Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1690
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: 98672
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:1593 original size:25 final size:25
Alignment explanation
Indices: 1551--1598 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1541 TTAATTTAAA
*
1551 AATAAATATAAATAATTTTATTTTT
1 AATAAATATAAATAATTTAATTTTT
*
1576 AATAAA-ATAACATCATTTAATTT
1 AATAAATATAA-ATAATTTAATTT
1599 CACCATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAAATATAAATAATTTAATTTTT
Found at i:2135 original size:3 final size:3
Alignment explanation
Indices: 2127--2163 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2117 ATCATTCTGC
2127 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2164 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2913 original size:24 final size:25
Alignment explanation
Indices: 2870--2919 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
2860 ATTAATGTAC
*
2870 TCATATTGTATTAGTATTATT-TTT
1 TCATATTGTACTAGTATTATTATTT
2894 TCATATTGTACTA-TATTTATTATTT
1 TCATATTGTACTAGTA-TTATTATTT
2919 T
1 T
2920 TCTTACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (25 bp):
TCATATTGTACTAGTATTATTATTT
Found at i:5169 original size:3 final size:3
Alignment explanation
Indices: 5163--5199 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5153 TTTTAAAATT
5163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5200 GCAGAATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5758 original size:25 final size:25
Alignment explanation
Indices: 5730--5777 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5720 ATTAATGGTG
*
5730 AAATTAAATGATGTTAT-TTTATTAA
1 AAATAAAATGAT-TTATATTTATTAA
*
5755 AAATAAAATTATTTATATTTATT
1 AAATAAAATGATTTATATTTATT
5778 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AAATAAAATGATTTATATTTATTAA
Found at i:8899 original size:19 final size:18
Alignment explanation
Indices: 8857--8900 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
8847 ATATTAAATG
* *
8857 TATTATGTTAATTATATT
1 TATTATGTCAATCATATT
8875 TAATTATGTCATATCATATT
1 T-ATTATGTCA-ATCATATT
8895 TATTAT
1 TATTAT
8901 ATGTTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATTATGTCAATCATATT
Found at i:9380 original size:44 final size:43
Alignment explanation
Indices: 9277--9397 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 43
9267 GACCATTCGT
* * * *
9277 TTACGTACAAATTGTAATGACAATACTATCCTTAAGATAGTCA
1 TTACGTATAAAGTGTAATGACAACACTATCCTTAAAATAGTCA
* * *
9320 TTACGTGTAAAGTGTAATGCCAACACTATCCTTAAAATCATTCA
1 TTACGTATAAAGTGTAATGACAACACTATCCTTAAAAT-AGTCA
** * ** *
9364 TTTGGTATAGAGTGTAATGGTAACACCATCCTTA
1 TTACGTATAAAGTGTAATGACAACACTATCCTTA
9398 TAGCGGCCTA
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 32 0.51
44 31 0.49
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (43 bp):
TTACGTATAAAGTGTAATGACAACACTATCCTTAAAATAGTCA
Found at i:9477 original size:32 final size:32
Alignment explanation
Indices: 9436--9498 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
9426 CTAAGTATAA
*
9436 ATAGAGTAACCCTTGCAAAGACATTGAATCCG
1 ATAGAGTAACCCTTGCAAAGACATGGAATCCG
*
9468 ATAGAGTAACCTTTGCAAAGACATGGAATCC
1 ATAGAGTAACCCTTGCAAAGACATGGAATCC
9499 CTCTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (32 bp):
ATAGAGTAACCCTTGCAAAGACATGGAATCCG
Found at i:10526 original size:2 final size:2
Alignment explanation
Indices: 10519--10545 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10509 TTTATTTGAT
10519 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
10546 TCTCTGATGG
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:11569 original size:21 final size:21
Alignment explanation
Indices: 11543--11582 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11533 GTAACAACAG
*
11543 TAAAATTAATTATTATAATAA
1 TAAAATTAAATATTATAATAA
11564 TAAAATTAAATATTATAAT
1 TAAAATTAAATATTATAAT
11583 GGTTAGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAATTAAATATTATAATAA
Found at i:11642 original size:22 final size:22
Alignment explanation
Indices: 11599--11642 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11589 GATGTATAGG
* *
11599 TGAGATTAAATATTATAGTGAT
1 TGAGATTAAATATAATAATGAT
11621 TGAGATTAAA-ATCAATAATGAT
