Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 160 of 196
Found at i:46965944 original size:6 final size:6
Alignment explanation
Indices: 46965935--46965967 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
46965925 TCTTCCATTT
46965935 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCC
46965968 CATCCTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (6 bp):
CCCTTC
Found at i:46970018 original size:126 final size:126
Alignment explanation
Indices: 46969783--46970118 Score: 548
Period size: 126 Copynumber: 2.7 Consensus size: 126
46969773 CGTTTCTGGT
*
46969783 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTTG
1 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
46969848 TGGACGCGATTTTGCTACAATAGGTCATGTAATAAACAAATTTTTT-TCTGATGCTTCTAAG
66 TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAACAAATTTTTTGT-TGACGCTTCTAAG
* * *
46969909 CAAATAGTATAAAATCGTTTCTACGAGAATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* ** * *
46969974 TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAGTTTTTTTGTTGACGTTTCTGAG
66 TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAACAAATTTTTTGTTGACGCTTCTAAG
*
46970035 CAAATAGTATAAAATCGCTTCTACCAGGATGATATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
46970100 TGGACGCGATTTTGCTACA
66 TGGACGCGATTTTGCTACA
46970119 GTAGCAAGTT
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
126 193 0.99
127 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (126 bp):
CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAACAAATTTTTTGTTGACGCTTCTAAG
Found at i:46973244 original size:10 final size:10
Alignment explanation
Indices: 46973229--46973253 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46973219 CAAATATAAC
46973229 ATTATGTAAA
1 ATTATGTAAA
46973239 ATTATGTAAA
1 ATTATGTAAA
46973249 ATTAT
1 ATTAT
46973254 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:46973421 original size:111 final size:110
Alignment explanation
Indices: 46973236--46973573 Score: 604
Period size: 111 Copynumber: 3.0 Consensus size: 110
46973226 AACATTATGT
* *
46973236 AAAATTATGTAAAATTATTAAGCCAAAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAA
1 AAAA-TATGTAAAATTATTAAGCC--AAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAA
46973301 CTAAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
63 CTAAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
46973349 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAAATTTATGAAATAAACT
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGT-AAAATTTATGAAATAAACT
46973414 AAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
65 AAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
46973460 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
*
46973525 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
66 AAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAA-TTATC
46973571 AAA
1 AAA
46973574 TTAAGTTAGG
Statistics
Matches: 220, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
110 80 0.36
111 117 0.53
112 19 0.09
113 4 0.02
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (110 bp):
AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
AAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:46973608 original size:29 final size:30
Alignment explanation
Indices: 46973574--46974020 Score: 301
Period size: 29 Copynumber: 14.8 Consensus size: 30
46973564 ATTTATCAAA
46973574 TTAAGTTAGGTTAGGGTTAGGGTTAGGG-T
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
*
46973603 TTAAGTTAGGTTA-----A-GGTT-GAGTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
* **
46973626 TTTAGTTAATTTA-GGTTAGGGTTAGGGTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
* **
46973655 TTTAGTTAATTTA-GGTTAGGGTTAGGGTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGG-TT
**
46973685 TTAA-TTAATTTA-GGTTAGGGTTAGGGTTTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGG---TT
46973716 AATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTT
1 --TTAAGTTAGGTTAGGGTTAGGGTTAGGG-TT
**
46973749 TTAA-TTAATTTA-GGTTAGGGTTAGGGTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
* **
46973777 TTTAGTTAATTTA-GGTTAGGGTTAGGGTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
* **
46973806 TTTAGTTAATTTA-GGTTAGGGTTAGGGTTTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGG---TT
*
46973838 AGTTAATTTAGGTTAGGGTTAGGGTTAGGGTTT
1 --TTAAGTTAGGTTAGGGTTAGGGTTAGGG-TT
**
46973871 TTAA-TTAAATTA-GGTTAGGGTTAGGGTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGG-TT
*
46973900 TTAA-TTAAGTTA-GGTTAGGGTTAGGGTTTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTAGGG---TT
46973931 AATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTTTT
1 --TTAAGTTAGGTTAGGGTTAGGGTTAGGG---TT
*
46973966 AATTAAATTAGGTTAGGGTTAGGGTTAGGGTTT
1 --TTAAGTTAGGTTAGGGTTAGGGTTAGGG-TT
46973999 TTAA-TT-GAGTTA-GGTTAGGGTT
1 TTAAGTTAG-GTTAGGGTTAGGGTT
46974021 TTCAATTAAA
Statistics
Matches: 370, Mismatches: 20, Indels: 56
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.01
23 15 0.04
24 1 0.00
27 1 0.00
28 9 0.02
29 184 0.50
30 23 0.06
31 18 0.05
32 2 0.01
33 17 0.05
34 22 0.06
35 76 0.21
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (30 bp):
TTAAGTTAGGTTAGGGTTAGGGTTAGGGTT
Found at i:46973759 original size:93 final size:92
Alignment explanation
Indices: 46973573--46974020 Score: 539
Period size: 93 Copynumber: 4.9 Consensus size: 92
46973563 AATTTATCAA
* * * * *
46973573 ATTAAGTTAGGTTAGGGTTAGGGTTAGGG----T--TTAAGTTAGGTTAAGGTT-GAGTTTTTAG
1 ATTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
*
46973631 TTAATTTAGGTTAGGGTTAGGG--TTT
66 TTAAGTTAGGTTAGGGTTAGGGTTTTT
*
46973656 -TT-AGTTAATTTA-GGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
1 ATTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
46973718 TTAAGTTAGGTTAGGGTTAGGGTTAGGGTTT
66 TTAAGTTAGGTTAGGGTTAGGGTT----TTT
* * *
46973749 -TTAA-TTAATTTA-GGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAG
1 ATTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
*
46973811 TTAATTTAGGTTAGGGTTAGGGTTTTT
66 TTAAGTTAGGTTAGGGTTAGGGTTTTT
* * *
46973838 AGTTAATTTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 A-TTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTA
46973903 ATTAAGTTAGGTTAGGGTTAGGGTTTTT
65 ATTAAGTTAGGTTAGGGTTAGGGTTTTT
*
46973931 AATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
1 -ATTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATT-AA-T---TTA-GGTTAGGGTTAGGG
*
46973996 TTTTTAATTGAGTTAGGTTAGGGTT
59 TTTTTAATTAAGTTAGGTTAGGGTT
46974021 TTCAATTAAA
Statistics
Matches: 321, Mismatches: 19, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
80 14 0.04
81 8 0.02
82 2 0.01
84 1 0.00
86 16 0.05
87 29 0.09
89 3 0.01
91 4 0.01
92 6 0.02
93 193 0.60
94 4 0.01
98 3 0.01
99 38 0.12
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (92 bp):
ATTAAGTTAAGTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
TTAAGTTAGGTTAGGGTTAGGGTTTTT
Found at i:46973783 original size:122 final size:122
Alignment explanation
Indices: 46973607--46974020 Score: 652
Period size: 122 Copynumber: 3.4 Consensus size: 122
46973597 TAGGGTTTAA
* * *
46973607 GTTA-GGTTAAGGTT-GAGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
1 GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
*
46973670 TTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAG
66 TTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
46973727 GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
1 GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
* * *
46973792 TTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAG
66 TTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
* * *
46973849 GTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
46973914 TTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAG
66 TTAGGGTTAGGGTTTTTAATTAA--T---TTA-GGTTAGGGTTAGGGTTTTTAATTAAATTAG
* *
46973977 GTTAGGGTTAGGGTTAGGGTTTTTAATTGAGTTAGGTTAGGGTT
1 GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTT
46974021 TTCAATTAAA
Statistics
Matches: 272, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
120 4 0.01
121 9 0.03
122 185 0.68
124 1 0.00
127 3 0.01
128 70 0.26
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (122 bp):
GTTAGGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
TTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
Found at i:46974016 original size:23 final size:24
Alignment explanation
Indices: 46973983--46974038 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
46973973 TTAGGTTAGG
*
46973983 GTTAGGGTTAGGGTTTTTAATTGA
1 GTTAGGGTTAGGGTTTTCAATTGA
*
46974007 GTTA-GGTTAGGGTTTTCAATTAA
1 GTTAGGGTTAGGGTTTTCAATTGA
*
46974030 ATTAGGGTT
1 GTTAGGGTT
46974039 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (24 bp):
GTTAGGGTTAGGGTTTTCAATTGA
Found at i:46974114 original size:26 final size:25
Alignment explanation
Indices: 46974084--46974132 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
46974074 CTTCAAAAAT
46974084 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
46974110 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
46974133 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:46974558 original size:18 final size:18
Alignment explanation
Indices: 46974531--46974565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46974521 CGAAAAAAGA
* *
46974531 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
46974549 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
46974566 AAACATACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:46975227 original size:7 final size:7
Alignment explanation
Indices: 46975217--46975241 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
46975207 TTATATACAT
46975217 AATACTA
1 AATACTA
46975224 AATACTA
1 AATACTA
46975231 AATACTA
1 AATACTA
46975238 AATA
1 AATA
46975242 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:46976225 original size:15 final size:16
