Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold537
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: 82277
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.29
Warning! 15129 characters in sequence are not A, C, G, or T
Found at i:3701 original size:29 final size:29
Alignment explanation
Indices: 3667--3791 Score: 128
Period size: 29 Copynumber: 4.2 Consensus size: 29
3657 AAAAAATTTG
*
3667 CATTTTGATCCCTCAAC-TTTCTAAAATTA
1 CATTTTGATCCCTAAACTTTTCT-AAATTA
* *
3696 CATTTT-AACCCTTTAACTTTTTCTAAATTA
1 CATTTTGATCCC-TAAAC-TTTTCTAAATTA
**
3726 CATTTCAATCCCTAAACTTTTCTAAATTA
1 CATTTTGATCCCTAAACTTTTCTAAATTA
* *
3755 CATTTTTACCCCTAAACTTTCTCTAAATTA
1 CATTTTGATCCCTAAACTTT-TCTAAATTA
*
3785 CGTTTTG
1 CATTTTG
3792 GCCCAAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
28 4 0.05
29 39 0.48
30 29 0.36
31 9 0.11
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (29 bp):
CATTTTGATCCCTAAACTTTTCTAAATTA
Found at i:3726 original size:30 final size:29
Alignment explanation
Indices: 3684--3790 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 29
3674 ATCCCTCAAC
*
3684 TTTCTAAAATTACATTTTAACCCTTTAACTT
1 TTTCT-AAATTACATTTTAACCC-TAAACTT
*
3715 TTTCTAAATTACATTTCAATCCCTAAAC-T
1 TTTCTAAATTACATTTTAA-CCCTAAACTT
*
3744 TTTCTAAATTACATTTTTACCCCTAAACTT
1 TTTCTAAATTACA-TTTTAACCCTAAACTT
* *
3774 TCTCTAAATTACGTTTT
1 TTTCTAAATTACATTTT
3791 GGCCCAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
29 26 0.39
30 33 0.49
31 8 0.12
ACGTcount: A:0.31, C:0.21, G:0.01, T:0.47
Consensus pattern (29 bp):
TTTCTAAATTACATTTTAACCCTAAACTT
Found at i:3737 original size:59 final size:59
Alignment explanation
Indices: 3674--3785 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
3664 TTGCATTTTG
* * * *
3674 ATCCCTCAAC-TTTCTAAAATTACATTTTAACCCTTTAACTTTTTCTAAATTACATTTCA
1 ATCCCTAAACTTTTCT-AAATTACATTTTAACCCCTAAACTTTCTCTAAATTACATTTCA
*
3733 ATCCCTAAACTTTTCTAAATTACATTTTTACCCCTAAACTTTCTCTAAATTAC
1 ATCCCTAAACTTTTCTAAATTACATTTTAACCCCTAAACTTTCTCTAAATTAC
3786 GTTTTGGCCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 42 0.89
60 5 0.11
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (59 bp):
ATCCCTAAACTTTTCTAAATTACATTTTAACCCCTAAACTTTCTCTAAATTACATTTCA
Found at i:3812 original size:59 final size:60
Alignment explanation
Indices: 3684--3814 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 60
3674 ATCCCTCAAC
* * * * *
3684 TTTCTAAAATTACATTTTAACCCTTTAACTTTTTCTAAATTACATTTCAATCCCTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACTTTCTCTAAATTACATTTCAAGCCCTAAAAT
* * **
3744 TTTCT-AAATTACATTTTTACCCCTAAACTTTCTCTAAATTACGTTT-TGGCCC-AAAAT
1 TTTCTAAAATTACATTTTAACCCCTAAACTTTCTCTAAATTACATTTCAAGCCCTAAAAT
3801 TTTCTCAAAATTAC
1 TTTCT-AAAATTAC
3815 GTTTAAGCCC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 9 0.15
58 3 0.05
59 43 0.72
60 5 0.08
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (60 bp):
TTTCTAAAATTACATTTTAACCCCTAAACTTTCTCTAAATTACATTTCAAGCCCTAAAAT
Found at i:3824 original size:29 final size:31
Alignment explanation
Indices: 3772--3834 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
3762 ACCCCTAAAC
* * *
3772 TTTCTCTAAATTACGTTT-TGGCCC-AAAAT
1 TTTCTCAAAATTACGTTTAAGCCCCAAAAAT
3801 TTTCTCAAAATTACGTTTAAGCCCCAAAAAT
1 TTTCTCAAAATTACGTTTAAGCCCCAAAAAT
3832 TTT
1 TTT
3835 GCTGCGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.59
30 4 0.14
31 8 0.28
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (31 bp):
TTTCTCAAAATTACGTTTAAGCCCCAAAAAT
Found at i:3829 original size:30 final size:29
Alignment explanation
Indices: 3759--3834 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