1 TGAGATTAAATAT-AATAATGAT
11643 ATATGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.36
Consensus pattern (22 bp):
TGAGATTAAATATAATAATGAT
Found at i:11700 original size:13 final size:15
Alignment explanation
Indices: 11672--11703 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
11662 CGTAACGGTA
11672 ATAATAAAATAAATT
1 ATAATAAAATAAATT
11687 ATAAT-AAA-AAATT
1 ATAATAAAATAAATT
11700 ATAA
1 ATAA
11704 AAGATATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAAAATAAATT
Found at i:11782 original size:19 final size:17
Alignment explanation
Indices: 11747--11783 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
11737 AACCTAAACC
11747 TATTTATATTTTTAAAT
1 TATTTATATTTTTAAAT
11764 TATTTGATATTTATTAAAT
1 TATTT-ATATTT-TTAAAT
11783 T
1 T
11784 GATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTATATTTTTAAAT
Found at i:13978 original size:40 final size:40
Alignment explanation
Indices: 13928--14005 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
13918 ATCAAGATAT
13928 TATTAGATTT-AATTAAATTTAAA-TAAATATATAATATTAA
1 TATTAGATTTAAATTAAA-TTAAATTAAATATAT-ATATTAA
* *
13968 TATTATATTTAAATTAAATTAAATTAAATTTATATATT
1 TATTAGATTTAAATTAAATTAAATTAAATATATATATT
14006 TATTTATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 19 0.56
41 15 0.44
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
TATTAGATTTAAATTAAATTAAATTAAATATATATATTAA
Found at i:14939 original size:2 final size:2
Alignment explanation
Indices: 14932--14962 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14922 CTTCAAATAC
*
14932 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14963 ATTATCATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19913 original size:56 final size:56
Alignment explanation
Indices: 19853--19997 Score: 129
Period size: 58 Copynumber: 2.6 Consensus size: 56
19843 ATTGGATTAA
* * *
19853 ATAAAATTTTAATATTAATATTATATTTAAATTTAATTTAAT-TTATA-TATTTTTTT
1 ATAAAA-TTTAATATTAATATTATATTTAAATTT-ATATAATATTAAATTAATTTTTT
* * * * *
19909 ATAAAA-TTAAAATAAAAATAATATTTTATAATGTTGTATAATATTAAATTAATTTTTT
1 ATAAAATTTAATATTAATATTATA-TTTA-AAT-TTATATAATATTAAATTAATTTTTT
19967 ATATAAA--TAATATTAATATTATATTTAAATT
1 ATA-AAATTTAATATTAATATTATATTTAAATT
19998 GAATGTAGCT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
54 13 0.18
55 5 0.07
56 17 0.24
57 10 0.14
58 23 0.32
59 3 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (56 bp):
ATAAAATTTAATATTAATATTATATTTAAATTTATATAATATTAAATTAATTTTTT
Found at i:20714 original size:2 final size:2
Alignment explanation
Indices: 20707--20735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20697 TATGAGCTTT
20707 TA 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 TA T
20736 GTTAATAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21793 original size:34 final size:34
Alignment explanation
Indices: 21747--21931 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
21737 GTAAAAACCA
*
21747 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
21781 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
21815 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
21849 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
21883 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
21916 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
21932 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:26024 original size:19 final size:19
Alignment explanation
Indices: 25997--26059 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
25987 TCACGTGTAC
* *
25997 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
26016 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
***
26035 AGTACATATATACGTGAAT
1 AGTACCCGTATACGTGAAT
26054 AGTACC
1 AGTACC
26060 TCGACAACCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:26407 original size:34 final size:34
Alignment explanation
Indices: 26361--26543 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
26351 GTAAAAACCA
*
26361 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
26395 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
26429 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
26463 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
