Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1170
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: 74508
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:880 original size:2 final size:2
Alignment explanation
Indices: 873--902 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
863 CCATAAATTT
873 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
903 TTCTACTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3742 original size:19 final size:19
Alignment explanation
Indices: 3715--3752 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3705 ATATATGTGA
*
3715 TAAAAATATTAA-TATTTT
1 TAAAAATATAAATTATTTT
3733 TAAAATATATAAATTATTTT
1 TAAAA-ATATAAATTATTTT
3753 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAAATATAAATTATTTT
Found at i:3758 original size:13 final size:13
Alignment explanation
Indices: 3742--3766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3732 TTAAAATATA
3742 TAAATTATTTTAT
1 TAAATTATTTTAT
3755 TAAATTATTTTA
1 TAAATTATTTTA
3767 AATTAAAATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTATTTTAT
Found at i:3773 original size:15 final size:15
Alignment explanation
Indices: 3742--3783 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3732 TTAAAATATA
3742 TAAATTATTTT--AT
1 TAAATTATTTTAAAT
3755 TAAATTATTTTAAAT
1 TAAATTATTTTAAAT
* *
3770 TAAAATAATTTAAA
1 TAAATTATTTTAAA
3784 AATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
15 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTATTTTAAAT
Found at i:4735 original size:3 final size:3
Alignment explanation
Indices: 4727--4773 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
4717 TATATTTTAG
4727 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
4773 A
1 A
4774 GTTTTTTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4884 original size:3 final size:3
Alignment explanation
Indices: 4876--4919 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4866 GAATAATGCT
4876 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4920 TGCTATAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5247 original size:15 final size:15
Alignment explanation
Indices: 5209--5255 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5199 CATTGATCAC
*
5209 TTTAGCATAAATA-T
1 TTTAGCACAAATACT
* *
5223 CTTAGTACAAATACT
1 TTTAGCACAAATACT
*
5238 TTTAGCACAATTACT
1 TTTAGCACAAATACT
5253 TTT
1 TTT
5256 GGTGTAATAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (15 bp):
TTTAGCACAAATACT
Found at i:5309 original size:45 final size:45
Alignment explanation
Indices: 5242--5328 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
5232 AATACTTTTA
* * *
5242 GCACAATTACTTTTGGTGTAATACTTTGACACAAGTATCATTCGG
1 GCACAATTACTTTTGATATAATACTTTGACACAAATATCATTCGG
* * * *
5287 GCACAGTTATTTTTGATATAATAGTTTGACATAAATATCATT
1 GCACAATTACTTTTGATATAATACTTTGACACAAATATCATT
5329 ATACCTTTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (45 bp):
GCACAATTACTTTTGATATAATACTTTGACACAAATATCATTCGG
Found at i:11414 original size:16 final size:16
Alignment explanation
Indices: 11393--11425 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11383 CTGGCCAACA
11393 GCTATGTGGTCTGTTG
1 GCTATGTGGTCTGTTG
11409 GCTATGTGGTCTGTTG
1 GCTATGTGGTCTGTTG
11425 G
1 G
11426 TAAAGTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.42
Consensus pattern (16 bp):
GCTATGTGGTCTGTTG
Found at i:13285 original size:2 final size:2
Alignment explanation
Indices: 13278--13305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13268 AAAAGTACTC
