Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012070.1 Corchorus capsularis cultivar CVL-1 contig12091, 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: 10548
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:218 original size:112 final size:112
Alignment explanation
Indices: 62--426 Score: 450
Period size: 113 Copynumber: 3.2 Consensus size: 112
52 GGCGCTTCAC
* *
62 CCTAAACGCCGCTAAATGGTGGAGTCTAAGGTTCAAAACGCCGCCATATTTAATGTTTCGGGGAA
1 CCTAAACGCCGCTAAATGGTGGCGTCTAA-GTTCAAAACGCCGCCATATTTAATTTTTCGGGGAA
*
127 ATGCAAAAAAACTCAAATTGAAGCCT-GAAAATAGCGGCGTCTGAGGT
65 ATGCAAAAAAACTCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT
* * ***
174 CCTAAACGCCGCTAAATGGCGGCGTCTGAA-TTACAATACGCCGCCATATTTAATTTTTCCAAAG
1 CCTAAACGCCGCTAAATGGTGGCGTCT-AAGTT-CAAAACGCCGCCATATTTAATTTTT-CGGGG
* ** * * * * *
238 AAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCT--TGT
63 AAATGCAAAAAAACTCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT
* *
286 CCCTAAACGCCGCTAAATGGTGGCGTCTAAGCTTCAAAACGCCGCCGTATTTAACTTTTTGGGGG
1 -CCTAAACGCCGCTAAATGGTGGCGTCTAAG-TTCAAAACGCCGCCATATTTAA-TTTTTCGGGG
351 AAATGCAAAAAAACATCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT
63 AAATGCAAAAAAAC-TCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT
* *
402 CCTGAACGCCGTTAAATGGTGGCGT
1 CCTAAACGCCGCTAAATGGTGGCGT
427 TTTGAGGGCC
Statistics
Matches: 209, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
111 2 0.01
112 52 0.25
113 80 0.38
114 50 0.24
115 23 0.11
116 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (112 bp):
CCTAAACGCCGCTAAATGGTGGCGTCTAAGTTCAAAACGCCGCCATATTTAATTTTTCGGGGAAA
TGCAAAAAAACTCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT
Found at i:304 original size:113 final size:111
Alignment explanation
Indices: 13--426 Score: 363
Period size: 113 Copynumber: 3.7 Consensus size: 111
3 ATTTTTTCGG
* * * **
13 AGAAACGTAAATTGAGTAAGAATG-AACCTAAAAAATAGCGGCG-CTTCACCCTAAACGCCGCTA
1 AGAAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCTTGTCCCTAAACGCCGCTA
* * **
76 AATGGTGGAGTCTAAGGTTCAAAACGCCGCCATATTTAATGTTTCGG
66 AATGGTGGCGTCTAA-GTTCAAAACGCCGCCATATTTAATTTTTCAA
* * ** * * * * * *
123 GGAAATGCAAAAAAACTCAAATTGAAGCCT-GAAAATAGCGGCGTCTGAGGT-CCTAAACGCCGC
1 AGAAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCT--TGTCCCTAAACGCCGC
* *
186 TAAATGGCGGCGTCTGAA-TTACAATACGCCGCCATATTTAATTTTTCCAA
64 TAAATGGTGGCGTCT-AAGTT-CAAAACGCCGCCATATTTAATTTTT-CAA
236 AGAAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCTTGTCCCTAAACGCCGCTA
1 AGAAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCTTGTCCCTAAACGCCGCTA
* ***
301 AATGGTGGCGTCTAAGCTTCAAAACGCCGCCGTATTTAACTTTTTGGG
66 AATGGTGGCGTCTAAG-TTCAAAACGCCGCCATATTTAA-TTTTTCAA
* * ** * * * * * *
349 GGAAATGCAAAAAAACATCAAATTGAAGCCTAAAAAATAGCGGCGTCTGAGGT-CCTGAACGCCG
1 AGAAATGTAAATTAA-GTAAAAATGAAACCTAAAAAATAGCGGCGTCT--TGTCCCTAAACGCCG
*
413 TTAAATGGTGGCGT
63 CTAAATGGTGGCGT
427 TTTGAGGGCC
Statistics
Matches: 241, Mismatches: 48, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
110 26 0.11
111 8 0.03
112 52 0.22
113 80 0.33
114 50 0.21
115 23 0.10
116 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (111 bp):
AGAAATGTAAATTAAGTAAAAATGAAACCTAAAAAATAGCGGCGTCTTGTCCCTAAACGCCGCTA
AATGGTGGCGTCTAAGTTCAAAACGCCGCCATATTTAATTTTTCAA
Found at i:524 original size:29 final size:29
Alignment explanation
Indices: 500--826 Score: 124
Period size: 27 Copynumber: 11.3 Consensus size: 29
490 CAATTTGTAT
500 TTTCTAAATATAATTTTTAACATTTATAA
1 TTTCTAAATATAATTTTTAACATTTATAA
*
529 TTTCTAAATATTATTTTT-A-A-TTATAA
1 TTTCTAAATATAATTTTTAACATTTATAA
* *
555 TTTCATTACATATATAATTTCT-A-A-TTATTAT
1 TTTC--TA-A-ATATAATTTTTAACATTTA-TAA
* *
586 TTTCTAAATATAATTTCTAAAAATTTATAA
1 TTTCTAAATATAATTT-TTAACATTTATAA
* *
616 TTTCCAAATATTATTTTCT--CA-TTATAA
1 TTTCTAAATATAATTTT-TAACATTTATAA
*
643 TTTCATTACATATATAATTTCTAA-ATATTAT--
1 TTTC--TA-A-ATATAATTTTTAACAT-TTATAA
* * *
674 TTTCTAATTATAATTTCATT-ACATATACAA
1 TTTCTAAATATAATTT--TTAACATTTATAA
* **
704 TTT-T-TATATAATTTTTAGA-AAATATAA
1 TTTCTAAATATAATTTTTA-ACATTTATAA
*
731 TTTCATTACATATATAATTTCTAA-ATATTAT--
1 TTTC--TA-A-ATATAATTTTTAACAT-TTATAA
*
762 TTTCTTAATATAATTTCATTAA-ATTTATAA
1 TTTCTAAATATAATTT--TTAACATTTATAA
* *
792 TTTCTGAATATTATTTTCTAA-A--TATAA
1 TTTCTAAATATAATTTT-TAACATTTATAA
819 TTTCTAAA
1 TTTCTAAA
827 CATATATATT
Statistics
Matches: 230, Mismatches: 31, Indels: 76
0.68 0.09 0.23
Matches are distributed among these distances:
26 12 0.05
27 58 0.25
28 24 0.10
29 39 0.17
30 51 0.22
31 26 0.11
32 2 0.01
33 18 0.08
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTCTAAATATAATTTTTAACATTTATAA
Found at i:557 original size:13 final size:13
Alignment explanation
Indices: 498--720 Score: 72
Period size: 13 Copynumber: 15.5 Consensus size: 13
488 TCCAATTTGT
*
498 ATTTTCTAAATATA
1 ATTTT-TAATTATA
512 ATTTTTAACATTTATA
1 ATTTTT-A-A-TTATA
* * *
528 ATTTCTAAATATT
1 ATTTTTAATTATA
541 ATTTTTAATTATA
1 ATTTTTAATTATA
554 ATTTCATTACATATATA
1 ATTT--TTA-AT-TATA
* *
571 ATTTCTAATTATT
1 ATTTTTAATTATA
*
584 ATTTTCTAAATATA
1 ATTTT-TAATTATA
*
598 ATTTCTAAAAATTTATA
1 ATTT-T--TAA-TTATA
** * *
615 ATTTCCAAATATT
1 ATTTTTAATTATA
*
628 ATTTTCTCATTATA
1 ATTTT-TAATTATA
642 ATTTCATTACATATATA
