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 116 of 132
Found at i:35250454 original size:18 final size:17
Alignment explanation
Indices: 35250416--35250459 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
35250406 CACCTTTAAA
35250416 TTTTCTTTTTAAATTCGT
1 TTTTC-TTTTAAATTCGT
35250434 TTTATCTTTTAAATTTC-T
1 TTT-TCTTTTAAA-TTCGT
35250452 TTTTCTTT
1 TTTTCTTT
35250460 ATTTTTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTCTTTTAAATTCGT
Found at i:35251288 original size:175 final size:175
Alignment explanation
Indices: 35250997--35251346 Score: 646
Period size: 175 Copynumber: 2.0 Consensus size: 175
35250987 GTATGTTCTC
35250997 TTCAAAATTCAATAATTGAAAATGGTACAAAATAAATTATGCCTTTAAGGATCGTATTTTAAATT
1 TTCAAAATTCAATAATTGAAAATGGTACAAAATAAATTATGCCTTTAAGGATCGTATTTTAAATT
* **
35251062 TCACTCGAGTTTTCAAACTTTAAACAATCAGGACCGGAAAATAATTGACAAGGTACCAATTTTGG
66 TCACTCGAGTATTCAAACTTTAAACAATCAGGACCAAAAAATAATTGACAAGGTACCAATTTTGG
*
35251127 GCGTGTGAGGGTGTTAATCCTTCCTCACACGTAACCGACTCCCGA
131 GCGTGTGAGGGTGTTAATCCTTCCTCACACGTAACCAACTCCCGA
*
35251172 TTCAAAATTCAATAATTGAAAATGGTACAAAATAAATTATGTCTTTAAGGATCGTATTTTAAATT
1 TTCAAAATTCAATAATTGAAAATGGTACAAAATAAATTATGCCTTTAAGGATCGTATTTTAAATT
35251237 TCACTCGAGTATTCAAACTTTAAACAATCAGGACCAAAAAATAATTGACAAGGTACCAATTTTGG
66 TCACTCGAGTATTCAAACTTTAAACAATCAGGACCAAAAAATAATTGACAAGGTACCAATTTTGG
*
35251302 GCGTGTGAGGGTGTTAATCCTTCCTCACATGTAACCAACTCCCGA
131 GCGTGTGAGGGTGTTAATCCTTCCTCACACGTAACCAACTCCCGA
35251347 ACACGTTTTT
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 169 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (175 bp):
TTCAAAATTCAATAATTGAAAATGGTACAAAATAAATTATGCCTTTAAGGATCGTATTTTAAATT
TCACTCGAGTATTCAAACTTTAAACAATCAGGACCAAAAAATAATTGACAAGGTACCAATTTTGG
GCGTGTGAGGGTGTTAATCCTTCCTCACACGTAACCAACTCCCGA
Found at i:35252814 original size:15 final size:15
Alignment explanation
Indices: 35252794--35252824 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35252784 AAAGAACTAC
35252794 TGTCTTAAAAGCAAA
1 TGTCTTAAAAGCAAA
35252809 TGTCTTAAAAGCAAA
1 TGTCTTAAAAGCAAA
35252824 T
1 T
35252825 CCACTCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TGTCTTAAAAGCAAA
Found at i:35258065 original size:30 final size:30
Alignment explanation
Indices: 35258029--35258089 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
35258019 CAATCTAGAG
35258029 AATAACAGAATTAAAAACTCAGGGAACTGC
1 AATAACAGAATTAAAAACTCAGGGAACTGC
35258059 AATAACAGAATTAAAAACTCAGGGAACTGC
1 AATAACAGAATTAAAAACTCAGGGAACTGC
35258089 A
1 A
35258090 TCTAAAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (30 bp):
AATAACAGAATTAAAAACTCAGGGAACTGC
Found at i:35259426 original size:78 final size:78
Alignment explanation
Indices: 35259297--35259456 Score: 304
Period size: 78 Copynumber: 2.1 Consensus size: 78
35259287 TTTCAAAACT
35259297 ATTTTCCTACAGGCAGGTGTAATTAGAAGTAGTTCTAGTGAAAAAGATGATTTTATTATGAGTTA
1 ATTTTCCTACAGGCAGGTGTAATTAGAAGTAGTTCTAGTGAAAAAGATGATTTTATTATGAGTTA
35259362 TAATTAATTTAAA
66 TAATTAATTTAAA
35259375 ATTTTCCTACAGGCAGGTGTAATTAGAAGT-GATTCTAGTGAAAAAGATGATTTTATTATGAGTT
1 ATTTTCCTACAGGCAGGTGTAATTAGAAGTAG-TTCTAGTGAAAAAGATGATTTTATTATGAGTT
35259439 ATAATTAATTTAAA
65 ATAATTAATTTAAA
35259453 ATTT
1 ATTT
35259457 GGTTATTTGT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
77 1 0.01
78 80 0.99
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (78 bp):
ATTTTCCTACAGGCAGGTGTAATTAGAAGTAGTTCTAGTGAAAAAGATGATTTTATTATGAGTTA
TAATTAATTTAAA
Found at i:35263046 original size:23 final size:24
Alignment explanation
Indices: 35263010--35263054 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
35263000 AAATTACATA
*
35263010 AAATAATTAATTTTTTA-AATTAT
1 AAATAAATAATTTTTTATAATTAT
*
35263033 AAATAAATATTTTTTTATAATT
1 AAATAAATAATTTTTTATAATT
35263055 TTTAATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATAAATAATTTTTTATAATTAT
Found at i:35264039 original size:3 final size:3
Alignment explanation
Indices: 35264031--35264063 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
35264021 ATCTTTCAAT
35264031 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35264064 CCATTTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35267648 original size:31 final size:29
Alignment explanation
Indices: 35267594--35267662 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
35267584 TGAAAAATAC
*
35267594 AAGACTAAAATTAAGTAATTTGAAAAGCACT
1 AAGACTAAAATTAAGTAAATTG--AAGCACT
* * * *
35267625 AAGACTAAACTTGATTAAATTGAAGTACT
1 AAGACTAAAATTAAGTAAATTGAAGCACT
35267654 AAGACTAAA
1 AAGACTAAA
35267663 TCTATAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
31 18 0.55
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (29 bp):
AAGACTAAAATTAAGTAAATTGAAGCACT
Found at i:35269021 original size:21 final size:21
Alignment explanation
Indices: 35268997--35269037 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35268987 TTTTTTCAAT
*
35268997 TATCTTAATTTTTTTTAATTA
1 TATCTTAATTTTTATTAATTA
*
35269018 TATCTTACTTTTTATTAATT
1 TATCTTAATTTTTATTAATT
35269038 TAGATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
TATCTTAATTTTTATTAATTA
Found at i:35269176 original size:24 final size:23
Alignment explanation
Indices: 35269119--35269177 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
35269109 AAAATAAAGC
*
35269119 ATAAAGATT-TATATTATTAATT
1 ATAAAGATTATATATTATAAATT
*
35269141 A-AATTGAATTATATATTATAAATT
1 ATAA-AG-ATTATATATTATAAATT
35269165 ATAAAGATT-TATA
1 ATAAAGATTATATA
35269178 CTCTACCCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 2 0.07
22 6 0.20
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (23 bp):
ATAAAGATTATATATTATAAATT
Found at i:35286273 original size:43 final size:43
Alignment explanation
Indices: 35286225--35286311 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
35286215 ACTTGTTGGC
* *
35286225 TTGATTACACTTGTCCTACATCTTCTAGCTTTTATGCAAATCA
1 TTGATTACACTTGTCCGACATCTTCTAACTTTTATGCAAATCA
* *
35286268 TTGATTACACTTGTCCGACATCTTTTAACTTTTATGTAAATCA
1 TTGATTACACTTGTCCGACATCTTCTAACTTTTATGCAAATCA
35286311 T
1 T
35286312 GTATCAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (43 bp):
TTGATTACACTTGTCCGACATCTTCTAACTTTTATGCAAATCA
Found at i:35290984 original size:31 final size:31
Alignment explanation
Indices: 35290946--35291008 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
35290936 ACATTGAGAA
35290946 TGAACATGGACA-AACCTATGTCCAGATTCAT
1 TGAACATGGACATAA-CTATGTCCAGATTCAT
*
35290977 TGAACATGGACATAACTTTGTCCAGATTCAT
1 TGAACATGGACATAACTATGTCCAGATTCAT
35291008 T
1 T
35291009 CTAGACTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (31 bp):
TGAACATGGACATAACTATGTCCAGATTCAT
Found at i:35301339 original size:18 final size:18
Alignment explanation
Indices: 35301316--35301361 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
35301306 TGTTTTTAAC
*
35301316 TAATATATTAATTAATAA
1 TAATATATTAATAAATAA
35301334 TAATAT-TATAATAAATAA
1 TAATATAT-TAATAAATAA
*
35301352 TAAAATATTA
1 TAATATATTA
35301362 TTATTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATATTAATAAATAA
Found at i:35303928 original size:18 final size:19
Alignment explanation
Indices: 35303873--35303934 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
35303863 ATTAATTATT
*
35303873 ATTTTTT-TGAAATTTATTTA
1 ATTTTTTAT-AAATTTA-ATA
35303893 ATATTTTTATAAATTTTAATA
1 AT-TTTTTATAAA-TTTAATA
35303914 ATTTTTTAT-AATTT-ATA
1 ATTTTTTATAAATTTAATA
35303931 ATTT
1 ATTT
35303935 AAAAAAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 7 0.18
18 3 0.08
19 2 0.05
20 9 0.24
21 12 0.32
22 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTTATAAATTTAATA
Found at i:35303932 original size:20 final size:21
Alignment explanation
Indices: 35303891--35303932 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
35303881 GAAATTTATT
35303891 TAATATTTTTATAAATTTTAA
1 TAATATTTTTATAAATTTTAA
35303912 TAAT-TTTTTAT-AATTTATAA
1 TAATATTTTTATAAATTT-TAA
35303932 T
1 T
35303933 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATTTTTATAAATTTTAA
Found at i:35304937 original size:24 final size:24
Alignment explanation
Indices: 35304908--35304957 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35304898 TTTACATATT
* *
35304908 TATTTTTA-AATTTATTAAATAATA
1 TATTTTTATAATAT-TTAAAAAATA
35304932 TATTTTTATAATATTTAAAAAATA
1 TATTTTTATAATATTTAAAAAATA
35304956 TA
1 TA
35304958 CATTTGCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTTATAATATTTAAAAAATA
Found at i:35305528 original size:20 final size:18
Alignment explanation
Indices: 35305495--35305533 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
35305485 TGATATTTTA
35305495 TTTAATTTTAATATATAT
1 TTTAATTTTAATATATAT
35305513 TTTAATTTTGACATATATAT
1 TTTAATTTT-A-ATATATAT
35305533 T
1 T
35305534 AAGAATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATTTTAATATATAT
Found at i:35305867 original size:11 final size:11
Alignment explanation
Indices: 35305851--35305898 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
35305841 AATTTTTCCC
*
35305851 TGTTATTTTGT
1 TGTTATGTTGT
*
35305862 TGTTATGTTAT
1 TGTTATGTTGT
* **
35305873 TGTTTTACTGT
1 TGTTATGTTGT
35305884 TGTTATGTTGT
1 TGTTATGTTGT
35305895 TGTT
1 TGTT
35305899 TTACTACCAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.10, C:0.02, G:0.21, T:0.67
Consensus pattern (11 bp):
TGTTATGTTGT
Found at i:35305884 original size:22 final size:22
Alignment explanation
Indices: 35305859--35305903 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35305849 CCTGTTATTT