26497 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
26530 CCATTTAATCAACA
1 CCATTTAATCAACA
26544 TCGGGGCATG
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:28418 original size:2 final size:2
Alignment explanation
Indices: 28413--28450 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28403 AGGTGACTTA
28413 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
28451 GTTGGGTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29949 original size:22 final size:22
Alignment explanation
Indices: 29923--29976 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
29913 GTGTTTTAAT
29923 TTTATTTTAAAAT-TTAAAAAAA
1 TTTATTTTAAAATATT-AAAAAA
* *
29945 TTTATTATTAATATATTAAATAA
1 TTTATT-TTAAAATATTAAAAAA
29968 -TTATTTTAA
1 TTTATTTTAA
29977 TTTTATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 11 0.39
23 11 0.39
24 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATTTTAAAATATTAAAAAA
Found at i:30061 original size:17 final size:17
Alignment explanation
Indices: 30025--30075 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
30015 ATGATAATAA
* *
30025 TTTATATTATATAAATTT
1 TTTATTTTAT-TATATTT
30043 TTTATTTTATTATA-TT
1 TTTATTTTATTATATTT
*
30059 TTTATTATTTTTATATT
1 TTTATT-TTATTATATT
30076 ATACTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.29
17 10 0.36
18 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTATATTT
Found at i:30063 original size:11 final size:11
Alignment explanation
Indices: 30047--30110 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
30037 AAATTTTTTA
30047 TTTTATTATAT
1 TTTTATTATAT
30058 TTTTATTAT-T
1 TTTTATTATAT
30068 TTTATATTATACT
1 TTT-TATTATA-T
**
30081 TTAAATTATAT
1 TTTTATTATAT
*
30092 TTTAATTAT-T
1 TTTTATTATAT
30102 TATTTATTA
1 T-TTTATTA
30111 AAATATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.13
11 30 0.67
12 6 0.13
13 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:39098 original size:11 final size:10
Alignment explanation
Indices: 39053--39114 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 10
39043 TGTTAGATTT
39053 AATTAAATTTA
1 AATTAAA-TTA
*
39064 AATAAATATATA
1 AATTAA-AT-TA
39076 ATATTAATATTA
1 A-ATTAA-ATTA
*
39088 TATTTAAATTA
1 -AATTAAATTA
39099 AATTAAATTA
1 AATTAAATTA
39109 AATTAA
1 AATTAA
39115 TATATTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 15 0.35
11 10 0.23
12 10 0.23
13 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTAAATTA
Found at i:40550 original size:5 final size:6
Alignment explanation
Indices: 40519--40549 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40509 ATATAATTTC
40519 AAATTA AAATTA AAATTA AAATT- AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
40550 TATATTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:46601 original size:5 final size:5
Alignment explanation
Indices: 46555--46614 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
46545 TACTAGATTT
* * *
46555 AATTA AATTTA AA-TA AA-TA TATAA AATTA ATATTA TATTTA AATTA
1 AATTA AA-TTA AATTA AATTA AATTA AATTA A-ATTA -AATTA AATTA
46601 AATTA AATTA AATT
1 AATTA AATTA AATT
46615 TATATATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 7 0.16
5 25 0.56
6 12 0.27
7 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:47975 original size:2 final size:2
Alignment explanation
Indices: 47917--47959 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
47907 TGTATGAGCT
47917 TA TA TA TA TA TA 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 TA TA TA TA TA TA
47959 T
1 T
47960 GTTAATAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48034 original size:6 final size:6
Alignment explanation
Indices: 48023--48053 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
48013 ATATATTTTT
48023 AAATTA AAATTA AAATTA AAA-TA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
48054 TATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:48047 original size:11 final size:12
Alignment explanation
Indices: 48023--48053 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
48013 ATATATTTTT
48023 AAATTAAAATTA
1 AAATTAAAATTA
48035 AAATTAAAA-TA
1 AAATTAAAATTA
48046 AAATTAAA
1 AAATTAAA
48054 TATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTAAAATTA
Found at i:48047 original size:17 final size:17
