Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 58 of 160
Found at i:12224748 original size:30 final size:30
Alignment explanation
Indices: 12224695--12224797 Score: 88
Period size: 30 Copynumber: 3.4 Consensus size: 30
12224685 TTGTTTATGA
* * * *
12224695 TAAGGATTCATTTAGGTATAAATTAACAG-T
1 TAAGAATTTATTTAGATACAAATTAA-AGAT
12224725 TAAGAATTTATTTAGATACAAATTAAAGAT
1 TAAGAATTTATTTAGATACAAATTAAAGAT
* *
12224755 TAA-AGATTTATTTA-ATTAAAAATTAAAAAT
1 TAAGA-ATTTATTTAGA-TACAAATTAAAGAT
12224785 TAA-AGATTTATTT
1 TAAGA-ATTTATTT
12224798 TGGTATAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.06
30 60 0.94
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (30 bp):
TAAGAATTTATTTAGATACAAATTAAAGAT
Found at i:12224837 original size:29 final size:29
Alignment explanation
Indices: 12224730--12224844 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 29
12224720 ACAGTTAAGA
* *
12224730 ATTTATTTAGATACAAATTAAAGATTAAAG
1 ATTTATTTAAATA-AAATTAAAAATTAAAG
*
12224760 ATTTATTTAATTAAAAATTAAAAATTAAAG
1 ATTTATTTAAAT-AAAATTAAAAATTAAAG
*** *
12224790 ATTTATTTTGGTATAA-TAAAAATATAAAG
1 ATTTATTTAAATAAAATTAAAAAT-TAAAG
* *
12224819 ACTTATTTAAATAAAATAATAAAATT
1 ATTTATTTAAATAAAATTA-AAAATT
12224845 TTAGGTTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
28 7 0.10
29 19 0.28
30 36 0.53
31 6 0.09
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (29 bp):
ATTTATTTAAATAAAATTAAAAATTAAAG
Found at i:12225702 original size:112 final size:108
Alignment explanation
Indices: 12225476--12225795 Score: 289
Period size: 112 Copynumber: 2.8 Consensus size: 108
12225466 ATTGAATTCT
* *
12225476 AAAATTTTTTTTTCATGTTTTCAATAAAAATTGCATTTTTATTTTAGAAATATCTTTTTTTCAAC
1 AAAATTTTTTTTT-ATGTTTTCAAAAAAAATT--ATTTTTATTTTAGAAA-AT-TTCTTTTCAAC
** * * * * *
12225541 AAAAATTGCGGTTCTAATCTTAAAAATGTTATTTTTATTTAATTCTAA
61 AAAAATTGCATTTTTTATCTTAAAAATGTTATCTATATTAAATTCTAA
* * * *
12225589 AAGATTTATTTTTTGATGTTTTCAACAAAGACTATTTTTATTTTAGAAAAGTTGTCTTTTCAACA
1 AAAATTT-TTTTTT-ATGTTTTCAAAAAAAATTATTTTTATTTTAGAAAA-TT-TCTTTTCAACA
* * * *
12225654 AAAATTGCATTTTTTATTTTAGAAATGTTGTCTATATTAAATTTTAA
62 AAAATTGCATTTTTTATCTTAAAAATGTTATCTATATTAAATTCTAA
* * *
12225701 AAAATAATTTTTTTATATATTTTCAAAAAAAATTACGTTTTTATCTTAAAAACATTATCTTTTCA
1 AAAAT--TTTTTTT-TATGTTTTCAAAAAAAATTA--TTTTTATTTTAGAAA-ATT-TCTTTTCA
* * *
12225766 ATAAAAATTGTATTTTTTATCTTACAAATG
59 ACAAAAATTGCATTTTTTATCTTAAAAATG
12225796 CCATTTTTGT
Statistics
Matches: 169, Mismatches: 29, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
111 2 0.01
112 67 0.40
113 26 0.15
114 24 0.14
115 49 0.29
116 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (108 bp):
AAAATTTTTTTTTATGTTTTCAAAAAAAATTATTTTTATTTTAGAAAATTTCTTTTCAACAAAAA
TTGCATTTTTTATCTTAAAAATGTTATCTATATTAAATTCTAA
Found at i:12226627 original size:99 final size:99
Alignment explanation
Indices: 12226502--12226696 Score: 381
Period size: 99 Copynumber: 2.0 Consensus size: 99
12226492 AAACTTTATT
12226502 AGTTGAAAACAAATATTTAAATTTATAAAAATTTAAATATACATGATCATTACCAGGTGTCCAAT
1 AGTTGAAAACAAATATTTAAATTTATAAAAATTTAAATATACATGATCATTACCAGGTGTCCAAT
12226567 TGTGTGACTAGGAATATAGCTTTGCATGTCATAA
66 TGTGTGACTAGGAATATAGCTTTGCATGTCATAA
*
12226601 AGTTTAAAACAAATATTTAAATTTATAAAAATTTAAATATACATGATCATTACCAGGTGTCCAAT
1 AGTTGAAAACAAATATTTAAATTTATAAAAATTTAAATATACATGATCATTACCAGGTGTCCAAT
12226666 TGTGTGACTAGGAATATAGCTTTGCATGTCA
66 TGTGTGACTAGGAATATAGCTTTGCATGTCA
12226697 GAATAGTCTC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (99 bp):
AGTTGAAAACAAATATTTAAATTTATAAAAATTTAAATATACATGATCATTACCAGGTGTCCAAT
TGTGTGACTAGGAATATAGCTTTGCATGTCATAA
Found at i:12226802 original size:91 final size:91
Alignment explanation
Indices: 12226647--12226824 Score: 338
Period size: 91 Copynumber: 2.0 Consensus size: 91
12226637 ATATACATGA
12226647 TCATTACCAGGTGTCCAATTGTGTGACTAGGAATATAGCTTTGCATGTCAGAATAGTCTCGATTT
1 TCATTACCAGGTGTCCAATTGTGTGACTAGGAATATAGCTTTGCATGTCAGAATAGTCTCGATTT
12226712 ATCATGCAATTACATTGATTTTCAAG
66 ATCATGCAATTACATTGATTTTCAAG
* *
12226738 TCATTACTAGGTGTTCAATTGTGTGACTAGGAATATAGCTTTGCATGTCAGAATAGTCTCGATTT
1 TCATTACCAGGTGTCCAATTGTGTGACTAGGAATATAGCTTTGCATGTCAGAATAGTCTCGATTT
12226803 ATCATGCAATTACATTGATTTT
66 ATCATGCAATTACATTGATTTT
12226825 TAAGGATAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (91 bp):
TCATTACCAGGTGTCCAATTGTGTGACTAGGAATATAGCTTTGCATGTCAGAATAGTCTCGATTT
ATCATGCAATTACATTGATTTTCAAG
Found at i:12227328 original size:61 final size:59
Alignment explanation
Indices: 12227212--12227399 Score: 160
Period size: 61 Copynumber: 3.1 Consensus size: 59
12227202 CCCTCTTCTT
* * * * * * * *
12227212 ATAATTAATCAAAATTATTATAATAAACTCCTATCATAATTACTGAACTATCCCTCCTACC
1 ATAACTAACCAAAATTAATATAAT-ATCTCTTATCATAATTAC-AAAATACCCCTCCTACC
* * * * *
12227273 CTAACTAACCAAAATTACTATAATGTCTTCTTATCATAATTACAAAAGTACCCCTCATACT
1 ATAACTAACCAAAATTAATATAATATC-TCTTATCATAATTACAAAA-TACCCCTCCTACC
* * * *
12227334 ATAATTGATCAAAATTAATATAATATCTCTTATACTATAATTATGAAAATACCCCTCCTACC
1 ATAACTAACCAAAATTAATATAATATCTCTTAT-C-ATAATTA-CAAAATACCCCTCCTACC
12227396 ATAA
1 ATAA
12227400 TTATGAAAAT
Statistics
Matches: 101, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
60 9 0.09
61 66 0.65
62 22 0.22
63 4 0.04
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (59 bp):
ATAACTAACCAAAATTAATATAATATCTCTTATCATAATTACAAAATACCCCTCCTACC
Found at i:12227416 original size:26 final size:26
Alignment explanation
Indices: 12227370--12227426 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
12227360 CTCTTATACT
12227370 ATAATTATGAAAATACCCCTCCTACC
1 ATAATTATGAAAATACCCCTCCTACC
* *
12227396 ATAATTATGAAAATGCTCCTCCTACC
1 ATAATTATGAAAATACCCCTCCTACC
*
12227422 CTAAT
1 ATAAT
12227427 GGCCAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.30
Consensus pattern (26 bp):
ATAATTATGAAAATACCCCTCCTACC
Found at i:12228739 original size:22 final size:23
Alignment explanation
Indices: 12228693--12228739 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
12228683 TTATATTTAA
* *
12228693 GATCTCATTTTTATATTTTGTTT
1 GATCTCATTATTATATTTTGGTT
*
12228716 GATCTTATTATTAT-TTTTGGTT
1 GATCTCATTATTATATTTTGGTT
12228738 GA
1 GA
12228740 GGAATCATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (23 bp):
GATCTCATTATTATATTTTGGTT
Found at i:12228961 original size:18 final size:18
Alignment explanation
Indices: 12228916--12228970 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
12228906 AAGGTTTTGT
*
12228916 TTTAGGGTTTAGG-T-AA
1 TTTAGGGTTTGGGTTAAA
*
12228932 TTT-GGGTATGGGTTAAA
1 TTTAGGGTTTGGGTTAAA
12228949 TTTAGGGTTTGGGTTAAA
1 TTTAGGGTTTGGGTTAAA
12228967 TTTA
1 TTTA
12228971 AGAGTTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 5 0.15
18 17 0.52
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (18 bp):
TTTAGGGTTTGGGTTAAA
Found at i:12229023 original size:22 final size:23
Alignment explanation
Indices: 12228981--12229054 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
12228971 AGAGTTTTGG
12228981 GGGTTTTAAGGTTCATAATTTT-
1 GGGTTTTAAGGTTCATAATTTTA
* *
12229003 GGGTTTTAAGGTT-TTGGATTTTA
1 GGGTTTTAAGGTTCAT-AATTTTA
*
12229026 GGGTTTT-AGGATTTCA-AAATTTA
1 GGGTTTTAAGG--TTCATAATTTTA
12229049 GGGTTT
1 GGGTTT
12229055 CAAAATTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 21 0.50
23 18 0.43
24 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (23 bp):
GGGTTTTAAGGTTCATAATTTTA
Found at i:12229039 original size:16 final size:15
Alignment explanation
Indices: 12228999--12229039 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12228989 AGGTTCATAA
*
12228999 TTTTGGGTTTTAAGG
1 TTTTGGATTTTAAGG
*
12229014 TTTTGGATTTTAGGG
1 TTTTGGATTTTAAGG
12229029 TTTTAGGATTT
1 TTTT-GGATTT
12229040 CAAAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (15 bp):
TTTTGGATTTTAAGG
Found at i:12229081 original size:16 final size:15
Alignment explanation
Indices: 12229030--12229086 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
12229020 ATTTTAGGGT
*
12229030 TTTAGGATTTCAAAA
1 TTTAGGGTTTCAAAA
12229045 TTTAGGGTTTCAAAA
1 TTTAGGGTTTCAAAA
*
12229060 TTTAGGGTTTCAAGAT
1 TTTAGGGTTTCAA-AA
12229076 TTTAGGGTTTC
1 TTTAGGGTTTC
12229087 GGGATTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 27 0.69
16 12 0.31
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (15 bp):
TTTAGGGTTTCAAAA
Found at i:12229094 original size:31 final size:30
Alignment explanation
Indices: 12229030--12229143 Score: 95
Period size: 31 Copynumber: 3.7 Consensus size: 30
12229020 ATTTTAGGGT
* ***
12229030 TTTAGGATTTCAAAATTTAGGGTTTCAAAA
1 TTTAGGATTTCAAATTTTAGGGTTTCGGGA
*
12229060 TTTAGGGTTTCAAGATTTTAGGGTTTCGGGA
1 TTTAGGATTTCAA-ATTTTAGGGTTTCGGGA
* * * *
12229091 TTTAAGATTTTAAAGGTTTAGGGTTTTGAGG-
1 TTTAGGATTTCAAA-TTTTAGGGTTTCG-GGA
*
12229122 TTTAGGATCTCAAGATTTTAGG
1 TTTAGGATTTCAA-ATTTTAGG
12229144 TTTTAGTTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
30 13 0.20
31 50 0.76
32 3 0.05
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.42
Consensus pattern (30 bp):
TTTAGGATTTCAAATTTTAGGGTTTCGGGA
Found at i:12230902 original size:48 final size:49
Alignment explanation
Indices: 12230812--12231061 Score: 157
Period size: 48 Copynumber: 4.9 Consensus size: 49
12230802 TTATATGTTT
* * *
12230812 TAATTTTTCTTACCTATACCGATGGTTAACGCCCGTCTGTATAGACTTG
1 TAATTTTTCTTACCTATACCGATGCTTAAAGCCCGTCAGTATAGACTTG
**
12230861 TAATTTTT-TTACCTATACCGATGCTTAAAGCTTGTCAGTATAGACTTG
1 TAATTTTTCTTACCTATACCGATGCTTAAAGCCCGTCAGTATAGACTTG
* * * * * *
12230909 TACGTTTTAATTTTCTTACTTATACAGAT-CGTTAATGCCCCTCAATATAGACTTATATG
1 TA------ATTTTTCTTACCTATACCGATGC-TTAAAGCCCGTCAGTATAGAC---T-TG
* * * * * *
12230968 TTTTAATTTTTCTTACCTATACCGACGGTTAATG-TCGTCAGTATAGATTTA
1 ---TAATTTTTCTTACCTATACCGATGCTTAAAGCCCGTCAGTATAGACTTG
* * *
12231019 TAATTTTTCTTACCTATACCAATACTTAACA-TCCGTCAGTATA
