Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013087.1 Corchorus capsularis cultivar CVL-1 contig13108, 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: 25815
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7216 original size:14 final size:14
Alignment explanation
Indices: 7197--7223 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7187 GGTATTTATG
7197 TTTGTGCTATATTT
1 TTTGTGCTATATTT
7211 TTTGTGCTATATT
1 TTTGTGCTATATT
7224 ATAAGTTTAG
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:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (14 bp):
TTTGTGCTATATTT
Found at i:8769 original size:17 final size:17
Alignment explanation
Indices: 8747--8779 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8737 AAAAGTTTTC
8747 CAAAAATCCAAAAAAAT
1 CAAAAATCCAAAAAAAT
*
8764 CAAAAATTCAAAAAAA
1 CAAAAATCCAAAAAAA
8780 AATCAAAAAA
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:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAAATCCAAAAAAAT
Found at i:11298 original size:61 final size:61
Alignment explanation
Indices: 11150--11299 Score: 183
Period size: 61 Copynumber: 2.4 Consensus size: 61
11140 AAAGCAATCA
* * *
11150 AAGACCAGTCTGTGGTCGACATTGAAAACTGAGAAAAACCTGTCTAAGGTCTGAAGCTAAAG
1 AAGACCAGTCTGTGGTCGACATT-AAAACTAAGAAAAACCTGTCTAAGGTCTGAAACCAAAG
* * *** * * *
11212 AAGATCAGTATGTGGTCGTTTTTAAAACTAATAAAGACCTGTCTGAGGTCTGAAACCAAAG
1 AAGACCAGTCTGTGGTCGACATTAAAACTAAGAAAAACCTGTCTAAGGTCTGAAACCAAAG
*
11273 AAGACCAGTCCGTGGTCGACATTAAAA
1 AAGACCAGTCTGTGGTCGACATTAAAA
11300 TTTGAGAATG
Statistics
Matches: 71, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
61 53 0.75
62 18 0.25
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (61 bp):
AAGACCAGTCTGTGGTCGACATTAAAACTAAGAAAAACCTGTCTAAGGTCTGAAACCAAAG
Found at i:11406 original size:62 final size:62
Alignment explanation
Indices: 11330--11447 Score: 200
Period size: 62 Copynumber: 1.9 Consensus size: 62
11320 GGTTAACTTT
* *
11330 AAAAACTAAGAAAGATCTGTCTGAGGTCTGAAACTGAAGAAGACCATTCCGTGGTCGACATG
1 AAAAACTAAGAAAGACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGTCCGTGGTCGACATG
* *
11392 AAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGCTGAAGAAGACCAGTCTGTGGTC
1 AAAAACTAAGAAAGACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGTCCGTGGTC
11448 TATATTGAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (62 bp):
AAAAACTAAGAAAGACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGTCCGTGGTCGACATG
Found at i:11409 original size:96 final size:96
Alignment explanation
Indices: 11235--11418 Score: 269
Period size: 96 Copynumber: 1.9 Consensus size: 96
11225 GGTCGTTTTT
* *
11235 AAAACTAATAAAGACCTGTCTGAGGTCTGAAACCAAAGAAGACCAGTCCGTGGTCGACATTAAAA
1 AAAACTAAGAAAGACCTGTCTGAGGTCTGAAACCAAAGAAGACCAGTCCGTGGTCGACATGAAAA
** * *
11300 TTTGAGAATGACCTGCCTGAGGTTAACTTTA
66 ACTAAGAAAGACCTGCCTGAGGTTAACTTTA
* ** *
11331 AAAACTAAGAAAGATCTGTCTGAGGTCTGAAACTGAAGAAGACCATTCCGTGGTCGACATGAAAA