13278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13306 GAAATGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15249 original size:16 final size:15
Alignment explanation
Indices: 15228--15260 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
15218 TTTATTTTTT
15228 AAAAAATTATATATTA
1 AAAAAATTATA-ATTA
15244 AAAAAATTATAATTA
1 AAAAAATTATAATTA
15259 AA
1 AA
15261 GTAATCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATTATAATTA
Found at i:15413 original size:24 final size:23
Alignment explanation
Indices: 15343--15415 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 23
15333 TATTTAAAAT
*
15343 AATATTAATTTATAATTAAATTTA
1 AATAATAATTTA-AATTAAATTTA
* *
15367 AATAATTTATTT-TATT--ATTTA
1 AATAA-TAATTTAAATTAAATTTA
15388 AATAATAATTTAAATTAAATTATA
1 AATAATAATTTAAATTAAATT-TA
15412 AATA
1 AATA
15416 TGTCTCTCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.13
21 13 0.33
23 6 0.15
24 10 0.26
25 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAATAATTTAAATTAAATTTA
Found at i:15414 original size:45 final size:49
Alignment explanation
Indices: 15321--15415 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
15311 TTAACTTAAC
15321 AATTTATTTCATTATTTAAAATAATATTAATTTATAATTAAATTTAAAT
1 AATTTATTTCATTATTTAAAATAATATTAATTTATAATTAAATTTAAAT
*
15370 AATTTATTTTATTATTT-AAAT-A-A-TAATTTA-AATTAAATTATAAAT
1 AATTTATTTCATTATTTAAAATAATATTAATTTATAATTAAATT-TAAAT
15415 A
1 A
15416 TGTCTCTCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
44 9 0.20
45 13 0.30
46 1 0.02
47 1 0.02
48 4 0.09
49 16 0.36
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (49 bp):
AATTTATTTCATTATTTAAAATAATATTAATTTATAATTAAATTTAAAT
Found at i:21254 original size:15 final size:15
Alignment explanation
Indices: 21234--21294 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
21224 AATTTAATAA
*
21234 TTTATTTAATTGTAT
1 TTTATTTAATTATAT
*
21249 TTTATTTATATTATTT
1 TTTATTTA-ATTATAT
21265 TTTATTTAATTATAT
1 TTTATTTAATTATAT
* *
21280 TATA-ATAATTATAT
1 TTTATTTAATTATAT
21294 T
1 T
21295 ATAAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
14 10 0.25
15 17 0.43
16 13 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTATTTAATTATAT
Found at i:21318 original size:15 final size:15
Alignment explanation
Indices: 21274--21320 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
21264 TTTTATTTAA
21274 TTATATTATAATAA-
1 TTATATTATAATAAT
*
21288 TTATATTATAAAAAT
1 TTATATTATAATAAT
21303 TTATA-TATTAATAAT
1 TTATATTA-TAATAAT
21318 TTA
1 TTA
21321 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATTATAATAAT
Found at i:21558 original size:21 final size:23
Alignment explanation
Indices: 21533--21576 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21523 TAACGTAATA
*
21533 TTAAT-AAATTATA-TTATATTT
1 TTAATAAAAATATATTTATATTT
21554 TTAATAAAAATATATTTATATTT
1 TTAATAAAAATATATTTATATTT
21577 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATAAAAATATATTTATATTT
Found at i:21558 original size:27 final size:27
Alignment explanation
Indices: 21535--21591 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
21525 ACGTAATATT
21535 AATA-AATTATATTATATTTTTAATAAA
1 AATATAATTATATT-TATTTTTAATAAA
* *
21562 AATATATTTATATTTATTTTTTATTAAA
1 AATATAATTATATTTA-TTTTTAATAAA
21590 AA
1 AA
21592 AAAGTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATAATTATATTTATTTTTAATAAA
Found at i:21577 original size:21 final size:21
Alignment explanation
Indices: 21533--21577 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21523 TAACGTAATA
* *
21533 TTAATAAATTATATTATATTT
1 TTAATAAAATATATTATATAT
21554 TTAATAAAAATATATT-TATAT
1 TTAAT-AAAATATATTATATAT