1 TAATTTTTCTTACCTATACCGATGCTTAA-AGCCCGTCAGTATA
12231062 AATTTATATT
Statistics
Matches: 154, Mismatches: 29, Indels: 36
0.70 0.13 0.16
Matches are distributed among these distances:
48 62 0.40
49 18 0.12
51 1 0.01
52 1 0.01
54 6 0.04
55 38 0.25
56 23 0.15
58 1 0.01
59 2 0.01
62 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (49 bp):
TAATTTTTCTTACCTATACCGATGCTTAAAGCCCGTCAGTATAGACTTG
Found at i:12231013 original size:55 final size:55
Alignment explanation
Indices: 12230861--12231139 Score: 193
Period size: 55 Copynumber: 5.1 Consensus size: 55
12230851 TATAGACTTG
* * * * *
12230861 TAATTTTT-TTACCTATACCGATGCTTAAAGCTTGTCAGTATAGACTTGTACGTTT
1 TAATTTTTCTTACCTATACCGACGCTTAATG-TCGTCAGTATAGACTTATATGTTT
* * * * *
12230916 TAA-TTTTCTTACTTATACAGATCG-TTAATGCCCCTCAATATAGACTTATATGTTT
1 TAATTTTTCTTACCTATACCGA-CGCTTAATG-TCGTCAGTATAGACTTATATGTTT
*
12230971 TAATTTTTCTTACCTATACCGACGGTTAATGTCGTCAGTATAGA-TT-TA-----
1 TAATTTTTCTTACCTATACCGACGCTTAATGTCGTCAGTATAGACTTATATGTTT
* ** ** * * *
12231019 TAATTTTTCTTACCTATACCAATACTTAACATCCGTCAGTATAAATTTATATTTTT
1 TAATTTTTCTTACCTATACCGACGCTTAATGT-CGTCAGTATAGACTTATATGTTT
* * * * * *
12231075 TAATTTTTTTTTACCTATACTGACGCTTAGA-GACTGTCAATATAGACTTGTATATTT
1 TAA-TTTTTCTTACCTATACCGACGCTTA-ATGTC-GTCAGTATAGACTTATATGTTT
12231132 TAATTTTT
1 TAATTTTT
12231140 TATTATATTT
Statistics
Matches: 175, Mismatches: 34, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
48 26 0.15
49 11 0.06
50 2 0.01
51 2 0.01
53 2 0.01
54 6 0.03
55 53 0.30
56 32 0.18
57 40 0.23
58 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (55 bp):
TAATTTTTCTTACCTATACCGACGCTTAATGTCGTCAGTATAGACTTATATGTTT
Found at i:12231073 original size:48 final size:47
Alignment explanation
Indices: 12230969--12231074 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 47
12230959 ACTTATATGT
* ** ** *
12230969 TTTA-ATTTTTCTTACCTATACCGACGGTTAATGTCGTCAGTATAGA
1 TTTATATTTTTCTTACCTATACCAACACTTAACATCGTCAGTATAAA
*
12231015 TTTATAATTTTTCTTACCTATACCAATACTTAACATCCGTCAGTATAAA
1 TTTAT-ATTTTTCTTACCTATACCAACACTTAACAT-CGTCAGTATAAA
12231064 TTTATATTTTT
1 TTTATATTTTT
12231075 TAATTTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.08
48 30 0.60
49 16 0.32
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.45
Consensus pattern (47 bp):
TTTATATTTTTCTTACCTATACCAACACTTAACATCGTCAGTATAAA
Found at i:12231275 original size:24 final size:24
Alignment explanation
Indices: 12231243--12231289 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12231233 TTTTTTTAAA
12231243 AATTATATTT-TCAATCATTAATATT
1 AATTATATTTAT-AATCA-TAATATT
12231268 AATT-TATTTATAATCATAATAT
1 AATTATATTTATAATCATAATAT
12231290 GATATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTATATTTATAATCATAATATT
Found at i:12238571 original size:25 final size:25
Alignment explanation
Indices: 12238537--12238584 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12238527 AATGAACCTA
12238537 TGTCAAACATTTCATAGTTATACTT
1 TGTCAAACATTTCATAGTTATACTT
12238562 TGTCAAACATTTCATAGTTATAC
1 TGTCAAACATTTCATAGTTATAC
12238585 ATATTCTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (25 bp):
TGTCAAACATTTCATAGTTATACTT
Found at i:12242949 original size:17 final size:17
Alignment explanation
Indices: 12242927--12242965 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12242917 ATAGGTTTTT
12242927 GGAGAAAGAAAACTGAA
1 GGAGAAAGAAAACTGAA
* *
12242944 GGAGAAAGGAAATTGAA
1 GGAGAAAGAAAACTGAA
12242961 GGAGA
1 GGAGA
12242966 TCGAGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.36, T:0.08
Consensus pattern (17 bp):
GGAGAAAGAAAACTGAA
Found at i:12252711 original size:17 final size:16
Alignment explanation
Indices: 12252684--12252715 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12252674 AAACTAGAAA
12252684 TCTCTTTTTTGGTTTC
1 TCTCTTTTTTGGTTTC
12252700 TCTCTCTTTTTGGTTT
1 TCTCT-TTTTTGGTTT
12252716 TTCTTTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.19, G:0.12, T:0.69
Consensus pattern (16 bp):
TCTCTTTTTTGGTTTC
Found at i:12260881 original size:2 final size:2
Alignment explanation
Indices: 12260874--12260906 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12260864 TTCCTTACAA
12260874 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12260907 TTTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12262515 original size:17 final size:18
Alignment explanation
Indices: 12262495--12262532 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
12262485 ATACCCCAAT
12262495 AATTAAAAAA-ATTCAAA
1 AATTAAAAAATATTCAAA
12262512 AATTAAAAAATTATTCAAA
1 AATTAAAAAA-TATTCAAA
12262531 AA
1 AA
12262533 AATGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAAAATATTCAAA
Found at i:12262670 original size:19 final size:20
Alignment explanation
Indices: 12262646--12262689 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
12262636 TAAAAATCTG
12262646 AAATTAAAAAATTTGTA-AA
1 AAATTAAAAAATTTGTATAA
* *
12262665 AAATTAGAAATTTTGTATAA
1 AAATTAAAAAATTTGTATAA
12262685 AAATT
1 AAATT
12262690 TTCAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATTAAAAAATTTGTATAA
Found at i:12262785 original size:19 final size:19
Alignment explanation
Indices: 12262763--12262828 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
12262753 AAAATCCAAG
12262763 AAAAATATAAAAAATTTTA
1 AAAAATATAAAAAATTTTA
* * *
12262782 AAAAACCAT-AAGAATTTAA
1 AAAAA-TATAAAAAATTTTA
*
12262801 AGAAAATCTAAAACAATTTTCA
1 A-AAAATATAAAA-AATTTT-A
12262823 AAAAAT
1 AAAAAT
12262829 TGGAAAAGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 15 0.43
20 8 0.23
21 10 0.29
22 2 0.06
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAAAATTTTA
Found at i:12263125 original size:27 final size:26
Alignment explanation
Indices: 12263095--12263160 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
12263085 AAATATAGAT
*
12263095 TTTTTAATTTTTTATAATGTTGAATTG
1 TTTTTAATTTTTCAT-ATGTTGAATTG
* *
12263122 TTTTTAATTTTTCATATTTTGACTTG
1 TTTTTAATTTTTCATATGTTGAATTG
12263148 TTTTTGAATTTTT
1 TTTTT-AATTTTT
12263161 AAAGTTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.67
Consensus pattern (26 bp):
TTTTTAATTTTTCATATGTTGAATTG
Found at i:12263168 original size:27 final size:26
Alignment explanation
Indices: 12263095--12263168 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
12263085 AAATATAGAT
* *
12263095 TTTTTAATTTTTTATAATGTTGAATTG
1 TTTTTAATTTTTCA-AATTTTGAATTG
* *
12263122 TTTTTAATTTTTCATATTTTGACTTG
1 TTTTTAATTTTTCAAATTTTGAATTG
12263148 TTTTTGAATTTTT-AAAGTTTT
1 TTTTT-AATTTTTCAAA-TTTT
12263169 TCTTTTCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 16 0.40
27 24 0.60
ACGTcount: A:0.23, C:0.03, G:0.09, T:0.65
Consensus pattern (26 bp):
TTTTTAATTTTTCAAATTTTGAATTG
Found at i:12263284 original size:18 final size:17
Alignment explanation
Indices: 12263261--12263309 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
12263251 TTGTTTTTTG
12263261 ATTTTTTGAATTGTTCA
1 ATTTTTTGAATTGTTCA
* *
12263278 TATTTTTTTACTTTGTTCA
1 -ATTTTTTGA-ATTGTTCA
12263297 ATTTTTTGGAATT
1 ATTTTTT-GAATT
12263310 CTTTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.63
Consensus pattern (17 bp):
ATTTTTTGAATTGTTCA
Found at i:12263286 original size:19 final size:18
Alignment explanation
Indices: 12263262--12263309 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
12263252 TGTTTTTTGA
12263262 TTTTTTGAATTGTTCATAT
1 TTTTTTGAATTGTTCA-AT
*
12263281 TTTTTT-ACTTTGTTCAAT
1 TTTTTTGA-ATTGTTCAAT
*
12263299 TTTTTGGAATT
1 TTTTTTGAATT
12263310 CTTTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTTTGAATTGTTCAAT
Found at i:12264804 original size:3 final size:3
Alignment explanation
Indices: 12264796--12264840 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12264786 AATGTGAAGG
12264796 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12264841 TGGGATTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12267097 original size:17 final size:18
Alignment explanation
Indices: 12267051--12267100 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
12267041 GGTCTAGAAG
12267051 GAAAAATTGTTAGGGTGT
1 GAAAAATTGTTAGGGTGT
* * *
12267069 TAAAAGATTGTT-TGTTGT
1 GAAAA-ATTGTTAGGGTGT
12267087 GAAAAATTGTTAGG
1 GAAAAATTGTTAGG
12267101 TTAGATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (18 bp):
GAAAAATTGTTAGGGTGT
Found at i:12267336 original size:17 final size:17
Alignment explanation
Indices: 12267314--12267346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12267304 TAATAACTTG
12267314 ATAAACTATAAGCAAAT
1 ATAAACTATAAGCAAAT
*
12267331 ATAAACTATAATCAAA
1 ATAAACTATAAGCAAA
12267347 GTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAACTATAAGCAAAT
Found at i:12275823 original size:17 final size:18
Alignment explanation
Indices: 12275801--12275834 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12275791 TGATGTTGTC
12275801 AATATTTTTT-TATTTGA
1 AATATTTTTTGTATTTGA
12275818 AATATTTTTTGTATTTG
1 AATATTTTTTGTATTTG
12275835 GTATATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
AATATTTTTTGTATTTGA
Found at i:12277626 original size:18 final size:18
Alignment explanation
Indices: 12277603--12277647 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
12277593 TGTGTGGCTT
12277603 GGCTCGACTTAGTAGCTA
1 GGCTCGACTTAGTAGCTA
12277621 GGCTCGACTTAGTAGCTA
1 GGCTCGACTTAGTAGCTA
*
12277639 GGTTCGACT
1 GGCTCGACT
12277648 GTGATGCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (18 bp):
GGCTCGACTTAGTAGCTA
Found at i:12278240 original size:42 final size:42
Alignment explanation
Indices: 12278197--12278561 Score: 218
Period size: 42 Copynumber: 8.8 Consensus size: 42
12278187 ACAAAACTCT
*
12278197 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCT
1 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * * * *
12278239 TCTAAACAAAGACACCACGACTTTGGAAAAATAAATTGCTCT
1 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * * *
12278281 TCTAAAT-AGAGGTACCACAACTTT-AAAAAAAAAAATGCTCC
1 TCT-AATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * * **
12278322 TC---T------CACCAAAACTTTTGAAAAGTAAAACGCTCC
1 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * ** *
12278355 TATAAAT-AGAGACACCATTACTTTGGAAAATAAAATAAAATGCTCC
1 TCT-AATCAGAGGCACCACAACTTTGG---A-AAAATAAATTGCTCC
* * * * * * *
12278401 TTTAAACAAAGGCACTATAACTTTTGAAAAGTAAATTGCTCC
1 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * * *
12278443 TCTAAACAGAGGCACCACGACTTTGCAAAAATAAATTTCTCC
1 TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* * * *
12278485 TCTAAAT-AGAGGCACCAAAACTTTGGAAATATAAATTACCCC
1 TCT-AATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
* **
12278527 TCTAAAT-AGAGACACCACAACTTTAAAAAAATAAA
1 TCT-AATCAGAGGCACCACAACTTTGGAAAAATAAA
12278562 ATAAAATGCT
Statistics
Matches: 251, Mismatches: 55, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
32 10 0.04
33 14 0.06
37 2 0.01
41 15 0.06
42 173 0.69
43 5 0.02
45 3 0.01
46 29 0.12
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.25
Consensus pattern (42 bp):
TCTAATCAGAGGCACCACAACTTTGGAAAAATAAATTGCTCC
Found at i:12278529 original size:84 final size:84
Alignment explanation
Indices: 12278325--12278608 Score: 232
Period size: 84 Copynumber: 3.3 Consensus size: 84
12278315 ATGCTCCTCT
* * * **
12278325 CACCAAAACTTTTGAAAAGTAAA--ACGCTCCTATAAATAGAGACACCATTACTTTGGAAAATAA
1 CACCAAAACTTTGGAAAAGTAAATTAC-C-CCTCTAAACAGAGACACCACAACTTT---AAA-AA
*
12278388 AATAAAATGCTCCTTTAAACAAAGG
60 AATAAAATGCTCCTCTAAACAAAGG
* * * * * * * **
12278413 CACTATAACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGCAAAAATAAA
1 CACCAAAACTTTGGAAAAGTAAATTACCCCTCTAAACAGAGACACCACAACTTTAAAAAAATAAA
* * * *
12278478 TTTCTCCTCTAAATAGAGG
66 ATGCTCCTCTAAACAAAGG
*
12278497 CACCAAAACTTTGGAAATA-TAAATTACCCCTCTAAATAGAGACACCACAACTTTAAAAAAATAA
1 CACCAAAACTTTGGAAA-AGTAAATTACCCCTCTAAACAGAGACACCACAACTTT----AAA-AA
12278561 AATAAAATGCTCCTCTAAACAAAGG
60 AATAAAATGCTCCTCTAAACAAAGG
* * *
12278586 CGCCATAACTTTTGAAAAGTAAA
1 CACCAAAACTTTGGAAAAGTAAA
12278609 ATACTCATCG
Statistics
Matches: 154, Mismatches: 33, Indels: 17
0.75 0.16 0.08
Matches are distributed among these distances:
84 66 0.43
85 2 0.01
88 44 0.29
89 41 0.27
90 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (84 bp):
CACCAAAACTTTGGAAAAGTAAATTACCCCTCTAAACAGAGACACCACAACTTTAAAAAAATAAA
ATGCTCCTCTAAACAAAGG
Found at i:12291383 original size:20 final size:21
Alignment explanation
Indices: 12291346--12291384 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12291336 CAACTTGTGC
*
12291346 TGAAAAATTTCATCAAAATCT
1 TGAAAAATTTCATAAAAATCT
*
12291367 TGAAAATTTTCA-AAAAAT
1 TGAAAAATTTCATAAAAAT
12291385 TTCCAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
TGAAAAATTTCATAAAAATCT
Found at i:12307466 original size:3 final size:3
Alignment explanation
Indices: 12307458--12307515 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
12307448 GGTTATATAG
12307458 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12307506 ATT ATT ATT A
1 ATT ATT ATT A
12307516 ACCTAGTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12309630 original size:23 final size:22
Alignment explanation
Indices: 12309588--12309634 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
12309578 TCTTTTACAA
*
12309588 CTTAGACATATCTCTCGGTTTAG
1 CTTAGACAAATCTCTCGG-TTAG
* *
12309611 CTTAGACAAATCTTTTGGTTAG
1 CTTAGACAAATCTCTCGGTTAG
12309633 CT
1 CT
12309635 ACCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (22 bp):
CTTAGACAAATCTCTCGGTTAG
Found at i:12310614 original size:60 final size:58
Alignment explanation
Indices: 12310498--12310678 Score: 265
Period size: 60 Copynumber: 3.1 Consensus size: 58
12310488 AGGTTTTATT
* * *
12310498 TTTTTAA-AAAAATTAATACTTCAACTTTTTCTTAAAAATATTTTTTTGAAAATTTTA
1 TTTTTAAGAAAAATTGATATTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTTA
* * *
12310555 TTTTTAAGAAAAATTGATATTTCCAACTTTTGCTCAAAAATATTTTTTTTAACAATTTTA
1 TTTTTAAGAAAAATTGATATTT-CAACTTTTCCTTAAAAATATTTTTTTGAA-AATTTTA
12310615 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAATTTTA
1 TTTTTAAGAAAAATTGATA-TTTCAACTTTTCCTTAAAAATATTTTTTTG-AAAATTTTA
12310675 TTTT
1 TTTT
12310679 ATATTATTTT
Statistics
Matches: 111, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
57 7 0.06
58 12 0.11
59 26 0.23
60 61 0.55
61 5 0.05
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (58 bp):
TTTTTAAGAAAAATTGATATTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTTA
Found at i:12311468 original size:13 final size:13
Alignment explanation
Indices: 12311452--12311480 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12311442 ATTTTTTCTC
12311452 TTCTTTTTGTGTT
1 TTCTTTTTGTGTT
12311465 TTC-TTTTGTGTT
1 TTCTTTTTGTGTT
12311477 TTCT
1 TTCT
12311481 ATGTAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.00, C:0.10, G:0.14, T:0.76
Consensus pattern (13 bp):
TTCTTTTTGTGTT
Found at i:12311951 original size:43 final size:42
Alignment explanation
Indices: 12311832--12312040 Score: 258
Period size: 42 Copynumber: 5.0 Consensus size: 42
12311822 GGTAAACAAA
* *
12311832 ACTCCTCTAAAC-GAAGGCTCAACGACTTTGAAAAAATAAATT
1 ACTCCTCTAAACAG-AGGCACCACGACTTTGAAAAAATAAATT
* * * * **
12311874 GCTCATCTAAATAGAAGCACCACGACTTCAAAAAAATAAATT
1 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
* * *
12311916 GCTCCTCTAAACAGAGGCAACACAACTTTGAAAAAATAAATT
1 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
* * *
12311958 ACTCCTATAAATAGAGGCATCACGACTTTGAAAAAAATAAATT
1 ACTCCTCTAAACAGAGGCACCACGACTTTG-AAAAAATAAATT
*
12312001 ACTCCTCTAAACAGAGGCACCATGACTTTGAAAAAATAAA
1 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAA
12312041 AAGCTCATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
42 102 0.72
43 39 0.28
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.22
Consensus pattern (42 bp):
ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
Found at i:12312014 original size:85 final size:84
Alignment explanation
Indices: 12311856--12312040 Score: 271
Period size: 85 Copynumber: 2.2 Consensus size: 84
12311846 AGGCTCAACG
* * *
12311856 ACTTTGAAAAAATAAATTGCTCATCTAAATAGAAGCACCACGACTTCAAAAAAATAAATTGCTCC
1 ACTTTGAAAAAATAAATTACTCATATAAATAGAAGCACCACGACTTCAAAAAAATAAATTACTCC
12311921 TCTAAACAGAGGCAACACA
66 TCTAAACAGAGGCAACACA
* * * *
12311940 ACTTTGAAAAAATAAATTACTCCTATAAATAGAGGCATCACGACTTTGAAAAAAATAAATTACTC
1 ACTTTGAAAAAATAAATTACTCATATAAATAGAAGCACCACGAC-TTCAAAAAAATAAATTACTC
* **
12312005 CTCTAAACAGAGGCACCATG
65 CTCTAAACAGAGGCAACACA
12312025 ACTTTGAAAAAATAAA
1 ACTTTGAAAAAATAAA
12312041 AAGCTCATTG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 39 0.43
85 51 0.57
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (84 bp):
ACTTTGAAAAAATAAATTACTCATATAAATAGAAGCACCACGACTTCAAAAAAATAAATTACTCC
TCTAAACAGAGGCAACACA
Found at i:12312260 original size:22 final size:23
Alignment explanation
Indices: 12312222--12312268 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
12312212 AAGGATTCAA
*
12312222 ATTTGCAAAATCTCAAGATTTGC
1 ATTTGCAAAATCTCAAGATTCGC
12312245 ATTTGC-AAAT-TGCAAGATTCGC
1 ATTTGCAAAATCT-CAAGATTCGC
12312267 AT
1 AT
12312269 CCAACATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 15 0.68
23 6 0.27
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (23 bp):
ATTTGCAAAATCTCAAGATTCGC
Found at i:12312568 original size:78 final size:79
Alignment explanation
Indices: 12312454--12312600 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 79
12312444 GTTTGACAAT
* * *
12312454 TCACATTCGATGAACTTTAGAGTTTCACACCTCAAAAATTTTTATTTGAAATTCAAAGATTCTCA
1 TCACATTCGATGAAATTTAGAGTTTCACACCTCAAAAATTCTCATTTGAAATTCAAAGATTCTCA
12312519 TTTGAGTTCGAAGA
66 TTTGAGTTCGAAGA
* * *
12312533 TCACATTCGAT-AAATTTTGGGTTTTACACCTCAAAAATTCTCATTTGAAATTCAAAGATTCTCA
1 TCACATTCGATGAAATTTAGAGTTTCACACCTCAAAAATTCTCATTTGAAATTCAAAGATTCTCA
12312597 TTTG
66 TTTG
12312601 GGAACTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 51 0.82
79 11 0.18
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (79 bp):
TCACATTCGATGAAATTTAGAGTTTCACACCTCAAAAATTCTCATTTGAAATTCAAAGATTCTCA
TTTGAGTTCGAAGA
Found at i:12312588 original size:21 final size:22
Alignment explanation
Indices: 12312562--12312619 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
12312552 GGTTTTACAC
12312562 CTCAAAAATTCTCATTT-GAAA
1 CTCAAAAATTCTCATTTGGAAA
* * *
12312583 TTCAAAGATTCTCATTTGGGAA
1 CTCAAAAATTCTCATTTGGAAA
12312605 CTCAAAAATTCTCAT
1 CTCAAAAATTCTCAT
12312620 CAAAAGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
CTCAAAAATTCTCATTTGGAAA
Found at i:12312996 original size:23 final size:23
Alignment explanation
Indices: 12312953--12312996 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12312943 TTGGAACAAG
* *
12312953 TTTCATCAACTGATCATCATTAT
1 TTTCATCAACTGACCACCATTAT
12312976 TTTCATC-ACTTGACCACCATT
1 TTTCATCAAC-TGACCACCATT
12312997 CATAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (23 bp):
TTTCATCAACTGACCACCATTAT
Found at i:12313885 original size:8 final size:8
Alignment explanation
Indices: 12313874--12313938 Score: 103
Period size: 8 Copynumber: 8.0 Consensus size: 8
12313864 TTTTCTCGTT
*
12313874 TTTTTTTA
1 TTTTTTCA
12313882 TTTTTTCA
1 TTTTTTCA
12313890 TTTTTTTCA
1 -TTTTTTCA
*
12313899 TTTTTTTA
1 TTTTTTCA
12313907 TTTTTTCA
1 TTTTTTCA
12313915 TTTTTTCA
1 TTTTTTCA
12313923 TTTTTTCA
1 TTTTTTCA
12313931 TTTTTTCA
1 TTTTTTCA
12313939 CCCATTATTG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
8 45 0.85
9 8 0.15
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:12313885 original size:9 final size:9
Alignment explanation
