Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1501
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: 104797
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:240 original size:23 final size:24
Alignment explanation
Indices: 197--242 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
187 AAATAGGATA
*
197 TTTTTTAATTTAGATTTTATTAAG
1 TTTTTTAATTTAGATTCTATTAAG
221 TTTTTTAATATTA-A-TCTATTAA
1 TTTTTTAAT-TTAGATTCTATTAA
243 TTATATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 10 0.50
25 3 0.15
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTTTAATTTAGATTCTATTAAG
Found at i:11612 original size:27 final size:27
Alignment explanation
Indices: 11562--11614 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11552 TTTAGGTTGG
*
11562 AAAAAATATGTGTTTAAAAAATTTAAT
1 AAAAAATATGTATTTAAAAAATTTAAT
*
11589 AAAAAATATG-ATTTAAGAATATTTAA
1 AAAAAATATGTATTTAA-AAAATTTAA
11615 ATGTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (27 bp):
AAAAAATATGTATTTAAAAAATTTAAT
Found at i:12069 original size:3 final size:3
Alignment explanation
Indices: 12061--12100 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12051 AAAGCGAGAA
12061 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12101 GATGATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12460 original size:20 final size:19
Alignment explanation
Indices: 12433--12473 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12423 AAAAGGAAAA
12433 AGAGGAAGAAAAAACAAAG
1 AGAGGAAGAAAAAACAAAG
* *
12452 AGAGAGAAGAAGAAAGAAAG
1 AGAG-GAAGAAAAAACAAAG
12472 AG
1 AG
12474 GAAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (19 bp):
AGAGGAAGAAAAAACAAAG
Found at i:13001 original size:35 final size:36
Alignment explanation
Indices: 12933--13013 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 36
12923 ACTTGCTTTA
*
12933 AAAAATTTAATTTTATTTTATTTCAACAGACGTATTT
1 AAAAA-TTATTTTTATTTTATTTCAACAGACGTATTT
12970 AAAAATTATTTTTATTTTATTTCAACA-ACGTATTT
1 AAAAATTATTTTTATTTTATTTCAACAGACGTATTT
13005 AAAAATTAT
1 AAAAATTAT
13014 AAAACAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 17 0.40
36 21 0.49
37 5 0.12
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (36 bp):
AAAAATTATTTTTATTTTATTTCAACAGACGTATTT
Found at i:13378 original size:12 final size:13
Alignment explanation
Indices: 13337--13386 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
13327 TATATTTAAA
13337 ATATTA-AATATT
1 ATATTATAATATT
*
13349 -TATTTTAATATT
1 ATATTATAATATT
*
13361 AAATTATAAT-TT
1 ATATTATAATATT
13373 ATATTATACATATT
1 ATATTATA-ATATT
13387 TTTGATATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 4 0.13
12 15 0.50
13 9 0.30
14 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTATAATATT
Found at i:13430 original size:18 final size:19
Alignment explanation
Indices: 13401--13436 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13391 ATATGTTTAT
13401 ATTATATTTTATTATATTA
1 ATTATATTTTATTATATTA
*
13420 ATTAT-TTTTATTGTATT
1 ATTATATTTTATTATATT
13437 TTTAATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTATATTTTATTATATTA
Found at i:13616 original size:24 final size:25
Alignment explanation
Indices: 13588--13641 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
13578 AATTTTAGAT
*
13588 ATAATAAAAATATAATATAATA-AA
1 ATAATAAAAATATAATAAAATATAA
*
13612 ATAATTAAAATATAATAAAATATAA
1 ATAATAAAAATATAATAAAATATAA
13637 A-AATA
1 ATAATA
13642 TAATATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
ATAATAAAAATATAATAAAATATAA
Found at i:13623 original size:19 final size:18
Alignment explanation
Indices: 13586--13646 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