1 AAAACTAAGAAAGACCTGTCTGAGGTCTGAAACCAAAGAAGACCAGTCCGTGGTCGACATGAAAA
*
11396 ACTAAGAAAGACCTGTCTGAGGT
66 ACTAAGAAAGACCTGCCTGAGGT
11419 CTGAAGCTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 77 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (96 bp):
AAAACTAAGAAAGACCTGTCTGAGGTCTGAAACCAAAGAAGACCAGTCCGTGGTCGACATGAAAA
ACTAAGAAAGACCTGCCTGAGGTTAACTTTA
Found at i:11474 original size:27 final size:28
Alignment explanation
Indices: 11400--11474 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
11390 TGAAAAACTA
11400 AGAAAGACCTGTCTGAGGTCTGAAGCTG
1 AGAAAGACCTGTCTGAGGTCTGAAGCTG
* * *
11428 A-AGAAGACCAGTCTGTGGTCT-ATA-TTG
1 AGA-AAGACCTGTCTGAGGTCTGA-AGCTG
*
11455 AGAAAGACCTGTCCGAGGTC
1 AGAAAGACCTGTCTGAGGTC
11475 AACTTTGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (28 bp):
AGAAAGACCTGTCTGAGGTCTGAAGCTG
Found at i:11522 original size:34 final size:37
Alignment explanation
Indices: 11451--11524 Score: 91
Period size: 40 Copynumber: 2.0 Consensus size: 37
11441 TGTGGTCTAT
11451 ATTGAGAAAGACCTGTCCGAGGTCAACTTTGATAATTGAA
1 ATTGAGAAAGACCTGTCCGAGGT--AC-TTGATAATTGAA
*
11491 ATTGAGAAAGACCTGTCTGAGGT-C-TGA-AATTGAA
1 ATTGAGAAAGACCTGTCCGAGGTACTTGATAATTGAA
11525 GAAGACTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 7 0.21
35 3 0.09
37 1 0.03
40 22 0.67
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (37 bp):
ATTGAGAAAGACCTGTCCGAGGTACTTGATAATTGAA
Found at i:11590 original size:28 final size:27
Alignment explanation
Indices: 11559--11716 Score: 75
Period size: 28 Copynumber: 5.2 Consensus size: 27
11549 GAAAATGAGA
11559 AAGACCTTTCTGAGGTCAAAAACTGAAG
1 AAGACCTTTCTGAGGTCAAAAACT-AAG
** *
11587 AAGACCAGTCTGTGGTCGACTTTAAAAACTAAG
1 AAGACCTTTCTGAGGT---C---AAAAACTAAG
*
11620 AAAGACCTTTCTGAGGTCAGAAACTAAAG
1 -AAGACCTTTCTGAGGTCAAAAACT-AAG
**
11649 AAGACCAGTCT-ATGGTCGACTTTGAAAACTAAG
1 AAGACCTTTCTGA-GGTC-A-----AAAACTAAG
*
11682 AAAGACCTTTCTGAGGTCAGAAACTGAAG
1 -AAGACCTTTCTGAGGTCAAAAACT-AAG
*
11711 ATGACC
1 AAGACC
11717 AGTCCGTGGT
Statistics
Matches: 98, Mismatches: 14, Indels: 36
0.66 0.09 0.24
Matches are distributed among these distances:
27 1 0.01
28 42 0.43
29 7 0.07
31 2 0.02
33 7 0.07
34 38 0.39
35 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (27 bp):
AAGACCTTTCTGAGGTCAAAAACTAAG
Found at i:11625 original size:34 final size:34
Alignment explanation
Indices: 11576--11762 Score: 109
Period size: 34 Copynumber: 5.9 Consensus size: 34
11566 TTCTGAGGTC
*
11576 AAAAACTGAAG-AAGACCAGTCTGTGGTCGACTTT
1 AAAAACT-AAGAAAGACCAGTCTGAGGTCGACTTT
**
11610 AAAAACTAAGAAAGACCTTTCTGAGGT---C---
1 AAAAACTAAGAAAGACCAGTCTGAGGTCGACTTT
*
11638 AGAAACTAA-AGAAGACCAGTCT-ATGGTCGACTTT
1 AAAAACTAAGA-AAGACCAGTCTGA-GGTCGACTTT
* **
11672 GAAAACTAAGAAAGACCTTTCTGAGGT---C---
1 AAAAACTAAGAAAGACCAGTCTGAGGTCGACTTT
* * * *
11700 AGAAACTGAAG-ATGACCAGTCCGTGGTCGACTTT
1 AAAAACT-AAGAAAGACCAGTCTGAGGTCGACTTT
* *
11734 AAAAACCAAGAAAGACCTGTCTGAGGTCG
