Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_382
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: 81862
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2611 original size:16 final size:16
Alignment explanation
Indices: 2590--2635 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
2580 AAAAACTTGA
*
2590 ATTAGAGGTGTATTGG
1 ATTAGAGGTGTAATGG
2606 ATTAGAGGTGTAATGG
1 ATTAGAGGTGTAATGG
*
2622 AATAGAGGTGTAAT
1 ATTAGAGGTGTAAT
2636 AGCAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (16 bp):
ATTAGAGGTGTAATGG
Found at i:2680 original size:45 final size:44
Alignment explanation
Indices: 2614--2708 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
2604 GGATTAGAGG
* *
2614 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
2659 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
2703 TGTAAT
1 TGTAAT
2709 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:2878 original size:25 final size:25
Alignment explanation
Indices: 2846--2900 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2836 TAATTTAATC
*
2846 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
2870 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
2895 ATATAT
1 ATATAT
2901 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:3082 original size:47 final size:46
Alignment explanation
Indices: 3031--3191 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
3021 GATTTAATAA
3031 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
3078 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
3119 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
3166 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
3192 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:8137 original size:123 final size:124
Alignment explanation
Indices: 7917--8206 Score: 503
Period size: 123 Copynumber: 2.3 Consensus size: 124
7907 TTATTTCGAG
* *
7917 TTGACGTTTCTG-GACAAATAGTATAAAATCGCGCCCTCGAGGATGCTAATTGGGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGT
*
7981 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATA-ATTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATATATTTTT
8040 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
* *
8105 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAATAAATATTTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATATATTTTT
*
8164 TTGACGTTTCTGAACAAATAGTATAAAATCGCGCCCTCGTGGA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGA
8207 CGCGATTTTG
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
123 111 0.70
124 48 0.30
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATATATTTTT
Found at i:11433 original size:56 final size:56
Alignment explanation
Indices: 11344--11468 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
11334 TATGTAAAAC
* **
11344 TATGTAAAATTATTAAGCCCAATAACTTCTGTTAATGGTTAGTAA-ATTTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGA-TTATCAAAT
*
11400 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
*
11456 TAGGTAAAATTAT
1 TATGTAAAATTAT
11469 GTTATGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 62 0.98
57 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
Found at i:11524 original size:29 final size:29
Alignment explanation
Indices: 11490--11731 Score: 396
Period size: 29 Copynumber: 8.4 Consensus size: 29
11480 TAAATAAATT
11490 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
11519 AGGTTAGGG-TTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
11547 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
11576 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
11605 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* * *
11634 AAGTTAGGGGTTTTAATCAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
11663 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* *
11692 GGGTTAAGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
11721 GGGTTAGGGTT
1 AGGTTAGGGTT
11732 AGGGTATGAA
Statistics
Matches: 199, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
28 28 0.14
29 171 0.86
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:11696 original size:23 final size:23
Alignment explanation
Indices: 11462--11609 Score: 98
Period size: 23 Copynumber: 5.7 Consensus size: 23
11452 AAATTAGGTA
* * *
11462 AAATTATGTTATGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAATT
11485 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
11508 AAATTAGGTTAAGGTTAGGGTTTTAATT
1 AAATTAGGTT-A-G---GGTTTTTAATT
11536 AAATTAGGTTAAGGTTAGGGTTTTTAATT
1 -AA--A--TT-AGGTTAGGGTTTTTAATT
*
11565 AAATTAGGTTAAGGTTAGGGGTTTTAATT
1 -AA--A--TT-AGGTTAGGGTTTTTAATT
11594 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
11610 AGGGTTTTTA
Statistics
Matches: 107, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
23 40 0.37
24 3 0.03
25 1 0.01
26 1 0.01
28 12 0.11
29 40 0.37
31 1 0.01
32 1 0.01
33 3 0.03
34 5 0.05
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:12968 original size:7 final size:7
Alignment explanation
Indices: 12958--12990 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
12948 TTATATACAT
12958 AATACTA
1 AATACTA
12965 AATACTA
1 AATACTA
12972 AATACTA
1 AATACTA
12979 AATACTA
1 AATACTA
*
12986 TATAC
1 AATAC
12991 CGGTCCCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:14231 original size:38 final size:37
Alignment explanation
Indices: 14142--14214 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
14132 GTCTCCAAAT
* * *
14142 TCACATTTCAATTC-AATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAAAATTCAATTTTTCACTTTCAA
*
14178 TCACAATTCAATTCAAAATTCAATTTTTCATTTTCAA
1 TCACAATTCAATTCAAAATTCAATTTTTCACTTTCAA
14215 ATCAATATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAAAATTCAATTTTTCACTTTCAA
Found at i:14442 original size:3 final size:3
Alignment explanation
Indices: 14434--14466 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
14424 AATCTCACTC
14434 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14467 CTTATACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16397 original size:11 final size:11
Alignment explanation
Indices: 16381--16459 Score: 83
Period size: 11 Copynumber: 7.2 Consensus size: 11
16371 TTTAAATAGG
16381 AATTTGAGAGA
1 AATTTGAGAGA
16392 AATTTGAGAGGA
1 AATTTGAGA-GA
16404 AA-TTGAGAGCA
1 AATTTGAGAG-A
*
16415 AA-TTCAGAGA
1 AATTTGAGAGA
16425 AATTTGAGAGA
1 AATTTGAGAGA
**
16436 ATATTAAAGAGA
1 A-ATTTGAGAGA
16448 AA-TTGAGAGA
1 AATTTGAGAGA
16458 AA
1 AA
16460 GGATTTAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
10 12 0.21
11 33 0.57
12 13 0.22
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.23
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:16424 original size:33 final size:33
Alignment explanation
Indices: 16387--16459 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
16377 TAGGAATTTG
*
16387 AGAGAAATTTGAGAGGAA-ATT-GAGAGCAAATTC
1 AGAGAAATTTGAGA-GAATATTAAAGAG-AAATTC
*
16420 AGAGAAATTTGAGAGAATATTAAAGAGAAATTG
1 AGAGAAATTTGAGAGAATATTAAAGAGAAATTC
16453 AGAGAAA
1 AGAGAAA
16460 GGATTTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 3 0.08
33 29 0.81
34 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.21
Consensus pattern (33 bp):
AGAGAAATTTGAGAGAATATTAAAGAGAAATTC
Found at i:21503 original size:33 final size:33
Alignment explanation
Indices: 21448--21527 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
21438 GTATATTGAT
*
21448 GATGCAGCCGTGTACAGCAATGCCGCGTGTATC
1 GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
* *
21481 GATGGAGCCGTGTGCAGGAATGCCGCGTGTATC
1 GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
21514 GATGGAGCCGTGTA
1 GATGGAGCCGTGTA
21528 TATCAGAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (33 bp):
GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
Found at i:22121 original size:27 final size:28
Alignment explanation
Indices: 22064--22121 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
22054 CAGCCCAGCC
** * *
22064 TAATTTATTATTTAATAATTAAAATTTA
1 TAATTTATTATTTAATAAAAAAAACTAA
*
22092 TAATTTTTTA-TTAATAAAAAAAACTAA
1 TAATTTATTATTTAATAAAAAAAACTAA
22119 TAA
1 TAA
22122 GCGAAGGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATTTATTATTTAATAAAAAAAACTAA
Found at i:22658 original size:19 final size:20
Alignment explanation
Indices: 22626--22694 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
22616 CATGTGGCAA
22626 AAAAATTATAAAAAATTATT
1 AAAAATTATAAAAAATTATT
* *
22646 AAAAGTTAT-AAAAGTTATT
1 AAAAATTATAAAAAATTATT
**
22665 AAATTTTAATAAAAAA-TA--
1 AAAAATT-ATAAAAAATTATT
22683 AAAAATTATAAA
1 AAAAATTATAAA
22695 TGTATCAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 14 0.35
20 12 0.30
21 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATTATAAAAAATTATT
Found at i:22667 original size:10 final size:10
Alignment explanation
Indices: 22626--22667 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
22616 CATGTGGCAA
*
22626 AAAAATTATA
1 AAAAATTATT
22636 AAAAATTATT
1 AAAAATTATT
*
22646 AAAAGTTA-T
1 AAAAATTATT
*
22655 AAAAGTTATT
1 AAAAATTATT
22665 AAA
1 AAA
22668 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:22836 original size:21 final size:20
Alignment explanation
Indices: 22810--22855 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
22800 TGTTGTGACA
22810 AAAATTGATAAAAAAATTAAT
1 AAAATTGAT-AAAAAATTAAT
* * *
22831 AAAATTTATAGAAAATTTAT
1 AAAATTGATAAAAAATTAAT
22851 AAAAT
1 AAAAT
22856 GCTTCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTGATAAAAAATTAAT
Found at i:22916 original size:20 final size:21
Alignment explanation
Indices: 22874--22916 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
22864 TAGTATGGTA
*
22874 TTTTTATATATTTCTTTATAC
1 TTTTTATATATTTCTTTAAAC
22895 TTTTTATA-ATTT-TCTTAAAC
1 TTTTTATATATTTCT-TTAAAC
22915 TT
1 TT
22917 AATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATATATTTCTTTAAAC
Found at i:23046 original size:23 final size:23
Alignment explanation
Indices: 23020--23065 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
23010 TTGTATTAAA
23020 ATTTAATCATTTTTATAATTTTT
1 ATTTAATCATTTTTATAATTTTT
* ** *
23043 ATTTATTTTTTTTTATCATTTTT
1 ATTTAATCATTTTTATAATTTTT
23066 TTTCACATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTTAATCATTTTTATAATTTTT
Found at i:23321 original size:7 final size:7
Alignment explanation
Indices: 23305--23349 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
23295 CCTTAAGCCT
*
23305 AAAAATA
1 AAAAAGA
23312 AAAAAGA
1 AAAAAGA
23319 AAAAAGAA
1 AAAAAG-A
23327 AAAAAGA
1 AAAAAGA
*
23334 AATAAGA
1 AAAAAGA
*
23341 AATAAGA
1 AAAAAGA
23348 AA
1 AA
23350 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAGA
Found at i:23329 original size:15 final size:15
Alignment explanation
Indices: 23311--23342 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23301 GCCTAAAAAT
23311 AAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAGA
*
23326 AAAAAAGAAATAAGA
1 AAAAAAGAAAAAAGA
23341 AA
1 AA
23343 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:23331 original size:22 final size:22
Alignment explanation
Indices: 23305--23354 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
23295 CCTTAAGCCT
*
23305 AAAAATAAAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
* *
23327 AAAAAGAAATAAGAAATAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
23349 ATAAAA
1 A-AAAA
23355 ATTATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAAGAA
Found at i:23350 original size:7 final size:7
Alignment explanation
Indices: 23315--23356 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
23305 AAAAATAAAA
*
23315 AAGAAAA
1 AAGAAAT
*
23322 AAGAAAAA
1 AAG-AAAT
23330 AAGAAAT
1 AAGAAAT
23337 AAGAAAT
1 AAGAAAT
23344 AAGAAAT
1 AAGAAAT
23351 AA-AAAT
1 AAGAAAT
23357 TATAAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 4 0.12
7 22 0.67
8 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (7 bp):
AAGAAAT
Found at i:29294 original size:7 final size:7
Alignment explanation
Indices: 29267--29301 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
29257 TAATGTTGTT
29267 TTTATTA
1 TTTATTA
*
29274 TTTCTTA
1 TTTATTA
*
29281 GTTATTA
1 TTTATTA
29288 TTTATTA
1 TTTATTA
29295 TTTATTA
1 TTTATTA
29302 ATAAAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:29994 original size:3 final size:3
Alignment explanation
Indices: 29986--30024 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29976 AAGTGAAAAT
29986 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30025 CCTCCCTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30239 original size:26 final size:26
Alignment explanation
Indices: 30165--30239 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
30155 TATTTATTTT
* * *
30165 TAAAAAACTAAAAAGTTCAAAACATA
1 TAAAAATCTAAAAAATTCAAAATATA
* **
30191 T-ATAAT-TTTAAAATTCACGAAATATA
1 TAAAAATCTAAAAAATTCA--AAATATA
30217 TAAAAATCTAAAAAATTCAAAAT
1 TAAAAATCTAAAAAATTCAAAAT
30240 TAAAGAATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
24 8 0.22
25 3 0.08
26 12 0.33
27 4 0.11
28 9 0.25
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (26 bp):
TAAAAATCTAAAAAATTCAAAATATA
Found at i:33444 original size:23 final size:23
