Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 21 of 28
Found at i:3142534 original size:30 final size:30
Alignment explanation
Indices: 3142493--3142563 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
3142483 ATGAAAGCAA
*
3142493 ATGCATTGAAATGAACATATGAGATGCATGT
1 ATGCATTGAAATGAACATATG-CATGCATGT
*
3142524 ATGCA-TGAAATGATCATATGCATGCATG-
1 ATGCATTGAAATGAACATATGCATGCATGT
*
3142552 AAGC-TTGAAATG
1 ATGCATTGAAATG
3142564 TTTATGTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.28
29 7 0.19
30 14 0.39
31 5 0.14
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (30 bp):
ATGCATTGAAATGAACATATGCATGCATGT
Found at i:3143764 original size:32 final size:32
Alignment explanation
Indices: 3143728--3143791 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3143718 TTTGTTCAGG
3143728 TTGTAATGTCTTGAAAAATTAAACAAAATATA
1 TTGTAATGTCTTGAAAAATTAAACAAAATATA
3143760 TTGTAATGTCTTGAAAAATTAAACAAAATATA
1 TTGTAATGTCTTGAAAAATTAAACAAAATATA
3143792 AAAAAAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (32 bp):
TTGTAATGTCTTGAAAAATTAAACAAAATATA
Found at i:3144281 original size:81 final size:81
Alignment explanation
Indices: 3144202--3144819 Score: 434
Period size: 81 Copynumber: 7.7 Consensus size: 81
3144192 GACCAAGGTA
* * * ** * *
3144202 AAACTGATAAAGCTAATGGGTTAGAAGGGTTAACTAGAGCAAAACTAATAAAGTTAACCAATTAA
1 AAACTGATAAAGCCAATGGGTTAGAAAGGTTAACCAGAGTGAAACTAATAAAGTTAACTAGTTAA
* * *
3144267 AAAGTTTGCCAAGGTG
66 AAGGTTGGCCAAGGCG
* * * * * *
3144283 AAACTGATAAAGCTAATGAGTTAGAAAGGTTGAA-CAG-GTGAAACCAGTAGAGTCAACTAGTTA
1 AAACTGATAAAGCCAATGGGTTAGAAAGGTT-AACCAGAGTGAAACTAATAAAGTTAACTAGTTA
* *
3144346 AAAGGTTGGCCAGGGCA
65 AAAGGTTGGCCAAGGCG
* * * *
3144363 AAACTGATAAAGCCAATGGGTTAGAAGGGTTGACCA-AGGTGAAA-TCGATAAAGTTAACTACTT
1 AAACTGATAAAGCCAATGGGTTAGAAAGGTTAACCAGA-GTGAAACT-AATAAAGTTAACTAGTT
* * *
3144426 AAAAGGTTGGCTAGGGCC
64 AAAAGGTTGGCCAAGGCG
* *** *
3144444 AAATTGATAAAGCCAACATGTTAGAAAGGTTAACCA-AGGTGAAACTGATAAAGTTAACTAGTTA
1 AAACTGATAAAGCCAATGGGTTAGAAAGGTTAACCAGA-GTGAAACTAATAAAGTTAACTAGTTA
*
3144508 AAAGGTTGGCCAGGGCG
65 AAAGGTTGGCCAAGGCG
* ** * * * *
3144525 AAA-TCGATAAAGCCAATGGGTTAGAAAGGTTGATGAGGGCGAAAC-AGATAAAGTCAACCAGTT
1 AAACT-GATAAAGCCAATGGGTTAGAAAGGTTAACCAGAGTGAAACTA-ATAAAGTTAACTAGTT
**
3144588 AAAAATTTGGCCAAGGCG
64 AAAAGGTTGGCCAAGGCG
* * * * * * * *
3144606 AAACTGATAAAGCTAACGGGTTAGAAA-GATAGACGAGGGTGAAACCAATAAAGTCAACTAATTA
1 AAACTGATAAAGCCAATGGGTTAGAAAGGTTA-ACCAGAGTGAAACTAATAAAGTTAACTAGTTA
* * *
3144670 AAAGGTTGGCTAGGGCA
65 AAAGGTTGGCCAAGGCG
* * * ** * * * * *
3144687 AAACCGATAAAACCAATGGGTTAGATAA-GTTGATTA-AG-GCAAAATCGATAAAGTCAACCAAT
1 AAACTGATAAAGCCAATGGGTTAGA-AAGGTTAACCAGAGTG-AAACT-AATAAAGTTAACTAGT
* *
3144749 TAAAAGGTTGGCCAGGGCA
63 TAAAAGGTTGGCCAAGGCG
* * * * *
3144768 AAACTAATAAAGCCAACT-AGTTA-AAAGGTTAGCCAGGGTGAAACCAATAAAG
1 AAACTGATAAAGCCAA-TGGGTTAGAAAGGTTAACCAGAGTGAAACTAATAAAG
3144820 CCAACGGGTT
Statistics
Matches: 428, Mismatches: 90, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
79 4 0.01
80 78 0.18
81 335 0.78
82 11 0.03
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (81 bp):
AAACTGATAAAGCCAATGGGTTAGAAAGGTTAACCAGAGTGAAACTAATAAAGTTAACTAGTTAA
AAGGTTGGCCAAGGCG
Found at i:3144483 original size:202 final size:202
Alignment explanation
Indices: 3144073--3144515 Score: 459
Period size: 202 Copynumber: 2.2 Consensus size: 202
3144063 AGAGGTTCGT
* * * * ** *
3144073 CAAGATGAAACTGAAAAAACTAACAAGTTAGAGGGGTTGACTAGGGTGAAACTAATAAAGTCAAC
1 CAAGGTGAAACTGATAAAGCTAA-TAGTTAGAAAGGTTGACTAGGGTGAAACCAATAAAGTCAAC
* * *
3144138 TAATTAAGAGGTTGGCTAGGGCAAGACTGATAAAGCCAACGGGTTAGAAGGATGGACCAAGGTAA
65 TAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACGGGTTAGAAGGATGGACCAAGGTAA
** * **
3144203 AACTGATAAAGCTAATGGGTTAGAAGGGTTAACTAGAGCAAAACTAATAAAGTTAACCAATTAAA
130 AACTGATAAAGCTAATGACTTAGAAAGGTTAACTAGAGCAAAACTAATAAAGCCAACCAATTAAA
**
3144268 AAGTTTGC
195 AAGTTAAC
* *
3144276 CAAGGTGAAACTGATAAAGCTAATGAGTTAGAAAGGTTGAAC-A-GGTGAAACCAGTAGAGTCAA
1 CAAGGTGAAACTGATAAAGCTAAT-AGTTAGAAAGGTTG-ACTAGGGTGAAACCAATAAAGTCAA
* * * * *
3144339 CTAGTTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAATGGGTTAGAAGGGTTGACCAAGGTG
64 CTAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACGGGTTAGAAGGATGGACCAAGGTA
* ** * * * * *
3144404 AAA-TCGATAAAGTTAACT-ACTTA-AAAGGTTGGCTAGGGCCAAATTGATAAAGCCAA-CATGT
129 AAACT-GATAAAGCTAA-TGACTTAGAAAGGTTAACTAGAGCAAAACTAATAAAGCCAACCA-AT
*
3144465 TAGAAAGGTTAAC
191 TA-AAAAGTTAAC
*
3144478 CAAGGTGAAACTGATAAAGTTAACTAGTTA-AAAGGTTG
1 CAAGGTGAAACTGATAAAGCTAA-TAGTTAGAAAGGTTG
3144516 GCCAGGGCGA
Statistics
Matches: 199, Mismatches: 34, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
200 2 0.01
201 36 0.18
202 124 0.62
203 35 0.18
204 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (202 bp):
CAAGGTGAAACTGATAAAGCTAATAGTTAGAAAGGTTGACTAGGGTGAAACCAATAAAGTCAACT
AATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACGGGTTAGAAGGATGGACCAAGGTAAA
ACTGATAAAGCTAATGACTTAGAAAGGTTAACTAGAGCAAAACTAATAAAGCCAACCAATTAAAA
AGTTAAC
Found at i:3144544 original size:162 final size:160
Alignment explanation
Indices: 3144249--3144865 Score: 618
Period size: 162 Copynumber: 3.8 Consensus size: 160
3144239 AGCAAAACTA
* * * * ** *
3144249 ATAAAGTTAACCAATTAAAAAGTTTGCCAAGGTGAAACTGATAAAGCTAA-TGAGTTAGAAAGGT
1 ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACT--GTTAGAAAGGT
* *
3144313 TGAA-C-AGGTGAAACCAGTAGAGTCAACTAGTTAAAAGGTTGGCCAGGGCAAAA-CTGATAAAG
64 T-AACCAAGGTGAAACCAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGCAAAATC-GATAAAG
* *
3144375 CCAATGGGTTAGAAGGGTTGACCAAGGTGAAATCG
127 CCAATGGGTTAGAA-GGTTGATCAAGGCGAAATCG
* * * * * *
3144410 ATAAAGTTAACTACTTAAAAGGTTGGCTAGGGCCAAATTGATAAAGCCAACATGTTAGAAAGGTT
1 ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAAC-TGTTAGAAAGGTT
** * *
3144475 AACCAAGGTGAAACTGATAAAGTTAACTAGTTAAAAGGTTGGCCAGGGCGAAATCGATAAAGCCA
65 AACCAAGGTGAAACCAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGCAAAATCGATAAAGCCA
* *
3144540 ATGGGTTAGAAAGGTTGATGAGGGCGAAA-CAG
130 ATGGGTTAG-AAGGTTGATCAAGGCGAAATC-G
* ** * * * * *
3144572 ATAAAGTCAACCAGTTAAAAATTTGGCCAAGGCGAAACTGATAAAGCTAACGGGTTAGAAA-GAT
1 ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAAC-TGTTAGAAAGGTT
* * * * * *
3144636 AGACGAGGGTGAAACCAATAAAGTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACC
65 A-ACCAAGGTGAAACCAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGCAAAATCGATAAAGCC
* * *
3144701 AATGGGTTAGATAAGTTGATTAAGGCAAAATCG
129 AATGGGTTAGA-AGGTTGATCAAGGCGAAATCG
*
3144734 ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTAATAAAGCCAACTAGTTA-AAAGGTT
1 ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACT-GTTAGAAAGGTT
* * * ** * * * *
3144798 AGCCAGGGTGAAACCAATAAAGCCAACGGGTTAGAAGGGTTGACCAAGGCAAAATCGATAAAGTC
65 AACCAAGGTGAAACCAATAAAGTCAACTAGTTA-AAAGGTTGGCCAGGGCAAAATCGATAAAGCC
3144863 AAT
129 AAT
3144866 CATTTAAAAG
Statistics
Matches: 374, Mismatches: 69, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
160 2 0.01
161 87 0.23
162 280 0.75
163 5 0.01
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (160 bp):
ATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCAAAACTGATAAAGCCAACTGTTAGAAAGGTTA
ACCAAGGTGAAACCAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGCAAAATCGATAAAGCCAA
TGGGTTAGAAGGTTGATCAAGGCGAAATCG
Found at i:3144739 original size:243 final size:242
Alignment explanation
Indices: 3144220--3144797 Score: 630
Period size: 243 Copynumber: 2.4 Consensus size: 242
3144210 AAAGCTAATG
* * * * * * *
3144220 GGTTAGAAGGGTTAA-CTAGAGCAAAACTAATAAAGTTAACCAATTAAAAAGTTTGCCAAGGTGA
1 GGTTAGAAAGGTTAACCAAG-GCAAAACTGATAAAGTTAACCAATTAAAAGGTTGGCCAGGGCGA
* * * *
3144284 AACTGATAAAGCTAATGAGTTAGAAAGGTTGAACAGGTGAAACCAGTAGAGTCAACTAGTTAAAA
65 AACTGATAAAGCCAATGAGTTAGAAAGGTTGAACAGGCGAAACCAGTAAAGTCAACCAGTTAAAA
* * * * * * * *
3144349 GGTTGGCCAGGGCAAAACTGATAAAGCCAATGGGTTAGAAGGGTTGACCAAGGTGAAATCGATAA
130 AGTTGGCCAAGGCAAAACTGATAAAGCCAACGGGTTAGAAAGATAGACCAAGGTGAAACCAATAA
* * * ** *
3144414 AGTTAACTACTTAAAAGGTTGGCTAGGGCCAAATTGATAAAGCCAACA
195 AGTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACCAACA
* ** * *
3144462 TGTTAGAAAGGTTAACCAAGGTGAAACTGATAAAGTTAACTAGTTAAAAGGTTGGCCAGGGCGAA
1 GGTTAGAAAGGTTAACCAAGGCAAAACTGATAAAGTTAACCAATTAAAAGGTTGGCCAGGGCGAA
* **
3144527 A-TCGATAAAGCCAATGGGTTAGAAAGGTTGATGAGGGCGAAA-CAGATAAAGTCAACCAGTTAA
66 ACT-GATAAAGCCAATGAGTTAGAAAGGTTGAACA-GGCGAAACCAG-TAAAGTCAACCAGTTAA
* * * * *
3144590 AAATTTGGCCAAGGCGAAACTGATAAAGCTAACGGGTTAGAAAGATAGACGAGGGTGAAACCAAT
128 AAAGTTGGCCAAGGCAAAACTGATAAAGCCAACGGGTTAGAAAGATAGACCAAGGTGAAACCAAT
**
3144655 AAAGTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACCAATG
193 AAAGTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACCAACA
* ** * *
3144705 GGTTAGATAA-GTTGATTAAGGCAAAA-TCGATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCA
1 GGTTAGA-AAGGTTAACCAAGGCAAAACT-GATAAAGTTAACCAATTAAAAGGTTGGCCAGGGCG
*
3144768 AAACTAATAAAGCCAACT-AGTTA-AAAGGTT
64 AAACTGATAAAGCCAA-TGAGTTAGAAAGGTT
3144798 AGCCAGGGTG
Statistics
Matches: 276, Mismatches: 52, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
241 1 0.00
242 88 0.32
243 183 0.66
244 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.21
Consensus pattern (242 bp):
GGTTAGAAAGGTTAACCAAGGCAAAACTGATAAAGTTAACCAATTAAAAGGTTGGCCAGGGCGAA
ACTGATAAAGCCAATGAGTTAGAAAGGTTGAACAGGCGAAACCAGTAAAGTCAACCAGTTAAAAA
GTTGGCCAAGGCAAAACTGATAAAGCCAACGGGTTAGAAAGATAGACCAAGGTGAAACCAATAAA
GTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACCAACA
Found at i:3144779 original size:121 final size:121
Alignment explanation
Indices: 3144647--3144905 Score: 340
Period size: 121 Copynumber: 2.1 Consensus size: 121
3144637 GACGAGGGTG
* * * * * *
3144647 AAACCAATAAAGTCAACTAATTAAAAGGTTGGCTAGGGCAAAACCGATAAAACCAATGGGTTAGA
1 AAACTAATAAAGCCAACTAATTAAAAGGTTAGCCAGGGCAAAACCAATAAAACCAACGGGTTAGA
** *
3144712 TA-AGTTGATTAAGGCAAAATCGATAAAGTCAACCAATTAAAAGGTTGGCCAGGGCA
66 -AGAGTTGACCAAGGCAAAATCGATAAAGTCAACCAATTAAAAGGTTGGCCAGGACA
* ** *
3144768 AAACTAATAAAGCCAACTAGTTAAAAGGTTAGCCAGGGTGAAACCAATAAAGCCAACGGGTTAGA
1 AAACTAATAAAGCCAACTAATTAAAAGGTTAGCCAGGGCAAAACCAATAAAACCAACGGGTTAGA
* * * *
3144833 AGGGTTGACCAAGGCAAAATCGATAAAGTCAATCATTTAAAAGGTTGGCCAGGATA
66 AGAGTTGACCAAGGCAAAATCGATAAAGTCAACCAATTAAAAGGTTGGCCAGGACA
*
3144889 AAACTGATAAAGCCAAC
1 AAACTAATAAAGCCAAC
3144906 GTGTTAGAAG
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
120 1 0.01
121 118 0.99
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (121 bp):
AAACTAATAAAGCCAACTAATTAAAAGGTTAGCCAGGGCAAAACCAATAAAACCAACGGGTTAGA
AGAGTTGACCAAGGCAAAATCGATAAAGTCAACCAATTAAAAGGTTGGCCAGGACA
Found at i:3144839 original size:81 final size:81
Alignment explanation
Indices: 3144754--3145934 Score: 498
Period size: 81 Copynumber: 14.6 Consensus size: 81
3144744 CCAATTAAAA
* * * * *
3144754 GGTTGGCCAGGGCAAAACTAATAAAGCCAACTAGTTAAAAGGTTAGCCAGGGTGAAACCAATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
3144819 GCCAACGGGTTAGAAG
66 GCCAACGGGTTAGAAG
* * * * *
3144835 GGTTGACCAAGGCAAAA-TCGATAAAGTCAA-TCATTTAAAAGGTTGGCCAGGATAAAACTGATA
1 GGTTGACCAAGGCAAAACT-AATAAAGTCAACT-AGTTAAAAGGTTGGCCAGGGTGAAACCGATA
*
3144898 AAGCCAACGTGTTAGAAG
64 AAGCCAACGGGTTAGAAG
* * * * * * ** * * *
3144916 GGTTGACTAAGGCGAAACTGATAAAGTCATCCAGTTAAAAAGTTGGTTAGAGCGAAACTGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
* * *
3144981 GCCAAAGGGTTAAAAA
66 GCCAACGGGTTAGAAG
* ** * *
3144997 GGTTGACCATGGCAAAACTAATAAAGTCAACTAGTTAAAAATTTGGCAAGGGTGAAATCGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
** *
3145062 GTTAATGGGTTAGAAG
66 GCCAACGGGTTAGAAG
* * * * * *
3145078 GGTTGACTAGGGCGAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAAGATGAAATCGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
* * *
3145143 GTCAACGGGTTACAAA
66 GCCAACGGGTTAGAAG
* * * * ** * ** * ** * * *** ** * *
3145159 GATTAACTAGGGGGTGACACCGATAAAGCCAACGGGTTAGAAGGGTAATCAGGGAAAAATCAATA
1 GGTTGACCA--AGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATA
* *** *
3145224 AAGTCAAATAGTTA-AAA
64 AAGCCAACGGGTTAGAAG
* * * * * * * * * * * *
3145241 GGTTGGCCAGGGTAAAACTGATAAA-ACTAA-TGGGTTAGATGCATTGACTAGGGCGAAACCGAT
1 GGTTGACCAAGGCAAAACTAATAAAGTC-AACT-AGTTAAAAG-GTTGGCCAGGGTGAAACCGAT
* ***
3145304 AAAGTCAACCAATTAG-AG
63 AAAGCCAACGGGTTAGAAG
* * *** * * * * * * * * * * **
3145322 GGGTCAATTAGGACGAAACTGATAAA-ACTGACAAGTTAGAGGGATTGACTAAGGCAAAACCGAT
1 GGTTGACCAAGG-CAAAACTAATAAAGTC-AACTAGTTAAAAGG-TTGGCCAGGGTGAAACCGAT
** ***
3145386 AAAATCAACCAATTAGAA-
63 AAAGCCAACGGGTTAGAAG
* * * ** * * * ** * ** **
3145404 GGCTGGCCATGGTGAAA-TCGATAAAGCCAA-TGAGTTAGAAGGGTTCACCAAGGCAAAAATGAT
1 GGTTGACCAAGGCAAAACT-AATAAAGTCAACT-AGTTA-AAAGGTTGGCCAGGGTGAAACCGAT
** *
3145467 AAAGCCAACGCATTAAAAG
63 AAAGCCAACGGGTTAGAAG
* * * * * *
3145486 GGTTGACC-AGGCAAAACTAATAAAGTGAACCAATTTAAAGGTTGGCCAGGGTAAAACTGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
* *
3145550 GCCAACGGGCTAGAAA
66 GCCAACGGGTTAGAAG
* * * * * * **
3145566 GGTTGGCCAGGGCAAAATTGATAGAGTCAACTAGCTAAAAGGTTGGCCAGGGTGAAATTGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
*
3145631 GCCAACAGGTTAGAAG
66 GCCAACGGGTTAGAAG
** * * *
3145647 GGTTGACCAAGGTGAAA-TCAATAAAGTTAATTAGTTAAAAGGTTGGCTAGGGTGAAACCGATAA
1 GGTTGACCAAGGCAAAACT-AATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAA
* * *
3145711 AGCTAATC-GGTTAAAAA
65 AGCCAA-CGGGTTAGAAG
* * * * * *
3145728 GGTTGACTAGGGCAAAACTAATAAAGTTAACTGGTTAAAAGGTTGGCCAGGGCGAAATCGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
* *
3145793 GCCAATGGGTTAGAAA
66 GCCAACGGGTTAGAAG
** * ** ** * * * ** *
3145809 GGTTGATGAGGGTGAAACCGATAAAGTCAACTAATTAAAAAGTTGGCAAGGGCAAAACTGATAAA
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
* ** * * *
3145874 GCTAATAGGCTAAAAA
66 GCCAACGGGTTAGAAG
* * ** **
3145890 GGTTGACGAGGGTGAAACCGATAAAGTCAACTAGTTAAAAGGTTG
1 GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTG
3145935 ACTAGGGCAA
Statistics
Matches: 849, Mismatches: 225, Indels: 52
0.75 0.20 0.05
Matches are distributed among these distances:
79 1 0.00
80 67 0.08
81 649 0.76
82 83 0.10
83 49 0.06
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (81 bp):
GGTTGACCAAGGCAAAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAGGGTGAAACCGATAAA
GCCAACGGGTTAGAAG
Found at i:3145402 original size:41 final size:41
Alignment explanation
Indices: 3145283--3145402 Score: 111
Period size: 41 Copynumber: 2.9 Consensus size: 41
3145273 GGTTAGATGC
* *
3145283 ATTGACTAGGGCGAAACCGATAAAGTCAACCAATTAGAGGG
1 ATTGACTAAGGCGAAACCGATAAAATCAACCAATTAGAGGG
* * * * * *
3145324 -GTCAATTAGGACGAAACTGATAAAA-CTGA-CAAGTTAGAGGG
1 ATTGACTAAGG-CGAAACCGATAAAATC-AACCAA-TTAGAGGG
*
3145365 ATTGACTAAGGCAAAACCGATAAAATCAACCAATTAGA
1 ATTGACTAAGGCGAAACCGATAAAATCAACCAATTAGA
3145403 AGGCTGGCCA
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
40 9 0.16
41 39 0.67
42 10 0.17
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (41 bp):
ATTGACTAAGGCGAAACCGATAAAATCAACCAATTAGAGGG
Found at i:3145487 original size:41 final size:40
Alignment explanation
Indices: 3145418--3145510 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
3145408 GGCCATGGTG
* *
3145418 AAATCGATAAAGCCAATGAGTTAGAAGGGTTCACCAAGGCAA
1 AAAT-GATAAAGCCAACGAGTTAAAAGGGTTCACC-AGGCAA
*
3145460 AAATGATAAAGCCAACGCA-TTAAAAGGGTTGACCAGGCAA
1 AAATGATAAAGCCAACG-AGTTAAAAGGGTTCACCAGGCAA
* *
3145500 AACTAATAAAG
1 AAATGATAAAG
3145511 TGAACCAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 15 0.33
41 25 0.56
42 5 0.11
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (40 bp):
AAATGATAAAGCCAACGAGTTAAAAGGGTTCACCAGGCAA
Found at i:3145568 original size:41 final size:40
Alignment explanation
Indices: 3145522--3145934 Score: 260
Period size: 41 Copynumber: 10.2 Consensus size: 40
3145512 GAACCAATTT
* * *
3145522 AAAGGTTGGCCAGGGTAAAACTGATAAAGCCAACGGGCTA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
** * * * * *
3145562 GAAAGGTTGGCCAGGGCAAAATTGATAGAGTCAACTAGCTA
1 -AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
* *
3145603 AAAGGTTGGCCAGGGTGAAATTGATAAAGCCAACAGGTTA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
* * * * ** * *
3145643 GAAGGGTTGACCAAGGTGAAA-TCAATAAAGTTAATTAGTTA
1 -AAAGGTTGGCCAGGGTGAAACT-GATAAAGCCAACTGGTTA
* * *
3145684 AAAGGTTGGCTAGGGTGAAACCGATAAAGCTAA-TCGGTTAA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACT-GGTT-A
* * ** * **
3145725 AAAGGTTGACTAGGGCAAAACTAATAAAGTTAACTGGTTA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
*
3145765 AAAGGTTGGCCAGGGCGAAA-TCGATAAAGCCAA-TGGGTTA
1 AAAGGTTGGCCAGGGTGAAACT-GATAAAGCCAACT-GGTTA
*** * * **
3145805 GAAAGGTTGATGAGGGTGAAACCGATAAAGTCAACTAATTA
1 -AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
* * ** * *
3145846 AAAAGTTGGCAAGGGCAAAACTGATAAAGCTAA-TAGGCTAA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACT-GG-TTA
* * * * *
3145887 AAAGGTTGACGAGGGTGAAACCGATAAAGTCAACTAGTTA
1 AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
3145927 AAAGGTTG
1 AAAGGTTG
3145935 ACTAGGGCAA
Statistics
Matches: 286, Mismatches: 72, Indels: 29
0.74 0.19 0.07
Matches are distributed among these distances:
39 4 0.01
40 127 0.44
41 152 0.53
42 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (40 bp):
AAAGGTTGGCCAGGGTGAAACTGATAAAGCCAACTGGTTA
Found at i:3145873 original size:243 final size:242
Alignment explanation
Indices: 3145479--3145941 Score: 559
Period size: 243 Copynumber: 1.9 Consensus size: 242
3145469 AGCCAACGCA
* * *
3145479 TTAAAAGGGTTGACCAGGCAAAACTAATAAAGTGAACCAATTTAAAGGTTGGCCAGGGTAAAACT
1 TTAAAAAGGTTGACCAGGCAAAACTAATAAAGTGAACCAATTAAAAGGTTGGCCAGGGGAAAACT
* ** * * *
3145544 GATAAAGCCAACGGGCTAGAAAGGTTGGCCAGGGCAAAATTGATAGAGTCAACTAGCTAAAAGGT
66 GATAAAGCCAACGGGCTAGAAAGGTTGACCAGGGCAAAACCGATAAAGTCAACTAACTAAAAAGT
* ** * * * * *
3145609 TGGCCAGGGTGAAATTGATAAAGCCAACAGGTTAGAAGGGTTGACCAAGGTGAAATCAATAAAGT
131 TGGCAAGGGCAAAACTGATAAAGCCAACAGGCTAAAAAGGTTGACCAAGGTGAAACCAATAAAGT
* * *
3145674 TAATTAGTTAAAAGGTTGGCTAGGGTGAAACCGATAAAGCTAATCGG
196 CAACTAGTTAAAAGGTTGACTAGGGTGAAACCGATAAAGCTAATCGG
* * *** *
3145721 TTAAAAAGGTTGACTAGGGCAAAACTAATAAAGTTAACTGGTTAAAAGGTTGGCCAGGGCGAAAT
1 TTAAAAAGGTTGACCA-GGCAAAACTAATAAAGTGAACCAATTAAAAGGTTGGCCAGGG-GAAAA
* * ** ** *
3145786 C-GATAAAGCCAATGGGTTAGAAAGGTTGATGAGGGTGAAACCGATAAAGTCAACTAATTAAAAA
64 CTGATAAAGCCAACGGGCTAGAAAGGTTGACCAGGGCAAAACCGATAAAGTCAACTAACTAAAAA
* * * * *
3145850 GTTGGCAAGGGCAAAACTGATAAAGCTAATAGGCTAAAAAGGTTGACGAGGGTGAAACCGATAAA
129 GTTGGCAAGGGCAAAACTGATAAAGCCAACAGGCTAAAAAGGTTGACCAAGGTGAAACCAATAAA
3145915 GTCAACTAGTTAAAAGGTTGACTAGGG
194 GTCAACTAGTTAAAAGGTTGACTAGGG
3145942 CAAAACTAAT
Statistics
Matches: 181, Mismatches: 38, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
242 14 0.08
243 163 0.90
244 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (242 bp):
TTAAAAAGGTTGACCAGGCAAAACTAATAAAGTGAACCAATTAAAAGGTTGGCCAGGGGAAAACT
GATAAAGCCAACGGGCTAGAAAGGTTGACCAGGGCAAAACCGATAAAGTCAACTAACTAAAAAGT
TGGCAAGGGCAAAACTGATAAAGCCAACAGGCTAAAAAGGTTGACCAAGGTGAAACCAATAAAGT
CAACTAGTTAAAAGGTTGACTAGGGTGAAACCGATAAAGCTAATCGG
Found at i:3145966 original size:40 final size:40
Alignment explanation
Indices: 3144080--3145966 Score: 367
Period size: 40 Copynumber: 46.6 Consensus size: 40
3144070 CGTCAAGATG
* * * ** **
3144080 AAACTGAAAAAACTAACAAGTTAGAGGGGTTGACTAGGGTG
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * * *
3144121 AAACTAATAAAGTCAACTAA-TTAAGAGGTTGGCTAGGGCA
1 AAACTGATAAAGCCAAC-AAGTTAAAAGGTTGACTAGGGCA
* ** * * * * *
3144161 AGACTGATAAAGCCAACGGGTTAGAAGGATGGACCAAGGTA
1 AAACTGATAAAGCCAACAAGTTAAAAGG-TTGACTAGGGCA
* *** * * *
3144202 AAACTGATAAAGCTAATGGGTTAGAAGGGTTAACTAGAGCA
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* ** * * *
3144243 AAACTAATAAAGTTAACCAA-TTAAAAAGTTTGCCAAGGTG--
1 AAACTGATAAAGCCAA-CAAGTT-AAAAGGTTGACTAGG-GCA
* **
3144283 AAACTGATAAAGCTAATGAGTTAGAAAGGTTGAAC-AGGTG-A
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTG-ACTAGG-GCA
* * * * * * *
3144324 AACCAG-TAGAGTCAACTAGTTAAAAGGTTGGCCAGGGCA
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
*** * *
3144363 AAACTGATAAAGCCAATGGGTTAGAAGGGTTGACCAAGGTG-A
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGA-CTAGG-GCA
* ** * * * *
3144405 AATC-GATAAAGTTAACTACTTAAAAGGTTGGCTAGGGCC
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* * * * * **
3144444 AAATTGATAAAGCCAACATGTTAGAAAGGTTAACCAAGGTG
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
** * * * *
3144485 AAACTGATAAAGTTAACTAGTTAAAAGGTTGGCCAGGGCG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
*** *
3144525 AAA-TCGATAAAGCCAATGGGTTAGAAAGGTTGA-TGAGGGCG
1 AAACT-GATAAAGCCAACAAGTTA-AAAGGTTGACT-AGGGCA
* * * ** * * * *
3144566 AAACAGATAAAGTCAACCAGTTAAAAATTTGGCCAAGGCG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* ** * * * **
3144606 AAACTGATAAAGCTAACGGGTTAGAAAGATAGACGAGGGTG
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
** * *
3144647 AAACCAATAAAGTCAACTAA-TTAAAAGGTTGGCTAGGGCA
1 AAACTGATAAAGCCAAC-AAGTTAAAAGGTTGACTAGGGCA
* * *** * *
3144687 AAACCGATAAAACCAATGGGTTAGATAA-GTTGATTAAGGCA
1 AAACTGATAAAGCCAACAAGTTA-A-AAGGTTGACTAGGGCA
* * *
3144728 AAA-TCGATAAAGTCAACCAA-TTAAAAGGTTGGCCAGGGCA
1 AAACT-GATAAAGCCAA-CAAGTTAAAAGGTTGACTAGGGCA
* * * **
3144768 AAACTAATAAAGCCAACTAGTTAAAAGGTT-AGCCAGGGTG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGA-CTAGGGCA
** ** * * *
3144808 AAACCAATAAAGCCAACGGGTTAGAAGGGTTGACCAAGGCA
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * * * **
3144849 AAA-TCGATAAAGTCAATC-ATTTAAAAGGTTGGCCAGGATA
1 AAACT-GATAAAGCCAA-CAAGTTAAAAGGTTGACTAGGGCA
** * * *
3144889 AAACTGATAAAGCCAACGTGTTAGAAGGGTTGACTAAGGCG
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * * * ** * *
3144930 AAACTGATAAAGTCATCCAGTTAAAAAGTTGGTTAGAGCG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* * *
3144970 AAACTGATAAAGCCAA-AGGGTTAAAAAGGTTGACCATGGCA
1 AAACTGATAAAGCCAACA-AGTT-AAAAGGTTGACTAGGGCA
* * * ** * * **
3145011 AAACTAATAAAGTCAACTAGTTAAAAATTTGGCAAGGGTG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
** *** * *
3145051 AAA-TCGATAAAGTTAATGGGTTAGAAGGGTTGACTAGGGCG
1 AAACT-GATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * * * * *
3145092 AAACTAATAAAGTCAACTAGTTAAAAGGTTGGCCAAGATG-A
1 AAACTGATAAAGCCAACAAGTTAAAAGGTT-GACTAG-GGCA
* * ** * * **
3145133 AATC-GATAAAGTCAACGGGTTACAAAGATTAACTAGGGGGTG
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTA--GGGCA
* * ** * * *
3145175 ACACCGATAAAGCCAACGGGTTAGAAGGGT-AATCAGGG-A
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACT-AGGGCA
* * * * * *
3145214 AAAATCAATAAAGTCAA-ATAGTTAAAAGGTTGGCCAGGGTA
1 AAACT-GATAAAGCCAACA-AGTTAAAAGGTTGACTAGGGCA
* * *** * * * *
3145255 AAACTGATAAAACTAATGGGTTAGATGCATTGACTAGGGCG
1 AAACTGATAAAGCCAACAAGTTAAAAG-GTTGACTAGGGCA
* * ** ** * * *
3145296 AAACCGATAAAGTCAACCAA-TTAGAGGGGTCAATTAGGACG
1 AAACTGATAAAGCCAA-CAAGTTA-AAAGGTTGACTAGGGCA
* ** * * *
3145337 AAACTGATAAAACTGACAAGTTAGAGGGATTGACTAAGGCA
1 AAACTGATAAAGCCAACAAGTTAAAAGG-TTGACTAGGGCA
* ** * * * *
3145378 AAACCGATAAAATCAACCAA-TTAGAAGGCTGGCCATGGTG-A
1 AAACTGATAAAGCCAA-CAAGTTAAAAGGTTGACTA-GG-GCA
* ** * * * *
3145419 AATC-GATAAAGCCAATGAGTTAGAAGGGTTCACCAAGGCA
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * *
3145459 AAAATGATAAAGCCAACGCA-TTAAAAGGGTTGACCA-GGCA