Indices: 12313855--12313936 Score: 86
Period size: 9 Copynumber: 9.6 Consensus size: 9
12313845 TGAGTCTTTC
12313855 TTTTTTC-T
1 TTTTTTCAT
*
12313863 TTTTTCTCGT
1 TTTTT-TCAT
*
12313873 TTTTTT-TT
1 TTTTTTCAT
12313881 ATTTTTTCAT
1 -TTTTTTCAT
12313891 TTTTTTCAT
1 TTTTTTCAT
12313900 TTTTTT-A-
1 TTTTTTCAT
12313907 TTTTTTCA-
1 TTTTTTCAT
12313915 TTTTTTCA-
1 TTTTTTCAT
12313923 TTTTTTCAT
1 TTTTTTCAT
12313932 TTTTT
1 TTTTT
12313937 CACCCATTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
7 6 0.09
8 24 0.36
9 29 0.44
10 7 0.11
ACGTcount: A:0.09, C:0.10, G:0.01, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:12316856 original size:28 final size:28
Alignment explanation
Indices: 12316825--12316892 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
12316815 TGATGTATAG
*
12316825 AATGAAATGATAATGATGCA-CGAAATTA
1 AATGAAATGATAATGATGCATCG-AATGA
*
12316853 AATGATATGATAATGATGCATCGAATGA
1 AATGAAATGATAATGATGCATCGAATGA
12316881 AATGAAAATGAT
1 AATG-AAATGAT
12316893 GCAGGTGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (28 bp):
AATGAAATGATAATGATGCATCGAATGA
Found at i:12318011 original size:58 final size:57
Alignment explanation
Indices: 12317938--12318113 Score: 203
Period size: 58 Copynumber: 3.0 Consensus size: 57
12317928 CTTTTATACA
12317938 AAGAAAATTGATACTTTCAACTTTTTTAAAAAATATTTTTTTAAAAATTTTATTTTT
1 AAGAAAATTGATACTTTCAACTTTTTTAAAAAATATTTTTTTAAAAATTTTATTTTT
* * * *
12317995 AAGGAAAATT-AGTACTTCCAACTTTTTCTCAGAAATATTTTTTTTTAATAATTTTATTTTT
1 AA-GAAAATTGA-TACTTTCAACTTTTT-T-A-AAAAATATTTTTTTAAAAATTTTATTTTT
* * *
12318056 AAAAAAATTGATATTTTCAACTTTTCCTT-AAAAATATTTTTTTGAAAATTTTTATTTT
1 AAGAAAATTGATACTTTCAACTTTT--TTAAAAAATATTTTTTT-AAAAATTTTATTTT
12318114 ATATTATTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 16
0.79 0.09 0.13
Matches are distributed among these distances:
57 3 0.03
58 33 0.33
59 13 0.13
60 19 0.19
61 30 0.30
62 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (57 bp):
AAGAAAATTGATACTTTCAACTTTTTTAAAAAATATTTTTTTAAAAATTTTATTTTT
Found at i:12318078 original size:60 final size:59
Alignment explanation
Indices: 12317941--12318113 Score: 192
Period size: 61 Copynumber: 2.9 Consensus size: 59
12317931 TTATACAAAG
* * *
12317941 AAAATTGATACTTTCAACTTTTT-TAAAAAATATTTTTTTAAAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTAAAATATTTTTTTTTAAAAATTTTATTTTTAAGA
* *
12317999 AAAATT-AGTACTTCCAACTTTTTCTCAGAAATATTTTTTTTTAATAATTTTATTTTTAA-A
1 AAAATTGA-TACTTTCAACTTTTTCT-A-AAATATTTTTTTTTAAAAATTTTATTTTTAAGA
* * * *
12318059 AAAATTGATATTTTCAACTTTTCCTTAAAA-ATATTTTTTTGAAAATTTTTATTTT
1 AAAATTGATACTTTCAACTTTTTC-TAAAATAT-TTTTTTTTAAAAATTTTATTTT
12318114 ATATTATTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
57 1 0.01
58 22 0.23
59 23 0.24
60 21 0.22
61 30 0.31
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTTCTAAAATATTTTTTTTTAAAAATTTTATTTTTAAGA
Found at i:12318199 original size:19 final size:19
Alignment explanation
Indices: 12318161--12318204 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12318151 AAATATTCTT
*
12318161 AAAAATAAACACATAAAAA
1 AAAAATAAACAAATAAAAA
* * *
12318180 ATAAATAAATAAATACAAA
1 AAAAATAAACAAATAAAAA
12318199 AAAAAT
1 AAAAAT
12318205 CAAAATGGCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAATAAACAAATAAAAA
Found at i:12319070 original size:18 final size:18
Alignment explanation
Indices: 12319042--12319088 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
12319032 AATTCAACTC
*
12319042 TTATT-TTTTTTTTATTT
1 TTATTATTTTTTTTACTT
* *
12319059 TTCTTATTTTTTTTCCTT
1 TTATTATTTTTTTTACTT
12319077 TTATTATTTTTT
1 TTATTATTTTTT
12319089 ATTTTTAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (18 bp):
TTATTATTTTTTTTACTT
Found at i:12323866 original size:2 final size:2
Alignment explanation
Indices: 12323859--12323900 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
12323849 AGCATAGTAT
12323859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
12323901 CTCCGAACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12324543 original size:30 final size:28
Alignment explanation
Indices: 12324507--12324607 Score: 102
Period size: 30 Copynumber: 3.6 Consensus size: 28
12324497 AAATTTAACT
12324507 ATTTATTTAGATATAAATTAAAGATAAATA
1 ATTTATTTA-ATATAAATTAAAGATAAA-A
*
12324537 ATTTATTTAATTACAAATTAAAGATTAAAA
1 ATTTATTTAA-TATAAATTAAAGA-TAAAA
* *
12324567 TTTTATTT-ATAT-AA-TAACGATATAAA
1 ATTTATTTAATATAAATTAAAGATA-AAA
12324593 ATTTATTTAA-ATAAA
1 ATTTATTTAATATAAA
12324608 ATTATAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
25 2 0.03
26 17 0.28
27 5 0.08
28 2 0.03
29 2 0.03
30 29 0.48
31 4 0.07
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (28 bp):
ATTTATTTAATATAAATTAAAGATAAAA
Found at i:12324576 original size:34 final size:30
Alignment explanation
Indices: 12324487--12324575 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
12324477 TTTAGGTACA
* * *
12324487 TACAAATTAAAAATTTAACTATTTATTTAGA-
1 TACAAATTAAAGA-TAAATTATTTATTTA-AT
* *
12324518 TATAAATTAAAGATAAATAATTTATTTAAT
1 TACAAATTAAAGATAAATTATTTATTTAAT
*
12324548 TACAAATTAAAGATTAAAAT-TTTATTTA
1 TACAAATTAAAGA-TAAATTATTTATTTA
12324576 TATAATAACG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 32 0.67
31 15 0.31
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
TACAAATTAAAGATAAATTATTTATTTAAT
Found at i:12326089 original size:34 final size:35
Alignment explanation
Indices: 12326033--12326098 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
12326023 TTTTATGACT
*
12326033 TATGGTTTTCCAAAATTTTTTTTTAAA-GATGAAAA
1 TATGGTTTTCCAAAA-TTCTTTTTAAAGGATGAAAA
*
12326068 TATGGTTTTCC-AACTTCTTTTTAAAGGATGA
1 TATGGTTTTCCAAAATTCTTTTTAAAGGATGA
12326099 CATGTGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 7 0.25
35 11 0.39
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (35 bp):
TATGGTTTTCCAAAATTCTTTTTAAAGGATGAAAA
Found at i:12328131 original size:353 final size:352
Alignment explanation
Indices: 12327483--12328187 Score: 1002
Period size: 353 Copynumber: 2.0 Consensus size: 352
12327473 CTTGGATATG
* * *
12327483 AAATGACGATAAATTAAGCTAAAACGTCCAAGGATTCGGTTTTCTTGCACATGTTGCATGTGGCC
1 AAATGACGATAAATTAAGCTAAAACATCCAAGGATTCGATTTTCTTGCACATGTTGCATGGGGCC
* ** * * * *
12327548 TGGGTTTGTCCCTAGTACATAGGAATTGAAAGCTTTTAAGTCATGCTTTTTCAAAGTATTCAGGA
66 TGGGTTCGTCCCTAGTACATAGGAATTGAAAGCTCCTAAGCCATACTGTTTCAAAGTATTCAAGA
* * * **
12327613 CAAGAAGAAAAGGGAAAGAACTAGGTTATAGTGCTGAAAAGGAAGGTCATGCCTTGTTGCCTTGA
131 CAAGAAGAAAAAGGAAAGAAATAGGTTATAGCGCTGAAAAGGAAGGTCACACCTTGTTGCCTTGA
* * * * * *
12327678 AGGCTTTTAACTCTCATGTTTTCAATTTTCTTTGCATGCTGACCAAAGGTTTTGAGGTTCACGTG
196 AGGCCTTTAACTCTCATATTTTCAATTTCCTTTGCATGCCGACCAAAGGTTTAGAGGTTCACGGG
* *
12327743 CATGTTTTGAATTCTGTTTCTCTTTGGGTTGTTGTACATGCTTCCAACTCCATTTGGCTTTCTGC
261 CATGTTTTGAATTCTGTTTCTCTTTGGGCTGTTGTACATGCTTCCAACTCCATGTGGCTTTCTGC
* *
12327808 ATTTTCTGTTCTCCTTCTCCTGCATGT
326 ATTTTCTCTTCTCATTCTCCTGCATGT
* * * * *
12327835 AAATGACTATAACTTAAGCTAAAACATCTAAGGATTCGATTTTCTTGCATATGTTGCATGGGGTC
1 AAATGACGATAAATTAAGCTAAAACATCCAAGGATTCGATTTTCTTGCACATGTTGCATGGGGCC
*
12327900 TGGGTTCGTCCCTAGTACATAGGAATTGAAAGCTCCTAAGCCATACTGTTTCGAAGTATTCAAGA
66 TGGGTTCGTCCCTAGTACATAGGAATTGAAAGCTCCTAAGCCATACTGTTTCAAAGTATTCAAGA
12327965 CAAGAAGAAAAAGGAGAAGAAATAGGTTATAGCG-TCGAAAAGGAAGGTCACACCTTGTTG-CTT
131 CAAGAAGAAAAAGGA-AAGAAATAGGTTATAGCGCT-GAAAAGGAAGGTCACACCTTGTTGCCTT
* *
12328028 GGAAGGCCTTTAACTTTCGTATTTTCAATTTCCTTTGCATGCCGACCAAAGGTTTA-AGGGTTCA
194 -GAAGGCCTTTAACTCTCATATTTTCAATTTCCTTTGCATGCCGACCAAAGGTTTAGA-GGTTCA
** * *
12328092 CGGGTTTGTTTTGAATTCTGTTTCTCTTTGGGCTGTTGTACATGGTTCCAACTTCATGTGGCTTT
257 CGGGCATGTTTTGAATTCTGTTTCTCTTTGGGCTGTTGTACATGCTTCCAACTCCATGTGGCTTT
* *
12328157 CTGTATTTTCTCTTCTCATTCTCTTGCATGT
322 CTGCATTTTCTCTTCTCATTCTCCTGCATGT
12328188 TGGCTTGTTG
Statistics
Matches: 310, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
352 133 0.43
353 177 0.57
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (352 bp):
AAATGACGATAAATTAAGCTAAAACATCCAAGGATTCGATTTTCTTGCACATGTTGCATGGGGCC
TGGGTTCGTCCCTAGTACATAGGAATTGAAAGCTCCTAAGCCATACTGTTTCAAAGTATTCAAGA
CAAGAAGAAAAAGGAAAGAAATAGGTTATAGCGCTGAAAAGGAAGGTCACACCTTGTTGCCTTGA
AGGCCTTTAACTCTCATATTTTCAATTTCCTTTGCATGCCGACCAAAGGTTTAGAGGTTCACGGG
CATGTTTTGAATTCTGTTTCTCTTTGGGCTGTTGTACATGCTTCCAACTCCATGTGGCTTTCTGC
ATTTTCTCTTCTCATTCTCCTGCATGT
Found at i:12330692 original size:3 final size:3
Alignment explanation
Indices: 12330686--12330728 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
12330676 CTACTAAAAA
*
12330686 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12330729 GGAAAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:12336916 original size:42 final size:42
Alignment explanation
Indices: 12336856--12336938 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
12336846 CACCCTAACA
*
12336856 AAAATTTCTCATTGATGCATCATATATAAAGAACAACCATAC
1 AAAATTTCTCATTAATGCATCATATATAAAGAACAACCATAC
* *
12336898 AAAATTTCTTATTAATGCATCATATATGAAGAACAACCATA
1 AAAATTTCTCATTAATGCATCATATATAAAGAACAACCATA
12336939 TAGTAGTGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (42 bp):
AAAATTTCTCATTAATGCATCATATATAAAGAACAACCATAC
Found at i:12342591 original size:50 final size:49
Alignment explanation
Indices: 12342500--12342724 Score: 202
Period size: 49 Copynumber: 4.6 Consensus size: 49
12342490 TCTAAAGCCT
* * *
12342500 ACAAGATTTTAAAATTCCAAAGCCTCTGTT-GGAAAGGAGCCATTTTTAG
1 ACAAGATTTTAAAGTTCCAAAGCCTCTATTGGGAAA-GAGCCATTTTCAG
* * *
12342549 ACAAGATGTTTAAAGTTCCAAAGCTTTTATTGGGAAAAAGCCATTTTCAG
1 ACAAGAT-TTTAAAGTTCCAAAGCCTCTATTGGGAAAGAGCCATTTTCAG
* * * * * * *
12342599 TCAAGATTTTTAAGTTCCAAAGCCTTTGTTGGGGATGAGCCATTTTCTG
1 ACAAGATTTTAAAGTTCCAAAGCCTCTATTGGGAAAGAGCCATTTTCAG
* * * * * *
12342648 AAAAGATTTTAAAATTTCAAAGCTTCTATTAAGG-AAGAGCCATTTTCAA
