Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3055
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: 31547
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:927 original size:285 final size:290
Alignment explanation
Indices: 361--928 Score: 925
Period size: 285 Copynumber: 2.0 Consensus size: 290
351 GAAATGTGAC
*
361 GGATCAAAAGGGACGAATAAGCTAATTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGTT
1 GGATCAAAAGGGACAAATAAGCTAATTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGTT
*
426 CCAATAAATACCTAAACATACCTAAACTTTTGGCCATTCAAATAGATTAGACTAATTTTTAATTA
66 CC----AATA-CTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTA
*
491 CTTAAAAATATTGCATAAATTTAATAACAAAATGGAGAATAAAAGAAACATGAAATTATACCTGT
126 CTTAAAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGT
* * ***
556 CAATTTGTTATTGTTAAGATAAAGCTCTCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTT
191 CAAATTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTT
621 CACCTGAAACGTATAATTAAATCGGTCAAAATTAT
256 CACCTGAAACGTATAATTAAATCGGTCAAAATTAT
656 GGATCAAAAGGGACAAATAAGCTAATTTCTGCCATAAGGTA-ATGGT-AACTTAGGATGTGGAGT
1 GGATCAAAAGGGACAAATAAGCTAA-TTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGT
*
719 TCC-A-A-T-AA-ATACCTAAACTTTTGGCAATTCAAATAGATTATTACTAATTTTTAATTACTT
65 TCCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTA-GACTAATTTTTAATTACTT
779 AAAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAA
129 AAAAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAA
* *
844 ATTGTTATTGCTAAGATAAAGAAATTGGAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCAC
194 ATTGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCAC
909 CTGAAACGTATAATTAAATC
259 CTGAAACGTATAATTAAATC
929 ATCACTTTAG
Statistics
Matches: 260, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
284 31 0.12
285 162 0.62
286 1 0.00
288 1 0.00
289 1 0.00
294 20 0.08
295 29 0.11
296 15 0.06
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (290 bp):
GGATCAAAAGGGACAAATAAGCTAATTCTGCCATAAGGTAGATGGTGAACTTAGGATGTGGAGTT
CCAATACTAAACATACCTAAACTTTTGGCAATTCAAATAGATTAGACTAATTTTTAATTACTTAA
AAATATTGCATAAATTTAATAACAAAATAGAGAATAAAAGAAACATGAAATTATACCTGTCAAAT
TGTTATTGCTAAGATAAAGAAATCGAAGAGAAGTCAAGTTTCCAATAACAAGAGGAATTTCACCT
GAAACGTATAATTAAATCGGTCAAAATTAT
Found at i:7626 original size:15 final size:15
Alignment explanation
Indices: 7591--7640 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
7581 AAATAATTAA
7591 AATAA-AACTAATAAT
1 AATAATAAC-AATAAT
7606 AATAATAACAATAAT
1 AATAATAACAATAAT
** *
7621 AATAATGGCAATGAT
1 AATAATAACAATAAT
7636 AATAA
1 AATAA
7641 CATTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 28 0.90
16 3 0.10
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATAACAATAAT
Found at i:8727 original size:12 final size:12
Alignment explanation
Indices: 8710--8740 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
8700 TAGTGGGCTG
8710 TTTGGGCTTGTT
1 TTTGGGCTTGTT
*
8722 TTTGGGTTTGTT
1 TTTGGGCTTGTT
8734 TTTGGGC
1 TTTGGGC
8741 AGGGCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.35, T:0.58
Consensus pattern (12 bp):
TTTGGGCTTGTT