Alignment explanation
Indices: 46976200--46976230 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
46976190 ATAATTATCT
46976200 AAAAATACTTAAATAA
1 AAAAATACTTAAATAA
46976216 AAAAAT-CTTAAATAA
1 AAAAATACTTAAATAA
46976231 TAATTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATACTTAAATAA
Found at i:46976342 original size:10 final size:10
Alignment explanation
Indices: 46976323--46976371 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
46976313 GCCATTGATG
*
46976323 AAAATATAAA
1 AAAATTTAAA
46976333 AAAATTTAAA
1 AAAATTTAAA
* *
46976343 ATTATTTTAAA
1 A-AAATTTAAA
*
46976354 AAAATATAAA
1 AAAATTTAAA
46976364 AAAATTTA
1 AAAATTTA
46976372 TAATTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:46976358 original size:31 final size:31
Alignment explanation
Indices: 46976323--46976387 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
46976313 GCCATTGATG
46976323 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
46976354 AAAATATAAAAAAATTTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
46976385 AAA
1 AAA
46976388 TAGATTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:46976370 original size:21 final size:21
Alignment explanation
Indices: 46976329--46976370 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46976319 GATGAAAATA
* **
46976329 TAAAAAAATTTAAAATTATTT
1 TAAAAAAATATAAAAAAATTT
46976350 TAAAAAAATATAAAAAAATTT
1 TAAAAAAATATAAAAAAATTT
46976371 ATAATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAAAATATAAAAAAATTT
Found at i:46980808 original size:52 final size:52
Alignment explanation
Indices: 46980745--46980846 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
46980735 ATCCAATAAA
46980745 GCCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAG
1 GCCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAG
* * ***
46980797 GCCAAGTGTGTCTTTGTGATACTATTTGTTCTGGTCTTATAGAAAAAAGG
1 GCCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGG
46980847 TTAGGGTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (52 bp):
GCCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAG
Found at i:46987741 original size:23 final size:26
Alignment explanation
Indices: 46987701--46987753 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
46987691 AATTATTAAT
*
46987701 AAAAAAAATTATATTTTAATC-TTTA
1 AAAAAAAAGTATATTTTAATCATTTA
*
46987726 AAAAAAAAGTA-A-TTTAATCATTTC
1 AAAAAAAAGTATATTTTAATCATTTA
46987750 AAAA
1 AAAA
46987754 TTTTAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 8 0.32
25 10 0.40
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAAAAAAGTATATTTTAATCATTTA
Found at i:46991034 original size:14 final size:14
Alignment explanation
Indices: 46991017--46991045 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46991007 TTGCATGGTT
46991017 GCAAATACATGCAC
1 GCAAATACATGCAC
46991031 GCAAATACATGCAC
1 GCAAATACATGCAC
46991045 G
1 G
46991046 TCTTTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (14 bp):
GCAAATACATGCAC
Found at i:46994498 original size:116 final size:117
Alignment explanation
Indices: 46994267--46994500 Score: 398
Period size: 116 Copynumber: 2.0 Consensus size: 117
46994257 TTGCTGAATT
* ** *
46994267 ATTATCATTCATTTTGAGTATGCAGAAAGCTTTATGATACAAAAGCACTGTTACTTTTGCAAATT
1 ATTATCATTCATTTTGAGTATGCAGAAAACTGCATCATACAAAAGCACTGTTACTTTTGCAAATT
46994332 CAAGTGATCCGTTTATTAAAGAATAAACTAATTCCAACCCAAATTAATTATA
66 CAAGTGATCCGTTTATTAAAGAATAAACTAATTCCAACCCAAATTAATTATA
*
46994384 ATTATCATTCATTTTGAGTATGCAGAAAACTGCATCATACAAAAGCACTTTTACTTTTGC-AATT
1 ATTATCATTCATTTTGAGTATGCAGAAAACTGCATCATACAAAAGCACTGTTACTTTTGCAAATT
* *
46994448 CAAGTGATCTGTTTATTGAAGAATAAACTAATTCCAACCCAAATTAATTATA
66 CAAGTGATCCGTTTATTAAAGAATAAACTAATTCCAACCCAAATTAATTATA
46994500 A
1 A
46994501 CTATTATGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
116 55 0.50
117 55 0.50
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (117 bp):
ATTATCATTCATTTTGAGTATGCAGAAAACTGCATCATACAAAAGCACTGTTACTTTTGCAAATT
CAAGTGATCCGTTTATTAAAGAATAAACTAATTCCAACCCAAATTAATTATA
Found at i:46995879 original size:16 final size:16
Alignment explanation
Indices: 46995846--46995879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46995836 TATAGTTGTT
* *
46995846 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
46995862 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
46995878 AA
1 AA
46995880 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:46998254 original size:19 final size:17
Alignment explanation
Indices: 46998213--46998250 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46998203 TTTTCCAATT
46998213 ATAAT-ATTTTTTAAAA
1 ATAATAATTTTTTAAAA
*
46998229 ATTATAATTTTTTAATAA
1 ATAATAATTTTTTAA-AA
46998247 ATAA
1 ATAA
46998251 ATAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATAATTTTTTAAAA
Found at i:46998620 original size:26 final size:26
Alignment explanation
Indices: 46998584--46998633 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
46998574 TGTTATAACT
46998584 TTTTTTTATTTACCAAAATATATATA
1 TTTTTTTATTTACCAAAATATATATA
*
46998610 TTTTTTTATTTACTAAAATATATA
1 TTTTTTTATTTACCAAAATATATA
46998634 AAAAAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTTTTATTTACCAAAATATATATA
Found at i:46999638 original size:14 final size:14
Alignment explanation
Indices: 46999619--46999646 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46999609 TTTTTGTATC
46999619 AATTTAATTATTCT
1 AATTTAATTATTCT
46999633 AATTTAATTATTCT
1 AATTTAATTATTCT
46999647 TGTTTCAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:47000135 original size:27 final size:27
Alignment explanation
Indices: 47000064--47000140 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
47000054 ATAACACGAG
**
47000064 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
47000091 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
47000118 TGGTGCCGCCAACAGGGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
47000141 CCACCCAGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.14, C:0.31, G:0.30, T:0.25
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:47000259 original size:28 final size:27
Alignment explanation
Indices: 47000198--47000259 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 27
47000188 TTTTGTTTTT
*
47000198 TTTATATATTTTGGTAAATAAAAAAAT
1 TTTATATATTTTGGTAAATAAAAAAAA
47000225 TTATATATATTTTGGTAAATAAAAAAAAA
1 TT-TATATATTTTGGTAAAT-AAAAAAAA
47000254 TTTATA
1 TTTATA
47000260 ACATTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 2 0.06
28 21 0.66
29 9 0.28
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAA
Found at i:47000683 original size:20 final size:21
Alignment explanation
Indices: 47000660--47000711 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
47000650 CTTATTTTCA
*
47000660 ATTTATTAATTTTATAAAA-T
1 ATTTATTAATTTTAGAAAATT
47000680 ATTT-TTAATGTTTAGAAAATT
1 ATTTATTAAT-TTTAGAAAATT
*
47000701 ATTTAGTAATT
1 ATTTATTAATT
47000712 GATTTAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 6 0.22
22 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
ATTTATTAATTTTAGAAAATT
Found at i:47001421 original size:28 final size:28
Alignment explanation
Indices: 47001390--47001451 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
47001380 ACAAAAACGA
*
47001390 TCTCTTTTTATTTAACCCAAACGGAATT
1 TCTCTTTTTATTTAACCCAAACGGAACT
* *
47001418 TCTC-TTTTCTTTAATCCAAACGGAACT
1 TCTCTTTTTATTTAACCCAAACGGAACT
47001445 TCTCTTT
1 TCTCTTT
47001452 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (28 bp):
TCTCTTTTTATTTAACCCAAACGGAACT
Found at i:47013837 original size:61 final size:61
Alignment explanation
Indices: 47013758--47013872 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
47013748 TATTTTTTAA
* * * * *
47013758 TTTTTAGAGTTAGGACTAAATTGACAATTTTTGTAAATATTGAGGACCAAATTTATTGAAT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTTATTGAAT
* * *
47013819 TTTTTTGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCTAAATTT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTT
47013873 GTTGGTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTTATTGAAT
Found at i:47015168 original size:23 final size:23
Alignment explanation
Indices: 47015142--47015194 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
47015132 ATAAGTGCCA
47015142 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
47015165 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
47015188 CACTGAT
1 CACTGAT
47015195 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:47015446 original size:18 final size:17
Alignment explanation
Indices: 47015420--47015458 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
47015410 ATTTTCCTTC
47015420 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
47015437 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
47015455 CACA
1 CACA
47015459 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:47017080 original size:21 final size:22
Alignment explanation
Indices: 47017049--47017089 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
47017039 TTTTTCAAAC
47017049 TATTAAATTAATTATTTTTAAG
1 TATTAAATTAATTATTTTTAAG
47017071 TATT-AATTAATTATTTTTA
1 TATTAAATTAATTATTTTTA
47017090 CATCTATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTAAATTAATTATTTTTAAG
Found at i:47020464 original size:17 final size:17
Alignment explanation
Indices: 47020431--47020488 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
47020421 TGGGGACGGT
47020431 AGAGAAA-AA-AA-AAG
1 AGAGAAAGAAGAAGAAG
*
47020445 AGAGAAAGGAGAAGAAG
1 AGAGAAAGAAGAAGAAG
47020462 AGA-AGAAGAAGAAGAAG
1 AGAGA-AAGAAGAAGAAG
*
47020479 AAAGAAAGAA
1 AGAGAAAGAA
47020489 AAAAAAGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.19
15 1 0.03
16 3 0.08
17 24 0.67
18 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAGAAGAAG
Found at i:47020667 original size:22 final size:22
Alignment explanation
Indices: 47020640--47020707 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