1 ACAAGATTTTAAAGTTCCAAAGCCTCTATT-GGGAAAGAGCCATTTTCAG
* * *
12342697 ACATGATTTTTAAAGTTTCAAAACCTCT
1 ACAAGA-TTTTAAAGTTCCAAAGCCTCT
12342725 GTTATTTTTT
Statistics
Matches: 141, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
49 80 0.57
50 56 0.40
51 5 0.04
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (49 bp):
ACAAGATTTTAAAGTTCCAAAGCCTCTATTGGGAAAGAGCCATTTTCAG
Found at i:12342713 original size:99 final size:100
Alignment explanation
Indices: 12342500--12342727 Score: 259
Period size: 99 Copynumber: 2.3 Consensus size: 100
12342490 TCTAAAGCCT
* * *
12342500 ACAAGA-TTTTAAAATTCCAAAGCCTCTGTTGGAAAGGAGCCATTTTTAGACAAGATGTTTAAAG
1 ACAAGATTTTTAAAGTTCCAAAGCCTCTGTTGGAAAGGAGCCATTTTTAGAAAAGATGTTTAAAA
* * *
12342564 TTCCAAAGCTTTTATTGGGAAAAAGCCATTTTCAG
66 TTCCAAAGCTTCTATTAGGAAAAAGCCATTTTCAA
* * ** *
12342599 TCAAGATTTTT-AAGTTCCAAAGCCTTTGTTGGGGATGAGCCATTTTCT-GAAAAGAT-TTTAAA
1 ACAAGATTTTTAAAGTTCCAAAGCCTCTGTTGGAAAGGAGCCATTTT-TAGAAAAGATGTTTAAA
* *
12342661 ATTTCAAAGCTTCTATTAAGG-AAGAGCCATTTTCAA
65 ATTCCAAAGCTTCTATT-AGGAAAAAGCCATTTTCAA
* * *
12342697 ACATGATTTTTAAAGTTTCAAAACCTCTGTT
1 ACAAGATTTTTAAAGTTCCAAAGCCTCTGTT
12342728 ATTTTTTTCT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
98 42 0.39
99 60 0.56
100 5 0.05
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (100 bp):
ACAAGATTTTTAAAGTTCCAAAGCCTCTGTTGGAAAGGAGCCATTTTTAGAAAAGATGTTTAAAA
TTCCAAAGCTTCTATTAGGAAAAAGCCATTTTCAA
Found at i:12342834 original size:12 final size:12
Alignment explanation
Indices: 12342817--12342842 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12342807 AAAATGATTC
12342817 AATAAAAATTTT
1 AATAAAAATTTT
12342829 AATAAAAATTTT
1 AATAAAAATTTT
12342841 AA
1 AA
12342843 ACTAATAAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAAAAATTTT
Found at i:12343608 original size:32 final size:33
Alignment explanation
Indices: 12343534--12343612 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
12343524 TTTATGACTC
* *
12343534 ATGGTTTTCTAACATTCTTTTTAAGGATGAGATT
1 ATGGTTTTCCAACATTCTTTTTAAGAATGAGA-T
12343568 ATGGTTTTCCAAC-TTCTTATTTTAAGAATGA-A-
1 ATGGTTTTCCAACATTC-T-TTTTAAGAATGAGAT
12343600 ATGGTTTTCCAAC
1 ATGGTTTTCCAAC
12343613 GGCTCTCAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 13 0.32
33 3 0.07
34 14 0.34
35 11 0.27
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (33 bp):
ATGGTTTTCCAACATTCTTTTTAAGAATGAGAT
Found at i:12351564 original size:27 final size:27
Alignment explanation
Indices: 12351529--12351581 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
12351519 TTTCCCTTTT
12351529 TCTTCTTCTTTTTTCTCTTCCTCTCTC
1 TCTTCTTCTTTTTTCTCTTCCTCTCTC
*
12351556 TCTTTTTCTTTTTTCTCTTCCTCTCT
1 TCTTCTTCTTTTTTCTCTTCCTCTCT
12351582 ATCTAGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (27 bp):
TCTTCTTCTTTTTTCTCTTCCTCTCTC
Found at i:12352383 original size:44 final size:43
Alignment explanation
Indices: 12352299--12352606 Score: 288
Period size: 44 Copynumber: 7.2 Consensus size: 43
12352289 TAGACTCCTC
* * * * *
12352299 AAATAACATAAAACTCCTCTAAGCAAAAGCTTC-ACGACTTTGAA
1 AAATAA-ATAAAGCTCCTCTAAACAGAGGC-TCAACAACTTTGAA
* * * *
12352343 AAGGTAAACAAAGCTCCTCTAAATAAAGGCTCAACAACTTTGGAA
1 AA-ATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTT-GAA
* * *
12352388 AAACAAATAAGGTTCCTCTAAACAGAGGCTCAACAACTTTGAAA
1 AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTG-AA
12352432 AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAA
1 AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAA
** *
12352475 AAAT--A-AAAGCTCCTCTAATTAGAGGCTTAACAACTTTAGAA
1 AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTT-GAA
* * * * * *
12352516 AAATAAATAATGCTCCTTTAATCGGAGGCTCCACAACTTTGGA
1 AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAA
* * *
12352559 AAATAAATAATA-CCCCTCTAAAC--ATGCTTAACAACTTTGAA
1 AAATAAATAA-AGCTCCTCTAAACAGAGGCTCAACAACTTTGAA
12352600 AAATAAA
1 AAATAAA
12352607 GCTCCTCAAC
Statistics
Matches: 220, Mismatches: 35, Indels: 21
0.80 0.13 0.08
Matches are distributed among these distances:
40 29 0.13
41 29 0.13
43 30 0.14
44 124 0.56
45 8 0.04
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (43 bp):
AAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAA
Found at i:12352544 original size:128 final size:124
Alignment explanation
Indices: 12352352--12352613 Score: 337
Period size: 128 Copynumber: 2.1 Consensus size: 124
12352342 AAAGGTAAAC
* *
12352352 AAAGCTCCTCTAAATAAAGGCTCAACAACTTTGGAAAAACAAATAAGGTTCCTCTAAACAGAGGC
1 AAAGCTCCTCTAAATAAAGGCTCAACAACTTTAGAAAAACAAATAAGGCTCCTCTAAACAGAGGC
*
12352417 TCAACAACTTTGAAAAAATAAATAA-AGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAAT
66 TCAACAACTTTG-AAAAATAAATAATA-CCCCTCTAAAC--AGGCTCAACAACTTTGAAAAAT
* * * * * * * *
12352479 AAAAGCTCCTCTAATTAGAGGCTTAACAACTTTAGAAAAATAAATAATGCTCCTTTAATCGGAGG
1 -AAAGCTCCTCTAAATAAAGGCTCAACAACTTTAGAAAAACAAATAAGGCTCCTCTAAACAGAGG
* * * *
12352544 CTCCACAACTTTGGAAAATAAATAATACCCCTCTAAACATGCTTAACAACTTTGAAAAAT
65 CTCAACAACTTTGAAAAATAAATAATACCCCTCTAAACAGGCTCAACAACTTTGAAAAAT
12352604 AAAGCTCCTC
1 AAAGCTCCTC
12352614 AACAATCATG
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
124 10 0.08
125 20 0.17
127 21 0.18
128 67 0.57
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (124 bp):
AAAGCTCCTCTAAATAAAGGCTCAACAACTTTAGAAAAACAAATAAGGCTCCTCTAAACAGAGGC
TCAACAACTTTGAAAAATAAATAATACCCCTCTAAACAGGCTCAACAACTTTGAAAAAT
Found at i:12352601 original size:84 final size:83
Alignment explanation
Indices: 12352335--12352606 Score: 287
Period size: 84 Copynumber: 3.2 Consensus size: 83
12352325 AAGCTTCACG
* * * * *
12352335 ACTTTGAAAAGGTAAACAAAGCTCCTCTAAATAAAGGCTCAACAACTTTGGAAAAACAAATAAGG
1 ACTTTGAAAA-ATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGG-AAAATAAATAA-G
* *
12352400 TTCCTCTAAACAGAGGCTCAACA
63 CTCCTCTAAAC--AGGCTTAACA
*
12352423 ACTTTGAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAAT-AA-AAGCT
1 ACTTTG-AAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATAAGCT
*
12352486 CCTCTAATTAGAGGCTTAACA
65 CCTCTAA--ACAGGCTTAACA
* * * * * *
12352507 ACTTTAGAAAAATAAATAATGCTCCTTTAATCGGAGGCTCCACAACTTTGGAAAATAAATAATAC
1 ACTTT-GAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATAA-GC
* *
12352572 CCCTCTAAACATGCTTAACA
64 TCCTCTAAACAGGCTTAACA
12352592 ACTTTGAAAAATAAA
1 ACTTTGAAAAATAAA
12352607 GCTCCTCAAC
Statistics
Matches: 158, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
84 76 0.48
85 20 0.13
86 5 0.03
87 12 0.08
88 41 0.26
89 4 0.03
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (83 bp):
ACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATAAGCTC
CTCTAAACAGGCTTAACA
Found at i:12353064 original size:22 final size:21
Alignment explanation
Indices: 12353011--12353065 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
12353001 GTTTCACATA
* *
12353011 TAAAATCTCAAAGATTCTCTTT
1 TAAAAT-TCAAAGACTCTCATT
*
12353033 TGAAATTCAAAGACTCTCATT
1 TAAAATTCAAAGACTCTCATT
12353054 TAAGAATTCAAA
1 TAA-AATTCAAA
12353066 ATTTCATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (21 bp):
TAAAATTCAAAGACTCTCATT
Found at i:12353081 original size:30 final size:30
Alignment explanation
Indices: 12353038--12353097 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12353028 TCTTTTGAAA
12353038 TTCAAAGACTCTCATTTAAGAATTCAAAAT
1 TTCAAAGACTCTCATTTAAGAATTCAAAAT
* * * *
12353068 TTCATAGATTCTCATTTGAGGATTCAAAAT
1 TTCAAAGACTCTCATTTAAGAATTCAAAAT
12353098 CTTGTCGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (30 bp):
TTCAAAGACTCTCATTTAAGAATTCAAAAT
Found at i:12354149 original size:7 final size:7
Alignment explanation
Indices: 12354139--12354217 Score: 60
Period size: 7 Copynumber: 11.6 Consensus size: 7
12354129 TCATTTTCTT
12354139 TTTTTCA
1 TTTTTCA
*
12354146 TTTTTTA
1 TTTTTCA
12354153 TTTTTCA
1 TTTTTCA
12354160 TTTTT--
1 TTTTTCA
*
12354165 TTTCTC-
1 TTTTTCA
12354171 TTTTTC-
1 TTTTTCA
*
12354177 TCTTTT-T
1 T-TTTTCA
12354184 TTTTTCA
1 TTTTTCA
12354191 TTGTTTCA
1 TT-TTTCA
*
12354199 TTTTTTCT
1 -TTTTTCA
12354207 TTTTTCA
1 TTTTTCA
12354214 TTTT
1 TTTT
12354218 ATATGTTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.07
6 10 0.17
7 34 0.58
8 9 0.15
9 2 0.03
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:12354149 original size:8 final size:8
Alignment explanation
Indices: 12354132--12354253 Score: 71
Period size: 8 Copynumber: 15.5 Consensus size: 8
12354122 TTTTCTCTCA
*
12354132 TTTTCTTT
1 TTTTCATT
12354140 TTTTCATT
1 TTTTCATT
12354148 TTTT-A-T
1 TTTTCATT
12354154 TTTTCATTTT
1 TTTTCA--TT
12354164 TTTTC-TCT
1 TTTTCAT-T
*
12354172 TTTTC-TC
1 TTTTCATT
12354179 TTTT--TT
1 TTTTCATT
12354185 TTTTCATT
1 TTTTCATT
*
12354193 GTTTCATT
1 TTTTCATT
12354201 TTTTC-TT
1 TTTTCATT
12354208 TTTTCATT
1 TTTTCATT
* *
12354216 TTAT-ATG
1 TTTTCATT
12354223 TTTTCAAATTT
1 TTTTC--A-TT
*
12354234 TTTTTATT
1 TTTTCATT
*
12354242 TTTTTATT
1 TTTTCATT
12354250 TTTT
1 TTTT
12354254 TACTATTGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
6 10 0.11
7 19 0.21
8 50 0.54
9 1 0.01
10 7 0.08
11 5 0.05
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:12354204 original size:40 final size:39
Alignment explanation
Indices: 12354122--12354206 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
12354112 TGAGTATTCA
* *
12354122 TTTTCTCTCATTTTCTTTTTTTCATTTTTTATTTTTCATT
1 TTTTCTCTCATTTTCTCTTTTT-ATTTTTCATTTTTCATT
* *
12354162 TTTTTTCTCTTTTTCTCTTTTT-TTTTTCATTGTTTCATT
1 TTTTCTCTCATTTTCTCTTTTTATTTTTCATT-TTTCATT
12354201 TTTTCT
1 TTTTCT
12354207 TTTTTCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 8 0.21
39 12 0.31
40 19 0.49
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (39 bp):
TTTTCTCTCATTTTCTCTTTTTATTTTTCATTTTTCATT
Found at i:12355656 original size:31 final size:31
Alignment explanation