35305859 TGTTGTTATGTTATTGTTTTAC
1 TGTTGTTATGTTATTGTTTTAC
*
35305881 TGTTGTTATGTTGTTGTTTTAC
1 TGTTGTTATGTTATTGTTTTAC
35305903 T
1 T
35305904 ACCATTTCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.20, T:0.64
Consensus pattern (22 bp):
TGTTGTTATGTTATTGTTTTAC
Found at i:35306043 original size:17 final size:18
Alignment explanation
Indices: 35306021--35306058 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
35306011 GTTGTAACAA
*
35306021 TATAAATATTATTTAA-G
1 TATAAAAATTATTTAATG
*
35306038 TATAAAAATTTTTTAATG
1 TATAAAAATTATTTAATG
35306056 TAT
1 TAT
35306059 TTTTAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAAAAATTATTTAATG
Found at i:35307018 original size:44 final size:45
Alignment explanation
Indices: 35306963--35307054 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 45
35306953 ATAATTATAA
* *
35306963 ATTACAATTATAATTATTTTTAAACATGTAATTATCACAACTTCT
1 ATTACAATTATAAGTATTTTTAAACATATAATTATCACAACTTCT
* *
35307008 ATTA-AATTATAAGTATTTTTAAATATATAATTATCACAATTTCT
1 ATTACAATTATAAGTATTTTTAAACATATAATTATCACAACTTCT
35307052 ATT
1 ATT
35307055 TTATTTCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (45 bp):
ATTACAATTATAAGTATTTTTAAACATATAATTATCACAACTTCT
Found at i:35312324 original size:2 final size:2
Alignment explanation
Indices: 35312319--35312344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35312309 AAAAGAAAAG
35312319 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
35312345 CCTCTGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35315905 original size:29 final size:29
Alignment explanation
Indices: 35315862--35315922 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
35315852 ATCACCCAAA
* *
35315862 AAATATTTTTACTAACTTTTAAGAAATTT
1 AAATATTTTTACTAACTTTTAAAAAATCT
* * *
35315891 AAATCTTTTTTCTAATTTTTAAAAAATCT
1 AAATATTTTTACTAACTTTTAAAAAATCT
35315920 AAA
1 AAA
35315923 ACCCCACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATATTTTTACTAACTTTTAAAAAATCT
Found at i:35331935 original size:9 final size:9
Alignment explanation
Indices: 35331916--35332009 Score: 59
Period size: 9 Copynumber: 10.4 Consensus size: 9
35331906 AGATAAATGT
35331916 AAAAT-TAA
1 AAAATATAA
35331924 AAAATATAA
1 AAAATATAA
*
35331933 AAAAAATAA
1 AAAATATAA
* *
35331942 TAATTATTTAA
1 -AA-AATATAA
* *
35331953 AGAGTATAA
1 AAAATATAA
*
35331962 AAATTATTAA
1 AAAATA-TAA
*
35331972 AAAATCT-A
1 AAAATATAA
* *
35331980 AATATGTAA
1 AAAATATAA
35331989 AAAAT-TAA
1 AAAATATAA
35331997 AAAATATAA
1 AAAATATAA
35332006 AAAA
1 AAAA
35332010 AACAGCTCAT
Statistics
Matches: 65, Mismatches: 15, Indels: 11
0.71 0.16 0.12
Matches are distributed among these distances:
8 19 0.29
9 32 0.49
10 10 0.15
11 4 0.06
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAATATAA
Found at i:35332006 original size:17 final size:17
Alignment explanation
Indices: 35331916--35332009 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
35331906 AGATAAATGT
35331916 AAAATTAAAAAATATAAA
1 AAAATTAAAAAATAT-AA
* * *
35331934 AAAAATAATAATTATTTAA
1 AAAATTAA-AA-AATATAA
* * *
35331953 AGAGTATAAAAATTATTAA
1 AAAAT-TAAAAAATA-TAA
* *
35331972 AAAATCT-AAATATGTAA
1 AAAAT-TAAAAAATATAA
35331989 AAAATTAAAAAATATAA
1 AAAATTAAAAAATATAA
35332006 AAAA
1 AAAA
35332010 AACAGCTCAT
Statistics
Matches: 54, Mismatches: 17, Indels: 11
0.66 0.21 0.13
Matches are distributed among these distances:
16 1 0.02
17 20 0.37
18 12 0.22
19 15 0.28
20 6 0.11
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATTAAAAAATATAA
Found at i:35332320 original size:21 final size:21
Alignment explanation
Indices: 35332294--35332338 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35332284 TAGTATTAAC
35332294 ATTTATGATTTAAAAAATATA
1 ATTTATGATTTAAAAAATATA
** * *
35332315 ATTTATTCTTTAATAAATTTA
1 ATTTATGATTTAAAAAATATA
35332336 ATT
1 ATT
35332339 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTATGATTTAAAAAATATA
Found at i:35332662 original size:12 final size:12
Alignment explanation
Indices: 35332641--35332675 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35332631 ATTTTCTTCA
35332641 TCATCATCGTTG
1 TCATCATCGTTG
* *
35332653 TCATCCTCGTCG
1 TCATCATCGTTG
35332665 TCATCATCGTT
1 TCATCATCGTT
35332676 ATCACTATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.40
Consensus pattern (12 bp):
TCATCATCGTTG
Found at i:35335834 original size:14 final size:15
Alignment explanation
Indices: 35335808--35335839 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
35335798 TTAAAATTTG
35335808 AAAAATACAGAAATT
1 AAAAATACAGAAATT
35335823 AAAAATAC-GAAATT
1 AAAAATACAGAAATT
35335837 AAA
1 AAA
35335840 GTACAATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAATACAGAAATT
Found at i:35337724 original size:19 final size:19
Alignment explanation
Indices: 35337662--35337730 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
35337652 ATTGTGTACC
*
35337662 AAATTATAAGAAAACTTAAATCA
1 AAATTATAA-AAAA-TTAAA--G
** *
35337685 AAATTATAAAAAGGTACAG
1 AAATTATAAAAAATTAAAG
35337704 AAATTATAAAAAATTAAAG
1 AAATTATAAAAAATTAAAG
*
35337723 AAAGTATA
1 AAATTATA
35337731 TCTTATAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 23 0.61
21 3 0.08
22 3 0.08
23 9 0.24
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.25
Consensus pattern (19 bp):
AAATTATAAAAAATTAAAG
Found at i:35338243 original size:10 final size:9
Alignment explanation
Indices: 35338203--35338263 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 9
35338193 TTCTAGACAA
35338203 TTTTAA-TT
1 TTTTAATTT
35338211 TTTTAACTTT
1 TTTTAA-TTT
*
35338221 TTATATATTT
1 TTTTA-ATTT
35338231 TTTTAGATTT
1 TTTTA-ATTT
35338241 TTTTGAAATTT
1 TTTT--AATTT
*
35338252 TTGTAATTT
1 TTTTAATTT
35338261 TTT
1 TTT
35338264 AAAAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 21 0.49
11 8 0.19
12 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (9 bp):
TTTTAATTT
Found at i:35338305 original size:19 final size:19
Alignment explanation
Indices: 35338284--35338319 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35338274 ATTTTGGAAT
*
35338284 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
35338302 TTTTAAAAATTATTTTAA
1 TTTTAAAAATTATTTTAA
35338320 GTTTGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:35340434 original size:509 final size:509
Alignment explanation
Indices: 35339477--35341006 Score: 3060
Period size: 509 Copynumber: 3.0 Consensus size: 509
35339467 CCAAATATCA
35339477 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
1 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
35339542 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
66 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
35339607 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
131 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
35339672 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
196 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
35339737 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
261 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
35339802 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
326 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
35339867 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
391 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
35339932 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
456 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
35339986 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
1 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
35340051 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
66 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
35340116 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
131 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
35340181 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
196 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
35340246 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
261 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
35340311 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
326 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
35340376 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
391 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
35340441 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
456 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
35340495 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
1 TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
35340560 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
66 TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
35340625 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
131 GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
35340690 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
196 GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
35340755 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
261 AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
35340820 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
326 AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
35340885 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
391 TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
35340950 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
456 TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
35341004 TGT
1 TGT
35341007 CCATAAAGCG
