Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011665.1 Corchorus capsularis cultivar CVL-1 contig11686, whole genome shotgun sequence
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: 51983
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1165 original size:125 final size:128
Alignment explanation
Indices: 956--1210 Score: 349
Period size: 125 Copynumber: 2.0 Consensus size: 128
946 TCTAGGCGTC
*
956 TATATTTTAGCCTTAATTTTTCACCCAATTTGCCTTTCTCGGAGAAAAATTAAAGATGGCGGCAT
1 TATATTTTAGCCTTAATTTTTCACCCAATTTGCCTTTCTCGGACAAAAATTAAAGATGGCGGCAT
* *
1021 CTTGGGGATCATACACCTCCATTTAGCGGCGTCCTGGGCCTCAGACGCCGCTATCTTCAATTT
66 CTTGGGGATCAGACACCTCCATTTAGCGGCGTCCTAGGCCTCAGACGCCGCTATCTTCAATTT
* * * * *
1084 TATATTTTAGCCTT-CTTTTTTATCCAATTTGTCTTTCTC-G-CAAAAATTAAAGATGGCGGCGT
1 TATATTTTAGCCTTAATTTTTCACCCAATTTGCCTTTCTCGGACAAAAATTAAAGATGGCGGCAT
* * * *
1146 -TT-GGAATGTCAGACGCCTCCATTTAGCGGCGTTCTAGGCCTTAGACGCCGCTATCTTCAATTT
66 CTTGGGGA--TCAGACACCTCCATTTAGCGGCGTCCTAGGCCTCAGACGCCGCTATCTTCAATTT
1209 TA
1 TA
1211 GTGAATAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
123 3 0.03
124 2 0.02
125 72 0.64
126 1 0.01
127 21 0.19
128 14 0.12
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (128 bp):
TATATTTTAGCCTTAATTTTTCACCCAATTTGCCTTTCTCGGACAAAAATTAAAGATGGCGGCAT
CTTGGGGATCAGACACCTCCATTTAGCGGCGTCCTAGGCCTCAGACGCCGCTATCTTCAATTT
Found at i:3540 original size:29 final size:29
Alignment explanation
Indices: 3486--3541 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3476 TTGAAGATTT
*
3486 ATTGAAGATAATTTCAAGAATTCAAGACC
1 ATTGAAGATAATTTCAAGAATGCAAGACC
* *
3515 ATTGAAGAATTATTTCAAGGA-GCAAGA
1 ATTGAAG-ATAATTTCAAGAATGCAAGA
3542 ATTGAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (29 bp):
ATTGAAGATAATTTCAAGAATGCAAGACC
Found at i:7044 original size:19 final size:18
Alignment explanation
Indices: 7011--7046 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7001 TTGAAATAAT
7011 TCTTCAATGATCTTCAAC
1 TCTTCAATGATCTTCAAC
*
7029 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7047 TAAGTCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAC
Found at i:8593 original size:16 final size:16
Alignment explanation
Indices: 8568--8598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8558 AGGAATAGGC
8568 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
8584 AATCATTCAAAGCAA
1 AATCAATCAAAGCAA
8599 AGCAATACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:13334 original size:19 final size:18
Alignment explanation
Indices: 13301--13336 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13291 TTGAAATAAT
13301 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
13319 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
13337 TAAGTCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:14437 original size:22 final size:22
Alignment explanation
Indices: 14405--14450 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
14395 CTAAAATGCA
* *
14405 GGACAAGTTCTGCCTAGAACTT
1 GGACAACTTCTGCCCAGAACTT
*
14427 GGACAACTTCTGCCCAGGACTT
1 GGACAACTTCTGCCCAGAACTT
14449 GG
1 GG
14451 TCTGTTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
GGACAACTTCTGCCCAGAACTT
Found at i:18191 original size:15 final size:15
Alignment explanation
Indices: 18171--18208 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18161 TCACCTCTTG
*
18171 TTATATAATTATATA
1 TTATATAATAATATA
18186 TTATATAATAATATA
1 TTATATAATAATATA
18201 TATATATA
1 T-TATATA
18209 TACTTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAATAATATA
Found at i:21678 original size:589 final size:589
Alignment explanation
Indices: 20562--21724 Score: 2256
Period size: 589 Copynumber: 2.0 Consensus size: 589
20552 CAATGGTTTT