Indices: 12355621--12355685 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
12355611 GAGTGGCTTC
12355621 AGATGATTGAGGGTAATCAAGTGGTTATTAT
1 AGATGATTGAGGGTAATCAAGTGGTTATTAT
12355652 AGATGATTGAGGGTAATCAAGTGGTTATTAT
1 AGATGATTGAGGGTAATCAAGTGGTTATTAT
12355683 AGA
1 AGA
12355686 GCTCTTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (31 bp):
AGATGATTGAGGGTAATCAAGTGGTTATTAT
Found at i:12363860 original size:25 final size:26
Alignment explanation
Indices: 12363814--12363862 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
12363804 AAATTTAGAG
* *
12363814 AAAATTTATCATCTAGAGATTTCTTA
1 AAAATTTACCATCTAGAAATTTCTTA
*
12363840 AAAATTTACCAT-TTGAAATTTCT
1 AAAATTTACCATCTAGAAATTTCT
12363863 AAGAATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (26 bp):
AAAATTTACCATCTAGAAATTTCTTA
Found at i:12364206 original size:16 final size:16
Alignment explanation
Indices: 12364167--12364213 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12364157 AAAATACTAA
*
12364167 GAAAAAAAAAACACAT
1 GAAAAAAAAAACAAAT
*
12364183 -AAACAAAAAAATAAAT
1 GAAA-AAAAAAACAAAT
*
12364199 GAAAAAAAAACCAAA
1 GAAAAAAAAAACAAA
12364214 ACAATACTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.79, C:0.11, G:0.04, T:0.06
Consensus pattern (16 bp):
GAAAAAAAAAACAAAT
Found at i:12371010 original size:18 final size:18
Alignment explanation
Indices: 12370987--12371021 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12370977 AAAAATACTC
12370987 ACATATTTTTATTATTAA
1 ACATATTTTTATTATTAA
12371005 ACATATTTTTATTATTA
1 ACATATTTTTATTATTA
12371022 TATTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ACATATTTTTATTATTAA
Found at i:12371022 original size:24 final size:25
Alignment explanation
Indices: 12370990--12371047 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
12370980 AATACTCACA
*
12370990 TATTTTTATTATTA-AACATATTTT
1 TATTATTATTATTATAACATATTTT
**
12371014 TATTATTA-TATTATATTATATTTT
1 TATTATTATTATTATAACATATTTT
12371038 TATTA-TATTA
1 TATTATTATTA
12371048 AAAAAATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATTATTATTATAACATATTTT
Found at i:12371091 original size:4 final size:4
Alignment explanation
Indices: 12371061--12371128 Score: 61
Period size: 4 Copynumber: 17.5 Consensus size: 4
12371051 AAATACTCAC
* * * * *
12371061 AAAT AAAT AGAT GAAT AAAT GAAT AAAT AAAA AAAT -TAT CAAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
12371108 AAAT -AAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AA
12371129 CCAAGCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
3 8 0.16
4 40 0.80
5 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12371110 original size:15 final size:14
Alignment explanation
Indices: 12371077--12371128 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
12371067 ATAGATGAAT
12371077 AAATGAATAAATAAAA
1 AAAT-AATAAAT-AAA
*
12371093 AAATTATCAAATAAA
1 AAATAAT-AAATAAA
12371108 AAATAATAAATAAA
1 AAATAATAAATAAA
12371122 TAAATAA
1 -AAATAA
12371129 CCAAGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.22
15 17 0.53
16 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
AAATAATAAATAAA
Found at i:12371139 original size:30 final size:31
Alignment explanation
Indices: 12371077--12371140 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
12371067 ATAGATGAAT
* * *
12371077 AAATGAATAAATAAAAAAATTATCAAATAAA
1 AAATGAATAAATAAAAAAATAACCAAACAAA
* *
12371108 AAAT-AATAAATAAATAAATAACCAAGCAAA
1 AAATGAATAAATAAAAAAATAACCAAACAAA
12371138 AAA
1 AAA
12371141 AATCTAAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (31 bp):
AAATGAATAAATAAAAAAATAACCAAACAAA
Found at i:12386846 original size:18 final size:18
Alignment explanation
Indices: 12386823--12386868 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
12386813 TGGGATATTC
12386823 ATGCATTATTTATAAGCT
1 ATGCATTATTTATAAGCT
12386841 ATGCATTATTTATAAGCT
1 ATGCATTATTTATAAGCT
12386859 ATGCATTATT
1 ATGCATTATT
12386869 AAGCAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
ATGCATTATTTATAAGCT
Found at i:12389970 original size:30 final size:30
Alignment explanation
Indices: 12389920--12389982 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
12389910 AAGATACTGT
12389920 AAAAACATATATTAACAAGCTCAACATAAG
1 AAAAACATATATTAACAAGCTCAACATAAG
* * *
12389950 AAAAATATATGTTAATAAGCTCAACATAAG
1 AAAAACATATATTAACAAGCTCAACATAAG
12389980 AAA
1 AAA
12389983 GTCTTACACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.08, T:0.22
Consensus pattern (30 bp):
AAAAACATATATTAACAAGCTCAACATAAG
Found at i:12395328 original size:2 final size:2
Alignment explanation
Indices: 12395321--12395354 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12395311 AAACAAATCC
12395321 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
12395355 GAAGAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12395509 original size:28 final size:27
Alignment explanation
Indices: 12395463--12395586 Score: 76
Period size: 28 Copynumber: 4.5 Consensus size: 27
12395453 CAAAGTCTGA
* *
12395463 AAATTC-AAAACTCTTTAAATTGATATC
1 AAATTCTAAAAATCTCTAAATTGA-ATC
*
12395490 AAATTCTAAAAATCTCTAAATTTGAAAC
1 AAATTCTAAAAATCTCTAAA-TTGAATC
* * *
12395518 TAAATTTTAAGAATC-CT-AATCTGAAAGC
1 -AAATTCTAAAAATCTCTAAAT-TG-AATC
* * *
12395546 AAATTCCAAAAATCCCTAAATTGGGATC
1 AAATTCTAAAAATCTCTAAATT-GAATC
12395574 AAATT-TCAAAAAT
1 AAATTCT-AAAAAT
12395587 TTCAAGATTT
Statistics
Matches: 76, Mismatches: 12, Indels: 17
0.72 0.11 0.16
Matches are distributed among these distances:
26 1 0.01
27 21 0.28
28 34 0.45
29 20 0.26
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.31
Consensus pattern (27 bp):
AAATTCTAAAAATCTCTAAATTGAATC
Found at i:12395559 original size:27 final size:27
Alignment explanation
Indices: 12395489--12395566 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
12395479 AAATTGATAT
*
12395489 CAAATTCTAAAAATCTCTAAATTTGAAA
1 CAAATTCTAAAAATC-CTAAATCTGAAA
* *
12395517 CTAAATTTTAAGAATCCT-AATCTGAAA
1 C-AAATTCTAAAAATCCTAAATCTGAAA
*
12395544 GCAAATTCCAAAAATCCCTAAAT
1 -CAAATTCTAAAAAT-CCTAAAT
12395567 TGGGATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 18 0.45
28 7 0.17
29 15 0.38
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (27 bp):
CAAATTCTAAAAATCCTAAATCTGAAA
Found at i:12409170 original size:18 final size:17
Alignment explanation
Indices: 12409139--12409186 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
12409129 CAAGGACAAA
12409139 AATATTTTTATTTTTTT
1 AATATTTTTATTTTTTT
*
12409156 AATATTTTTGTTTTTTTT
1 AATATTTTT-ATTTTTTT
*
12409174 AATTATTATTATT
1 AA-TATTTTTATT
12409187 ATTATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
AATATTTTTATTTTTTT
Found at i:12409181 original size:3 final size:3
Alignment explanation
Indices: 12409175--12409219 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12409165 GTTTTTTTTA
12409175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12409220 TGCTTAAGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12412462 original size:13 final size:13
Alignment explanation
Indices: 12412433--12412465 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12412423 ACTAAATTGG
12412433 ATATTCTAATATT
1 ATATTCTAATATT
12412446 ATATT-TAATATT
1 ATATTCTAATATT
12412458 CATATTCT
1 -ATATTCT
12412466 TTCAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 10 0.56
14 1 0.06
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTCTAATATT
Found at i:12414521 original size:16 final size:16
Alignment explanation
Indices: 12414450--12414513 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
12414440 TTTATCCAAT
*
12414450 TAAAAAATAATATGAAAA
1 TAAAAAA-AATA-AAAAA
*
12414468 TAGAAAAAATCAAAAAA
1 TAAAAAAAAT-AAAAAA
**
12414485 TGTAAAAAATAAAAAA
1 TAAAAAAAATAAAAAA
12414501 TAAAAAAAATAAA
1 TAAAAAAAATAAA
12414514 GAAAAAAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 17 0.44
17 15 0.38
18 7 0.18
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (16 bp):
TAAAAAAAATAAAAAA
Found at i:12416684 original size:3 final size:3
Alignment explanation
Indices: 12416617--12416668 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
12416607 ATCAAAAAAT
12416617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12416665 TTA T
1 TTA T
12416669 CAAATGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12417133 original size:16 final size:17
Alignment explanation
Indices: 12417112--12417159 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
12417102 AGTATTTCAG
12417112 TAATTTAATATGTA-GT
1 TAATTTAATATGTATGT
*
12417128 TAATTTTATAT-TATGT
1 TAATTTAATATGTATGT
12417144 TAAAATTTAATATGTA
1 T--AATTTAATATGTA
12417160 ATTTAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 13 0.50
18 9 0.35
19 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (17 bp):
TAATTTAATATGTATGT
Found at i:12417361 original size:116 final size:116
Alignment explanation
Indices: 12417135--12417354 Score: 248
Period size: 116 Copynumber: 1.9 Consensus size: 116
12417125 AGTTAATTTT
* * * * ** *
12417135 ATATTATGTTAAAATTTAATATGTAATTTAAAAGTGGTATTATGGCAATTTTTGAATAAAATGTC
1 ATATTATATTAAAATTTAATATATAATTTAAAAGTAGTATTATAGCAATTTTCAAATAAAATATC
* *
12417200 ACATGTGAAATTTCTATGAAACAATGACAATGGTATTTTAGTAATTTAATA
66 ACATGTGAAATTTCTATGAAACAATCACAATGGCATTTTAGTAATTTAATA
*** *
12417251 ATATTATATTAAAATTTAATATATAATTTAATAAG-AGTATTATATTTATTTTCAAATAAATTAT
1 ATATTATATTAAAATTTAATATATAATTTAA-AAGTAGTATTATAGCAATTTTCAAATAAAATAT
* * *
12417315 CACATGT-CAATCTTCTATGAAGCTATCACAA-GGACATTTT
65 CACATGTGAAAT-TTCTATGAAACAATCACAATGG-CATTTT
12417355 TATAATTATG
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
115 5 0.06
116 77 0.91
117 3 0.04
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (116 bp):
ATATTATATTAAAATTTAATATATAATTTAAAAGTAGTATTATAGCAATTTTCAAATAAAATATC