47020630 TGGATTAGAA
*
47020640 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTGTAATTT
47020662 TTTTGTATGAATATTGTAA-TT
1 TTTTGTATGAATATTGTAATTT
*
47020683 TTTT-TATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
47020704 TTTT
1 TTTT
47020708 ATAATTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 14 0.33
21 11 0.26
22 18 0.42
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.60
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:47020690 original size:20 final size:20
Alignment explanation
Indices: 47020640--47020865 Score: 104
Period size: 21 Copynumber: 10.4 Consensus size: 20
47020630 TGGATTAGAA
* *
47020640 TTTTGTATGAATATTCTAATT
1 TTTTTTATGAATATTGTAA-T
47020661 TTTTTGTATGAATATTGTAAT
1 TTTTT-TATGAATATTGTAAT
47020682 TTTTTTATGAATATTGTAAT
1 TTTTTTATGAATATTGTAAT
* *
47020702 TATTTTAT-AATTAAATTTGTATT
1 TTTTTTATGAA-T--A-TTGTAAT
*
47020725 TATAGTTTTA-G-AT-TAGT-A-
1 T-T--TTTTATGAATATTGTAAT
*
47020743 TTTTGTATGAATATTGTAATTTT
1 TTTTTTATGAATATTGTAA---T
*
47020766 ATAATTTTATATGAATATTGCAAT
1 -T--TTTT-TATGAATATTGTAAT
47020790 TTTTTGTATGAATATTGTAAT
1 TTTTT-TATGAATATTGTAAT
* *
47020811 GTCTAGATATACTGTAATATTGTAAT
1 -T-T--TTTTA-TG-AATATTGTAAT
47020837 TTTTTGTATGAATATTGTAAT
1 TTTTT-TATGAATATTGTAAT
*
47020858 TATTTTAT
1 TTTTTTAT
47020866 AATTAATTTG
Statistics
Matches: 159, Mismatches: 18, Indels: 57
0.68 0.08 0.24
Matches are distributed among these distances:
15 4 0.03
16 1 0.01
17 3 0.02
18 4 0.03
19 3 0.02
20 29 0.18
21 43 0.27
22 18 0.11
23 11 0.07
24 6 0.04
25 5 0.03
26 19 0.12
27 13 0.08
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTTTTATGAATATTGTAAT
Found at i:47020702 original size:103 final size:107
Alignment explanation
Indices: 47020595--47020810 Score: 264
Period size: 103 Copynumber: 2.0 Consensus size: 107
47020585 TATTAATTAT
* * * *
47020595 TAATTA-TAAATTATCTATATTTAGTGTTTATAG-TTTGGATTAGAATTTTGTATGAATATTCTA
1 TAATTATTAAATAAT-TAAATTT-GTATTTATAGTTTTAGATTAGAATTTTGTATGAATATTCTA
* *
47020658 A-TT-T-TTTTGTATGAATATTGTAATTTTTT-TATGAATATTG
64 ATTTATATTTTATATGAATATTGCAATTTTTTGTATGAATATTG
** * *
47020698 TAATTATTTTATAATTAAATTTGTATTTATAGTTTTAGATTAGTATTTTGTATGAATATTGTAAT
1 TAATTATTAAATAATTAAATTTGTATTTATAGTTTTAGATTAGAATTTTGTATGAATATTCTAA-
47020763 TTTATAATTTTATATGAATATTGCAATTTTTTGTATGAATATTG
65 TTTAT-ATTTTATATGAATATTGCAATTTTTTGTATGAATATTG
47020807 TAAT
1 TAAT
47020811 GTCTAGATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
102 9 0.09
103 40 0.42
104 5 0.05
105 2 0.02
106 1 0.01
108 23 0.24
109 15 0.16
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (107 bp):
TAATTATTAAATAATTAAATTTGTATTTATAGTTTTAGATTAGAATTTTGTATGAATATTCTAAT
TTATATTTTATATGAATATTGCAATTTTTTGTATGAATATTG
Found at i:47021051 original size:37 final size:37
Alignment explanation
Indices: 47021000--47021080 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
47020990 CATATAAAGT
*
47021000 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGATTAA
47021038 TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
47021075 TTATAA
1 TTATAA
47021081 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 38 0.90
38 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
Found at i:47024259 original size:22 final size:22
Alignment explanation
Indices: 47024232--47024273 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
47024222 AATACCTTAT
*
47024232 TTTTTTTCTTCT-TTTCCTTCC
1 TTTTTTTCTTCTGCTTCCTTCC
47024253 TTTTTTTCTTCTGCTTCCTTC
1 TTTTTTTCTTCTGCTTCCTTC
47024274 TTATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTCTTCTGCTTCCTTCC
Found at i:47024261 original size:18 final size:18
Alignment explanation
Indices: 47024234--47024283 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
47024224 TACCTTATTT
*
47024234 TTTTTCTTCTTTTCCTTCC
1 TTTTT-TTCTTCTCCTTCC
*
47024253 TTTTTTTCTTCTGCTTCC
1 TTTTTTTCTTCTCCTTCC
47024271 TTCTTATTTCTTC
1 TT-TT-TTTCTTC
47024284 CGTTTCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTTTCTTCTCCTTCC
Found at i:47024374 original size:27 final size:27
Alignment explanation
Indices: 47024344--47024421 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
47024334 ATCAGACCAT
*
47024344 TGGCGCCTCTCAG-TATGGCACCAATAA
1 TGGCGCCTCTCAGATA-GGCACCAACAA
* * *
47024371 TGGCGCCTCCCAGATAGGCACCACCAT
1 TGGCGCCTCTCAGATAGGCACCAACAA
* *
47024398 TGGCGCCTCTGAGATAGGCGCCAA
1 TGGCGCCTCTCAGATAGGCACCAA
47024422 TACTATGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 40 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (27 bp):
TGGCGCCTCTCAGATAGGCACCAACAA
Found at i:47025137 original size:56 final size:56
Alignment explanation
Indices: 47025070--47025181 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
47025060 CATTCCGGTG
47025070 TAAATTTTGGTTGGTACCGGTCGTATT-AGTCTGTACTAGTTGATTTCTCCCATACC
1 TAAATTTTGGTTGGTACCGGTCGT-TTCAGTCTGTACTAGTTGATTTCTCCCATACC
47025126 TAAATTTTGGTTGGTACCGGTCGTTTCAGTCTGTACTAGTTGATTTCTCCCATACC
1 TAAATTTTGGTTGGTACCGGTCGTTTCAGTCTGTACTAGTTGATTTCTCCCATACC
47025182 GATCAAAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 2 0.04
56 53 0.96
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (56 bp):
TAAATTTTGGTTGGTACCGGTCGTTTCAGTCTGTACTAGTTGATTTCTCCCATACC
Found at i:47026196 original size:17 final size:17
Alignment explanation
Indices: 47026151--47026196 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
47026141 AAACTATAAC
47026151 AAAATTATTT--TTTAA
1 AAAATTATTTAATTTAA
*
47026166 AATATT-TTTAAATTTAA
1 AAAATTATTT-AATTTAA
47026183 AAAATTATTTAATT
1 AAAATTATTTAATT
47026197 ATTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 5 0.20
17 14 0.56
18 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATTATTTAATTTAA
Found at i:47030410 original size:21 final size:20
Alignment explanation
Indices: 47030363--47030452 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
47030353 TTATCTGATA
* *
47030363 AAAAAATAAATTAATTTATT
1 AAAAAATAAATTTATTTATC
47030383 AGAAAAATAAATTTATTTATC
1 A-AAAAATAAATTTATTTATC
** * *
47030404 AATAAAATAAAAATA-CTGT-
1 AA-AAAATAAATTTATTTATC
47030423 -AAAAATAAATTTATTTATC
1 AAAAAATAAATTTATTTATC
47030442 AATAAAATAAA
1 AA-AAAATAAA
47030453 AATACTGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
17 10 0.19
18 3 0.06
20 5 0.09
21 36 0.67
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAAATAAATTTATTTATC
Found at i:47030436 original size:38 final size:38
Alignment explanation
Indices: 47030385--47030463 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
47030375 AATTTATTAG
47030385 AAAAATAAATTTATTTATCAATAAAATAAAAATACTGT
1 AAAAATAAATTTATTTATCAATAAAATAAAAATACTGT
47030423 AAAAATAAATTTATTTATCAATAAAATAAAAATACTGT
1 AAAAATAAATTTATTTATCAATAAAATAAAAATACTGT
47030461 AAA
1 AAA
47030464 CTTCACCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (38 bp):
AAAAATAAATTTATTTATCAATAAAATAAAAATACTGT
Found at i:47033182 original size:39 final size:39
Alignment explanation
Indices: 47033139--47033233 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
47033129 CCCGGTGCTT
47033139 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
47033178 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
* *
47033217 GTCCCTGTGGTTGGTGT
1 GTCCCTGTTGTCGGTGT
47033234 TGAGGTAGGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.04, C:0.20, G:0.39, T:0.37
Consensus pattern (39 bp):
GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
Found at i:47033229 original size:24 final size:24
Alignment explanation
Indices: 47033193--47033284 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
47033183 TGTTGTCGGT
* *
47033193 GTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTGGTTGGTGTGGTAGGA
*
47033217 GTCCCTGTGGTTGGTGTTGAGGTAGGC
1 GTCCCTGTGGTTGGTG-T--GGTAGGA
* * *
47033244 GTCCCTGTGGTCGGTGTCGTCGGA
1 GTCCCTGTGGTTGGTGTGGTAGGA
*
47033268 GTCCCTGTGGATGGTGT
1 GTCCCTGTGGTTGGTGT
47033285 TGTGCTTGTA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
24 33 0.59
25 1 0.02
26 1 0.02
27 21 0.38
ACGTcount: A:0.07, C:0.18, G:0.42, T:0.33
Consensus pattern (24 bp):
GTCCCTGTGGTTGGTGTGGTAGGA
Found at i:47034758 original size:19 final size:19
Alignment explanation
Indices: 47034679--47034764 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 19
47034669 TCGAATTTAA
* *
47034679 ATTTATTTAAAAATATAAA
1 ATTTTTTTAAAAATATAAT
* *
47034698 ATTATTTTT-ATATTATAAT
1 ATT-TTTTTAAAAATATAAT
*
47034717 ATTTAAATTTT--AAATAT-AC
1 ATTT---TTTTAAAAATATAAT
47034736 ATTTTTTTAAAAATATAAT
1 ATTTTTTTAAAAATATAAT
*
47034755 ATTTTATTAA
1 ATTTTTTTAA
47034765 CTCCATTGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.08
18 7 0.14
19 28 0.55
20 8 0.16
21 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTTAAAAATATAAT
Found at i:47035602 original size:16 final size:16
Alignment explanation
Indices: 47035556--47035608 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
47035546 TACTATTTAA
*
47035556 AATTTAAAATAATAAAA
1 AATTTAAAAT-ATAAAT
*
47035573 AATTT---ATATTAAT
1 AATTTAAAATATAAAT
47035586 AATTTAAAATATAAAT
1 AATTTAAAATATAAAT
47035602 AATTTAA
1 AATTTAA
47035609 TATGTATGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
16 14 0.47
17 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAATATAAAT
Found at i:47035621 original size:29 final size:29
Alignment explanation
Indices: 47035552--47035607 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
47035542 ATAATACTAT
47035552 TTAA-AATTTAAAATAATAAAAAATTTATA
1 TTAATAATTTAAAAT-ATAAAAAATTTATA
*
47035581 TTAATAATTTAAAATATAAATAATTTA
1 TTAATAATTTAAAATATAAAAAATTTA
47035608 ATATGTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TTAATAATTTAAAATATAAAAAATTTATA
Found at i:47041741 original size:39 final size:38
Alignment explanation
Indices: 47041693--47041881 Score: 118
Period size: 39 Copynumber: 4.8 Consensus size: 38
47041683 GTTTAGTTAT
*
47041693 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAAC
1 TAAT-ATTATTGTTAGTTAGTATTATTATTAGT-AAAAAC