1 AAACTGATAAAGCCAAC-AAGTTAAAA-GGTTGACTAGGGCA
* ** * * * *
3145499 AAACTAATAAAGTGAACCAA-TTTAAAGGTTGGCCAGGGTA
1 AAACTGATAAAGCCAA-CAAGTTAAAAGGTTGACTAGGGCA
** * * *
3145539 AAACTGATAAAGCCAACGGGCTAGAAAGGTTGGCCAGGGCA
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGACTAGGGCA
* * * * * * * **
3145580 AAATTGATAGAGTCAACTAGCTAAAAGGTTGGCCAGGGTG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* * * *
3145620 AAATTGATAAAGCCAACAGGTTAGAAGGGTTGACCAAGGTG-A
1 AAACTGATAAAGCCAACAAGTTA-AAAGGTTGA-CTAGG-GCA
* * ** ** * **
3145662 AATC-AATAAAGTTAATTAGTTAAAAGGTTGGCTAGGGTG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* * *
3145701 AAACCGATAAAGCTAATC-GGTTAAAAAGGTTGACTAGGGCA
1 AAACTGATAAAGCCAA-CAAGTT-AAAAGGTTGACTAGGGCA
* ** ** * * *
3145742 AAACTAATAAAGTTAACTGGTTAAAAGGTTGGCCAGGGCG
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
*** **
3145782 AAA-TCGATAAAGCCAATGGGTTAGAAAGGTTGA-TGAGGGTG
1 AAACT-GATAAAGCCAACAAGTTA-AAAGGTTGACT-AGGGCA
* * * * *
3145823 AAACCGATAAAGTCAACTAA-TTAAAAAGTTGGCAAGGGCA
1 AAACTGATAAAGCCAAC-AAGTTAAAAGGTTGACTAGGGCA
* * * * * **
3145863 AAACTGATAAAGCTAATAGGCTAAAAAGGTTGACGAGGGTG
1 AAACTGATAAAGCCAACAAG-TTAAAAGGTTGACTAGGGCA
* * *
3145904 AAACCGATAAAGTCAACTAGTTAAAAGGTTGACTAGGGCA
1 AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
* *
3145944 AAACTAATAAAACCAACAAGTTA
1 AAACTGATAAAGCCAACAAGTTA
3145967 GAGGTAAATA
Statistics
Matches: 1304, Mismatches: 446, Indels: 193
0.67 0.23 0.10
Matches are distributed among these distances:
38 4 0.00
39 53 0.04
40 599 0.46
41 588 0.45
42 41 0.03
43 19 0.01
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.20
Consensus pattern (40 bp):
AAACTGATAAAGCCAACAAGTTAAAAGGTTGACTAGGGCA
Found at i:3156039 original size:20 final size:21
Alignment explanation
Indices: 3155986--3156039 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3155976 ATTTACCTGC
* *
3155986 ATGTATCGATAC-ATTATTCA
1 ATGTATCGATACAATGATTAA
3156006 ATGTATCGATACAATGA-TAA
1 ATGTATCGATACAATGATTAA
3156026 ATGTATCGATACAA
1 ATGTATCGATACAA
3156040 AACTTATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATGATTAA
Found at i:3156860 original size:52 final size:51
Alignment explanation
Indices: 3156773--3157150 Score: 270
Period size: 52 Copynumber: 7.4 Consensus size: 51
3156763 GGTGCTAATA
* * * *
3156773 TGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGATACGAAGAATGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATA-GAAGAATGCCAATG
* * *
3156825 TGCTGATTCATGGCCAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AGAAGAATGCCAATG
* * * *
3156877 TGCTAATTCAAGGCCAGCGACATTGGGCTTAGGAATGTTA-AAG-ATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GATAGAAGAATGCCAATG
* * * * *
3156929 TGTTGATTCAAGGCCAGCGATATCGAACTTAAAGATA-AAG-GTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAGAAGAATGCCAATG
*** * * * *
3156978 CATTGATTCAAGGCCAGTGACGTTGGACTTAAATATACGAAGAATGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATA-GAAGAATGCCAATG
* * * * *
3157030 TACTGATTCACGGCCAGCAACATT-GAGCTTAGGAATGTTA-AAG-ATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGA-CTTA--AA-GATAGAAGAATGCCAATG
** * ** * *
3157082 TGCTGATTCAAGGCCAATGATATCAGACTTCAAGAT-GAAG-GTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAGAAGAATGCCAATG
* *
3157131 CGTTGATTCAAGGCCAGCGA
1 TGCTGATTCAAGGCCAGCGA
3157151 ATGCTAATTC
Statistics
Matches: 255, Mismatches: 58, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
49 70 0.27
50 4 0.02
51 5 0.02
52 158 0.62
53 9 0.04
54 5 0.02
55 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (51 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAGAAGAATGCCAATG
Found at i:3157053 original size:153 final size:153
Alignment explanation
Indices: 3156760--3157150 Score: 471
Period size: 153 Copynumber: 2.5 Consensus size: 153
3156750 TAAGGATGAG
* * * * ** * *
3156760 AAAGGTGCTAATATGCTGATTCAAGGCTAGCGATATTGGGCTTAAAGATACGAAGAATGTCAATG
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAACTTAAAGATA--AAG-GTGCCAATG
* * * * *
3156825 TGCTGATTCATGGCCAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATGTGCTAATTCAAGG
63 CGTTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAATGCCAATGTACTAATTCAAGG
* *
3156890 CCAGCGACATTGGGCTTAGGAATGTT
128 CCAGCAACATTGAGCTTAGGAATGTT
* *
3156916 AAAGATGCCAATATGTTGATTCAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGCCAATGCAT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGCCAATGCGT
* * * * * * *
3156981 TGATTCAAGGCCAGTGACGTTGGACTTAAATAT-ACGAAGAATGTCAATGTACTGATTCACGGCC
66 TGATTCAAGGCCAGCGACATTAGACTTAAAGATGA-GAAGAATGCCAATGTACTAATTCAAGGCC
3157045 AGCAACATTGAGCTTAGGAATGTT
130 AGCAACATTGAGCTTAGGAATGTT
** * *
3157069 AAAGATGCCAATATGCTGATTCAAGGCCAATGATATC-AGACTTCAAGATGAAGGTGCCAATGCG
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGA-ACTTAAAGATAAAGGTGCCAATGCG
3157133 TTGATTCAAGGCCAGCGA
65 TTGATTCAAGGCCAGCGA
3157151 ATGCTAATTC
Statistics
Matches: 202, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
152 2 0.01
153 154 0.76
154 3 0.01
156 43 0.21
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (153 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGCCAATGCGT
TGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAATGCCAATGTACTAATTCAAGGCCA
GCAACATTGAGCTTAGGAATGTT
Found at i:3157251 original size:52 final size:49
Alignment explanation
Indices: 3157169--3157340 Score: 173
Period size: 52 Copynumber: 3.4 Consensus size: 49
3157159 TCACGACCAA
* *
3157169 CGACATTAGACTTGAAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAG
1 CGACATTGGACTTAAAGAT-A-AAG-ATGCCAATGTGCTGATTCAAGGCCAG
* * * *
3157221 CGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAACGCCAG
1 CGACATTGGACTTA--AA-GATAAAGATGCCAATGTGCTGATTCAAGGCCAG
* * * * * * *
3157273 CAATATTGGATTTAAAGATGATGGTGCCAATGTGTTGATTCAAGGCCAG
1 CGACATTGGACTTAAAGATAAAGATGCCAATGTGCTGATTCAAGGCCAG
3157322 CGACATTGGACTTAAAGAT
1 CGACATTGGACTTAAAGAT
3157341 GAGAAGGATG
Statistics
Matches: 97, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
49 42 0.43
50 2 0.02
52 45 0.46
53 3 0.03
54 3 0.03
55 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (49 bp):
CGACATTGGACTTAAAGATAAAGATGCCAATGTGCTGATTCAAGGCCAG
Found at i:3157321 original size:49 final size:49
Alignment explanation
Indices: 3157196--3157342 Score: 141
Period size: 49 Copynumber: 2.9 Consensus size: 49
3157186 ATGAGAAGAA
* * * * * * * *
3157196 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGA
1 TGCCAATATGCTGATTCAACGCCAGCAACATTGGACTTA--AA-GATGATGG
* *
3157248 TGCCAATATGCTGATTCAACGCCAGCAATATTGGATTTAAAGATGATGG
1 TGCCAATATGCTGATTCAACGCCAGCAACATTGGACTTAAAGATGATGG
* * * *
3157297 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
1 TGCCAATATGCTGATTCAACGCCAGCAACATTGGACTTAAAGATGA
3157343 GAAGGATGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
49 44 0.56
50 2 0.03
52 33 0.42
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAACGCCAGCAACATTGGACTTAAAGATGATGG
Found at i:3157401 original size:43 final size:43
Alignment explanation
Indices: 3157353--3157434 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
3157343 GAAGGATGAT
* * * *
3157353 AAAGGTGCTAATATGCTGATTAAAGGCCAGCGATATTGGACTC
1 AAAGGTACCAATATGCTGATTAAAGGCCAACGACATTGGACTC
* * *
3157396 AAAGGTACCAATGTGTTGATTCAAGGCCAACGACATTGG
1 AAAGGTACCAATATGCTGATTAAAGGCCAACGACATTGG
3157435 GCTTAAAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (43 bp):
AAAGGTACCAATATGCTGATTAAAGGCCAACGACATTGGACTC
Found at i:3157891 original size:15 final size:14
Alignment explanation
Indices: 3157848--3157882 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3157838 CGTTCTCGAC
*
3157848 AAAAGTTCTTGACA
1 AAAATTTCTTGACA
3157862 AAAATTTCTTGACA
1 AAAATTTCTTGACA
*
3157876 ACAATTT
1 AAAATTT
3157883 TGTTGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (14 bp):
AAAATTTCTTGACA
Found at i:3168515 original size:20 final size:20
Alignment explanation
Indices: 3168490--3168543 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
3168480 ATTTGCCTGC
3168490 ATGTATCGATACATTGA-ATA
1 ATGTATCGATACATT-ATATA
3168510 ATGTATCGATACATTATATA
1 ATGTATCGATACATTATATA
3168530 ATGTATCGATACAT
1 ATGTATCGATACAT
3168544 CTAGGTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTATATA
Found at i:3169231 original size:22 final size:22
Alignment explanation
Indices: 3169176--3169219 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3169166 GTTAAGAATG
3169176 ATTAAGAAAATTAACTTATTAA
1 ATTAAGAAAATTAACTTATTAA
3169198 ATTAAGAAAATTAACTTATTAA
1 ATTAAGAAAATTAACTTATTAA
3169220 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTAAGAAAATTAACTTATTAA
Found at i:3170114 original size:16 final size:18
Alignment explanation
Indices: 3170089--3170125 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3170079 TTTTATGTAG
*
3170089 TATTAGGTTAT-GT-ATA
1 TATTAAGTTATAGTCATA
3170105 TATTAAGTTATAGTCATA
1 TATTAAGTTATAGTCATA
3170123 TAT
1 TAT
3170126 ATATTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTAAGTTATAGTCATA
Found at i:3170129 original size:22 final size:22
Alignment explanation
Indices: 3170101--3170171 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3170091 TTAGGTTATG
*
3170101 TATATATTAAGTTATAGTCATA
1 TATATATTAAGTTATAGTAATA
* *
3170123 TATATATTTAGTTATACTAATA
1 TATATATTAAGTTATAGTAATA
* * * *
3170145 TGTACATTGAGTTATAGTGATA
1 TATATATTAAGTTATAGTAATA
3170167 TATAT
1 TATAT
3170172 TTATATATGC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.46
Consensus pattern (22 bp):
TATATATTAAGTTATAGTAATA
Found at i:3170278 original size:24 final size:24
Alignment explanation
Indices: 3170251--3170297 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3170241 TTAGGGGTAG
*
3170251 TTAAATCATCATATTTACATTTAT
1 TTAAATCATCATATGTACATTTAT
*
3170275 TTAAATCATCATATGTATATTTA
1 TTAAATCATCATATGTACATTTA
3170298 ATTGTAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAATCATCATATGTACATTTAT
Found at i:3170311 original size:22 final size:21
Alignment explanation
Indices: 3170283--3170340 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
3170273 ATTTAAATCA
*
3170283 TCATATGTATATTTAATTGTAG
1 TCATATGTATATTTAATT-AAG
*
3170305 TCATATGTACATTCT-ATTAAG
1 TCATATGTATATT-TAATTAAG
3170326 TCATATGTATATTTA
1 TCATATGTATATTTA
3170341 GTTATAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 14 0.45
22 15 0.48
23 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (21 bp):
TCATATGTATATTTAATTAAG
Found at i:3170358 original size:20 final size:20
Alignment explanation
Indices: 3170333--3170373 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3170323 AAGTCATATG
*
3170333 TATATTTAGTTATAATCATA
1 TATATTCAGTTATAATCATA
*
3170353 TATATTCAGTTATAATTATA
1 TATATTCAGTTATAATCATA
3170373 T
1 T
3170374 GTGCATGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATTCAGTTATAATCATA
Found at i:3170372 original size:18 final size:19
Alignment explanation
Indices: 3170328--3170373 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3170318 CTATTAAGTC
* *
3170328 ATATGTATATTTAGTTATA
1 ATATATATATTCAGTTATA
3170347 ATCATATATATTCAGTTATA
1 AT-ATATATATTCAGTTATA
3170367 AT-TATAT
1 ATATATAT
3170374 GTGCATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 2 0.08
20 17 0.71
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (19 bp):
ATATATATATTCAGTTATA
Found at i:3177940 original size:89 final size:90
Alignment explanation
Indices: 3177836--3178016 Score: 292
Period size: 89 Copynumber: 2.0 Consensus size: 90
3177826 CCGATCTAGT
* * * *
3177836 CCGAGTTGACTAAAAAAGTTAACAACCCGAAATCGACCGATTCGAACCTGAAAATGACCTGAACC
1 CCGAGTTGACTAAAAAAGTTAACAACCCAAAATCGACCGATCCGAACCCGAAAATGACCCGAACC
