Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 276 of 290
Found at i:88459043 original size:30 final size:29
Alignment explanation
Indices: 88459009--88459071 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
88458999 TTATAAAAAA
* *
88459009 TTTATAATTTTTAATAAATTTTAAATATTT
1 TTTATAATTTTTAATAAAATTT-AATAATT
* *
88459039 TTTATATTTTTTATTAAAATTTAATAATT
1 TTTATAATTTTTAATAAAATTTAATAATT
88459068 TTTA
1 TTTA
88459072 GACTATGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTATAATTTTTAATAAAATTTAATAATT
Found at i:88459066 original size:50 final size:49
Alignment explanation
Indices: 88458977--88459071 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
88458967 ATTTCTATAT
*
88458977 ATTTTATAATTTTTTATGATTTTTATAAAAAATTTATAATTTTTAATAA
1 ATTTTAAAATTTTTTATGATTTTTATAAAAAATTTATAATTTTTAATAA
*
88459026 ATTTTAAATATTTTTTAT-ATTTTT-TATTAAAATTTAATAATTTTTA
1 ATTTTAAA-ATTTTTTATGATTTTTATA-AAAAATTT-ATAATTTTTA
88459072 GACTATGACA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
48 2 0.05
49 20 0.49
50 19 0.46
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (49 bp):
ATTTTAAAATTTTTTATGATTTTTATAAAAAATTTATAATTTTTAATAA
Found at i:88459071 original size:10 final size:10
Alignment explanation
Indices: 88459012--88459071 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
88459002 TAAAAAATTT
88459012 ATAATTTTTA
1 ATAATTTTTA
*
88459022 ATAAATTTTA
1 ATAATTTTTA
*
88459032 A-ATATTTTTT
1 ATA-ATTTTTA
*
88459042 ATATTTTTTA
1 ATAATTTTTA
* **
88459052 TTAAAATTTA
1 ATAATTTTTA
88459062 ATAATTTTTA
1 ATAATTTTTA
88459072 GACTATGACA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
9 1 0.03
10 34 0.94
11 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:88461705 original size:11 final size:11
Alignment explanation
Indices: 88461689--88461726 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
88461679 ATTCAACCTT
88461689 AATAAATTTGA
1 AATAAATTTGA
*
88461700 AATAAA-TAG-
1 AATAAATTTGA
88461709 AATAAATTTGA
1 AATAAATTTGA
88461720 AATAAAT
1 AATAAAT
88461727 AGAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.26
10 4 0.17
11 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (11 bp):
AATAAATTTGA
Found at i:88461714 original size:20 final size:20
Alignment explanation
Indices: 88461689--88461732 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
88461679 ATTCAACCTT
88461689 AATAAATTTGAAATAAATAG
1 AATAAATTTGAAATAAATAG
88461709 AATAAATTTGAAATAAATAG
1 AATAAATTTGAAATAAATAG
88461729 AATA
1 AATA
88461733 TTATGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (20 bp):
AATAAATTTGAAATAAATAG
Found at i:88467076 original size:29 final size:29
Alignment explanation
Indices: 88467036--88467093 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
88467026 GGAGATGCCA
88467036 CTCTCTTAGCTGATGACTCTGGCAGTCCT
1 CTCTCTTAGCTGATGACTCTGGCAGTCCT
88467065 CTCTCTTAGCTGATGACTCTGGCAGTCCT
1 CTCTCTTAGCTGATGACTCTGGCAGTCCT
88467094 ATATTTCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.21, T:0.34
Consensus pattern (29 bp):
CTCTCTTAGCTGATGACTCTGGCAGTCCT
Found at i:88468029 original size:9 final size:9
Alignment explanation
Indices: 88468017--88468041 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
88468007 AAAATTTTAA
88468017 AAATTATAT
1 AAATTATAT
88468026 AAATTATAT
1 AAATTATAT
88468035 AAATTAT
1 AAATTAT
88468042 TTCATGTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATTATAT
Found at i:88468637 original size:12 final size:12
Alignment explanation
Indices: 88468620--88468649 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
88468610 CAAAACAGTG
88468620 GAAAACCAACAA
1 GAAAACCAACAA
88468632 GAAAACCAACAA
1 GAAAACCAACAA
88468644 GAAAAC
1 GAAAAC
88468650 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.23, G:0.10, T:0.00
Consensus pattern (12 bp):
GAAAACCAACAA
Found at i:88469121 original size:19 final size:19
Alignment explanation
Indices: 88469097--88469138 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
88469087 ATAAGTAAAG
88469097 AAATTATTAAAAAATAGTT
1 AAATTATTAAAAAATAGTT
88469116 AAATTATTAAAAAATAGTT
1 AAATTATTAAAAAATAGTT
88469135 AAAT
1 AAAT
88469139 AAACATGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTATTAAAAAATAGTT
Found at i:88482815 original size:22 final size:22
Alignment explanation
Indices: 88482787--88482829 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
88482777 TATTTCGACG
88482787 TAGTTACTTTTGTTTGAAATGA
1 TAGTTACTTTTGTTTGAAATGA
88482809 TAGTTACTTTTGTTTGAAATG
1 TAGTTACTTTTGTTTGAAATG
88482830 TTGGTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.51
Consensus pattern (22 bp):
TAGTTACTTTTGTTTGAAATGA
Found at i:88486494 original size:20 final size:20
Alignment explanation
Indices: 88486444--88486494 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
88486434 TAAAATAATA
*
88486444 TTATATT-AATTATATATGT
1 TTATATTAAATTATATATAT
* *
88486463 TGA-ATAATAATTATATATAT
1 TTATATTA-AATTATATATAT
88486483 TTATATTAAATT
1 TTATATTAAATT
88486495 CTTAATCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 17 0.71
21 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTATATTAAATTATATATAT
Found at i:88486634 original size:39 final size:40
Alignment explanation
Indices: 88486575--88486664 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 40
88486565 TATATTTATA
* * *
88486575 TTTAATACAACAAAATATTTATTATATTTAT-TTGTATTT
1 TTTAATATAACAAAACATTTATTATATTTATGTAGTATTT
*
88486614 TTTAATATAATAAAACATTTATTATATTTATGGTAGTATTT
1 TTTAATATAACAAAACATTTATTATATTTAT-GTAGTATTT
88486655 TTTAATATAA
1 TTTAATATAA
88486665 ATATTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 28 0.62
41 17 0.38
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (40 bp):
TTTAATATAACAAAACATTTATTATATTTATGTAGTATTT
Found at i:88493526 original size:17 final size:17
Alignment explanation
Indices: 88493504--88493537 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88493494 ATCCACTAAT
*
88493504 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
88493521 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
88493538 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:88498165 original size:17 final size:17
Alignment explanation
Indices: 88498143--88498176 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88498133 ATCCACTAAT
*
88498143 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
88498160 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
88498177 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:88503461 original size:14 final size:14
Alignment explanation
Indices: 88503442--88503483 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
88503432 CTCCTAAACT
88503442 ACCCCACTAACTCC
1 ACCCCACTAACTCC
* *
88503456 ACCCCATTAA-GCC
1 ACCCCACTAACTCC
88503469 ACCCCACTAACTCC
1 ACCCCACTAACTCC
88503483 A
1 A
88503484 TTACCCTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.31, C:0.52, G:0.02, T:0.14
Consensus pattern (14 bp):
ACCCCACTAACTCC
Found at i:88503855 original size:3 final size:3
Alignment explanation
Indices: 88503847--88503968 Score: 60
Period size: 3 Copynumber: 41.0 Consensus size: 3
88503837 AGGGGGAGAG
*
88503847 TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT TACT T-T TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * * *
88503890 T-T TA- TAT ATATT TAT TAC CAT TATT TATT TATT TAT TAT TAG TAA
1 TAT TAT TAT -TA-T TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT
* * * *
88503935 CA- TAT TGT TAT TTT TAT TAT TAT T-T TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
88503969 AATGGCACTA
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
2 13 0.14
3 62 0.67
4 17 0.18
5 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:88508019 original size:20 final size:21
Alignment explanation
Indices: 88507978--88508021 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
88507968 GAGGGATCAA
*
88507978 ATGCTGGAGTCCCAGAAAAAC
1 ATGCTGGAGTCACAGAAAAAC
*
88507999 ATGCTGGA-TCACAGAACAAC
1 ATGCTGGAGTCACAGAAAAAC
88508019 ATG
1 ATG
88508022 ATAAGCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (21 bp):
ATGCTGGAGTCACAGAAAAAC
Found at i:88516177 original size:45 final size:45
Alignment explanation
Indices: 88516126--88516251 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
88516116 AATCATCAGC
* * *
88516126 CTTATCTTCACTGAGCAGGAGT-GAGGCAGG-CTAAATATATCAGAT
1 CTTATCTTCGCTGAGCAGGAGTGGA-GCAGGTC-AAATACAGCAGAT