20562 AAAAATTTCACATTCCAAACTAAAATTCATTTAAAATACTATATGGGTAAACTTAAAATTCACAT
1 AAAAATTTCACATTCCAAACTAAAATTCATTTAAAATACTATATGGGTAAACTTAAAATTCACAT
*
20627 GAATATATGATCATACGTATGATTTAGCCTCGATTACGTGGTAACTCCTACGGACTCGAGTCCAT
66 GAATATATGATCATACGTATGATTTAGCCTCGATTACGTGGTAACTCCCACGGACTCGAGTCCAT
* *
20692 AGGACCATCACTCTTTAATACTATTGGGTTAATGTGTTTGGTTTTCAAAATAAATTCTACCTTAT
131 AGGACCATCACTCTTTAATACTATTGGGTTAATGAGTTTGGTTTTCAAAATAAATTCTACATTAT
*
20757 TTTACATTAATACGACATTAATTGTGTTTACATTGTCTTTTGTTTGTTTAATTAATGTTGAATTA
196 TTTACATGAATACGACATTAATTGTGTTTACATTGTCTTTTGTTTGTTTAATTAATGTTGAATTA
20822 ATTAGATGTGATCATGTGAATGAGTTTTTGTCTTTTTCTCACATGGTTGATCACTTAAATATCCC
261 ATTAGATGTGATCATGTGAATGAGTTTTTGTCTTTTTCTCACATGGTTGATCACTTAAATATCCC
20887 TCTAAACTTAACATTTTTGCTTGAAATGCATTGTCTTTGTATGACATTTTATCATAAGGTGTAAT
326 TCTAAACTTAACATTTTTGCTTGAAATGCATTGTCTTTGTATGACATTTTATCATAAGGTGTAAT
20952 TAGTGCTGTTTCCACCATTTTCCTTGGTTATTAGCTTTAGCCTTCGGTTCCCGGTAAAAAATTAT
391 TAGTGCTGTTTCCACCATTTTCCTTGGTTATTAGCTTTAGCCTTCGGTTCCCGGTAAAAAATTAT
*
21017 TGGAATTTCCGGGTCTTTTGTTGAAGAATCCGATCCAAACAAGTTGATTTGATTAGACTCCATTT
456 TGGAATTTCCGGGTCTTTTGTAGAAGAATCCGATCCAAACAAGTTGATTTGATTAGACTCCATTT
21082 GTTTACTCATTTTTAGATTTTCTTCCTAACGTATAGTTTGGTTTTTGCAATTGTAAAAACAAAAT
521 GTTTACTCATTTTTAGATTTTCTTCCTAACGTATAGTTTGGTTTTTGCAATTGTAAAAACAAAAT
21147 TTAA
586 TTAA
21151 AAAAATTTCACATTCCAAACTAAAATTCATTTAAAATACTATATGGGTAAACTTAAAATTCACAT
1 AAAAATTTCACATTCCAAACTAAAATTCATTTAAAATACTATATGGGTAAACTTAAAATTCACAT
21216 GAATATATGATCATACGTATGATTTAGCCTCGATTACGTGGTAACTCCCACGGACTCGAGTCCAT
66 GAATATATGATCATACGTATGATTTAGCCTCGATTACGTGGTAACTCCCACGGACTCGAGTCCAT
21281 AGGACCATCACTCTTTAATACTATTGGGTTAATGAGTTTGGTTTTCAATAA-AAATTCTACATTA
131 AGGACCATCACTCTTTAATACTATTGGGTTAATGAGTTTGGTTTTCAA-AATAAATTCTACATTA
*
21345 TTTTGCATGAATACGACATTAATTGTGTTTACATTGTCTTTTGTTTGTTTAATTAATGTTGAATT
195 TTTTACATGAATACGACATTAATTGTGTTTACATTGTCTTTTGTTTGTTTAATTAATGTTGAATT
21410 AATTAGATGTGATCATGTGAATGAGTTTTTGTCTTTTTCTCACATGGTTGATCACTTAAATATCC
260 AATTAGATGTGATCATGTGAATGAGTTTTTGTCTTTTTCTCACATGGTTGATCACTTAAATATCC
21475 CTCTAAACTTAACATTTTTGCTTGAAATGCATTGTCTTTGTATGACATTTTATCATAAGGTGTAA
325 CTCTAAACTTAACATTTTTGCTTGAAATGCATTGTCTTTGTATGACATTTTATCATAAGGTGTAA
21540 TTAGTGCTGTTTCCACCATTTTCCTTGGTTATTAGCTTTAGCCTTCGGTTCCCGGTAAAAAATTA
390 TTAGTGCTGTTTCCACCATTTTCCTTGGTTATTAGCTTTAGCCTTCGGTTCCCGGTAAAAAATTA
21605 TTGGAATTTCCGGGTCTTTTGTAGAAGAATCCGATCCAAACAAGTTGATTTGATTAGACTCCATT
455 TTGGAATTTCCGGGTCTTTTGTAGAAGAATCCGATCCAAACAAGTTGATTTGATTAGACTCCATT
21670 TGTTTACTCATTTTTAGATTTTCTTCCTAACGTATAGTTTGGTTTTTGCAATTGT
520 TGTTTACTCATTTTTAGATTTTCTTCCTAACGTATAGTTTGGTTTTTGCAATTGT
21725 CTTTCGCCGG
Statistics
Matches: 567, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
589 565 1.00
590 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (589 bp):
AAAAATTTCACATTCCAAACTAAAATTCATTTAAAATACTATATGGGTAAACTTAAAATTCACAT
GAATATATGATCATACGTATGATTTAGCCTCGATTACGTGGTAACTCCCACGGACTCGAGTCCAT
AGGACCATCACTCTTTAATACTATTGGGTTAATGAGTTTGGTTTTCAAAATAAATTCTACATTAT
TTTACATGAATACGACATTAATTGTGTTTACATTGTCTTTTGTTTGTTTAATTAATGTTGAATTA
ATTAGATGTGATCATGTGAATGAGTTTTTGTCTTTTTCTCACATGGTTGATCACTTAAATATCCC
TCTAAACTTAACATTTTTGCTTGAAATGCATTGTCTTTGTATGACATTTTATCATAAGGTGTAAT
TAGTGCTGTTTCCACCATTTTCCTTGGTTATTAGCTTTAGCCTTCGGTTCCCGGTAAAAAATTAT
TGGAATTTCCGGGTCTTTTGTAGAAGAATCCGATCCAAACAAGTTGATTTGATTAGACTCCATTT
GTTTACTCATTTTTAGATTTTCTTCCTAACGTATAGTTTGGTTTTTGCAATTGTAAAAACAAAAT
TTAA
Found at i:22479 original size:21 final size:21
Alignment explanation
Indices: 22426--22485 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
22416 TTTGGAGCAA
*
22426 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
22447 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