21575 TTA
1 TTA
21578 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATAAAATATATTATATAT
Found at i:25113 original size:8 final size:8
Alignment explanation
Indices: 25097--25134 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
25087 TTTTTATATT
*
25097 TATATATA
1 TATAAATA
25105 TATAAATA
1 TATAAATA
*
25113 TAAAAATA
1 TATAAATA
25121 TA-AAATA
1 TATAAATA
25128 TATAAAT
1 TATAAAT
25135 GCATAACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TATAAATA
Found at i:25266 original size:12 final size:12
Alignment explanation
Indices: 25243--25298 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
25233 TACCATATTC
*
25243 ATATTATTTTTT
1 ATATTATATTTT
*
25255 ATGTTATATTTT
1 ATATTATATTTT
*
25267 ATATTTTATTTT
1 ATATTATATTTT
25279 A-ATTAT-TTTT
1 ATATTATATTTT
25289 ATATTATATT
1 ATATTATATT
25299 CGGATTGTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.14
11 9 0.24
12 23 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:26878 original size:38 final size:38
Alignment explanation
Indices: 26829--27006 Score: 230
Period size: 38 Copynumber: 4.7 Consensus size: 38
26819 TTGAATTAGT
* * *
26829 TGACGGTTAGAGAATTCAATTTGAAATTGACTGGCAGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
*
26867 TGACGGCTAGAGAATTCAATTTGAAATTGGTTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* *
26905 TGACGGCTAGAGAATTTAATTTGAAATTGGCCGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
* * * *
26943 TGACGACTAGAGAATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
** *
26981 TGGTGGCTAGAGAATTCCAAATTGAA
1 TGACGGCTAGAGAATT-CAATTTGAA
27007 CTCTCTTTGA
Statistics
Matches: 123, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 116 0.94
39 7 0.06
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.28
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
Found at i:30578 original size:38 final size:38
Alignment explanation
Indices: 30535--30688 Score: 245
Period size: 38 Copynumber: 4.1 Consensus size: 38
30525 TTGAATTAGT
* *
30535 TGACGGTTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGC
*
30573 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGC
*
30611 TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGT
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGC
* * *
30649 TGACGACTAGAGAATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGC
30687 TG
1 TG
30689 GTGGCTGGTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 109 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCCGGCGGC
Found at i:32066 original size:3 final size:3
Alignment explanation
Indices: 32060--32089 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
32050 ATAAAAAAAG
32060 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
32090 AAGTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:36267 original size:11 final size:12
Alignment explanation
Indices: 36251--36288 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
36241 TATATTCATG
36251 TATTTAT-ATCA
1 TATTTATAATCA
36262 TATTTATAAT-A
1 TATTTATAATCA
*
36273 TTTTTATAATCA
1 TATTTATAATCA
36285 TATT
1 TATT
36289 GTATTATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATAATCA
Found at i:37840 original size:13 final size:13
Alignment explanation
Indices: 37822--37846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37812 ATTACTCAAA
37822 TGTATCGATACAT
1 TGTATCGATACAT
37835 TGTATCGATACA
1 TGTATCGATACA
37847 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37899 original size:52 final size:52
Alignment explanation
Indices: 37855--37982 Score: 247
Period size: 52 Copynumber: 2.5 Consensus size: 52