* * **
47041733 TAATATTATTATCATGGTTAGTTATTAGGATTAGTAAAAACCC
1 TAATATTATTGT--TAGTTAG-TATTATTATTAGTAAAAA--C
* * ****
47041776 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTAC
1 TAA-TATTATTGTTAGTTAGTATTATTATTAGTAAAAAC
*
47041814 ATTATATTATTGTTAGTTAGTATTATT-TTGAGT-AAAAC
1 -TAATATTATTGTTAGTTAGTATTATTATT-AGTAAAAAC
* *
47041852 TATTATTATTGTTA-TT-GTGTTAGTTATTAG
1 TAATATTATTGTTAGTTAGTATTA-TTATTAG
47041882 GATTAGTGGT
Statistics
Matches: 116, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
35 5 0.04
36 6 0.05
37 14 0.12
38 12 0.10
39 26 0.22
40 14 0.12
41 16 0.14
42 11 0.09
43 5 0.04
44 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (38 bp):
TAATATTATTGTTAGTTAGTATTATTATTAGTAAAAAC
Found at i:47044728 original size:8 final size:8
Alignment explanation
Indices: 47044696--47044751 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
47044686 GGAATTGAGC
47044696 TAATGTTG
1 TAATGTTG
**
47044704 TAAAATTG
1 TAATGTTG
*
47044712 TTATG-TG
1 TAATGTTG
47044719 TAATGTTG
1 TAATGTTG
47044727 TAATGTTG
1 TAATGTTG
47044735 TAATGTTG
1 TAATGTTG
*
47044743 CAATGTTG
1 TAATGTTG
47044751 T
1 T
47044752 TTTAACACCC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 6 0.15
8 33 0.85
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (8 bp):
TAATGTTG
Found at i:47047096 original size:154 final size:156
Alignment explanation
Indices: 47046902--47047202 Score: 441
Period size: 157 Copynumber: 1.9 Consensus size: 156
47046892 TGCCTGCAAC
* * *
47046902 TTAAAAAAGAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCCCGAATTTT
1 TTAAAAAAGAATTTAGAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTT
* *
47046967 ATTACTTT-A-AAAAATATAATATTTTC-TAATTTTATTGTATTACATTATTTTAGTACATTATG
66 ATTACTTTAATAAAAATATAATATTTTCGT-ATTTTATTATATTACATTATTTAAGTACATTATG
47047029 TTTGAAAT-TCATTAATTTAGTGAGTTT
130 TTTGAAATGT-ATTAATTTAGTGAGTTT
* * *
47047056 TTAAAATA-AATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCTCGGATTT
1 TTAAAAAAGAATTTAGAAAAA-AACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTT
* *
47047120 TATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTAAGTACATTAT
65 TATTACTTT-AATAAAAATATAATATTTTCGTATTTTATTATATTACATTATTTAAGTACATTAT
47047185 GTTTGAAATGTATTAATT
129 GTTTGAAATGTATTAATT
47047203 AATTCTATTT
Statistics
Matches: 131, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
153 11 0.08
154 55 0.42
156 1 0.01
157 62 0.47
158 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (156 bp):
TTAAAAAAGAATTTAGAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTT
ATTACTTTAATAAAAATATAATATTTTCGTATTTTATTATATTACATTATTTAAGTACATTATGT
TTGAAATGTATTAATTTAGTGAGTTT
Found at i:47047276 original size:119 final size:119
Alignment explanation
Indices: 47047153--47047369 Score: 310
Period size: 119 Copynumber: 1.8 Consensus size: 119
47047143 TATTTTCGTA
* * **
47047153 TTTTATTATTTTACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAATTCTATTTTTTTT
1 TTTTATTATTTAACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCTATTTTTTAA
*
47047218 A-AAATAGTAAAAAACTCTTATTTCTGCCCTTTAAAAAAATATACTACTTTTTAT
66 ATAAAT-GTAAAAAACTCTTATTTCGGCCCTTTAAAAAAATATACTACTTTTTAT
* * * * * *
47047272 TTTTATTATTTAACATTATTTTAGTACATTATGTTTTAAATTTATTAATTTAGTGTGTTTTTTAA
1 TTTTATTATTTAACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCTATTTTTTAA
*
47047337 ATAAATTTAAAAAACTCTTATTTCGGCCCTTTA
66 ATAAATGTAAAAAACTCTTATTTCGGCCCTTTA
47047370 CTCGTATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
119 81 0.95
120 4 0.05
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.52
Consensus pattern (119 bp):
TTTTATTATTTAACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCTATTTTTTAA
ATAAATGTAAAAAACTCTTATTTCGGCCCTTTAAAAAAATATACTACTTTTTAT
Found at i:47047433 original size:152 final size:151
Alignment explanation
Indices: 47047252--47047752 Score: 589
Period size: 152 Copynumber: 3.3 Consensus size: 151
47047242 TGCCCTTTAA
* * *
47047252 AAAAATATACTACTTTTTATTTTTATTATTTAACATTATTTTAGTACATTATGTTTTAAATTTAT
1 AAAAATATACTATTTTTTA-TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* * *
47047317 TAATTTAGTGTGTTTTTTAAATAAATTTAAAAAACTCTTATTTCGGCCCTTTACTCGTATTTTTT
65 TAATTTAGTATGTTTTTTAAATAAATTTAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTT
47047382 CCCGAATTTTATTACTTTCAAT
130 CCCGAATTTTATTACTTTCAAT
* *
47047404 AAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAATATACTATTTTT-TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* * * * * *** * *
47047469 TAAGTAATTCTATTTTTTTTTTAAATTTAGTAAAATACCCTTATTTCGACCCTTTGTTCGTATTT
65 TAATTTAGTATGTTTTTTAAATAAATTTA--AAAA-ACCCTTATTTCGGCCCTTTGCTCGTA-TT
*
47047534 TTTTCTCCGGATTTTATTACTTT--A-
126 TTTTC-CCGAATTTTATTACTTTCAAT
* * *
47047558 CAAAATATACGATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
1 AAAAATATACTATTTT-TTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* * * * *
47047623 TAATTTAGTATGTTTTCTAAATAAAGTTCAAAAAATAACCCTTATTTCGGCCATTTGCTTGT-CT
65 TAATTTAGTATGTTTTTTAAATAAA-TT--TAAAA-AACCCTTATTTCGGCCCTTTGCTCGTATT
*
47047687 TTTTCCCAAATTTTATTACTTTCAAT
126 TTTTCCCGAATTTTATTACTTTCAAT
* *
47047713 AAAAATATA-TATTTTTTATTTTGTTATTTTACATTTTTTT
1 AAAAATATACTATTTTTTATTTTATTATTTTACATTATTTT
47047753 CGGATTTTAT
Statistics
Matches: 290, Mismatches: 45, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
152 93 0.32
153 30 0.10
154 84 0.29
155 58 0.20
156 8 0.03
157 17 0.06
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (151 bp):
AAAAATATACTATTTTTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATT
AATTTAGTATGTTTTTTAAATAAATTTAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTC
CCGAATTTTATTACTTTCAAT
Found at i:47047463 original size:271 final size:275
Alignment explanation
Indices: 47046971--47047523 Score: 834
Period size: 271 Copynumber: 2.0 Consensus size: 275
47046961 AATTTTATTA
*
47046971 CTTTAAAAAATATAATATTTTCTAATTTTATTGTATTACATTATTTTAGTACATTATGTTTGAAA
1 CTTTAAAAAATATAATATTTTCTAATTTTATTATATTACATTATTTTAGTACATTATGTTTGAAA
*
47047036 TTCATTAATTTAGTGAGTTTTTAAAATAAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTC
66 TTCATTAATTTAGTGAGTTTTTAAAATAAATTT--AAAAATAACCCTTATTTCGGCCCTTTACTC
* *
47047101 GTATTTTTTTCTCGGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
129 GTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
*
47047166 CATTATTTAAGTACATTATGTTTGAAATGTATTAATTAATTCTA-TTTTTTTTAAA-ATAGTAAA
194 CATTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTTTAAATATAGTAAA
*
47047229 AAACTCTTATTTCTG-CC
259 AAACCCTTATTTC-GACC
* * *
47047246 CTTTAAAAAAATATACTACTTTT-TATTTTTATTAT-TTAACATTATTTTAGTACATTATGTTTT
1 CTTT-AAAAAATATAATA-TTTTCTAATTTTATTATATT-ACATTATTTTAGTACATTATGTTTG
* * * *
47047309 AAATTTATTAATTTAGTGTGTTTTTTAAATAAATTT-AAAA-AACTCTTATTTCGGCCCTTTACT
63 AAATTCATTAATTTAGTGAGTTTTTAAAATAAATTTAAAAATAACCCTTATTTCGGCCCTTTACT
*
47047372 CGTA-TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTT
128 CGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTT
* *
47047436 ACATTATTTTAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTTTTAAATTTAGTA
193 ACATTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTA-TTTTTTTTTAAATATAGTA
*
47047501 AAATACCCTTATTTCGACC
257 AAAAACCCTTATTTCGACC
47047520 CTTT
1 CTTT
47047524 GTTCGTATTT
Statistics
Matches: 254, Mismatches: 17, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
271 100 0.39
272 25 0.10
273 16 0.06
274 24 0.09
275 6 0.02
276 79 0.31
277 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (275 bp):
CTTTAAAAAATATAATATTTTCTAATTTTATTATATTACATTATTTTAGTACATTATGTTTGAAA
TTCATTAATTTAGTGAGTTTTTAAAATAAATTTAAAAATAACCCTTATTTCGGCCCTTTACTCGT
ATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACA
TTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTTTAAATATAGTAAAAA
ACCCTTATTTCGACC
Found at i:47048107 original size:21 final size:19
Alignment explanation
Indices: 47048081--47048130 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
47048071 TTATTTATTT
47048081 CTTTCTTTTTCCTTCCTTCC
1 CTTTCTTTTTCC-TCCTTCC
* *
47048101 CTCTTCTTCTT-CTCCTTTC
1 CT-TTCTTTTTCCTCCTTCC
47048120 CTTTCTTTTTC
1 CTTTCTTTTTC
47048131 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 3 0.12
21 7 0.28
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
CTTTCTTTTTCCTCCTTCC
Found at i:47048147 original size:14 final size:14
Alignment explanation
Indices: 47048107--47048153 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
47048097 TTCCCTCTTC
47048107 TTCTTCTCCTTTCCT
1 TTCTTCTCCTTT-CT
* *
47048122 TTCTTTTTCTTTCT
1 TTCTTCTCCTTTCT
*
47048136 TTCTTCTCCTTTCC
1 TTCTTCTCCTTTCT
47048150 TTCT
1 TTCT
47048154 CCATCCCACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCTTCTCCTTTCT
Found at i:47048294 original size:5 final size:5
Alignment explanation
Indices: 47048286--47048360 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
47048276 TGGGGTGGAG
* *
47048286 AAGGA AAGGA GAA-GA AA-GA AAGAA AATGA AAGGA GAA-GA AAGGA AAGGA
1 AAGGA AAGGA -AAGGA AAGGA AAGGA AAGGA AAGGA -AAGGA AAGGA AAGGA
* *
47048335 AAGGA GAA-G- AAGAA AAGGG AAGGA AA
1 AAGGA -AAGGA AAGGA AAGGA AAGGA AA
47048361 AAGAAAGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
3 2 0.04
4 8 0.15
5 39 0.71
6 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (5 bp):
AAGGA
Found at i:47048326 original size:10 final size:11
Alignment explanation
Indices: 47048282--47048343 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 11
47048272 CTGGTGGGGT
47048282 GGAGAAGGAAA
1 GGAGAAGGAAA
47048293 GGAGAA-GAAA
1 GGAGAAGGAAA
* *
47048303 GAAAGAAAATGAAA
1 G---GAGAAGGAAA
47048317 GGAGAA-GAAA
1 GGAGAAGGAAA
47048327 GGA-AAGGAAA
1 GGAGAAGGAAA
47048337 GGAGAAG
1 GGAGAAG
47048344 AAGAAAAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 2 0.05
10 19 0.44
11 13 0.30
13 4 0.09
14 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.39, T:0.02
Consensus pattern (11 bp):
GGAGAAGGAAA
Found at i:47048326 original size:20 final size:20