22468 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
22486 CAAGTTATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:28605 original size:6 final size:6
Alignment explanation
Indices: 28596--28622 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28586 AAAGCAAAGC
28596 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
28623 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:28637 original size:13 final size:13
Alignment explanation
Indices: 28619--28653 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28609 AATCTAAATC
*
28619 TAAAGCAGATTAA
1 TAAAGCAAATTAA
28632 TAAAGCAAATTAA
1 TAAAGCAAATTAA
28645 TAAAGCAAA
1 TAAAGCAAA
28654 CAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:36064 original size:15 final size:14
Alignment explanation
Indices: 36044--36077 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
36034 TTTTGGGGGA
36044 AAAGAAAGATAGTT
1 AAAGAAAGATAGTT
*
36058 CAAAGAAAGTTAGTT
1 -AAAGAAAGATAGTT
36073 AAAGA
1 AAAGA
36078 GTGTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGAAAGATAGTT
Found at i:38317 original size:40 final size:40
Alignment explanation
Indices: 38259--38356 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
38249 ACCAATTTTA
* *
38259 TTATTTTCCAAAAGTCTTCTCCTGGAATTATTAAAAACTT
1 TTATTTTCCAAAAGTCTTCTCCTGGAATTACTAAAAACAT
* * * *
38299 TTATTTTCCAAAAATCTTCTCTTGGATTTGCTAAAAACAT
1 TTATTTTCCAAAAGTCTTCTCCTGGAATTACTAAAAACAT
38339 TTATTTTCCAAAAGTCTT
1 TTATTTTCCAAAAGTCTT
38357 GGAATTGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (40 bp):
TTATTTTCCAAAAGTCTTCTCCTGGAATTACTAAAAACAT
Found at i:38480 original size:14 final size:14
Alignment explanation
Indices: 38461--38493 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
38451 AGAACATGAT
38461 TTTTTGAAAAACAA
1 TTTTTGAAAAACAA
*
38475 TTTTTGAAAAACAC
1 TTTTTGAAAAACAA
38489 TTTTT
1 TTTTT
38494 ATTGCATCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAAACAA
Found at i:39587 original size:50 final size:49
Alignment explanation
Indices: 39517--39947 Score: 442
Period size: 50 Copynumber: 8.7 Consensus size: 49
39507 AGAGAAAACT
* * *
39517 GGACCTTCCGACTGGGAAGGGGAATTTTGGGAAACAAATAAAGAGATAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAATAG
* *
39566 GAACCTTCCGACCTGGGAAGGGGCATTTTTGGAAACAAATAAAGAGAATAG
1 GGACCTTCCGACC-GGGAAGGGGCATTTTGGGAAACAAATAAAGA-AATAG
* *
39617 GGACCTTCCGACCGGGAAGCGGCATTTTGGAAAACAAATAAAGAAA-ACG
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAATA-G
* *
39666 AGGACCTTCCGACCGGGAAGGGGCATTTT-GG-AATAAACAAAGAAAACTA-
1 -GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAG-AAA-TAG
* * * * *
39715 TGACCTTTCGACCAGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAG-AAATAG
* * * * * * *
39765 GGACCTTCCAACCAGGAAGGGGGCACTTTTTGAAAACAAACAAAGAAAACAA
1 GGACCTTCCGACCGGGAA-GGGGCA-TTTTGGGAAACAAATAAAG-AAATAG
* * *
39817 GGATCTTCCGACCGGGAAGGGGCATTTTAGGAAACAAATAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAG-AAATAG
* * *
39867 GGACCTTCCGACCGGGAAGGGCCATTTTTGG-AATAAATAAAGAAATTA-
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAA-TAG
* * *
39915 TGACCTTCCGACCGGGAAGGGGCTTTTTTGGAA
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGGAA
39948 TAAGTAACTG
Statistics
Matches: 325, Mismatches: 43, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
48 65 0.20
49 33 0.10
50 162 0.50
51 28 0.09
52 37 0.11
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (49 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAATAG
Found at i:39750 original size:98 final size:99
Alignment explanation
Indices: 39509--39935 Score: 510
Period size: 98 Copynumber: 4.3 Consensus size: 99
39499 AAATGTGAAG