ACATGTGAAATTTCTATGAAACAATCACAATGGCATTTTAGTAATTTAATA
Found at i:12417718 original size:28 final size:29
Alignment explanation
Indices: 12417680--12417735 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12417670 CAAGGGGTGA
*
12417680 TTTTATGTGGTAT-G-AGAATGTTAGATTC
1 TTTTATGTGGT-TGGCAGAAAGTTAGATTC
*
12417708 TTTTATTTGGTTGGCAGAAAGTTAGATT
1 TTTTATGTGGTTGGCAGAAAGTTAGATT
12417736 ACTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 11 0.46
29 12 0.50
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (29 bp):
TTTTATGTGGTTGGCAGAAAGTTAGATTC
Found at i:12418212 original size:63 final size:61
Alignment explanation
Indices: 12418145--12418327 Score: 167
Period size: 62 Copynumber: 3.0 Consensus size: 61
12418135 AGACTAATTA
* ** * *
12418145 AATCAAATACTATGTCATTTTTTTAATATAGGAACAT-CATAATTGATATAGAAAGAAATTTTT
1 AATCAAATACTATGTC-GTTTTGGAATATA--AAAATCCATAATTGATATAGAAAAAAATTTTT
*
12418208 AATCAAATACTATGTCGTTTTGGAATATAAAAATGCCATAATTGATATAGAAAAAAATTTTA
1 AATCAAATACTATGTCGTTTTGGAATATAAAAAT-CCATAATTGATATAGAAAAAAATTTTT
* * * ** *
12418270 AATTAGATATTACATCAGCTTTT--AATATAAAAATGCCATAATTGAGATA-AAAAAAATT
1 AATCAAATACTATGTC-G-TTTTGGAATATAAAAAT-CCATAATTGATATAGAAAAAAATT
12418328 AAATACATAT
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
60 4 0.04
61 9 0.09
62 70 0.67
63 17 0.16
64 4 0.04
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (61 bp):
AATCAAATACTATGTCGTTTTGGAATATAAAAATCCATAATTGATATAGAAAAAAATTTTT
Found at i:12418248 original size:62 final size:62
Alignment explanation
Indices: 12418182--12418327 Score: 181
Period size: 62 Copynumber: 2.4 Consensus size: 62
12418172 ATAGGAACAT
* * **
12418182 CATAATTGATATAGAAAGAAATTTTTAATCAAATACTATGTC-G-TTTTGGAATATAAAAATGC
1 CATAATTGATATAGAAAAAAATTTTAAATCAAATACTACATCAGCTTTT--AATATAAAAATGC
* * *
12418244 CATAATTGATATAGAAAAAAATTTTAAATTAGATATTACATCAGCTTTTAATATAAAAATGC
1 CATAATTGATATAGAAAAAAATTTTAAATCAAATACTACATCAGCTTTTAATATAAAAATGC
*
12418306 CATAATTGAGATA-AAAAAAATT
1 CATAATTGATATAGAAAAAAATT
12418328 AAATACATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 9 0.12
62 60 0.81
63 1 0.01
64 4 0.05
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (62 bp):
CATAATTGATATAGAAAAAAATTTTAAATCAAATACTACATCAGCTTTTAATATAAAAATGC
Found at i:12418736 original size:11 final size:11
Alignment explanation
Indices: 12418707--12418735 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12418697 TTATTGATTA
12418707 CCAATTTTGTT
1 CCAATTTTGTT
12418718 CCAATTTTGTT
1 CCAATTTTGTT
12418729 CC-ATTTT
1 CCAATTTT
12418736 TTTCTTAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (11 bp):
CCAATTTTGTT
Found at i:12419915 original size:23 final size:23
Alignment explanation
Indices: 12419889--12419935 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12419879 TAGTTATATA
12419889 TAATTGCTACTGTTGAGAATTTG
1 TAATTGCTACTGTTGAGAATTTG
12419912 TAATTGCTACTGTTGAGAATTTG
1 TAATTGCTACTGTTGAGAATTTG
12419935 T
1 T
12419936 TTTAAGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (23 bp):
TAATTGCTACTGTTGAGAATTTG
Found at i:12422243 original size:24 final size:24
Alignment explanation
Indices: 12422200--12422262 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
12422190 ATGATTCTAT
* * *
12422200 ATTTTTTTATTAATACAATTCATA
1 ATTTTTTCATTTATACAATTCAGA
* *
12422224 ATTTTTTCATTTATATAATTGAGA
1 ATTTTTTCATTTATACAATTCAGA
* *
12422248 ATTTATTCATATATA
1 ATTTTTTCATTTATA
12422263 AAAGTTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTTTTTCATTTATACAATTCAGA
Found at i:12426872 original size:30 final size:30
Alignment explanation
Indices: 12426808--12426913 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
12426798 TATTATATTT
* * ** *
12426808 AAATAAGTTTTTAATTTTTAATTTACATCC
1 AAATAAGTCTTTAACTTTTAATTTGTATCA
12426838 AAATAAGTCTTTAACTTTTAATTTGTATCA
1 AAATAAGTCTTTAACTTTTAATTTGTATCA
* * * *
12426868 AAATAAATCTTTAAATTTTTTATTTGTA-CTT
1 AAATAAGTCTTT-AACTTTTAATTTGTATC-A
*
12426899 AAATAAGTTTTTAAC
1 AAATAAGTCTTTAAC
12426914 AAAAATCTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
30 39 0.63
31 23 0.37
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (30 bp):
AAATAAGTCTTTAACTTTTAATTTGTATCA
Found at i:12426912 original size:31 final size:31
Alignment explanation
Indices: 12426780--12426912 Score: 98
Period size: 31 Copynumber: 4.4 Consensus size: 31
12426770 GCTTTATTTC
* * * *
12426780 AATAAGTATTTATATTTTTA-TTATA-TTTA
1 AATAAGTCTTTAAATTTTTATTTGTACTCTA
* * *
12426809 AATAAGT-TTTTAATTTTTAATT-TACATCCA
1 AATAAGTCTTTAAATTTTTATTTGTAC-TCTA
* * *
12426839 AATAAGTCTTTAACTTTTAATTTGTA-TCAA
1 AATAAGTCTTTAAATTTTTATTTGTACTCTA
*
12426869 AATAAATCTTTAAATTTTTTATTTGTACT-TA
1 AATAAGTCTTTAAA-TTTTTATTTGTACTCTA
*
12426900 AATAAGTTTTTAA
1 AATAAGTCTTTAA
12426913 CAAAAATCTT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
28 12 0.15
29 9 0.11
30 24 0.29
31 34 0.41
32 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (31 bp):
AATAAGTCTTTAAATTTTTATTTGTACTCTA
Found at i:12427007 original size:28 final size:30
Alignment explanation
Indices: 12426941--12427021 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
12426931 CATTTAAAAC
* *
12426941 ATAAGTTTATTTGGATATAAATCAAAATATA
1 ATAA-TTTATTTGAATATAAATAAAAATATA
*
12426972 ATGATTTATTTGAATAT-AATAAAAATATA
1 ATAATTTATTTGAATATAAATAAAAATATA
12427001 A-AATTTATTT-AA-A-AAATAAAA
1 ATAATTTATTTGAATATAAATAAAA
12427022 TAATTCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
26 8 0.18
27 2 0.04
28 8 0.18
29 12 0.27
30 12 0.27
31 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (30 bp):
ATAATTTATTTGAATATAAATAAAAATATA
Found at i:12429915 original size:25 final size:25
Alignment explanation
Indices: 12429849--12429970 Score: 77
Period size: 25 Copynumber: 4.5 Consensus size: 25
12429839 ATGAGAACGG
*
12429849 TAATATAATATAAATTTTTTATTAGACATA
1 TAATATAA-ATATATTTTTTATT--A-A-A
12429879 TATATAGTAAATATATTTTTTATTAAA
1 TA-ATA-TAAATATATTTTTTATTAAA
*
12429906 TAATATAAAT-TATTATTTTAAATTAAT
1 TAATATAAATATATT-TTTT--ATTAAA
* *
12429933 TAAAATTAATATA-TTTTTATTTAAA
1 TAATATAAATATATTTTTTA-TTAAA
* *
12429958 AAATATTAATATA
1 TAATATAAATATA
12429971 CATTGATAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
24 5 0.06
25 24 0.31
26 7 0.09
27 17 0.22
28 3 0.04
29 1 0.01
30 2 0.03
31 16 0.21
32 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATATAAATATATTTTTTATTAAA
Found at i:12430025 original size:19 final size:20
Alignment explanation
Indices: 12429978--12430030 Score: 56
Period size: 23 Copynumber: 2.6 Consensus size: 20
12429968 ATACATTGAT
12429978 AAAAAATTACATAAATATATAA
1 AAAAAATTA-A-AAATATATAA
*
12430000 AATAAAATTAAAAATA-ATTA
1 AA-AAAATTAAAAATATATAA
12430020 AAAAAA-TAAAA
1 AAAAAATTAAAA
12430031 TTTTCTCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 5 0.17
21 5 0.17
22 3 0.10
23 7 0.24
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATTAAAAATATATAA
Found at i:12430563 original size:7 final size:7
Alignment explanation
Indices: 12430553--12430585 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12430543 TTTGTTTTTG
12430553 TTTTTAA
1 TTTTTAA
12430560 TTTTTAA
1 TTTTTAA
12430567 -TTTTAA
1 TTTTTAA
12430573 TTTTTAA
1 TTTTTAA
12430580 TATTTT
1 T-TTTT
12430586 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:12430570 original size:13 final size:13
Alignment explanation
Indices: 12430554--12430580 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12430544 TTGTTTTTGT
12430554 TTTTAATTTTTAA
1 TTTTAATTTTTAA
12430567 TTTTAATTTTTAA
1 TTTTAATTTTTAA
12430580 T
1 T
12430581 ATTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:12430667 original size:9 final size:10
Alignment explanation
Indices: 12430646--12430678 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12430636 AATTAAAAAT
12430646 AAAATTTTGA
1 AAAATTTTGA
12430656 AAAATTTT-A
1 AAAATTTTGA
12430665 AAAATTATTGA
1 AAAATT-TTGA
12430676 AAA
1 AAA
12430679 TAGAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 10 0.48
11 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (10 bp):
AAAATTTTGA
Found at i:12430864 original size:22 final size:22
Alignment explanation
Indices: 12430862--12430908 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12430852 ATTAATATAA
12430862 TATTTGTTAATATAATATTATT
1 TATTTGTTAATATAATATTATT
*
12430884 TACTTGTTAATATAATATTATT
1 TATTTGTTAATATAATATTATT
12430906 TAT
1 TAT
12430909 CAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTGTTAATATAATATTATT
Found at i:12430880 original size:37 final size:37
Alignment explanation
Indices: 12430799--12431068 Score: 107
Period size: 37 Copynumber: 7.6 Consensus size: 37
12430789 TACTAATAAA
* * * * *
12430799 ATAATATT-TTTATTATATAAATATTATATTAATAAAG
1 ATAATATTATTTATT-TATTAATATAATATTTATTAAT
*
12430836 A-ACATATTATTTATTTATTAATATAATATTTGTTAAT
1 ATA-ATATTATTTATTTATTAATATAATATTTATTAAT
* *
12430873 ATAATATTATTTACTTGTTAATATAATA-TTATT--T
1 ATAATATTATTTATTTATTAATATAATATTTATTAAT
*
12430907 ATCAATA-TA-TTATTT-TT-ATATATTATATTA-TAA-
1 AT-AATATTATTTATTTATTAATATAATAT-TTATTAAT
* * * * * *
12430940 ATAATA-TA-TTAATAAATAATATTATAATATATTAAA
1 ATAATATTATTTATTTATTAATATAAT-ATTTATTAAT
* * *
12430976 ATAATA-TATTGA-TAAATAA-ATAATATTATATTAAT
1 ATAATATTATTTATTTATTAATATAATATT-TATTAAT
* *
12431011 A-AATA-AATAATATTATATTAATA-AATA-TTATT-AT
1 ATAATATTAT-TTATT-TATTAATATAATATTTATTAAT
*
12431045 ATTA-ATTATATTATATTATTAATA
1 ATAATATTAT-TTAT-TTATTAATA
12431069 ACAAAAGAAA
Statistics
Matches: 182, Mismatches: 29, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
31 7 0.04
32 13 0.07
33 11 0.06
34 24 0.13
35 40 0.22
36 23 0.13
37 56 0.31
38 8 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATAATATTATTTATTTATTAATATAATATTTATTAAT
Found at i:12430915 original size:18 final size:17
Alignment explanation
Indices: 12430846--12431068 Score: 73