3177901 CGAAATGATC-GAACCTAAAATGAC
66 CGAAATGATCTGAACCTAAAATGAC
* * *
3177925 CCGAGTTGACTAAAAATGTTAACAACCCAAAATCGATCGATCCGAACCCGAAAATGACCCGAACT
1 CCGAGTTGACTAAAAAAGTTAACAACCCAAAATCGACCGATCCGAACCCGAAAATGACCCGAACC
3177990 CGAAATGATCTGAACCTAAAATGAC
66 CGAAATGATCTGAACCTAAAATGAC
3178015 CC
1 CC
3178017 AAACCCAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 68 0.81
90 16 0.19
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (90 bp):
CCGAGTTGACTAAAAAAGTTAACAACCCAAAATCGACCGATCCGAACCCGAAAATGACCCGAACC
CGAAATGATCTGAACCTAAAATGAC
Found at i:3178011 original size:32 final size:32
Alignment explanation
Indices: 3177975--3178035 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3177965 TCCGAACCCG
* * * *
3177975 AAAATGACCCGAACTCGAAATGATCTGAACCT
1 AAAATGACCCAAACCCAAAATGACCTGAACCT
3178007 AAAATGACCCAAACCCAAAATGACCTGAA
1 AAAATGACCCAAACCCAAAATGACCTGAA
3178036 TAATTAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (32 bp):
AAAATGACCCAAACCCAAAATGACCTGAACCT
Found at i:3178820 original size:15 final size:15
Alignment explanation
Indices: 3178800--3178846 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3178790 CTGAATGTTA
3178800 AACCCAATTGACCCG
1 AACCCAATTGACCCG
* *
3178815 AACCCAAAATGACCTG
1 AACCC-AATTGACCCG
3178831 AACCCAATTGACCCG
1 AACCCAATTGACCCG
3178846 A
1 A
3178847 GCGTTAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.38, C:0.36, G:0.13, T:0.13
Consensus pattern (15 bp):
AACCCAATTGACCCG
Found at i:3178935 original size:16 final size:16
Alignment explanation
Indices: 3178882--3178927 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3178872 CGAAATGACT
*
3178882 CGAACCCAAAACAATC
1 CGAACCCAAAATAATC
* * *
3178898 CGAACTCGAAATGATC
1 CGAACCCAAAATAATC
3178914 CGAACCCAAAATAA
1 CGAACCCAAAATAA
3178928 CTCGAACCTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.30, G:0.11, T:0.11
Consensus pattern (16 bp):
CGAACCCAAAATAATC
Found at i:3178950 original size:48 final size:49
Alignment explanation
Indices: 3178874--3178966 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 49
3178864 CTCAAATCCG
* * *
3178874 AAATGACTCGAACCCAAAACAATCCGAACTCG-AAATGATCCGAACCCA
1 AAATAACTCGAACCCAAAACAACCCGAACTCGAAAATGACCCGAACCCA
* * * *
3178922 AAATAACTCGAACCTAAAGCGACCCGAACTTGAAAATGACCCGAA
1 AAATAACTCGAACCCAAAACAACCCGAACTCGAAAATGACCCGAA
3178967 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
48 26 0.70
49 11 0.30
ACGTcount: A:0.44, C:0.29, G:0.14, T:0.13
Consensus pattern (49 bp):
AAATAACTCGAACCCAAAACAACCCGAACTCGAAAATGACCCGAACCCA
Found at i:3183132 original size:22 final size:23
Alignment explanation
Indices: 3183083--3183133 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
3183073 AGGCTTTAGG
*
3183083 AATGTACATATGACTCTACAACTT
1 AATGTACATATGAC-CTACAACTA
*
3183107 AATGTACATATGA-CTATAACTA
1 AATGTACATATGACCTACAACTA
3183129 AATGT
1 AATGT
3183134 CGATATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (23 bp):
AATGTACATATGACCTACAACTA
Found at i:3183309 original size:22 final size:23
Alignment explanation
Indices: 3183279--3183344 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
3183269 TCAAAACACA
* *
3183279 GAATATACATATAACTCTAA-TT
1 GAATGTACATATAACTATAACTT
* *
3183301 GAATGTACATTTCACTATAACTT
1 GAATGTACATATAACTATAACTT
*
3183324 -AATGTACATATGACTATAACT
1 GAATGTACATATAACTATAACT
3183345 AAACATACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (23 bp):
GAATGTACATATAACTATAACTT
Found at i:3183353 original size:22 final size:22
Alignment explanation
Indices: 3183314--3183356 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3183304 TGTACATTTC
* **
3183314 ACTATAACTTAATGTACATATG
1 ACTATAACTAAACATACATATG
3183336 ACTATAACTAAACATACATAT
1 ACTATAACTAAACATACATAT
3183357 TAATAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (22 bp):
ACTATAACTAAACATACATATG
Found at i:3183673 original size:242 final size:239
Alignment explanation
Indices: 3183336--3183801 Score: 559
Period size: 242 Copynumber: 1.9 Consensus size: 239
3183326 TGTACATATG
* *
3183336 ACTATAACTAAACATACATATTAATAAAATACTCCTTAAACACTTTTCAATTATTGTACAGAACA
1 ACTATAACTAAACATACATATCAATAAAATACTCCTTAAACACTTCTCAATTATTGTACAGAACA
** *
3183401 ATGTCTCATGTAAATTTTTTAAGCCATTCAACATAATAAATATATAAACTATGTATATATGACAA
66 ATGTCTCACATAAATTTTTTAAACCATTCAACATAATAAATATATAAACTATG----TATGACAA
* * * *
3183466 AAA-TGGGATATACATA-TA-AAAATAGAATGTACTTGTAAATATAATTGAATGTACAT-ATCAA
127 AAACT-GGATATACATATTAGAAAATAAAATGTACATGTAAATATAACTAAATGTACATAAT-AA
*
3183527 AACACAGAATGTACATA-AGACTCTAACTGAATGTACAATTAAATATATAA
190 AACACAGAACGTACATATA-ACTCTAACTGAATGTACAATTAAATATATAA
* * * * *
3183577 ACTATAATTGAACATACATATCAATCAAAATATTCCTTAAATACTTCT-AATCTATTGTGCAGAA
1 ACTATAACTAAACATACATATCAAT-AAAATACTCCTTAAACACTTCTCAAT-TATTGTACAGAA
* * * *
3183641 TAGTG-CTTCACATAAATTTTTTAAACCATTCAACATATTAAATGTATAAACTATGTATGACAAA
64 CAATGTC-TCACATAAATTTTTTAAACCATTCAACATAATAAATATATAAACTATGTATGACAAA
* ** *
3183705 AACTGGATATGCATATTAGAAAATAAAATGTACATGTCTATATAACTAAATGTACATAATAGAAC
128 AACTGGATATACATATTAGAAAATAAAATGTACATGTAAATATAACTAAATGTACATAATAAAAC
* * *
3183770 ACAGAACGTTCATATAACTTTAATTGAATGTA
193 ACAGAACGTACATATAACTCTAACTGAATGTA
3183802 TATTTTACTA
Statistics
Matches: 191, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
238 21 0.11
239 3 0.02
240 62 0.32
241 29 0.15
242 76 0.40
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (239 bp):
ACTATAACTAAACATACATATCAATAAAATACTCCTTAAACACTTCTCAATTATTGTACAGAACA
ATGTCTCACATAAATTTTTTAAACCATTCAACATAATAAATATATAAACTATGTATGACAAAAAC
TGGATATACATATTAGAAAATAAAATGTACATGTAAATATAACTAAATGTACATAATAAAACACA
GAACGTACATATAACTCTAACTGAATGTACAATTAAATATATAA
Found at i:3183833 original size:22 final size:22
Alignment explanation
Indices: 3183808--3183850 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3183798 TGTATATTTT
3183808 ACTATAACTCAATATACATATG
1 ACTATAACTCAATATACATATG
* *
3183830 ACTATAATTGAATATACATAT
1 ACTATAACTCAATATACATAT
3183851 CAATCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (22 bp):
ACTATAACTCAATATACATATG
Found at i:3185729 original size:20 final size:20
Alignment explanation
Indices: 3185704--3185769 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
3185694 CTACTACTAT
3185704 TTGTATCGATACATGGCATA
1 TTGTATCGATACATGGCATA
*
3185724 TTGTATC---A-AT-ACA-A
1 TTGTATCGATACATGGCATA
3185738 -TGTATCGATACATGGCATA
1 TTGTATCGATACATGGCATA
3185757 TTGTATCGATACA
1 TTGTATCGATACA
3185770 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 6 0.16
14 1 0.03
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 1 0.03
20 19 0.51
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGCATA
Found at i:3185776 original size:13 final size:13
Alignment explanation
Indices: 3185758--3185782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3185748 CATGGCATAT
3185758 TGTATCGATACAA
1 TGTATCGATACAA
3185771 TGTATCGATACA
1 TGTATCGATACA
3185783 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3185793 original size:33 final size:33
Alignment explanation
Indices: 3185705--3185802 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
3185695 TACTACTATT
*
3185705 TGTATCGATACATGGCATATTGTATCAATACAA
1 TGTATCGATACATGGCATATTGTATCGATACAA
3185738 TGTATCGATACATGGCATATTGTATCGATACAA
1 TGTATCGATACATGGCATATTGTATCGATACAA
3185771 TGTATCGATACATGAAG-A-ATTGTATCGATACA
1 TGTATCGATACATG--GCATATTGTATCGATACA
3185803 TTGTCCCAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
33 60 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGGCATATTGTATCGATACAA
Found at i:3187416 original size:15 final size:15
Alignment explanation
Indices: 3187396--3187430 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3187386 AACCATCAAA
3187396 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
3187411 GATGATGATGATAAT
1 GATGATGAAGATAAT
3187426 GATGA
1 GATGA
3187431 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:3193768 original size:20 final size:20
Alignment explanation
Indices: 3193726--3193779 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
3193716 TTCTACTATT
* *
3193726 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAATGAA
3193747 TGTATCGATACATAAATGAA
1 TGTATCGATACATAAATGAA
3193767 TGTATCGATACAT
1 TGTATCGATACAT
3193780 GTCTCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAATGAA
Found at i:3205217 original size:2 final size:2
Alignment explanation
Indices: 3205210--3205235 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3205200 TGATTAAGTG
3205210 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3205236 ATTTTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3206261 original size:19 final size:20
Alignment explanation
Indices: 3206220--3206264 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
3206210 TTGAAAATAC
3206220 TTTTTGCACTTACTTTAATT
1 TTTTTGCACTTACTTTAATT
3206240 TTTTTGCACTTACTTTAATT
1 TTTTTGCACTTACTTTAATT
3206260 TTTTT
1 TTTTT
3206265 ACTTGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTGCACTTACTTTAATT
Found at i:3208329 original size:20 final size:20
Alignment explanation
Indices: 3208304--3208359 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3208294 GTAGTTTAGA
*
3208304 GTATCGATACATTTTGTAAT
1 GTATCGATATATTTTGTAAT
* *
3208324 GTATCGATATATTGTGTATT
1 GTATCGATATATTTTGTAAT
*
3208344 GTATCAATATATTTTG
1 GTATCGATATATTTTG
3208360 ATATGCATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (20 bp):
GTATCGATATATTTTGTAAT
Found at i:3209506 original size:39 final size:38
Alignment explanation
Indices: 3209457--3209565 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
3209447 AAGATCAACG
*
3209457 AAATTTATATAAATCCAAATATACA-AAAAAATATCAATC
1 AAATTCATATAAAT-CAAATATACATAAAAAA-ATCAATC
**
3209496 AAATTCATATAAAATCAAATATTTATAAAAAAATCAATC
1 AAATTCATAT-AAATCAAATATACATAAAAAAATCAATC
* *
3209535 AAATTCATATAAGATCAAATATGCATTAAAA
1 AAATTCATATAA-ATCAAATATACATAAAAA
3209566 GACCATGATA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.03
39 49 0.80
40 10 0.16
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (38 bp):
AAATTCATATAAATCAAATATACATAAAAAAATCAATC
Found at i:3209509 original size:23 final size:22
Alignment explanation
Indices: 3209483--3209546 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
3209473 AAATATACAA
3209483 AAAAATATCAATCAAATTCATAT
1 AAAAA-ATCAATCAAATTCATAT
* *
3209506 --AAAATCAA--ATATTTATA-
1 AAAAAATCAATCAAATTCATAT
3209523 AAAAAATCAATCAAATTCATAT
1 AAAAAATCAATCAAATTCATAT
3209545 AA
1 AA
3209547 GATCAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
18 7 0.22
19 8 0.25
20 5 0.16
21 10 0.31
22 2 0.06
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATCAATCAAATTCATAT
Found at i:3214519 original size:31 final size:32
Alignment explanation
Indices: 3214452--3214530 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
3214442 GATGCATTGA
3214452 AGAATGTATCGATACATTTGGGCAAAAAACCT
1 AGAATGTATCGATACATTTGGGCAAAAAACCT
* * **
3214484 AGAATGTATTGATAGATTTGGG-TTAAAA-CT
1 AGAATGTATCGATACATTTGGGCAAAAAACCT
3214514 CAGAATGTATCGATACA
1 -AGAATGTATCGATACA
3214531 ATGAAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 18 0.45
32 20 0.50
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (32 bp):
AGAATGTATCGATACATTTGGGCAAAAAACCT
Found at i:3214632 original size:20 final size:20
Alignment explanation
Indices: 3214589--3214661 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
3214579 GACATGGTCC
***
3214589 TGTATCGATACATTTCAGACA
1 TGTATCGATACA-TTCACTTA
*
3214610 TGTATTGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
3214630 TGTATCGATACATTCACTTT
1 TGTATCGATACATTCACTTA
*
3214650 TGTATCAATACA
1 TGTATCGATACA