* * * * *
88516171 CTTATCTTCGCTTAACAAGAGTGGAGCAGGTCAGATACAGCGGAT
1 CTTATCTTCGCTGAGCAGGAGTGGAGCAGGTCAAATACAGCAGAT
* *
88516216 CTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAAT
1 CTTATCTTCGCTGAGCAGGAGTGGAGCAGGTCAAAT
88516252 TTCAGCAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
45 62 0.95
46 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
CTTATCTTCGCTGAGCAGGAGTGGAGCAGGTCAAATACAGCAGAT
Found at i:88516199 original size:135 final size:135
Alignment explanation
Indices: 88515712--88516182 Score: 694
Period size: 135 Copynumber: 3.5 Consensus size: 135
88515702 GATTACAGAT
* * * ** * *
88515712 ATCATCAGCCTTAACTTCACTAAGTAATAGTAAAGCAGGTTAAATATAGCAGATCTTATCTTCGC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCAGATCTTATCTTCGC
* * * *
88515777 TGACCAGGAGTGGAGCAGATCGAATTTTGGTGAATATTATCTCCACGTACTGGTGATGGAGCAGA
66 TGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCACGTACTGGCGATGGAGCAGA
88515842 TTCCA
131 TTCCA
* * *
88515847 ATCATCAGGCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAGTATAGCAGATCTTATCTTCGT
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCAGATCTTATCTTCGC
88515912 TGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCACGTACTGGCGATGGAGCAGA
66 TGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCACGTACTGGCGATGGAGCAGA
88515977 TTCCA
131 TTCCA
* * *
88515982 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCATATATTGTCTTCGC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCAGATCTTATCTTCGC
* * * *
88516047 TGAGCAGGAGCGGAGCAGATCGAATTTTGGTAAATCTTATCTCC-CTGT-GTCGACAATGGAGCA
66 TGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCAC-GTACT-GGCGATGGAGCA
*
88516110 GATTCAA
129 GATTCCA
* *
88516117 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAGGCAGGCTAAATATATCAGATCTTATCTTCGC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCAGATCTTATCTTCGC
88516182 T
66 T
88516183 TAACAAGAGT
Statistics
Matches: 304, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
134 2 0.01
135 302 0.99
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (135 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATATAGCAGATCTTATCTTCGC
TGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATCTCCACGTACTGGCGATGGAGCAGA
TTCCA
Found at i:88528346 original size:23 final size:24
Alignment explanation
Indices: 88528302--88528348 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
88528292 TGTAAATTTA
88528302 AAATTTAGTCTCTTTATTTTTTTTT
1 AAATTTAGTCTCTTTA-TTTTTTTT
88528327 AAATTTAGTCT-TTCTATTTTTT
1 AAATTTAGTCTCTT-TATTTTTT
88528349 AGATTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (24 bp):
AAATTTAGTCTCTTTATTTTTTTT
Found at i:88528566 original size:12 final size:12
Alignment explanation
Indices: 88528551--88528576 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88528541 TTTGTAAATT
88528551 TTATTTTTATAA
1 TTATTTTTATAA
88528563 TTATTTTTATAA
1 TTATTTTTATAA
88528575 TT
1 TT
88528577 TATATGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTTTATAA
Found at i:88533118 original size:22 final size:23
Alignment explanation
Indices: 88533090--88533132 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
88533080 TCATGAAAAT
88533090 AAATTTA-AATTTTTAAAAATGA
1 AAATTTATAATTTTTAAAAATGA
**
88533112 AAATTTATGTTTTTTAAAAAT
1 AAATTTATAATTTTTAAAAAT
88533133 TATAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
AAATTTATAATTTTTAAAAATGA
Found at i:88533143 original size:24 final size:23
Alignment explanation
Indices: 88533099--88533143 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
88533089 TAAATTTAAA
*
88533099 TTTTTAAAAATGAAAATTTATGT
1 TTTTTAAAAATGAAAAATTATGT
*
88533122 TTTTTAAAAATTATAAAATTAT
1 TTTTTAAAAATGA-AAAATTAT
88533144 TTTACAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTTTAAAAATGAAAAATTATGT
Found at i:88536931 original size:34 final size:33
Alignment explanation
Indices: 88536892--88536972 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
88536882 CCAGATTAGG
*
88536892 AAAAAGGGTTAAGTTCAGGTACCAAATTGGACCA
1 AAAAAGGGTTAAGTTCAGGTACCAAATTAGA-CA
* * ** *
88536926 AAAAAGTGTCAAGTTTGGGTACTAAATTAGACA
1 AAAAAGGGTTAAGTTCAGGTACCAAATTAGACA
* *
88536959 GAAAAGGATTAAGT
1 AAAAAGGGTTAAGT
88536973 ATCAACTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
33 12 0.32
34 25 0.68
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (33 bp):
AAAAAGGGTTAAGTTCAGGTACCAAATTAGACA
Found at i:88537020 original size:31 final size:32
Alignment explanation
Indices: 88536979--88537062 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 32
88536969 AAGTATCAAC
* * *
88536979 TTAAGAAAAAATGTCAAATTTAGA-TGCTAAA
1 TTAAAAAAAAATGTCAAATTTAGAGTACGAAA
*
88537010 TTAAAAAAAAA--TCAAAATTA-AGTACGAAA
1 TTAAAAAAAAATGTCAAATTTAGAGTACGAAA
*
88537039 TTAAGAAAAAAATGTCAAGTTTAG
1 TTAA-AAAAAAATGTCAAATTTAG
88537063 GAAAAACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
28 1 0.02
29 17 0.40
30 7 0.17
31 10 0.24
32 7 0.17
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (32 bp):
TTAAAAAAAAATGTCAAATTTAGAGTACGAAA
Found at i:88537882 original size:23 final size:22
Alignment explanation
Indices: 88537834--88537883 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
88537824 TCTGAATCTT
* *
88537834 TAAATTCAAAAAATAGAAAGAT
1 TAAATTCAAAAAATAGAAAAAA
* *
88537856 TAAATTCTTAAAAATATAAAAAA
1 TAAATTC-AAAAAATAGAAAAAA
88537879 TAAAT
1 TAAAT
88537884 AACAAATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
TAAATTCAAAAAATAGAAAAAA
Found at i:88542184 original size:19 final size:20
Alignment explanation
Indices: 88542157--88542200 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
88542147 AAAATTGAAA
* *
88542157 ATTTGGAATTTTTATAAA-T
1 ATTTAGAATTTTTAAAAATT
88542176 ATTTAGAATTTTTAAAAATT
1 ATTTAGAATTTTTAAAAATT
88542196 ATTTA
1 ATTTA
88542201 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTAGAATTTTTAAAAATT
Found at i:88545058 original size:10 final size:10
Alignment explanation
Indices: 88545043--88545092 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
88545033 TAATTCTAGG
88545043 ATTTAT-TTT
1 ATTTATCTTT
88545052 CATTTATCTTT
1 -ATTTATCTTT
*
88545063 AATTATCTTT
1 ATTTATCTTT
88545073 ATTTAT-TTGT
1 ATTTATCTT-T
88545083 ATTTATCTTT
1 ATTTATCTTT
88545093 TAGAATTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:88553017 original size:10 final size:10
Alignment explanation
Indices: 88553004--88553063 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
88552994 TATTTCTAGG
88553004 ATTTAT-TTT
1 ATTTATCTTT
88553013 CATTTATCTTT
1 -ATTTATCTTT
88553024 ATTTATCTTT
1 ATTTATCTTT
*
88553034 AATTATCTTT
1 ATTTATCTTT
88553044 ATTTAT-TTGT
1 ATTTATCTT-T
88553054 ATTTATCTTT
1 ATTTATCTTT
88553064 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:88566218 original size:68 final size:68
Alignment explanation
Indices: 88566135--88566280 Score: 240
Period size: 68 Copynumber: 2.2 Consensus size: 68
88566125 ATTAGCAAAA
* * *
88566135 ATAT-AAAATATAAGTAGATTGGAAAGATTTGTTCTAAAATATAATTTATAAAATACCATTAAAA
1 ATATAAAAATGTAAGTAGATTGGAAAGATTTGTTATAAAATATAATTTACAAAATACCATTAAAA
88566199 ATT
66 ATT
* *
88566202 ATATAAAAATGTAAGTAGATTGGAAAGATTTGTTATAAAATATAATTTGCAAAATATCATTAAAA
1 ATATAAAAATGTAAGTAGATTGGAAAGATTTGTTATAAAATATAATTTACAAAATACCATTAAAA
88566267 ATT
66 ATT
88566270 ATATAAAAATG
1 ATATAAAAATG
88566281 ACGAGAGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
67 4 0.05
68 69 0.95
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.35
Consensus pattern (68 bp):
ATATAAAAATGTAAGTAGATTGGAAAGATTTGTTATAAAATATAATTTACAAAATACCATTAAAA
ATT
Found at i:88573077 original size:13 final size:13
Alignment explanation
Indices: 88573059--88573089 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
88573049 TTTCAAACCC
88573059 TAGAATTTTTAAA
1 TAGAATTTTTAAA
*
88573072 TAGAATTTTTCAA
1 TAGAATTTTTAAA
88573085 TAGAA
1 TAGAA
88573090 AAACTCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (13 bp):
TAGAATTTTTAAA
Found at i:88573423 original size:24 final size:22
Alignment explanation
Indices: 88573396--88573439 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
88573386 CCTTAGAAGG
88573396 AAAAAATATATATATGCGAACCTT
1 AAAAAA-AT-TATATGCGAACCTT
*
88573420 AAAAAAATTGTATGCGAACC
1 AAAAAAATTATATGCGAACC
88573440 CTTGGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (22 bp):
AAAAAAATTATATGCGAACCTT
Found at i:88573703 original size:15 final size:15
Alignment explanation