Alignment explanation
Indices: 47048301--47048371 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
47048291 AAGGAGAAGA
*
47048301 AAGAAAGAAAATGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
*
47048321 AAGAAAGGAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
* *
47048341 AAG-AAGAAAAGGGAAGGAAA
1 AAGAAAGAAAAGGAAAGG-AG
47048361 AAGAAAGAAAA
1 AAGAAAGAAAA
47048372 AAAAATAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 12 0.27
20 25 0.57
21 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAAGGAG
Found at i:47048357 original size:24 final size:24
Alignment explanation
Indices: 47048286--47048360 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
47048276 TGGGGTGGAG
*
47048286 AAGGAAAGGAGAAGAA-AGAAAGAA
1 AAGGAAAGGAGAAGAAGA-AAAGGA
*
47048310 AATGAAA-G-G-AGAAG-AAAGGA
1 AAGGAAAGGAGAAGAAGAAAAGGA
*
47048330 AAGGAAAGGAGAAGAAGAAAAGGG
1 AAGGAAAGGAGAAGAAGAAAAGGA
47048354 AAGGAAA
1 AAGGAAA
47048361 AAGAAAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 2 0.05
23 6 0.14
24 18 0.43
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (24 bp):
AAGGAAAGGAGAAGAAGAAAAGGA
Found at i:47049162 original size:153 final size:149
Alignment explanation
Indices: 47048696--47049548 Score: 943
Period size: 153 Copynumber: 5.7 Consensus size: 149
47048686 ATAAAATCTA
* * *
47048696 AAAAAAATATAAAATAACAAAATAAAAAATATATATATTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATAAAAAATA-ATATATTTTT-TT-AAAGTAATAAAATTCGGGA
* *
47048761 AAAAATACGAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTTAACAAACACATTAAA
63 AAAAATACGAACAAAGGGCCGAAATAAGGG-T-TTTTTT-AAATTTATTTAAAAAACA-AATAAA
*
47048826 TTAATAAATTTCAAACATAATGTACT
124 TTAATAAATTTAAAACATAATGTACT
* * * * *
47048852 AAAATAATGTACAATAATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGAAAA
1 AAAATAATGTAAAATAATAAAA-TAAAAAATAATATATTTTTTTAAAGTAATAAAATTCGGGAAA
** * * *
47048917 AAATACGAACAAAGGGCCGAAATAA-GAATATTTTACTAATTTA--AAAAAAACAGAATTAATTA
65 AAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTA--AATTTATTTAAAAAACA-AATAAATTA
* *
47048979 ATACATTTCAAACATAATGTACT
127 ATAAATTTAAAACATAATGTACT
*
47049002 AAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATA-AAAAATAATATATTTTT-TT-AAAGTAATAAAATTCGGGA
* ** * *
47049067 AAAAATACTAGTAAACGGCCGAAATAAGGCTTTTTTTAAATTTATTTAAAAAACAAACTAAATTA
63 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACAAA-TAAATTA
47049132 ATAAATTTAAAACATAATGTACT
127 ATAAATTTAAAACATAATGTACT
*
47049155 AAAATAATGTAAAATAATAAAAATAAAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGGAA
1 AAAATAATGTAAAATAAT-AAAATAAAAAATAATATATTTTTTTAAAGTAATAAAATTC-GGG-A
* * *
47049220 AAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTTACTAAA-TTA---AAAAAACAGAATTAAT
63 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT--TAAATTTATTTAAAAAACA-AATAAAT
* *
47049281 TAATACATTTCAAACATAATG---T
125 TAATAAATTTAAAACATAATGTACT
** *
47049303 AAAATAA--TAAAATACA-AAAAT--AAAAT-AT-T-TTAATTGAAAGTAATAAAATTCGGGAAA
1 AAAATAATGTAAAATA-ATAAAATAAAAAATAATATATTTTTTTAAAGTAATAAAATTCGGGAAA
** *
47049360 AAATACGAGTAAAGGGCCGAAATAAGGGTTACTTTTCTAAATTTATTTAAAAAACACACTAAATT
65 AAATACGAACAAAGGGCCGAAATAAGGGTT--TTTT-TAAATTTATTTAAAAAACA-AATAAATT
* *
47049425 AATGAATTTAAAATATAATGTACT
126 AATAAATTTAAAACATAATGTACT
* * *
47049449 AAAATAATGTAAAATAATAAAATTAGAAAATAGTATA-TTTTTTAAAGTATTAAAATTCGGGGAA
1 AAAATAATGTAAAATAATAAAA-TAAAAAATAATATATTTTTTTAAAGTAATAAAATTC-GGG-A
47049513 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
63 AAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
47049549 ACTAATTTTT
Statistics
Matches: 596, Mismatches: 64, Indels: 77
0.81 0.09 0.10
Matches are distributed among these distances:
138 30 0.05
139 8 0.01
140 26 0.04
141 1 0.00
142 1 0.00
143 35 0.06
145 5 0.01
146 15 0.03
147 2 0.00
148 19 0.03
149 3 0.01
150 74 0.12
151 63 0.11
152 57 0.10
153 129 0.22
154 57 0.10
155 36 0.06
156 27 0.05
157 8 0.01
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.30
Consensus pattern (149 bp):
AAAATAATGTAAAATAATAAAATAAAAAATAATATATTTTTTTAAAGTAATAAAATTCGGGAAAA
AATACGAACAAAGGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACAAATAAATTAATAA
ATTTAAAACATAATGTACT
Found at i:47049205 original size:303 final size:296
Alignment explanation
Indices: 47048696--47049556 Score: 1236
Period size: 303 Copynumber: 2.9 Consensus size: 296
47048686 ATAAAATCTA
*
47048696 AAAAAAATATAAAATAACAAAATAAAAAATATATATATTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAAT-TAAAATAA-AAAAT-AAAAATA-ATATATTTTTATTGAAAGTAATAAAATTCGGGA
** * * *
47048761 AAAAATACGAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTTAACAAACACATTAAA
62 AAAAATACGAGTAAAGGGCCGAAATAA-GGCT-TTTTTT-AAATTTATTTAAAAAACACACTAAA
* *
47048826 TTAATAAATTTCAAACATAATGTACTAAAATAATGTACAATAATAAAATTAGAAAATAGTATATT
124 TTAATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATT
* ** *
47048891 TTTTAAAAGTAATAAAATTC-GGAAAAAAATACGAACAAAGGGCCGAAATAAGAATATTTTACTA
189 TTTTTAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTA
47048955 ATTTAAAAAAAACAGAATTAATTAATACATTTCAAACATAATGTACT
254 ATTT-AAAAAAACAGAATTAATTAATACATTTCAAACATAATG---T
*
47049002 AAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGA
1 AAAATAAT-TAAAATAA-AAAATA--AAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* * *
47049067 AAAAATACTAGTAAACGGCCGAAATAAGGCTTTTTTTAAATTTATTTAAAAAACAAACTAAATTA
62 AAAAATACGAGTAAAGGGCCGAAATAAGGCTTTTTTTAAATTTATTTAAAAAACACACTAAATTA
* *
47049132 ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAAATAAAAAATAGTATATTTTT
127 ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
* * *
47049197 TTAAAGTAATAAAATTCGGGGAAAAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTTACTAAA
192 TTAAAGTAATAAAATTC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAT
47049262 TTAAAAAAACAGAATTAATTAATACATTTCAAACATAATGT
256 TTAAAAAAACAGAATTAATTAATACATTTCAAACATAATGT
*
47049303 AAAATAA-TAAAATACAAAAAT----A-AA-ATATTTTAATTGAAAGTAATAAAATTCGGGAAAA
1 AAAATAATTAAAATA-AAAAATAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAA
*
47049361 AATACGAGTAAAGGGCCGAAATAAGGGTTACTTTTCTAAATTTATTTAAAAAACACACTAAATTA
65 AATACGAGTAAAGGGCCGAAATAAGGCTT--TTTT-TAAATTTATTTAAAAAACACACTAAATTA
* *
47049426 ATGAATTTAAAATATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATA-TTTT
127 ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
*
47049490 TTAAAGTATTAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAT
192 TTAAAGTAATAAAATTC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAT
47049555 TT
256 TT
47049557 TTTTTGAAGT
Statistics
Matches: 510, Mismatches: 37, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
291 58 0.11
292 2 0.00
293 72 0.14
294 84 0.16
299 12 0.02
300 1 0.00
301 8 0.02
303 102 0.20
304 44 0.09
305 46 0.09
306 75 0.15
307 6 0.01
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (296 bp):
AAAATAATTAAAATAAAAAATAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAAA
ATACGAGTAAAGGGCCGAAATAAGGCTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATAA
ATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAA
AGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAATTTAAA
AAAACAGAATTAATTAATACATTTCAAACATAATGT
Found at i:47049469 original size:143 final size:140
Alignment explanation
Indices: 47049158--47049553 Score: 416
Period size: 138 Copynumber: 2.8 Consensus size: 140
47049148 ATGTACTAAA
** *
47049158 ATAATGTAAAATAATAAAAATA-AAAAATAGTATATTTT--TTTAAAGTAATAAAATTCGGGGAA
1 ATAATGTAAAATAAT-AAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAA
* * *
47049220 AAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACAGAATTAATTAAT
65 AAAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACACAATAAATTAAT
*
47049285 ACATTTCAAAC
130 ACATTTAAAAC
47049296 ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTC-GGG-AA
1 ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAAA
*
47049359 AAAATACG-AGTAAAGGGCCGAAATAAGGGTTACTTTT-CTAAATTTATTTAAAAAACACACTAA
66 AAAATACGAAG-AAAGGGCCGAAATAAGGGTT--TTTTACTAAA-TTA---AAAAAACACAATAA
*
47049422 ATTAATGA-ATTTAAAAT
124 ATTAAT-ACATTTAAAAC
* * *
47049439 ATAATGTACTAAAATAATGTAAAATA-ATAAAATTAGAAAATAGTATATT-TTTTAAAGTATTAA
1 ATAATG---TAAAATAA--TAAAATACA-AAAA-T--AAAATA-T-T-TTAATTGAAAGTAATAA
*
47049502 AATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAA
54 AATTCGGGGAAAAAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAA
47049554 TTTTTTTTGA
Statistics
Matches: 218, Mismatches: 13, Indels: 38
0.81 0.05 0.14
Matches are distributed among these distances:
137 8 0.04
138 58 0.27
139 8 0.04
140 24 0.11
143 30 0.14
144 1 0.00
146 8 0.04
147 1 0.00
148 11 0.05
149 1 0.00
151 6 0.03
152 1 0.00
153 21 0.10
154 9 0.04
155 30 0.14
156 1 0.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAAA
AAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACACAATAAATTAATA
CATTTAAAAC
Found at i:47052966 original size:43 final size:42
Alignment explanation
Indices: 47052900--47053069 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 42
47052890 ATAGGATTTC
47052900 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
47052943 CGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
*
47052986 CGTATT-TGATT-CGTGTAAGACC-CTATCTGGGACAG-TGGCAT
1 CG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
47053027 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
47053070 TGTACGAGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 20
0.80 0.06 0.15
Matches are distributed among these distances:
40 2 0.02
41 28 0.26
42 10 0.09
43 63 0.58
44 6 0.06
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (42 bp):
CGATTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:47053057 original size:84 final size:84
Alignment explanation
Indices: 47052912--47053069 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
47052902 ATATGTGTTA
* * * *
47052912 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