Found at i:8967 original size:43 final size:43
Alignment explanation
Indices: 8900--9000 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
8890 TCCAATGCGT
* * *
8900 CTTGTTGCTTCAATCTACTCCACTGCACATCA-AAGAGATAC-GG
1 CTTGTAGCTTCAATCCACTCCACTGCACATCAGAA-AGAT-CTGA
* * *
8943 CTTTTAGCTTCAATCCACTTCACTGCACTTCAGAAAGATCTGA
1 CTTGTAGCTTCAATCCACTCCACTGCACATCAGAAAGATCTGA
8986 CTTGTAGCTTCAATC
1 CTTGTAGCTTCAATC
9001 TTCTTCGCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 46 0.94
44 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (43 bp):
CTTGTAGCTTCAATCCACTCCACTGCACATCAGAAAGATCTGA
Found at i:9408 original size:44 final size:43
Alignment explanation
Indices: 9363--9521 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 43
9353 TTATTTTAAT
*
9363 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAAT-GCTTCAAC
** * ** *
9407 CTGCTCTGCTGCAACTTCAGGGAGATAAGATTGGTGTCTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATG-CTTCAAC
* * * *
9451 CTACTCCACTGCTACTTCAGCGAGATAAGGTTTGCAAT--TTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGAT-AGGATT--AATGCTTCAAC
9495 CTGCTCCACTGCAACTTCAAGGG-GATA
1 CTGCTCCACTGCAACTTC-AGGGAGATA
9522 ATGTTTGATA
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
43 2 0.02
44 80 0.89
45 7 0.08
47 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (43 bp):
CTGCTCCACTGCAACTTCAGGGAGATAGGATTAATGCTTCAAC
Found at i:9692 original size:45 final size:45
Alignment explanation
Indices: 9655--10322 Score: 911
Period size: 45 Copynumber: 14.9 Consensus size: 45
9645 CAAGATATGT
9655 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * *
9700 TATCTTTAGTCTACTTTGCTGCCAATATAGGAAGACAAAACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* **
9745 TATCTT-TGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
9790 TATCTTCAGTCTAC-TCGCTGCTAATACAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
9834 TATATTC-GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * * *
9879 TATCTTCAATCAACTTCGTTGACAATACAGGAAGACAAGACATGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * * **
9924 TATCTTC-GATCTACTTCGTTGCCAATATAGTAAGACAAGATATGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
9969 TATCTTCAGTCTACTTCGCTGCCAATATAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* * *
10014 TATCTT-TGATCTACTTCACTGCCAATATAGGAAGACAAGACCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
10059 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAAACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
10104 TATCTTCAGTCTTCTTCGCTGCCAATACAGGAAGACAAGACCTGT
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
10149 TATCTTTAATCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
*
10194 TATCTTC-GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* *
10239 TATCTTCAGTCTACTTCGCTACCAATACAGGAAGATAAGACCT-C
1 TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
* **
10283 TATCTT-TGATCTACTTCATTGCCAATACAGGAAGACAAGA
1 TATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAGA
10323 TCTGTTATTT
Statistics
Matches: 553, Mismatches: 58, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.00