* * * *
39509 AGAAAACT-GGACCTTCCGACTGGGAAGGGGA-ATTTTGGGAAACAAATAAAG-AGATAGGAACC
1 AGAAAACTAGGACCTTCCGACCGGGAA-GGGACATTTTGGGAAACAAATAAAGAAAACAGGGACC
*
39571 TTCCGACCTGGGAAGGGGCATTTTTGGAAACAAATAA
65 TTCCGACC-GGGAAGGGGCATTTTTGG-AACAAACAA
* *
39608 AGAGAA-TAGGGACCTTCCGACCGGGAAGCGG-CATTTTGGAAAACAAATAAAGAAAAC-GAGGA
1 AGAAAACTA-GGACCTTCCGACCGGGAAG-GGACATTTTGGGAAACAAATAAAGAAAACAG-GGA
*
39670 CCTTCCGACCGGGAAGGGGCA-TTTTGGAATAAACAA
63 CCTTCCGACCGGGAAGGGGCATTTTTGGAACAAACAA
* * *
39706 AGAAAACTATGACCTTTCGACCAGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * *
39771 TCCAACCAGGAAGGGGGCACTTTTTGAAAACAAACAA
66 TCCGACCGGGAA-GGGGCA-TTTTTG-GAACAAACAA
* * * *
39808 AGAAAACAAGGATCTTCCGACCGGGAAGGGGCATTTTAGGAAACAAATAAAGAAAACAGGGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
* * *
39873 TCCGACCGGGAAGGGCCATTTTTGGAATAAATAA
66 TCCGACCGGGAAGGGGCATTTTTGGAACAAACAA
* *
39907 AG-AAATTATGACCTTCCGACCGGGAAGGG
1 AGAAAACTAGGACCTTCCGACCGGGAAGGG
39936 GCTTTTTTGG
Statistics
Matches: 281, Mismatches: 34, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
97 2 0.01
98 93 0.33
99 30 0.11
100 56 0.20
101 24 0.09
102 76 0.27
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.17
Consensus pattern (99 bp):
AGAAAACTAGGACCTTCCGACCGGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
TCCGACCGGGAAGGGGCATTTTTGGAACAAACAA
Found at i:39873 original size:200 final size:198
Alignment explanation
Indices: 39509--39935 Score: 578
Period size: 200 Copynumber: 2.2 Consensus size: 198
39499 AAATGTGAAG
* * * *
39509 AGAAAACT-GGACCTTCCGACTGGGAAGGGGAATTTTGGGAAACAAATAAAGAGATAGGAACCTT
1 AGAAAACTATGACCTTCCGACCGGGAA-GGGAATTTTGGGAAACAAATAAAGAAACAGGAACCTT
* * * * * * *
39573 CCGACCTGGGAAGGGGCATTTTTGGAAACAAATAAAGAGAATAGGGACCTTCCGACCGGGAAGCG
65 CCAACCTAGGAAGGGGCATTTTTGAAAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAAGCG
*
39638 GCATTTTGGAAAACAAATAAAGAAAACGAGGACCTTCCGACCGGGAAGGGGCA-TTTTGGAATAA
130 GCATTTTGGAAAACAAATAAAGAAAACGAGGACCTTCCGACCGGGAAGGGCCATTTTTGGAATAA
39702 ACAA
195 ACAA
* * *
39706 AGAAAACTATGACCTTTCGACCAGGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
1 AGAAAACTATGACCTTCCGACCGGGAAGGGA-ATTTTGGGAAACAAATAAAG-AAACAGGAACCT
*
39771 TCCAACC-AGGAAGGGGGCACTTTTTGAAAACAAACAAAGAAAACAAGGATCTTCCGACCGGGAA
64 TCCAACCTAGGAA-GGGGCA-TTTTTGAAAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAA
*
39835 GGGGCATTTTAGG-AAACAAATAAAGAAAAC-AGGGACCTTCCGACCGGGAAGGGCCATTTTTGG
127 GCGGCATTTT-GGAAAACAAATAAAGAAAACGA-GGACCTTCCGACCGGGAAGGGCCATTTTTGG
*
39898 AATAAATAA
190 AATAAACAA
*
39907 AG-AAATTATGACCTTCCGACCGGGAAGGG
1 AGAAAACTATGACCTTCCGACCGGGAAGGG
39936 GCTTTTTTGG
Statistics
Matches: 201, Mismatches: 21, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
197 12 0.06
198 38 0.19
199 22 0.11
200 111 0.55
201 18 0.09
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.17
Consensus pattern (198 bp):
AGAAAACTATGACCTTCCGACCGGGAAGGGAATTTTGGGAAACAAATAAAGAAACAGGAACCTTC
CAACCTAGGAAGGGGCATTTTTGAAAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAAGCGG
CATTTTGGAAAACAAATAAAGAAAACGAGGACCTTCCGACCGGGAAGGGCCATTTTTGGAATAAA
CAA
Found at i:39962 original size:43 final size:43
Alignment explanation
Indices: 39868--39995 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
39858 AGAAAACAGG
* *
39868 GACCTTCCGACCGGGAAGGGCCATTTTTGGAATAAATAAAGAAATTAT
1 GACCTTCCGACCGGGAAGGGGCATTTTTGG----AAT-AAGAAACTAT
* * *
39916 GACCTTCCGACCGGGAAGGGGCTTTTTTGGAATAAGTAACTGT
1 GACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAAACTAT
* *
39959 GACCTTCCGACCGGGAACGGGCATTTTTGAAATAAGA
1 GACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA
39996 GAAGAAAACG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
43 40 0.56