37845 CACTGATCTT
37855 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
37907 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
37959 TGTATCGATACATGCAGGCAAATT
1 TGTATCGATACATGCAGGCAAATT
37983 CTCATATTTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:41084 original size:2 final size:2
Alignment explanation
Indices: 41077--41119 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
41067 CTCATTTTAA
41077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
41119 A
1 A
41120 ATCATGTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41886 original size:27 final size:27
Alignment explanation
Indices: 41846--41898 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
41836 TATAAAATTT
* *
41846 ATTTATATATAAATATTTTATAATTAC
1 ATTTAAATACAAATATTTTATAATTAC
*
41873 ATTTAAATACAAATATTTTTTAATTA
1 ATTTAAATACAAATATTTTATAATTA
41899 TTAAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAAATACAAATATTTTATAATTAC
Found at i:42619 original size:20 final size:21
Alignment explanation
Indices: 42596--42640 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
42586 AAAATATAGA
42596 GATATAATGTGT-ATTATATC
1 GATATAATGTGTAATTATATC
* *
42616 GATATACTTTGTAATTATATC
1 GATATAATGTGTAATTATATC
42637 GATA
1 GATA
42641 CATTTACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (21 bp):
GATATAATGTGTAATTATATC
Found at i:42868 original size:15 final size:15
Alignment explanation
Indices: 42848--42876 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42838 CTGCAATCTC
42848 TTTTTATTATTTTAT
1 TTTTTATTATTTTAT
42863 TTTTTATTATTTTA
1 TTTTTATTATTTTA
42877 ATTAAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTATTTTAT
Found at i:43204 original size:19 final size:17
Alignment explanation
Indices: 43170--43206 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43160 TTATATAAAA
43170 TATATTAAAATATTTAT
1 TATATTAAAATATTTAT
*
43187 TATATTAACATATTT-T
1 TATATTAAAATATTTAT
43203 TATA
1 TATA
43207 AATAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTAAAATATTTAT
Found at i:43289 original size:16 final size:16
Alignment explanation
Indices: 43252--43293 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
43242 AAATCAAACT
43252 ATAAATTTAAATTATC
1 ATAAATTTAAATTATC
*
43268 AAAAATTTAAATTAT-
1 ATAAATTTAAATTATC
43283 ATTAAATTTAA
1 A-TAAATTTAA
43294 TTTCAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATTTAAATTATC
Found at i:43576 original size:13 final size:13
Alignment explanation
Indices: 43558--43585 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43548 AACACCTTAA
43558 CTTTATGTGATTG
1 CTTTATGTGATTG
43571 CTTTATGTGATTG
1 CTTTATGTGATTG
43584 CT
1 CT
43586 GATGTTAACT
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:0.14, C:0.11, G:0.21, T:0.54
Consensus pattern (13 bp):
CTTTATGTGATTG
Found at i:45177 original size:55 final size:55
Alignment explanation
Indices: 45118--45222 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
45108 ATGATAAAGA
* *
45118 TTGAAGTTCATGCCCGC-AACAAGACTCTTGTGGGTCACCTTGGCCATGATTGAGG
1 TTGAAGTTCACG-CAGCTAACAAGACTCTTGTGGGTCACCTTGGCCATGATTGAGG
* *
45173 TTGAAGTTCACGCAGCTAATAGGACTCTTGTGGGTCACCTTGGCCATGAT
1 TTGAAGTTCACGCAGCTAACAAGACTCTTGTGGGTCACCTTGGCCATGAT
45223 CTGTTTGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 3 0.07
55 42 0.93
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.29
Consensus pattern (55 bp):
TTGAAGTTCACGCAGCTAACAAGACTCTTGTGGGTCACCTTGGCCATGATTGAGG
Found at i:45403 original size:16 final size:16
Alignment explanation