Statistics
Matches: 1021, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
509 1021 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (509 bp):
TGTGAAATTTTCAGTTGCCTTATACTTAGGAAATATGATTAATTAGTTTGAAATTCAATGCTTGA
TCTCTAATCTCGGGTTTATATTAGTTAGTTTAGTAAGTTCAATCTTCGTAGGATCATTTTGAGAT
GGACTCCTTTTCATAGAGAACATGTCACTCCGGATGGTACTACAATATGCCCATGTTCAAAGTGT
GTGAATAGGGAGTCTCATAATATCAAGGATACTTAGATTTGGGTTTAATTCGGGTTGTAGAAGAT
AGGTACATCATGGGGAAAATGGACAACATCTCCACTTCCGATGACGAAATGGGAGACATTCTGTT
AGACAACAAGGGAGAACTTACTATAATATTGGAAGAGAAACAACTGATGATTTGGAGAATTTGCC
TATTCCTAAAAGTGTTCAATACAAAGGAGATAACTCATTGGAAGAGTTAGAATAAGAGCTGTACA
TCGGGTGTAAGCAATATTCTGTGCTTAATTTTATTGTAAAGATGATGAACAACT
Found at i:35341775 original size:18 final size:19
Alignment explanation
Indices: 35341716--35341785 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
35341706 TTTCACAACA
35341716 AAAATTACAAAATAATTT-T
1 AAAATT-CAAAATAATTTAT
* *
35341735 AAAATTTTAAAATAATTTTT
1 AAAA-TTCAAAATAATTTAT
35341755 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
35341773 AAAATTCCAAAAT
1 AAAATT-CAAAAT
35341786 TTATAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.24
19 27 0.60
20 7 0.16
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:35341789 original size:17 final size:17
Alignment explanation
Indices: 35341748--35341791 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
35341738 ATTTTAAAAT
*
35341748 AATTTTTAAAATTCAAA
1 AATTTATAAAATTCAAA
*
35341765 ATATTTATAAAATTCCAA
1 A-ATTTATAAAATTCAAA
35341783 AATTTATAA
1 AATTTATAA
35341792 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTATAAAATTCAAA
Found at i:35341811 original size:11 final size:11
Alignment explanation
Indices: 35341797--35341829 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
35341787 TATAATTTTT
35341797 AAAAAATT--A
1 AAAAAATTAAA
35341806 AAAAAATTAAA
1 AAAAAATTAAA
35341817 AAAAAATTAAA
1 AAAAAATTAAA
35341828 AA
1 AA
35341830 TATATAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:35343036 original size:257 final size:257
Alignment explanation
Indices: 35342571--35343076 Score: 746
Period size: 257 Copynumber: 2.0 Consensus size: 257
35342561 CAATCATTTA
*
35342571 CATAAGCACATATTAAGCCCAAAAACCAACTCAACCTAGGAACATGCCATACTTAAACAAAACGA
1 CATAAACACATATTAAGCCCAAAAACCAACTCAACCTAGGAACATGCCATACTT--ACAAAACGA
* *
35342636 GATTTATACAAACATTGTTGAGTCGGGGGATCACTTCTTAGATGTTGGATCTATTGCTCGAACTC
64 GATTTATACAAACATTGTTGAGTCGGGGGATCACTTCTTAGATGCTGGATCTACTGCTCGAACTC
* ** * **
35342701 TTGGGAATCTATTATACATGTGCACGGAGAAAACAAACTGTACACTGAGCAATAAAGCTCAATGG
129 TCGGGAATCTATTATACATGCACACAGAGAAAACAAACCATACACTGAGCAATAAAGCTCAATGG
*
35342766 TACCTTCATAAAACATAGTAAATAAACATAACATTACTAACTTGTTATATTACATTACATATATG
194 TACCTTCATAAAACAAAGTAAATAAACATAACATTACT-ACTTGTTATATTACATTACATATATG
** * * * *
35342831 CATAAACACATATTAAGCCCCCAAACCAACTCAATCTAGGTACATGCCATACTT-TAAAATGAGA
1 CATAAACACATATTAAGCCCAAAAACCAACTCAACCTAGGAACATGCCATACTTACAAAACGAGA
*
35342895 TTTATACAAACATTGTTGAGTCGAGGGG-TCACTTCTTGGATGCTGGATCTACTGCTCGAACTCT
66 TTTATACAAACATTGTTGAGTCG-GGGGATCACTTCTTAGATGCTGGATCTACTGCTCGAACTCT
* * * *** *
35342959 CGGTAATCTATTCTACTTGCACACAGAGAAAACAAACCATATGTTGAGTAATAAAGCTCAATGGT
130 CGGGAATCTATTATACATGCACACAGAGAAAACAAACCATACACTGAGCAATAAAGCTCAATGGT
35343024 ACCTTCATAAAACAAAGTAAATAAACATAACATTACTACTTGTTATATTACAT
195 ACCTTCATAAAACAAAGTAAATAAACATAACATTACTACTTGTTATATTACAT
35343077 ATATGCATAA
Statistics
Matches: 221, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
256 16 0.07
257 152 0.69
258 4 0.02
260 49 0.22
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (257 bp):
CATAAACACATATTAAGCCCAAAAACCAACTCAACCTAGGAACATGCCATACTTACAAAACGAGA
TTTATACAAACATTGTTGAGTCGGGGGATCACTTCTTAGATGCTGGATCTACTGCTCGAACTCTC
GGGAATCTATTATACATGCACACAGAGAAAACAAACCATACACTGAGCAATAAAGCTCAATGGTA
CCTTCATAAAACAAAGTAAATAAACATAACATTACTACTTGTTATATTACATTACATATATG
Found at i:35346127 original size:12 final size:12
Alignment explanation
Indices: 35346110--35346205 Score: 54
Period size: 12 Copynumber: 7.8 Consensus size: 12
35346100 ATAACATTTA
*
35346110 AACAACCAAAAT
1 AACAACAAAAAT
35346122 AACAACAAAAAT
1 AACAACAAAAAT
*
35346134 AGCAA-AAATAGCA-
1 AACAACAAA-A--AT
* *
35346147 ACACAACTAAAAC
1 A-ACAACAAAAAT
35346160 AGA-AACAAAAAT
1 A-ACAACAAAAAT
* *
35346172 AATAGCAAAAAT
1 AACAACAAAAAT
*
35346184 AGCAACAAAAAT
1 AACAACAAAAAT
*
35346196 AACAGCAAAA
1 AACAACAAAA
35346206 CAATAGAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
11 4 0.06
12 50 0.78
13 3 0.05
14 5 0.08
15 2 0.03
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:35346182 original size:24 final size:24
Alignment explanation
Indices: 35346155--35346205 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
35346145 CAACACAACT
*
35346155 AAAACAGAAACAAAAATAATAGCA
1 AAAACAGAAACAAAAATAACAGCA
* *
35346179 AAAATAGCAACAAAAATAACAGCA
1 AAAACAGAAACAAAAATAACAGCA
35346203 AAA
1 AAA
35346206 CAATAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.71, C:0.14, G:0.08, T:0.08
Consensus pattern (24 bp):
AAAACAGAAACAAAAATAACAGCA
Found at i:35347987 original size:183 final size:183
Alignment explanation
Indices: 35347674--35348052 Score: 627
Period size: 183 Copynumber: 2.1 Consensus size: 183
35347664 AACCAAGATT
*
35347674 CAAAGTCTTGATAATCTTGCTCAACTCCAAGGATGCTCAAATCCCATCCAAAGTTGGTCCTCAAT
1 CAAAATCTTGATAATCTTGCTCAACTCCAAGGATGCTCAAATCCCATCCAAAGTTGGTCCTCAAT
* * *
35347739 TTTTGTGATCTTTTGAGCTTGTCAAGTAGGCTTTGTAGAAGGTTAAGCCCAACATGTTATTGGGC
66 TTTTGTGATCTTTTGAGCTTGTCAAGTAGGCTTTGTAAAAGGATAAACCCAACATGTTATTGGGC
* **
35347804 TGAAAATTGGGCCCTTATACTCGCATCAACATGTTT-CTAAACAACATTGAAAG
131 TGAAAATTGAGCCCCCATACTCGCATCAACATGTTTCCT-AACAACATTGAAAG
* *
35347857 CAAAATCTTGATAATCTTGCTCAACTCCAAGGATGCTCGAATCCCATCCAAAGTTGGTCCTTGAA
1 CAAAATCTTGATAATCTTGCTCAACTCCAAGGATGCTCAAATCCCATCCAAAGTTGGTCC-TCAA
*
35347922 -TTTTGTGATCTTTTGAGCTTGTCAAGTAGGCTTTGTAAAAGGATAAACCCAACATGTTCTTGGG
65 TTTTTGTGATCTTTTGAGCTTGTCAAGTAGGCTTTGTAAAAGGATAAACCCAACATGTTATTGGG
*
35347986 CTGAAAATTGAGCCCCCATAGTCGCATCAACATGTTTCCTAACAACATTGAAAG
130 CTGAAAATTGAGCCCCCATACTCGCATCAACATGTTTCCTAACAACATTGAAAG
35348040 CAAAATCTTGATA
1 CAAAATCTTGATA
35348053 CAAAGCTTAT
Statistics
Matches: 183, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
183 178 0.97
184 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (183 bp):
CAAAATCTTGATAATCTTGCTCAACTCCAAGGATGCTCAAATCCCATCCAAAGTTGGTCCTCAAT
TTTTGTGATCTTTTGAGCTTGTCAAGTAGGCTTTGTAAAAGGATAAACCCAACATGTTATTGGGC
TGAAAATTGAGCCCCCATACTCGCATCAACATGTTTCCTAACAACATTGAAAG
Found at i:35361938 original size:2 final size:2
Alignment explanation
Indices: 35361931--35361956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35361921 CGATCAATCC
35361931 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
35361957 AACTGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35367468 original size:12 final size:12
Alignment explanation
Indices: 35367452--35367508 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
35367442 CACAAACAAG
*
35367452 CTCGTTTATTGG
1 CTCGTTTATTGA
**
35367464 CTCGTTTATAAA
1 CTCGTTTATTGA
35367476 CTCGTTTATTGA
1 CTCGTTTATTGA
35367488 CTCGTTTA-TGA
1 CTCGTTTATTGA
35367499 CTCGTTTATT
1 CTCGTTTATT
35367509 TATTAATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 11 0.28
12 28 0.72
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:35367646 original size:23 final size:23
Alignment explanation
Indices: 35367606--35367682 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
35367596 ATTGTTCGTG
* *
35367606 ACATGTTCAATTATATGTTTATGA
1 ACATGTTCGATTA-ATGTTAATGA
* **
35367630 ACATGTTCGTTTAATGTTCGTGA
1 ACATGTTCGATTAATGTTAATGA
*
35367653 ACATATTCGATTAA-GTTAAATGA
1 ACATGTTCGATTAATGTT-AATGA
35367676 ACATGTT
1 ACATGTT
35367683 TGTGGACATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
22 3 0.07
23 29 0.67
24 11 0.26
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (23 bp):
ACATGTTCGATTAATGTTAATGA
Found at i:35369144 original size:24 final size:24
Alignment explanation
Indices: 35369117--35369164 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35369107 TGCTCGTCAT
35369117 GACCTTGAGCAACGACGTCGCCAC
1 GACCTTGAGCAACGACGTCGCCAC
35369141 GACCTTGAGCAACGACGTCGCCAC
1 GACCTTGAGCAACGACGTCGCCAC
35369165 ATGGACTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (24 bp):
GACCTTGAGCAACGACGTCGCCAC
Found at i:35370081 original size:24 final size:23
Alignment explanation
Indices: 35370054--35370109 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
35370044 AACATCCAAG
35370054 TTACACTTTAATTAAAA-ATTATCA
1 TTACACTTTAA-TAAAATATT-TCA
*
35370078 TTACACATTTCATAAAATATTTCA
1 TTACAC-TTTAATAAAATATTTCA
35370102 TTACACTT
1 TTACACTT
35370110 GGTGAGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 20 0.69
25 7 0.24
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (23 bp):
TTACACTTTAATAAAATATTTCA
Found at i:35380321 original size:23 final size:24
Alignment explanation
Indices: 35380275--35380326 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
35380265 TTAAGTTGTT
****
35380275 GCCTTTGAGTCTTTGTTTGTTAA-
1 GCCTTTGAGTCTTTGTGCAATAAG
35380298 GCCTTTGAGTCTTTGTGCAATAAG
1 GCCTTTGAGTCTTTGTGCAATAAG
35380322 GCCTT
1 GCCTT
35380327 CATCTCACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.44
Consensus pattern (24 bp):
GCCTTTGAGTCTTTGTGCAATAAG
Found at i:35384341 original size:15 final size:15
Alignment explanation
Indices: 35384317--35384350 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35384307 TTCTTAAATT