3214662 AATTGTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 34 0.76
21 11 0.24
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:3215395 original size:61 final size:60
Alignment explanation
Indices: 3215313--3215516 Score: 230
Period size: 61 Copynumber: 3.4 Consensus size: 60
3215303 TACGACACTA
* * * *
3215313 GACTTAAAGATGATAAGAATGAGAAAAGTGCTAATGAGCTGATTCAAGGCCAATAACATC
1 GACTTAAAAATGAGAAGAATGAGAAAAGTGCTAATGAGCTGATTCAAGGCCAACAATATC
* * *
3215373 AGACTTAAAAATGAGAAAAATGATAAAGGTGCTAAT-ATGCTGATTCAAGGCCAACAATATTC
1 -GACTTAAAAATGAGAAGAATGAGAAAAGTGCTAATGA-GCTGATTCAAGGCCAACAATA-TC
** * * * * * *
3215435 GACTTAAGGATGATAAGGATGAGAAGAGTGCCAATGTGCTGATTCAAGGCCAACGATATC
1 GACTTAAAAATGAGAAGAATGAGAAAAGTGCTAATGAGCTGATTCAAGGCCAACAATATC
3215495 GAACTTAAAAATGAGAAGAATG
1 G-ACTTAAAAATGAGAAGAATG
3215517 CTAATGTACA
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
60 4 0.03
61 111 0.95
62 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.22
Consensus pattern (60 bp):
GACTTAAAAATGAGAAGAATGAGAAAAGTGCTAATGAGCTGATTCAAGGCCAACAATATC
Found at i:3215824 original size:33 final size:33
Alignment explanation
Indices: 3215787--3216149 Score: 174
Period size: 33 Copynumber: 11.2 Consensus size: 33
3215777 TAGAAGGAGA
* * *
3215787 TGCCACTGACTTATGTAGGCTTTTGAAAAAGGC
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* * *
3215820 TGCCA-TCGCCTTGTGTGGGCTTTAGAAGAAGGG
1 TGCCACT-GACTTGTGTGGGCTTTAGAAAAAGGC
* * *
3215853 TGCCACTAACTTGTGTGGGCTTTAG-AAAGGGAT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGG-C
* ** * * * * *
3215886 TGACACCAACTTGAGTAGGCTTTTG-AGAAGGT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* * *
3215918 TGCCACCGACATGTGTGGGC-TTA-AAAAGGGC
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* * * *
3215949 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* ** * * *
3215982 TGCTACCAACTTGTGTAGGCTTTAG--AAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* * * *
3216013 TAG-AACTAACTTGTGTGGGCTTTAGAAAAGGGT
1 T-GCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* ** * *
3216046 TACCACCAACTTGTGTGGGTTTTAG--AAAGGT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
* * * * * *
3216077 TGCCACCGACTTATGTAGGCTTTAGAGAAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
*
3216110 TGCTA-TCGACTTGTGTGGGCTTTGAAGAAAAAGG-
1 TGCCACT-GACTTGTGTGGGCTTT--AGAAAAAGGC
3216144 TGCCAC
1 TGCCAC
3216150 AAAGTTGTGG
Statistics
Matches: 260, Mismatches: 54, Indels: 30
0.76 0.16 0.09
Matches are distributed among these distances:
31 76 0.29
32 25 0.10
33 147 0.57
34 5 0.02
35 7 0.03
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (33 bp):
TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGC
Found at i:3216003 original size:64 final size:64
Alignment explanation
Indices: 3215812--3216131 Score: 299
Period size: 64 Copynumber: 5.0 Consensus size: 64
3215802 TAGGCTTTTG
* * * *
3215812 AAAAA-GGCTGCCATCGCCTTGTGTGGGCTTTAGAAGAAGGG-TGCCACTAACTTGTGTGGGCTT
1 AAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGGTTGCCACCAACTTGTGTGGGC-T
3215875 T
64 T
* * * * * * * *
3215876 AGAAAGGGATTGACACCAACTTGAGTAGGCTTTTGAGAA-GGTTGCCACCGACATGTGTGGGCTT
1 AAAAAGGG-TTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTT
* * *
3215940 AAAAAGGGCTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCTACCAACTTGTGTAGGCTT
1 AAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTT
* * * ** * * *
3216004 TAGAAGGGTTAG-AACTAACTTGTGTGGGCTTTAGAAAAGGGTTACCACCAACTTGTGTGGGTTT
1 AAAAAGGGTT-GCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGG-CT
3216068 T
64 T
* * * * * *
3216069 AGAAA-GGTTGCCACCGACTTATGTAGGCTTTAGAGAAGGGTTGCTATCGACTTGTGTGGGCTT
1 AAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTT
3216132 TGAAGAAAAA
Statistics
Matches: 201, Mismatches: 48, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
63 27 0.13
64 128 0.64
65 28 0.14
66 18 0.09
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (64 bp):
AAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTT
Found at i:3216098 original size:128 final size:127
Alignment explanation
Indices: 3215812--3216136 Score: 388
Period size: 128 Copynumber: 2.5 Consensus size: 127
3215802 TAGGCTTTTG
* * * *
3215812 AAAAAGGCTGCCATCGCCTTGTGTGGGCTTTAGAAGAAGGG-TGCCACTAACTTGTGTGGGCTTT
1 AAAAAGGCTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGGTTGCTACCAACTTGTGTGGGCTTT
* * * *
3215876 AGAAAGGGATTGACACCAACTTGAGTAGGCTTTTGAGAAGGTTGCCACCGACATGTGTGGGCTT
65 AG-AAGGGATTGACACCAACTTGAGTAGGCTTTAGAAAAGGTTACCACCAACATGTGTGGGCTT
*
3215940 AAAAAGGGCTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCTACCAACTTGTGTAGGCTTT
1 AAAAA-GGCTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCTACCAACTTGTGTGGGCTTT
* * * * *
3216005 AGAAGGG-TTAGA-ACTAACTTGTGTGGGCTTTAGAAAAGGGTTACCACCAACTTGTGTGGGTTT
65 AGAAGGGATT-GACACCAACTTGAGTAGGCTTTAGAAAA-GGTTACCACCAACATGTGTGGG-CT
3216068 T
127 T
* * * * * *
3216069 AGAAAGGTTGCCACCGACTTATGTAGGCTTTAGAGAAGGGTTGCTATCGACTTGTGTGGGCTTT-
1 AAAAAGGCTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCTACCAACTTGTGTGGGCTTTA
3216133 GAAG
66 GAAG
3216137 AAAAAGGTGC
Statistics
Matches: 171, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
127 26 0.15
128 91 0.53
129 54 0.32
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.28
Consensus pattern (127 bp):
AAAAAGGCTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCTACCAACTTGTGTGGGCTTTA
GAAGGGATTGACACCAACTTGAGTAGGCTTTAGAAAAGGTTACCACCAACATGTGTGGGCTT
Found at i:3216313 original size:62 final size:61
Alignment explanation
Indices: 3216229--3216737 Score: 432
Period size: 62 Copynumber: 8.3 Consensus size: 61
3216219 ATTGACTTGG
*
3216229 GTGGGCTTTGAAGAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
1 GTGGACTTTGAA-AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
3216291 GTGGACTTTGATAAAAAAGGTGCCAC-GATGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
1 GTGGACTTTGA-AAAAAAGGTGCCACAGA-GTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
* *
3216353 GTGGACTTTGAAGAAAATGGTGCCACAGAGTTATGGACTTTGAAGAAAA--GTG-CATCGGAGTT
1 GTGGACTTTGAA-AAAAAGGTGCCACAGAGTTGTGGACTTT-AA-AAAAGGGTGCCA-CGGAGTT
* **
3216415 GTAGACTTT-AAAAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAAGTGCCACGGAGTT
1 GTGGACTTTGAAAAAAAGGTGCCACAGAGTTGTGGACTTT-AA-AAAAGGGTGCCACGGAGTT
** *** * ** * *
3216477 GTGGACTTT-AAAAAGGGGTGCCGTGGAGTTGTGGACCTTGAAAAAAAATGTGCCTCAGAGTT
1 GTGGACTTTGAAAAAAAGGTGCCACAGAGTTGTGGA-CTT-TAAAAAAGGGTGCCACGGAGTT
* * * * * *
3216539 ATGGACTTTG--AAAAAGATGCCACATAGTTGTGCACTTTAGAAAAA-GTTGCCACGGAGAT
1 GTGGACTTTGAAAAAAAGGTGCCACAGAGTTGTGGACTTTA-AAAAAGGGTGCCACGGAGTT
* * * * * * * **
3216598 ATAGAATTTGAAGAAAAAGGTGCCAAAGAGTTGTAGATTTTAAAAAAAAGGG-GCTATAGAGTT
1 GTGGACTTTGAA-AAAAAGGTGCCACAGAGTTGTGGACTTT--AAAAAAGGGTGCCACGGAGTT
* ** ** * * *
3216661 GTGGACTTT-AAGAGGA-GTGCCACAGAGTTGTGGACTTTAAAAAAGACTACCACGAAGTA
1 GTGGACTTTGAAAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
3216720 GTGGACTTT-AAGAAAAAG
1 GTGGACTTTGAA-AAAAAG
3216738 ATTGGGTGCC
Statistics
Matches: 360, Mismatches: 64, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
58 7 0.02
59 34 0.09
60 63 0.17
61 25 0.07
62 195 0.54
63 30 0.08
64 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (61 bp):
GTGGACTTTGAAAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTT
Found at i:3216354 original size:92 final size:91
Alignment explanation
Indices: 3216242--3216737 Score: 349
Period size: 92 Copynumber: 5.4 Consensus size: 91
3216232 GGCTTTGAAG
*
3216242 AAAAAGGTGCCACAGAGTTGTGGACTTT-AA-AAAAGGGTGCCACGGAGTTGTGGACTTTGATAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGA-AA
*
3216305 AAAAGGTGCCA-C-GATGTTGTGGACTTTA
65 AAAA-GTG-CATCGGA-GTTGTAGACTTTA
* * * * *
3216333 AAAAAGGGTGCCACGGAGTTGTGGACTTTGAAGAAAATGGTGCCACAGAGTTATGGACTTTGAAG
1 AAAAA-GGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGAAA
3216398 AAAAGTGCATCGGAGTTGTAGACTTTAA
65 AAAAGTGCATCGGAGTTGTAGACTTT-A
*
3216426 AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAAGTGCCACGGAGTTGTGGACTTT-AAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAA
** * * *
3216490 AGGGGTGCCGT-GGAGTTGTGGACCTTGAAA
66 A-AAGTG-CATCGGAGTTGTAGA-CTT--TA
* * * * ** * *
3216520 AAAAATGTGCCTCAGAGTTATGGACTTT---GAAAAAGATGCCACATAGTTGTGCACTTT-AGAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAA
* * *
3216581 AAAGTTGCCA-CGGAGATATAGAATTTGAA
66 AAAG-TG-CATCGGAGTTGTAGACTTT--A
* * * * * * ** *
3216610 GAAAAAGGTGCCAAAGAGTTGTAGA-TTTTAAAAAAAAGGGGCTATAGAGTTGTGGACTTT-AAG
1 -AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGAAA
** * *
3216673 AGGAGTGCCA-CAGAGTTGTGGACTTTA
65 AAAAGTG-CATCGGAGTTGTAGACTTTA
* * *
3216700 AAAAAGACTACCAC-GAAGTAGTGGACTTT-AAGAAAAAG
1 AAAAAG-GTGCCACAG-AGTTGTGGACTTTGAAGAAAAAG
3216738 ATTGGGTGCC
Statistics
Matches: 322, Mismatches: 61, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
89 7 0.02
90 27 0.08
91 73 0.23
92 116 0.36
93 46 0.14
94 53 0.16
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.24
Consensus pattern (91 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTTGAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAA
AAAGTGCATCGGAGTTGTAGACTTTA
Found at i:3216530 original size:154 final size:152
Alignment explanation
Indices: 3216234--3216644 Score: 499
Period size: 154 Copynumber: 2.7 Consensus size: 152
3216224 CTTGGGTGGG
*
3216234 CTTTGAAGAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACTT
1 CTTTGAAG-AAAA-GTGCCACAGAGTTGT-GACTTTAAAAAAAGGTGCCACGGAGTTGTGGACTT
*
3216299 TGATA-AAAAAGGTGCCACGATGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACTTTG
63 TGA-AGAAAAAGGTGCCACGA-GTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACCTTG
*
3216363 AAGAAAATGGTGCCACAGAGTTATGGA
126 AAAAAAATGGTGCCACAGAGTTATGGA
* *
3216390 CTTTGAAGAAAAGTG-CATCGGAGTTGTAGACTTTAAAAAAAGGTGCCACAGAGTTGTGGACTTT
1 CTTTGAAGAAAAGTGCCA-CAGAGTTGT-GACTTTAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* * **
3216454 GAAGAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAAGGGGTGCCGTGGAGTTGTGGACCTTGAA
64 GAAGAAAAAGGTGCCAC-GAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACCTTG-A
*
3216519 AAAAAAT-GTGCCTCAGAGTTATGGA
127 AAAAAATGGTGCCACAGAGTTATGGA
* * * * * * *
3216544 CTTTG-A-AAAAGATGCCACATAGTTGTGCACTTTAGAAAAAGTTGCCACGGAGATATAGAATTT
1 CTTTGAAGAAAAG-TGCCACAGAGTTGTG-ACTTTAAAAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
3216607 GAAGAAAAAGGTGCCAAAGAGTTGTAGATTTTAAAAAA
64 GAAGAAAAAGGTGCC-ACGAGTTGTGGACTTTAAAAAA
3216645 AAGGGGCTAT
Statistics
Matches: 222, Mismatches: 25, Indels: 19
0.83 0.09 0.07
Matches are distributed among these distances:
152 6 0.03
153 72 0.32
154 123 0.55
155 13 0.06
156 8 0.04
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (152 bp):
CTTTGAAGAAAAGTGCCACAGAGTTGTGACTTTAAAAAAAGGTGCCACGGAGTTGTGGACTTTGA
AGAAAAAGGTGCCACGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACCTTGAAAAA
AATGGTGCCACAGAGTTATGGA
Found at i:3216661 original size:154 final size:151
Alignment explanation
Indices: 3216241--3216706 Score: 482
Period size: 154 Copynumber: 3.1 Consensus size: 151
3216231 GGGCTTTGAA
*
3216241 GAAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACTTTGATA-A
1 GAAAAAGATGCCACAGAGTTGT-GACTTTAAAAAA-GGTGCCACGGAGTTGTGGACTTTGA-AGA
* * * *
3216305 AAAAGGTGCC-ACGATGTTGTGGACTTTAAAAAAGGGTGCCACGGAGTTGTGGACTTTGAAGAAA
63 AAAAGGTGCCAAAGA-GTTGTGGACTTTAAAAAAGGGTGCCATGGAGTTGTGGACCTTGAAAAAA
3216369 ATGGTGCCACAGAGTTATGGACTTT
127 ATGGTGCCACAGAGTTATGGACTTT
* *
3216394 GAAGAAA-AGTG-CATCGGAGTTGTAGACTTTAAAAAAAGGTGCCACAGAGTTGTGGACTTTGAA
1 GAA-AAAGA-TGCCA-CAGAGTTGT-GACTTT-AAAAAAGGTGCCACGGAGTTGTGGACTTTGAA
* ** * *