Indices: 88573683--88573732 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
88573673 CCCCTGTACA
*
88573683 AACCCTAGGTGTGCG
1 AACCCTAGATGTGCG
88573698 AACCCTAGATGTGCG
1 AACCCTAGATGTGCG
***
88573713 -ACCCTTTTTGTGCG
1 AACCCTAGATGTGCG
88573727 AACCCT
1 AACCCT
88573733 TGTACGAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (15 bp):
AACCCTAGATGTGCG
Found at i:88577197 original size:21 final size:21
Alignment explanation
Indices: 88577173--88577231 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
88577163 TTAAAACAAG
88577173 TGAAGAAAAAGAAAAAGAGAA
1 TGAAGAAAAAGAAAAAGAGAA
* *
88577194 TGAA-AAAGAGCAAAAAGAGAT
1 TGAAGAAAAAG-AAAAAGAGAA
88577215 TGAGAGTGAAAAAGAAA
1 TGA-A--GAAAAAGAAA
88577232 TTGAAGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.17
21 16 0.53
22 1 0.03
24 3 0.10
25 5 0.17
ACGTcount: A:0.64, C:0.02, G:0.25, T:0.08
Consensus pattern (21 bp):
TGAAGAAAAAGAAAAAGAGAA
Found at i:88577210 original size:27 final size:27
Alignment explanation
Indices: 88577178--88577229 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
88577168 ACAAGTGAAG
88577178 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
88577205 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
88577230 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:88580570 original size:104 final size:104
Alignment explanation
Indices: 88580443--88580644 Score: 386
Period size: 104 Copynumber: 1.9 Consensus size: 104
88580433 AATATTACGT
88580443 GTATGTAGTATGTCATACTCATAACCAGTCATATGAACGTCATTCACACATCAAAACCTACCATT
1 GTATGTAGTATGTCATACTCATAACCAGTCATATGAACGTCATTCACACATCAAAACCTACCATT
88580508 AGCGTTATAAAGGTCTTTTCATCAGTTAGGGGTAAAACA
66 AGCGTTATAAAGGTCTTTTCATCAGTTAGGGGTAAAACA
*
88580547 GTATGTAGTATGTCATACTCATAACCAGTCATATGAATGTCATTCACACATCAAAACCTACCATT
1 GTATGTAGTATGTCATACTCATAACCAGTCATATGAACGTCATTCACACATCAAAACCTACCATT
*
88580612 AGCGTTATAAAGGTCTTTTTATCAGTTAGGGGT
66 AGCGTTATAAAGGTCTTTTCATCAGTTAGGGGT
88580645 TCGGTAATTT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (104 bp):
GTATGTAGTATGTCATACTCATAACCAGTCATATGAACGTCATTCACACATCAAAACCTACCATT
AGCGTTATAAAGGTCTTTTCATCAGTTAGGGGTAAAACA
Found at i:88585291 original size:18 final size:18
Alignment explanation
Indices: 88585268--88585303 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
88585258 CTTCAAAAAG
88585268 AATGGCTTCACAAGATCA
1 AATGGCTTCACAAGATCA
88585286 AATGGCTTCACAAGATCA
1 AATGGCTTCACAAGATCA
88585304 CATCGATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
AATGGCTTCACAAGATCA
Found at i:88592337 original size:26 final size:26
Alignment explanation
Indices: 88592301--88592352 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
88592291 ATAAATGGAG
88592301 TAAGCATTAAGCTTAGTAAGCACGTA
1 TAAGCATTAAGCTTAGTAAGCACGTA
*
88592327 TAAGTATTAAGCTTAGTAAGCACGTA
1 TAAGCATTAAGCTTAGTAAGCACGTA
88592353 ATATAGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (26 bp):
TAAGCATTAAGCTTAGTAAGCACGTA
Found at i:88593566 original size:47 final size:47
Alignment explanation
Indices: 88593497--88593590 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
88593487 ATATTCAACA
88593497 ATGGCATATCTCAAAATCTTTAACGGTTTTAAAAACGAAGGTACGGG
1 ATGGCATATCTCAAAATCTTTAACGGTTTTAAAAACGAAGGTACGGG
88593544 ATGGCATATCTCAAAATCTTTAACGGTTTTAAAAACGAAGGTACGGG
1 ATGGCATATCTCAAAATCTTTAACGGTTTTAAAAACGAAGGTACGGG
88593591 TCAGCTAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (47 bp):
ATGGCATATCTCAAAATCTTTAACGGTTTTAAAAACGAAGGTACGGG
Found at i:88603219 original size:227 final size:227
Alignment explanation
Indices: 88602824--88603278 Score: 883
Period size: 227 Copynumber: 2.0 Consensus size: 227
88602814 ATAATTAAGG
*
88602824 ATGTCTAATATTTTAAATAGATTAGTTGAAACAAAATGCCGTCAAAGTGACCTCTTTTGTGTAGG
1 ATGTCTAATATTTTAAATAGATTAGTTGAAACAAAATGCCGTCAAAGTGACCTCTTTTGTGTAGA
*
88602889 TAAGCTTATTTAAATTATTAAGATGATTATATGTTTTTGTGATTCATGTGTTTATTAATTGACTT
66 TAACCTTATTTAAATTATTAAGATGATTATATGTTTTTGTGATTCATGTGTTTATTAATTGACTT
*
88602954 AAAGGTAAGTTAATATTTGGTAGAATTTCAACGACATCTGTGGTGATAAATGTGTGACAATTATA
131 AAAGGTAAGTTAATATTTGGTAGAATTTCAACGACATCTATGGTGATAAATGTGTGACAATTATA
88603019 AGGTACTTTATGTGAGCAATAAGTTAGTCCAA
196 AGGTACTTTATGTGAGCAATAAGTTAGTCCAA
88603051 ATGTCTAATATTTTAAATAGATTAGTTGAAACAAAATGCCGTCAAAGTGACCTCTTTTGTGTAGA
1 ATGTCTAATATTTTAAATAGATTAGTTGAAACAAAATGCCGTCAAAGTGACCTCTTTTGTGTAGA
88603116 TAACCTTATTTAAATTATTAAGATGATTATATGTTTTTGTGATTCATGTGTTTATTAATTGACTT
66 TAACCTTATTTAAATTATTAAGATGATTATATGTTTTTGTGATTCATGTGTTTATTAATTGACTT
88603181 AAAGGTAAGTTAATATTTGGTAGAATTTCAACGACATCTATGGTGATAAATGTGTGACAATTATA
131 AAAGGTAAGTTAATATTTGGTAGAATTTCAACGACATCTATGGTGATAAATGTGTGACAATTATA
88603246 AGGTACTTTATGTGAGCAATAAGTTAGTCCAA
196 AGGTACTTTATGTGAGCAATAAGTTAGTCCAA
88603278 A
1 A
88603279 GATTGATTCA
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
227 225 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (227 bp):
ATGTCTAATATTTTAAATAGATTAGTTGAAACAAAATGCCGTCAAAGTGACCTCTTTTGTGTAGA
TAACCTTATTTAAATTATTAAGATGATTATATGTTTTTGTGATTCATGTGTTTATTAATTGACTT
AAAGGTAAGTTAATATTTGGTAGAATTTCAACGACATCTATGGTGATAAATGTGTGACAATTATA
AGGTACTTTATGTGAGCAATAAGTTAGTCCAA
Found at i:88608057 original size:7 final size:7
Alignment explanation
Indices: 88608045--88608114 Score: 86
Period size: 7 Copynumber: 9.9 Consensus size: 7
88608035 AAATCTAGGG
88608045 AGGGTTT
1 AGGGTTT
88608052 AGGGTTT
1 AGGGTTT
*
88608059 ATGGTTTT
1 A-GGGTTT
*
88608067 AGGGCTT
1 AGGGTTT
*
88608074 AGTGTTT
1 AGGGTTT
*
88608081 AGGGCTT
1 AGGGTTT
*
88608088 AAGGTTT
1 AGGGTTT
88608095 AGGGTTT
1 AGGGTTT
88608102 AGGGTTT
1 AGGGTTT
88608109 AGGGTT
1 AGGGTT
88608115 GATTTGTTAG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
7 46 0.88
8 6 0.12
ACGTcount: A:0.16, C:0.03, G:0.39, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:88608584 original size:61 final size:60
Alignment explanation
Indices: 88608456--88608585 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 60
88608446 GACCACACGC
* *
88608456 CCGTGTCTATTTAGTAGACTTTAACACGACCTAAGCCACCTCACACGGGCGTGGAAAATG
1 CCGTGTCTATTTAGTAGACTTTAACACGACCTAAGCCACATCACACGGGCATGGAAAATG
* * * * *
88608516 CCTGTGTCTATTTAGTAGACTTTAGCACGGCTTAAGCCACATCACACGGGCATGGCACATGG
1 CC-GTGTCTATTTAGTAGACTTTAACACGACCTAAGCCACATCACACGGGCATGGAAAAT-G
88608578 CCGTGTCT
1 CCGTGTCT
88608586 CTATCGAGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
60 2 0.03
61 56 0.92
62 3 0.05
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (60 bp):
CCGTGTCTATTTAGTAGACTTTAACACGACCTAAGCCACATCACACGGGCATGGAAAATG
Found at i:88609608 original size:26 final size:24
Alignment explanation
Indices: 88609568--88609627 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
88609558 TTATTTCATT
* * *
88609568 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
88609592 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
88609618 AAATAAATAT
1 AAATAAATAT
88609628 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:88609639 original size:22 final size:22
Alignment explanation
Indices: 88609598--88609656 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
88609588 ATAATAAATC
* *
88609598 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
88609618 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
88609640 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
88609657 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:88609733 original size:15 final size:16
Alignment explanation
Indices: 88609703--88609735 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
88609693 AAATAGTTAT
88609703 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
88609720 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
88609735 A
1 A
88609736 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:88613972 original size:44 final size:44
Alignment explanation
Indices: 88613909--88614037 Score: 185
Period size: 44 Copynumber: 3.0 Consensus size: 44
88613899 GGCGTTCGAT
*
88613909 ACGCCCGTGCCCACCACCCGTGGTCGAAACTATCAAAATAACAC
1 ACGCCCGTGCCCACCACCCGTGGTCGAAACTGTCAAAATAACAC
* * *
88613953 ACGCCCGTACCCACCACCCGTGGTCGAAATTGTCAAAAT--GAC
1 ACGCCCGTGCCCACCACCCGTGGTCGAAACTGTCAAAATAACAC
*
88613995 A-GCCCGTGCCCACCA-TCGTGGTCGAAACTGTCAAAATAACAC
1 ACGCCCGTGCCCACCACCCGTGGTCGAAACTGTCAAAATAACAC
88614037 A
1 A
88614038 GGGGTGGGAG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
40 20 0.27
41 13 0.17
42 6 0.08
44 36 0.48