Alignment explanation
Indices: 48021--48053 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48011 AAATATATTT
*
48021 TTAAATTAAAATTAAAA
1 TTAAAATAAAATTAAAA
48038 TTAAAATAAAATTAAA
1 TTAAAATAAAATTAAA
48054 TATATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAAAATTAAAA
Found at i:52147 original size:16 final size:17
Alignment explanation
Indices: 52130--52187 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
52120 TTTAAAATAA
52130 TTTATATTTATATAAAT
1 TTTATATTTATATAAAT
52147 TTTAATATATTA-AT-AA-
1 TTT-ATAT-TTATATAAAT
*
52163 TTTATA-TAATATAAAT
1 TTTATATTTATATAAAT
52179 TTTATATTT
1 TTTATATTT
52188 TATCATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 5 0.15
16 9 0.27
17 6 0.18
18 6 0.18
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATATTTATATAAAT
Found at i:52150 original size:27 final size:27
Alignment explanation
Indices: 52120--52171 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
52110 TTTAATATCA
*
52120 TTTAAAATAATTTAT-ATTTATATAAAT
1 TTTAAAAT-ATTAATAATTTATATAAAT
*
52147 TTTAATATATTAATAATTTATATAA
1 TTTAAAATATTAATAATTTATATAA
52172 TATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAAAATATTAATAATTTATATAAAT
Found at i:52250 original size:31 final size:32
Alignment explanation
Indices: 52182--52254 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
52172 TATAAATTTT
* * * **
52182 ATATTTTATCATATTTTTATTATTTTTTATATT
1 ATATTTTA-AATATTTTTATAATTTTTAATAAA
52215 ATATTTTAAATATTTTTA-AATTTTTAATAAA
1 ATATTTTAAATATTTTTATAATTTTTAATAAA
52246 ATATTTTAA
1 ATATTTTAA
52255 TTTTACAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 18 0.51
32 9 0.26
33 8 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
ATATTTTAAATATTTTTATAATTTTTAATAAA
Found at i:57064 original size:2 final size:2
Alignment explanation
Indices: 57057--57089 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57047 ACAACTTCAA
57057 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
57090 AAATTATAAT
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:59674 original size:30 final size:30
Alignment explanation
Indices: 59623--59680 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59613 TTATTTCATC
* *
59623 ATCACCTACATTTATTATAATTTATTTTGA
1 ATCACCTAAATTTAATATAATTTATTTTGA
59653 ATCA-CTAAATTTAATATTAATTTATTTT
1 ATCACCTAAATTTAATA-TAATTTATTTT
59681 TATATGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (30 bp):
ATCACCTAAATTTAATATAATTTATTTTGA
Found at i:60840 original size:2 final size:2
Alignment explanation
Indices: 60833--60867 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60823 ATTATAATTC
60833 AT 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 AT A
60868 AGTCGTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61091 original size:18 final size:20
Alignment explanation
Indices: 61054--61093 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
61044 AAATATAAGT
*
61054 ATAATTTTTATAATTTATAA
1 ATAAATTTTATAATTTATAA
61074 ATAAATTTTAT-A-TTATAA
1 ATAAATTTTATAATTTATAA
61092 AT
1 AT
61094 TAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAATTTTATAATTTATAA
Found at i:61361 original size:19 final size:19
Alignment explanation
Indices: 61329--61370 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
61319 AATTTTAAAA
61329 ATTAAAAAAATATTATT-AT
1 ATTAAAAAAATATT-TTAAT
* *
61348 ATTAAATAATTATTTTAAT
1 ATTAAAAAAATATTTTAAT
61367 ATTA
1 ATTA
61371 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTAAAAAAATATTTTAAT
Found at i:61447 original size:17 final size:17
Alignment explanation
Indices: 61423--61457 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61413 ATTATATAAA
61423 TTTTTTATTTTT-ATAT
1 TTTTTTATTTTTAATAT
61439 TTTTATTATTTTTAATAT
1 TTTT-TTATTTTTAATAT
61457 T
1 T
61458 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTATTTTTAATAT
Found at i:61459 original size:23 final size:24
Alignment explanation
Indices: 61424--61488 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
61414 TTATATAAAT
* * *
61424 TTTTTATTTTTATATTTT-TATTA
1 TTTTTAATATTATATTTTAAATTA
61447 TTTTTAATATTATATTTTAAATTA
1 TTTTTAATATTATATTTTAAATTA
61471 TATTTTAATTATT-TATTT
1 T-TTTTAA-TATTATATTT
