explanation
Indices: 34194331--34194471 Score: 264
Period size: 50 Copynumber: 2.8 Consensus size: 50
34194321 TGATGGATAA
34194331 GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCTGATGGTTGG
1 GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCTGATGGTTGG
34194381 GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCTGATGGTTGG
1 GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCTGATGGTTGG
* *
34194431 GTAGATTAAGGACAATTGCAAATCAATGAGCTATCAATTCT
1 GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCT
34194472 CTCACAACTG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (50 bp):
GCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTCTGATGGTTGG
Found at i:34216480 original size:2 final size:2
Alignment explanation
Indices: 34216469--34216517 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
34216459 TTAAAACAAT
34216469 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34216510 TA TA TA TA
1 TA TA TA TA
34216518 AAATAATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34220121 original size:17 final size:17
Alignment explanation
Indices: 34220099--34220133 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34220089 TTAAATTTTA
34220099 ATAATAATATAATATAT
1 ATAATAATATAATATAT
*
34220116 ATAATAATATATTATAT
1 ATAATAATATAATATAT
34220133 A
1 A
34220134 ATTATTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATATAATATAT
Found at i:34220134 original size:12 final size:12
Alignment explanation
Indices: 34220105--34220141 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34220095 TTTAATAATA
34220105 ATATAATATA-T
1 ATATAATATATT
34220116 ATAATAATATATT
1 AT-ATAATATATT
34220129 ATATAAT-TATT
1 ATATAATATATT
34220140 AT
1 AT
34220142 TGAAATCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 13 0.54
13 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATAATATATT
Found at i:34221048 original size:23 final size:23
Alignment explanation
Indices: 34221020--34221063 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34221010 AATGTGTAAA
*
34221020 TATTTTTATAAAATAAAATTTAT
1 TATTTTAATAAAATAAAATTTAT
* *
34221043 TATTTTAATAAATTATAATTT
1 TATTTTAATAAAATAAAATTT
34221064 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTTAATAAAATAAAATTTAT
Found at i:34225533 original size:8 final size:9
Alignment explanation
Indices: 34225493--34225530 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
34225483 TTTTTTTTCA
34225493 TTTAAAATT
1 TTTAAAATT
34225502 TTTAAAATT
1 TTTAAAATT
34225511 TTTAAAATT
1 TTTAAAATT
34225520 TTTAAAATT
1 TTTAAAATT
34225529 TT
1 TT
34225531 AAATTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTAAAATT
Found at i:34230580 original size:16 final size:16
Alignment explanation
Indices: 34230541--34230584 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
34230531 GAAAAAAAAT
34230541 TTAAT-TATT-TTTTA
1 TTAATATATTATTTTA
*
34230555 -TAA-ATTTTATTTTA
1 TTAATATATTATTTTA
34230569 TTAATATATTATTTTA
1 TTAATATATTATTTTA
34230585 AATGTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 5 0.21
15 3 0.12
16 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTAATATATTATTTTA
Found at i:34232953 original size:9 final size:10
Alignment explanation
Indices: 34232936--34232979 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
34232926 TCTTAACAAA
34232936 AATTACAAAAT
1 AATT-CAAAAT
34232947 AA-TCAAAAT
1 AATTCAAAAT
* *
34232956 AATTTAAAAA
1 AATTCAAAAT
34232966 AATTCAAAAT
1 AATTCAAAAT
34232976 AATT
1 AATT
34232980 TCTTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 8 0.29
10 18 0.64
11 2 0.07
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTCAAAAT
Found at i:34233013 original size:19 final size:20
Alignment explanation
Indices: 34232942--34233014 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
34232932 CAAAAATTAC
34232942 AAAATAATCAAAATAATTTA-
1 AAAA-AATCAAAATAATTTAT
*
34232962 AAAAAATTCAAAATAATTTCT
1 AAAAAA-TCAAAATAATTTAT
* * *
34232983 TAAAATTAAAAAT-ATTTAT
1 AAAAAATCAAAATAATTTAT
34233002 AAAAAATCAAAAT
1 AAAAAATCAAAAT
34233015 TTATATTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 17 0.40
20 22 0.51
21 4 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATCAAAATAATTTAT
Found at i:34233067 original size:18 final size:18
Alignment explanation
Indices: 34233043--34233092 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
34233033 AATTTCTTTT
34233043 AAAAATTCTAAAAATATA
1 AAAAATTCTAAAAATATA
* * * *
34233061 TAAAATTTTAAAATTTTA
1 AAAAATTCTAAAAATATA
34233079 AAAAATTTCTAAAA
1 AAAAA-TTCTAAAA
34233093 TAATAACTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATTCTAAAAATATA
Found at i:34246682 original size:10 final size:10
Alignment explanation
Indices: 34246631--34246695 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
34246621 CAAAACATAG
34246631 AAAATTATTTA
1 AAAATTA-TTA
*
34246642 AAAACTATTA
1 AAAATTATTA
* *
34246652 AGAATGA-TA
1 AAAATTATTA
*
34246661 AGAAATTGTTA
1 A-AAATTATTA
34246672 AAAATTATT-
1 AAAATTATTA
*
34246681 AAAATTAATA
1 AAAATTATTA
34246691 AAAAT
1 AAAAT
34246696 CTAGAAATTG
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
9 11 0.26
10 22 0.52
11 9 0.21
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (10 bp):
AAAATTATTA
Found at i:34251052 original size:3 final size:3
Alignment explanation
Indices: 34251044--34251068 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34251034 AAAAAATTCT
34251044 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
34251069 GGTAGTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34262578 original size:31 final size:30
Alignment explanation
Indices: 34262540--34262613 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
34262530 TTAAATGAAT
34262540 TATTTTTTATTATT-TGGATATTGTTAATAAA
1 TATTTTTTATT-TTAT-GATATTGTTAATAAA
* *
34262571 TATTTTTTTAGTTTTATGATATTTTTATTAAA
1 TA-TTTTTTA-TTTTATGATATTGTTAATAAA
*
34262603 TATTTTATATT
1 TATTTTTTATT
34262614 CAGATTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 2 0.05
31 8 0.22
32 24 0.65
33 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (30 bp):
TATTTTTTATTTTATGATATTGTTAATAAA
Done.