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.16
Consensus pattern (44 bp):
ACGCCCGTGCCCACCACCCGTGGTCGAAACTGTCAAAATAACAC
Found at i:88616110 original size:30 final size:29
Alignment explanation
Indices: 88616076--88616156 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
88616066 ATTTTTGAAG
* *
88616076 ACTTTTATTTATTATTTAT-TATTTTTATTT
1 ACTTTTATTT-TTATTTATCT-TTTTAAATT
*
88616106 ACTTTTATCTTTATTTATCTTTTTAAATT
1 ACTTTTATTTTTATTTATCTTTTTAAATT
88616135 ACTTTT-TATTTTATTTATCTTT
1 ACTTTTAT-TTTTATTTATCTTT
88616157 AATACTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 1 0.02
29 34 0.76
30 10 0.22
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (29 bp):
ACTTTTATTTTTATTTATCTTTTTAAATT
Found at i:88616113 original size:16 final size:16
Alignment explanation
Indices: 88616076--88616128 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
88616066 ATTTTTGAAG
88616076 ACTTTTATTTATTATTT
1 ACTTTTATTT-TTATTT
88616093 A---TTATTTTTATTT
1 ACTTTTATTTTTATTT
*
88616106 ACTTTTATCTTTATTT
1 ACTTTTATTTTTATTT
88616122 ATCTTTT
1 A-CTTTT
88616129 TAAATTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
16 12 0.39
17 6 0.19
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (16 bp):
ACTTTTATTTTTATTT
Found at i:88623029 original size:29 final size:29
Alignment explanation
Indices: 88622996--88623052 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
88622986 GGTCCAACAC
* *
88622996 ATGACCTTTCACATGGCTATGTGTCACAA
1 ATGACCTATCACATGGCCATGTGTCACAA
88623025 ATGACCTATCACATGGCCATGTGTCACA
1 ATGACCTATCACATGGCCATGTGTCACA
88623053 TACGGCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (29 bp):
ATGACCTATCACATGGCCATGTGTCACAA
Found at i:88623061 original size:29 final size:29
Alignment explanation
Indices: 88622998--88623066 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
88622988 TCCAACACAT
* * *
88622998 GACCTTTCACATGGCTATGTGTCACAAAT
1 GACCTATCACATGGCCATGTGTCACAAAC
*
88623027 GACCTATCACATGGCCATGTGTCACATAC
1 GACCTATCACATGGCCATGTGTCACAAAC
* *
88623056 GGCCTACCACA
1 GACCTATCACA
88623067 CAGTTTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
GACCTATCACATGGCCATGTGTCACAAAC
Found at i:88625695 original size:13 final size:14
Alignment explanation
Indices: 88625672--88625700 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
88625662 AGCTTACACC
88625672 AAAACCAAAAAAAT
1 AAAACCAAAAAAAT
88625686 AAAA-CAAAAAAAT
1 AAAACCAAAAAAAT
88625699 AA
1 AA
88625701 TAATAAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACCAAAAAAAT
Found at i:88626931 original size:3 final size:3
Alignment explanation
Indices: 88626923--88626961 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
88626913 TACTTATGTA
88626923 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
88626962 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:88627629 original size:13 final size:13
Alignment explanation
Indices: 88627611--88627658 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
88627601 ATGATAGAGT
88627611 TAATTTAATCTTA
1 TAATTTAATCTTA
*
88627624 TAATTTATATTTTAA
1 TAATTTA-ATCTT-A
*
88627639 TTATTTAATCTTA
1 TAATTTAATCTTA
88627652 TAATTTA
1 TAATTTA
88627659 TATTTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 14 0.48
14 8 0.28
15 7 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (13 bp):
TAATTTAATCTTA
Found at i:88627649 original size:28 final size:28
Alignment explanation
Indices: 88627613--88627668 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
88627603 GATAGAGTTA
88627613 ATTTAATCTTATAATTTATATTTTAATT
1 ATTTAATCTTATAATTTATATTTTAATT
88627641 ATTTAATCTTATAATTTATATTTTAATT
1 ATTTAATCTTATAATTTATATTTTAATT
88627669 CCATGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTAATCTTATAATTTATATTTTAATT
Found at i:88630245 original size:25 final size:26
Alignment explanation
Indices: 88630208--88630260 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
88630198 GTCTAATGAG
*
88630208 AATAGTTTATTAAA-TAAAAATAAAAT
1 AATACTTTATTAAAGT-AAAATAAAAT
*
88630234 AATACTTT-TTAAAGTAGAATAAAAT
1 AATACTTTATTAAAGTAAAATAAAAT
88630259 AA
1 AA
88630261 CATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (26 bp):
AATACTTTATTAAAGTAAAATAAAAT
Found at i:88633311 original size:15 final size:15
Alignment explanation
Indices: 88633270--88633318 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
88633260 TAATCAAAAT
88633270 TAGATAAAATTATCA
1 TAGATAAAATTATCA
**** *
88633285 TAGACCCCATTATAA
1 TAGATAAAATTATCA
88633300 TAGATAAAATTATCA
1 TAGATAAAATTATCA
88633315 TAGA
1 TAGA
88633319 AGTCTCTGTA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (15 bp):
TAGATAAAATTATCA
Found at i:88637207 original size:21 final size:23
Alignment explanation
Indices: 88637181--88637238 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
88637171 TTAAAAAACA
*
88637181 ATAATA-AATAA-AATAGTAAAT
1 ATAATATAATAATAATACTAAAT
*
88637202 ATAATAGTAAAAATAATACTAAAT
1 ATAATA-TAATAATAATACTAAAT
88637226 ATAATATAATAAT
1 ATAATATAATAAT
88637239 TATTGATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 6 0.19
23 10 0.32
24 15 0.48
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAATATAATAATAATACTAAAT
Found at i:88637215 original size:14 final size:12
Alignment explanation
Indices: 88637180--88637231 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
88637170 ATTAAAAAAC
*
88637180 AATAATAAATAA
1 AATAGTAAATAA
*
88637192 AATAGTAAATAT
1 AATAGTAAATAA
88637204 AATAGTAAA-AA
1 AATAGTAAATAA
* *
88637215 TAATACTAAATAT
1 -AATAGTAAATAA
88637228 AATA
1 AATA
88637232 TAATAATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (12 bp):
AATAGTAAATAA
Found at i:88637867 original size:24 final size:23
Alignment explanation
Indices: 88637819--88637868 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
88637809 TGTGATTTCT
**
88637819 TATTTTTTTATTTTTTTGTACTA
1 TATTTTTTTATTTTTTAATACTA
88637842 TATTTTTTTATATGTTTTAATA-TA
1 TATTTTTTTAT-T-TTTTAATACTA
88637866 TAT
1 TAT
88637869 GTGAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 6 0.26
25 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TATTTTTTTATTTTTTAATACTA
Found at i:88639441 original size:12 final size:12
Alignment explanation
Indices: 88639426--88639450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88639416 AATAAAGAGG
88639426 AAAATAAAAAAT
1 AAAATAAAAAAT
88639438 AAAATAAAAAAT
1 AAAATAAAAAAT
88639450 A
1 A
88639451 CACCTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:88640149 original size:21 final size:21
Alignment explanation
Indices: 88640125--88640189 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
88640115 ATACTATATA
88640125 TATACATATTATATATATTCT
1 TATACATATTATATATATTCT
** * * *
88640146 TATAGTTGTTTTATATA-T-A
1 TATACATATTATATATATTCT
88640165 TATACATATTATATATATTCT
1 TATACATATTATATATATTCT
88640186 TATA
1 TATA
88640190 GTTGTTTTAT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
21 17 0.53
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (21 bp):
TATACATATTATATATATTCT
Found at i:88640159 original size:23 final size:23
Alignment explanation
Indices: 88640133--88640203 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
88640123 TATATACATA
88640133 TTATATATATTCTTATAGTTGTT
1 TTATATATATTCTTATAGTTGTT
** *
88640156 TTATATATA----TATA--CATA
1 TTATATATATTCTTATAGTTGTT
88640173 TTATATATATTCTTATAGTTGTT
1 TTATATATATTCTTATAGTTGTT
88640196 TTATATAT
1 TTATATAT
88640204 TATTATTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 10 0.28
19 4 0.11
21 4 0.11
23 18 0.50
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATATATTCTTATAGTTGTT
Found at i:88640160 original size:19 final size:19
Alignment explanation
Indices: 88640138--88640201 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
88640128 ACATATTATA
88640138 TATATTCTTATAGTTGTTT
1 TATATTCTTATAGTTGTTT
* ** *
88640157 TATATAT-ATATACATATTAT
1 TATAT-TCTTATAGTTGTT-T
88640177 ATATATTCTTATAGTTGTTT
1 -TATATTCTTATAGTTGTTT
88640197 TATAT
1 TATAT
88640202 ATTATTATTG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 17 0.52
20 4 0.12
21 12 0.36
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (19 bp):
TATATTCTTATAGTTGTTT
Found at i:88640163 original size:40 final size:40
Alignment explanation
Indices: 88640119--88640203 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
88640109 AAATTAATAC
88640119 TATATATATACATATTATATATATTCTTATAGTTGTTTTA
1 TATATATATACATATTATATATATTCTTATAGTTGTTTTA