44 3 0.04
48 28 0.39
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (43 bp):
GACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAAACTAT
Found at i:40037 original size:91 final size:91
Alignment explanation
Indices: 39868--40038 Score: 204
Period size: 91 Copynumber: 1.9 Consensus size: 91
39858 AGAAAACAGG
* * ** *
39868 GACCTTCCGACCGGGAAGGGCCATTTTTGGAATAAATAAAGAAATTATGACCTTCCGACCGGGAA
1 GACCTTCCGACCGGGAAGGGCCATTTTTGAAATAAAGAAAGAAACGATGACCTTCCGACCGAGAA
****
39933 GGGGCTTTTTTGGAATAAGTAACTGT
66 GGGGCAAACTTGGAATAAGTAACTGT
*
39959 GACCTTCCGACCGGGAACGGG-CATTTTTGAAAT-AAGAGAAGAAAACGGTGACCTTCCGACCGA
1 GACCTTCCGACCGGGAA-GGGCCATTTTTGAAATAAAGA-AAG-AAACGATGACCTTCCGACCGA
40022 GAA-GGGCAAACTTGGAA
63 GAAGGGGCAAACTTGGAA
40039 ACTAAACAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
90 3 0.04
91 41 0.61
92 23 0.34
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (91 bp):
GACCTTCCGACCGGGAAGGGCCATTTTTGAAATAAAGAAAGAAACGATGACCTTCCGACCGAGAA
GGGGCAAACTTGGAATAAGTAACTGT
Found at i:40097 original size:41 final size:40
Alignment explanation
Indices: 40009--40132 Score: 139
Period size: 41 Copynumber: 3.0 Consensus size: 40
39999 GAAAACGGTG
* *
40009 ACCTTCCGACCGA-GAAGGGC-AAACTTGGAAACTAAACAAC
1 ACCTTCCGA-TGAGGAAGGGCAAAAC-AGGAAACTAAACAAC
40049 ACCTTCCGAT-AGGGAAGGGCAAAAC-GAGAAATCTAAACAAC
1 ACCTTCCGATGA-GGAAGGGCAAAACAG-GAAA-CTAAACAAC
*
40090 ACCTTCCGGTGAGGAAGGGCAAAACAGGAAAACTAAACAAC
1 ACCTTCCGATGAGGAAGGGCAAAACAGG-AAACTAAACAAC
40131 AC
1 AC
40133 GCAAACTGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 15
0.81 0.02 0.16
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 20 0.27
41 47 0.64
42 5 0.07
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (40 bp):
ACCTTCCGATGAGGAAGGGCAAAACAGGAAACTAAACAAC
Found at i:40136 original size:25 final size:25
Alignment explanation
Indices: 40111--40157 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40101 AGGAAGGGCA
*
40111 AAACAGGAAAA-CTAAACAACACGC
1 AAACAGAAAAAGCTAAACAACACGC
*
40135 AAACTGAAAAAGCTAAACAACAC
1 AAACAGAAAAAGCTAAACAACAC
40158 CTTCCGACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.60, C:0.23, G:0.11, T:0.06
Consensus pattern (25 bp):
AAACAGAAAAAGCTAAACAACACGC
Found at i:40812 original size:51 final size:51
Alignment explanation
Indices: 40707--41025 Score: 269
Period size: 51 Copynumber: 6.3 Consensus size: 51
40697 GTCTCAATTT
* * * * *
40707 TTTATTTACAAATTAAT-CAAAATTCAATCTTTTAGTTCATAGATTTCACC
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGATTTCATC
* * *
40757 TTTATTTACAAATTGATCCAGAGTTTAATCATTTAGTTCAAAGATCTT-ATT
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGAT-TTCATC
* * *
40808 TTTATTTACAAATTAAT-CACAAGTTCAATCATTTAATTCAAAGATCTCATC
1 TTTATTTACAAATTAATCCA-AAGTTTAATCATTTAGTTCAAAGATTTCATC
* * *
40859 TTTATTTACAAATTAATCAAAAGTTTAATTA-TTAGCTT-AAAGATTTCACC
1 TTTATTTACAAATTAATCCAAAGTTTAATCATTTAG-TTCAAAGATTTCATC
* * * * *
40909 TTTA-TCACCAAATTAATCCAAAGTTTCATCTTTTAATTCAAA-AGTTTCATT
1 TTTATTTA-CAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGA-TTTCATC
** ** * * * *
40960 TTTATTTACAAATTTCTTAAAAGATTCAATC-TTTCACTT-AAACATTTAATC
1 TTTATTTACAAATTAATCCAAAG-TTTAATCATTT-AGTTCAAAGATTTCATC
41011 TTTATTTACAAATTA
1 TTTATTTACAAATTA
41026 CTTAAAAATC
Statistics
Matches: 216, Mismatches: 39, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
49 2 0.01
50 58 0.27
51 142 0.66
52 14 0.06
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTATTTACAAATTAATCCAAAGTTTAATCATTTAGTTCAAAGATTTCATC
Found at i:40934 original size:152 final size:152
Alignment explanation
Indices: 40707--41025 Score: 373
Period size: 152 Copynumber: 2.1 Consensus size: 152
40697 GTCTCAATTT
* * * *