13576 ATAATTTTAG
*
13586 ATATAATAAAA-AT-ATA
1 ATATAATAAAATATAAAA
*
13602 ATATAATAAAATAATTAAA
1 ATATAATAAAAT-ATAAAA
13621 ATATAATAAAATATAAAA
1 ATATAATAAAATATAAAA
13639 ATATAATA
1 ATATAATA
13647 TCAATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.28
18 15 0.38
19 14 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAATAAAATATAAAA
Found at i:13652 original size:24 final size:22
Alignment explanation
Indices: 13590--13652 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 22
13580 TTTTAGATAT
13590 AATAAAAATATAATATAAT-AA
1 AATAAAAATATAATATAATAAA
* *
13611 AAT--AATTAAAATATAATAAA
1 AATAAAAATATAATATAATAAA
13631 ATATAAAAATATAATATCAATA
1 A-ATAAAAATATAATAT-AATA
13653 TTATATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 12 0.36
20 3 0.09
21 5 0.15
23 9 0.27
24 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAAAATATAATATAATAAA
Found at i:13664 original size:6 final size:5
Alignment explanation
Indices: 13586--13718 Score: 66
Period size: 5 Copynumber: 26.8 Consensus size: 5
13576 ATAATTTTAG
* * *
13586 ATATA ATAAAA ATATA ATATA ATA-A A-ATA ATTAAA ATATA ATAAA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA
* * * * *
13636 A-A-A ATATA ATATCA ATATT ATATG A-AT- ATATA ATCATA TTAAA AT-TT
1 ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
*
13683 ATATA ATATAA ATTAGTA ATATA TTA-A ATATA ATAT
1 ATATA ATAT-A A-TA-TA ATATA ATATA ATATA ATAT
13719 TTAACATATG
Statistics
Matches: 97, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
3 4 0.04
4 15 0.15
5 53 0.55
6 20 0.21
7 4 0.04
8 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:14085 original size:2 final size:2
Alignment explanation
Indices: 14078--14123 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
14068 TTCAAATAGC
14078 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
14120 AT AT
1 AT AT
14124 TGCATCGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14744 original size:24 final size:24
Alignment explanation
Indices: 14708--14753 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
14698 AATTTAAATA
*
14708 TTATTAATAATATTATTTAATTTT
1 TTATTAATAATATGATTTAATTTT
* *
14732 TTATTTATTATATGATTTAATT
1 TTATTAATAATATGATTTAATT
14754 GATTCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATTAATAATATGATTTAATTTT
Found at i:18627 original size:17 final size:18
Alignment explanation
Indices: 18607--18644 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
18597 CATTAATAAA
18607 TATTAAATATAAATAT-T
1 TATTAAATATAAATATAT
18624 TATTAAATATAAATATAT
1 TATTAAATATAAATATAT
18642 TAT
1 TAT
18645 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATATAAATATAT
Found at i:20912 original size:3 final size:3
Alignment explanation
Indices: 20906--20941 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
20896 AACTGAAAAA
*
20906 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20942 TTATGATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28304 original size:19 final size:19
Alignment explanation
Indices: 28280--28316 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28270 TAATTTAAAT
* *
28280 AAATATAATTATTTAATAA
1 AAATATAAATATTAAATAA
28299 AAATATAAATATTAAATA
1 AAATATAAATATTAAATA
28317 TATGTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATAAATATTAAATAA
Found at i:28919 original size:25 final size:26
Alignment explanation
Indices: 28880--28930 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
28870 ACATCATTCA
* *
28880 TATATTTTATAATATTATATTATTAT
1 TATATTTTAAAATATTATATAATTAT
*
28906 TATA-TTTAAAATATTTTATAATTAT
1 TATATTTTAAAATATTATATAATTAT
28931 ATAAGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATATTTTAAAATATTATATAATTAT
Found at i:31451 original size:57 final size:57
Alignment explanation
Indices: 31363--31474 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
31353 ACCGTACGGC
* *
31363 ACAATTAGGGTTGGATTTTGGGCTCAACTTAACACCCTAAAGAGATGAAGAGAAATT
1 ACAATTAGGGTTGGATTTTGGGCTCAACTTAACAACATAAAGAGATGAAGAGAAATT
*
31420 ACAATTAGGGTTGGATTTTGGGCTGAACTTAACAACATAAAGAGATGAAGAGAAA
1 ACAATTAGGGTTGGATTTTGGGCTCAACTTAACAACATAAAGAGATGAAGAGAAA
31475 GCCCAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (57 bp):
ACAATTAGGGTTGGATTTTGGGCTCAACTTAACAACATAAAGAGATGAAGAGAAATT
Found at i:31724 original size:16 final size:16
Alignment explanation
Indices: 31690--31732 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
31680 TTTTAAATAT
*
31690 TATTTTTTTATTAATA
1 TATTTTTTTATTAACA
31706 TATTTTTTTACTT-ACA
1 TATTTTTTTA-TTAACA
31722 TATTTTGTTTA
1 TATTTT-TTTA
31733 GAAAATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTTTTTTATTAACA
Found at i:33266 original size:3 final size:3
Alignment explanation
Indices: 33258--33285 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33248 CATTCTCGTT
33258 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
33286 AACTCAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:43509 original size:48 final size:48
Alignment explanation
Indices: 43429--43573 Score: 229
Period size: 48 Copynumber: 3.0 Consensus size: 48
43419 AGCATTATTG
* *
43429 CAATAATAAGTCAATCCCCTAACAAACAATTGGTACTCGAGTAGAGCA
1 CAATTATACGTCAATCCCCTAACAAACAATTGGTACTCGAGTAGAGCA
43477 CAATTATACGTCAATCCCCTAACAAACAATTGGTAC-CAGAGTAGAGCA
1 CAATTATACGTCAATCCCCTAACAAACAATTGGTACTC-GAGTAGAGCA
* * *
43525 CAATTATACATCAATCCCCTAACAAACAATTGGTATTAGAGTAGAGCA
1 CAATTATACGTCAATCCCCTAACAAACAATTGGTACTCGAGTAGAGCA
43573 C
1 C
43574 TTCCATGAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
47 1 0.01
48 89 0.99
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (48 bp):
CAATTATACGTCAATCCCCTAACAAACAATTGGTACTCGAGTAGAGCA
Found at i:49865 original size:17 final size:16
Alignment explanation
Indices: 49824--49866 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
49814 TGACCGGTTC
*
49824 AATTATAATAAAAAAA
1 AATTAAAATAAAAAAA
*
49840 AATTAAAATAAACAAA
1 AATTAAAATAAAAAAA
49856 AATTAGAAATA
1 AATTA-AAATA
49867 CTTCAGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AATTAAAATAAAAAAA
Found at i:56954 original size:2 final size:2
Alignment explanation
Indices: 56947--56976 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56937 TGAATCCCAC
56947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56977 ATCAAGTTTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57102 original size:2 final size:2
Alignment explanation
Indices: 57095--57121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57085 GTTATTTCTT
57095 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57122 TTTATTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58598 original size:7 final size:7
Alignment explanation
Indices: 58586--58628 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
58576 ATAATAAATT
58586 ATATAAA
1 ATATAAA
58593 ATATAAA
1 ATATAAA
*
58600 ATATAAT
1 ATATAAA
58607 ATAATAAA
1 AT-ATAAA
58615 ATATATAA
1 ATATA-AA
58623 ATATAA
1 ATATAA
58629 TTAAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 19 0.59
8 13 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATATAAA
Found at i:58612 original size:17 final size:17
Alignment explanation
Indices: 58579--58637 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
58569 AATTATTATA
* *
58579 ATAAATTAT-ATAAAAT
1 ATAAAATATAATATAAT
58595 ATAAAATATAATATAAT