61489 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 16 0.44
24 5 0.14
25 11 0.31
26 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTAATATTATATTTTAAATTA
Found at i:61462 original size:14 final size:13
Alignment explanation
Indices: 61433--61488 Score: 68
Period size: 12 Copynumber: 4.6 Consensus size: 13
61423 TTTTTTATTT
61433 TTATATTTT--TA
1 TTATATTTTAATA
61444 TTAT-TTTTAATA
1 TTATATTTTAATA
61456 TTATATTTTAA-A
1 TTATATTTTAATA
61468 TTATATTTTAATTA
1 TTATATTTTAA-TA
61482 TT-TATTT
1 TTATATTT
61489 ATTAAAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.10
11 4 0.10
12 18 0.45
13 11 0.28
14 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATTTTAATA
Found at i:61487 original size:25 final size:26
Alignment explanation
Indices: 61443--61510 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
61433 TTATATTTTT
61443 ATTAT-TTTTAA-TATTATATT-TTAA
1 ATTATATTTTAATTATT-TATTATTAA
61467 ATTATATTTTAATTATTTATTTATTAA
1 ATTATATTTTAATTATTTA-TTATTAA
61494 A--ATATTTTAATT-TTTAT
1 ATTATATTTTAATTATTTAT
61511 CAGATTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.03
24 9 0.22
25 19 0.47
26 6 0.15
27 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTATATTTTAATTATTTATTATTAA
Found at i:61517 original size:25 final size:25
Alignment explanation
Indices: 61470--61519 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
61460 ATTTTAAATT
**
61470 ATATTTTAATTATTTATTTATTAAA
1 ATATTTTAATTATTTATAGATTAAA
61495 ATATTTTAATT-TTTATCAGATTAAA
1 ATATTTTAATTATTTAT-AGATTAAA
61520 TGTGTCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATTTTAATTATTTATAGATTAAA
Found at i:62056 original size:45 final size:46
Alignment explanation
Indices: 61984--62079 Score: 142
Period size: 45 Copynumber: 2.1 Consensus size: 46
61974 TTTTTAACAA
* *
61984 ACAAAAGTATCTGTTTTAACCTTTAATCATCAACGTATCTTAGGCT
1 ACAAGAGTATCTGTTTTAACCTTTAATCATCAACGCATCTTAGGCT
62030 ACAAGAGTATCTG-TTTAA-CTTCTAATCATCAACGCATCTTAGGCT
1 ACAAGAGTATCTGTTTTAACCTT-TAATCATCAACGCATCTTAGGCT
*
62075 GCAAG
1 ACAAG
62080 CCATTGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 3 0.07
45 31 0.67
46 12 0.26
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (46 bp):
ACAAGAGTATCTGTTTTAACCTTTAATCATCAACGCATCTTAGGCT
Found at i:63804 original size:2 final size:2
Alignment explanation
Indices: 63797--63829 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63787 ATGTTGGCAC
63797 TA TA TA 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 TA TA TA T
63830 TGCTTTGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65408 original size:4 final size:4
Alignment explanation
Indices: 65399--65426 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
65389 ACCAAATTAT
65399 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
65427 ACCTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:66916 original size:2 final size:2
Alignment explanation
Indices: 66909--66951 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
66899 AATCAGTTAT
66909 TA TA TA TA TA TA 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 TA TA TA TA TA TA
66951 T
1 T
66952 GTGGGTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68092 original size:3 final size:3
Alignment explanation
Indices: 68086--68112 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
68076 AGAAGAAGAA
68086 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
68113 AACAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:70225 original size:3 final size:3
Alignment explanation
Indices: 70219--70247 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
70209 TATTTATTTC
70219 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
70248 AGTATGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:70303 original size:23 final size:23
Alignment explanation
Indices: 70273--70343 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
70263 AAAGCTAAGA
70273 TTCAAATTGCTTACATATGTTTG
1 TTCAAATTGCTTACATATGTTTG
70296 TTCAAATTGCTTACATATGTTTG
1 TTCAAATTGCTTACATATGTTTG
70319 TTCAAATTGCTTACATATGTTTG
1 TTCAAATTGCTTACATATGTTTG
70342 TT
1 TT
70344 TACTTTGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (23 bp):
TTCAAATTGCTTACATATGTTTG
Found at i:71241 original size:20 final size:21
Alignment explanation