Indices: 45384--45415 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45374 TTTAAATAAT
45384 TTTATATTTATAAATA
1 TTTATATTTATAAATA
45400 TTTATATTTATAAATA
1 TTTATATTTATAAATA
45416 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATATTTATAAATA
Found at i:45468 original size:19 final size:19
Alignment explanation
Indices: 45428--45484 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
45418 TAATTTAAAT
*
45428 TTTTTTATTTTTATTATAA
1 TTTTTTATTTTTAATATAA
*
45447 TTTTTTATTTTTAAATATAT
1 TTTTTTATTTTT-AATATAA
45467 TTTAATTTAATTTTTAAT
1 TTT--TTT-ATTTTTAAT
45485 TATTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 12 0.38
20 8 0.25
22 6 0.19
23 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTATTTTTAATATAA
Found at i:45469 original size:18 final size:18
Alignment explanation
Indices: 45421--45510 Score: 54
Period size: 18 Copynumber: 5.4 Consensus size: 18
45411 AAATAAATAA
45421 TTTAAAT-T-TTTTTATT
1 TTTAAATATATTTTTATT
*
45437 TTT-ATTATAATTTTTTATT
1 TTTAAATAT-A-TTTTTATT
*
45456 TTTAAATATA-TTTTA-A
1 TTTAAATATATTTTTATT
*
45472 TTT--A-AT-TTTTAATT
1 TTTAAATATATTTTTATT
*
45486 ATTAAATATATTTTTATT
1 TTTAAATATATTTTTATT
*
45504 ATTAAAT
1 TTTAAAT
45511 TTTTATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
13 6 0.11
14 3 0.05
15 2 0.04
16 8 0.14
17 7 0.12
18 14 0.25
19 12 0.21
20 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAATATATTTTTATT
Found at i:45478 original size:30 final size:30
Alignment explanation
Indices: 45433--45518 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
45423 TAAATTTTTT
* *
45433 TATTTTTATTATAATTTTTTATTTTTAAATA
1 TATTTTAATT-TAATTTTTTATTATTAAATA
*
45464 TATTTTAATTTAATTTTTAATTATTAAATA
1 TATTTTAATTTAATTTTTTATTATTAAATA
* *
45494 TATTTTTATTATTAAATTTTTATTA
1 TA-TTTTAAT-TTAATTTTTTATTA
45519 ATATTCTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 20 0.43
31 15 0.32
32 12 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TATTTTAATTTAATTTTTTATTATTAAATA
Found at i:46129 original size:19 final size:18
Alignment explanation
Indices: 46086--46129 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
46076 TTAAATTTAT
46086 TTTTAAAAATAAAAATATA
1 TTTT-AAAATAAAAATATA
*
46105 TATTAAAATAAAAATAATA
1 TTTTAAAATAAAAAT-ATA
46124 TTTTAA
1 TTTTAA
46130 TAATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTAAAATAAAAATATA
Found at i:46132 original size:17 final size:18
Alignment explanation
Indices: 46091--46125 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46081 TTTATTTTTA
46091 AAAATAAAAATATATATT
1 AAAATAAAAATATATATT
46109 AAAATAAAAATA-ATATT
1 AAAATAAAAATATATATT
46126 TTAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAAAAATATATATT
Found at i:46180 original size:23 final size:20
Alignment explanation
Indices: 46123--46183 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 20
46113 TAAAAATAAT
*
46123 ATTTTAATAATTTAATAAAA
1 ATTTTAAAAATTTAATAAAA
46143 ATTTTAATATTAATTTAAGTAAAAAA
1 ATTTTAA-A--AATTTAA-T--AAAA
46169 ATTTTAAAAATTTAA
1 ATTTTAAAAATTTAA
46184 ATCATAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 7 0.21
23 14 0.41
24 1 0.03
25 1 0.03
26 11 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTTAAAAATTTAATAAAA
Found at i:46223 original size:20 final size:20
Alignment explanation
Indices: 46189--46231 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
46179 TTTAAATCAT
46189 AATTTAATATAAAAT-TAAA
1 AATTTAATATAAAATATAAA
*
46208 AATTTAAATTTAAAATATAAA
1 AATTT-AATATAAAATATAAA
46229 AAT
1 AAT
46232 ATTTTAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTAATATAAAATATAAA
Found at i:46311 original size:31 final size:31
