Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013588.1 Corchorus capsularis cultivar CVL-1 contig13609, 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: 73671
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2454 original size:17 final size:16
Alignment explanation
Indices: 2414--2464 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
2404 GATGTAATCT
*
2414 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
2430 TTGTATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
2447 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
2464 T
1 T
2465 GGGGGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:5620 original size:26 final size:26
Alignment explanation
Indices: 5584--5633 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
5574 ACCATAAGGC
5584 AGGAGCATTAAGCCGTTAGGCGAATG
1 AGGAGCATTAAGCCGTTAGGCGAATG
*
5610 AGGAGCTTTAAGCCGTTAGGCGAA
1 AGGAGCATTAAGCCGTTAGGCGAA
5634 ATATCACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.20
Consensus pattern (26 bp):
AGGAGCATTAAGCCGTTAGGCGAATG
Found at i:8870 original size:28 final size:27
Alignment explanation
Indices: 8821--8881 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
8811 CGGCCCCGAA
* * *
8821 ATATATATACTATTTTTTTATACATAAT
1 ATATATATACTATGTGTATATACAT-AT
*
8849 ATATATATACTATGTGTATATATATAT
1 ATATATATACTATGTGTATATACATAT
8876 ATATAT
1 ATATAT
8882 TTATTAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (27 bp):
ATATATATACTATGTGTATATACATAT
Found at i:8992 original size:20 final size:18
Alignment explanation
Indices: 8967--9011 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
8957 ACATATGTTT
8967 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
8987 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
9005 TACTAAT
1 TACTAAT
9012 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:9671 original size:42 final size:42
Alignment explanation
Indices: 9599--9680 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
9589 CTAAACTTCA
9599 TTATATGAACAATAATTATATAAATATATAAGTACTAAATCAG
1 TTATATGAACAAT-ATTATATAAATATATAAGTACTAAATCAG
* * * *
9642 TTATATGAATAAT-TTATGATAAATTTATAATTAGTAAAT
1 TTATATGAACAATATTAT-ATAAATATATAAGTACTAAAT
9681 TTTTTTTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 4 0.12
42 18 0.53
43 12 0.35
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (42 bp):
TTATATGAACAATATTATATAAATATATAAGTACTAAATCAG
Found at i:10851 original size:70 final size:71
Alignment explanation
Indices: 10770--10915 Score: 249
Period size: 70 Copynumber: 2.1 Consensus size: 71
10760 ATTAATATGG
*
10770 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGT-
1 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
10834 AAACTA
66 AAACTA
* *
10840 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAATTAAAAATAGAGTTTTTAGTTGACTA
1 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
*
10905 AAATTA
66 AAACTA
10911 TAAAA
1 TAAAA
10916 GTTTAAGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
70 61 0.86
71 10 0.14
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (71 bp):
TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
AAACTA
Found at i:11613 original size:33 final size:31
Alignment explanation
Indices: 11571--11697 Score: 98
Period size: 33 Copynumber: 3.9 Consensus size: 31
11561 AACTGCTCAT
11571 GCCGCCCTAGGGGGGCGGCTGAGCCATGGTAGG
1 GCCGCCC-AGGGGGGCGGCTGAGCCATGGTA-G
* *
11604 GCCGCCCTAGGGGAGCGGCCTG-GCCATGGTAAT
1 GCCGCCC-AGGGGGGCGG-CTGAGCCATGGT-AG
*
11637 GCCGCACCAGGGGGACGGC--ATGCCATGGCTAG
1 GCCGC-CCAGGGGGGCGGCTGA-GCCATGG-TAG
***
11669 GCCGTCCCCCTGGGGCGGCTGAGCCATGG
1 GCCG-CCCAGGGGGGCGGCTGAGCCATGG
11698 CCAAGCCGCC
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
32 22 0.29
33 47 0.62
34 7 0.09
ACGTcount: A:0.13, C:0.31, G:0.43, T:0.13
Consensus pattern (31 bp):
GCCGCCCAGGGGGGCGGCTGAGCCATGGTAG
Found at i:11714 original size:33 final size:33
Alignment explanation
Indices: 11658--11752 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
11648 GGGACGGCAT
11658 GCCATGGCTAGGCCGTCCCCCTGGGGCGGCT-GA
1 GCCATGGCTAGGCCG-CCCCCTGGGGCGGCTCGA
* * *
11691 GCCATGGCCAAGCCGCCCTCCTGGGGCGGCTCTA
1 GCCATGGCTAGGCCGCCC-CCTGGGGCGGCTCGA
*
11725 -CCATGGATAGGCCGCCCCCTGGGGCGGC
1 GCCATGGCTAGGCCGCCCCCTGGGGCGGC
11753 ACCGGTACTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 14 0.26