1 AAAAACTAAGAAAGACCAGTCTGAGGTCG
11763 GAGAATAAAG
Statistics
Matches: 111, Mismatches: 23, Indels: 38
0.65 0.13 0.22
Matches are distributed among these distances:
27 2 0.02
28 36 0.32
29 3 0.03
31 4 0.04
33 6 0.05
34 58 0.52
35 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (34 bp):
AAAAACTAAGAAAGACCAGTCTGAGGTCGACTTT
Found at i:11636 original size:62 final size:62
Alignment explanation
Indices: 11495--11839 Score: 367
Period size: 62 Copynumber: 5.6 Consensus size: 62
11485 ATTGAAATTG
* * * * * * * *
11495 AGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACTAGTATGTGGTTGA-TATTGAAAA-TG
1 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGACCAGTCTGTGGTCGACT-TTAAAAACTA
*
11556 AGAAAGACCTTTCTGAGGTCAAAAACTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTA
1 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTA
* * *
11618 AGAAAGACCTTTCTGAGGTCAGAAACTAAAGAAGACCAGTCTATGGTCGACTTTGAAAACTA
1 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTA
* * *
11680 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGATGACCAGTCCGTGGTCGACTTTAAAAACCA
1 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTA
* ** * * * * *
11742 AGAAAGACCTGTCTGAGGTCGGAGAATAAAGAGGAAGATCAG-CTTGTGGTTGACTTT--TAATT
1 AGAAAGACCTTTCTGAGGTC--AGAA-ACTGAAGAAGACCAGTC-TGTGGTCGACTTTAAAAACT
*
11804 G
62 A
* * *
11805 AGAAAGACCTTTCTGAAGTCGGAAACTAAAGAAGA
1 AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGA
11840 AAATGACGAA
Statistics
Matches: 240, Mismatches: 38, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
60 7 0.03
61 52 0.22
62 135 0.56
63 20 0.08
64 5 0.02
65 21 0.09
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (62 bp):
AGAAAGACCTTTCTGAGGTCAGAAACTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTA
Found at i:11919 original size:47 final size:47
Alignment explanation
Indices: 11868--11966 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 47
11858 AAACCAATTG
** *
11868 TGGTCACCAAATTGTAGAC-TCGCATGGAAGCGAGAAAAGACCGACTA
1 TGGTCACCAAATTGTA-ACTTCGCATAAAAGCGAGAAAAGACCAACTA
* * *
11915 TGGTCACCAAATTGTAACTTTGCATAAAAGTGAGAAAAGACCAACTT
1 TGGTCACCAAATTGTAACTTCGCATAAAAGCGAGAAAAGACCAACTA
11962 TGGTC
1 TGGTC
11967 GAAGGACCGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 2 0.04
47 43 0.96
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (47 bp):
TGGTCACCAAATTGTAACTTCGCATAAAAGCGAGAAAAGACCAACTA
Found at i:12028 original size:48 final size:48
Alignment explanation
Indices: 11942--12246 Score: 391
Period size: 48 Copynumber: 6.4 Consensus size: 48
11932 CTTTGCATAA
* ***
11942 AAGTGA-GAAAAGACCAACTTTGGTC-GAAGGACCGCTGACTCACATGG
1 AAGTGAGGAAAA-ACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
* * * * *
11989 AAGTAAGGAAACACCAATTTAGGTGGGAAGGATTTCTGACTCACATGG
1 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
* * *
12037 AAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTACTGACTCATATGG
1 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