44 74 0.13
45 473 0.86
46 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (45 bp):
TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAGACCTGC
Found at i:11653 original size:6 final size:6
Alignment explanation
Indices: 11642--11697 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
11632 TTGGCCTTTC
* *
11642 CTTTTT CTTTTT C-TTTT CTTCTT CTTTTT C-TTTT -TTTTT CTTGTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
11687 -TTTTT ATTTTT
1 CTTTTT CTTTTT
11698 TTGATTGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 17 0.40
6 25 0.60
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:11658 original size:11 final size:10
Alignment explanation
Indices: 11643--11699 Score: 69
Period size: 11 Copynumber: 5.3 Consensus size: 10
11633 TGGCCTTTCC
11643 TTTTTCTTTT
1 TTTTTCTTTT
11653 TCTTTTCTTCTT
1 T-TTTTCTT-TT
11665 CTTTTTCTTTT
1 -TTTTTCTTTT
11676 TTTTTCTTGTT
1 TTTTTCTT-TT
*
11687 TTTTTATTTT
1 TTTTTCTTTT
11697 TTT
1 TTT
11700 GATTGAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 14 0.33
11 18 0.43
12 9 0.21
13 1 0.02
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:11669 original size:22 final size:22
Alignment explanation
Indices: 11642--11699 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
11632 TTGGCCTTTC
11642 CTTTTTCTTTTTCTTTTCTTCTT
1 CTTTTTCTTTTT-TTTTCTTCTT
*
11665 CTTTTTCTTTTTTTTTCTTGTT
1 CTTTTTCTTTTTTTTTCTTCTT
*
11687 -TTTTTATTTTTTT
1 CTTTTTCTTTTTTT
11700 GATTGAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 12 0.36
22 9 0.27
23 12 0.36
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (22 bp):
CTTTTTCTTTTTTTTTCTTCTT
Found at i:21518 original size:17 final size:17
Alignment explanation
Indices: 21496--21787 Score: 136
Period size: 17 Copynumber: 16.5 Consensus size: 17
21486 AACACGAAAG
*
21496 TTTTTGAATCACAAGAA
1 TTTTTGAAACACAAGAA
*
21513 TTTTTGAAAACCCGAA-AA
1 TTTTTG-AAACAC-AAGAA
*
21531 TTTTTAGAAACATGAAG-A
1 TTTTT-GAAACA-CAAGAA
* *
21549 TTTTTGAAACACGACAA
1 TTTTTGAAACACAAGAA
21566 TTTTTGAAACACAAGAA
1 TTTTTGAAACACAAGAA
* * *
21583 TTTTTTTTAAAGCGCAA-AC
1 --TTTTTGAAA-CACAAGAA
* *
21602 TTTTTTAAA-ACACTGAAA
1 TTTTTGAAACACA-AG-AA
* *
21620 TTTGTGAAACACGAGAA
1 TTTTTGAAACACAAGAA
*
21637 TTGTTGAAAACACGAA-AA
1 TTTTTG-AAACAC-AAGAA
* *
21655 TTTTTGAAA-ATATGAAAA
1 TTTTTGAAACACA--AGAA
*
21673 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACAAGAA
*
21691 TTTTTGAAACACAAAAA
1 TTTTTGAAACACAAGAA
21708 TTTTTAGAAA-ACAAGAAAA
1 TTTTT-GAAACACAAG--AA
* *
21727 CTTTTTGAATCACTAGAA
1 -TTTTTGAAACACAAGAA
*
21745 -TTTTGAAA-ACACGTAAA
1 TTTTTGAAACACAAG--AA
*
21762 TTTTTGAAACATC-GGAA
1 TTTTTGAAACA-CAAGAA
21779 TTTTTGAAA
1 TTTTTGAAA
21788 ACATGTGGAT
Statistics
Matches: 213, Mismatches: 32, Indels: 60
0.70 0.10 0.20
Matches are distributed among these distances:
15 6 0.03
16 9 0.04
17 80 0.38
18 77 0.36
19 25 0.12
20 16 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACAAGAA
Found at i:21532 original size:18 final size:18
Alignment explanation
Indices: 21484--21790 Score: 224
Period size: 18 Copynumber: 17.3 Consensus size: 18
21474 GATTTAAAAA
*