1 ATAAAATATAATATAAT
58612 A-AAATATATAAATATAAT
1 ATAAA-ATAT-AATATAAT
58630 -TAAAATAT
1 ATAAAATAT
58638 TACGTAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 11 0.30
17 15 0.41
18 11 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAATATAATATAAT
Found at i:58904 original size:2 final size:2
Alignment explanation
Indices: 58891--58923 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
58881 CCCTCCTTTA
*
58891 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58924 ATACACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:59204 original size:22 final size:22
Alignment explanation
Indices: 59157--59204 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
59147 TTTTAAAAAA
* * *
59157 ATTTTAAAAATATTTTTTTATT
1 ATTTTAAAAATAATTATTAATT
59179 -TTTTAAAAATAATTATTAATT
1 ATTTTAAAAATAATTATTAATT
59200 ATTTT
1 ATTTT
59205 TAATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTAAAAATAATTATTAATT
Found at i:60032 original size:25 final size:26
Alignment explanation
Indices: 59985--60034 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
59975 TATATTAGAG
* *
59985 TAAAAATTTTAAATTTATTAATAATA
1 TAAAAATTTTAAATTGATAAATAATA
*
60011 TAAAAATTTTCAATTGA-AAATAAT
1 TAAAAATTTTAAATTGATAAATAAT
60035 GATATGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAAAATTTTAAATTGATAAATAATA
Found at i:60526 original size:2 final size:2
Alignment explanation
Indices: 60519--60551 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60509 TAACAACAAC
60519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60552 GAAGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61038 original size:23 final size:24
Alignment explanation
Indices: 61002--61047 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
60992 ATACTATTAA
*
61002 ATTATATATTATTATATAACATTT
1 ATTATATATCATTATATAACATTT
*
61026 ATTATA-ATCATTATTTAACATT
1 ATTATATATCATTATATAACATT
61048 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATATATCATTATATAACATTT
Found at i:71298 original size:37 final size:37
Alignment explanation
Indices: 71257--71327 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
71247 GTAGCTTGGC
*
71257 CAATCCACTATGATTATTAGTATTTGGGTGGCAGTGT
1 CAATCCACTATGATTATTAGAATTTGGGTGGCAGTGT
*
71294 CAATCCACTATGATTGTTAGAATTTGGGTGGCAG
1 CAATCCACTATGATTATTAGAATTTGGGTGGCAG
71328 CGCTAATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (37 bp):
CAATCCACTATGATTATTAGAATTTGGGTGGCAGTGT
Found at i:71336 original size:37 final size:37
Alignment explanation
Indices: 71257--71338 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
71247 GTAGCTTGGC
* *
71257 CAATCCACTATGATTATTAGTATTTGGGTGGCAGTGT
1 CAATCCACTATGATTATTAGAATTTGGGTGGCAGCGT
*
71294 CAATCCACTATGATTGTTAGAATTTGGGTGGCAGCG-
1 CAATCCACTATGATTATTAGAATTTGGGTGGCAGCGT
71330 CTAATCCAC
1 C-AATCCAC
71339 GAAAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.02
37 40 0.98
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (37 bp):
CAATCCACTATGATTATTAGAATTTGGGTGGCAGCGT
Found at i:72730 original size:3 final size:3
Alignment explanation
Indices: 72722--72762 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
72712 TTACTCTTTA
72722 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
72763 AAATTTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:72910 original size:24 final size:24
Alignment explanation
Indices: 72882--72928 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
72872 AAAAAAATCT
*
72882 TAAATTTGGTA-AAAGAAAATAAA
1 TAAAATTGGTATAAAGAAAATAAA
* *
72905 TAAAATTGTTATAAGGAAAATAAA
1 TAAAATTGGTATAAAGAAAATAAA
72929 AATTGGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (24 bp):