35384317 TTTTTCTTTTAGTTG
1 TTTTTCTTTTAGTTG
* *
35384332 TTTTTGTTTTATTTG
1 TTTTTCTTTTAGTTG
35384347 TTTT
1 TTTT
35384351 CATAAATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTAGTTG
Found at i:35384618 original size:10 final size:10
Alignment explanation
Indices: 35384523--35384577 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
35384513 TATTTATTGA
*
35384523 TAAAAACTATT
1 TAAAAATTA-T
35384534 TAAAAATTAT
1 TAAAAATTAT
*
35384544 TAATAATTA-
1 TAAAAATTAT
35384553 TAAGAAATTA-
1 TAA-AAATTAT
35384563 TAAAAATTTAT
1 TAAAAA-TTAT
35384574 TAAA
1 TAAA
35384578 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 6 0.16
10 20 0.53
11 12 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:35385221 original size:10 final size:9
Alignment explanation
Indices: 35385208--35385265 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
35385198 TTTTTATGCT
35385208 TTTTATAATA
1 TTTT-TAATA
35385218 TTTTGTAA-A
1 TTTT-TAATA
*
35385227 -TTTTATTAA
1 TTTTTAAT-A
35385236 TTTTTAATA
1 TTTTTAATA
35385245 TTTTT-ATA
1 TTTTTAATA
35385253 TTTTTAGATA
1 TTTTTA-ATA
35385263 TTT
1 TTT
35385266 ATTCATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.05
8 11 0.28
9 8 0.20
10 19 0.47
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTAATA
Found at i:35385221 original size:28 final size:27
Alignment explanation
Indices: 35385190--35385361 Score: 79
Period size: 28 Copynumber: 6.1 Consensus size: 27
35385180 TTTTAGTTTG
**
35385190 TTTTGTAATTTTTATGCTTTTTATAATA
1 TTTTGTAATTTTTATGAATTTT-TAATA
* *
35385218 TTTTGTAAATTTTATTAATTTTTAATA
1 TTTTGTAATTTTTATGAATTTTTAATA
*
35385245 TTTT-TATATTTTTA-GATATTTATTCATAA
1 TTTTGTA-ATTTTTATGA-ATTT-TTAAT-A
* *
35385274 TTCATATAA-TTTTAT-AATTTTTAAGT-
1 TT-TTGTAATTTTTATGAATTTTTAA-TA
* * *
35385300 TTTTTTACATTTTTATAACATTTATAATAAA
1 TTTTGTA-ATTTTTATGA-ATTTTTAAT--A
*
35385331 TTTTG-CATTTTTAT-ATATTTTTAAATA
1 TTTTGTAATTTTTATGA-ATTTTT-AATA
35385358 TTTT
1 TTTT
35385362 TATGATTTTA
Statistics
Matches: 112, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.03
26 6 0.05
27 33 0.29
28 35 0.31
29 27 0.24
30 2 0.02
31 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTGTAATTTTTATGAATTTTTAATA
Found at i:35385247 original size:18 final size:18
Alignment explanation
Indices: 35385215--35385265 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
35385205 GCTTTTTATA
35385215 ATATTTTGTAA-ATTTTATT
1 ATATTTT-TAATATTTT-TT
35385234 A-ATTTTTAATA-TTTTT
1 ATATTTTTAATATTTTTT
35385250 ATATTTTTAGATATTT
1 ATATTTTTA-ATATTT
35385266 ATTCATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.11
17 13 0.46
18 9 0.32
19 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
ATATTTTTAATATTTTTT
Found at i:35385295 original size:9 final size:9
Alignment explanation
Indices: 35385190--35385327 Score: 77
Period size: 9 Copynumber: 15.0 Consensus size: 9
35385180 TTTTAGTTTG
*
35385190 TTTTGTAAT
1 TTTTATAAT
**
35385199 TTTTATGCT
1 TTTTATAAT
35385208 TTTTATAAT
1 TTTTATAAT
* *
35385217 ATTTTGTAAA
1 -TTTTATAAT
35385227 TTTTATTAAT
1 TTTTA-TAAT
35385237 TTTTA-ATAT
1 TTTTATA-AT
35385246 TTTTAT-AT
1 TTTTATAAT
*
35385254 TTTTAGATAT
1 TTTTATA-AT
35385264 TTATTCATAAT
1 TT-TT-ATAAT
**
35385275 TCATATAA-
1 TTTTATAAT
35385283 TTTTATAAT
1 TTTTATAAT
*
35385292 TTTTA-AGT
1 TTTTATAAT
*
35385300 TTTTTTACAT
1 TTTTATA-AT
*
35385310 TTTTATAAC
1 TTTTATAAT
*
35385319 ATTTATAAT
1 TTTTATAAT
35385328 AAATTTTGCA
Statistics
Matches: 96, Mismatches: 22, Indels: 22
0.69 0.16 0.16
Matches are distributed among these distances:
8 20 0.21
9 42 0.44
10 27 0.28
11 5 0.05
12 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:35385369 original size:29 final size:28
Alignment explanation
Indices: 35385207--35385370 Score: 88
Period size: 29 Copynumber: 5.8 Consensus size: 28
35385197 ATTTTTATGC
*
35385207 TTTTTATAATATTTTGTA-AATTTTAT-TAA
1 TTTTTA-AATATTTT-TATATTTTTATAT-A
*
35385236 TTTTT-AATATTTTTATATTTTTAGATA
1 TTTTTAAATATTTTTATATTTTTATATA
* ** *
35385263 TTTATT-CATAATTCATATAATTTTATA-A
1 TTT-TTAAAT-ATTTTTATATTTTTATATA
* * *
35385291 TTTTTAAGTTTTTTTACATTTTTATA-A
1 TTTTTAAATATTTTTATATTTTTATATA
** * **
35385318 CATTTATAATAAATTTTGCATTTTTATATA
1 TTTTTA-AAT-ATTTTTATATTTTTATATA
35385348 TTTTTAAATATTTTTATGATTTT
1 TTTTTAAATATTTTTAT-ATTTT
35385371 AAGTATAAAA
Statistics
Matches: 101, Mismatches: 25, Indels: 18
0.70 0.17 0.12
Matches are distributed among these distances:
26 2 0.02
27 37 0.37
28 17 0.17
29 40 0.40
30 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTTAAATATTTTTATATTTTTATATA
Found at i:35397176 original size:18 final size:18
Alignment explanation
Indices: 35397153--35397195 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35397143 GAATAGATTT
35397153 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
35397171 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
35397189 TTAATTA
1 TTAATTA
35397196 CTAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:35411337 original size:28 final size:30
Alignment explanation
Indices: 35411306--35411361 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
35411296 ATGTAATTAT
*
35411306 ATACATGA-ACTTTGATTT-ATGCAATTTC
1 ATACATGATACTTTGATTTGATCCAATTTC
*
35411334 ATACATGATATTTTGATTTGATCCAATT
1 ATACATGATACTTTGATTTGATCCAATT
35411362 CTTGTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 9 0.38
30 7 0.29
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (30 bp):
ATACATGATACTTTGATTTGATCCAATTTC
Found at i:35411563 original size:30 final size:30
Alignment explanation
Indices: 35411495--35411566 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
35411485 GATTAAATCA
*
35411495 AAATTAAAATTTCAAGTATACATTTGAACC
1 AAATTAAAATTTCAAGTATACAATTGAACC
* * * * *
35411525 ACAATTAAAATTTTACGTGTATAATTGCACC
1 A-AATTAAAATTTCAAGTATACAATTGAACC
35411556 AAATTAAAATT
1 AAATTAAAATT
35411567 CATACATAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTATACAATTGAACC
Found at i:35415166 original size:16 final size:16
Alignment explanation
Indices: 35415129--35415166 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35415119 TAATATGTTG
35415129 TCATAAAGAACTAATT
1 TCATAAAGAACTAATT
*
35415145 TAATAAAGAA-TATATT
1 TCATAAAGAACTA-ATT
35415161 TCATAA
1 TCATAA
35415167 CTATAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (16 bp):
TCATAAAGAACTAATT
Found at i:35415631 original size:91 final size:90
Alignment explanation
Indices: 35415524--35415755 Score: 249
Period size: 90 Copynumber: 2.6 Consensus size: 90
35415514 GTACTTTTTT
* * * *
35415524 TAAAATGTCCATTGTGGTACTTGTATTTTGAAAATGTATAATATGATACTTAAACTATTAATTTG
1 TAAAATATCCAATGTGGTACTTATATTTTGAAAATGT-TAATATGATACTTAAACTATTAATTTA
35415589 TCTATTATTTAATA-CT-TGTACTTTCA
65 TCTATTATTTAATACCTATGT--TTTCA
* * *
35415615 TAAAATATGCAATGTGGTA-TATATATTTTGAAAATGTTCAATATGGTA-TTGAACTATTAATTT
1 TAAAATATCCAATGTGGTACT-TATATTTTGAAAATGTT-AATATGATACTTAAACTATTAATTT
* * *
35415678 ATGTATTATTTAGTACCTATGTTTTTA
64 ATCTATTATTTAATACCTATGTTTTCA
* * *
35415705 TAAAATGTCCAATATGGTACTTATACGTTT-AAAATGTTTAATATGATACTT
1 TAAAATATCCAATGTGGTACTTATA-TTTTGAAAATG-TTAATATGATACTT
35415756 GGACTATCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
90 66 0.56
91 49 0.42
92 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (90 bp):
TAAAATATCCAATGTGGTACTTATATTTTGAAAATGTTAATATGATACTTAAACTATTAATTTAT
CTATTATTTAATACCTATGTTTTCA
Found at i:35415723 original size:90 final size:87
Alignment explanation
Indices: 35415518--35415778 Score: 267
Period size: 91 Copynumber: 2.9 Consensus size: 87
35415508 GTACATGTAC
* * * *
35415518 TTTTTTTAAAATGTCCATTGTGGTACTTGTATTTTGAAAATGTATAATATGATACTTAAACTATT
1 TTTTTATAAAATGTCCAATGTGGTACTTATATTTTGAAAATGT-TAATATGATACTTGAACTATT
*
35415583 AATTTGTCTATTATTTAATACTTG
65 AATTT-TGTATTATTTAATACTTG
* * * *
35415607 TACTTTCATAAAATATGCAATGTGGTA-TATATATTTTGAAAATGTTCAATATGGTA-TTGAACT
1 T--TTTTATAAAATGTCCAATGTGGTACT-TATATTTTGAAAATGTT-AATATGATACTTGAACT
*
35415670 ATTAATTTATGTATTATTTAGTACCTATG
62 ATTAATTT-TGTATTATTTAATA-CT-TG
* * *
35415699 TTTTTATAAAATGTCCAATATGGTACTTATACGTTT-AAAATGTTTAATATGATACTTGGACTAT
1 TTTTTATAAAATGTCCAATGTGGTACTTATA-TTTTGAAAATG-TTAATATGATACTTGAACTAT
*
35415763 CAATATTTGTATTATT
64 TAAT-TTTGTATTATT
35415779 ATGAGCATGA
Statistics
Matches: 142, Mismatches: 19, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
89 1 0.01
90 66 0.46
91 70 0.49
92 5 0.04
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (87 bp):
TTTTTATAAAATGTCCAATGTGGTACTTATATTTTGAAAATGTTAATATGATACTTGAACTATTA
ATTTTGTATTATTTAATACTTG
Found at i:35421833 original size:95 final size:95
Alignment explanation
Indices: 35421712--35421943 Score: 303
Period size: 94 Copynumber: 2.5 Consensus size: 95
35421702 ACATTAAAAT
* * * * *
35421712 TTTAAAAATAATTTAA-AAATAAAATTTTGTATTTAAGTCAAAATGGAA-TTCGAATTTTATATA
1 TTTAAAAATAATTAAATAAATAAAATTTTGTATTTAAATCAAAAT-GAAGTTCAAATTCTATACA
35421775 TTATCATGGTTACCCCA-TTAAAATTTTACAA
65 TTATCATGGTTA-CCCAGTTAAAATTTTACAA
* *
35421806 TTTAAAAATAACTAAATAAATAAAA-TTTGTATTTAAATCAAAATGAAGTTTAAATTCTATACAT
1 TTTAAAAATAATTAAATAAATAAAATTTTGTATTTAAATCAAAATGAAGTTCAAATTCTATACAT
* * *
35421870 TATCATTGTTATCCAGTTAAAATTTTATAA
66 TATCATGGTTACCCAGTTAAAATTTTACAA
*
35421900 TTTAAAAATAATTAAATAAGTAAAATTATT-TATTTAAATCAAAA
1 TTTAAAAATAATTAAATAAATAAAATT-TTGTATTTAAATCAAAA
35421944 ATAAATTTTT
Statistics
Matches: 121, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
93 6 0.05
94 90 0.74
95 23 0.19