47052977 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
47052996 TCGTGTAAGACC-CTATCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTG
1 TCGTGTAAGACCAC-ATCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
47053058 GGACGTTGGCAT
63 GGACATTGGCAT
47053070 TGTACGAGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:47053259 original size:16 final size:17
Alignment explanation
Indices: 47053230--47053261 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47053220 TGAATTGATG
47053230 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
47053247 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
47053262 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:47055949 original size:76 final size:77
Alignment explanation
Indices: 47055867--47056075 Score: 219
Period size: 76 Copynumber: 2.7 Consensus size: 77
47055857 ACTAACACAA
47055867 TAACAATAATAATAGTTTTTTACTCAA-AATAATACTAACTAACAATAATAATTAGAG-TTTTAC
1 TAACAATAATAATAGTTTTTTACT-AACAATAATACTAACTAACAATAATAATTAGAGTTTTTAC
47055930 TAAAAATAATAAC
65 TAAAAATAATAAC
* **** * *
47055943 TAACAATAAT-ATAATGTAAAAACTAACAATCATACTAACTAA-AATAATAATTAGGGTTTTTAC
1 TAACAATAATAATAGT-TTTTTACTAACAATAATACTAACTAACAATAATAATTAGAGTTTTTAC
***
47056006 TAATCCTAATAAC
65 TAAAAATAATAAC
* * * *
47056019 TAACCATAATAATATTAGTTTTTTACTAATAATAATACTAAGTAACAATAATTATTA
1 TAA-C--AATAATAATAGTTTTTTACTAACAATAATACTAACTAACAATAATAATTA
47056076 ATAACTAAAC
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
75 19 0.18
76 47 0.45
77 1 0.01
79 25 0.24
80 13 0.12
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (77 bp):
TAACAATAATAATAGTTTTTTACTAACAATAATACTAACTAACAATAATAATTAGAGTTTTTACT
AAAAATAATAAC
Found at i:47055952 original size:37 final size:38
Alignment explanation
Indices: 47055867--47056070 Score: 125
Period size: 37 Copynumber: 5.3 Consensus size: 38
47055857 ACTAACACAA
** *
47055867 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGAGTTTTACT-AAAATAATAATAAC
47055906 TAACAATAATAATTAGAGTTTTACT-AAA-AATAATAAC
1 TAACAATAATAA-TAGAGTTTTACTAAAATAATAATAAC
*** * *
47055943 TAACAATAAT-ATA-ATGTAAAAACTAACAATCATACTAAC
1 TAACAATAATAATAGA-GT-TTTACTAA-AATAATAATAAC
* **
47055982 TAA-AATAATAATTAGGGTTTTTACT--AATCCTAATAAC
1 TAACAATAATAA-TAGAG-TTTTACTAAAATAATAATAAC
* * * *
47056019 TAACCATAATAATATTAGTTTTTTACTAATAATAATACTAAG
1 TAACAATAATAATA-GAG--TTTTACTAA-AATAATAATAAC
47056061 TAACAATAAT
1 TAACAATAAT
47056071 TATTAATAAC
Statistics
Matches: 127, Mismatches: 22, Indels: 29
0.71 0.12 0.16
Matches are distributed among these distances:
34 1 0.01
35 4 0.03
36 4 0.03
37 34 0.27
38 19 0.15
39 31 0.24
40 16 0.13
41 1 0.01
42 17 0.13
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (38 bp):
TAACAATAATAATAGAGTTTTACTAAAATAATAATAAC
Found at i:47055985 original size:23 final size:23
Alignment explanation
Indices: 47055940--47055986 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
47055930 TAAAAATAAT
*
47055940 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
47055963 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
47055986 A
1 A
47055987 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:47056695 original size:21 final size:22
Alignment explanation
Indices: 47056655--47056700 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
47056645 TGGCCAGTAC
*
47056655 AAATAACAAAAACAATAGCA-A
1 AAATAACAAAAACAACAGCAGA
47056676 AAATAACAACAAA-AACAGCAGA
1 AAATAACAA-AAACAACAGCAGA
47056698 AAA
1 AAA
47056701 ATAGCAGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.72, C:0.15, G:0.07, T:0.07
Consensus pattern (22 bp):
AAATAACAAAAACAACAGCAGA
Found at i:47057370 original size:14 final size:12
Alignment explanation
Indices: 47057337--47057366 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
47057327 AACACCAAAA
47057337 TTGAGAGGAAAT
1 TTGAGAGGAAAT
47057349 TT-AGAGGAAAT
1 TTGAGAGGAAAT
47057360 TTGAGAG
1 TTGAGAG
47057367 AGGATTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (12 bp):
TTGAGAGGAAAT
Found at i:47059117 original size:9 final size:8
Alignment explanation
Indices: 47059103--47059178 Score: 59
Period size: 9 Copynumber: 9.1 Consensus size: 8
47059093 TGAAATGTAC
47059103 ATTTTAAA
1 ATTTTAAA
47059111 TATTTTAAA
1 -ATTTTAAA
47059120 TATTTTTAAA
1 -A-TTTTAAA
47059130 A-TTTAAA
1 ATTTTAAA
47059137 ATTTTAAAA
1 ATTTT-AAA
47059146 ATATTTAAA
1 AT-TTTAAA
* *
47059155 A-TAT-AC
1 ATTTTAAA
47059161 ATTTTAAA
1 ATTTTAAA
47059169 ATTTATAAA
1 ATTT-TAAA
47059178 A
1 A
47059179 CAAACAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
6 2 0.04
7 11 0.20
8 8 0.14
9 25 0.45
10 10 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTTTAAA
Found at i:47059225 original size:25 final size:25
Alignment explanation
Indices: 47059110--47059225 Score: 59
Period size: 25 Copynumber: 4.7 Consensus size: 25
47059100 TACATTTTAA
*
47059110 ATATTTTAAATATTTTTAAAATTTAA-
1 ATATTTTAAATA-TTTTAAAA-ATAAT
*
47059136 A-ATTTTAAAAATATTT-AAAAT-AT
1 ATATTTTAAATAT-TTTAAAAATAAT
* *
47059159 ACATTTTAAA-ATTTATAAAACAAACAAT
1 ATATTTTAAATATTT-T--AA-AAATAAT
* *
47059187 AAATTTT--AT-CTTTAAAAATAAT
1 ATATTTTAAATATTTTAAAAATAAT
47059209 ATATTTTAAATATTTTA
1 ATATTTTAAATATTTTA
47059226 TAATATTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 27
0.66 0.08 0.26
Matches are distributed among these distances:
22 15 0.22
23 7 0.10
24 14 0.20
25 17 0.25
26 5 0.07
27 3 0.04
28 8 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTTTAAATATTTTAAAAATAAT
Found at i:47059256 original size:22 final size:22
Alignment explanation
Indices: 47059217--47059306 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
47059207 ATATATTTTA
* *
47059217 AATATTTTATAATATTAAAAAAT
1 AATA-TTTAAAATTTTAAAAAAT
*
47059240 TATATTTAAAATTTTAAAAAAT
1 AATATTTAAAATTTTAAAAAAT
*
47059262 AATATTATAAAACATTTT-AAATAT
1 AATATT-T-AAA-ATTTTAAAAAAT
*
47059286 ACAT-TTT-AAATTTTATAAAAT
1 A-ATATTTAAAATTTTAAAAAAT
47059307 CAGTAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
20 5 0.09
21 6 0.11
22 21 0.38
23 5 0.09
24 11 0.20
25 7 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTTAAAATTTTAAAAAAT
Found at i:47059881 original size:23 final size:22
Alignment explanation
Indices: 47059855--47059912 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
47059845 TTTTTCTTTG
*
47059855 TTTTTCTTTATTTACTTTTTCAA
1 TTTTTCTTTATTT-CTTTGTCAA
* *
47059878 TTTTTTTTTATTTCTTTGTCAT
1 TTTTTCTTTATTTCTTTGTCAA
*
47059900 TTCTTTGTTTATT
1 TT-TTTCTTTATT
47059913 ATTTGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTCTTTATTTCTTTGTCAA
Found at i:47059952 original size:18 final size:20
Alignment explanation
Indices: 47059929--47059971 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
47059919 TTTATAATAT
*
47059929 TATTTTTTAA-ATT-TTAAA
1 TATTTTTTAATATTATAAAA
47059947 TATTTTTTAATATTATAAAA
1 TATTTTTTAATATTATAAAA
47059967 TATTT
1 TATTT
47059972 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 3 0.14
20 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTTAATATTATAAAA
Found at i:47060040 original size:13 final size:13
Alignment explanation
Indices: 47060024--47060071 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
47060014 TGTTTTTATA
47060024 ATATTTTAAATAT
1 ATATTTTAAATAT
47060037 ATATTTT-AA-A-
1 ATATTTTAAATAT
47060047 A-ATTTTAAATAT
1 ATATTTTAAATAT
*
47060059 AATTTTTTAAATA
1 -ATATTTTAAATA
47060072 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 2 0.07
12 2 0.07
13 8 0.28
14 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:47060054 original size:22 final size:23
Alignment explanation
Indices: 47060017--47060074 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
47060007 TATTATTTGT
*
47060017 TTTTATAATATTTTAAATAT-ATA
1 TTTTA-AAAATTTTAAATATAATA
*
47060040 TTTTAAAAATTTTAAATATAATT
1 TTTTAAAAATTTTAAATATAATA
47060063 TTTTAAATAATT
1 TTTTAAA-AATT
47060075 ATTTTTAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.42
23 14 0.45
24 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAAAAATTTTAAATATAATA
Found at i:47060137 original size:23 final size:22
Alignment explanation
Indices: 47060104--47060154 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
47060094 CGTTTTCAAA
*
47060104 AAAAATTATATTTAAAATTTTTT
1 AAAAATAATATTT-AAATTTTTT
47060127 AAAAATAATATTTAAATTTTTT
1 AAAAATAATATTTAAATTTTTT
47060149 AAAAAT
1 AAAAAT
47060155 TTTAAATGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAATAATATTTAAATTTTTT
Found at i:47060211 original size:21 final size:22
Alignment explanation
Indices: 47060176--47060217 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
47060166 GCACCGAGTA
*
47060176 AAATATTATTTTTAAAAATTTT
1 AAATATTAATTTTAAAAATTTT
47060198 AAATA-TAATTTTAAAAATTT
1 AAATATTAATTTTAAAAATTT
47060218 CGAATATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTAATTTTAAAAATTTT
Found at i:47060223 original size:21 final size:21
Alignment explanation
Indices: 47060176--47060224 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
47060166 GCACCGAGTA
* *
47060176 AAATATTATTTTTAAAAATTTT
1 AAATA-TAATTTTAAAAATTTC
47060198 AAATATAATTTTAAAAATTTC
1 AAATATAATTTTAAAAATTTC
*
47060219 GAATAT
1 AAATAT
47060225 CTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATAATTTTAAAAATTTC
Found at i:47060291 original size:23 final size:22
Alignment explanation
Indices: 47060245--47060294 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
47060235 AATTTTTAAA
* *
47060245 AAAAT-TATATTTAAAAATTTT
1 AAAATATACATTTAAAAATTAT
47060266 AAAATATACATTTAAAATATTAT
1 AAAATATACATTTAAAA-ATTAT
47060289 AAAATA
1 AAAATA
47060295 AAAAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATATACATTTAAAAATTAT
Found at i:47060333 original size:24 final size:23
Alignment explanation
Indices: 47060290--47060334 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
47060280 AAATATTATA
**
47060290 AAATAAAAAAAAACTGAAAAAGT
1 AAATAAAAAAAAACAAAAAAAGT
47060313 AAATAAAGAAAAAACAAAAAAA
1 AAATAAA-AAAAAACAAAAAAA