3749 AAATTACATT
* * *
3759 TTTA-CCCCTAAACTTTCTCTAAATTACG
1 TTTAGCCCCAAAATTTTCTCAAAATTACG
* *
3787 TTTTGGCCCAAAATTTTCTCAAAATTACG
1 TTTAGCCCCAAAATTTTCTCAAAATTACG
3816 TTTAAGCCCCAAAAATTTT
1 TTT-AGCCCC-AAAATTTT
3835 GCTGCGTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 3 0.08
29 23 0.61
30 4 0.11
31 8 0.21
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTAGCCCCAAAATTTTCTCAAAATTACG
Found at i:4135 original size:3 final size:3
Alignment explanation
Indices: 4129--4177 Score: 53
Period size: 3 Copynumber: 14.7 Consensus size: 3
4119 CGGTTTTGAG
4129 GAA GAA GAA GAA GAA GAA GAAA GAAA GAAA GAAA GAA GAA GAAA GAA
1 GAA GAA GAA GAA GAA GAA G-AA G-AA G-AA G-AA GAA GAA G-AA GAA
4176 GA
1 GA
4178 GGGAAAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 26 0.59
4 18 0.41
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4154 original size:4 final size:4
Alignment explanation
Indices: 4145--4195 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
4135 GAAGAAGAAG
** *
4145 AAGA AAGA AAGA AAGA AAG- AAG- AAGA AAG- AAGA GGGA AAGA AAAA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
4190 AAGA AA
1 AAGA AA
4196 AAATTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 9 0.23
4 30 0.77
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:4165 original size:25 final size:28
Alignment explanation
Indices: 4133--4194 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
4123 TTTGAGGAAG
* *
4133 AAGAAGAAG-AAGAAGAAAGAAAGAAAGA
1 AAGAAGAAGAAAGAAG-AGGAAAGAAAAA
4161 AAGAAGAAGAAAGAAGAGGGAAAGAAAAA
1 AAGAAGAAGAAAGAAGA-GGAAAGAAAAA
4190 AAGAA
1 AAGAA
4195 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (28 bp):
AAGAAGAAGAAAGAAGAGGAAAGAAAAA
Found at i:4522 original size:16 final size:15
Alignment explanation
Indices: 4494--4539 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
4484 GCAGGCCGAA
4494 AAAAGGAAA-AAAAAG
1 AAAA-GAAAGAAAAAG
4509 AGAAAGAAAGAAAAAG
1 A-AAAGAAAGAAAAAG
4525 AAAAGAAAAGAAAAA
1 AAAAG-AAAGAAAAA
4540 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:4548 original size:26 final size:25
Alignment explanation
Indices: 4492--4557 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
4482 CAGCAGGCCG
* *
4492 AAAAAAGGAAAAAAAAGAGAAAGAA
1 AAAAAAAGAAAAAAAAGAGAAAAAA
*
4517 AGAAAAAGAAAAGAAAAGA-AAAAAA
1 AAAAAAAGAAAA-AAAAGAGAAAAAA
*
4542 TAAAAAAATAAAAAAA
1 -AAAAAAAGAAAAAAA
4558 GGGTTCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 18 0.53
26 16 0.47
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAAGAGAAAAAA
Found at i:4549 original size:16 final size:15
Alignment explanation
Indices: 4492--4558 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
4482 CAGCAGGCCG
*
4492 AAAAAAGGAAAAAAA
1 AAAAAAAGAAAAAAA
* * *
4507 AGAGAAAGAAAGAAA
1 AAAAAAAGAAAAAAA
* *
4522 AAGAAAAGAAAAGAA
1 AAAAAAAGAAAAAAA
* *
4537 AAAAATA-AAAAAAT
1 AAAAAAAGAAAAAAA
4551 AAAAAAAG
1 AAAAAAAG
4559 GGTTCAATTT
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:4556 original size:10 final size:10
Alignment explanation
Indices: 4492--4557 Score: 62
Period size: 10 Copynumber: 6.4 Consensus size: 10
4482 CAGCAGGCCG
*
4492 AAAAAAGGAA
1 AAAAAAGAAA
*
4502 AAAAAAGAGA
1 AAAAAAGAAA
*
4512 AAGAAAGAAA
1 AAAAAAGAAA
4522 AAGAAAAGAAA
1 AA-AAAAGAAA
4533 AGAAAAA-AATA
1 A-AAAAAGAA-A
*
4544 AAAAAATAAA
1 AAAAAAGAAA
4554 AAAA
1 AAAA
4558 GGGTTCAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
10 30 0.64
11 16 0.34
12 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:4557 original size:24 final size:26
Alignment explanation