88640159 TATATATATACATATTATATATATTCTTATAGTTGTTTTA
1 TATATATATACATATTATATATATTCTTATAGTTGTTTTA
88640199 TATAT
1 TATAT
88640204 TATTATTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (40 bp):
TATATATATACATATTATATATATTCTTATAGTTGTTTTA
Found at i:88640200 original size:21 final size:21
Alignment explanation
Indices: 88640136--88640209 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
88640126 ATACATATTA
88640136 TATATATTCTTATAGTTGTTT
1 TATATATTCTTATAGTTGTTT
* ** * *
88640157 TATATA-T-ATATACATATTA
1 TATATATTCTTATAGTTGTTT
88640176 TATATATTCTTATAGTTGTTT
1 TATATATTCTTATAGTTGTTT
*
88640197 TATATATTATTAT
1 TATATATTCTTAT
88640210 TGTTCCTAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 25 0.62
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.58
Consensus pattern (21 bp):
TATATATTCTTATAGTTGTTT
Found at i:88652600 original size:43 final size:43
Alignment explanation
Indices: 88652537--88652714 Score: 164
Period size: 43 Copynumber: 4.1 Consensus size: 43
88652527 CTAGAATCAG
* *
88652537 TGAATTCACCAGACCTTAACCCCCTAAGTAGTAGGGTAACAGGT
1 TGAATTC-GCAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
* * *
88652581 TGAATTCGCAGATCTTAACCCCCTAAGCAGTAGGGAAACAGAT
1 TGAATTCGCAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
* * * **
88652624 CGAAGAT-G-ATGAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCA
1 TGAA-TTCGCA-GA-CCTTAACCCCCTAAGCAGTAGGGTAAC-AGGT
* * * *
88652669 T-AATTTGCAGGCCTTAACCCCCTAAGCAGTAGGGTAATAGGC
1 TGAATTCGCAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
88652711 TGAA
1 TGAA
88652715 AATTAAAGAT
Statistics
Matches: 108, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.04
43 65 0.60
44 36 0.33
45 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (43 bp):
TGAATTCGCAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
Found at i:88652924 original size:44 final size:43
Alignment explanation
Indices: 88652854--88652978 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
88652844 CTAAATGTAC
*
88652854 AGACCTTAAACCCC-TAAGCAGTAGGGTAATAGGTTGAATTCAA
1 AGACCTT-AACCCCTTAAGCAGTAGGGTAATAGGCTGAATTCAA
* * * * * ***
88652897 AGGGCTTTAACCCCTTAAGCAGTAGGGTAACAAGCCGAATTTGC
1 A-GACCTTAACCCCTTAAGCAGTAGGGTAATAGGCTGAATTCAA
88652941 AGACCTTAACCCCTTAAGCAGTAGGGTAATAGGCTGAA
1 AGACCTTAACCCCTTAAGCAGTAGGGTAATAGGCTGAA
88652979 AATTACAGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
43 39 0.59
44 27 0.41
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (43 bp):
AGACCTTAACCCCTTAAGCAGTAGGGTAATAGGCTGAATTCAA
Found at i:88653598 original size:23 final size:23
Alignment explanation
Indices: 88653571--88653624 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
88653561 CAATTTTGGG
*
88653571 CCCAAAACCCCTAACCTAATTTA
1 CCCAAAACCCCTAACCCAATTTA
88653594 CCCAAAACCCCTAACCCAATTTA
1 CCCAAAACCCCTAACCCAATTTA
88653617 CCCAAAAC
1 CCCAAAAC
88653625 ACTAAACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.17
Consensus pattern (23 bp):
CCCAAAACCCCTAACCCAATTTA
Found at i:88654846 original size:21 final size:21
Alignment explanation
Indices: 88654822--88654884 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
88654812 ATACTATATA
88654822 TATACATATTATATATATTCT
1 TATACATATTATATATATTCT
** * *
88654843 TATAGTTGTT-T-TATA-T-A
1 TATACATATTATATATATTCT
88654860 TATACATATTATATATATTCT
1 TATACATATTATATATATTCT
88654881 TATA
1 TATA
88654885 GTTGTTTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
17 7 0.23
18 2 0.07
19 8 0.27
20 2 0.07
21 11 0.37
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (21 bp):
TATACATATTATATATATTCT
Found at i:88654859 original size:38 final size:38
Alignment explanation
Indices: 88654816--88654898 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
88654806 AAATTAATAC
88654816 TATATATATACATATTATATATATTCTTATAGTTGTTT
1 TATATATATACATATTATATATATTCTTATAGTTGTTT
88654854 TATATATATACATATTATATATATTCTTATAGTTGTTT
1 TATATATATACATATTATATATATTCTTATAGTTGTTT
88654892 TATATAT
1 TATATAT
88654899 TATTATTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (38 bp):
TATATATATACATATTATATATATTCTTATAGTTGTTT
Found at i:88654895 original size:21 final size:21
Alignment explanation
Indices: 88654833--88654904 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
88654823 ATACATATTA
88654833 TATATATTCTTATAGTTGTTT
1 TATATATTCTTATAGTTGTTT
** * *
88654854 TATATA----TATACATATTA
1 TATATATTCTTATAGTTGTTT
88654871 TATATATTCTTATAGTTGTTT
1 TATATATTCTTATAGTTGTTT
*
88654892 TATATATTATTAT
1 TATATATTCTTAT
88654905 TGTTCCTAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
17 13 0.34
21 25 0.66
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (21 bp):
TATATATTCTTATAGTTGTTT
Found at i:88655247 original size:2 final size:2
Alignment explanation
Indices: 88655240--88655286 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
88655230 TTTATATCTC
*
88655240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
88655281 GT AT AT
1 AT AT AT
88655287 TTTCCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:88656596 original size:10 final size:10
Alignment explanation
Indices: 88656581--88656619 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
88656571 TTCTGGGAAG
88656581 ATACTACAAT
1 ATACTACAAT
*
88656591 ATACTATCATAG
1 ATACTA-CA-AT
88656603 ATACTACAAT
1 ATACTACAAT
88656613 ATACTAC
1 ATACTAC
88656620 CATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.56
11 4 0.16
12 7 0.28
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (10 bp):
ATACTACAAT
Found at i:88656604 original size:22 final size:22
Alignment explanation
Indices: 88656579--88656623 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
88656569 TCTTCTGGGA
*
88656579 AGATACTACAATATACTATCAT
1 AGATACTACAATATACTACCAT
88656601 AGATACTACAATATACTACCAT
1 AGATACTACAATATACTACCAT
88656623 A
1 A
88656624 AATAAATGCT
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:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (22 bp):
AGATACTACAATATACTACCAT
Found at i:88658095 original size:70 final size:70
Alignment explanation
Indices: 88657977--88658112 Score: 227
Period size: 70 Copynumber: 1.9 Consensus size: 70
88657967 GGTATGGGTT
* *
88657977 AATAATCAAGTGTTAGTATTTTTACCCAATAATGTTATAAAGGGTGTAGGTTCAAACCCCACCAA
1 AATAATCAAGTGGTAGTATTTTTACCCAAGAATGTTATAAAGGGTGTAGGTTCAAACCCCACCAA
88658042 GATCA
66 GATCA
* * *
88658047 AATAGTCAAGTGGTAGTATTTTTACCCAGGAATGTTATAAAGGGTGTAGGTTCAAACCTCACCAA
1 AATAATCAAGTGGTAGTATTTTTACCCAAGAATGTTATAAAGGGTGTAGGTTCAAACCCCACCAA
88658112 G
66 G
88658113 CTAAATGCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (70 bp):
AATAATCAAGTGGTAGTATTTTTACCCAAGAATGTTATAAAGGGTGTAGGTTCAAACCCCACCAA
GATCA
Found at i:88659463 original size:17 final size:16
Alignment explanation
Indices: 88659432--88659465 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
88659422 GCTAAAGGTC
88659432 ATAAAAATTAAAAAAA
1 ATAAAAATTAAAAAAA
88659448 ATAAAATATTATAAAAAA
1 ATAAAA-ATTA-AAAAAA
88659466 GTCCTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAAAAATTAAAAAAA
Found at i:88663671 original size:15 final size:15
Alignment explanation
Indices: 88663624--88663672 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
88663614 CCCCTATCAC
*
88663624 CACCTCTTCCACCAC
1 CACCTCTTCCACCAT
* *
88663639 CTCCTCTTCC-TC-T
1 CACCTCTTCCACCAT
88663652 C-CCTCTTCCACCAT
1 CACCTCTTCCACCAT
88663666 CACCTCT
1 CACCTCT
88663673 GCCCCTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 3 0.11
15 14 0.52
ACGTcount: A:0.12, C:0.57, G:0.00, T:0.31
Consensus pattern (15 bp):
CACCTCTTCCACCAT
Found at i:88664137 original size:23 final size:23
Alignment explanation
Indices: 88664118--88664180 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
88664108 TAAAAAATGC
88664118 TAATACAATTACATATAAAATTT
1 TAATACAATTACATATAAAATTT
*
88664141 TAATA-AATATAAAT-TAAAAATTT
1 TAATACAAT-TACATAT-AAAATTT
88664164 TAATACAATTACATATA
1 TAATACAATTACATATA
88664181 TAGGATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATACAATTACATATAAAATTT
Found at i:88664200 original size:46 final size:46
Alignment explanation
Indices: 88664118--88664207 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
88664108 TAAAAAATGC
*
88664118 TAATACAATTACATATAAAATTTTAATAAATATAAATTAAAAATTT
1 TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
* *
88664164 TAATACAATTACATATATAGGATATTAA-ATAT-TAAATTAAAAAT
1 TAATACAATTACATATA-A-AATATTAATAAATATAAATTAAAAAT