*
12085 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTACTGACTCACATGG
1 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
* * * *
12133 AAGTGAGGAAATACCAACTTGTGTC-GTAGGATTTTTGACTCACATGG
1 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
* * * *
12180 AAGTGAGGAAAGACCAACTTGGGTCGAAACGATTTCTGACTCACATGA
1 AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
12228 AAGTGAGGAAAAACCAACT
1 AAGTGAGGAAAAACCAACT
12247 GCCAACTTGG
Statistics
Matches: 225, Mismatches: 30, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
47 57 0.25
48 168 0.75
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (48 bp):
AAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTTCTGACTCACATGG
Found at i:12055 original size:95 final size:95
Alignment explanation
Indices: 11942--12246 Score: 396
Period size: 95 Copynumber: 3.2 Consensus size: 95
11932 CTTTGCATAA
* *** * * *
11942 AAGTGAGAAAAGACCAACTTTGGTCGAAGGACCGCTGACTCACATGGAAGTAAGGAAACACCAAT
1 AAGTGAGGAAAGACCAACTTTGGTCGAAGGATTACTGACTCACATGGAAGTGAGGAAAAACCAAC
* *
12007 TTAGGTGGGAAGGATTTCTGACTCACATGG
66 TTGGGTCGGAAGGATTTCTGACTCACATGG
* *
12037 AAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTACTGACTCATATGGAAGTGAGGAAAAACCAA
1 AAGTGAGGAAAGACCAACTTTGGTC-GAAGGATTACTGACTCACATGGAAGTGAGGAAAAACCAA
*
12102 CTTGGGTCGGAAGGATTACTGACTCACATGG
65 CTTGGGTCGGAAGGATTTCTGACTCACATGG
* * ** *
12133 AAGTGAGGAAATACCAAC-TTGTGTCGTAGGATTTTTGACTCACATGGAAGTGAGGAAAGACCAA
1 AAGTGAGGAAAGACCAACTTTG-GTCGAAGGATTACTGACTCACATGGAAGTGAGGAAAAACCAA
* * *
12197 CTTGGGTCGAAACGATTTCTGACTCACATGA
65 CTTGGGTCGGAAGGATTTCTGACTCACATGG
*
12228 AAGTGAGGAAAAACCAACT
1 AAGTGAGGAAAGACCAACT
12247 GCCAACTTGG
Statistics
Matches: 183, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
95 103 0.56
96 80 0.44
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (95 bp):
AAGTGAGGAAAGACCAACTTTGGTCGAAGGATTACTGACTCACATGGAAGTGAGGAAAAACCAAC
TTGGGTCGGAAGGATTTCTGACTCACATGG
Found at i:12179 original size:143 final size:143
Alignment explanation
Indices: 11941--12246 Score: 429
Period size: 143 Copynumber: 2.1 Consensus size: 143
11931 ACTTTGCATA
* *
11941 AAAGTGA-GAAAAGACCAACTTTGGTCGAAGGACCGCTGACTCACATGGAAGTAAGGAAACACCA
1 AAAGTGAGGAAAA-ACCAACTTGGGTCGAAGGACCACTGACTCACATGGAAGTAAGGAAACACCA
* * * *
12005 ATTTAGGTGGGAAGGATTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGAT
65 ACTTAGGTGCGAAGGATTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTGGGTCGAAACGAT
*
12070 TACTGACTCATATG
130 TACTGACTCACATG
* ** * *
12084 GAAGTGAGGAAAAACCAACTTGGGTCGGAAGGATTACTGACTCACATGGAAGTGAGGAAATACCA
1 AAAGTGAGGAAAAACCAACTTGGGTC-GAAGGACCACTGACTCACATGGAAGTAAGGAAACACCA
* *
12149 ACTT--GTGTCGTAGGATTTTTGACTCACATGGAAGTGAGGAAAGACCAACTTGGGTCGAAACGA
65 ACTTAGGTG-CGAAGGATTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTGGGTCGAAACGA
*
12212 TTTCTGACTCACATG
129 TTACTGACTCACATG
12227 AAAGTGAGGAAAAACCAACT
1 AAAGTGAGGAAAAACCAACT
12247 GCCAACTTGG