Indices: 71201--71242 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
71191 TTTTCCTTTT
* *
71201 TTATATTCAAAATATACTAAA
1 TTATATTCAAAATACAATAAA
71222 TTATA-TCAAAATACAATAAA
1 TTATATTCAAAATACAATAAA
71242 T
1 T
71243 AAATTCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
TTATATTCAAAATACAATAAA
Found at i:71654 original size:21 final size:20
Alignment explanation
Indices: 71628--71668 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
71618 TGAATTCAAA
71628 TTTTAATATTAAAATTTTTTT
1 TTTTAA-ATTAAAATTTTTTT
*
71649 TTTTAAATTATAATTTTTTT
1 TTTTAAATTAAAATTTTTTT
71669 ATAATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATTAAAATTTTTTT
Found at i:75931 original size:20 final size:20
Alignment explanation
Indices: 75908--75956 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
75898 TTTAAATTAT
75908 TATATATTTATAAACTTTAA
1 TATATATTTATAAACTTTAA
* * *
75928 TATATATATATAAATTTTGA
1 TATATATTTATAAACTTTAA
75948 TATAT-TTTA
1 TATATATTTA
75957 ATATTTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TATATATTTATAAACTTTAA
Found at i:76800 original size:4 final size:5
Alignment explanation
Indices: 76769--76798 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
76759 TATTAAATAA
*
76769 TAATT TAATT TAAAT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT
76799 AAAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:77255 original size:23 final size:23
Alignment explanation
Indices: 77225--77268 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
77215 TAAAAAAGGA
77225 ATATTGAAGAGCCAAAACAATAT
1 ATATTGAAGAGCCAAAACAATAT
*
77248 ATATTGAAGAGCCAGAACAAT
1 ATATTGAAGAGCCAAAACAAT
77269 CTCATGCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (23 bp):
ATATTGAAGAGCCAAAACAATAT
Found at i:79896 original size:18 final size:18
Alignment explanation
Indices: 79864--79898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
79854 TCAAATAGAT
**
79864 ATTATTTTTTTATTTAAA
1 ATTATTTTTAAATTTAAA
79882 ATTATTTTTAAATTTAA
1 ATTATTTTTAAATTTAA
79899 TATTTTAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTATTTTTAAATTTAAA
Found at i:80170 original size:15 final size:15
Alignment explanation
Indices: 80150--80179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
80140 AATCAATTTG
80150 ATTAATTATTAAATT
1 ATTAATTATTAAATT
*
80165 ATTAATTTTTAAATT
1 ATTAATTATTAAATT
80180 TGATAACTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTATTAAATT
Found at i:80299 original size:23 final size:23
Alignment explanation
Indices: 80265--80321 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
80255 ATATATTTTT
* * *
80265 TATAATAGTTTTAAATTATATTA
1 TATAATAATTTTAAATAATAATA
*
80288 TATAATAATTTTTATATAATAATA
1 TATAATAA-TTTTAAATAATAATA
80312 TA-AATAATTT
1 TATAATAATTT
80322 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 12 0.41
24 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATAATAATTTTAAATAATAATA
Found at i:83230 original size:18 final size:18
Alignment explanation
Indices: 83207--83243 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
83197 AGGCTCGAAA
83207 TTCCTAACTCTGATTCGC
1 TTCCTAACTCTGATTCGC
**
83225 TTCCTATTTCTGATTCGC
1 TTCCTAACTCTGATTCGC
83243 T
1 T
83244 GGGATCAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.30, G:0.11, T:0.46
Consensus pattern (18 bp):
TTCCTAACTCTGATTCGC
Found at i:84587 original size:15 final size:16
Alignment explanation
Indices: 84561--84590 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
84551 TTAAAATGTT
84561 TAATTAAATAAAATTA
1 TAATTAAATAAAATTA
84577 TAATT-AATAAAATT
1 TAATTAAATAAAATT
84591 TTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAATAAAATTA
Found at i:85507 original size:17 final size:19
Alignment explanation
Indices: 85485--85520 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
85475 ATACCACTTT
85485 AAATAT-ACA-AAAAATAA
1 AAATATAACATAAAAATAA
85502 AAATATAACATAAAAATAA
1 AAATATAACATAAAAATAA
85521 TTAAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATATAACATAAAAATAA
Found at i:85943 original size:20 final size:20
Alignment explanation
Indices: 85900--85964 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 20
85890 ATACATAAAT
*
85900 TTTTTCTTGTCCTTTCT-TTCC