Period size: 15 Copynumber: 12.7 Consensus size: 17
12430836 AACATATTAT
12430846 TTATTTATTAATATAATA
1 TTATTTA-TAATATAATA
*
12430864 TT-TGT-TAATATAATA
1 TTATTTATAATATAATA
12430879 TTATTTACTTGTTAATATAATA
1 TTATTTA-----TAATATAATA
*
12430901 TTATTTATCA-AT-ATA
1 TTATTTATAATATAATA
12430916 TTATTT-T--TAT-ATA
1 TTATTTATAATATAATA
12430929 TTATATTATAA-ATAATA
1 TTAT-TTATAATATAATA
*
12430946 -TATTAATAA-ATAATA
1 TTATTTATAATATAATA
*
12430961 TTATAATATATTAAAATAATA
1 TTAT--T-TA-TAATATAATA
*
12430982 -TATTGATAAATAAATAATA
1 TTATTTAT-AAT--ATAATA
12431001 TTATATTAATAA-ATAAATA
1 TTAT-TT-ATAATAT-AATA
*
12431020 ATATTATATTAATA-AATA
1 TTATT-TA-TAATATAATA
12431038 TTATTATATTAAT-T-ATA
1 TTATT-TA-TAATATAATA
12431055 TTATATTATTAATA
1 TTAT-TTA-TAATA
12431069 ACAAAAGAAA
Statistics
Matches: 163, Mismatches: 10, Indels: 64
0.69 0.04 0.27
Matches are distributed among these distances:
13 9 0.06
14 3 0.02
15 33 0.20
16 13 0.08
17 24 0.15
18 25 0.15
19 18 0.11
20 10 0.06
21 9 0.06
22 19 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (17 bp):
TTATTTATAATATAATA
Found at i:12431005 original size:22 final size:22
Alignment explanation
Indices: 12430950--12431037 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
12430940 ATAATATATT
12430950 AATAAATAATA-T-TA-TAATA
1 AATAAATAATATTATATTAATA
* * * *
12430969 TATTAA-AATAATATATTGATA
1 AATAAATAATATTATATTAATA
12430990 AATAAATAATATTATATTAATA
1 AATAAATAATATTATATTAATA
12431012 AATAAATAATATTATATTAATA
1 AATAAATAATATTATATTAATA
12431034 AATA
1 AATA
12431038 TTATTATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.07
19 5 0.09
20 2 0.03
21 8 0.14
22 39 0.67
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
AATAAATAATATTATATTAATA
Found at i:12431005 original size:40 final size:37
Alignment explanation
Indices: 12430925--12431046 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 37
12430915 ATTATTTTTA
*
12430925 TATATTATATTATAAATAATATATTAATAAATAATAT
1 TATAATATATTATAAATAATATATTAATAAATAATAT
*
12430962 TATAATATATTA-AAATAATATATTGATAAATAA-AT
1 TATAATATATTATAAATAATATATTAATAAATAATAT
* * *
12430997 AATATTATATTAATAAATAAATAATATTATATTAATAAATAT
1 TATAATATATT-ATAAAT-AAT-ATATTA-ATAAAT-AATAT
*
12431039 TATTATAT
1 TATAATAT
12431047 TAATTATATT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
35 11 0.16
36 21 0.30
37 15 0.22
38 3 0.04
39 5 0.07
40 5 0.07
41 2 0.03
42 7 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (37 bp):
TATAATATATTATAAATAATATATTAATAAATAATAT
Found at i:12431052 original size:22 final size:22
Alignment explanation
Indices: 12430947--12431052 Score: 95
Period size: 22 Copynumber: 5.2 Consensus size: 22
12430937 TAAATAATAT
*
12430947 ATTAATAAATAATATTATAATA
1 ATTAATAAATAATATTATATTA
*
12430969 TATT-A-AAAT-A-A-TATATTG
1 -ATTAATAAATAATATTATATTA
*
12430987 ATAAATAAATAATATTATATTA
1 ATTAATAAATAATATTATATTA
*
12431009 ATAAATAAATAATA-T-TA-T-
1 ATTAATAAATAATATTATATTA
*
12431027 ATTAATAAATATTATTATATTA
1 ATTAATAAATAATATTATATTA
12431049 ATTA
1 ATTA
12431053 TATTATATTA
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
17 2 0.03
18 18 0.26
19 7 0.10
20 6 0.09
21 7 0.10
22 25 0.37
23 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTAATAAATAATATTATATTA
Found at i:12431058 original size:14 final size:14
Alignment explanation
Indices: 12431022--12431062 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12431012 AATAAATAAT
12431022 ATTATATTA-A-TA
1 ATTATATTATATTA
*
12431034 AATATTATTATATTA
1 ATTA-TATTATATTA
12431049 ATTATATTATATTA
1 ATTATATTATATTA
12431063 TTAATAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.12
13 5 0.21
14 11 0.46
15 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATATTATATTA
Found at i:12431060 original size:22 final size:19
Alignment explanation
Indices: 12430782--12431069 Score: 85
Period size: 18 Copynumber: 15.8 Consensus size: 19
12430772 TGATGTTATA
* *
12430782 ATTATTATACTAATAAAAT
1 ATTATTATATTAATAATAT
* *
12430801 AATATTTTTATTATATAA-AT
1 ATTA-TTATATTA-ATAATAT
* * *
12430821 ATTA-TATTAATAAAGAACAT
1 ATTATTA-T-ATTAATAATAT
*
12430841 ATTATT-TATTTATTAATAT
1 ATTATTATA-TTAATAATAT
* *
12430860 AATATT-TGTTAAT-ATAAT
1 ATTATTATATTAATAAT-AT
**
12430878 ATTATT-TACTTGTTAATAT
1 ATTATTATA-TTAATAATAT
*
12430897 AATATTAT-TT-ATCAATAT
1 ATTATTATATTAAT-AATAT
12430915 ATTATT-T-TT-AT-ATAT
1 ATTATTATATTAATAATAT
12430930 -TATATTATA--AATAATAT
1 AT-TATTATATTAATAATAT
12430947 ATTA--ATA--AATAATAT
1 ATTATTATATTAATAATAT
*
12430962 -TATAATATATTAA-AATA-
1 AT-TATTATATTAATAATAT
12430979 ATATATTGATA--AATAA-AT
1 AT-TATT-ATATTAATAATAT
*
12430997 AATATTATATTAATAAATAAAT
1 ATTATTATATTAAT-AAT--AT
*
12431019 AATATTATATTAATAA-AT
1 ATTATTATATTAATAATAT
12431037 ATTATTATATTAAT--TAT
1 ATTATTATATTAATAATAT
12431054 ATTA-TATTATTAATAA
1 ATTATTA-TATTAATAA
12431070 CAAAAGAAAC
Statistics
Matches: 208, Mismatches: 24, Indels: 74
0.68 0.08 0.24
Matches are distributed among these distances:
14 2 0.01
15 21 0.10
16 8 0.04
17 37 0.18
18 57 0.27
19 37 0.18
20 23 0.11
21 7 0.03
22 16 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
ATTATTATATTAATAATAT
Found at i:12431065 original size:40 final size:40
Alignment explanation
Indices: 12430777--12431065 Score: 162
Period size: 40 Copynumber: 7.3 Consensus size: 40
12430767 TATAGTGATG
*
12430777 TTATAATTATTATACTAATAAAATAATATT-T-TT-ATTATA
1 TTATAA-TATTATATTAAT-AAATAATATTATATTAATTATA
* *
12430816 -TA-AATATTATATTAATAAAGAACATATTAT-TTATTTATTA
1 TTATAATATTATATTAATAAA-TA-ATATTATATTAATTA-TA
* * * *
12430856 ATATAATATT-TGTTAAT--ATAATATTAT-TTACTTGTTA
1 TTATAATATTATATTAATAAATAATATTATATTAATT-ATA
* * *
12430893 ATATAATATTAT-TT-ATCAAT-ATATTATTTTTATATATTATA
1 TTATAATATTATATTAATAAATAATATTA--TAT-TA-ATTATA
* *
12430934 TTATAAATAATATATTAATAAATAATATTATAATATATTA-A
1 TTAT-AATATTATATTAATAAATAATATTATATTA-ATTATA
* * *
12430975 -AATAATA-TATTGATAAATAAATAATATTATATTAA-TAAA
1 TTATAATATTA-T-ATTAATAAATAATATTATATTAATTATA
* *
12431014 TAAATAATATTATATTAATAAATATTATTATATTAATTATA
1 T-TATAATATTATATTAATAAATAATATTATATTAATTATA
*
12431055 TTATATTATTA
1 TTATAATATTA
12431066 ATAACAAAAG
Statistics
Matches: 201, Mismatches: 22, Indels: 53
0.73 0.08 0.19
Matches are distributed among these distances:
35 3 0.01
36 14 0.07
37 39 0.19
38 13 0.06
39 12 0.06
40 54 0.27
41 28 0.14
42 24 0.12
43 3 0.01
44 5 0.02
45 6 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (40 bp):
TTATAATATTATATTAATAAATAATATTATATTAATTATA
Found at i:12431213 original size:7 final size:7
Alignment explanation
Indices: 12431201--12431239 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
12431191 AAAGTATTTA
12431201 AAAATAT
1 AAAATAT
12431208 AAAATAT
1 AAAATAT
12431215 AAAATAT
1 AAAATAT
*
12431222 AAAACAT
1 AAAATAT
*
12431229 AAAACAT
1 AAAATAT
12431236 AAAA
1 AAAA
12431240 CGTAGAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAT
Found at i:12447373 original size:5 final size:5
Alignment explanation
Indices: 12447358--12447387 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
12447348 TGCCAAATTT
12447358 TAAAA -AAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
12447388 TTAAGCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:12447433 original size:33 final size:33
Alignment explanation
Indices: 12447387--12447962 Score: 667
Period size: 33 Copynumber: 17.5 Consensus size: 33
12447377 TAAAATAAAA
* *
12447387 TTTAAGCCTAGTTTATCTGGCC-TCAAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
12447420 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
12447453 TTTAAGCTCAGTTTATCTGGCC-TCAAATGAAGA
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
* * * *
12447486 TTTAAGCCTAATTTATTTGACCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
12447519 TTTAAGCCTAGTTTATCTGGCCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
12447552 TTTAAGCTCAGTTTATCTGGTCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * **
12447585 TTTAAGCCCAGTTTATCTAGCCATTAATGAATT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
12447618 TTTAAGTCCAGTTTATCTGGCCATGAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * *
12447651 TTTAAGCCCAGCTTATCTGGCCATGAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
12447684 TTTAAGCCCAGCTTATCTGGCCATGAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
12447717 TTTAAGCCCAGTTTATTTGGCCATCAATAAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * *
12447750 TTTAAGCCCAGTTTATCTGACCATTAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * * *
12447783 TTTAAGCCTAGTTTATCTGACCATTAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * * *
12447816 TTTAAGCCCAGCTTATCTGGCCATTAATGAGGT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * *
12447849 TTTAAACCCAGTTTATCTGG-CTTCAAATGAAGA
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
* **
12447882 TTTAAACCCAGTTTATCTGGCC-TCAAATGAAAA
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
* * **
12447915 TTTAAGCCCAGTTTAGCTGGCCTTCAAT-AAAA
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
12447947 TTTAAGCCAAGTTTAT
1 TTTAAGCCCAGTTTAT
12447963 TTAGCCCCAA
Statistics
Matches: 481, Mismatches: 56, Indels: 13
0.87 0.10 0.02
Matches are distributed among these distances:
32 22 0.05
33 452 0.94
34 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (33 bp):
TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
Found at i:12448168 original size:21 final size:21
Alignment explanation
Indices: 12448142--12448193 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
12448132 AAGGGATATT
12448142 TGCATTTGCATCACTTACATC
1 TGCATTTGCATCACTTACATC
* *
12448163 TGCATTTGCATCACTTGCATT
1 TGCATTTGCATCACTTACATC
*
12448184 TGCACTTGCA
1 TGCATTTGCA
12448194 CAAGATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.38
Consensus pattern (21 bp):
TGCATTTGCATCACTTACATC
Done.