21484 AAAACACGAAAGTTTTTG
1 AAAACACGAAAATTTTTG
*
21502 -AATCAC-AAGAATTTTTG
1 AAAACACGAA-AATTTTTG
*
21519 AAAACCCGAAAATTTTT-
1 AAAACACGAAAATTTTTG
* *
21536 AGAAACATGAAGATTTTTG
1 A-AAACACGAAAATTTTTG
*
21555 -AAACACGACAATTTTTG
1 AAAACACGAAAATTTTTG
* ** *
21572 AAACACAAGAATTTTTTTT
1 AAA-ACACGAAAATTTTTG
* * * *
21591 AAAGCGC-AAACTTTTTT
1 AAAACACGAAAATTTTTG
*
21608 AAAACACTG-AAATTTGTG
1 AAAACAC-GAAAATTTTTG
* *
21626 -AAACACGAGAATTGTTG
1 AAAACACGAAAATTTTTG
21643 AAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* *
21661 AAAATATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
21679 AAAACACAAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
21697 -AAACACAAAAATTTTTAG
1 AAAACACGAAAATTTTT-G
*
21715 AAAACAAGAAAACTTTTTG
1 AAAACACGAAAA-TTTTTG
* * *
21734 -AATCACTAGAA-TTTTG
1 AAAACACGAAAATTTTTG
*
21750 AAAACACGTAAATTTTTG
1 AAAACACGAAAATTTTTG
*
21768 -AAACATCG-GAATTTTTG
1 AAAACA-CGAAAATTTTTG
21785 AAAACA
1 AAAACA
21791 TGTGGATTTT
Statistics
Matches: 225, Mismatches: 46, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
16 8 0.04
17 88 0.39
18 99 0.44
19 25 0.11
20 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:21589 original size:36 final size:35
Alignment explanation
Indices: 21485--21787 Score: 196
Period size: 35 Copynumber: 8.6 Consensus size: 35
21475 ATTTAAAAAA
* *
21485 AAACACGAAAGTTTTTGAATCACAAG-AATTTTTG
1 AAACACGAAAATTTTTGAAACACAAGAAATTTTTG
* *
21519 AAAACCCGAAAATTTTT-AGAA-ACATGAAGATTTTTG
1 -AAACACGAAAATTTTTGA-AACACAAGAA-ATTTTTG
* * *
21555 AAACACGACAATTTTTGAAACACAAGAATTTTTTTT
1 AAACACGAAAATTTTTGAAACACAAGAA-ATTTTTG
* * * * *
21591 AAA-GCGCAAACTTTTTTAAA-ACACTGAAATTTGTG
1 AAACACG-AAAATTTTTGAAACACA-AGAAATTTTTG
* * *
21626 AAACACGAGAATTGTTGAAA-ACACGAAAATTTTTG
1 AAACACGAAAATTTTTGAAACACAAG-AAATTTTTG
* *
21661 AAAATATGAAAATTTTTGAAAACACAA-AAATTTTTG
1 -AAACACGAAAATTTTTG-AAACACAAGAAATTTTTG
*
21697 AAACACAAAAATTTTTAGAAA-ACAAGAAAACTTTTTG
1 AAACACGAAAATTTTT-GAAACACAAG-AAA-TTTTTG
* * * *
21734 AATCACTAGAA-TTTTGAAA-ACACGTAAATTTTTG
1 AAACACGAAAATTTTTGAAACACAAG-AAATTTTTG
*
21768 AAACATCG-GAATTTTTGAAA
1 AAACA-CGAAAATTTTTGAAA
21788 ACATGTGGAT
Statistics
Matches: 210, Mismatches: 40, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
34 23 0.11
35 100 0.48
36 67 0.32
37 17 0.08
38 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (35 bp):
AAACACGAAAATTTTTGAAACACAAGAAATTTTTG
Found at i:21684 original size:54 final size:52
Alignment explanation
Indices: 21484--21770 Score: 201
Period size: 53 Copynumber: 5.4 Consensus size: 52
21474 GATTTAAAAA
* * * *
21484 AAAACACGAAAGTTTTTGAATCACAAG--AATTTTTGAAAACCCGAA-AATTTTT
1 AAAACACGAAAATTTTTGAA-AACAAGAAAATTTTTG-AAACAC-AAGAATTTTG
* * * * *
21536 AGAAACATGAAGATTTTTG-AAACACGACAATTTTTGAAACACAAGAATTTTTTT
1 A-AAACACGAAAATTTTTGAAAACAAGAAAATTTTTGAAACACAAGAA--TTTTG
* * * * * * *
21590 TAAA-GCGCAAACTTTTTTAAAACACTG-AAATTTGTGAAACACGAGAATTGTTG
1 AAAACACG-AAAATTTTTGAAAACA-AGAAAATTTTTGAAACACAAGAATT-TTG
* * *
21643 AAAACACGAAAATTTTTGAAAATATGAAAATTTTTGAAAACACAAAAATTTTTG
1 AAAACACGAAAATTTTTGAAAACAAGAAAATTTTTG-AAACACAAGAA-TTTTG
* * *
21697 -AAACACAAAAATTTTTAGAAAACAAGAAAACTTTTTGAATCACTAGAATTTTG