Alignment explanation
Indices: 46273--46369 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
46263 TAATATATCG
**
46273 ATGTCTTGGTTTCTTCTTAGCAGCATCCAGA
1 ATGTCTTGGTTTCTTCCCAGCAGCATCCAGA
*
46304 ATGTCTTGGTTTCTTCCCAGCAGTATCCAGA
1 ATGTCTTGGTTTCTTCCCAGCAGCATCCAGA
* * * * *
46335 ATGTC-TAGTGTCTTCCGAGCAGTATCCAAA
1 ATGTCTTGGTTTCTTCCCAGCAGCATCCAGA
46365 ATGTC
1 ATGTC
46370 CAGTTCTGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 26 0.44
31 33 0.56
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (31 bp):
ATGTCTTGGTTTCTTCCCAGCAGCATCCAGA
Found at i:46780 original size:9 final size:9
Alignment explanation
Indices: 46762--46791 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
46752 CTATGGCTTT
*
46762 TTATTTTTA
1 TTATTGTTA
46771 TTATTGTTA
1 TTATTGTTA
46780 TTATTGTTA
1 TTATTGTTA
46789 TTA
1 TTA
46792 ATAGTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (9 bp):
TTATTGTTA
Found at i:46819 original size:10 final size:10
Alignment explanation
Indices: 46798--46833 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
46788 ATTAATAGTT
46798 TATTTAATAAA
1 TATTT-ATAAA
46809 TATTTATAAA
1 TATTTATAAA
*
46819 TATTTATTAA
1 TATTTATAAA
46829 TATTT
1 TATTT
46834 TTACTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTATAAA
Found at i:47401 original size:26 final size:24
Alignment explanation
Indices: 47361--47411 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
47351 AAATCGTTGT
*
47361 TAAAATTATTTTATTTTATTTTTA
1 TAAAATTATTTTATTTTAATTTTA
47385 TAAAATATATATTTATTTTAATTTTA
1 TAAAAT-TAT-TTTATTTTAATTTTA
47411 T
1 T
47412 TTTATTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.25
25 3 0.12
26 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TAAAATTATTTTATTTTAATTTTA
Found at i:59921 original size:14 final size:14
Alignment explanation
Indices: 59880--59922 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
59870 ATAAATTTAA
* *
59880 ATTTTAAATTTTAAT
1 ATTTTTAATTTT-TT
*
59895 ATTTATAATTTTTT
1 ATTTTTAATTTTTT
59909 ATTTTTAATTTTTT
1 ATTTTTAATTTTTT
59923 TATAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTTAATTTTTT
Found at i:60585 original size:22 final size:20
Alignment explanation
Indices: 60558--60601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
60548 CGTATACTAA
60558 TATTATATTCTCATGTTATTTT
1 TATTATATT-TCAT-TTATTTT
*
60580 TATTATATTTTATTTATTTT
1 TATTATATTTCATTTATTTT
60600 TA
1 TA
60602 AGATATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 9 0.43
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTATATTTCATTTATTTT
Found at i:62725 original size:36 final size:36
Alignment explanation
Indices: 62661--62751 Score: 95
Period size: 36 Copynumber: 2.6 Consensus size: 36
62651 TAAATACGGT
62661 AATATT-AAATATAAT-T-ATATGAATATATATGAAA
1 AATATTAAAATATAATATAATATGAATATATAT-AAA
62695 AATAATTAAAATATAATATAATAT-AA-ATATATAAA
1 AAT-ATTAAAATATAATATAATATGAATATATATAAA
* * *
62730 TATTTTAAAAT-TTATATAATAT
1 AATATTAAAATATAATATAATAT
62752 TAATTATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
33 10 0.20
34 10 0.20
35 8 0.16
36 15 0.30
37 3 0.06
38 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (36 bp):
AATATTAAAATATAATATAATATGAATATATATAAA
Found at i:62747 original size:33 final size:33
Alignment explanation
Indices: 62694--62801 Score: 103
Period size: 33 Copynumber: 3.2 Consensus size: 33
62684 TATATATGAA
*
62694 AAATA-ATTAAAATATAATATAATATAAATATAT
1 AAATATATTAAAAT-TTATATAATATAAATATAT
* *
62727 AAATATTTTAAAATTTATATAATATTAAT-TAT
1 AAATATATTAAAATTTATATAATATAAATATAT
* * * *
62759 TAATATATAAAAAATTATATAAATATAAAATATCTT