3216457 GAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAAGGGGTGCCGTGGAGTTGTGGACCTTGAAAAA
61 GAAAAAGGTGCCAAAGAGTTGTGGACTTTAAAAAAGGGTGCCATGGAGTTGTGGACCTTG-AAAA
*
3216522 AAAT-GTGCCTCAGAGTTATGGACTTT
125 AAATGGTGCCACAGAGTTATGGACTTT
* * * * * *
3216548 GAAAAAGATGCCACATAGTTGTGCACTTTAGAAAAAGTTGCCACGGAGATATAGAATTTGAAGAA
1 GAAAAAGATGCCACAGAGTTGTG-ACTTTA-AAAAAGGTGCCACGGAGTTGTGGACTTTGAAGAA
* * * * * * **
3216613 AAAGGTGCCAAAGAGTTGTAGATTTTAAAAAAAAGGG-GCTATAGAGTTGTGGA-CTTTAAGAGG
64 AAAGGTGCCAAAGAGTTGTGGACTTT--AAAAAAGGGTGCCATGGAGTTGTGGACCTTGAAAAAA
*
3216676 A--GTGCCACAGAGTTGTGGACTTT
127 ATGGTGCCACAGAGTTATGGACTTT
*
3216699 AAAAAAGA
1 GAAAAAGA
3216707 CTACCACGAA
Statistics
Matches: 263, Mismatches: 37, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
151 27 0.10
152 6 0.02
153 75 0.29
154 132 0.50
155 23 0.09
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (151 bp):
GAAAAAGATGCCACAGAGTTGTGACTTTAAAAAAGGTGCCACGGAGTTGTGGACTTTGAAGAAAA
AGGTGCCAAAGAGTTGTGGACTTTAAAAAAGGGTGCCATGGAGTTGTGGACCTTGAAAAAAATGG
TGCCACAGAGTTATGGACTTT
Found at i:3221549 original size:70 final size:70
Alignment explanation
Indices: 3221466--3221600 Score: 270
Period size: 70 Copynumber: 1.9 Consensus size: 70
3221456 GCACAGTATT
3221466 TGTCGGGGAAACAATCAAACCTTTTGTTTACTCCCACTTTACCATTTTTATTAAAATAACACTCA
1 TGTCGGGGAAACAATCAAACCTTTTGTTTACTCCCACTTTACCATTTTTATTAAAATAACACTCA
3221531 ATATG
66 ATATG
3221536 TGTCGGGGAAACAATCAAACCTTTTGTTTACTCCCACTTTACCATTTTTATTAAAATAACACTCA
1 TGTCGGGGAAACAATCAAACCTTTTGTTTACTCCCACTTTACCATTTTTATTAAAATAACACTCA
3221601 TCACATGATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.36
Consensus pattern (70 bp):
TGTCGGGGAAACAATCAAACCTTTTGTTTACTCCCACTTTACCATTTTTATTAAAATAACACTCA
ATATG
Found at i:3223034 original size:13 final size:13
Alignment explanation
Indices: 3223016--3223041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3223006 CAATTTTTTG
3223016 TGTATCGATACAT
1 TGTATCGATACAT
3223029 TGTATCGATACAT
1 TGTATCGATACAT
3223042 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3225440 original size:21 final size:21
Alignment explanation
Indices: 3225416--3225462 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3225406 TTTGATGCTG
3225416 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
3225436 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
3225457 ATTTTG
1 ATTTTG
3225463 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:3225601 original size:13 final size:13
Alignment explanation
Indices: 3225583--3225621 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3225573 ATAATCACCC
*
3225583 TGTATCGATACAG
1 TGTATCGATACAA
3225596 TGTATCGATACAA
1 TGTATCGATACAA
3225609 TGTATCGATACAA
1 TGTATCGATACAA
3225622 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3225632 original size:20 final size:20
Alignment explanation
Indices: 3225607--3225645 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3225597 GTATCGATAC
3225607 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3225627 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
3225646 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3227717 original size:15 final size:15
Alignment explanation
Indices: 3227697--3227727 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3227687 ATTTCGTTTG
*
3227697 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3227712 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3227727 G
1 G
3227728 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3229560 original size:21 final size:21
Alignment explanation
Indices: 3229531--3229575 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3229521 AAGTTTTCAT
*
3229531 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3229551 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3229573 TTT
1 TTT
3229576 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3231811 original size:13 final size:13
Alignment explanation
Indices: 3231793--3231818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3231783 CAATTTTTTG
3231793 TGTATCGATACAT
1 TGTATCGATACAT
3231806 TGTATCGATACAT
1 TGTATCGATACAT
3231819 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3234536 original size:21 final size:20
Alignment explanation
Indices: 3234485--3234538 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
3234475 CATTTTAGAC
3234485 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
3234505 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
3234525 ATTGTATTGATACA
1 A-TGTATCGATACA
3234539 AATTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:3237347 original size:78 final size:79
Alignment explanation
Indices: 3237216--3237418 Score: 232
Period size: 79 Copynumber: 2.6 Consensus size: 79
3237206 CAACGATGTT
* * * ** * *
3237216 TTTATTTCCAAAACACCAATTTTCCACCATCAGGGG-TACTCCAACCCTGTTA-TTCCCGAGGGG
1 TTTATTTCTAAAACATCAATTTTTCACCAT-AGGGGATACTCCAACCCCATTATTTCCC-AAGCG
* *
3237279 ATACT-CTAACCTGGC
64 ATACTCCAAACCCGGC
* * * *
3237294 TTTATTTTTAAAACATCAATTTTTCACAATTGGGGATACTCCAACCCCATTATTTCTCAAGCGAT
1 TTTATTTCTAAAACATCAATTTTTCACCATAGGGGATACTCCAACCCCATTATTTCCCAAGCGAT
3237359 ACTCCAAACCCGGC
66 ACTCCAAACCCGGC
* *
3237373 CTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACC
1 TTTATTTCTAAAACATCAATTTTTCACCATAGGGGATACTCCAACC
3237419 TTGGTTATAT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 4 0.04
78 47 0.45
79 54 0.51
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (79 bp):
TTTATTTCTAAAACATCAATTTTTCACCATAGGGGATACTCCAACCCCATTATTTCCCAAGCGAT
ACTCCAAACCCGGC
Found at i:3243369 original size:13 final size:13
Alignment explanation
Indices: 3243351--3243377 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3243341 ACATTATGCT
3243351 TTGTATCGATACA
1 TTGTATCGATACA
3243364 TTGTATCGATACA
1 TTGTATCGATACA
3243377 T
1 T
3243378 GTTCATTGTA
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:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3243407 original size:20 final size:19
Alignment explanation
Indices: 3243361--3243417 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
3243351 TTGTATCGAT
*
3243361 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
3243380 TCATTGTATTGATACATGG
1 ACATTGTATCGATACATGG
3243399 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
3243418 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:3243488 original size:20 final size:20
Alignment explanation
Indices: 3243446--3243496 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3243436 CTACCACTGT
* *
3243446 TTGTATCGATACATGGTACA
1 TTGTATAGATACATGATACA
*
3243466 TTGTATTGATACATGATGA-A
1 TTGTATAGATACATGAT-ACA
3243486 TTGTATAGATA
1 TTGTATAGATA
3243497 TATTGCTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGTATAGATACATGATACA
Found at i:3249617 original size:20 final size:20
Alignment explanation
Indices: 3249592--3249630 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3249582 GAAATTTTCC
*
3249592 AGAATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
3249612 AGAATGTATCGATACATTG
1 AGAATGTATCGATACATTG
3249631 TATCGATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:3249634 original size:13 final size:13
Alignment explanation
Indices: 3249616--3249641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3249606 TATTGAAGAA
3249616 TGTATCGATACAT
1 TGTATCGATACAT
3249629 TGTATCGATACAT
1 TGTATCGATACAT
3249642 GGGTTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3249803 original size:20 final size:20
Alignment explanation
Indices: 3249762--3249806 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3249752 AATCTTTTAC
*
3249762 AAATTCTTCATTTTCACTTCA
1 AAATACTTCATTTTCAC-TCA
3249783 AAATACTTCATTTTTCA-TCA
1 AAATACTTCA-TTTTCACTCA
3249803 AAAT
1 AAAT
3249807 TATCAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATACTTCATTTTCACTCA
Found at i:3252207 original size:20 final size:19
Alignment explanation
Indices: 3252161--3252217 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
3252151 TTGTATTGAT
*
3252161 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
3252180 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
3252199 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
3252218 AAATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:3252271 original size:20 final size:20
Alignment explanation
Indices: 3252246--3252299 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3252236 CTACCACTGT
*
3252246 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
3252266 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
3252286 TTGTATCGATACAT
1 TTGTATCGATACAT
3252300 TACTTCTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:3259876 original size:15 final size:15
Alignment explanation
Indices: 3259856--3259894 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
3259846 TTTTTTTTTT
3259856 CAAAAAAAAACAAAA
1 CAAAAAAAAACAAAA
3259871 CAAAAAAAAACAAAA
1 CAAAAAAAAACAAAA
3259886 -AAAGAAAAA
1 CAAA-AAAAA
3259895 GAGAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAACAAAA
Found at i:3261233 original size:59 final size:60
Alignment explanation
Indices: 3260878--3261433 Score: 647
Period size: 61 Copynumber: 9.2 Consensus size: 60
3260868 CTTTCAATCT
* * * * * *
3260878 TCAAAGAGCAGGGCAC-TTTCCTTTCAATGCCCACACATGTTGGTGGCACCTTCTAGTCC
1 TCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * * *
3260937 TC-AAGAGCAGGATGACTTTTCCATTTAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * * * *
3260997 TCAAAGAGCAGGACACCTTTTCC-TTTAGAAGACCATACAAGTTGGTGGCACCTTTCAATCC
1 TCAAAGAGCAGGAC-GCTTTTCCTTTTA-AAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* *
3261058 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCT
1 TCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * *
3261119 TCAAAGAGTAGGACGCCTTTTCTTTTTAAATCCCACACAAGTTGGTGGCACCTTCCAGTCC
1 TCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* *
3261180 TCAAAGAGCAGGATGC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAATCC
1 TCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * *
3261239 TCAAAGAGCAAGATG-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCC
1 TCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * * * *
3261298 TTAAAGAGCAGGATGC-TTTCCTTTCAAAGCTCACACAAGTTGGTGGCACCTTCTAGTCC
1 TCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * * ** ** **
3261357 TCAAAGATCAGGGCACTTTCTCCTTGAAAAAAGCCCACATGAGTTGGTGGCACCTTTAAGTCC
1 TCAAAGAGCAGGACGCTTT-TCCTT--TTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
3261420 TCAAAGAGCAGGAC
1 TCAAAGAGCAGGAC
3261434 ACACTTCATT
Statistics
Matches: 432, Mismatches: 52, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
58 9 0.02
59 163 0.38
60 45 0.10
61 170 0.39
62 4 0.01
63 41 0.09
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (60 bp):
TCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
Found at i:3261513 original size:42 final size:43
Alignment explanation
Indices: 3261417--3261517 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 43
3261407 CACCTTTAAG
*
3261417 TCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTTTCCTTTG
1 TCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTTTCCTTTA
* * * * * *
3261460 TCCTTAGAGAGCATGACGCATTTTATTTCCTTTTTTT-CTTTA
1 TCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTTTCCTTTA
3261502 TCCTCAAAGAGCAGGA
1 TCCTCAAAGAGCAGGA
3261518 TGTACTCCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 17 0.35
43 31 0.65
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (43 bp):
TCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTTTCCTTTA
Found at i:3261604 original size:34 final size:34
Alignment explanation