88664208 AATATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 29 0.74
47 4 0.10
48 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (46 bp):
TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
Found at i:88665360 original size:7 final size:7
Alignment explanation
Indices: 88665348--88665455 Score: 67
Period size: 7 Copynumber: 15.1 Consensus size: 7
88665338 ACTAATTAAT
88665348 CTAAACC
1 CTAAACC
88665355 CTAAACC
1 CTAAACC
*
88665362 TCTTAACCC
1 -C-TAAACC
*
88665371 CT-ATCC
1 CTAAACC
*
88665377 CATAAACA
1 C-TAAACC
*
88665385 CTAAACT
1 CTAAACC
88665392 CTAAACC
1 CTAAACC
*
88665399 CTTACACC
1 C-TAAACC
* *
88665407 TTAAACT
1 CTAAACC
88665414 CT-AACC
1 CTAAACC
*
88665420 CTAACCC
1 CTAAACC
88665427 CTAAACC
1 CTAAACC
*
88665434 CTAAATC
1 CTAAACC
* *
88665441 ATAATCC
1 CTAAACC
88665448 CTAAACC
1 CTAAACC
88665455 C
1 C
88665456 ATAATTCATC
Statistics
Matches: 75, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
6 9 0.12
7 51 0.68
8 10 0.13
9 5 0.07
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:88665535 original size:46 final size:46
Alignment explanation
Indices: 88665482--88665569 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
88665472 CTTCAAATAC
*
88665482 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAGCCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAGCCA
88665528 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAA
88665570 ATCATAAACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAGCCA
Found at i:88665568 original size:21 final size:21
Alignment explanation
Indices: 88665498--88665582 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
88665488 ACTCCTAAAC
*
88665498 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* * *
88665519 CTTAAGCCATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
88665544 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
88665565 CTTAAATCATAAACCATA
1 CTTAAACCATAAACCATA
88665583 AACTATAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
21 30 0.60
22 3 0.06
24 3 0.06
25 14 0.28
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:88665933 original size:82 final size:80
Alignment explanation
Indices: 88665748--88666149 Score: 432
Period size: 81 Copynumber: 5.0 Consensus size: 80
88665738 TTATATGACT
* * * * * *
88665748 TTTAGCGCCGTTTCTTCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGCGTTTTACAAAAGCGC
1 TTTAGCGGCGTTT-TCCATAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTCCAAAAGCGC
*
88665813 CGCTAATGCTCTGGTC
65 CGCTAATGCTCTAGTC
*
88665829 TTTAGCGGCGTTTTGCCATAAGCGCCTCTAATGCTCTGGTCTTTAGCGGCGTTTTGCCAAAAGCG
1 TTTAGCGGCGTTTT-CCATAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTT-CCAAAAGCG
88665894 CCGCTAATGCTCTAGTC
64 CCGCTAATGCTCTAGTC
* * * * *
88665911 ATTAGCGGCGGTTTTCCTTAAGCGGCGCTAATGCTCTGGTCATTATCGGCGCTTTTCCAAAAGCG
1 TTTAGCGGC-GTTTTCCATAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTTTCCAAAAGCG
* *
88665976 GCGCTAATGCTCTGGTC
64 CCGCTAATGCTCTAGTC
* * * *
88665993 TTTAGCGGCGTTTTACAAAAGCGCCGCTAATGCTC-AGTCTTTAGCGGCGTTTTACCAAAACCGC
1 TTTAGCGGCGTTTTCCATAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTT-CCAAAAGCGC
*
88666057 CGCTAATGCT-TAGTT
65 CGCTAATGCTCTAGTC
* * * ** * ** *
88666072 TTTAGCGGCGTTTTCTACTAAAACGCCGTTGTTGCTCT-GTTTTTAGCGGCGTTTTATAAAAAAC
1 TTTAGCGGCGTTTTCCA-T-AAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTT-CCAAAAGC
*
88666136 GCCGCTATTGCTCT
63 GCCGCTAATGCTCT
88666150 GTATTTTAAA
Statistics
Matches: 272, Mismatches: 40, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
79 22 0.08
80 30 0.11
81 115 0.42
82 96 0.35
83 9 0.03
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (80 bp):
TTTAGCGGCGTTTTCCATAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTCCAAAAGCGCC
GCTAATGCTCTAGTC
Found at i:88666151 original size:40 final size:41
Alignment explanation
Indices: 88665764--88666150 Score: 439
Period size: 41 Copynumber: 9.5 Consensus size: 41
88665754 GCCGTTTCTT
* *
88665764 CAAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGCGTTTTA-
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
*
88665804 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTGC
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
* * *
88665845 CATAAGCGCCTCTAATGCTCTGGTCTTTAGCGGCGTTTTGC
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
* *
88665886 CAAAAGCGCCGCTAATGCTCTAGTCATTAGCGGCGGTTTT-C
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGC-GTTTTAC
** * * *
88665927 CTTAAGCGGCGCTAATGCTCTGGTCATTATCGGCGCTTTT-C
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTTTAC
*
88665968 CAAAAGCGGCGCTAATGCTCTGGTCTTTAGCGGCGTTTTA-
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
*
88666008 CAAAAGCGCCGCTAATGCTC-AGTCTTTAGCGGCGTTTTAC
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
* * *
88666048 CAAAACCGCCGCTAATGCT-TAGTTTTTAGCGGCGTTTTCTAC
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTT-TAC
* * ** * *
88666090 TAAAA-CGCCGTTGTTGCTCT-GTTTTTAGCGGCGTTTTAT
1 CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
* * *
88666129 AAAAAACGCCGCTATTGCTCTG
1 CAAAAGCGCCGCTAATGCTCTG
88666151 TATTTTAAAA
Statistics
Matches: 306, Mismatches: 30, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
39 24 0.08
40 108 0.35
41 161 0.53
42 13 0.04
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTAC
Found at i:88671506 original size:21 final size:21
Alignment explanation
Indices: 88671482--88671537 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
88671472 TTAGCTTGTC
*
88671482 TTATTTTTATTTTTGCCTTTA
1 TTATTTTTATTTTTGCCCTTA
* *
88671503 TTATTGTTATTTTATTCCCTTA
1 TTATTTTTATTTT-TGCCCTTA
*
88671525 TT-TGTTTATTTTT
1 TTATTTTTATTTTT
88671538 TTATGTACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 20 0.69
22 8 0.28
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATTTTTATTTTTGCCCTTA
Found at i:88673447 original size:18 final size:18
Alignment explanation
Indices: 88673424--88673465 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
88673414 TTCAAGGTGC
88673424 AATTAATTTAAAATT-TTT
1 AATTAA-TTAAAATTATTT
*
88673442 AATTAATTAAATTTATTT
1 AATTAATTAAAATTATTT
88673460 AATTAA
1 AATTAA
88673466 AAAACTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAATTAAAATTATTT
Found at i:88676520 original size:15 final size:16
Alignment explanation
Indices: 88676490--88676533 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
88676480 AAAATGTAAT
88676490 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
88676506 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
*
88676521 TTTTTTCATTTTA
1 -TTTATCATTTTA
88676534 TAAATTAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:88676532 original size:16 final size:16
Alignment explanation
Indices: 88676486--88676536 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
88676476 GTAAAAAATG
88676486 TAATTTTATCATTTTAA
1 TAATTTTATCATTTT-A
88676503 TAA-TTTAT-ATTTTTA
1 TAATTTTATCA-TTTTA
*
88676518 TAATTTTTTCATTTTA
1 TAATTTTATCATTTTA
88676534 TAA
1 TAA
88676537 ATTAGTACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATCATTTTA
Found at i:88677700 original size:23 final size:23
Alignment explanation
Indices: 88677668--88677720 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
88677658 TTAGTGGCTA
* *
88677668 GTATTTTGTGATGCCTTTTTGGC
1 GTATTCTGTGATGCCTTTGTGGC
88677691 GTATTCTGTGATGCCTTTGTGGC
1 GTATTCTGTGATGCCTTTGTGGC
*
88677714 ATATTCT
1 GTATTCT
88677721 ATGACATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (23 bp):
GTATTCTGTGATGCCTTTGTGGC
Found at i:88678678 original size:137 final size:137
Alignment explanation
Indices: 88678432--88678704 Score: 494
Period size: 137 Copynumber: 2.0 Consensus size: 137
88678422 TTGGCGTATA
88678432 TGTAAGTGCCTATATTAAATAAGCATCTGTCAAAGACTGAAAACAAATTCAGAATCTTTAAGTTG
1 TGTAAGTGCCTATATTAAATAAGCATCTGTCAAAGACTGAAAACAAATTCAGAATCTTTAAGTTG
*
88678497 TGGAAATCAACAGTAAACATTCAAAGGTAACTTGGATTGAAATTCACTAAGTCCGTTGAACTTAT
66 TGGAAATCAACAGTAAACATTCAAAGGTAACTTAGATTGAAATTCACTAAGTCCGTTGAACTTAT
88678562 TAGTGTT
131 TAGTGTT
* *
88678569 TGTAAGTGCCTATATTAGAA-AAGTATCTGTCAAAGACTGAAAACAAATTTAGAATCTTTAAGTT
1 TGTAAGTGCCTATATTA-AATAAGCATCTGTCAAAGACTGAAAACAAATTCAGAATCTTTAAGTT
*
88678633 GTGGAAATCAACAGTAAACATTCAAAGGTAACTTAGATTGAAATTCACTAAGTTCGTTGAACTTA
65 GTGGAAATCAACAGTAAACATTCAAAGGTAACTTAGATTGAAATTCACTAAGTCCGTTGAACTTA
88678698 TTAGTGT