Alignment explanation
Indices: 33399--33444 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33389 AATTGGCCGG
* *
33399 AATTAAATTATTTTATTTAAAAA
1 AATTAAATTATTTAATATAAAAA
* *
33422 AATTAATTTATTTAATATCAAAA
1 AATTAAATTATTTAATATAAAAA
33445 TCGAGAGGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTAAATTATTTAATATAAAAA
Found at i:34962 original size:30 final size:30
Alignment explanation
Indices: 34926--34985 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34916 TGTGGCAATC
34926 CACATACTTTTATAAAAATTCAAAAGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
34956 CACATACTTTTATAAAAATTCAAAAGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
34986 AATAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (30 bp):
CACATACTTTTATAAAAATTCAAAAGAATT
Found at i:48345 original size:41 final size:42
Alignment explanation
Indices: 48263--48350 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
48253 GTATTTTTCA
*
48263 AAAGTTTATGTTAATATTCAAAACCAAAATAATTATTAGTGT
1 AAAGTTTATGTTAATATTCAAAACCAAAATAATTAATAGTGT
* ** * *
48305 AAAGTTTATGTTAGTATT-TTAATCAATATAATTAATAGTGT
1 AAAGTTTATGTTAATATTCAAAACCAAAATAATTAATAGTGT
*
48346 TAAGT
1 AAAGT
48351 GATTGAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 22 0.56
42 17 0.44
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (42 bp):
AAAGTTTATGTTAATATTCAAAACCAAAATAATTAATAGTGT
Found at i:50061 original size:16 final size:15
Alignment explanation
Indices: 50040--50103 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 15
50030 TTGAAATTAA
50040 ATTATATATATTTATT
1 ATTATATAT-TTTATT
*
50056 ATTATA-ATTTTATA
1 ATTATATATTTTATT
* *
50070 ATTTTATAATTTTAAT
1 ATTATAT-ATTTTATT
* *
50086 AGTGTATATTTTATT
1 ATTATATATTTTATT
50101 ATT
1 ATT
50104 TAAAAAGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 10 0.26
15 11 0.29
16 17 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTATATATTTTATT
Found at i:50070 original size:8 final size:8
Alignment explanation
Indices: 50057--50083 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
50047 ATATTTATTA
50057 TTATAATT
1 TTATAATT
50065 TTATAATT
1 TTATAATT
50073 TTATAATT
1 TTATAATT
50081 TTA
1 TTA
50084 ATAGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATAATT
Found at i:50075 original size:22 final size:23
Alignment explanation
Indices: 50041--50103 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
50031 TGAAATTAAA
50041 TTATATATATTTATTATTATAAT-T
1 TTATA-AT-TTTATTATTATAATAT
* *
50065 TTATAATTTTATAATTTTAATAGT
1 TTATAATTTTATTATTATAATA-T
*
50089 GTAT-ATTTTATTATT
1 TTATAATTTTATTATT
50104 TAAAAAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (23 bp):
TTATAATTTTATTATTATAATAT
Found at i:51730 original size:25 final size:25
Alignment explanation
Indices: 51689--51738 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
51679 TTTTTAATCA
51689 ATATATCTACATACTATAT-TTTTT
1 ATATATCTACATACTATATGTTTTT
51713 ATATATGCTACA-ATCTATATGTTTTT
1 ATATAT-CTACATA-CTATATGTTTTT
51739 TTTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (25 bp):
ATATATCTACATACTATATGTTTTT
Found at i:51975 original size:26 final size:24
Alignment explanation
Indices: 51927--51974 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
51917 ACATATGCAC
51927 ATACTTACATTTTTATTTTATATA
1 ATACTTACATTTTTATTTTATATA
*
51951 ATACTTACAGTTTTT-TTCTATATA
1 ATACTTACA-TTTTTATTTTATATA
51975 TGTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATACTTACATTTTTATTTTATATA
Found at i:67380 original size:6 final size:6
Alignment explanation
Indices: 67371--67395 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
67361 AATTCTGTTC
67371 CTTTTA CTTTTA CTTTTA CTTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA C
67396 ACATTGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
CTTTTA
Found at i:70371 original size:3 final size:3
Alignment explanation
Indices: 70365--70389 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
70355 TTCTTCTTCA
70365 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
70390 GTAACAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:70874 original size:3 final size:3
Alignment explanation
Indices: 70866--70903 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
70856 TGAGAAGCCA
70866 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
70904 AGTGGAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.