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
142 3 0.02
143 100 0.69
144 41 0.28
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (143 bp):
AAAGTGAGGAAAAACCAACTTGGGTCGAAGGACCACTGACTCACATGGAAGTAAGGAAACACCAA
CTTAGGTGCGAAGGATTTCTGACTCACATGGAAGTGAGGAAAGACCAACTTGGGTCGAAACGATT
ACTGACTCACATG
Found at i:14337 original size:14 final size:13
Alignment explanation
Indices: 14318--14365 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
14308 ACCCGAAACC
14318 TTTTGAAAACTCAT
1 TTTTGAAAAC-CAT
*
14332 TTTTGAAAACCTT
1 TTTTGAAAACCAT
*
14345 TTCTTGAAAACAAT
1 TT-TTGAAAACCAT
14359 TTTTGAA
1 TTTTGAA
14366 TAATGTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:17009 original size:48 final size:49
Alignment explanation
Indices: 16936--17058 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 49
16926 ACTTGTCTTT
* * * * *
16936 CGTCCGGAAAGGCCATTTTAAGAAAAAGCGAGT-AAAACTAACGCCTTC
1 CGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAACTAACGCCTTC
* **
16984 CGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTGAAAAATTAGTGCCTTC
1 CGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGT-AAAAACTAACGCCTTC
*
17034 CGTCCGGGAAGGGCGTTTTGGGAAA
1 CGTCCGGGAAGGGCGTTTTAGGAAA
17059 CAAATGAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 28 0.44
50 36 0.56
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (49 bp):
CGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAACTAACGCCTTC
Found at i:17128 original size:49 final size:50
Alignment explanation
Indices: 17029--17157 Score: 190
Period size: 49 Copynumber: 2.6 Consensus size: 50
17019 AAAATTAGTG
* * * **
17029 CCTTCCGTCCGGGAA-GGGCGTTTTGGGAAACAAATGAAGAAAGTTGGGA
1 CCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACTGGGA
*
17078 CCTTCCGACCAGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACT-GGA
1 CCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACTGGGA
17127 CCTTCCGACCGGGAAGGGGCATTTTGGGAAA
1 CCTTCCGACCGGGAAGGGGCATTTTGGGAAA
17158 AGCAAGTAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 46 0.64
50 26 0.36
ACGTcount: A:0.31, C:0.19, G:0.32, T:0.19
Consensus pattern (50 bp):
CCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAAAACTGGGA
Found at i:18520 original size:18 final size:18
Alignment explanation
Indices: 18497--18537 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
18487 AAAGGGGAAG
18497 GAAGAAAG-AGAGGAATCT
1 GAAGAAAGAAG-GGAATCT
18515 GAAGAAAGAAGGGAATCT
1 GAAGAAAGAAGGGAATCT
18533 GAAGA
1 GAAGA
18538 CTACTCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.51, C:0.05, G:0.34, T:0.10
Consensus pattern (18 bp):
GAAGAAAGAAGGGAATCT
Found at i:20947 original size:28 final size:28
Alignment explanation
Indices: 20916--20971 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
20906 CAAAATTACC
20916 CAAATCCTATTTATGTAAACTAAAATGT
1 CAAATCCTATTTATGTAAACTAAAATGT
* *
20944 CAAATCCTATTTATGTAAGCTAAGATGT
1 CAAATCCTATTTATGTAAACTAAAATGT