40707 TTTATTTACAAATTAATCAAAATTCAATCTTTTAGTTCATAGATTTCACCTTTATTTACAAATTG
1 TTTATTTACAAATTAATCAAAATTCAATCTATTAGTTCAAAGATTTCACCTTTATTCACAAATTA
* * *
40772 ATCCAGAGTTTAATCATTTAGTTC-AAAGATCTT-ATTTTTATTTACAAATTAATCACAAG-TTC
66 ATCCAAAGTTTAATCATTTAATTCAAAAG-T-TTCATTTTTATTTACAAATTAATCAAAAGATTC
* *
40834 AATCATTT-AATTCAAAGATCTCATC
129 AATC-TTTCAATT-AAACATCTAATC
*
40859 TTTATTTACAAATTAATCAAAAGTTTAAT-TATTAGCTT-AAAGATTTCACCTTTA-TCACCAAA
1 TTTATTTACAAATTAATCAAAA-TTCAATCTATTAG-TTCAAAGATTTCACCTTTATTCA-CAAA
* * ** *
40921 TTAATCCAAAGTTTCATCTTTTAATTCAAAAGTTTCATTTTTATTTACAAATTTCTTAAAAGATT
63 TTAATCCAAAGTTTAATCATTTAATTCAAAAGTTTCATTTTTATTTACAAATTAATCAAAAGATT
* *
40986 CAATCTTTCACTTAAACATTTAATC
128 CAATCTTTCAATTAAACATCTAATC
41011 TTTATTTACAAATTA
1 TTTATTTACAAATTA
41026 CTTAAAAATC
Statistics
Matches: 143, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
151 4 0.03
152 118 0.83
153 21 0.15
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (152 bp):
TTTATTTACAAATTAATCAAAATTCAATCTATTAGTTCAAAGATTTCACCTTTATTCACAAATTA
ATCCAAAGTTTAATCATTTAATTCAAAAGTTTCATTTTTATTTACAAATTAATCAAAAGATTCAA
TCTTTCAATTAAACATCTAATC
Found at i:40950 original size:20 final size:20
Alignment explanation
Indices: 40921--40963 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40911 TATCACCAAA
40921 TTAATCC-AAAGTTTCATCTT
1 TTAATCCAAAAGTTTCAT-TT
*
40941 TTAATTCAAAAGTTTCATTT
1 TTAATCCAAAAGTTTCATTT
40961 TTA
1 TTA
40964 TTTACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATCCAAAAGTTTCATTT
Found at i:41431 original size:18 final size:20
Alignment explanation
Indices: 41391--41432 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
41381 TATATCGGAC
*
41391 TCCTCCTTTTATTCTTCTTT
1 TCCTCCTTTTATTCTTCTGT
*
41411 TCCT-CTTTTCTT-TTCTGT
1 TCCTCCTTTTATTCTTCTGT
41429 TCCT
1 TCCT
41433 TCCTCGCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (20 bp):
TCCTCCTTTTATTCTTCTGT
Found at i:44150 original size:18 final size:17
Alignment explanation
Indices: 44115--44168 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
44105 TATGCAATGC
44115 AAATGCCTAAACAATTA
1 AAATGCCTAAACAATTA
*
44132 AAATGTCTAAACAAATTA
1 AAATGCCTAAAC-AATTA
* *
44150 AGATGCCT-ACCAATTA
1 AAATGCCTAAACAATTA
44166 AAA
1 AAA
44169 CGGATATGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 7 0.23
17 13 0.42
18 11 0.35
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATGCCTAAACAATTA
Found at i:45698 original size:19 final size:22
Alignment explanation
Indices: 45674--45718 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
45664 TCTAAAAACC
45674 TTTTGA-AAAAC-ATTT-TTCT
1 TTTTGACAAAACAATTTCTTCT
*
45693 TTTTGACAAATCAATTTCTTCT
1 TTTTGACAAAACAATTTCTTCT
45715 TTTT
1 TTTT
45719 TTGGGAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 4 0.18
22 8 0.36
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTGACAAAACAATTTCTTCT
Found at i:46341 original size:13 final size:13
Alignment explanation
Indices: 46286--46342 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
46276 TTAAAAACTA
46286 AAAACC-TTTTTG
1 AAAACCATTTTTG
*
46298 AAAACTCATTTTCG
1 AAAAC-CATTTTTG
*
46312 AAAACCTTTTCTTG
1 AAAACCATTT-TTG
*
46326 AAAACAATTTTTG
1 AAAACCATTTTTG
46339 AAAA
1 AAAA
46343 ACACTCTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
12 5 0.14
13 12 0.32
14 20 0.54
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:49188 original size:50 final size:50
Alignment explanation
Indices: 49121--49834 Score: 830
Period size: 50 Copynumber: 14.5 Consensus size: 50
49111 AAATGTGAAG
* *
49121 AGAAAAC-TGGACCTTCCGACTGGGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
*
49170 AGAGAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* * *