TAAAATTGGTATAAAGAAAATAAA
Found at i:74075 original size:31 final size:33
Alignment explanation
Indices: 74024--74086 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 33
74014 ATCATACATA
*
74024 AAATAATTTTATATTGTTATAAATTATAATTAC
1 AAATAATTATATATTGTTATAAATTATAATTAC
74057 AAATAATTATATA-T-TTATAAATTATAATTA
1 AAATAATTATATATTGTTATAAATTATAATTA
74087 TATTTCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 16 0.55
32 1 0.03
33 12 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (33 bp):
AAATAATTATATATTGTTATAAATTATAATTAC
Found at i:74154 original size:20 final size:20
Alignment explanation
Indices: 74108--74154 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
74098 ACTCACAATA
*
74108 TTAATTTAGTCAATATTTAT
1 TTAATTTAGTCAATAATTAT
* *
74128 GTGATTTA-TCAATAAATTAT
1 TTAATTTAGTCAAT-AATTAT
74148 TTAATTT
1 TTAATTT
74155 TTAGTTTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAATTTAGTCAATAATTAT
Found at i:76525 original size:9 final size:9
Alignment explanation
Indices: 76511--76746 Score: 65
Period size: 9 Copynumber: 26.2 Consensus size: 9
76501 TTAAATTCAA
76511 AAAAATTAT
1 AAAAATTAT
*
76520 AAAAATCCA-
1 AAAAAT-TAT
76529 AAAAATT-T
1 AAAAATTAT
*
76537 AAAATAATTCT
1 -AAA-AATTAT
76548 AAAAATT-T
1 AAAAATTAT
76556 AAAAATT-T
1 AAAAATTAT
*
76564 AAAAA-AAT
1 AAAAATTAT
76572 AAAAAATTAT
1 -AAAAATTAT
76582 -AAAATTAT
1 AAAAATTAT
*
76590 AAAACTCTAT
1 AAAAAT-TAT
* * *
76600 AATATTTAAAA
1 AAAAATT--AT
76611 ACAAAATTCA-
1 A-AAAATT-AT
76621 AAAAATTAT
1 AAAAATTAT
* *
76630 AAAAAATAA
1 AAAAATTAT
**
76639 AAATAAAAAT
1 AAA-AATTAT
76649 AAAAACTTCAT
1 AAAAA-TT-AT
*
76660 -AAATTTA-
1 AAAAATTAT
76667 AAAAATCT-T
1 AAAAAT-TAT
*
76676 TAAAATTAT
1 AAAAATTAT
76685 -AAAATTAT
1 AAAAATTAT
76693 --AAATTAT
1 AAAAATTAT
76700 --AAATTAT
1 AAAAATTAT
76707 AAAAAAATGTAT
1 --AAAAAT-TAT
76719 -AAAATTCA-
1 AAAAATT-AT
* *
76727 AAAAAATAA
1 AAAAATTAT
76736 AAAAATTAT
1 AAAAATTAT
76745 AA
1 AA
76747 TTTTTGAATT
Statistics
Matches: 175, Mismatches: 23, Indels: 58
0.68 0.09 0.23
Matches are distributed among these distances:
7 14 0.08
8 40 0.23
9 76 0.43
10 28 0.16
11 10 0.06
12 7 0.04
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:76530 original size:19 final size:19
Alignment explanation
Indices: 76503--76593 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
76493 TAGTCTTTTT
76503 AAATTCAAAAAAATTATAA
1 AAATTCAAAAAAATTATAA
* *
76522 AAATCCAAAAAATTTA-AA
1 AAATTCAAAAAAATTATAA
*
76540 ATAATTC-TAAAAATT-TAA
1 A-AATTCAAAAAAATTATAA
*
76558 AAATTTAAAAAAA-TA-AA
1 AAATTCAAAAAAATTATAA
*
76575 AAATT--ATAAAATTATAA
1 AAATTCAAAAAAATTATAA
76592 AA
1 AA
76594 CTCTATAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.09
16 2 0.03
17 16 0.28
18 17 0.29
19 18 0.31
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTCAAAAAAATTATAA
Found at i:76533 original size:18 final size:18
Alignment explanation
Indices: 76503--76593 Score: 82
Period size: 17 Copynumber: 5.1 Consensus size: 18
76493 TAGTCTTTTT
76503 AAATTCAAAAAAATTATAA
1 AAATTC-AAAAAATTATAA
*
76522 AAATCCAAAAAATT-TAAA
1 AAATTCAAAAAATTAT-AA
*
76540 ATAATTCTAAAAATT-TAA
1 A-AATTCAAAAAATTATAA
* *
76558 AAATTTAAAAAAATA-AA
1 AAATTCAAAAAATTATAA
*
76575 AAATT-ATAAAATTATAA
1 AAATTCAAAAAATTATAA
76592 AA
1 AA
76594 CTCTATAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.12
17 22 0.37
18 14 0.23
19 17 0.28
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTCAAAAAATTATAA
Found at i:76545 original size:28 final size:27
Alignment explanation
Indices: 76503--76593 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
76493 TAGTCTTTTT
*
76503 AAATTCAAAAAAATTATAAAAATCCAAA