20972 TTTAAGCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (28 bp):
CAAATCCTATTTATGTAAACTAAAATGT
Found at i:21041 original size:16 final size:16
Alignment explanation
Indices: 21020--21050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21010 AAATGAAGTC
21020 AAGGCAAAAATGCAAA
1 AAGGCAAAAATGCAAA
*
21036 AAGGCAACAATGCAA
1 AAGGCAAAAATGCAA
21051 CAAAACTAAA
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:0.58, C:0.16, G:0.19, T:0.06
Consensus pattern (16 bp):
AAGGCAAAAATGCAAA
Found at i:22138 original size:91 final size:91
Alignment explanation
Indices: 21983--22163 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
21973 TTTTTTGCTA
* * * *
21983 ACTCCCGGATCTCCATAATTAAGCAAACTCATTCTCATAACATTGTTTCCTTCTTGGTGATCTCC
1 ACTCCCGAATCTCCATAATAAAGCAAACTCATTCCCATAACATTGTTTCCTTCTTGGTCATCTCC
*
22048 ATGAGCAATTAAACACAAACTAACAC
66 ACGAGCAATTAAACACAAACTAACAC
* * *
22074 ACTCCCGAATCTCCATAATAAAGCAAGCTCATTCCCATAATATTGGTTT-CTTCTTGTTCATCTC
1 ACTCCCGAATCTCCATAATAAAGCAAACTCATTCCCATAACATT-GTTTCCTTCTTGGTCATCTC
*
22138 CACGAGCAATTAAACATAAACTAACA
65 CACGAGCAATTAAACACAAACTAACA
22164 AAGCAGCACA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 76 0.95
92 4 0.05
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (91 bp):
ACTCCCGAATCTCCATAATAAAGCAAACTCATTCCCATAACATTGTTTCCTTCTTGGTCATCTCC
ACGAGCAATTAAACACAAACTAACAC
Found at i:22993 original size:27 final size:28
Alignment explanation
Indices: 22955--23007 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
22945 GTAAATAATC
22955 TTTTAAGAAAGATTATAGGTAATTTTTT
1 TTTTAAGAAAGATTATAGGTAATTTTTT
22983 TTTTAA-AAAGATTATAGGTAATTTT
1 TTTTAAGAAAGATTATAGGTAATTTT
23008 CAAGGCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (28 bp):
TTTTAAGAAAGATTATAGGTAATTTTTT
Found at i:23448 original size:9 final size:10
Alignment explanation
Indices: 23425--23473 Score: 66
Period size: 9 Copynumber: 5.1 Consensus size: 10
23415 TCTATGTGGC
*
23425 ATTTTTTATT
1 ATTTTTTAAT
23435 ATTTTTTAAT
1 ATTTTTTAAT
23445 -TTTTTTAAT
1 ATTTTTTAAT
*
23454 ATTTTTTGAT
1 ATTTTTTAAT
23464 -TTTTTTAAT
1 ATTTTTTAAT
23473 A
1 A
23474 ATTTCATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:23450 original size:19 final size:19
Alignment explanation
Indices: 23426--23473 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
23416 CTATGTGGCA
*
23426 TTTTTTATTATTTTTTAAT
1 TTTTTTAATATTTTTTAAT
*
23445 TTTTTTAATATTTTTTGAT
1 TTTTTTAATATTTTTTAAT
23464 TTTTTTAATA
1 TTTTTTAATA
23474 ATTTCATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTAATATTTTTTAAT
Found at i:24759 original size:15 final size:15
Alignment explanation
Indices: 24726--24757 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24716 TTACGGCTGG
24726 AAACAAACATAAATC
1 AAACAAACATAAATC
24741 AAACAAACA-AAATC
1 AAACAAACATAAATC
24755 AAA
1 AAA
24758 ACTTTCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.72, C:0.19, G:0.00, T:0.09
Consensus pattern (15 bp):
AAACAAACATAAATC
Done.