33 39 0.72
34 1 0.02
ACGTcount: A:0.11, C:0.39, G:0.37, T:0.14
Consensus pattern (33 bp):
GCCATGGCTAGGCCGCCCCCTGGGGCGGCTCGA
Found at i:11926 original size:33 final size:33
Alignment explanation
Indices: 11826--12017 Score: 239
Period size: 33 Copynumber: 5.9 Consensus size: 33
11816 AAGTAGTCTT
* *
11826 GCCGCCCTAGT-GGGACGGCT-AGCCGTGGTAGA
1 GCCGCCCTAGTGGGGA-GGCTCCGCCGTGGCAGA
* * *
11858 GCCGTCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * *
11890 GCCGTCCTAGTGGGGCGGCTCCGCCGTGGCATA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
11923 GCCGCCCTAGTGGGGAGGCTCCACCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
11956 GCCGCCCTAGTGGGGAGGCACCGCCGTCGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
11989 GCCGTCCTAGTGGGGAGGCTCC-CCGTGGC
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGC
12018 TAAGGGCAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
32 51 0.36
33 92 0.64
ACGTcount: A:0.12, C:0.32, G:0.41, T:0.15
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:18480 original size:14 final size:14
Alignment explanation
Indices: 18449--18550 Score: 125
Period size: 14 Copynumber: 7.2 Consensus size: 14
18439 AATATGCAGG
*
18449 AAACAGAATCCAAAA
1 AAACAGAAT-CTAAA
*
18464 AAATAGAATCTAAA
1 AAACAGAATCTAAA
* *
18478 AAACAAAATCCAAA
1 AAACAGAATCTAAA
18492 AAACAGAATCTAAAA
1 AAACAGAATCT-AAA
*
18507 AAACAGAATCCAAA
1 AAACAGAATCTAAA
*
18521 AAACAGAAT-AAAA
1 AAACAGAATCTAAA
18534 AAACAGAATCTAAA
1 AAACAGAATCTAAA
18548 AAA
1 AAA
18551 TTACAAACAT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
13 12 0.16
14 42 0.56
15 21 0.28
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11
Consensus pattern (14 bp):
AAACAGAATCTAAA
Found at i:18482 original size:29 final size:28
Alignment explanation
Indices: 18449--18550 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 28
18439 AATATGCAGG
*
18449 AAACAGAATCCAAAAAAATAGAATCTAAA
1 AAACAGAATCC-AAAAAACAGAATCTAAA
*
18478 AAACAAAATCCAAAAAACAGAATCTAAAA
1 AAACAGAATCCAAAAAACAGAATCT-AAA
*
18507 AAACAGAATCCAAAAAACAGAAT-AAAA
1 AAACAGAATCCAAAAAACAGAATCTAAA
*
18534 AAACAGAATCTAAAAAA
1 AAACAGAATCCAAAAAA
18551 TTACAAACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 19 0.28
28 13 0.19
29 35 0.52
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11
Consensus pattern (28 bp):
AAACAGAATCCAAAAAACAGAATCTAAA
Found at i:18497 original size:43 final size:42
Alignment explanation
Indices: 18449--18550 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 42
18439 AATATGCAGG
* * * *
18449 AAACAGAATCCAAAAAAATAGAATCTAAAAAACAAAATCCAAA
1 AAACAGAATCTAAAAAAACAGAATCCAAAAAACAAAAT-AAAA
*
18492 AAACAGAATCTAAAAAAACAGAATCCAAAAAACAGAATAAAA
1 AAACAGAATCTAAAAAAACAGAATCCAAAAAACAAAATAAAA
18534 AAACAGAATCTAAAAAA
1 AAACAGAATCTAAAAAA
18551 TTACAAACAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 20 0.37
43 34 0.63
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11
Consensus pattern (42 bp):
AAACAGAATCTAAAAAAACAGAATCCAAAAAACAAAATAAAA
Found at i:19980 original size:18 final size:19
Alignment explanation
Indices: 19949--19984 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19939 CAATATGCAG
19949 AAAACAGAATTAAAAAAAA
1 AAAACAGAATTAAAAAAAA
19968 AAAACAGAA-TAAAAAAA
1 AAAACAGAATTAAAAAAA
19985 CAGACTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.08
Consensus pattern (19 bp):
AAAACAGAATTAAAAAAAA
Found at i:28352 original size:17 final size:17
Alignment explanation
Indices: 28330--28365 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28320 CTTCCCTTTT
28330 ATTGTTTGATATAAAGG
1 ATTGTTTGATATAAAGG
*
28347 ATTGTTTGGTATAAAGG
1 ATTGTTTGATATAAAGG
28364 AT
1 AT
28366 AAAATAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (17 bp):
ATTGTTTGATATAAAGG
Found at i:29440 original size:2 final size:2
Alignment explanation
Indices: 29433--29475 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
29423 AGATTATTAT
29433 TA TA TA TA T- TA TA TA TA T- TA TA T- TA TA TA TA T- 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
29471 TA TA T
1 TA TA T
29476 GGTATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:29444 original size:9 final size:9
Alignment explanation
Indices: 29430--29475 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
29420 TATAGATTAT
29430 TATTATATA
1 TATTATATA
29439 TATTATATA