Indices: 4500--4558 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
4490 CGAAAAAAGG
4500 AAAAAAAAGAGAAAGAAAGAAAAAGAA
1 AAAAAAA-GAGAAAGAAAGAAAAAGAA
* *
4527 AAGAAAAGA-AAA-AAATAAAAA-AA
1 AAAAAAAGAGAAAGAAAGAAAAAGAA
4550 TAAAAAAAG
1 -AAAAAAAG
4559 GGTTCAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 15 0.54
25 3 0.11
26 2 0.07
27 6 0.21
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (26 bp):
AAAAAAAGAGAAAGAAAGAAAAAGAA
Found at i:5137 original size:18 final size:17
Alignment explanation
Indices: 5081--5137 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
5071 TAAAAAATCG
*
5081 AAAAATTT-GTGTTTAA
1 AAAAATTTCGTGTTTTA
* * *
5097 AAAAATCTCCGTGGTTTC
1 AAAAAT-TTCGTGTTTTA
5115 AAAAATATTCGTGTTTTA
1 AAAAAT-TTCGTGTTTTA
5133 AAAAA
1 AAAAA
5138 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 24 0.77
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTA
Found at i:5201 original size:35 final size:35
Alignment explanation
Indices: 5162--5649 Score: 491
Period size: 35 Copynumber: 13.8 Consensus size: 35
5152 AGAATCTGTT
* *
5162 TTTC-AAATTTTTCGTGTTTTCAAAAAATTCCCTTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAATTCCCGTG
* * *
5197 TTTCAATAATCTTCGTGTTTTCAAAAATTCCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
* *
5232 TTTCAAAAATTTTCATGTTTTCAAAAATTCCCATG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
* * **
5267 TTTTAAAAATTTTTGTGTTTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
** *
5302 TTTCAAAAATCCTCGTGTTTTCAAAAATTCCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
* * * *
5337 TTCCAAAAAATTTCGTGTTTCCAAAAATTCCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
* *
5372 ATTCAAAAAATTTTCGTGTTTTCTAAAAATTTCCGTG
1 TTTC-AAAAATTTTCGTGTTTTC-AAAAATTCCCGTG
*
5409 TTTCAAAAATTTTCATGTTTTCAAAAAATTCCCGTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAATTCCCGTG
* ** *
5445 TTTTAAAAA-TTTCTGTGTTTTCAAAAATTTTCATG
1 TTTCAAAAATTTTC-GTGTTTTCAAAAATTCCCGTG
* * * *
5480 TTTTCAAAAAATTTCCATGTTTT-AAAAATTTCAGTG
1 -TTTC-AAAAATTTTCGTGTTTTCAAAAATTCCCGTG
* ***
5516 -TTCTAAAATATTTTTGTGTTTTCAAAAATTTTTGTG
1 TTTC-AAAA-ATTTTCGTGTTTTCAAAAATTCCCGTG
** *
5552 TTTCAAAAATCCTCGTGTTTTCAAAAATTCCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
**
5587 TTTCAAAAATTTTCGTGTTTTCAAAAATTTTTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAA-TTCCCGTG
*
5623 TTTTCAAAAATTCTCGTG-TTTCAAAAA
1 -TTTCAAAAATTTTCGTGTTTTCAAAAA
5650 CTTTCGTGTT
Statistics
Matches: 374, Mismatches: 67, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
34 7 0.02
35 204 0.55
36 116 0.31
37 44 0.12
38 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (35 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTCCCGTG
Found at i:5235 original size:17 final size:16
Alignment explanation
Indices: 5171--5715 Score: 320
Period size: 18 Copynumber: 30.6 Consensus size: 16
5161 TTTTCAAATT
5171 TTTCGTGTTTTCAAAAAA
1 TTTCGTG-TTTC-AAAAA
* * *
5189 TTCCCTTGTTTCAATAA
1 TT-TCGTGTTTCAAAAA
5206 TCTTCGTGTTTTCAAAAA
1 T-TTCGTG-TTTCAAAAA
*
5224 TTCCGGTGTTTCAAAAA
1 TTTC-GTGTTTCAAAAA
*
5241 TTTTCATGTTTTCAAAAA
1 -TTTCGTG-TTTCAAAAA
* * *
5259 TTCCCATGTTTTAAAAA
1 TT-TCGTGTTTCAAAAA
*
5276 TTTTTGTGTTTTCAAAAA
1 -TTTCGTG-TTTCAAAAA
5294 TTTTCGTGTTTCAAAAA
1 -TTTCGTGTTTCAAAAA
*
5311 TCCTCGTGTTTTCAAAAA
1 T-TTCGTG-TTTCAAAAA
* *
5329 TTCCGGTGTTCCAAAAAA
1 TTTC-GTGTTTC-AAAAA
5347 TTTCGTGTTTCCAAAAA
1 TTTCGTGTTT-CAAAAA
* *
5364 TTCCGGTGATTCAAAAAA
1 TTTC-GTGTTTC-AAAAA
5382 TTTTCGTGTTTTCTAAAAA
1 -TTTCGTG-TTTC-AAAAA
5401 TTTCCGTGTTTCAAAAA
1 TTT-CGTGTTTCAAAAA
*
5418 TTTTCATGTTTTCAAAAAA
1 -TTTCGTG-TTTC-AAAAA
* *
5437 TTCCCGTGTTTTAAAAA