96 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (95 bp):
TTTAAAAATAATTAAATAAATAAAATTTTGTATTTAAATCAAAATGAAGTTCAAATTCTATACAT
TATCATGGTTACCCAGTTAAAATTTTACAA
Found at i:35422267 original size:45 final size:48
Alignment explanation
Indices: 35422160--35422267 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 48
35422150 TGTTGGTATT
* **
35422160 TGATTTTATTTATTTTTGCTTCTTTTCTTGGATTAAATTAATGTATTTA
1 TGATGTTATTTATTTTTGCTTCTTTTCTTGGATTAAATTAATG-ACGTA
* *
35422209 TGATTTTTATTTATTTTTGCTTCTTTTCTTGGATTAAATTAATG-CGTG
1 TGA-TGTTATTTATTTTTGCTTCTTTTCTTGGATTAAATTAATGACGTA
35422257 TG-TGTT-TTTAT
1 TGATGTTATTTAT
35422268 CAAATTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
45 5 0.09
46 3 0.06
48 3 0.06
49 3 0.06
50 40 0.74
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (48 bp):
TGATGTTATTTATTTTTGCTTCTTTTCTTGGATTAAATTAATGACGTA
Found at i:35422275 original size:50 final size:50
Alignment explanation
Indices: 35422171--35422276 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
35422161 GATTTTATTT
* * **
35422171 ATTTTTGCTTCTTTTCTTGGATTAAATTAATGTATTTATGATTTTTATTT
1 ATTTTTGCTTCTTTTCTTGGATTAAATTAATGCATGTATGATTTTTATAA
* *
35422221 ATTTTTGCTTCTTTTCTTGGATTAAATTAATGCGTGTGTG-TTTTTATCAA
1 ATTTTTGCTTCTTTTCTTGGATTAAATTAATGCATGTATGATTTTTAT-AA
35422271 ATTTTT
1 ATTTTT
35422277 AATTTCAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
49 7 0.14
50 42 0.86
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.59
Consensus pattern (50 bp):
ATTTTTGCTTCTTTTCTTGGATTAAATTAATGCATGTATGATTTTTATAA
Found at i:35422489 original size:23 final size:24
Alignment explanation
Indices: 35422460--35422512 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
35422450 AAAAAAATTA
35422460 TTATTTTAATATAAATTAAATTGAT
1 TTATTTTAATAT-AATTAAATTGAT
*
35422485 TT-TTTTAATATAATTAAATTGAA
1 TTATTTTAATATAATTAAATTGAT
35422508 TTATT
1 TTATT
35422513 ACGCTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 13 0.50
24 11 0.42
25 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTATTTTAATATAATTAAATTGAT
Found at i:35422495 original size:24 final size:23
Alignment explanation
Indices: 35422454--35422512 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 23
35422444 TCTAAGAAAA
35422454 AAATT-ATTATTTTAATATAAATT
1 AAATTGATTATTTTAATAT-AATT
*
35422477 AAATTGATTTTTTTAATATAATT
1 AAATTGATTATTTTAATATAATT
35422500 AAATTGAATTATT
1 AAATTG-ATTATT
35422513 ACGCTAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
AAATTGATTATTTTAATATAATT
Found at i:35422572 original size:27 final size:28
Alignment explanation
Indices: 35422526--35422578 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
35422516 CTAATCTTTT
*
35422526 GTTAATTTTTTAGTATTTTTATAGAACG
1 GTTAAATTTTTAGTATTTTTATAGAACG
35422554 GTTAAATTTTTAGTA-TTTTATAGAA
1 GTTAAATTTTTAGTATTTTTATAGAA
35422579 ATTATGTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (28 bp):
GTTAAATTTTTAGTATTTTTATAGAACG
Found at i:35426374 original size:161 final size:161
Alignment explanation
Indices: 35426185--35426502 Score: 537
Period size: 161 Copynumber: 2.0 Consensus size: 161
35426175 AATAAGGTGA
*
35426185 CTTTTACAAGAGTTAGTTAAACCCCTTACAGCTGTGGCTGTTACTCCCTAAACGCACTGTTTTAC
1 CTTTTACAAGAGTTAGTTAAACCCCTTACAGCTGTGGCCGTTACTCCCTAAACGCACTGTTTTAC
* * * * *
35426250 TAAATCTATACACACCGTTTCAGTAATACCACACACACTCAACGCATCGTTTTACCCTTGTTATT
66 TAAATCTATACACACCATTTCAGTAACACCACACACACTCAACGCATCATTTTACCCTTATTATA
35426315 CACTTTTCCTATTTTTTATATTTACCCGCGG
131 CACTTTTCCTATTTTTTATATTTACCCGCGG
**
35426346 CTTTTACAAGAGTTAGTTAAGTCCCTTACAGCTGTGGCCGTTACTCCCTAAACGCACTGTTTTAC
1 CTTTTACAAGAGTTAGTTAAACCCCTTACAGCTGTGGCCGTTACTCCCTAAACGCACTGTTTTAC
** *
35426411 TAAATCTATATGCACCATTTCAGTAACACCGCACACACTCAACGCATCATTTTACCCTTATTATA
66 TAAATCTATACACACCATTTCAGTAACACCACACACACTCAACGCATCATTTTACCCTTATTATA
35426476 CACTTTTCCTATTTTTTATATTTACCC
131 CACTTTTCCTATTTTTTATATTTACCC
35426503 CATAACAGCA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
161 146 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.36
Consensus pattern (161 bp):
CTTTTACAAGAGTTAGTTAAACCCCTTACAGCTGTGGCCGTTACTCCCTAAACGCACTGTTTTAC
TAAATCTATACACACCATTTCAGTAACACCACACACACTCAACGCATCATTTTACCCTTATTATA
CACTTTTCCTATTTTTTATATTTACCCGCGG
Found at i:35427876 original size:18 final size:17
Alignment explanation
Indices: 35427853--35427886 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35427843 ACTATAGTAT
35427853 TTATTTTATAATTAAAAA
1 TTATTTTATAA-TAAAAA
35427871 TTATTTTATAATAAAA
1 TTATTTTATAATAAAA
35427887 TAATATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTTTATAATAAAAA
Found at i:35427893 original size:18 final size:18
Alignment explanation
Indices: 35427854--35427894 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35427844 CTATAGTATT
*
35427854 TATTTTATAATTAAAAAT
1 TATTTTATAATTAAAAAA
35427872 TATTTTATAA-TAAAATAA
1 TATTTTATAATTAAAA-AA
35427890 TATTT
1 TATTT
35427895 CGTAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTATAATTAAAAAA
Found at i:35428471 original size:16 final size:16
Alignment explanation
Indices: 35428452--35428486 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
35428442 AATTTCACCC
*
35428452 ATAAATAAAACGATTA
1 ATAAATAAAACAATTA
35428468 ATAAATAAAACAATTA
1 ATAAATAAAACAATTA
35428484 ATA
1 ATA
35428487 GATATGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
ATAAATAAAACAATTA
Found at i:35433144 original size:51 final size:52
Alignment explanation
Indices: 35433085--35433220 Score: 188
Period size: 51 Copynumber: 2.7 Consensus size: 52
35433075 TTTAATTTTT
*
35433085 AAATTTTAAATTAATAAAGGT-AAAATTACACTTTGACCCCTAAAAATGATA
1 AAATTTTAATTTAATAAAGGTAAAAATTACACTTTGACCCCTAAAAATGATA
***
35433136 AAATTTTAATTTAAT-ACTTTAAAAATTACACTTTGACCCCTAAAAATGATA
1 AAATTTTAATTTAATAAAGGTAAAAATTACACTTTGACCCCTAAAAATGATA
***
35433187 AAATTTTAATTTAAT-ACTTTAAAAATTACACTTT
1 AAATTTTAATTTAATAAAGGTAAAAATTACACTTT
35433221 TACTATCATA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 2 0.03
51 78 0.98
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (52 bp):
AAATTTTAATTTAATAAAGGTAAAAATTACACTTTGACCCCTAAAAATGATA
Found at i:35433243 original size:51 final size:50
Alignment explanation
Indices: 35433106--35433220 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 50
35433096 TAATAAAGGT
*
35433106 AAAATTACACTTTGACCCCTAAAAATGATAAAATTTTAATTTAATACTTTA
1 AAAATTACACTTTGACCCATAAAAAT-ATAAAATTTTAATTTAATACTTTA
*
35433157 AAAATTACACTTTGACCCCTAAAAATGATAAAATTTTAATTTAATACTTTA
1 AAAATTACACTTTGACCCATAAAAAT-ATAAAATTTTAATTTAATACTTTA
35433208 AAAATTACACTTT
1 AAAATTACACTTT
35433221 TACTATCATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.37
Consensus pattern (50 bp):
AAAATTACACTTTGACCCATAAAAATATAAAATTTTAATTTAATACTTTA
Found at i:35436967 original size:17 final size:16
Alignment explanation
Indices: 35436929--35436973 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
35436919 AAATAATTTA
*
35436929 ATTAATAAATTAATTT
1 ATTAATAAATTAATTG
35436945 AGTTAATTAAATTAATTG
1 A-TTAA-TAAATTAATTG
35436963 ATTAAATAAAT
1 ATT-AATAAAT
35436974 AATATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 11 0.44
18 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
ATTAATAAATTAATTG
Found at i:35437030 original size:18 final size:17
Alignment explanation
Indices: 35436999--35437032 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35436989 AGAAAATTTA
*
35436999 TATTATGTTGGATAAAT
1 TATTATGTTCGATAAAT
35437016 TATTCATGTTCGATAAA
1 TATT-ATGTTCGATAAA
35437033 AGTTCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TATTATGTTCGATAAAT
Found at i:35437294 original size:21 final size:21
Alignment explanation
Indices: 35437268--35437307 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35437258 GCCATATAGT
35437268 TTTTATTTTCTCAAAAATAAA
1 TTTTATTTTCTCAAAAATAAA
*
35437289 TTTTATTTTCTCAAGAATA
1 TTTTATTTTCTCAAAAATA
35437308 TTCATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTATTTTCTCAAAAATAAA
Found at i:35442553 original size:22 final size:22
Alignment explanation
Indices: 35442528--35442581 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
35442518 CAATGTTTTG
*
35442528 TGTCTCGAGACAAA-TGCCACAA
1 TGTCTCGAGACAAACTACC-CAA
*
35442550 TGTCTTGAGACAAACTACCCAA
1 TGTCTCGAGACAAACTACCCAA
35442572 TGTCTCGAGA
1 TGTCTCGAGA
35442582 TAAGCATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (22 bp):
TGTCTCGAGACAAACTACCCAA
Found at i:35444724 original size:2 final size:2
Alignment explanation
Indices: 35444717--35444766 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
35444707 ATATTTTGTG
35444717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35444759 AT AT AT AT
1 AT AT AT AT
35444767 GGATATGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35451288 original size:28 final size:28
Alignment explanation
Indices: 35451243--35451299 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
35451233 ATTTAATAAT
* *
35451243 TATAAAAATATTTAAAAAAATTAAAAAA
1 TATAAAAATATTCAAAAAAATCAAAAAA
*
35451271 TATAAAAAT-TTCATAAAAACTCAAAAAA
1 TATAAAAATATTCA-AAAAAATCAAAAAA
35451299 T
1 T
35451300 TAACATGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (28 bp):
TATAAAAATATTCAAAAAAATCAAAAAA
Found at i:35451923 original size:16 final size:16
Alignment explanation
Indices: 35451899--35451932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35451889 ATTAAAATAT
* *
35451899 AAATTACAAACACAAA
1 AAATAACAAAAACAAA
35451915 AAATAACAAAAACAAA
1 AAATAACAAAAACAAA
35451931 AA
1 AA