1 AAATATATTAAAATTTATAT-AATAT-AAATAT-AT
62795 AAATATA
1 AAATATA
62802 ATTATAATAC
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
32 19 0.32
33 23 0.38
34 10 0.17
35 1 0.02
36 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATATATTAAAATTTATATAATATAAATATAT
Found at i:63043 original size:11 final size:11
Alignment explanation
Indices: 63024--63089 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
63014 AAAATATTTA
* *
63024 TATACTTATGT
1 TATATTTATAT
63035 TATATTTATAT
1 TATATTTATAT
*
63046 TATTTTTTATAT
1 TA-TATTTATAT
63058 TATATTT-TAAT
1 TATATTTAT-AT
*
63069 TATATTTTTAT
1 TATATTTATAT
*
63080 CATATTTATA
1 TATATTTATA
63090 AACATATTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
10 1 0.02
11 34 0.74
12 11 0.24
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:63056 original size:12 final size:12
Alignment explanation
Indices: 63039--63079 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
63029 TTATGTTATA
63039 TTTATATTATTT
1 TTTATATTATTT
*
63051 TTTATATTATAT
1 TTTATATTATTT
63063 TTTA-ATTATATT
1 TTTATATTAT-TT
63075 TTTAT
1 TTTAT
63080 CATATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:63060 original size:23 final size:23
Alignment explanation
Indices: 63029--63089 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
63019 ATTTATATAC
* *
63029 TTATGTTATATTTATATTATTTT
1 TTATATTATATTTATATTATATT
63052 TTATATTATATTT-TAATTATATT
1 TTATATTATATTTAT-ATTATATT
*
63075 TT-TATCATATTTATA
1 TTATATTATATTTATA
63090 AACATATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATATTATATTTATATTATATT
Found at i:63956 original size:3 final size:3
Alignment explanation
Indices: 63940--63980 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
63930 GGGAGTGTGA
*
63940 AGG AGG A-G ACGG AGG AGG AGG AGG AGG AGG AAG AGG AGG AG
1 AGG AGG AGG A-GG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
63981 ACAAGGGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.61, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:72484 original size:47 final size:45
Alignment explanation
Indices: 72427--72519 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 45
72417 AAAGCTCGAA
72427 TCCATTGCAATTTGAGCCCGACAA-TAATTTGAATCTGAGCCTTAAAC
1 TCCATTGCAATTTGAGCCCGA-AACTAATTTG-ATCTGA-CCTTAAAC
72474 TCCATTGCAATTTGAGCCCGAAACTAATTTGATCTGACCTTAAAC
1 TCCATTGCAATTTGAGCCCGAAACTAATTTGATCTGACCTTAAAC
72519 T
1 T
72520 GATCCAATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
45 9 0.20
46 8 0.18
47 28 0.62
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (45 bp):
TCCATTGCAATTTGAGCCCGAAACTAATTTGATCTGACCTTAAAC
Found at i:72497 original size:24 final size:24
Alignment explanation
Indices: 72427--72498 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
72417 AAAGCTCGAA
72427 TCCATTGCAATTTGAGCCCGACAA-
1 TCCATTGCAATTTGAGCCCGA-AAC
* * **
72451 T-AATTTG-AATCTGAGCCTTAAAC
1 TCCA-TTGCAATTTGAGCCCGAAAC
72474 TCCATTGCAATTTGAGCCCGAAAC
1 TCCATTGCAATTTGAGCCCGAAAC
72498 T
1 T
72499 AATTTGATCT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
22 2 0.06
23 15 0.42
24 19 0.53
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (24 bp):
TCCATTGCAATTTGAGCCCGAAAC
Found at i:74234 original size:18 final size:17
Alignment explanation
Indices: 74190--74234 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
74180 TATACAATCA
74190 ATATTATTATAATTATAT
1 ATATTA-TATAATTATAT
**
74208 ATAGCATATAATTAATAT
1 ATATTATATAATT-ATAT
74226 ATATTATAT
1 ATATTATAT
74235 CATGTACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATATTATATAATTATAT
Done.