1 TT-TCGTGTTTCAAAAA
5454 TTTCTGTGTTTTCAAAAA
1 TTTC-GTG-TTTCAAAAA
*
5472 TTTTCATGTTTTCAAAAAA
1 -TTTCGTG-TTTC-AAAAA
* *
5491 TTTCCATGTTTTAAAAA
1 TTT-CGTGTTTCAAAAA
5508 TTTCAGTG-TTCTAAAATA
1 TTTC-GTGTTTC-AAAA-A
*
5526 TTTTTGTGTTTTCAAAAA
1 -TTTCGTG-TTTCAAAAA
*
5544 TTTTTGTGTTTCAAAAA
1 -TTTCGTGTTTCAAAAA
*
5561 TCCTCGTGTTTTCAAAAA
1 T-TTCGTG-TTTCAAAAA
*
5579 TTCCGGTGTTTCAAAAA
1 TTTC-GTGTTTCAAAAA
5596 TTTTCGTGTTTTCAAAAA
1 -TTTCGTG-TTTCAAAAA
5614 TTTTTCGTGTTTTCAAAAA
1 --TTTCGTG-TTTCAAAAA
5633 TTCTCGTGTTTCAAAAA
1 TT-TCGTGTTTCAAAAA
*
5650 CTTTCGTGTTTTTTTTTTAAAAA
1 -TTTCGTG------TTTCAAAAA
* *
5673 TTTAGTGCTTC-AAAA
1 TTTCGTGTTTCAAAAA
5688 TTCTCGTGTTTCAAAAA
1 TT-TCGTGTTTCAAAAA
5705 CTTTCGTGTTT
1 -TTTCGTGTTT
5716 TTTTAAAAAA
Statistics
Matches: 427, Mismatches: 49, Indels: 103
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.01
16 15 0.04
17 151 0.35
18 174 0.41
19 64 0.15
20 3 0.01
22 6 0.01
23 8 0.02
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (16 bp):
TTTCGTGTTTCAAAAA
Found at i:5703 original size:55 final size:53
Alignment explanation
Indices: 5629--5757 Score: 204
Period size: 53 Copynumber: 2.4 Consensus size: 53
5619 CGTGTTTTCA
* *
5629 AAAATTCTCGTGTTTCAAAAACTTTCGTGTTTTTTTTTTAAAAATTTAGTGCTTC
1 AAAATTCTCGTGTTTCAAAAACTTTCGTG--TTTTTTTAAAAAAATTAGTGCTTC
*
5684 AAAATTCTCGTGTTTCAAAAACTTTCGTGTTTTTTTAAAAAAATTCGTGCTTC
1 AAAATTCTCGTGTTTCAAAAACTTTCGTGTTTTTTTAAAAAAATTAGTGCTTC
*
5737 AAAATTCTCGTGTTTTAAAAA
1 AAAATTCTCGTGTTTCAAAAA
5758 TAAAAGTCTC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
53 41 0.59
55 29 0.41
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (53 bp):
AAAATTCTCGTGTTTCAAAAACTTTCGTGTTTTTTTAAAAAAATTAGTGCTTC
Found at i:5758 original size:17 final size:17
Alignment explanation
Indices: 5173--5661 Score: 271
Period size: 17 Copynumber: 27.5 Consensus size: 17
5163 TTCAAATTTT
5173 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTT--AAAAATTC
* * * *
5192 CCTTGTTTCAATAA-TC
1 TCGTGTTTTAAAAATTC
5208 TTCGTGTTTTCAAAAATTC
1 -TCGTGTTTT-AAAAATTC
* *
5227 -CGGTGTTTCAAAAATTT
1 TC-GTGTTTTAAAAATTC
*
5244 TCATGTTTTCAAAAATTC
1 TCGTGTTTT-AAAAATTC
* * *
5262 CCATGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTC
* *
5279 TTGTGTTTTCAAAAATTT
1 TCGTGTTTT-AAAAATTC
* *
5297 TCGTGTTTCAAAAATCC
1 TCGTGTTTTAAAAATTC
5314 TCGTGTTTTCAAAAATTC
1 TCGTGTTTT-AAAAATTC
**
5332 -CGGTGTTCCAAAAAATT-
1 TC-GTGTT-TTAAAAATTC
*
5349 TCGTGTTTCCAAAAATTC
1 TCGTGTTT-TAAAAATTC
** *
5367 -CGGTGATTCAAAAAATTT
1 TC-GTG-TTTTAAAAATTC
5385 TCGTGTTTTCTAAAAATT-
1 TCGTG-TTT-TAAAAATTC
* *
5403 TCCGTGTTTCAAAAATTT
1 T-CGTGTTTTAAAAATTC
*
5421 TCATGTTTTCAAAAAATTC
1 TCGTGTTTT--AAAAATTC
*
5440 CCGTGTTTTAAAAATT-
1 TCGTGTTTTAAAAATTC
*
5456 TCTGTGTTTTCAAAAATTT
1 TC-GTGTTTT-AAAAATTC
*
5475 TCATGTTTTCAAAAAATT-
1 TCGTGTTTT--AAAAATTC
*
5493 TCCATGTTTTAAAAATT-
1 T-CGTGTTTTAAAAATTC
* *
5510 TCAGTGTTCTAAAATATTT
1 TC-GTGTTTTAAAA-ATTC
* *
5529 TTGTGTTTTCAAAAATTT
1 TCGTGTTTT-AAAAATTC
* * *
5547 TTGTGTTTCAAAAATCC
1 TCGTGTTTTAAAAATTC
5564 TCGTGTTTTCAAAAATTC
1 TCGTGTTTT-AAAAATTC
* *
5582 -CGGTGTTTCAAAAATTT
1 TC-GTGTTTTAAAAATTC
*
5599 TCGTGTTTTCAAAAATTTT
1 TCGTGTTTT-AAAAA-TTC
5618 TCGTGTTTTCAAAAATTC
1 TCGTGTTTT-AAAAATTC
*
5636 TCGTGTTTCAAAAACTT-
1 TCGTGTTTTAAAAA-TTC
5653 TCGTGTTTT
1 TCGTGTTTT
5662 TTTTTTAAAA
Statistics
Matches: 375, Mismatches: 59, Indels: 74
0.74 0.12 0.15
Matches are distributed among these distances:
16 4 0.01
17 148 0.39
18 147 0.39
19 76 0.20
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTC
Found at i:6392 original size:14 final size:16
Alignment explanation