1 AAATTTAAAAAAATTATAAAAAT-CAAA
* * **
76531 AAATTTAAAATAATTCTAAAAATTTAA
1 AAATTTAAAAAAATTATAAAAATCAAA
* *
76558 AAATTTAAAAAAA-TA-AAAAATTATA
1 AAATTTAAAAAAATTATAAAAATCAAA
76583 AAATTATAAAA
1 AAATT-TAAAA
76594 CTCTATAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 13 0.25
26 6 0.11
27 14 0.26
28 20 0.38
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAATTTAAAAAAATTATAAAAATCAAA
Found at i:76559 original size:7 final size:8
Alignment explanation
Indices: 76529--76593 Score: 58
Period size: 8 Copynumber: 7.5 Consensus size: 8
76519 TAAAAATCCA
76529 AAAAATTT
1 AAAAATTT
76537 AAAATAATTCT
1 -AAA-AATT-T
76548 AAAAATTT
1 AAAAATTT
76556 AAAAATTT
1 AAAAATTT
**
76564 AAAAAAAT
1 AAAAATTT
*
76572 AAAAAATT
1 AAAAATTT
76580 ATAAAATTAT
1 A-AAAATT-T
76590 AAAA
1 AAAA
76594 CTCTATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 23 0.48
9 15 0.31
10 9 0.19
11 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAAATTT
Found at i:76633 original size:8 final size:8
Alignment explanation
Indices: 76574--76710 Score: 85
Period size: 8 Copynumber: 17.5 Consensus size: 8
76564 AAAAAAATAA
76574 AAAATTAT
1 AAAATTAT
76582 AAAATTAT
1 AAAATTAT
76590 AAAACTCTAT
1 AAAA-T-TAT
*
76600 AATATT-T
1 AAAATTAT
*
76607 AAAA--AC
1 AAAATTAT
*
76613 AAAATTCAA
1 AAAATT-AT
76622 AAAATTAT
1 AAAATTAT
*
76630 AAAA-AAT
1 AAAATTAT
76637 AAAA--AT
1 AAAATTAT
*
76643 AAAAATA-
1 AAAATTAT
76650 AAAACTTCAT
1 AAAA-TT-AT
* *
76660 AAATTTAA
1 AAAATTAT
*
76668 AAAATCTTT
1 AAAAT-TAT
76677 AAAATTAT
1 AAAATTAT
76685 AAAATTAT
1 AAAATTAT
76693 -AAATTAT
1 AAAATTAT
76700 -AAATTAT
1 AAAATTAT
76707 AAAA
1 AAAA
76711 AAATGTATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
6 10 0.10
7 28 0.27
8 38 0.37
9 18 0.17
10 9 0.09
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAATTAT
Found at i:76662 original size:30 final size:30
Alignment explanation
Indices: 76606--76662 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
76596 CTATAATATT
*
76606 TAAAAACAAAATTCAAAAAATTATAAAAAA
1 TAAAAACAAAAATCAAAAAATTATAAAAAA
* *
76636 TAAAAATAAAAAT-AAAAACTTCATAAA
1 TAAAAACAAAAATCAAAAAATT-ATAAA
76663 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
TAAAAACAAAAATCAAAAAATTATAAAAAA
Found at i:76687 original size:42 final size:43
Alignment explanation
Indices: 76641--76738 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
76631 AAAAATAAAA
*
76641 ATAAAAATAAAAACTTCATAAATT-T-AAAAAATCTTTAAAATT-
1 ATAAAAATAAAAA-TT-ATAAATTATAAAAAAATCTATAAAATTC
* * *
76683 ATAAAATTATAAATTATAAATTATAAAAAAATGTATAAAATTC
1 ATAAAAATAAAAATTATAAATTATAAAAAAATCTATAAAATTC
*
76726 AAAAAAATAAAAA
1 ATAAAAATAAAAA
76739 AATTATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 7 0.15
41 3 0.07
42 26 0.57
43 10 0.22
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (43 bp):
ATAAAAATAAAAATTATAAATTATAAAAAAATCTATAAAATTC
Found at i:76698 original size:7 final size:7
Alignment explanation
Indices: 76678--76709 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
76668 AAAATCTTTA
76678 AAATTAT
1 AAATTAT
76685 AAAATTAT
1 -AAATTAT
76693 AAATTAT
1 AAATTAT
76700 AAATTAT
1 AAATTAT
76707 AAA
1 AAA
76710 AAAATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATTAT
Found at i:76903 original size:20 final size:20
Alignment explanation
Indices: 76819--76912 Score: 59
Period size: 20 Copynumber: 4.6 Consensus size: 20
76809 TTTTTATAAT
*
76819 ATTTTGAATTTTATTATTTGAA
1 ATTTTTAATTTTATT-TTTG-A
* *
76841 ATTTTTATAATTTACTTTT-A
1 ATTTTTA-ATTTTATTTTTGA
** *
76861 ATTTTATAGA-TTT-TTAATAA
1 ATTTT-TA-ATTTTATTTTTGA
76881 ATTTTTAATTTTATTTTTGA
1 ATTTTTAATTTTATTTTTGA
*
76901 ATTTTGAATTTT
1 ATTTTTAATTTT