1 TATTATATA
29448 TATTATAT-
1 TATTATATA
29456 TA-TATATA
1 TATTATATA
29464 T-TATATATA
1 TAT-TATATA
29473 TAT
1 TAT
29476 GGTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 5 0.15
8 3 0.09
9 24 0.73
10 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATATA
Found at i:29460 original size:23 final size:24
Alignment explanation
Indices: 29415--29473 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 24
29405 AGGTTTTGAC
*
29415 ATTAGTATAGATTATTATTATATAT
1 ATTA-TATATATTATTATTATATAT
29440 ATTATATATATTA-TATTATATAT
1 ATTATATATATTATTATTATATAT
29463 ATTATATATAT
1 ATTATATATAT
29474 ATGGTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 21 0.64
24 8 0.24
25 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTATATATATTATTATTATATAT
Found at i:30122 original size:30 final size:31
Alignment explanation
Indices: 30062--30136 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
30052 AAATTTGGTG
30062 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTGCTCAATTAACTCAACTTC
* *
30093 AGGGACTCAATTGCTC-ATTAAGTTC-ACTTC
1 AGGGACCCAATTGCTCAATTAA-CTCAACTTC
*
30123 AGGGACCCATTTGC
1 AGGGACCCAATTGC
30137 ACATTTGCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAATTAACTCAACTTC
Found at i:31480 original size:16 final size:16
Alignment explanation
Indices: 31461--31505 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
31451 TAAGTCGGGT
31461 TCGGGTTAAATTTGGG
1 TCGGGTTAAATTTGGG
* *
31477 TCGGGTT-GATTCTGGT
1 TCGGGTTAAATT-TGGG
31493 TCGGGTTAAATTT
1 TCGGGTTAAATTT
31506 AGGTTAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.42
Consensus pattern (16 bp):
TCGGGTTAAATTTGGG
Found at i:31496 original size:32 final size:32
Alignment explanation
Indices: 31455--31561 Score: 142
Period size: 32 Copynumber: 3.3 Consensus size: 32
31445 CAAACTTAAG
**
31455 TCGGGTTCGGGTTAAATTTGGGTCGGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTTAGGTTGAT
* * *
31487 TCTGGTTCGGGTTAAATTTAGGTTAAGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTTAGGTTGAT
* * *
31519 TCGGGTTCGGGTCAATTTTGGGTTAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTTAGGTTGAT
31551 TCGGGTTCGGG
1 TCGGGTTCGGG
31562 CTCGGATTGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.15, C:0.09, G:0.36, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAATTTGGGTTAGGTTGAT
Found at i:31727 original size:20 final size:20
Alignment explanation
Indices: 31694--31732 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31684 CATAAATGAA
*
31694 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
31714 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
31733 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:33220 original size:15 final size:15
Alignment explanation
Indices: 33200--33232 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
33190 CACCCAATTG
33200 TTTG-TTTTGTTCTTT
1 TTTGTTTTTGTT-TTT
33215 TTTGTTTTTGTTTTT
1 TTTGTTTTTGTTTTT
33230 TTT
1 TTT
33233 AGAAATACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (15 bp):
TTTGTTTTTGTTTTT
Found at i:33712 original size:3 final size:3
Alignment explanation
Indices: 33704--33739 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
33694 GGTAGAAAAT
33704 TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA
33740 CACTTGGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45289 original size:14 final size:15
Alignment explanation
Indices: 45270--45306 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
45260 TCTAGGATTT
45270 ATTTATTTA-TTATC
1 ATTTATTTACTTATC
45284 ATTTATTTATCTTATC
1 ATTTATTTA-CTTATC
45300 A-TTATTT
1 ATTTATTT
45307 TTTTATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATTTACTTATC
Found at i:45306 original size:19 final size:18
Alignment explanation
Indices: 45266--45314 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
45256 AAAATCTAGG
*
45266 ATTTATTTATTTATTATC
1 ATTTATTTATTTATCATC
*
45284 ATTTATTTATCTTATCATT
1 ATTTATTTAT-TTATCATC
*
45303 ATTTTTTTATTT
1 ATTTATTTATTT
45315 CTTTTCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTATTTATCATC
Found at i:46551 original size:20 final size:20
Alignment explanation
Indices: 46517--46554 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46507 AGTCCAAAGG
*
46517 GGGGGCGGTGGCTAGTAAAA
1 GGGGGCGGTAGCTAGTAAAA
*
46537 GGGGGCGGTATCTAGTAA
1 GGGGGCGGTAGCTAGTAA