Indices: 6353--6395 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
6343 TTTCTCAAAA
6353 TCTTCTCTTTCTTCTC
1 TCTTCTCTTTCTTCTC
6369 TCTTGCTCTTTCTTC-C
1 TCTT-CTCTTTCTTCTC
6385 TCTT-TCTTTCT
1 TCTTCTCTTTCT
6396 CCTATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.27
16 9 0.35
17 10 0.38
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (16 bp):
TCTTCTCTTTCTTCTC
Found at i:11240 original size:281 final size:282
Alignment explanation
Indices: 10725--11288 Score: 1112
Period size: 281 Copynumber: 2.0 Consensus size: 282
10715 AGGCAAAGGA
10725 ATACGCATCACCTTATCTCCGTTACTTTTTCTGTTATGGAGAGATTGTTGAAGATTTCAAGAATC
1 ATACGCATCA-CTTATCTCCGTTACTTTTTCTGTTATGGAGAGATTGTTGAAGATTTCAAGAATC
10790 AACGAAAGGAACTTAAATTGAGGAAACAGAGGGTGAAAACTCGTGTCGATGAGGCTAAAAGGCAA
65 AACGAAAGGAACTTAAATTGAGGAAACAGAGGGTGAAAACTCGTGTCGATGAGGCTAAAAGGCAA
10855 ATTAAGGTCATCTATGAAGACGTTGAAGACTGGCTTAGAAGGGCTGAGAAAGAACTGGAAGAAAC
130 ATTAAGGTCATCTATGAAGACGTTGAAGACTGGCTTAGAAGGGCTGAGAAAGAACTGGAAGAAAC
10920 CCAGAACTTCGAAGAGGAAATAGATGGCGTCAAGCGGTTCAAATGGTGTCCTCAATGGAGCTGGC
195 CCAGAACTTCGAAGAGGAAATAGATGGCGTCAAGCGGTTCAAATGGTGTCCTCAATGGAGCTGGC
10985 GATATCGTTTAAGTAAGAAACTG
260 GATATCGTTTAAGTAAGAAACTG
11008 ATACGCATCA-TTATCTCCGTTACTTTTTCTGTTATGGAGAGATTGTTGAAGATTTCAAGAATCA
1 ATACGCATCACTTATCTCCGTTACTTTTTCTGTTATGGAGAGATTGTTGAAGATTTCAAGAATCA
11072 ACGAAAGGAACTTAAATTGAGGAAACAGAGGGTGAAAACTCGTGTCGATGAGGCTAAAAGGCAAA
66 ACGAAAGGAACTTAAATTGAGGAAACAGAGGGTGAAAACTCGTGTCGATGAGGCTAAAAGGCAAA
11137 TTAAGGTCATCTATGAAGACGTTGAAGACTGGCTTAGAAGGGCTGAGAAAGAACTGGAAGAAACC
131 TTAAGGTCATCTATGAAGACGTTGAAGACTGGCTTAGAAGGGCTGAGAAAGAACTGGAAGAAACC
11202 CAGAACTTCGAAGAGGAAATAGATGGCGTCAAGCGGTTCAAATGGTGTCCTCAATGGAGCTGGCG
196 CAGAACTTCGAAGAGGAAATAGATGGCGTCAAGCGGTTCAAATGGTGTCCTCAATGGAGCTGGCG
11267 ATATCGTTTAAGTAAGAAACTG
261 ATATCGTTTAAGTAAGAAACTG
11289 GCAGAGAAGA
Statistics
Matches: 281, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
281 271 0.96
283 10 0.04
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (282 bp):
ATACGCATCACTTATCTCCGTTACTTTTTCTGTTATGGAGAGATTGTTGAAGATTTCAAGAATCA
ACGAAAGGAACTTAAATTGAGGAAACAGAGGGTGAAAACTCGTGTCGATGAGGCTAAAAGGCAAA
TTAAGGTCATCTATGAAGACGTTGAAGACTGGCTTAGAAGGGCTGAGAAAGAACTGGAAGAAACC
CAGAACTTCGAAGAGGAAATAGATGGCGTCAAGCGGTTCAAATGGTGTCCTCAATGGAGCTGGCG
ATATCGTTTAAGTAAGAAACTG
Found at i:11937 original size:12 final size:12
Alignment explanation
Indices: 11920--11944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11910 TGTCAAAGCT
11920 GCACCTGTTGAA
1 GCACCTGTTGAA
11932 GCACCTGTTGAA
1 GCACCTGTTGAA
11944 G
1 G
11945 ACAATATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (12 bp):
GCACCTGTTGAA
Found at i:27967 original size:87 final size:87
Alignment explanation
Indices: 27820--27995 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
27810 CTCAAAACAA
* *
27820 ATACACTTACACAAAATATAAATATAGTTTCTCCTCTCTCAATTTCTAGTTACCACTAGTTATAC
1 ATACACTTACACAAAATATAAATATAGTTTCCCCTCTCTCAATTTCTAGTTACCAATAGTTATAC
27885 ACTCACAATTCACTCTTTGCAT
66 ACTCACAATTCACTCTTTGCAT
27907 ATACACTTACACAAAATATAAATATAGTTTCCCCTCTCTCAATTTCTAGTTACCAATAGTTATAC
1 ATACACTTACACAAAATATAAATATAGTTTCCCCTCTCTCAATTTCTAGTTACCAATAGTTATAC
27972 ACTCACAATTCACTCTTTGCAT
66 ACTCACAATTCACTCTTTGCAT
27994 AT
1 AT
27996 TTCCACTCTT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (87 bp):
ATACACTTACACAAAATATAAATATAGTTTCCCCTCTCTCAATTTCTAGTTACCAATAGTTATAC
ACTCACAATTCACTCTTTGCAT
Found at i:40255 original size:15 final size:15
Alignment explanation
Indices: 40235--40281 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
40225 TTGTTAGAGC
*
40235 AAATAAAATTATTTT