Indices: 3261492--3261621 Score: 107
Period size: 34 Copynumber: 3.6 Consensus size: 34
3261482 TTATTTCCTT
* *
3261492 TTTTTCTTTATCCTCAAAGAGCAGGATGTACTCC
1 TTTTCCTTTATCCTCAAAGAGCAGAATGTACTCC
* * * ** * *
3261526 TTTGTCCTTTGTCTTCAAGGAAAAAGACCCATTTCATTCTC
1 TTT-TCCTTTATCCTCAAAG-AGCAGA---ATGT-ACTC-C
3261567 TTTTCCTTTATCCTCAAAGAGCAGAATGTACTCC
1 TTTTCCTTTATCCTCAAAGAGCAGAATGTACTCC
*
3261601 TTTTCCTTTATCCTTAAAGAG
1 TTTTCCTTTATCCTCAAAGAG
3261622 TAGGACACAT
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
34 24 0.33
35 15 0.21
36 6 0.08
39 7 0.10
40 16 0.22
41 4 0.06
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (34 bp):
TTTTCCTTTATCCTCAAAGAGCAGAATGTACTCC
Found at i:3261644 original size:75 final size:74
Alignment explanation
Indices: 3261484--3261644 Score: 186
Period size: 75 Copynumber: 2.2 Consensus size: 74
3261474 GACGCATTTT
* * *
3261484 ATTTCC-TTT-TTTTCTTTATCCTCAAAGAGCAGGATGTACTCCTTTGTCCTTTGTCTTCAAGGA
1 ATTTCCTTTTCTTTTCTTTATCCTCAAAGAGCAGAATGTACTCCTTTGTCCTTTATCTTCAAAGA
*
3261547 AAAAGACCC
66 AAAAGACAC
* *
3261556 ATTTCATTCTCTTTTCCTTTATCCTCAAAGAGCAGAATGTACTCCTTT-TCCTTTATCCTT-AAA
1 ATTTCCTTTTCTTTT-CTTTATCCTCAAAGAGCAGAATGTACTCCTTTGTCCTTTAT-CTTCAAA
** *
3261619 GAGTAGGACAC
64 GAAAAAGACAC
3261630 ATTTTCCTTTTCTTT
1 A-TTTCCTTTTCTTT
3261645 CCCCTTCTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
72 5 0.07
73 2 0.03
74 21 0.29
75 45 0.62
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (74 bp):
ATTTCCTTTTCTTTTCTTTATCCTCAAAGAGCAGAATGTACTCCTTTGTCCTTTATCTTCAAAGA
AAAAGACAC
Found at i:3262287 original size:50 final size:50
Alignment explanation
Indices: 3262212--3262306 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
3262202 TTTTTACAAT
* *
3262212 TTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATACATTATTCA
1 TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTATTCA
*
3262262 TTGTATCGATACATTTTAGGTTTTACCCAGATGTATCGATACATT
1 TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATT
3262307 TAGGCATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (50 bp):
TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTATTCA
Found at i:3264778 original size:51 final size:51
Alignment explanation
Indices: 3264702--3264820 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
3264692 TTATTTTTGA
* ** *
3264702 GGGGATACTCCAACCTCGGTTTTATTTTTAAAACATAGATTTTTCACAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATAGATTTTTCACAATC
* * *
3264753 GGGGATACTCTAACCCCGGCCTTATTTCTAAAACATTGATTTTTCACCATC
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATAGATTTTTCACAATC
3264804 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
3264821 ATTATTTCTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATAGATTTTTCACAATC
Found at i:3264920 original size:78 final size:79
Alignment explanation
Indices: 3264756--3264907 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
3264746 CACAATCGGG
* * ** * *
3264756 GATACTCTAACCCCGGCCTTATTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCC
1 GATACTCCAACCTCGGTTTTATTTCCAAAACATTGATTTTCCACCATCGGGGATACTCCAACCCC
3264821 ATTATTTCTAAAAA
66 ATTATTTCTAAAAA
* *
3264835 GATACTCCAACCTCGGTTTTATTTCCAAAACATTGATTTTCCACCAT-TGGGATACTCCAACCCT
1 GATACTCCAACCTCGGTTTTATTTCCAAAACATTGATTTTCCACCATCGGGGATACTCCAACCCC
3264899 ATTATTTCT
66 ATTATTTCT
3264908 GAGGGGGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 24 0.37
79 41 0.63
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCTCGGTTTTATTTCCAAAACATTGATTTTCCACCATCGGGGATACTCCAACCCC
ATTATTTCTAAAAA
Found at i:3269034 original size:19 final size:20
Alignment explanation
Indices: 3269010--3269063 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3269000 ATATTATGCT
* *
3269010 TTGTATTGATACATGTTC-A
1 TTGTATCGATACATGCTCAA
*
3269029 TTGTATCGATACATACTCAA
1 TTGTATCGATACATGCTCAA
3269049 TTGTATCGATACATG
1 TTGTATCGATACATG
3269064 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:3277813 original size:19 final size:20
Alignment explanation
Indices: 3277786--3277835 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3277776 ATCCAGAAGC
*
3277786 ATCGATACATGTTC-ATTGT
1 ATCGATACATGCTCAATTGT
* *
3277805 ATTGATACATACTCAATTGT
1 ATCGATACATGCTCAATTGT
3277825 ATCGATACATG
1 ATCGATACATG
3277836 AAACTGGCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
ATCGATACATGCTCAATTGT
Found at i:3277898 original size:13 final size:13
Alignment explanation
Indices: 3277880--3277907 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3277870 CGATACATGG
3277880 TACATTGTATCGA
1 TACATTGTATCGA
3277893 TACATTGTATCGA
1 TACATTGTATCGA
3277906 TA
1 TA
3277908 TATAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3280071 original size:13 final size:13
Alignment explanation
Indices: 3280053--3280081 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3280043 TGTTGGGCAT
3280053 AATGTATCGATAC
1 AATGTATCGATAC
3280066 AATGTATCGATAC
1 AATGTATCGATAC
3280079 AAT
1 AAT
3280082 TCTTCATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3280096 original size:33 final size:33
Alignment explanation
Indices: 3280054--3280165 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 33
3280044 GTTGGGCATA
* *
3280054 ATGTATCGATACAATGTATCGATACAATTCTTC
1 ATGTATCGATACAATATATCAATACAATTCTTC
*
3280087 ATGTATCGATACAATATATCAATACAATTTTTC
1 ATGTATCGATACAATATATCAATACAATTCTTC
* *
3280120 ATGTATTGATACAATATATCAATACAATGTC-CC
1 ATGTATCGATACAATATATCAATACAAT-TCTTC
*
3280153 ATGTATTGATACA
1 ATGTATCGATACA
3280166 TTTCACTTAG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
33 71 0.99
34 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACAATATATCAATACAATTCTTC
Found at i:3280239 original size:19 final size:20
Alignment explanation
Indices: 3280194--3280246 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
3280184 GTACCAGTTT
3280194 CATGTATCGATACAATTAAG
1 CATGTATCGATACAATTAAG
*
3280214 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTAAG
*
3280233 TATGTATCGATACA
1 CATGTATCGATACA
3280247 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Found at i:3283879 original size:113 final size:112
Alignment explanation
Indices: 3283673--3283897 Score: 263
Period size: 113 Copynumber: 2.0 Consensus size: 112
3283663 AACTTAGAAG
* * * * * *
3283673 AACATCAAATTTGTCTGATTTTCATAGAAATTCATATTTTTTACATTCTGATCCATTCGTGCCTA
1 AACATCAAATTTGTCTAATTTTCAAAAAAAATCATATTTTATACATTCTAATCCATTCGTGCCTA
* * * * *
3283738 GGAAAATGGGGCACGTATCATCTGAGTTTTGAAAATTTTGAGCCCAAC
66 GAAAAATGGGACACGTACCATATCAGTTTTG-AAATTTTGAGCCCAAC
* *
3283786 AACATCAAATTTGTCTAATTTTCAAAAAAAATCATATTTTATATGA-TCTAATCCATTTGTGCCT
1 AACATCAAATTTGTCTAATTTTCAAAAAAAATCATATTTTATA-CATTCTAATCCATTCGTGCCT
* * * * *
3283850 AGAAAAATGGGATATGTACCCTATCAGTTTTGAAATTTTTAGGCCAAC
65 AGAAAAATGGGACACGTACCATATCAGTTTTGAAATTTTGAGCCCAAC
3283898 CAGAATTTCC
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
112 14 0.15
113 78 0.84
114 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (112 bp):
AACATCAAATTTGTCTAATTTTCAAAAAAAATCATATTTTATACATTCTAATCCATTCGTGCCTA
GAAAAATGGGACACGTACCATATCAGTTTTGAAATTTTGAGCCCAAC
Found at i:3284200 original size:44 final size:43
Alignment explanation
Indices: 3284148--3284274 Score: 105
Period size: 44 Copynumber: 2.9 Consensus size: 43
3284138 TAAAATGCTT
*
3284148 ACATTTGCATTTTAGAAAACATTGGCATTTGCATCATTTCATAT
1 ACATTTGCATTTTAGAAAACATT-GCATTTGCATCATTTCATAC
* * * * *
3284192 GCATTTGCAACTTTATTG-ATAC-TTGCAATTGCATCATTTCATGC
1 ACATTTGC-A-TTT-TAGAAAACATTGCATTTGCATCATTTCATAC
* * **
3284236 ACATGTGCATTTTACATGACATTAGCATTTGCATCATTT
1 ACATTTGCATTTTAGAAAACATT-GCATTTGCATCATTT
3284275 TGTAAGAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
41 1 0.02
42 5 0.08
43 3 0.05
44 44 0.69
45 3 0.05
46 6 0.09
47 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (43 bp):
ACATTTGCATTTTAGAAAACATTGCATTTGCATCATTTCATAC
Found at i:3284270 original size:88 final size:88
Alignment explanation
Indices: 3284148--3284372 Score: 261
Period size: 88 Copynumber: 2.6 Consensus size: 88
3284138 TAAAATGCTT
* * * *
3284148 ACATTTGCATTTTAGAAAACATTGGCATTTGCATCATTTCATATGCATTTGCAACTTTATTGATA
1 ACATCTGCATTTTAGATAACATTAGCATTTGCATCATTTCATATGCATTTGCAACTTTATTGAAA
* *
3284213 CTTGCAATTGCATCATTTCATGC
66 CTTACAATTGCATCATTTCATAC
* * * ** * * *
3284236 ACATGTGCATTTTACATGACATTAGCATTTGCATCATTTTGTAAGAATTTGCCACTTTATTGAAA
1 ACATCTGCATTTTAGATAACATTAGCATTTGCATCATTTCATATGCATTTGCAACTTTATTGAAA
* **
3284301 CTTACAGTTGCATTGTTTCATAC
66 CTTACAATTGCATCATTTCATAC
* * * *
3284324 ATATCTACACTTTAGATAACATTAGTATTTGCATCATTTCATATGCATT
1 ACATCTGCATTTTAGATAACATTAGCATTTGCATCATTTCATATGCATT
3284373 GGCCATTTTA
Statistics
Matches: 110, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
88 110 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (88 bp):
ACATCTGCATTTTAGATAACATTAGCATTTGCATCATTTCATATGCATTTGCAACTTTATTGAAA
CTTACAATTGCATCATTTCATAC
Found at i:3286267 original size:20 final size:20
Alignment explanation
Indices: 3286242--3286306 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
3286232 TACAAGCCAA
3286242 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATTTTTGG
3286262 TGTATCGATAC-A----T--
1 TGTATCGATACAATTTTTGG
3286275 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATTTTTGG
3286295 TGTATCGATACA
1 TGTATCGATACA
3286307 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATTTTTGG
Found at i:3286280 original size:13 final size:13
Alignment explanation
Indices: 3286262--3286320 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
3286252 CAATTTTTGG
3286262 TGTATCGATACAT
1 TGTATCGATACAT
3286275 TGTATCGATACAATTTTT
1 TGTATCGATAC-A----T
3286293 GGTGTATCGATACAT
1 --TGTATCGATACAT
3286308 TGTATCGATACAT
1 TGTATCGATACAT
3286321 ACTTGGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3286284 original size:33 final size:33
Alignment explanation
Indices: 3286242--3286338 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
3286232 TACAAGCCAA
3286242 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATTTTTGGTGTATCGATACAT
3286275 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATTTTTGGTGTATCGATACAT
**
3286308 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATTTTTGGTGTATCGATACA
3286339 AGTTTGGCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 18 0.29
33 44 0.71
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATTTTTGGTGTATCGATACAT
Found at i:3288718 original size:21 final size:21
Alignment explanation
Indices: 3288694--3288739 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3288684 TTTGATGCTG
3288694 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
3288714 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
3288735 ATTTT
1 ATTTT
3288740 ACAAAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:3288878 original size:13 final size:13
Alignment explanation
Indices: 3288860--3288896 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3288850 TATAAACCCC
3288860 CTGTATCGATACA
1 CTGTATCGATACA
3288873 CTGTATCGATACA
1 CTGTATCGATACA
*
3288886 ATGTATCGATA
1 CTGTATCGATA
3288897 TAAAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:3290993 original size:15 final size:15
Alignment explanation
Indices: 3290973--3291002 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3290963 GTTCATCAAT
3290973 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
3290988 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
3291003 CTCAATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:3295105 original size:13 final size:13
Alignment explanation
Indices: 3295087--3295144 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
3295077 CAATTTTTGG
3295087 TGTATCGATACAT
1 TGTATCGATACAT