130 TTAGTGT
88678705 CTGTTGTTAG
Statistics
Matches: 131, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
137 129 0.98
138 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (137 bp):
TGTAAGTGCCTATATTAAATAAGCATCTGTCAAAGACTGAAAACAAATTCAGAATCTTTAAGTTG
TGGAAATCAACAGTAAACATTCAAAGGTAACTTAGATTGAAATTCACTAAGTCCGTTGAACTTAT
TAGTGTT
Found at i:88679213 original size:18 final size:19
Alignment explanation
Indices: 88679176--88679223 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
88679166 CGAGTTGATC
88679176 CAAATAACTTGATAATTAACT
1 CAAATAACTTG--AATTAACT
88679197 CAAATAACTTG-ATTAACT
1 CAAATAACTTGAATTAACT
88679215 CAAATAACT
1 CAAATAACT
88679224 CAAACTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.59
21 11 0.41
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (19 bp):
CAAATAACTTGAATTAACT
Found at i:88682106 original size:40 final size:40
Alignment explanation
Indices: 88682042--88682118 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
88682032 GATGGGTACC
* *
88682042 TTATGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCAT
1 TTATGGTGTGCAGGGATGGATGGGTCGATTATATCCCCAT
* *
88682082 TTATGGTGTGCAGGGATGGGTGGGTCGATTTTATCCC
1 TTATGGTGTGCAGGGATGGATGGGTCGATTATATCCC
88682119 AGCTTGGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.16, C:0.13, G:0.35, T:0.36
Consensus pattern (40 bp):
TTATGGTGTGCAGGGATGGATGGGTCGATTATATCCCCAT
Found at i:88686850 original size:5 final size:5
Alignment explanation
Indices: 88686819--88686849 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
88686809 TCACTAGTTA
*
88686819 GGTTG GGTTG GGTTG GGTTG GGTTG GTTTG G
1 GGTTG GGTTG GGTTG GGTTG GGTTG GGTTG G
88686850 TGAGTAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
GGTTG
Found at i:88689952 original size:17 final size:16
Alignment explanation
Indices: 88689930--88689969 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
88689920 AAAAAAAGTG
*
88689930 ATAAAAAGTACAAAAAA
1 ATAAAAACTA-AAAAAA
*
88689947 ATAAAATCTAAAAAAA
1 ATAAAAACTAAAAAAA
88689963 ATAAAAA
1 ATAAAAA
88689970 AATATTCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (16 bp):
ATAAAAACTAAAAAAA
Found at i:88692988 original size:14 final size:15
Alignment explanation
Indices: 88692969--88693025 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
88692959 AATCTTTAAG
88692969 GATATG-CAATCTTA
1 GATATGACAATCTTA
88692983 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
88693000 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
88693019 GATATGA
1 GATATGA
88693026 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:88693010 original size:36 final size:38
Alignment explanation
Indices: 88692969--88693047 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
88692959 AATCTTTAAG
88692969 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
88693005 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
88693045 GAT
1 GAT
88693048 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:88693016 original size:19 final size:19
Alignment explanation
Indices: 88692969--88693047 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
88692959 AATCTTTAAG
88692969 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
88692988 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
88693005 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
88693024 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
88693045 GAT
1 GAT
88693048 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:88700650 original size:31 final size:31
Alignment explanation
Indices: 88700592--88700650 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
88700582 GGTGCAATTA
* *
88700592 TATAAATGAAACTTTTATTGTGGTTCAAATG
1 TATAAATGAAACTTTCATTGTGATTCAAATG
* *
88700623 TATACATGAAACTTTCATTTTGATTCAA
1 TATAAATGAAACTTTCATTGTGATTCAA
88700651 TCATACACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (31 bp):
TATAAATGAAACTTTCATTGTGATTCAAATG
Found at i:88701914 original size:24 final size:24
Alignment explanation
Indices: 88701899--88701950 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
88701889 AATCAATGTC
*
88701899 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
88701923 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
88701947 AAAT
1 AAAT
88701951 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:88704429 original size:6 final size:6
Alignment explanation
Indices: 88704403--88704515 Score: 54
Period size: 6 Copynumber: 18.3 Consensus size: 6
88704393 AATAAACATT
* * * *
88704403 ATCAGA A-CTAGA ATCAAA ATGAGA ATGAGA ATCAGA ATCAGA ATCAGGTG
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* * * *
88704453 AT-AGA ATCAGA ATTAG- GTGACAGA ATCAAA ATCAGT ATCAGGTA A-CAGA
1 ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
*
88704502 ATCAGA ACCAGA AT
1 ATCAGA ATCAGA AT
88704516 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
5 6 0.08
6 62 0.77
7 8 0.10
8 4 0.05
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:88704460 original size:19 final size:19
Alignment explanation
Indices: 88704435--88704487 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
88704425 GAATGAGAAT
88704435 CAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGGTGA
* *
88704454 TAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGGTGA
*
88704473 CAGAATCAAAATCAG
1 CAGAATCAGAATCAG
88704488 TATCAGGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTGA
Found at i:88704461 original size:25 final size:25
Alignment explanation
Indices: 88704430--88704515 Score: 85
Period size: 25 Copynumber: 3.7 Consensus size: 25
88704420 AATGAGAATG
88704430 AGAATCAGAATCAGAATCAGGT---
1 AGAATCAGAATCAGAATCAGGTGAC
*
88704452 -G-AT-AGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
* * *
88704474 AGAATCAAAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTGAC
*
88704499 AGAATCAGAACCAGAAT
1 AGAATCAGAATCAGAAT
88704516 GTGAATGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
19 15 0.30
20 2 0.04
21 1 0.02
23 1 0.02
24 2 0.04
25 29 0.58
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTGAC
Found at i:88704680 original size:27 final size:26
Alignment explanation
Indices: 88704639--88704739 Score: 121
Period size: 27 Copynumber: 3.8 Consensus size: 26
88704629 CTGCCATAAT
* *
88704639 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
88704666 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
88704692 AGATATTTGTGGCATAGCCACCAGAAAT
1 AGATA-TTGTGGCAGAGCCACCAG-AAC
* *
88704720 AGATAATGTGGCAAAGCCAC
1 AGATATTGTGGCAGAGCCAC
88704740 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.11
27 52 0.79
28 7 0.11
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:88704926 original size:22 final size:22
Alignment explanation
Indices: 88704898--88704962 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
88704888 GCAAATACGT
*
88704898 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
88704920 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
**
88704942 TTGGCGTAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
88704963 AATAATTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:88705426 original size:27 final size:27
Alignment explanation
Indices: 88705396--88705529 Score: 187
Period size: 27 Copynumber: 5.0 Consensus size: 27
88705386 GGGGAAAATG
* * * *
88705396 GTAATTTTACCCCACAAGGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
88705423 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
88705450 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
88705477 GTAATTCTACCTTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
88705504 GTAATTCTACCCTACAGGGGTATTTC
1 GTAATTCTACCCTACAGGGGTATTTC
88705530 GATAATTTTG
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 95 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:88705442 original size:54 final size:55
Alignment explanation
Indices: 88705384--88705496 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 55
88705374 TTAACACCCT
88705384 AGGGGGAAAAT-GGTAATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
1 AGGGGGAAAATCGGT-ATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
* ** * * * *
88705438 A-GGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTAC
1 AGGGGGAAAATCGGTATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
88705492 AGGGG
1 AGGGG
88705497 TATTTCAGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
53 10 0.20