49220 ACAAAAC-GAGGACCTTCCGACCGGGAAGGGGCATTTT-GG-AATAAACAA
1 AGAAAACAG-GGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* *
49268 AGAAAACTA-GGACCTTCCGACCGAGAAGGGACATTTTGGGAAACAAATAA
1 AGAAAAC-AGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* * * * * *
49318 AGAAAACAGGGACCTTCCAACCAGGAAGAGGCACTTTT-GAAAACAGACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCA-TTTTGGGAAACAAATAA
* * * * *
49368 AGAAAACAAGGATCTTCCGACCGGGAAGGGGCATTTT-GG-AATAAGTGA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
** * * * *
49416 AGAAAATTGTGACCTTCCGACCGGGAAGGGGCATTTTGAGAAGCAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* *
49466 AGAAAACAAGGACCTTCCGACCGAGAAGGGGCATTTTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* * *
49516 AGAGAACAGGGA-CTTCCGACTGGGAAGGGG-A-ATTGGGAAACAAATAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
** * * * *
49563 AGAAAACAACGACCTTCCGACCGGAAAGGGACATTTT-GG-AATAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* * *
49611 AGAAAACTA-GGACCTTCCAACCGGGAAGGGACATTTTAGGAAACAAATAA
1 AGAAAAC-AGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* * *
49661 AGAAAACAGGGACCTTCC-ACCCAGGAAGGGGCACTTTT-GAAAACAAACAA
1 AGAAAACAGGGACCTTCCGA-CCGGGAAGGGGCA-TTTTGGGAAACAAATAA
* * *
49711 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAGCAAACAA
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
* *
49761 AAAAACACAGGGACCTTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAA
1 AGAAA-ACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
49812 AGAAAACAGGGACCTTCCGACCG
1 AGAAAACAGGGACCTTCCGACCG
49835 AGTGTCGCAA
Statistics
Matches: 560, Mismatches: 83, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
47 24 0.04
48 130 0.23
49 46 0.08
50 306 0.55
51 54 0.10
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.15
Consensus pattern (50 bp):
AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAA
Found at i:49397 original size:148 final size:148
Alignment explanation
Indices: 49121--49834 Score: 881
Period size: 148 Copynumber: 4.8 Consensus size: 148
49111 AAATGTGAAG
* * *
49121 AGAAAACT-GGACCTTCCGACTGGGAAGGGGCATTTTGGGAAACAAATAAAGAGAACAGGGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGGACCT
*
49185 TCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAACAAAAC-GAGGACCTTCCGACCGGGAAGG
66 TCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAG-GGACCTTCCGACCGGGAAGG
*
49249 GGCATTTTGGAATAAACAA
130 GGCATTTTGGAACAAACAA
* * *
49268 AGAAAACTAGGACCTTCCGACCGAGAAGGGACATTTTGGGAAACAAATAAAGAAAACAGGGACCT
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGGACCT
* * * * * * * *
49333 TCCAACCAGGAAGAGGCACTTTT-GAAAACAGACAAAGAAAACAAGGATCTTCCGACCGGGAAGG
66 TCCGACCGGGAAGGGGCA-TTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCGACCGGGAAGG
* ***
49397 GGCATTTTGGAATAAGTGA
130 GGCATTTTGGAACAAACAA
* * * *
49416 AGAAAA-TTGTGACCTTCCGACCGGGAAGGGGCATTTTGAGAAGCAAACAAAGAAAACAAGGACC
1 AGAAAACTAG-GACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGGACC
* * *
49480 TTCCGACCGAGAAGGGGCATTTTGGGAAACAAATAAAGAGAACAGGGA-CTTCCGACTGGGAAGG
65 TTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCGACCGGGAAGG
* * *
49544 GG-AATTGGGAAACAAATAA
130 GGCATTTTGG-AACAAACAA
* * * * *
49563 AGAAAACAACGACCTTCCGACCGGAAAGGGACATTTT-GG-AATAAACAAAGAAAACTA-GGACC
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAAAC-AGGGACC
* * * *
49625 TTCCAACCGGGAAGGGACATTTTAGGAAACAAATAAAGAAAACAGGGACCTTCC-ACCCAGGAAG
65 TTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCGA-CCGGGAAG
*
49689 GGGCACTTTTGAAAACAAACAA
129 GGGCA-TTTTG-GAACAAACAA
* * *
49711 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAGCAAACAAAAAAACACAGGGACC
1 AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAA-ACAGGGACC