35451933 CTTCAATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAACAAAAACAAA
Found at i:35457063 original size:17 final size:17
Alignment explanation
Indices: 35457041--35457097 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
35457031 CCTTTCATTT
35457041 TTTAACCTTCAATCTTC
1 TTTAACCTTCAATCTTC
* ** ***
35457058 TTTAACTTTCTTTGACC
1 TTTAACCTTCAATCTTC
*
35457075 TTTAACCTTCCATCTTC
1 TTTAACCTTCAATCTTC
35457092 TTTAAC
1 TTTAAC
35457098 TTCCCTTGAT
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.21, C:0.28, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAACCTTCAATCTTC
Found at i:35457079 original size:34 final size:34
Alignment explanation
Indices: 35457041--35457134 Score: 125
Period size: 34 Copynumber: 2.8 Consensus size: 34
35457031 CCTTTCATTT
* * *
35457041 TTTAACCTTCAATCTTCTTTAACTTTCTTTGACC
1 TTTAACCTTCCATCTTCTTTAACTTCCCTTGACC
*
35457075 TTTAACCTTCCATCTTCTTTAACTTCCCTTGATC
1 TTTAACCTTCCATCTTCTTTAACTTCCCTTGACC
** *
35457109 TTTAATATTCCATCTTCCTTAACTTC
1 TTTAACCTTCCATCTTCTTTAACTTC
35457135 TCATATTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (34 bp):
TTTAACCTTCCATCTTCTTTAACTTCCCTTGACC
Found at i:35462562 original size:34 final size:34
Alignment explanation
Indices: 35462524--35462614 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
35462514 CCTTTCATCT
** * *
35462524 TTTAACCTTCCATCTTCCTTAATTTCCTTTGACC
1 TTTAACCTTCCATCTTCCTTAACCTCCCTTAACC
* * *
35462558 TTTAACCTTCCGTCTTCTTTAACCTCCCTTAATC
1 TTTAACCTTCCATCTTCCTTAACCTCCCTTAACC
*
35462592 GTTAACCTTCCATCTTCCTTAAC
1 TTTAACCTTCCATCTTCCTTAAC
35462615 TTTTCATATT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.19, C:0.34, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTAACCTTCCATCTTCCTTAACCTCCCTTAACC
Found at i:35462577 original size:17 final size:17
Alignment explanation
Indices: 35462557--35462614 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
35462547 TTCCTTTGAC
*
35462557 CTTTAACCTTCCGTCTT
1 CTTTAACCTTCCATCTT
* * **
35462574 CTTTAACCTCCCTTAAT
1 CTTTAACCTTCCATCTT
*
35462591 CGTTAACCTTCCATCTT
1 CTTTAACCTTCCATCTT
*
35462608 CCTTAAC
1 CTTTAAC
35462615 TTTTCATATT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.19, C:0.36, G:0.03, T:0.41
Consensus pattern (17 bp):
CTTTAACCTTCCATCTT
Found at i:35464068 original size:6 final size:6
Alignment explanation
Indices: 35464016--35464067 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
35464006 CACTTCCCAC
* *
35464016 CCAATA CCAATA CCAATA CCAATA CCAATA CCAATA CCAACA CCAACA
1 CCAATA CCAATA CCAATA CCAATA CCAATA CCAATA CCAATA CCAATA
35464064 CCAA
1 CCAA
35464068 CGCTACAGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (6 bp):
CCAATA
Found at i:35467400 original size:23 final size:23
Alignment explanation
Indices: 35467374--35467539 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
35467364 AGTGCTGGGC
35467374 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35467397 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
35467416 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
35467436 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
35467459 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
35467483 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
35467507 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35467530 ATCAGAGAGC
1 AACAGAGAGC
35467540 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 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 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:35467434 original size:39 final size:39
Alignment explanation
Indices: 35467380--35467454 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
35467370 GGGCAACAGA
*
35467380 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
35467419 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
35467455 GCTAATCGGA
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:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:35467493 original size:48 final size:46
Alignment explanation
Indices: 35467419--35467539 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
35467409 ACAAAGTACT
* * *
35467419 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
35467465 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
35467513 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
35467540 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:35473538 original size:11 final size:11
Alignment explanation
Indices: 35473517--35473551 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
35473507 CTCGATCAAG
35473517 TTTTAATATATT
1 TTTTAA-ATATT
35473529 TTTTAAATATT
1 TTTTAAATATT
35473540 TTTGTAAATATT
1 TTT-TAAATATT
35473552 AATGCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:35481796 original size:176 final size:176
Alignment explanation
Indices: 35481502--35481853 Score: 632
Period size: 176 Copynumber: 2.0 Consensus size: 176
35481492 TTTTGAGTTC
* *
35481502 CTTATTAGCTTAAGTTGGAAGGATAGCTCCTAAATCCTAACATATATACAAGCACAGTGAATCCA
1 CTTATTAACTTAAGTTGGAAGGATAGCTCCTAAATCCTAACATAAATACAAGCACAGTGAATCCA
35481567 ATCAACTTTCACAGCAAGATTACAGGGCCTAAGATTCAATTTTAAAGTTAAGTTTCGAATGAAGA
66 ATCAACTTTCACAGCAAGATTACAGGGCCTAAGATTCAATTTTAAAGTTAAGTTTCGAATGAAGA
* *
35481632 TTTTGAGTTGATCGTAAATACTTAATTGGTGACTCTTCGTCGGCTT
131 TTCTGAGTTGATCGTAAATACTTAAATGGTGACTCTTCGTCGGCTT
*
35481678 CTTATTAACTTAAGTTGGAAGGATAGCTCTTAAATCCTAACATAAATACAAGCACAGTGAATCCA
1 CTTATTAACTTAAGTTGGAAGGATAGCTCCTAAATCCTAACATAAATACAAGCACAGTGAATCCA
* *
35481743 ATCAACTTTCACAGCAAGATTACAGGGCCTAAGATTCAATTTTAAAGTTAAGTTTCGGATGAATA
66 ATCAACTTTCACAGCAAGATTACAGGGCCTAAGATTCAATTTTAAAGTTAAGTTTCGAATGAAGA
*
35481808 TTCTGGGTTGATCGTAAATACTTAAATGGTGACTCTTCGTCGGCTT
131 TTCTGAGTTGATCGTAAATACTTAAATGGTGACTCTTCGTCGGCTT
35481854 TTTAATTTGT
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
176 168 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (176 bp):
CTTATTAACTTAAGTTGGAAGGATAGCTCCTAAATCCTAACATAAATACAAGCACAGTGAATCCA
ATCAACTTTCACAGCAAGATTACAGGGCCTAAGATTCAATTTTAAAGTTAAGTTTCGAATGAAGA
TTCTGAGTTGATCGTAAATACTTAAATGGTGACTCTTCGTCGGCTT
Found at i:35489967 original size:28 final size:28
Alignment explanation
Indices: 35489916--35489977 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
35489906 TTAATTTACT
* * * *
35489916 ATTCTCGATTTGTTATTTTCAATTGTTA
1 ATTCTCGATTTGTTATTCTAAATTATCA
35489944 ATTCTCGATATT-TTATTCTAAATTATCA
1 ATTCTCGAT-TTGTTATTCTAAATTATCA
35489972 ATTCTC
1 ATTCTC
35489978 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (28 bp):
ATTCTCGATTTGTTATTCTAAATTATCA
Found at i:35500859 original size:15 final size:16
Alignment explanation
Indices: 35500825--35500864 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
35500815 GAAAAGATAC
*
35500825 TTAAAATTTGTGTAAG
1 TTAAAATTTGTATAAG
*
35500841 TTAAATTTTGTATAA-
1 TTAAAATTTGTATAAG
35500856 TTAAAATTT
1 TTAAAATTT
35500865 CAATATACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TTAAAATTTGTATAAG
Found at i:35501791 original size:15 final size:14
Alignment explanation
Indices: 35501757--35501787 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35501747 TAAAATTTTG
35501757 TTTAATAAAAAAAA
1 TTTAATAAAAAAAA
*
35501771 TTTAATAAACAAAA
1 TTTAATAAAAAAAA
35501785 TTT
1 TTT
35501788 TAATGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTAATAAAAAAAA
Found at i:35502774 original size:73 final size:73
Alignment explanation
Indices: 35502677--35502823 Score: 249
Period size: 73 Copynumber: 2.0 Consensus size: 73
35502667 TACAAACCAA
* *
35502677 AATTCAAATAGATTTTTCCTCCGATCTTCGATATTGACCATCAGATCGACTTGAATCTAAGGTAT
1 AATTCAAATAGATTTTTCCTCCGATCTTCGACACTGACCATCAGATCGACTTGAATCTAAGGTAT
*
35502742 GTTCTTCT
66 GTTATTCT
* *
35502750 AATTCAGATAGATTTTTCCTCCGATCTTCGACACTGACCATCAGATCGACTTGCATCTAAGGTAT
1 AATTCAAATAGATTTTTCCTCCGATCTTCGACACTGACCATCAGATCGACTTGAATCTAAGGTAT
35502815 GTTATTCT
66 GTTATTCT
35502823 A
1 A
35502824 CTCGATAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (73 bp):
AATTCAAATAGATTTTTCCTCCGATCTTCGACACTGACCATCAGATCGACTTGAATCTAAGGTAT
GTTATTCT
Found at i:35507585 original size:24 final size:26
Alignment explanation
Indices: 35507533--35507582 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
35507523 ATAAATAAGA
35507533 AATATATTAAATTATTAAATTAAAAAT
1 AATATATTAAATTATTAAA-TAAAAAT
35507560 AATATATTAAATTATTAAA-AAAA
1 AATATATTAAATTATTAAATAAAA
35507583 TAAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
27 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATATTAAATTATTAAATAAAAAT
Found at i:35508447 original size:95 final size:94
Alignment explanation
Indices: 35508273--35508447 Score: 214
Period size: 95 Copynumber: 1.9 Consensus size: 94
35508263 GTAATCCTTG
** *
35508273 ATTTTGTGAAGTTATCTTTTATATTTTAAATTTGTTTATTTAAAATTGTTAATAAAAATTATTTA
1 ATTTTGTGAAAATATCTTTTATATTTCAAATTTGTTTATTTAAAATTGTT-ATAAAAATTATTTA
* **
35508338 AAAGTTTGGTTATATATCTATAATATTTTT
65 AAAATTTGAATATATATCTATAATATTTTT
* *
35508368 ATTTTGTGAAAATATTTTTTATATTTCAAATTTATTTTATTT-AAATTG-T-TAAAAATTATTTT
1 ATTTTGTGAAAATATCTTTTATATTTCAAATTT-GTTTATTTAAAATTGTTATAAAAATTA-TTT
35508430 AAAAATTTGACA-ATATAT
64 AAAAATTTGA-ATATATAT
35508448 TTGATTTTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
92 9 0.13
93 17 0.25
94 1 0.01
95 35 0.51
96 7 0.10
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (94 bp):
ATTTTGTGAAAATATCTTTTATATTTCAAATTTGTTTATTTAAAATTGTTATAAAAATTATTTAA
AAATTTGAATATATATCTATAATATTTTT
Found at i:35513376 original size:20 final size:20