1 TTTTTCTT-T-CTTTCTCTTTC
*
85921 TTTTTCTTTTTTTCTCTTTC
1 TTTTTCTTTCTTTCTCTTTC
85941 --TTTCTTTCTTTCTCTCTT-
1 TTTTTCTTTCTTTCTCT-TTC
85959 TTTTTC
1 TTTTTC
85965 ACTTATGTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.38
19 7 0.19
20 8 0.22
21 8 0.22
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTCTTTC
Found at i:85944 original size:4 final size:4
Alignment explanation
Indices: 85911--85964 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
85901 TTTTCTTGTC
* * *
85911 CTTT CTTT CCTT -TTT CTTT -TTT -TCT CTTT CTTT CTTT CTTT CTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
85956 CTTT TTTT C
1 CTTT CTTT C
85965 ACTTATGTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 7 0.17
4 33 0.82
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:89387 original size:15 final size:15
Alignment explanation
Indices: 89364--89411 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
89354 GAAACCGTAA
*
89364 ATTAGATATTATAAT
1 ATTAAATATTATAAT
* *
89379 ATTAAATATAATTAT
1 ATTAAATATTATAAT
*
89394 ATAAAATATTATATAT
1 ATTAAATATTATA-AT
89410 AT
1 AT
89412 AATAATTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATATTATAAT
Found at i:89404 original size:22 final size:23
Alignment explanation
Indices: 89371--89424 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
89361 TAAATTAGAT
* *
89371 ATTATAATATTA-A-ATATAATT
1 ATTAAAATATTATATATATAATA
89392 ATATAAAATATTATATATATAATA
1 AT-TAAAATATTATATATATAATA
89416 ATTAAAATA
1 ATTAAAATA
89425 GATACGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 9 0.32
23 8 0.29
24 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATATTATATATATAATA
Found at i:89497 original size:27 final size:28
Alignment explanation
Indices: 89450--89522 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
89440 TTTAAATTTT
*
89450 ATATAATATAAAT-TATTAATAAATTAAA
1 ATATAATATAAATATATAAAT-AATTAAA
* *
89478 CT-TAATATAAATATA-AAATATTTAAA
1 ATATAATATAAATATATAAATAATTAAA
89504 ATATAATA-AAATATATAAA
1 ATATAATATAAATATATAAA
89523 AAAGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 14 0.37
27 21 0.55
28 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATAATATAAATATATAAATAATTAAA
Found at i:89515 original size:10 final size:9
Alignment explanation
Indices: 89488--89523 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
89478 CTTAATATAA
89488 ATATAAAAT
1 ATATAAAAT
*
89497 ATTTAAAAT
1 ATATAAAAT
89506 ATAATAAAAT
1 AT-ATAAAAT
89516 ATATAAAA
1 ATATAAAA
89524 AAGACATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATAAAAT
Found at i:94204 original size:2 final size:2
Alignment explanation
Indices: 94197--94228 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
94187 CTACTAATTA
94197 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
94229 GTAGATGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95122 original size:18 final size:18
Alignment explanation
Indices: 95099--95158 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
95089 ATAATACATT
95099 TAAATATTATTAATATAA
1 TAAATATTATTAATATAA
* * *
95117 TAAATA-AATATAATACATT
1 TAAATATTAT-TAATATA-A
95136 TAAATATTATTAATATAA
1 TAAATATTATTAATATAA
95154 TAAAT
1 TAAAT
95159 TAAATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 17 0.52
19 12 0.36
20 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATTATTAATATAA
Found at i:95123 original size:37 final size:37
Alignment explanation
Indices: 95074--95166 Score: 177
Period size: 37 Copynumber: 2.5 Consensus size: 37
95064 GAAACTAAAT
95074 ATATAATAAATAAATATAATACATTTAAATATTATTA
1 ATATAATAAATAAATATAATACATTTAAATATTATTA
95111 ATATAATAAATAAATATAATACATTTAAATATTATTA
1 ATATAATAAATAAATATAATACATTTAAATATTATTA
95148 ATATAATAAATTAAATATA
1 ATATAATAAA-TAAATATA
95167 TATTATCTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 47 0.85
38 8 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (37 bp):
ATATAATAAATAAATATAATACATTTAAATATTATTA
Found at i:95141 original size:15 final size:13
Alignment explanation
Indices: 95074--95166 Score: 67
Period size: 13 Copynumber: 7.4 Consensus size: 13
95064 GAAACTAAAT
*
95074 ATATAATAAATAA
1 ATATAATAATTAA
95087 ATATAATACATTTAA
1 ATATAATA-A-TTAA
95102 ATAT--T-ATT-A
1 ATATAATAATTAA
*
95111 ATATAATAAATAA