1 AAAACACGAAAATTTTT-GAAAACAAGAAAA-TTTTTGAAACACAAGAATTTTG
*
21750 AAAACACGTAAATTTTTGAAA
1 AAAACACGAAAATTTTTGAAA
21771 CATCGGAATT
Statistics
Matches: 185, Mismatches: 33, Indels: 33
0.74 0.13 0.13
Matches are distributed among these distances:
51 6 0.03
52 14 0.08
53 82 0.44
54 74 0.40
55 9 0.05
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (52 bp):
AAAACACGAAAATTTTTGAAAACAAGAAAATTTTTGAAACACAAGAATTTTG
Found at i:21781 original size:71 final size:68
Alignment explanation
Indices: 21526--21790 Score: 200
Period size: 71 Copynumber: 3.7 Consensus size: 68
21516 TTGAAAACCC
* **
21526 GAAAATTTTT-AGAAACA-TGAAGATTTTTGAAACACGACAATTTTTGAAACACAAGAATTTTTT
1 GAAAATTTTTGA-AAACACT-AA-ATTTTTGAAACACG-GAATTTTTGAAA-ACAAGAAAATTTT
* **
21589 TTAAA-GC
61 TGAAATAT
* * * * *
21596 GCAAACTTTTTTAAAACACTGAAATTTGTGAAACACGAGAATTGTTGAAAACACGAAAATTTTTG
1 G-AAAATTTTTGAAAACACT-AAATTTTTGAAACACG-GAATTTTTGAAAACAAGAAAATTTTTG
21661 AAAATAT
63 -AAATAT
* **
21668 GAAAATTTTTGAAAACACAAAAATTTTTGAAACACAAAAATTTTTAGAAAACAAGAAAACTTTTT
1 GAAAATTTTTGAAAACAC-TAAATTTTTGAAACAC-GGAATTTTT-GAAAACAAGAAAA-TTTTT
21733 G-AATCACT
62 GAAAT-A-T
*
21741 -AGAA-TTTTGAAAACACGTAAATTTTTGAAACATCGGAATTTTTGAAAACA
1 GAAAATTTTTGAAAACAC-TAAATTTTTGAAACA-CGGAATTTTTGAAAACA
21791 TGTGGATTTT
Statistics
Matches: 160, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
70 19 0.12
71 111 0.69
72 23 0.14
73 7 0.04
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (68 bp):
GAAAATTTTTGAAAACACTAAATTTTTGAAACACGGAATTTTTGAAAACAAGAAAATTTTTGAAA
TAT
Found at i:21799 original size:18 final size:18
Alignment explanation
Indices: 21745--21801 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
21735 ATCACTAGAA
* *
21745 TTTTGAAAACACGTAAAT
1 TTTTGAAAACATGTGAAT
21763 TTTTG-AAACATCG-GAAT
1 TTTTGAAAACAT-GTGAAT
*
21780 TTTTGAAAACATGTGGAT
1 TTTTGAAAACATGTGAAT
21798 TTTT
1 TTTT
21802 TTTTACACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTTGAAAACATGTGAAT
Found at i:22021 original size:20 final size:21
Alignment explanation
Indices: 21985--22028 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
21975 GACAAAAAAA
*
21985 TTTTGAAACACAGGAATTTTT
1 TTTTGAAACACACGAATTTTT
22006 TTTTGAAA-ACACGAATTTTT
1 TTTTGAAACACACGAATTTTT
22026 TTT
1 TTT
22029 GAATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (21 bp):
TTTTGAAACACACGAATTTTT
Found at i:22366 original size:10 final size:10
Alignment explanation
Indices: 22346--22415 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 10
22336 AATTGAACCC
22346 TTTTC-TCTT
1 TTTTCTTCTT
22355 TTTTCTTC-T
1 TTTTCTTCTT
22364 TTTT-TTCTT
1 TTTTCTTCTT
22373 TTTTCTT-TT
1 TTTTCTTCTT
22382 TTTCTCTGT-TT
1 TTT-TCT-TCTT
*
22393 TTTTCCGTC-T
1 TTTT-CTTCTT
*
22403 TTCTCTTCTT
1 TTTTCTTCTT
22413 TTT
1 TTT
22416 CTTTTTGGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.06
9 23 0.47
10 16 0.33
11 7 0.14
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:22372 original size:18 final size:17
Alignment explanation
Indices: 22346--22394 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
22336 AATTGAACCC