Alignment explanation
Indices: 35513353--35513395 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
35513343 CCTCTAACCC
35513353 GAATCGCGAACACAAACCTT
1 GAATCGCGAACACAAACCTT
* *
35513373 GAATCTCGAACTCAAACCTT
1 GAATCGCGAACACAAACCTT
35513393 GAA
1 GAA
35513396 CCCGAATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (20 bp):
GAATCGCGAACACAAACCTT
Found at i:35513909 original size:3 final size:3
Alignment explanation
Indices: 35513901--35513925 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35513891 GTGCATCATG
35513901 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
35513926 GCGAGAGATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35514102 original size:13 final size:13
Alignment explanation
Indices: 35514086--35514113 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35514076 ATTTAGATTT
35514086 ATGATTGATAAAA
1 ATGATTGATAAAA
35514099 ATGATTGATAAAA
1 ATGATTGATAAAA
35514112 AT
1 AT
35514114 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGATTGATAAAA
Found at i:35519847 original size:29 final size:29
Alignment explanation
Indices: 35519777--35519836 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
35519767 GCTTGCTTTT
**
35519777 TGGTAATTTGACTTGAGATTAGTAATAGC
1 TGGTAATTTGACTCAAGATTAGTAATAGC
35519806 TGGTAATTTGACTCAAGATTAGTAATAGC
1 TGGTAATTTGACTCAAGATTAGTAATAGC
35519835 TG
1 TG
35519837 TATGTTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (29 bp):
TGGTAATTTGACTCAAGATTAGTAATAGC
Found at i:35523860 original size:28 final size:29
Alignment explanation
Indices: 35523827--35523883 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
35523817 TTATAATAAT
35523827 TGGATTAAATTAATTTTT-TATTATTAAA
1 TGGATTAAATTAATTTTTATATTATTAAA
* *
35523855 TGGATTAATTTTATTTTTATATTATTAAA
1 TGGATTAAATTAATTTTTATATTATTAAA
35523884 AAAATCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
TGGATTAAATTAATTTTTATATTATTAAA
Found at i:35529134 original size:2 final size:2
Alignment explanation
Indices: 35529127--35529169 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35529117 TTTTACATTA
35529127 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
35529169 T
1 T
35529170 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:35529174 original size:2 final size:2
Alignment explanation
Indices: 35529169--35529231 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
35529159 TCTCTCTCTC
35529169 TA TA TA 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
35529211 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
35529232 TCTTTTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35531696 original size:62 final size:61
Alignment explanation
Indices: 35531568--35531752 Score: 255
Period size: 61 Copynumber: 3.0 Consensus size: 61
35531558 GTTGACACCT
* * * * *
35531568 CCTTTTCTCGTGGAAAAAATTTCAAATTTTTTTGGTATTGGCCATCAAATGACCAACAC-CC
1 CCTTTTCTCG-AGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACTCC
* *
35531629 TCTTTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGACCATCAAATGGCCGACACTCC
1 -CCTTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACTCC
* **
35531691 CCTTTTCTCGAGAAAAAAATTTAAATTTTTTTTATGTTGGCCATCAAATGGCCGACACTCC
1 CCTTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACTCC
35531752 C
1 C
35531753 TATTTCAATT
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
61 99 0.90
62 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (61 bp):
CCTTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACTCC
Found at i:35532131 original size:63 final size:62
Alignment explanation
Indices: 35532032--35532320 Score: 307
Period size: 63 Copynumber: 4.7 Consensus size: 62
35532022 TTGTCATGCA
*
35532032 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGGAGGGTGTCGACCATTTG
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAGG-GGGTGTCGACCATTTG
* * *
35532095 ATGGCCAACACAAAAAAAATTTTAATTTTTTTCTCGAG--AAAAGGGGTGTGTCGACTATTTG
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAGGGG-GTGTCGACCATTTG
* * * * * *
35532156 ATAGCCAACACAAAAAAAAATTAAATTTTTTTCTCGAGAAAAAATAGAGGTGTCGGCCATTTG
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAA-GGGGGTGTCGACCATTTG
* * * * * * * * ***
35532219 ATGGCTAACACCACAAAAATTAAAATTTTATTCT-TA-AGAAAAGGGGATGTCGCCCATACA
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAGGGGGTGTCGACCATTTG
* *
35532279 ATGGCCAATACCAAAAAAATTTAAATTTTTTTTCTCGTGAAA
1 ATGGCCAACACCAAAAAAATTTAAA-TTTTTTTCTCGAGAAA
35532321 TTCAAATGGC
Statistics
Matches: 185, Mismatches: 34, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
60 34 0.18
61 67 0.36
62 1 0.01
63 81 0.44
64 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (62 bp):
ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAGGGGGTGTCGACCATTTG
Found at i:35532294 original size:124 final size:124
Alignment explanation
Indices: 35532030--35532320 Score: 352
Period size: 124 Copynumber: 2.3 Consensus size: 124
35532020 TATTGTCATG
* *
35532030 CAATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGGAGGGTGTCGACCATTTG
1 CAATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAAGAGGGTGTCGACCATTTG
** * * * * *
35532095 ATGGCCAACACAAAAAAAATTTTAATTTTTTTCTCGAGAAAAGGGGTGTGTCGACTATT
66 ATGGCCAACACAAAAAAAATTAAAATTTTATTCTCAAGAAAAGGGGTATGTCGACCATA
** * * * *
35532154 TGATAGCCAACACAAAAAAAAATTAAATTTTTTTCTCGAGAAAAAATAGA-GGTGTCGGCCATTT
1 CAATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAA-AGAGGGTGTCGACCATTT
* * * * *
35532218 GATGGCTAACACCACAAAAATTAAAATTTTATTCTTAAGAAAAGGGG-ATGTCGCCCATA
65 GATGGCCAACACAAAAAAAATTAAAATTTTATTCTCAAGAAAAGGGGTATGTCGACCATA
* *
35532277 CAATGGCCAATACCAAAAAAATTTAAATTTTTTTTCTCGTGAAA
1 CAATGGCCAACACCAAAAAAATTTAAA-TTTTTTTCTCGAGAAA
35532321 TTCAAATGGC
Statistics
Matches: 138, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
123 29 0.21
124 107 0.78
125 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (124 bp):
CAATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAAAGAGGGTGTCGACCATTTG
ATGGCCAACACAAAAAAAATTAAAATTTTATTCTCAAGAAAAGGGGTATGTCGACCATA
Found at i:35532960 original size:18 final size:18
Alignment explanation
Indices: 35532937--35532973 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35532927 TGATACGTGT
*
35532937 GTATTTTTTTTAAATACG
1 GTATTTTATTTAAATACG
*
35532955 GTATTTTATTTATATACG
1 GTATTTTATTTAAATACG
35532973 G
1 G
35532974 AAATACGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
GTATTTTATTTAAATACG
Found at i:35533346 original size:100 final size:98
Alignment explanation
Indices: 35533212--35533403 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 98
35533202 TGACACCCAT
* *
35533212 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTAGCCATCAAATGG-TCGACACCCCCCTTT
1 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCT-GACA--CCCCTCT
*
35533276 TTTCTCGAGAAAAAAATTTTAAATTTTTTTGCCCCC
63 TTTCTCGAGAAAAAAAATTTAAATTTTTTTGCCCCC
*
35533312 TTTTCTCGAGGAAAAAAATTCAAA-TTTTTTGGTGTTGGCCATCAAATGGCTGACACCCCTCTTT
1 TTTTCTCGA-GAAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCTGACACCCCTCTTT
*
35533376 TCTCGAGAAAAAAAATTTAATTTTTTTT
65 TCTCGAGAAAAAAAATTTAAATTTTTTT
35533404 ATGTTGGTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
98 34 0.40
100 37 0.44
101 14 0.16
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (98 bp):
TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCTGACACCCCTCTTTT
CTCGAGAAAAAAAATTTAAATTTTTTTGCCCCC
Found at i:35533377 original size:61 final size:61
Alignment explanation
Indices: 35533307--35533476 Score: 218
Period size: 61 Copynumber: 2.8 Consensus size: 61
35533297 AATTTTTTTG
* *
35533307 CCCC-CTTTTCTCGAGGAAAAAAATTCAAATTTTTTGGTGTTGGCCATCAAATGGCTGACA
1 CCCCTCTTTTCTCGAGGAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
* * ** **
35533367 CCCCTCTTTTCTCGAGAAAAAAAATTTAATTTTTTTTATGTTGGTTATCAAATGGCCGACA
1 CCCCTCTTTTCTCGAGGAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
* *
35533428 CCCCTTTTTTTCCCGA-GAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
1 CCCC-TCTTTTCTCGAGGAAAAAAATTTAAA-TTTTTTGGTGTTGGCCAT
35533477 TGCATGATAG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 4 0.04
61 64 0.70
62 23 0.25
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (61 bp):
CCCCTCTTTTCTCGAGGAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA
Found at i:35533379 original size:161 final size:160
Alignment explanation
Indices: 35533147--35533465 Score: 419
Period size: 161 Copynumber: 2.0 Consensus size: 160
35533137 GGTCGTCACA
* * * * ***
35533147 CCCTATTTCTCGAGAAAAAAAATTTAACTTTTTTTTGTGTTGGCTATTGCATAGCTGACACCCAT
1 CCCTATTTCTCGAGAAAAAAAATTCAACATTTTTTGGTGTTGGCCATCAAATAGCTGACACCCAT
* *
35533212 TTTTCTCGAG-AAAAAAATTTAAATTTTTTTGGTGTTAGCCATCAAATGGTCGACACCCCCCTTT
66 TTTTCTCGAGAAAAAAAATTT-AATTTTTTTGATGTTAGCCATCAAATGGCCGACA-CCCCCTTT
*
35533276 TTTCTCGAGAAAAAAATTTTAAATTTTTTTGCC
129 TTTCCCGAGAAAAAAA-TTTAAATTTTTTTGCC
* * *
35533309 CCCT-TTTCTCGAGGAAAAAAATTCAA-ATTTTTTGGTGTTGGCCATCAAATGGCTGACACCCCT
1 CCCTATTTCTCGAGAAAAAAAATTCAACATTTTTTGGTGTTGGCCATCAAATAGCTGACACCCAT
* * ** *
35533372 CTTTTCTCGAGAAAAAAAATTTAATTTTTTTTATGTTGGTTATCAAATGGCCGACACCCCTTTTT
66 -TTTTCTCGAGAAAAAAAATTTAATTTTTTTGATGTTAGCCATCAAATGGCCGACACCCCCTTTT
35533437 TTCCCGAGAAAAAAATTTAAATTTTTTTG
130 TTCCCGAGAAAAAAATTTAAATTTTTTTG
35533466 GTGTTGGCCA
Statistics
Matches: 137, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
159 14 0.10
160 51 0.37
161 58 0.42
162 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (160 bp):