76913 TATAATTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
18 1 0.02
19 7 0.12
20 30 0.54
21 3 0.05
22 9 0.16
23 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTTAATTTTATTTTTGA
Found at i:76929 original size:37 final size:37
Alignment explanation
Indices: 76870--76940 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
76860 AATTTTATAG
*
76870 ATTTTTAATAAATTTTTAATTTTATTTTTGAATTTTGA
1 ATTTTTAATAAATTTTTAATTTT-TTTTTAAATTTTGA
* *
76908 ATTTTT-ATAATTTTTTGATTTTTTTTTAAATTT
1 ATTTTTAATAAATTTTTAATTTTTTTTTAAATTT
76941 AAAAAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 10 0.33
37 14 0.47
38 6 0.20
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (37 bp):
ATTTTTAATAAATTTTTAATTTTTTTTTAAATTTTGA
Found at i:81019 original size:39 final size:39
Alignment explanation
Indices: 80917--81025 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
80907 TTTTATTTAT
** * * *
80917 ATCTTATAAAAATTAATATGCTTAAATATAACAGTTTAT
1 ATCTTATAAAAATTAAGGTGCTTAGATATAACAGCTTAC
* *
80956 ATCTTATAGAAATTAAGGTGCTTAGATATAATAGCTTAC
1 ATCTTATAAAAATTAAGGTGCTTAGATATAACAGCTTAC
* *
80995 ATCTTATAAAAACTAAGGTGCTTAGTTATAA
1 ATCTTATAAAAATTAAGGTGCTTAGATATAA
81026 GACTTAAAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (39 bp):
ATCTTATAAAAATTAAGGTGCTTAGATATAACAGCTTAC
Found at i:84086 original size:12 final size:13
Alignment explanation
Indices: 84057--84088 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
84047 AAAAATACTC
84057 ATTTTATTTATTT
1 ATTTTATTTATTT
84070 A-TTTATTT-TTT
1 ATTTTATTTATTT
84081 ATTTTATT
1 ATTTTATT
84089 CAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 13 0.72
13 1 0.06
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:85495 original size:7 final size:7
Alignment explanation
Indices: 85485--85518 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
85475 CATAATATTT
85485 AAATATA
1 AAATATA
85492 AAATATA
1 AAATATA
85499 AAATATA
1 AAATATA
85506 AAAT-TA
1 AAATATA
*
85512 ATATATA
1 AAATATA
85519 TTATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAATATA
Found at i:85523 original size:25 final size:24
Alignment explanation
Indices: 85486--85532 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
85476 ATAATATTTA
85486 AATATAAAATATAAAATATAAAATT
1 AATATAAAATATAAAAT-TAAAATT
* * *
85511 AATATATATTATATAATTAAAA
1 AATATAAAATATAAAATTAAAA
85533 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATATAAAATATAAAATTAAAATT
Found at i:85666 original size:21 final size:20
Alignment explanation
Indices: 85649--85692 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
85639 ATTTAAATTT
85649 TTTTAAATATTAAATAAA-A
1 TTTTAAATATTAAATAAATA
85668 TTTTAAAT-TTAAATAAATA
1 TTTTAAATATTAAATAAATA
*
85687 ATTTAA
1 TTTTAA
85693 TTTATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAAATATTAAATAAATA
Found at i:85681 original size:18 final size:19
Alignment explanation
Indices: 85649--85684 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
85639 ATTTAAATTT
85649 TTTTAAATATTAAATAAAA
1 TTTTAAATATTAAATAAAA
85668 TTTTAAAT-TTAAATAAA
1 TTTTAAATATTAAATAAA
85685 TAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTAAATATTAAATAAAA
Found at i:85694 original size:18 final size:18
Alignment explanation
Indices: 85650--85702 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
85640 TTTAAATTTT
*
85650 TTTAAATATTAAATAAAAT
1 TTTAAAT-TTAAATAAAAA
85669 TTTAAATTTAAATAAATAA
1 TTTAAATTTAAATAAA-AA
*
85688 TTTAATTTATAAATA
1 TTTAAATT-TAAATA
85703 TGTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 9 0.30
19 15 0.50
20 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAATTTAAATAAAAA
Done.