46555 TCCACTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.11, G:0.47, T:0.18
Consensus pattern (20 bp):
GGGGGCGGTAGCTAGTAAAA
Found at i:47564 original size:14 final size:14
Alignment explanation
Indices: 47545--47572 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47535 CGCTCCCTTC
47545 TTTTCTCTTCCTAA
1 TTTTCTCTTCCTAA
47559 TTTTCTCTTCCTAA
1 TTTTCTCTTCCTAA
47573 ATTCTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTCTCTTCCTAA
Found at i:52239 original size:27 final size:28
Alignment explanation
Indices: 52203--52270 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
52193 ATTCTAGGGA
* *
52203 ACTAATTTTGAATGGGA-AACTGTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
52230 ACTAACTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
52257 ACTAACTTGGAATG
1 ACTAACTTTGAATG
52271 AGAGTCTGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:56627 original size:27 final size:28
Alignment explanation
Indices: 56594--56661 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
56584 ATTCTAGGGA
*
56594 ACTAACTTTGAATGGGA-AACTGTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
56621 ACTAACTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
56648 ACTAACTTGGAATG
1 ACTAACTTTGAATG
56662 AGAGTCTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:58093 original size:5 final size:5
Alignment explanation
Indices: 58083--58117 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
58073 TATTTTCACA
58083 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
58118 TATTGATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:61605 original size:109 final size:106
Alignment explanation
Indices: 61378--61655 Score: 335
Period size: 109 Copynumber: 2.7 Consensus size: 106
61368 TTTTAATTTT
* *
61378 AATTTTAATTTAGG-TAAAACTTGGTG-AATTAGTTATATATTTTATTTCTAAAACCC--T-ATA
1 AATTTTAATTTGGGCT-AAACTTGGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
* * * *
61438 ACAAT--ATTATTGATTATGGAATTTACCCTTAAAATAAAAA
65 ACAATAAATTATTAATTATGAAATTTACCATCAAAATAAAAA
* *
61478 AA--TTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAATA
1 AATTTTAATTTGG-GCTAAACTTGGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
61541 ACAATAAATTATTAATT-TGAAATTTACCATCAAAATAAAAATAA
65 ACAATAAATTATTAATTATGAAATTTACCATCAAAAT--AAA-AA
*
61585 AATTTTAATTTTGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATTTCT-AAACACTATAATA
1 AATTTTAA-TTTGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
*
61649 ATAATAA
65 ACAATAA
61656 TAATAATAAT
Statistics
Matches: 152, Mismatches: 12, Indels: 20
0.83 0.07 0.11
Matches are distributed among these distances:
98 8 0.05
99 10 0.07
100 31 0.20
102 1 0.01
103 8 0.05
104 16 0.11
105 9 0.06
106 3 0.02
107 4 0.03
108 18 0.12
109 39 0.26
110 5 0.03
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
AATTTTAATTTGGGCTAAACTTGGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATAA
CAATAAATTATTAATTATGAAATTTACCATCAAAATAAAAA
Found at i:61651 original size:3 final size:3
Alignment explanation
Indices: 61643--61688 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
61633 TCTAAACACT
*
61643 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
61689 AGATGACACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:63761 original size:22 final size:22
Alignment explanation
Indices: 63733--63784 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
63723 TTGAACAATG
63733 CTGCATCAAAACTAAATCATTA
1 CTGCATCAAAACTAAATCATTA
63755 CTGCATCAAAACTAAATCATTA
1 CTGCATCAAAACTAAATCATTA
63777 CTGCATCA
1 CTGCATCA
63785 TAATTACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (22 bp):
CTGCATCAAAACTAAATCATTA
Found at i:69006 original size:33 final size:32
Alignment explanation
Indices: 68923--69062 Score: 111
Period size: 33 Copynumber: 4.2 Consensus size: 32
68913 AAAGGATCAT
* **
68923 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC
* * *
68956 GTGTCCGGGTGTAGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
* *
68989 GTGGCCGGTGATGGCCGGGCATCTCCATGTTGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * * * *
69022 ATGGTCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC
69055 GTGGCCGG
1 GTGGCCGG
69063 ATCTCCGAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
32 8 0.09
33 77 0.89
34 2 0.02
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Done.