54 36 0.73
55 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (55 bp):
AGGGGGAAAATCGGTATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
Found at i:88705551 original size:27 final size:27
Alignment explanation
Indices: 88705521--88705624 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
88705511 TACCCTACAG
88705521 GGGTATTTCGATAATTTTGTAAATCGA
1 GGGTATTTCGATAATTTTGTAAATCGA
*** *
88705548 GGGTAAAACGATAATTCTGTAAATC-A
1 GGGTATTTCGATAATTTTGTAAATCGA
* ** * *
88705574 GGGGTACTTT-GGTAATTTTACAAGTTGA
1 -GGGTA-TTTCGATAATTTTGTAAATCGA
*
88705602 GGGTATTTC-AGTAATTTGGTAAA
1 GGGTATTTCGA-TAATTTTGTAAA
88705625 CTAAAGTATT
Statistics
Matches: 54, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
26 4 0.07
27 49 0.91
28 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTGTAAATCGA
Found at i:88705563 original size:81 final size:81
Alignment explanation
Indices: 88705413--88705565 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
88705403 TACCCCACAA
* ** *** *
88705413 GGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGG
1 GGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACAATACAAGGGTAAAACGA
88705478 TAATTCTACCTTACAG
66 TAATTCTACCTTACAG
* * *
88705494 GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTTTGTA-AAT-CGAGGGTAAAAC
1 GGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGAT-A-TTTCTACAATACAAGGGTAAAAC
88705557 GATAATTCT
64 GATAATTCT
88705566 GTAAATCAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 53 0.88
82 2 0.03
83 5 0.08
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (81 bp):
GGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACAATACAAGGGTAAAACGA
TAATTCTACCTTACAG
Found at i:88709787 original size:255 final size:253
Alignment explanation
Indices: 88709324--88709832 Score: 869
Period size: 255 Copynumber: 2.0 Consensus size: 253
88709314 TAGTACCAGC
* * *
88709324 TACACTATCCAAATGCAACTTCAGTTAAAATTTAATTTGCATCTGAAAGGCAACTTGACTTGACA
1 TACACTATCCAAATGCAACATCAATTAAAACTTAATTTGCATCTGAAAGGCAACTTGACTTGACA
*
88709389 TATTTGATTAGCATTATTTGATCAATAAACCTAGACTCTTTAAGTACATTTGAGGATTTTAAGAA
66 TATTTGATTAGCATTATTTGATCAATAAACCTAGACTCTTTAAGTACATTCGAGGATTTTAAGAA
* * *
88709454 CACTTTATTAAAGTTAAAACATGGAGAAAATCAAGTCAAAGAAGGATTTTTGAAGACTTTCAAAT
131 CACTTTATTAAAGTCAAAACATGAAGAAAATCAAGTCAAACAAGGATTTTTGAAGACTTTCAAAT
* *
88709519 GTCATCCAGTTTCTTTAATTGAAGATATTTGTTTTCTAAAGAATATTGCACTGAGAAT
196 GTCATCAAGTTTCTTTAATTGAAGATATTTGTTTTCTAAAGAATATTACACTGAGAAT
*
88709577 TACACTATCTAAATGCAACATCAATTAAAACTTAATTTGCATCT-AAATGGCAA-TGTGACTTGA
1 TACACTATCCAAATGCAACATCAATTAAAACTTAATTTGCATCTGAAA-GGCAACT-TGACTTGA
*
88709640 CATATTTGATTAGCATTATTTGATCAATAAACCTAGACTCTTTAAGTATACCTTCGAGGATTTTA
64 CATATTTGATTAGCATTATTTGATCAATAAACCTAGACTCTTTAAG--TACATTCGAGGATTTTA
88709705 AGAACACTTTATTAAAGTCAAAACATGAAGAAAATCAAGTCAAACAAGGATTTTTGAAGACTTTC
127 AGAACACTTTATTAAAGTCAAAACATGAAGAAAATCAAGTCAAACAAGGATTTTTGAAGACTTTC
88709770 AAATGTCATCAAGTTTCTTTAATTGAAGATATTTGTTTTCTAAAGAATATTACACTGAGAAT
192 AAATGTCATCAAGTTTCTTTAATTGAAGATATTTGTTTTCTAAAGAATATTACACTGAGAAT
88709832 T
1 T
88709833 TTATCTGTTA
Statistics
Matches: 241, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
252 4 0.02
253 99 0.41
255 138 0.57
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (253 bp):
TACACTATCCAAATGCAACATCAATTAAAACTTAATTTGCATCTGAAAGGCAACTTGACTTGACA
TATTTGATTAGCATTATTTGATCAATAAACCTAGACTCTTTAAGTACATTCGAGGATTTTAAGAA
CACTTTATTAAAGTCAAAACATGAAGAAAATCAAGTCAAACAAGGATTTTTGAAGACTTTCAAAT
GTCATCAAGTTTCTTTAATTGAAGATATTTGTTTTCTAAAGAATATTACACTGAGAAT
Found at i:88711581 original size:45 final size:45
Alignment explanation
Indices: 88711531--88711637 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
88711521 GTAGCAGTAG
* * *
88711531 CAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCTGTAA
1 CAGTAACGGTAACAGTAGTCAACACACAAAGTGTC-GAATCGGTAA
* * *
88711576 CAGTAATGGTAACAATAGTCGACACACAAAGTGTCGAATCGGTAA
1 CAGTAACGGTAACAGTAGTCAACACACAAAGTGTCGAATCGGTAA
*
88711621 TAGTAACGGTAACAGTA
1 CAGTAACGGTAACAGTA
88711638 ACAGTAGTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (45 bp):
CAGTAACGGTAACAGTAGTCAACACACAAAGTGTCGAATCGGTAA
Found at i:88711646 original size:51 final size:51
Alignment explanation
Indices: 88711533--88711652 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 51
88711523 AGCAGTAGCA
* * * *
88711533 GTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAATG
1 GTAACAGTAACAGTAGTCGACACACAAAGTGCTGAATCGGTAACAGTAACG
*
88711584 GTAAC----A-A-TAGTCGACACACAAAGTG-TCGAATCGGTAATAGTAACG
1 GTAACAGTAACAGTAGTCGACACACAAAGTGCT-GAATCGGTAACAGTAACG
*
88711629 GTAACAGTAACAGTAGTCGGCACA
1 GTAACAGTAACAGTAGTCGACACA
88711653 TAAGTGCCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
44 1 0.02
45 36 0.64
46 1 0.02
47 1 0.02
49 1 0.02
50 1 0.02
51 15 0.27
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (51 bp):
GTAACAGTAACAGTAGTCGACACACAAAGTGCTGAATCGGTAACAGTAACG
Found at i:88712291 original size:13 final size:13
Alignment explanation
Indices: 88712273--88712298 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88712263 TTTCTTCTAT
88712273 ATAATATAATATA
1 ATAATATAATATA
88712286 ATAATATAATATA
1 ATAATATAATATA
88712299 CTTAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:88712318 original size:26 final size:26
Alignment explanation
Indices: 88712288--88712337 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
88712278 ATAATATAAT
*
88712288 AATATA-ATATACTTAATTATTAAACA
1 AATATATATAT-CTTAATTAATAAACA
*
88712314 AATATATATATTTTAATTAATAAA
1 AATATATATATCTTAATTAATAAA
88712338 ATCTTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATATATATCTTAATTAATAAACA
Found at i:88718418 original size:45 final size:45
Alignment explanation
Indices: 88718351--88718445 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
88718341 GCAATAACAA
* * ** * *
88718351 TAACAGTATTCAACACATAAAGTGTTGAATCTGTAACAGTAATGG
1 TAACAATATTCAACACACAAAGTGTCAAATCGGTAACAGTAACGG
* *
88718396 TAACAATATTCGATACACAAAGTGTCAAATCGGTAACAGTAACGG
1 TAACAATATTCAACACACAAAGTGTCAAATCGGTAACAGTAACGG
88718441 TAACA
1 TAACA
88718446 GTAACAGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (45 bp):
TAACAATATTCAACACACAAAGTGTCAAATCGGTAACAGTAACGG
Found at i:88718443 original size:12 final size:12
Alignment explanation
Indices: 88718426--88718450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88718416 AGTGTCAAAT
88718426 CGGTAACAGTAA
1 CGGTAACAGTAA
88718438 CGGTAACAGTAA
1 CGGTAACAGTAA
88718450 C
1 C
88718451 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:88718824 original size:14 final size:14
Alignment explanation
Indices: 88718805--88718843 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
88718795 TCAGTTCATT
*
88718805 AAATACGTACCTTA
1 AAATACTTACCTTA
88718819 AAATACTTACCTTA
1 AAATACTTACCTTA
88718833 AAATACTTACC
1 AAATACTTACC
88718844 ACACATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATACTTACCTTA
Found at i:88719107 original size:5 final size:5
Alignment explanation
Indices: 88719097--88719129 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
88719087 TGTTTCTTTT
88719097 ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
88719130 CTTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.08
4 2 0.08
5 22 0.85
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:88719122 original size:13 final size:13
Alignment explanation
Indices: 88719104--88719129 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88719094 TTTATATAAT
88719104 ATAATATAATATA
1 ATAATATAATATA
88719117 ATAATATAATATA
1 ATAATATAATATA
88719130 CTTAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:88725154 original size:18 final size:18
Alignment explanation
Indices: 88725131--88725168 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
88725121 ATGATAACAT
88725131 ACGAAAGATAATAATCTA
1 ACGAAAGATAATAATCTA
88725149 ACGAAAGATAATAATCTA
1 ACGAAAGATAATAATCTA
88725167 AC
1 AC
88725169 TATGGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (18 bp):
ACGAAAGATAATAATCTA
Found at i:88735094 original size:3 final size:3
Alignment explanation
Indices: 88735076--88735126 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
88735066 TTAAATACTC
* *
88735076 TTA TTA TTT TTA -TA TTA TTAA TT- TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
88735120 TGTA TTA
1 T-TA TTA
88735127 GTTTATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Done.