22346 TTTTCTCTTTTTTCTTCT
1 TTTTCTCTTTTTTCTT-T
*
22364 TTTTTTCTTTTTTCTTT
1 TTTTCTCTTTTTTCTTT
22381 TTTTCTCTGTTTTT
1 TTTTCTCT-TTTTT
22395 TTCCGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTCTCTTTTTTCTTT
Found at i:22380 original size:15 final size:16
Alignment explanation
Indices: 22355--22386 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22345 CTTTTCTCTT
22355 TTTTCTTCTTTTTTTC
1 TTTTCTTCTTTTTTTC
22371 TTTT-TTCTTTTTTTC
1 TTTTCTTCTTTTTTTC
22386 T
1 T
22387 CTGTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTCTTTTTTTC
Found at i:22396 original size:20 final size:19
Alignment explanation
Indices: 22346--22421 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
22336 AATTGAACCC
22346 TTTTCTCTTTTTTCTTC-TT
1 TTTTCTCTTTTTT-TTCTTT
22365 TTTT-TC--TTTTTTCTTT
1 TTTTCTCTTTTTTTTCTTT
**
22381 TTTTCTCTGTTTTTTTCCGT
1 TTTTCTCT-TTTTTTTCTTT
* *
22401 CTTTCTCTTCTTTTTCTTT
1 TTTTCTCTTTTTTTTCTTT
22420 TT
1 TT
22422 GGCCTGTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.07
16 10 0.22
17 2 0.04
18 2 0.04
19 13 0.29
20 15 0.33
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTCTCTTTTTTTTCTTT
Found at i:22674 original size:7 final size:7
Alignment explanation
Indices: 22657--22757 Score: 57
Period size: 7 Copynumber: 14.0 Consensus size: 7
22647 TAAAAAATAA
22657 TTTTC-T
1 TTTTCTT
22663 TTTTCTT
1 TTTTCTT
22670 TTTTC-T
1 TTTTCTT
*
22676 TCTTCTT
1 TTTTCTT
*
22683 TCTTCTT
1 TTTTCTT
22690 CCCCTTTTCTT
1 ----TTTTCTT
*
22701 CTTTCTT
1 TTTTCTT
*
22708 TCTTCTT
1 TTTTCTT
22715 TATTT-TT
1 T-TTTCTT
22722 TCTTTCTT
1 T-TTTCTT
*
22730 TCTTCTT
1 TTTTCTT
22737 TTTT-TT
1 TTTTCTT
*
22743 CTTTCTT
1 TTTTCTT
22750 TTTCTCTT
1 TTT-TCTT
22758 CTCCTTCATT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
6 15 0.20
7 44 0.59
8 9 0.12
11 6 0.08
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTT
Found at i:22708 original size:4 final size:4
Alignment explanation
Indices: 22695--22750 Score: 57
Period size: 4 Copynumber: 14.8 Consensus size: 4
22685 TTCTTCCCCT
* *
22695 TTTC -TTC TTTC TTTC -TTC TTTA TTT- TTTC TTTC TTTC -TTC TTTTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC
22740 TTTC TTTC TTT
1 TTTC TTTC TTT
22751 TTCTCTTCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
3 12 0.27
4 30 0.68
5 2 0.05
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:22709 original size:11 final size:11
Alignment explanation
Indices: 22658--22759 Score: 99
Period size: 11 Copynumber: 9.5 Consensus size: 11
22648 AAAAAATAAT
22658 TTTCTTT-TTC
1 TTTCTTTCTTC
22668 TTT-TTTCTTC
1 TTTCTTTCTTC
22678 -TTCTTTCTTC
1 TTTCTTTCTTC
*
22688 TTCCCCTTTTCTTC
1 TT--TC-TTTCTTC
22702 TTTCTTTCTTC
1 TTTCTTTCTTC
* *
22713 TTTATTTTTTC
1 TTTCTTTCTTC
22724 TTTCTTTCTTC
1 TTTCTTTCTTC
22735 TTT-TTT-TTC
1 TTTCTTTCTTC
22744 TTTCTTT-TTC
1 TTTCTTTCTTC
22754 TCTTCT
1 T-TTCT
22760 CCTTCATTCA
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
9 11 0.14
10 23 0.29
11 33 0.42
12 1 0.01
13 1 0.01
14 9 0.12
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:23205 original size:29 final size:30
Alignment explanation
Indices: 23098--23223 Score: 123