47060335 ATGAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (23 bp):
AAATAAAAAAAAACAAAAAAAGT
Found at i:47063566 original size:17 final size:17
Alignment explanation
Indices: 47063544--47063578 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47063534 TGCTTTTGAG
*
47063544 TTTTCTGTTCTGTTTGC
1 TTTTCTGTTCTGCTTGC
*
47063561 TTTTCTTTTCTGCTTGC
1 TTTTCTGTTCTGCTTGC
47063578 T
1 T
47063579 GTTCGAGAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.14, T:0.66
Consensus pattern (17 bp):
TTTTCTGTTCTGCTTGC
Found at i:47074707 original size:11 final size:12
Alignment explanation
Indices: 47074690--47074722 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
47074680 GTATAATTTA
47074690 AAAAAATTATAT
1 AAAAAATTATAT
*
47074702 -AAAAATAATAT
1 AAAAAATTATAT
47074713 AAAAAATTAT
1 AAAAAATTAT
47074723 TCTAAGAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:47076075 original size:44 final size:44
Alignment explanation
Indices: 47075983--47076076 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
47075973 AGATAGAAAG
* * * *
47075983 AAAGTTTATATAGGATGATGATGTTAATGTATTGTTGTCCCTTA
1 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
*
47076027 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTC
1 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
47076071 AAAGTT
1 AAAGTT
47076077 AAGTTATGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (44 bp):
AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
Found at i:47077970 original size:14 final size:13
Alignment explanation
Indices: 47077951--47078007 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
47077941 ATTTAGCCGA
47077951 ATATGCATCACCAC
1 ATATGCATCA-CAC
47077965 ATATGCAT-ACAC
1 ATATGCATCACAC
*
47077977 ATAGTTACATCATCAC
1 ATA--TGCATCA-CAC
47077993 ATATGCAT-ACAC
1 ATATGCATCACAC
47078005 ATA
1 ATA
47078008 GCTCACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 12 0.32
13 2 0.05
14 16 0.43
15 1 0.03
16 6 0.16
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (13 bp):
ATATGCATCACAC
Found at i:47078280 original size:43 final size:43
Alignment explanation
Indices: 47078233--47078314 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
47078223 TAATCACAGA
47078233 TCGATGCC-ACTGTCCCAGACAG-GATCTTACACGAAAACATAAT
1 TCGATGCCAAC-GTCCCAGAC-GTGATCTTACACGAAAACATAAT
* *
47078276 TCGATGCCAACGTCCCGGACGTGGTCTTACACGAAAACA
1 TCGATGCCAACGTCCCAGACGTGATCTTACACGAAAACA
47078315 CAAATTGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.91
44 2 0.06
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (43 bp):
TCGATGCCAACGTCCCAGACGTGATCTTACACGAAAACATAAT
Found at i:47084185 original size:25 final size:27
Alignment explanation
Indices: 47084133--47084187 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
47084123 TAAATGTCTA
47084133 TTTTCGTAATTAATCAATTTTCCCTATAT
1 TTTTCGTAATTAATCAATTTT--CTATAT
*
47084162 TTTTCGTAATTAAT-TATTTT-TATAT
1 TTTTCGTAATTAATCAATTTTCTATAT
47084187 T
1 T
47084188 ATTTAGGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
28 5 0.20
29 14 0.56
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTCGTAATTAATCAATTTTCTATAT
Found at i:47086348 original size:6 final size:6
Alignment explanation
Indices: 47086337--47086362 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47086327 AGCTGTGATT
47086337 TCCATC TCCATC TCCATC TCCATC TC
1 TCCATC TCCATC TCCATC TCCATC TC
47086363 TAACCAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCATC
Found at i:47087452 original size:7 final size:7
Alignment explanation
Indices: 47087437--47087466 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
47087427 ATAGTGTCTA
*
47087437 GTGTCTG
1 GTGTTTG
47087444 GTGTTTG
1 GTGTTTG
47087451 GTGTTTG
1 GTGTTTG
47087458 GTGTTTG
1 GTGTTTG
47087465 GT
1 GT
47087467 CCCTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.43, T:0.53
Consensus pattern (7 bp):
GTGTTTG
Found at i:47112931 original size:11 final size:11
Alignment explanation
Indices: 47112909--47112981 Score: 76
Period size: 11 Copynumber: 6.6 Consensus size: 11
47112899 AACTAATCTT
47112909 CTCTCAAATTTC
1 CTCTC-AATTTC
47112921 CTCTCAATTTC
1 CTCTCAATTTC
* *
47112932 TTCTAAATTTC
1 CTCTCAATTTC
*
47112943 CTCTCAATTTG
1 CTCTCAATTTC
*
47112954 CTCTCAAATTC
1 CTCTCAATTTC
**
47112965 CTCAAAATTT-
1 CTCTCAATTTC
47112975 CTCTCAA
1 CTCTCAA
47112982 GTCCATATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
10 5 0.10
11 39 0.80
12 5 0.10
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:47112932 original size:22 final size:22
Alignment explanation
Indices: 47112907--47112981 Score: 100
Period size: 22 Copynumber: 3.4 Consensus size: 22
47112897 CAAACTAATC
47112907 TTCTCTCAAATTTCCTCTCAAT
1 TTCTCTCAAATTTCCTCTCAAT
47112929 TTCT-TCTAAATTTCCTCTCAAT
1 TTCTCTC-AAATTTCCTCTCAAT
**
47112951 TTGCTCTCAAA-TTCCTCAAAAT
1 TT-CTCTCAAATTTCCTCTCAAT
47112973 TTCTCTCAA
1 TTCTCTCAA
47112982 GTCCATATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.19
22 32 0.67
23 5 0.10
24 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (22 bp):
TTCTCTCAAATTTCCTCTCAAT
Found at i:47112958 original size:33 final size:32
Alignment explanation
Indices: 47112907--47112981 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
47112897 CAAACTAATC
* * *
47112907 TTCTCTCAAATTTCCTCTCAATTTCTTCTAAAT
1 TTCTCTC-AATTTCCTCTCAAATTCCTCAAAAT
*
47112940 TTCCTCTCAATTTGCTCTCAAATTCCTCAAAAT
1 TT-CTCTCAATTTCCTCTCAAATTCCTCAAAAT
47112973 TTCTCTCAA
1 TTCTCTCAA
47112982 GTCCATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.19
33 25 0.68
34 5 0.14
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (32 bp):
TTCTCTCAATTTCCTCTCAAATTCCTCAAAAT
Found at i:47114295 original size:16 final size:17
Alignment explanation
Indices: 47114274--47114309 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
47114264 TACAGTAAGC
47114274 TTTTTTAATATAT-ATA
1 TTTTTTAATATATAATA
*
47114290 TTTTTTAATTTATAATA
1 TTTTTTAATATATAATA
47114307 TTT
1 TTT
47114310 AGATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAATATATAATA
Found at i:47115263 original size:12 final size:12
Alignment explanation
Indices: 47115248--47115272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47115238 TTGTAAGTTT
47115248 TGCAACAAAAGG
1 TGCAACAAAAGG
47115260 TGCAACAAAAGG
1 TGCAACAAAAGG
47115272 T
1 T
47115273 TCTCATGTTG
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:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (12 bp):
TGCAACAAAAGG
Found at i:47128190 original size:20 final size:20
Alignment explanation
Indices: 47128167--47128205 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47128157 CAAATGTGTT
*
47128167 AAAATTATTAATTAAAATAA
1 AAAAATATTAATTAAAATAA
**
47128187 AAAAATATTTTTTAAAATA
1 AAAAATATTAATTAAAATA
47128206 CTAATTACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATATTAATTAAAATAA
Found at i:47128320 original size:30 final size:30
Alignment explanation
Indices: 47128276--47128343 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
47128266 TTAAATTTTA
* *
47128276 TAAATAATTAATATTT-ATTTCTTAAAAATAT
1 TAAA-AATTAATATTTCATATATT-AAAATAT
* *
47128307 TTAAAATTTATATTTCATATATTAAAATAT
1 TAAAAATTAATATTTCATATATTAAAATAT
47128337 TAAAAAT
1 TAAAAAT
47128344 AAGTTATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAATTAATATTTCATATATTAAAATAT
Found at i:47131353 original size:23 final size:23
Alignment explanation
Indices: 47131287--47131341 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
47131277 AAAATTTATA
47131287 AATATTTTATACTATAAAATATT
1 AATATTTTATACTATAAAATATT
47131310 AATATTTTATACTATAAAATATT
1 AATATTTTATACTATAAAATATT
47131333 AATATTTTA
1 AATATTTTA
47131342 ATTATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTTATACTATAAAATATT
Found at i:47131533 original size:18 final size:18
Alignment explanation
Indices: 47131506--47131540 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47131496 TATATGTGAT
47131506 ATTAATTA-TTATAAAAC
1 ATTAATTATTTATAAAAC
47131523 ATTATATTATTTATAAAA
1 ATTA-ATTATTTATAAAA
47131541 ATAATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATTATTTATAAAAC
Found at i:47131547 original size:18 final size:18
Alignment explanation
Indices: 47131510--47131548 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47131500 TGTGATATTA
*
47131510 ATTATTATAAAACATTAT
1 ATTATTATAAAACATAAT
47131528 ATTATTTATAAAA-ATAAT
1 ATTA-TTATAAAACATAAT
47131546 ATT
1 ATT
47131549 TGATTGCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATTATAAAACATAAT
Found at i:47137793 original size:18 final size:19
Alignment explanation
Indices: 47137756--47137793 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
47137746 TTATAAATAT
*
47137756 AAATAAAAACTCTTGTAAA
1 AAATAAAAACTCTTGCAAA
*
47137775 AAATAAAACCTCTT-CAAA
1 AAATAAAAACTCTTGCAAA
47137793 A
1 A
47137794 CAAGTCTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (19 bp):
AAATAAAAACTCTTGCAAA
Found at i:47146013 original size:4 final size:4
Alignment explanation
Indices: 47146006--47146036 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
47145996 GTTTCACCAA
47146006 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCA
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCA
47146037 CAAAACCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.52, G:0.00, T:0.23
Consensus pattern (4 bp):
CCAT
Found at i:47148920 original size:23 final size:23
Alignment explanation
Indices: 47148890--47148933 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47148880 TTGGTTTGGT
*
47148890 TTTTAAAA-ATATTTTCTATTTTA
1 TTTTAAAATA-ATTTTATATTTTA
47148913 TTTTAAAATAATTTTATATTT
1 TTTTAAAATAATTTTATATTT
47148934 GAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAAATAATTTTATATTTTA
Found at i:47148928 original size:16 final size:18
Alignment explanation
Indices: 47148907--47148943 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
47148897 AATATTTTCT
*
47148907 ATTTTAT-TTT-AAAATA
1 ATTTTATATTTGAAAAAA
47148923 ATTTTATATTTGAAAAAA