1 AAATAAAAGTATTTT
*
40250 AAATAACAGTATTTT
1 AAATAAAAGTATTTT
* *
40265 AAATAATAGTAATTT
1 AAATAAAAGTATTTT
40280 AA
1 AA
40282 TTTTTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (15 bp):
AAATAAAAGTATTTT
Found at i:42480 original size:38 final size:39
Alignment explanation
Indices: 42417--42494 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
42407 GAAATCAAAA
42417 ATCAAAAATTGTTTTAATTCAAATCATGAATATTCAATC
1 ATCAAAAATTGTTTTAATTCAAATCATGAATATTCAATC
42456 ATCAAAAATTG-TTTAATTCAAATCATGAATATTCAATC
1 ATCAAAAATTGTTTTAATTCAAATCATGAATATTCAATC
42494 A
1 A
42495 AATTTTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 28 0.72
39 11 0.28
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (39 bp):
ATCAAAAATTGTTTTAATTCAAATCATGAATATTCAATC
Found at i:42508 original size:33 final size:36
Alignment explanation
Indices: 42421--42513 Score: 104
Period size: 38 Copynumber: 2.6 Consensus size: 36
42411 TCAAAAATCA
*
42421 AAAATTGTTTTAATTCAAATCATGAATATTCAATCATC
1 AAAATTG-TTAAATTCAAATCATGAATATTCAA-CATC
*
42459 AAAAATTGTTTAATTCAAATCATGAATATTC-A-ATC
1 -AAAATTGTTAAATTCAAATCATGAATATTCAACATC
42494 -AAATT-TTAATATTCAAATCA
1 AAAATTGTTAA-ATTCAAATCA
42514 CAAATTTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
32 3 0.06
33 15 0.29
35 3 0.06
37 1 0.02
38 23 0.44
39 7 0.13
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (36 bp):
AAAATTGTTAAATTCAAATCATGAATATTCAACATC
Found at i:42524 original size:19 final size:18
Alignment explanation
Indices: 42483--42525 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
42473 TCAAATCATG
*
42483 AATATTCAATCAAATTTT
1 AATATTCAATCAAAATTT
42501 AATATTCAAATCACAAATTT
1 AATATTC-AATCA-AAATTT
42521 -ATATT
1 AATATT
42526 TTCTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTCAATCAAAATTT
Found at i:42659 original size:15 final size:15
Alignment explanation
Indices: 42639--42668 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42629 GATCAAATTG
*
42639 ATTAAATGTGTAAAT
1 ATTAAATGTCTAAAT
42654 ATTAAATGTCTAAAT
1 ATTAAATGTCTAAAT
42669 TTATTATTAA
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:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTAAATGTCTAAAT
Found at i:43138 original size:8 final size:8
Alignment explanation
Indices: 43127--43155 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
43117 TACCTTTATT
43127 ATTTTAAA
1 ATTTTAAA
43135 ATTTTAAA
1 ATTTTAAA
43143 ATTTTAAA
1 ATTTTAAA
43151 ATTTT
1 ATTTT
43156 CTAAAGAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATTTTAAA
Found at i:44515 original size:8 final size:8
Alignment explanation
Indices: 44504--44532 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
44494 TACCTTTATT
44504 ATTTTAAA
1 ATTTTAAA
44512 ATTTTAAA
1 ATTTTAAA
44520 ATTTTAAA
1 ATTTTAAA
44528 ATTTT
1 ATTTT
44533 CTAAAGAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATTTTAAA
Found at i:46400 original size:32 final size:32
Alignment explanation
Indices: 46364--46434 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
46354 AGAAATAGAT
*
46364 AAAAATACAAAAGAATTTCAAAAAATCAA-AAA
1 AAAAATACAAAAAAATTTCAAAAAAT-AACAAA
** * *
46396 AAAAATTTAAAAAAATTTTAAGAAATAACAAA
1 AAAAATACAAAAAAATTTCAAAAAATAACAAA
46428 AAAAATA
1 AAAAATA
46435 TGGAAAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.20
Consensus pattern (32 bp):
AAAAATACAAAAAAATTTCAAAAAATAACAAA
Found at i:53983 original size:24 final size:25
Alignment explanation
Indices: 53938--53998 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 25
53928 CTTCATGCTA
*
53938 TATTTTTTT-AATTTTATGATTTTTT
1 TATTTTTTTGAATTTCA-GATTTTTT
53963 TATTTTTTTGAATTTCA-ATTTTTT