CCCTATTTCTCGAGAAAAAAAATTCAACATTTTTTGGTGTTGGCCATCAAATAGCTGACACCCAT
TTTTCTCGAGAAAAAAAATTTAATTTTTTTGATGTTAGCCATCAAATGGCCGACACCCCCTTTTT
TCCCGAGAAAAAAATTTAAATTTTTTTGCC
Found at i:35533841 original size:60 final size:59
Alignment explanation
Indices: 35533777--35533986 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 59
35533767 CCATTTGATG
*
35533777 GCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGGGGTGTCAACCATGCAAT
1 GCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGAGGTGTCAACCATGCAAT
* * * **
35533836 AGCCAACACCAAAAAAATTTAAAATTTTTTTTTCGAGAAAAGGAGGTGTCGGCCATGCAAT
1 -GCCAACACCAAAAAAATTT-GAATTTTTTTCTCGAAAAAAGGAGGTGTCAACCATGCAAT
* * ** ***
35533897 GACTAACA-CAAAAAAAATTGAATTTTTTTTCTCGAGAAAAAGGA-GTGTCGGCCATTTGAT
1 G-CCAACACCAAAAAAATTTGAA-TTTTTTTCTCGA-AAAAAGGAGGTGTCAACCATGCAAT
* * *
35533957 GGACAACACCCAAAAATTTTGAATTTTTTT
1 -GCCAACACCAAAAAAATTTGAATTTTTTT
35533987 TCTAATAAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.02
60 65 0.52
61 58 0.46
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (59 bp):
GCCAACACCAAAAAAATTTGAATTTTTTTCTCGAAAAAAGGAGGTGTCAACCATGCAAT
Found at i:35533988 original size:61 final size:61
Alignment explanation
Indices: 35533774--35533989 Score: 237
Period size: 61 Copynumber: 3.6 Consensus size: 61
35533764 TGGCCATTTG
* * **
35533774 ATGGCCAACACCAAAAAAATTTGAA-TTTTTTTCTCGA-AAAAAGGGGGTGTCAACCATGCA
1 ATGGACAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAA-GGAGTGTCGGCCATGCA
* * *
35533834 ATAGCCAACACCAAAAAAATTTAAAATTTTTTTT-TCGAG-AAAAGGAGGTGTCGGCCATGCA
1 ATGGACAACACCAAAAAAATTT-GAATTTTTTTTCTCGAGAAAAAGGA-GTGTCGGCCATGCA
* ***
35533895 AT-GACTAACA-CAAAAAAAATTGAATTTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATTTG
1 ATGGAC-AACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATGCA
* *
35533955 ATGGACAACACCCAAAAATTTTGAATTTTTTTTCT
1 ATGGACAACACCAAAAAAATTTGAATTTTTTTTCT
35533990 AATAAAAAAG
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
59 10 0.08
60 57 0.43
61 59 0.44
62 7 0.05
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (61 bp):
ATGGACAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAAGGAGTGTCGGCCATGCA
Found at i:35548507 original size:21 final size:20
Alignment explanation
Indices: 35548469--35548517 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
35548459 ATAATCATAT
35548469 TTAAAATATAATTATATTT-A
1 TTAAAA-ATAATTATATTTAA
*
35548489 TATAAAAATAATATTTATTTAA
1 T-TAAAAATAAT-TATATTTAA
35548511 TTAAAAA
1 TTAAAAA
35548518 ACTTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAATAATTATATTTAA
Found at i:35548717 original size:3 final size:3
Alignment explanation
Indices: 35548711--35548745 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35548701 ATTATTGTCA
35548711 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35548746 ATTTCTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35559052 original size:51 final size:50
Alignment explanation
Indices: 35558987--35559218 Score: 160
Period size: 51 Copynumber: 4.7 Consensus size: 50
35558977 TATTTTAAAG
* * * *
35558987 AAAAATTTTAAATTTTTAACAAAGTTTTGATTTTTTCTAACTATTCCAAA
1 AAAAAGTTTGAATTTTTAACAAAATATTGATTTTTTCTAACTATTCCAAA
*
35559037 ATAAAAGTTTGAATTTTTAAGCAAAATAGTGA---TTT-T--CT-TT--AAA
1 A-AAAAGTTTGAATTTTTAA-CAAAATATTGATTTTTTCTAACTATTCCAAA
* *** * ** **
35559080 AAAAAGTTTAGATTTTTTAA-AAAATAAAAATATGTTTTTTAGTTATTTTAAA
1 AAAAAGTTT-GAATTTTTAACAAAATATTGAT-T-TTTTCTAACTATTCCAAA
* * *
35559132 GAAAAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTCTAACTATTCCAAA
1 -AAAAAGTTTGAATTTTTAACAAAATATTGATTTTTTCTAACTATTCCAAA
*
35559183 ATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTT
1 A-AAAAGTTTGAATTTTTAA-CAAAATATTGATTTT
35559219 CTTTAAAAAA
Statistics
Matches: 138, Mismatches: 26, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
41 7 0.05
42 8 0.06
43 13 0.09
45 2 0.01
46 5 0.04
47 1 0.01
48 1 0.01
49 4 0.03
50 4 0.03
51 46 0.33
52 32 0.23
53 15 0.11
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.44
Consensus pattern (50 bp):
AAAAAGTTTGAATTTTTAACAAAATATTGATTTTTTCTAACTATTCCAAA
Found at i:35559136 original size:146 final size:146
Alignment explanation
Indices: 35558858--35559365 Score: 759
Period size: 146 Copynumber: 3.4 Consensus size: 146
35558848 TTTGGGAAAT
* * * * ** *
35558858 GTTTTGATTTTTT-TAAACAATTTCGAAATAAAAGTTTTGATTTTTTTTAAGTGAAATAGTTATT
1 GTTTTGATTTTTTCT-AACTATTCCAAAATAAAAG-TTTGA--ATTTTTAAGCAAAATAGTGATT
* *
35558922 TTCTTTAAAAAAAGAAAGTTTATA-TTTTTAAAAAATAAAAATCTGTTTTTTTAGTTATTTTAAA
62 TTCTTT--AAAAA-AAAGTTTAGATTTTTTAAAAAATAAAAATATG-TTTTTTAGTTATTTTAAA
*
35558986 GAAAAATTTTAAATTTTTAACAAA
123 GAAAAAGTTTAAATTTTTAACAAA
35559010 GTTTTGATTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCT
1 GTTTTGATTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCT
35559075 TTAAAAAAAAGTTTAGATTTTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAGT
66 TTAAAAAAAAGTTTAGATTTTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAGT
35559140 TTAAATTTTTAACAAA
131 TTAAATTTTTAACAAA
35559156 GTTTTGATTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCT
1 GTTTTGATTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCT
35559221 TTAAAAAAAAGTTTAGATTTTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAGT
66 TTAAAAAAAAGTTTAGATTTTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAGT
35559286 TTAAATTTTTAACAAA
131 TTAAATTTTTAACAAA
* * * * * * * *
35559302 GTTTTGATTTTTTTTTAACTATTTCGAAATCAAAGTTTGGATTTTTGAGTAAAGTAGTGATTTT
1 GTTTTGA-TTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTT
35559366 TGTTTAATCA
Statistics
Matches: 335, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
146 203 0.61
147 73 0.22
149 24 0.07
151 5 0.01
152 29 0.09
153 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (146 bp):
GTTTTGATTTTTTCTAACTATTCCAAAATAAAAGTTTGAATTTTTAAGCAAAATAGTGATTTTCT
TTAAAAAAAAGTTTAGATTTTTTAAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGAAAAAGT
TTAAATTTTTAACAAA
Found at i:35563442 original size:24 final size:24
Alignment explanation
Indices: 35563400--35563445 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35563390 ATTTTATCTT
* *
35563400 GGATTTTAAGAACTGTTTTGGATG
1 GGATTTTAAAAACTATTTTGGATG
*
35563424 GGATTTTAAAAATTATTTTGGA
1 GGATTTTAAAAACTATTTTGGA
35563446 GGCTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (24 bp):
GGATTTTAAAAACTATTTTGGATG
Found at i:35564945 original size:29 final size:29
Alignment explanation
Indices: 35564908--35564965 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
35564898 TTCAAACTTG
*
35564908 ACACATTTTCTAATTTGGTACCTAAATTT
1 ACACATTTTCTAAGTTGGTACCTAAATTT
* * *
35564937 ACACTTTTTTTAAGTTGGTACTTAAATTT
1 ACACATTTTCTAAGTTGGTACCTAAATTT
35564966 TTTGGGGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (29 bp):
ACACATTTTCTAAGTTGGTACCTAAATTT
Found at i:35566783 original size:23 final size:24
Alignment explanation
Indices: 35566733--35566783 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
35566723 GGTGAGAGAT
* *
35566733 CTTTGTTTGTTTTTATTTGATTAG
1 CTTTTTTTGTTTTTAATTGATTAG
35566757 -TTTTTTTGTTTTTAATTGA-TAG
1 CTTTTTTTGTTTTTAATTGATTAG
35566779 CTTTT
1 CTTTT
35566784 ACCTATGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.69
Consensus pattern (24 bp):
CTTTTTTTGTTTTTAATTGATTAG
Found at i:35569374 original size:10 final size:10
Alignment explanation
Indices: 35569359--35569412 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
35569349 TAATAATTAT
35569359 AAAAATATAG
1 AAAAATATAG
35569369 AAAAATAT--
1 AAAAATATAG
* *
35569377 AAAATTAT-T
1 AAAAATATAG
*
35569386 AAAAAT-TAT
1 AAAAATATAG
35569395 AAAAATATAG
1 AAAAATATAG
35569405 AAAAATAT
1 AAAAATAT
35569413 TTTACAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.21
9 12 0.32
10 18 0.47
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (10 bp):
AAAAATATAG
Found at i:35569377 original size:18 final size:18
Alignment explanation
Indices: 35569356--35569412 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
35569346 CGATAATAAT
35569356 TATAAAAATATAGAAAAA
1 TATAAAAATATAGAAAAA
* *
35569374 TATAAAATTATTA-AAAAT
1 TATAAAAATA-TAGAAAAA
35569392 TATAAAAATATAGAAAAA
1 TATAAAAATATAGAAAAA
35569410 TAT
1 TAT
35569413 TTTACAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 29 0.88
19 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
TATAAAAATATAGAAAAA
Found at i:35569608 original size:18 final size:18
Alignment explanation
Indices: 35569585--35569639 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
35569575 AAAAATTATT
35569585 ATAATTTTATAATTTTTA
1 ATAATTTTATAATTTTTA
*
35569603 ATAATTTTCTATATTTTGTA
1 ATAATTTTATA-ATTTT-TA
*
35569623 A-CATTTTAATAATTTTT
1 ATAATTTT-ATAATTTTT
35569640 TTCTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 11 0.35
19 15 0.48
20 5 0.16
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
ATAATTTTATAATTTTTA
Found at i:35569650 original size:22 final size:22
Alignment explanation
Indices: 35569616--35569682 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
35569606 ATTTTCTATA
* *
35569616 TTTTGTAACATTTT-AATAATTT
1 TTTTCTAAAATTTTAAAT-ATTT
35569638 TTTTCTAAAATTTTAAATATTT
1 TTTTCTAAAATTTTAAATATTT
* * *
35569660 TTGTAT-ATATTTTAAATATTT
1 TTTTCTAAAATTTTAAATATTT
35569681 TT
1 TT
35569683 CTATAATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.41
22 20 0.51
23 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTTCTAAAATTTTAAATATTT
Done.