1 ATTTTATATTTGAAAAAA
47148941 ATT
1 ATT
47148944 AAAAAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTATATTTGAAAAAA
Found at i:47157260 original size:20 final size:22
Alignment explanation
Indices: 47157217--47157264 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
47157207 CTACTAAAAA
*
47157217 TTAAAGAAAAACATCAAAGATT
1 TTAAAGAAAAACATAAAAGATT
* *
47157239 TTAAA-AAAATCATAAAAGTTT
1 TTAAAGAAAAACATAAAAGATT
47157260 TTAAA
1 TTAAA
47157265 TTTTGAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (22 bp):
TTAAAGAAAAACATAAAAGATT
Found at i:47157484 original size:112 final size:113
Alignment explanation
Indices: 47157321--47157536 Score: 364
Period size: 112 Copynumber: 1.9 Consensus size: 113
47157311 GAGTTCTATA
* *
47157321 TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAAATCTTCAAAATCAAAACTATGAACTTTTTA
1 TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTAA
47157386 ATATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
66 ATATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
* **
47157434 TTTTAAAATAAAAAA-AATGATTTTTTG-AAAAAAGCTCTTCAAAATCAAAACTATGAACTTCTA
1 TTTTAAAATAAAAAACAAT-AATTTTTGAAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTA
47157497 AATATTAGATCTGAAATATATAAAAATAGAAAATCCAATT
65 AATATTAGATCTGAAATATATAAAAATAGAAAATCCAATT
47157537 GCAGTTTTAG
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 75 0.77
113 22 0.23
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (113 bp):
TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTAA
ATATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
Found at i:47160985 original size:184 final size:174
Alignment explanation
Indices: 47160685--47161054 Score: 429
Period size: 184 Copynumber: 2.1 Consensus size: 174
47160675 AGGGGCATCA
* * * *
47160685 TCTTCCAATTCCGCAACATGTATCAAGCCATCTTCAGTGAAAATATGGAGCATGGACAAGGTATG
1 TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAGGTATG
* * * * *
47160750 TGAAAGTTTGGGAATCGTAGTAGGAGTGATGCCATCATTACTTTCAGCATTGAGAGGGAACTGAA
66 TGAAAGTTGGGGAATCGTAGTAGGAGTGATACCAACATCACTTTCAGCATTGAGAGGGAACCGAA
* * *
47160815 GAGCCTCCAAAAAAATC-AGAGGCATTAAAGAGTAATGCAGCGTCG
131 GAGCC-CCAAAAAAATCGA-AGGCATTAAAAAGTAAAGCAGAGTCG
* * *
47160860 TCTTCCAATTCCTCAACATATATCAAACTATCTTCACTGAAAACATGGAGCATTGACAAGATATG
1 TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAG----G
* *
47160925 ATGATCGTGTGAAAGTTGGGGAATCGTAGTAGGGGT-ATTATCAACATCACTTTCAGCATTGAGA
62 -T-A---TGTGAAAGTTGGGGAATCGTAGTAGGAGTGA-TACCAACATCACTTTCAGCATTGAGA
* * *
47160989 GGGAACCGAAGAGCCCCCAGAAAATCGAAGGCATTAAAAAGTAAAGCGGAGTCG
121 GGGAACCGAAGAGCCCCAAAAAAATCGAAGGCATTAAAAAGTAAAGCAGAGTCG
*
47161043 TCTTCCATTTCC
1 TCTTCCAATTCC
47161055 ATACTGTCTT
Statistics
Matches: 163, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
175 53 0.33
179 1 0.01
180 1 0.01
181 1 0.01
183 43 0.26
184 64 0.39
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (174 bp):
TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAGGTATG
TGAAAGTTGGGGAATCGTAGTAGGAGTGATACCAACATCACTTTCAGCATTGAGAGGGAACCGAA
GAGCCCCAAAAAAATCGAAGGCATTAAAAAGTAAAGCAGAGTCG
Found at i:47163336 original size:18 final size:18
Alignment explanation
Indices: 47163315--47163349 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47163305 TGAGTTTTCG
47163315 AATTCAAATAACTCGAAC
1 AATTCAAATAACTCGAAC
* *
47163333 AATTCGAATAATTCGAA
1 AATTCAAATAACTCGAA
47163350 TATCAAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTCAAATAACTCGAAC
Found at i:47163427 original size:30 final size:30
Alignment explanation
Indices: 47163393--47163451 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
47163383 AACTCCCAAA
* *
47163393 CCTTTTTACTTTTC-CCTCAAAACTTTTACT
1 CCTTTTCAC-TTTCTCCCCAAAACTTTTACT
47163423 CCTTTTCACTTTCCTCCCCAAAACTTTTA
1 CCTTTTCACTTT-CTCCCCAAAACTTTTA
47163452 TTCCCCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 9 0.36
31 13 0.52
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (30 bp):
CCTTTTCACTTTCTCCCCAAAACTTTTACT
Found at i:47163741 original size:17 final size:16
Alignment explanation
Indices: 47163707--47163737 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
47163697 CCCATTTACT
47163707 TTCCCTCAAACTTTTA
1 TTCCCTCAAACTTTTA
47163723 TTCCCTCAAACTTTT
1 TTCCCTCAAACTTTT
47163738 TATTTTCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTCAAACTTTTA
Found at i:47163769 original size:20 final size:21
Alignment explanation
Indices: 47163724--47163769 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
47163714 AAACTTTTAT
*
47163724 TCCCTCAAACTTTTTATTTTC
1 TCCCTCAAACTTTTTATTCTC
*
47163745 CCCCT-AAAC-TTTTACTTCTC
1 TCCCTCAAACTTTTTA-TTCTC
47163765 TCCCT
1 TCCCT
47163770 TTACTCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (21 bp):
TCCCTCAAACTTTTTATTCTC
Found at i:47178330 original size:31 final size:31
Alignment explanation
Indices: 47178290--47178350 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
47178280 AAAATAACAA
*
47178290 TTCAGTAACTTAAAAT-AAAAATTTTGAATAG
1 TTCAATAACTT-AAATGAAAAATTTTGAATAG
*
47178321 TTCAATAACTTAAATGAAAACTTTTGAATA
1 TTCAATAACTTAAATGAAAAATTTTGAATA
47178351 ACTAAATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (31 bp):
TTCAATAACTTAAATGAAAAATTTTGAATAG
Found at i:47179173 original size:22 final size:22
Alignment explanation
Indices: 47179125--47179166 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47179115 CTTTGGAATA
* *
47179125 TTATTTTAAAGAAAGTGGGTAG
1 TTATTGTAAAGAAAGTGAGTAG
47179147 TTATTGTAAAGAAAGTGAGT
1 TTATTGTAAAGAAAGTGAGT
47179167 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (22 bp):
TTATTGTAAAGAAAGTGAGTAG
Found at i:47185600 original size:32 final size:32
Alignment explanation
Indices: 47185564--47185630 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
47185554 ACATGACAGC
*
47185564 CTGGTGGAGGGCCTGCCACAGGCGACACTGGA
1 CTGGTGGAGGGCCTGCCACAGGCGACACCGGA
*
47185596 CTGGTGGAGGGCCTGCTACAGGCGACACCGGA
1 CTGGTGGAGGGCCTGCCACAGGCGACACCGGA
47185628 CTG
1 CTG
47185631 AAATGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.40, T:0.13
Consensus pattern (32 bp):
CTGGTGGAGGGCCTGCCACAGGCGACACCGGA
Found at i:47197955 original size:16 final size:16
Alignment explanation
Indices: 47197934--47197979 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
47197924 TCTTAATCCT
47197934 TTATTTGTTTATTTAG
1 TTATTTGTTTATTTAG
* *
47197950 TTATTTGTTTGTTTAT
1 TTATTTGTTTATTTAG
* *
47197966 TTATATCTTTATTT
1 TTATTTGTTTATTT
47197980 GAAATTTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (16 bp):
TTATTTGTTTATTTAG
Found at i:47197980 original size:20 final size:20
Alignment explanation
Indices: 47197932--47197980 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
47197922 TCTCTTAATC
47197932 CTTTATTTGTTTATTTAGTT
1 CTTTATTTGTTTATTTAGTT
* *
47197952 ATTTGTTTGTTTATTTA-TAT
1 CTTTATTTGTTTATTTAGT-T
47197972 CTTTATTTG
1 CTTTATTTG
47197981 AAATTTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.69
Consensus pattern (20 bp):
CTTTATTTGTTTATTTAGTT
Found at i:47198720 original size:107 final size:106
Alignment explanation
Indices: 47198534--47198755 Score: 322
Period size: 107 Copynumber: 2.1 Consensus size: 106
47198524 CATCAAAAAG
* * *
47198534 AAACTTTCAAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
*
47198599 GTTTCAATTTCTCGTTTGACCAAATAGCAAAATATCCTTT-TT
66 GTTTCAATTTCTCGTTCGACCAAATAGCAAAATAT--TTTCTT
* * * * *
47198641 AAACTTTCAAAACGAGGCAATGTTTTGTGTTTGAAAATTCGAGAGAACGTACCCTAACGTGCTGG
1 AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
*
47198706 GTTTCAATTTCTCGTTCGACCAAATAGCTAAATATTTTCTT
66 GTTTCAATTTCTCGTTCGACCAAATAGCAAAATATTTTCTT
47198747 -AACTTTCAA
1 AAACTTTCAA
47198756 TCAATATTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
105 12 0.12
106 2 0.02
107 90 0.87
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (106 bp):
AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
GTTTCAATTTCTCGTTCGACCAAATAGCAAAATATTTTCTT
Found at i:47201338 original size:75 final size:74
Alignment explanation
Indices: 47201117--47201451 Score: 440
Period size: 74 Copynumber: 4.5 Consensus size: 74
47201107 AACATGTGAA
* * *
47201117 CTGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
**
47201182 CGGCGTGTC
66 CAACGTGTC
* * *
47201191 CCGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAAGCAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAA-CAGAAATTGAAAATACC
47201254 TCAACGTGTC
65 TCAACGTGTC
* * *
47201264 TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAA-CAGAAATTGAAAATACC
*
47201329 TCAATGTGTC
65 TCAACGTGTC
* * * * * *
47201339 TTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGACAACAGAAATTTAAATTACCT
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
*
47201404 CAGCGTGTC
66 CAACGTGTC
* * *
47201413 CTGAGGCTCAACTCATTTCTTGCAATATGAGCTGATTTT
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
47201452 GGAAAAGTAG
Statistics
Matches: 230, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
72 8 0.03
73 55 0.24
74 88 0.38
75 79 0.34
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (74 bp):
CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
CAACGTGTC
Found at i:47201867 original size:73 final size:73
Alignment explanation
Indices: 47201748--47201884 Score: 220
Period size: 73 Copynumber: 1.9 Consensus size: 73
47201738 ATAAGTTAAA
* * *
47201748 AAACAGAAATGGAAAATACCTCAGCCTGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGG
1 AAACAGAAATGGAAAATACCTCAGCCTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGG
47201813 TTTTTGCC
66 TTTTTGCC
* * *
47201821 AAACAGTAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACAGAAATGGAAAATACCTCAGCCTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
47201885 ATTTAGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 58 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (73 bp):
AAACAGAAATGGAAAATACCTCAGCCTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGG
TTTTTGCC
Done.