Period size: 29 Copynumber: 4.3 Consensus size: 30
23088 GGGGCCAATG
*
23098 TGTAATTTTAAGAAAATTTAGGGGTCAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
* * ** *
23128 TATAATTT-AAAAAAACCTAGTGGAT-AAAA
1 TGTAATTTCAAGAAAATTTAG-GGGTCAAAA
**
23157 CATAATTTCAAGAAAATTTAGGGGTCAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
* * *
23187 TGCAATTTCAA-AAAATTTAGGGGACGAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
23216 TGTAATTT
1 TGTAATTT
23224 TTTTTAAAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
29 46 0.60
30 31 0.40
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (30 bp):
TGTAATTTCAAGAAAATTTAGGGGTCAAAA
Found at i:23222 original size:59 final size:59
Alignment explanation
Indices: 23098--23223 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
23088 GGGGCCAATG
* * * *
23098 TGTAATTTTAAGAAAATTTAGGGGTCAAAATATAATTTAAAAAAACCTAGTGGATAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAATACAATTTAAAAAAACCTAGGGGACAAAA
** * * ** *
23157 CATAATTTCAAGAAAATTTAGGGGTCAAAATGCAATTTCAAAAAATTTAGGGGACGAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAATACAATTTAAAAAAACCTAGGGGACAAAA
23216 TGTAATTT
1 TGTAATTT
23224 TTTTTAAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (59 bp):
TGTAATTTCAAGAAAATTTAGGGGTCAAAATACAATTTAAAAAAACCTAGGGGACAAAA
Found at i:23699 original size:78 final size:79
Alignment explanation
Indices: 23449--24197 Score: 762
Period size: 78 Copynumber: 9.5 Consensus size: 79
23439 CGTGTGACTT
* * * *
23449 GAGGCTGAACTCACCTCTAGCAATATGAGTTGATTTTTTTTGAAAGAACAGAAATTTTAAAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAA-AACAGAAA-ATT-AAAAAA
* * *
23514 TACCTC-GATATGAGCCT
63 TACCTCAG-CATGTGCCC
* * * * * * * *
23531 GATGCTCAACTCACCTTTCACAATATGAGTTGA-TTGTTT-GAAAAGCA-TAAATTGAAAATTAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATTAAAAAATAC
23593 CTCAGC--GTGACCC
66 CTCAGCATGTG-CCC
*
23606 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACA-AAAATTGAAAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATTAAAAAATAC
23670 CTCAGCATGTGCCC
66 CTCAGCATGTGCCC
** * *
23684 GAGGCTCAACTCACCTCTCTTAATATGAGTTGATTTTTTTTGAAAAGCAG-AAATTAAAAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATTAAAAAATAC
*
23748 CTCAGCGTGTGACCC
66 CTCAGCATGTG-CCC
* * *
23763 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT--AAAAATAGAAATTTAAATGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATTAAA--AAAT
*
23826 ACCTCGGCATGTGACCC
64 ACCTCAGCATGTG-CCC
** *
23843 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAG-AAATTGAAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGGAAAAACAGAAAATTAAAAAATA
23907 CCTCAGC--GTGACCC
65 CCTCAGCATGTG-CCC
* * *
23921 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGGAAAAAATAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGG-AAAAACAGAAAATT-AAA-AAA
*
23986 TACCTC-GACATGTGTCC
63 TACCTCAG-CATGTGCCC
* * * **
24003 GAGGCTCAACTCACCTCTCGTAATATGAGTTAATTTTTTTGGAAAAAATAGAATTTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGG-AAAAACAGAAAATT-AAA-AAA
* *
24068 TATCTC-GACATGTGTCC
63 TACCTCAG-CATGTGCCC
* * * *