1 ATATAATAATTAA
95124 ATATAATACATTTAA
1 ATATAATA-A-TTAA
95139 ATAT--T-ATT-A
1 ATATAATAATTAA
95148 ATATAATAAATTAA
1 ATATAAT-AATTAA
95162 ATATA
1 ATATA
95167 TATTATCTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
9 10 0.16
10 4 0.06
11 4 0.06
12 2 0.03
13 22 0.34
14 8 0.12
15 14 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATAATTAA
Found at i:95149 original size:19 final size:19
Alignment explanation
Indices: 95090--95150 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
95080 TAAATAAATA
95090 TAATACATTTAAATATTAT
1 TAATACATTTAAATATTAT
* * *
95109 TAATATA-ATAAATA-AAT
1 TAATACATTTAAATATTAT
95126 ATAATACATTTAAATATTAT
1 -TAATACATTTAAATATTAT
95146 TAATA
1 TAATA
95151 TAATAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 12 0.36
19 17 0.52
20 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATACATTTAAATATTAT
Found at i:95154 original size:24 final size:24
Alignment explanation
Indices: 95123--95171 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
95113 ATAATAAATA
*
95123 AATATAATACATTTAAATAT-TATT
1 AATATAATA-AATTAAATATATATT
95147 AATATAATAAATTAAATATATATT
1 AATATAATAAATTAAATATATATT
95171 A
1 A
95172 TCTTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AATATAATAAATTAAATATATATT
Found at i:95188 original size:33 final size:31
Alignment explanation
Indices: 95119--95217 Score: 76
Period size: 33 Copynumber: 3.1 Consensus size: 31
95109 TAATATAATA
* * *
95119 AATAAA-TATAATACATTTAAATATTATTAATAT
1 AATAAATTA-AATA-ATTTATAT-TTATTATTTT
*
95152 AATAAATTAAATATATATTATCTTTATTATTTT
1 AATAAATTAAATA-AT-TTATATTTATTATTTT
* *
95185 AATATATTTAATAATTTATATTT-TTATATTT
1 AATAAATTAAATAATTTATATTTATTAT-TTT
95216 AA
1 AA
95218 ATTTATATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 4 0.07
31 12 0.22
32 2 0.04
33 31 0.56
34 6 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAAATTAAATAATTTATATTTATTATTTT
Found at i:95226 original size:22 final size:24
Alignment explanation
Indices: 95174--95226 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
95164 ATATATTATC
95174 TTTAT-TATTTTAATATATTTAATA
1 TTTATATATTTT-ATATATTTAATA
*
95198 ATT-TATATTTT-TATATTTAA-A
1 TTTATATATTTTATATATTTAATA
95219 TTTATATA
1 TTTATATA
95227 ATTACAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 1 0.04
24 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATATATTTTATATATTTAATA
Found at i:95297 original size:22 final size:22
Alignment explanation
Indices: 95269--95310 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
95259 TTATAATCTA
95269 TCAATTATAAATATGTATTGGC
1 TCAATTATAAATATGTATTGGC
*
95291 TCAATTATAAATGTGTATTG
1 TCAATTATAAATATGTATTG
95311 ATTCAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (22 bp):
TCAATTATAAATATGTATTGGC
Found at i:95316 original size:22 final size:22
Alignment explanation
Indices: 95269--95322 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
95259 TTATAATCTA
*
95269 TCAATTATAAATATGTATTGGC
1 TCAATTATAAATATGTATTGAC
* *
95291 TCAATTATAAATGTGTATTGAT
1 TCAATTATAAATATGTATTGAC
95313 TCAATGTATA
1 TCAAT-TATA
95323 CCACATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (22 bp):
TCAATTATAAATATGTATTGAC
Found at i:95913 original size:25 final size:25
Alignment explanation
Indices: 95853--95915 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 25
95843 AATTTAAAAT
95853 ATAAAAATATTAA-ATAATAATTATA
1 ATAAAAA-ATTAATATAATAATTATA
*
95878 AT-ATAAA-TAATA-AATAATTATAA
1 ATAAAAAATTAATATAATAATTAT-A
95901 ATAAAAAATTAATAT
1 ATAAAAAATTAATAT
95916 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 12 0.39
23 5 0.16
24 7 0.23
25 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAAAAAATTAATATAATAATTATA
Found at i:95925 original size:18 final size:18
Alignment explanation
Indices: 95858--95925 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
95848 AAAATATAAA
*
95858 AATAT-TAAATAATAATT
1 AATATATAAATAAAAATT
95875 -ATAATATAAATAATAAA-T
1 AAT-ATATAAATAA-AAATT
95893 AAT-TATAAATAAAAAATT
1 AATATATAAAT-AAAAATT
*
95911 AATATTTAAATAAAA
1 AATATATAAATAAAA
95926 TATTTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
16 2 0.05
17 12 0.29
18 18 0.43
19 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATATAAATAAAAATT
Done.