3295100 TGTATCGATACATACTT
1 TGTATCGATAC--A--T
3295117 GGTGTATCGATACAT
1 --TGTATCGATACAT
3295132 TGTATCGATACAT
1 TGTATCGATACAT
3295145 ACTTGGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
15 2 0.05
17 2 0.05
19 11 0.28
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3295124 original size:19 final size:19
Alignment explanation
Indices: 3295100--3295162 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
3295090 ATCGATACAT
3295100 TGTATCGATACATACTTGG
1 TGTATCGATACATACTTGG
3295119 TGTATCGATAC--A--T--
1 TGTATCGATACATACTTGG
3295132 TGTATCGATACATACTTGG
1 TGTATCGATACATACTTGG
3295151 TGTATCGATACA
1 TGTATCGATACA
3295163 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATACTTGG
Found at i:3295124 original size:32 final size:32
Alignment explanation
Indices: 3295067--3295162 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
3295057 TACAAGCCAA
**
3295067 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATAC-ATACTTGGTGTATCGATACAT
3295100 TGTATCGATACATACTTGGTGTATCGATACAT
1 TGTATCGATACATACTTGGTGTATCGATACAT
3295132 TGTATCGATACATACTTGGTGTATCGATACA
1 TGTATCGATACATACTTGGTGTATCGATACA
3295163 AGTTTGGCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.82
33 11 0.18
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATACTTGGTGTATCGATACAT
Found at i:3295169 original size:19 final size:17
Alignment explanation
Indices: 3295067--3295163 Score: 75
Period size: 19 Copynumber: 5.8 Consensus size: 17
3295057 TACAAGCCAA
3295067 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA---TTGG
3295087 TGTATCGATAC-A-T--
1 TGTATCGATACAATTGG
3295100 TGTATCGATACATACTTGG
1 TGTATCGATACA-A-TTGG
3295119 TGTATCGATAC-A-T--
1 TGTATCGATACAATTGG
3295132 TGTATCGATACATACTTGG
1 TGTATCGATACA-A-TTGG
3295151 TGTATCGATACAA
1 TGTATCGATACAA
3295164 GTTTGGCTAC
Statistics
Matches: 65, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 3 0.05
18 1 0.02
19 24 0.37
20 11 0.17
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (17 bp):
TGTATCGATACAATTGG
Found at i:3295626 original size:46 final size:46
Alignment explanation
Indices: 3295556--3295666 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 46
3295546 ACTATACCTT
* * *
3295556 GTCAAACCT-TTTTCATTCTAGTTTGATGTAATGGTTCTTGCCCTA
1 GTCAAACATCTTTTCATTCTAGTTTGATATAATGGTTCTCGCCCTA
* **
3295601 GTCAAACATCTTTTCATTACT-GTTTGATATGATGGTTCTCGCTTTA
1 GTCAAACATCTTTTCATT-CTAGTTTGATATAATGGTTCTCGCCCTA
3295647 GTCAAACATCTTTTCATTCT
1 GTCAAACATCTTTTCATTCT
3295667 CATTTGACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
45 10 0.17
46 46 0.79
47 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (46 bp):
GTCAAACATCTTTTCATTCTAGTTTGATATAATGGTTCTCGCCCTA
Found at i:3295824 original size:35 final size:35
Alignment explanation
Indices: 3295724--3295812 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 35
3295714 TGGTTTTCGC
*
3295724 CCTAGTCAAACGTCTTTTCATTCCCATTTGTCTGTA
1 CCTAGTCAAAC-TCTTTTCATTCCCATTTGACTGTA
* *
3295760 CTTGGTCAAACTCTTTTCATTCCCATTTGACTGTA
1 CCTAGTCAAACTCTTTTCATTCCCATTTGACTGTA
3295795 CCTAGTCAAACTCTTTTC
1 CCTAGTCAAACTCTTTTC
3295813 GTTACTGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 39 0.81
36 9 0.19
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (35 bp):
CCTAGTCAAACTCTTTTCATTCCCATTTGACTGTA
Found at i:3296045 original size:81 final size:81
Alignment explanation
Indices: 3295855--3296058 Score: 205
Period size: 81 Copynumber: 2.5 Consensus size: 81
3295845 TTAAACATCT
* * * ** *
3295855 TTTTCATTACCATTTGACGTCATGGTTCT-GCCCTGCTCAAACATTTTTTCATTCCCGTTTAAGT
1 TTTTCATTACTATTTGACATGATGGTTCTCGCCCTGCTCAAACATCATTTCATTCCCGTTTAACT
3295919 ATACCCAGTCAAACTC
66 ATACCCAGTCAAACTC
** * * *** * * *
3295935 TTTTTGTTACTATTTGGCCTGACAATTCTCGCCTTAG-TCAAACATCATTTCATTCTCGTTTGAC
1 TTTTCATTACTATTTGACATGATGGTTCTCGCCCT-GCTCAAACATCATTTCATTCCCGTTTAAC
* *
3295999 TATGCCTAGTCAAACTC
65 TATACCCAGTCAAACTC
* *
3296016 TTTTCATTACTATTTGACATGATGGTTCTCACCCTGGTCAAAC
1 TTTTCATTACTATTTGACATGATGGTTCTCGCCCTGCTCAAAC
3296059 TTTTTTCATT
Statistics
Matches: 95, Mismatches: 26, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
80 21 0.22
81 73 0.77
82 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (81 bp):
TTTTCATTACTATTTGACATGATGGTTCTCGCCCTGCTCAAACATCATTTCATTCCCGTTTAACT
ATACCCAGTCAAACTC
Found at i:3296130 original size:46 final size:45
Alignment explanation
Indices: 3296007--3296164 Score: 221
Period size: 45 Copynumber: 3.5 Consensus size: 45
3295997 ACTATGCCTA
*
3296007 GTCAAACTCTTTTCATTACTATTTGACATGATGGTTCTCACCCTG
1 GTCAAACTCTTTTCATTACTATTTGACATGATGGTTCTCGCCCTG
* *
3296052 GTCAAACTTTTTTCATTACTATTTGACGTGATGGTTCTCGCCCTG
1 GTCAAACTCTTTTCATTACTATTTGACATGATGGTTCTCGCCCTG
* *
3296097 GTCAAACATCTTTTCATT-CTAGTTTGACATGATGGTTCTTGCCCTA
1 GTCAAAC-TCTTTTCATTACTA-TTTGACATGATGGTTCTCGCCCTG
*
3296143 GTCAAACATATTTTCATT-CTAT
1 GTCAAAC-TCTTTTCATTACTAT
3296165 CACTACCTGA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 53 0.51
46 50 0.49
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (45 bp):
GTCAAACTCTTTTCATTACTATTTGACATGATGGTTCTCGCCCTG
Found at i:3302294 original size:24 final size:24
Alignment explanation
Indices: 3302267--3302312 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3302257 ATAGGGTTGA
*
3302267 AGTATTCTTGATAAATAAAATTTT
1 AGTATTCTTGATAAAGAAAATTTT
* *
3302291 AGTATTTTTGATGAAGAAAATT
1 AGTATTCTTGATAAAGAAAATT
3302313 GACGTGAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (24 bp):
AGTATTCTTGATAAAGAAAATTTT
Found at i:3304389 original size:24 final size:20
Alignment explanation
Indices: 3304346--3304470 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
3304336 AATAAACTAG
3304346 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
3304366 ATGTATCGATACATCTAGGTAAAAAAACAAA
1 ATGTATCGATACA--T---T----AAA-A-A
*
3304397 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTAAAAA
* * ***
3304417 ATGTATTGATACATTCATCC
1 ATGTATCGATACATTAAAAA
*
3304437 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTAAAAA
*
3304457 ATGTATCAATACAT
1 ATGTATCGATACAT
3304471 CTGGGTAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 57 0.70
21 1 0.01
22 3 0.04
25 1 0.01
26 1 0.01
29 4 0.05
30 1 0.01
31 14 0.17
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:3307236 original size:19 final size:19
Alignment explanation
Indices: 3307212--3307279 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
3307202 AATTCAACGA
3307212 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3307231 TTTGTATCAATAC--AA--
1 TTTGTATCGATACATAAGT
*
3307246 --TGTATCGATTCATAAGT
1 TTTGTATCGATACATAAGT
*
3307263 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3307280 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
13 9 0.23
15 2 0.05
17 2 0.05
19 26 0.67
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3307250 original size:32 final size:32
Alignment explanation
Indices: 3307214--3307276 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3307204 TTCAACGATT
*
3307214 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
* *
3307246 TGTATCGATTCATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
3307277 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:3307337 original size:13 final size:13
Alignment explanation
Indices: 3307319--3307344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3307309 CATTTTTCTG
3307319 TGTATCGATACAT
1 TGTATCGATACAT
3307332 TGTATCGATACAT
1 TGTATCGATACAT
3307345 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3307341 original size:33 final size:33
Alignment explanation
Indices: 3307299--3307365 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3307289 GCCAAGGAAA
***
3307299 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3307332 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3307365 T
1 T
3307366 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3309827 original size:54 final size:51
Alignment explanation
Indices: 3309711--3309833 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
3309701 CAATTCTCCG
* * *
3309711 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
*
3309762 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAACACAAATTTTCT-A
*
3309816 CAATCGAGGATACTCCAA
1 CAATCGGGGATACTCCAA
3309834 TCTCGTTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 31 0.50
53 1 0.02
54 30 0.48
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
Found at i:3309868 original size:28 final size:28
Alignment explanation
Indices: 3309818--3309894 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
3309808 ATTTTTCACA
* * * **
3309818 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
3309846 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
3309874 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3309895 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:3309997 original size:79 final size:79
Alignment explanation
Indices: 3309848--3310051 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
3309838 GTTATTTCAT
** * **
3309848 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAATAT
* * *
3309913 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
3309927 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCAATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAAT-A
3309991 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
3310006 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC
3310052 GTTATTATCT
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 100 0.97
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:3312015 original size:63 final size:63
Alignment explanation
Indices: 3311912--3312055 Score: 191
Period size: 63 Copynumber: 2.3 Consensus size: 63
3311902 TCACGCTCCT
* * *
3311912 ATGTATTGATACTTTTCATAATGTATCAATATATTCATTTGAAATTTATAACCGTTGGGCCCA
1 ATGTATCGATACTTTTCATAATGTATCAATACATTCATTTGAAATTTATAACCGTTAGGCCCA
* * * *
3311975 ATGTATCGATACTTTTCATAATGTATCGATACATGT-ATTTGATATTTATAGCCGTTAGGCTCA
1 ATGTATCGATACTTTTCATAATGTATCAATACAT-TCATTTGAAATTTATAACCGTTAGGCCCA
* *
3312038 ATGTATCAATACATTTCA
1 ATGTATCGATACTTTTCA
3312056 CCATATATTG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 70 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (63 bp):
ATGTATCGATACTTTTCATAATGTATCAATACATTCATTTGAAATTTATAACCGTTAGGCCCA
Found at i:3312069 original size:63 final size:63
Alignment explanation
Indices: 3311948--3312070 Score: 156
Period size: 63 Copynumber: 2.0 Consensus size: 63
3311938 CAATATATTC
* * * * *
3311948 ATTTGAAATTTATAACCGTTGGGCCCAATGTATCGATACTTTTCATAATGTATCGATACATGT
1 ATTTGAAATTTATAACCGTTAGGCCCAATGTATCAATACATTTCACAATATATCGATACATGT
* * * * *
3312011 ATTTGATATTTATAGCCGTTAGGCTCAATGTATCAATACATTTCACCATATATTGATACA
1 ATTTGAAATTTATAACCGTTAGGCCCAATGTATCAATACATTTCACAATATATCGATACA
3312071 ATCCTTCATG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (63 bp):
ATTTGAAATTTATAACCGTTAGGCCCAATGTATCAATACATTTCACAATATATCGATACATGT
Found at i:3312096 original size:13 final size:13
Alignment explanation
Indices: 3312078--3312107 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3312068 ACAATCCTTC
3312078 ATGTATCGATACA
1 ATGTATCGATACA
3312091 ATGTATCGATACA
1 ATGTATCGATACA
3312104 ATGT
1 ATGT
3312108 GAGTTTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3312787 original size:16 final size:16
Alignment explanation
Indices: 3312749--3312790 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
3312739 TTGTTAAGAC
3312749 TTGTAAATAT-AGGCT
1 TTGTAAATATAAGGCT
3312764 TTGTAAATATAAGG-T
1 TTGTAAATATAAGGCT
3312779 TTGGTAAATATA
1 TT-GTAAATATA
3312791 GGACATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (16 bp):
TTGTAAATATAAGGCT
Done.