24085 GAGGCTCAACTCACCTCT-GTAATATGAGTTGA--CTTTTGAAAAAACAGAAATTTAAAAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATT-AAA-AAAT
* *
24147 ACCTCGGCATG-ACCC
64 ACCTCAGCATGTGCCC
*
24162 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
24198 AAAAAAAAAC
Statistics
Matches: 581, Mismatches: 61, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
74 2 0.00
75 32 0.06
76 15 0.03
77 62 0.11
78 167 0.29
79 56 0.10
80 69 0.12
81 35 0.06
82 133 0.23
83 10 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (79 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAGAAAATTAAAAAATAC
CTCAGCATGTGCCC
Found at i:23871 original size:237 final size:237
Alignment explanation
Indices: 23449--24197 Score: 871
Period size: 237 Copynumber: 3.2 Consensus size: 237
23439 CGTGTGACTT
* *
23449 GAGGCTGAACTCACCTCTAGCAATATGAGTTGATTTTTTTTGAAAGAACAGAAATTTTAAAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAA-AACAGAAA-TTTAAAAAAA
* * * * * * * **
23514 TACCTCG-ATATGAGCCTGATGCTCAACTCACCTTTCACAATATGAGTTGATTGTTTGAAAAGCA
64 TACCTCGCATGTGA-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAATA
* * * *
23578 TAAA-TTGAA-AATTACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
128 GAAATTTAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
23639 TTTTTTTGGAAAAACAAAAATTGAAAAATACCTCAGCATGTGCCC
193 TTTTTTTGAAAAAACAAAAATTGAAAAATACCTCAGCATGTGCCC
** *
23684 GAGGCTCAACTCACCTCTCTTAATATGAGTTGATTTTTTTTGAAAAGCAGAAA-TT-AAAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAAAATA
* *
23747 CCTCAGCGTGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAATAGA
66 CCTC-GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAATAGA
23812 AATTTAAATGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
130 AATTTAAA-GAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
** *
23877 TTTTTTTTTAAAAACAGAAATTGAAAAATACCTCAGC--GTGACCC
193 TTTTTTTGAAAAAACAAAAATTGAAAAATACCTCAGCATGTG-CCC
* * *
23921 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGGAAAAAATAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAA-AAA
* * *
23986 TACCTCGACATGTG-TCCGAGGCTCAACTCACCTCTCGTAATATGAGTTAATTTTTTTGGAAAAA
64 TACCTCG-CATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT---AAAA
* * * * *
24050 ATAGAATTTTAAAAGAAATATCTCGACATGTG-TCCGAGGCTCAACTCACCTCT-GTAATATGAG
125 ATAGAAATTT-AAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
24113 TTGA--CTTTTGAAAAAACAGAAATTTAAAAGAAATACCTCGGCATG-ACCC
189 TTGATTTTTTTGAAAAAACA-AAAATT-GAA-AAATACCTCAGCATGTGCCC
*
24162 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
24198 AAAAAAAAAC
Statistics
Matches: 442, Mismatches: 49, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
231 12 0.03
232 47 0.11
233 8 0.02
234 7 0.02
235 51 0.12
236 3 0.01
237 81 0.18
238 54 0.12
239 6 0.01
240 45 0.10
241 75 0.17
242 20 0.05
243 30 0.07
244 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (237 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAAAATA
CCTCGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAATAGAA
ATTTAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTTGAAAAAACAAAAATTGAAAAATACCTCAGCATGTGCCC
Done.