1 TATTTTTTTGAATTTCAGATTTTTT
53987 TA-TTTTTTGAAT
1 TATTTTTTTGAAT
53999 ATTTTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.29
24 9 0.26
25 9 0.26
26 6 0.18
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (25 bp):
TATTTTTTTGAATTTCAGATTTTTT
Found at i:54139 original size:25 final size:25
Alignment explanation
Indices: 54117--54167 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
54107 AATTAAGTGT
54117 TATATATATATATATATTAAAGTAAA
1 TATA-ATATATATATATTAAAGTAAA
54143 TATAATATATATAATATTAAA-TAAA
1 TATAATATATAT-ATATTAAAGTAAA
54168 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TATAATATATATATATTAAAGTAAA
Found at i:54430 original size:24 final size:24
Alignment explanation
Indices: 54403--54452 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
54393 AAGGTTAAAA
54403 TTTAAATAGAAGGGTAAAATGACT
1 TTTAAATAGAAGGGTAAAATGACT
*
54427 TTTAAATATAAGGGTAAAATGACT
1 TTTAAATAGAAGGGTAAAATGACT
54451 TT
1 TT
54453 CTTATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (24 bp):
TTTAAATAGAAGGGTAAAATGACT
Found at i:62391 original size:35 final size:36
Alignment explanation
Indices: 62352--62426 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 36
62342 ATAGCAAAAC
62352 TACGTTGAAAG-AAATGGAGAAAGGAGGAAAACAAA
1 TACGTTGAAAGAAAATGGAGAAAGGAGGAAAACAAA
62387 TACGTTGAAAGAAATTAAATGGAGAAAGGAGGAAAACAAA
1 TACGTTGAAAG--A--AAATGGAGAAAGGAGGAAAACAAA
62427 GGGAGAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
35 11 0.31
40 24 0.69
ACGTcount: A:0.55, C:0.05, G:0.27, T:0.13
Consensus pattern (36 bp):
TACGTTGAAAGAAAATGGAGAAAGGAGGAAAACAAA
Found at i:64383 original size:15 final size:15
Alignment explanation
Indices: 64365--64400 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
64355 CAGATAAAAT
64365 TATTTTAAATAATAG
1 TATTTTAAATAATAG
64380 TATTTTAAATAATAG
1 TATTTTAAATAATAG
64395 TATTTT
1 TATTTT
64401 CATTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTTTAAATAATAG
Found at i:70490 original size:95 final size:94
Alignment explanation
Indices: 70220--70628 Score: 348
Period size: 94 Copynumber: 4.3 Consensus size: 94
70210 TCATCATCCG
* * * * * * *
70220 TAATTATTCATCATAAAACTAATGAAAAAGTAAGAGCGTGAAGAAATCATCAACGATGCCTGTGT
1 TAATTATTCATCATAAAAATAAT-AGAAAGTAACAAC-TGAATAATTCATCAACAATGCC--TGT
* ** * * **
70285 CTCACTACCAAAAGTGGTGAAGACTCTTCATACG
62 CCCA-TGGCGAAAGTGGTGAAGACTCTTGATAAT
* * * *
70319 TAATGATTCTTCATAAAAATAATAGAAAGTAAC-A--GAATAATTCGTCAACAATGCCTGTCGCA
1 TAATTATTCATCATAAAAATAATAGAAAGTAACAACTGAATAATTCATCAACAATGCCTGTCCCA
*
70381 GTGGCGAAACTGGTGAAGGA-TCTTGATAAT
66 -TGGCGAAAGTGGTGAA-GACTCTTGATAAT
* * * * * *
70411 TTATTAATCATCATAAAAATAATAGAAA-CAACAACGTGAAGAATTCATCAACAATACCTTTCCC
1 TAATTATTCATCATAAAAATAATAGAAAGTAACAAC-TGAATAATTCATCAACAATGCCTGTCCC
* * *
70475 ACTGGCAAAAGTGGTGAAGACCCTTCG-TACT
65 A-TGGCGAAAGTGGTGAAGACTCTT-GATAAT
* * * * *
70506 TAATTATTCATCATAAAAATAGTA-ACAAGTAGCAGCATCAATAATTCATCAACGATGCCTGTCC
1 TAATTATTCATCATAAAAATAATAGA-AAGTAACAAC-TGAATAATTCATCAACAATGCCTGTCC
70570 CA-GGCGAAAGTGGTGAAGACTCTTGATAAT
64 CATGGCGAAAGTGGTGAAGACTCTTGATAAT
*
70600 TAATTATTCATCATAAAAATAATAAAAAG
1 TAATTATTCATCATAAAAATAATAGAAAG
70629 GTGACCGCGT
Statistics
Matches: 249, Mismatches: 50, Indels: 27
0.76 0.15 0.08
Matches are distributed among these distances:
91 3 0.01
92 50 0.20
93 3 0.01
94 69 0.28
95 67 0.27
96 29 0.12
98 8 0.03
99 20 0.08
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (94 bp):
TAATTATTCATCATAAAAATAATAGAAAGTAACAACTGAATAATTCATCAACAATGCCTGTCCCA
TGGCGAAAGTGGTGAAGACTCTTGATAAT
Found at i:70586 original size:189 final size:188
Alignment explanation