*
49776 TTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAAAGAAAACAGGGACCTTCCGACCG
65 TTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCGACCG
49835 AGTGTCGCAA
Statistics
Matches: 482, Mismatches: 67, Indels: 32
0.83 0.12 0.06
Matches are distributed among these distances:
145 63 0.13
146 21 0.04
147 69 0.14
148 250 0.52
149 6 0.01
150 12 0.02
151 60 0.12
152 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.15
Consensus pattern (148 bp):
AGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAAAGAAAACAGGGACCT
TCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGG
GCATTTTGGAACAAACAA
Found at i:50691 original size:14 final size:14
Alignment explanation
Indices: 50672--50698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50662 TTCTTACTAA
50672 ACTTAATTACCCTT
1 ACTTAATTACCCTT
50686 ACTTAATTACCCT
1 ACTTAATTACCCT
50699 GAATTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTACCCTT
Found at i:50728 original size:35 final size:34
Alignment explanation
Indices: 50683--51338 Score: 680
Period size: 35 Copynumber: 19.1 Consensus size: 34
50673 CTTAATTACC
*
50683 CTTACTTAATTACCCTGAATTAAGTTACTTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTA-TTACTGA
*
50718 CTTACTTAATTACCCTGAATTAAGCTACTTATTGACTTA
1 CTTACTTAATTACCCTGAATTAAG----TTATT-ACTGA
* *
50757 ATTACTTAATTACCCTGAATTAAGTTATTTGCTGA
1 CTTACTTAATTACCCTGAATTAAGTTA-TTACTGA
*
50792 CTTACTTAATTACCCTGAATTAAGTTGATTACTAA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* * * *
50827 ATTACTTAATTACCCTAAATTAAGTTAATAAATGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* * *
50862 ATTTCTTAATTACCCTGAATCAAG---TTACTG-
1 CTTACTTAATTACCCTGAATTAAGTTATTACTGA
*
50892 CTTTACTTAATTTCCCTGAATTAAG---TTACT-A
1 C-TTACTTAATTACCCTGAATTAAGTTATTACTGA
* *
50923 ATTGAC-T--TTA--CTTAATTAAGTTGATTACTGA
1 CTT-ACTTAATTACCCTGAATTAAGTT-ATTACTGA
*
50954 CTTACTTAATTACCGTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* *
50989 CTTACTTAATTACCCTGAACTAAGTTGGTTACTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
*
51024 CTTACTTAATTACCCTGAATTAAGTTGATTATTG-
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* *
51058 CATTGCTTAATTACCCTGAATTAAGTCGATTACTGA
1 C-TTACTTAATTACCCTGAATTAAGT-TATTACTGA
* * *
51094 CTCACTTAGTTACCCTGAATTAAGTTGATTACCGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
*
51129 CTTACTTAATTTCCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
*
51164 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* * *
51199 CTGACTTAAATACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* *
51234 ATTACTTAATTACCCTAAATTAAGTTA--A-TGA
1 CTTACTTAATTACCCTGAATTAAGTTATTACTGA
*
51265 CTCACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTT-ATTACTGA
* *
51300 TTTACTTAATTACCCTGAATTAAGTTACTTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTA-TTACTGA
51335 CTTA
1 CTTA
51339 ATTACTCTGA
Statistics
Matches: 528, Mismatches: 64, Indels: 58
0.81 0.10 0.09
Matches are distributed among these distances:
26 9 0.02
28 2 0.00
30 10 0.02
31 61 0.12
32 2 0.00
33 3 0.01
34 4 0.01
35 402 0.76
36 4 0.01
38 2 0.00
39 29 0.05
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (34 bp):
CTTACTTAATTACCCTGAATTAAGTTATTACTGA
Found at i:50940 original size:26 final size:25
Alignment explanation
Indices: 50910--50965 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
50900 AATTTCCCTG
*
50910 AATTAAGTT-ACTAATTGACTTTACTT
1 AATTAAGTTGA-TAACTGAC-TTACTT
*
50936 AATTAAGTTGATTACTGACTTACTT
1 AATTAAGTTGATAACTGACTTACTT
50961 AATTA
1 AATTA
50966 CCGTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 15 0.56
27 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (25 bp):
AATTAAGTTGATAACTGACTTACTT
Done.