Indices: 70220--70623 Score: 467
Period size: 189 Copynumber: 2.1 Consensus size: 188
70210 TCATCATCCG
* * * * * * * *
70220 TAATTATTCATCATAAAACTAATGAAAAAGTAAGAGCGTGAAGAAATCATCAACGATGCCTGTGT
1 TAATTAATCATCATAAAAATAAT-AGAAA-CAACAACGTGAAGAAATCATCAACAATACCTGTGT
* * *
70285 CTCACTACCAAAAGTGGTGAAGACTCTTCATACGTAATGATTCTTCATAAAAATAATAGAAAGTA
64 CCCACTACCAAAAGTGGTGAAGACCCTTCATACGTAATGATTCATCATAAAAATAATAGAAAGTA
* * *
70350 ACAGAATAATTCGTCAACAATGCCTGTCGCAGTGGCGAAACTGGTGAAGGA-TCTTGATAAT
129 ACACAATAATTCATCAACAATGCCTGTCCCAG-GGCGAAACTGGTGAA-GACTCTTGATAAT
* *
70411 TTATTAATCATCATAAAAATAATAGAAACAACAACGTGAAGAATTCATCAACAATACCT-T-TCC
1 TAATTAATCATCATAAAAATAATAGAAACAACAACGTGAAGAAATCATCAACAATACCTGTGTCC
** * * * *
70474 CACTGGCAAAAGTGGTGAAGACCCTTCGTACTTAATTATTCATCATAAAAATAGTA-ACAAGTAG
66 CACTACCAAAAGTGGTGAAGACCCTTCATACGTAATGATTCATCATAAAAATAATAGA-AAGTA-
* *
70538 CAGCATCAATAATTCATCAACGATGCCTGTCCCA-GGCGAAAGTGGTGAAGACTCTTGATAAT
129 -A-CA-CAATAATTCATCAACAATGCCTGTCCCAGGGCGAAACTGGTGAAGACTCTTGATAAT
*
70600 TAATTATTCATCATAAAAATAATA
1 TAATTAATCATCATAAAAATAATA
70624 AAAAGGTGAC
Statistics
Matches: 181, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
186 1 0.01
187 55 0.30
188 3 0.02
189 72 0.40
190 6 0.03
191 44 0.24
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (188 bp):
TAATTAATCATCATAAAAATAATAGAAACAACAACGTGAAGAAATCATCAACAATACCTGTGTCC
CACTACCAAAAGTGGTGAAGACCCTTCATACGTAATGATTCATCATAAAAATAATAGAAAGTAAC
ACAATAATTCATCAACAATGCCTGTCCCAGGGCGAAACTGGTGAAGACTCTTGATAAT
Found at i:72520 original size:44 final size:44
Alignment explanation
Indices: 72471--72584 Score: 167
Period size: 44 Copynumber: 2.6 Consensus size: 44
72461 TGGCTTTCTA
* *
72471 ATTCTCGAATCTGTGTTTCTGATCATTTCCTTTTTTGCTTCCAT
1 ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTACAT
* *
72515 ATTCTCAAATCTGTGTTTGTGGTCATTTCCTTTTTTGCTTACAT
1 ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTACAT
*
72559 ATTCT-GAAATCTGTGTCTGTGATCAT
1 ATTCTCG-AATCTGTGTTTGTGATCAT
72585 CACCAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (44 bp):
ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTACAT
Found at i:73486 original size:51 final size:51
Alignment explanation
Indices: 73422--73525 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
73412 TATTCGAGTC
*
73422 AATTTGAGTTTATCCAAATAACTTAATTAACTCAAATAACTCGAACTAGTT
1 AATTCGAGTTTATCCAAATAACTTAATTAACTCAAATAACTCGAACTAGTT
* *
73473 AATTCGAGTTTATCCGAATAACTTAATTAACTCAAATAACTTGAACTAGTT
1 AATTCGAGTTTATCCAAATAACTTAATTAACTCAAATAACTCGAACTAGTT
73524 AA
1 AA
73526 ATCAAAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (51 bp):
AATTCGAGTTTATCCAAATAACTTAATTAACTCAAATAACTCGAACTAGTT
Found at i:76583 original size:27 final size:27
Alignment explanation
Indices: 76534--76592 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 27
76524 CTTCATGCTA
*
76534 TATTTTTTTAATTTTATAGTTTTTTTT
1 TATTTTTTTAATTTCATAGTTTTTTTT
76561 TATTTTTTTGAATTTCA-A---TTTTTT
1 TATTTTTTT-AATTTCATAGTTTTTTTT
76585 TATTTTTT
1 TATTTTTT
76593 GAATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.47
27 10 0.33
28 6 0.20
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (27 bp):
TATTTTTTTAATTTCATAGTTTTTTTT
Found at i:76831 original size:24 final size:24
Alignment explanation
Indices: 76804--76855 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
76794 AAAGGTGAAA
76804 TTTTAAATAGAAGGGTAAAATGAC
1 TTTTAAATAGAAGGGTAAAATGAC
*
76828 TTTTAAATGGAAGGGTAAAATGAC
1 TTTTAAATAGAAGGGTAAAATGAC
76852 TTTT
1 TTTT
76856 TTATAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (24 bp):
TTTTAAATAGAAGGGTAAAATGAC
Done.