1 ATTT--TTA-AT-TATA
* * *
659 ATTTCTAAATATT
1 ATTTTTAATTATA
672 ATTTTCTAATTATA
1 ATTTT-TAATTATA
*
686 ATTTCATTACATATACA
1 ATTT--TTA-AT-TATA
703 ATTTTT-A-TATA
1 ATTTTTAATTATA
714 ATTTTTA
1 ATTTTTA
721 GAAAATATAA
Statistics
Matches: 154, Mismatches: 33, Indels: 46
0.66 0.14 0.20
Matches are distributed among these distances:
11 9 0.06
13 40 0.26
14 40 0.26
15 15 0.10
16 19 0.12
17 31 0.20
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTTAATTATA
Found at i:580 original size:30 final size:29
Alignment explanation
Indices: 523--822 Score: 118
Period size: 30 Copynumber: 10.3 Consensus size: 29
513 TTTTTAACAT
* *
523 TTATAATTTC--TAA-ATATTATTTTTAA
1 TTATAATTTCATTAATATATAATTTCTAA
549 TTATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTCATTA-ATATATAATTTCTAA
*
579 TTATTATTT--TCTAA-ATATAATTTCTAAAAA
1 TTATAATTTCAT-TAATATATAATTTCT---AA
* *
609 TTTATAATTTCCA--AATAT-TATTTTCTCA
1 -TTATAATTT-CATTAATATATAATTTCTAA
637 TTATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTCATTA-ATATATAATTTCTAA
* *
667 ATATTATTT--TCTAAT-TATAATTTC--A
1 TTATAATTTCAT-TAATATATAATTTCTAA
* * ** *
692 TTA-CATATACAATTTTTATATAATTTTTAGAAA
1 TTATAAT-TTC-ATTAATATATAATTTCT---AA
*
725 ATATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTCATTA-ATATATAATTTCTAA
* *
755 ATATTATTTTC-TT-A-ATATAATTTCATTAAA
1 TTA-TAATTTCATTAATATATAATTTC--T-AA
* *
785 TTTATAATTTC-TGAATAT-TATTTTCTAA
1 -TTATAATTTCATTAATATATAATTTCTAA
*
813 ATATAATTTC
1 TTATAATTTC
823 TAAACATATA
Statistics
Matches: 209, Mismatches: 28, Indels: 73
0.67 0.09 0.24
Matches are distributed among these distances:
24 2 0.01
25 4 0.02
26 12 0.06
27 50 0.24
28 21 0.10
29 11 0.05
30 52 0.25
31 32 0.15
32 7 0.03
33 16 0.08
34 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (29 bp):
TTATAATTTCATTAATATATAATTTCTAA
Found at i:615 original size:44 final size:44
Alignment explanation
Indices: 497--873 Score: 446
Period size: 44 Copynumber: 8.6 Consensus size: 44
487 TTCCAATTTG
*
497 TATTTTCTAAATATAATTT--TTAACATTTATAATTTCTAAATAT
1 TATTTTCTAAATATAATTTCATT-ACATATATAATTTCTAAATAT
* *
540 TATTTT-TAATTATAATTTCATTACATATATAATTTCTAATTAT
1 TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAATAT
* * * *
583 TATTTTCTAAATATAATTTC-TAAAAATTTATAATTTCCAAATAT
1 TATTTTCTAAATATAATTTCAT-TACATATATAATTTCTAAATAT
* *
627 TATTTTCTCATTATAATTTCATTACATATATAATTTCTAAATAT
1 TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAATAT
* * * *
671 TATTTTCTAATTATAATTTCATTACATATACAATTTTTATATAAT
1 TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAAT-AT
***
716 T-TTTAGAAAATATAATTTCATTACATATATAATTTCTAAATAT
1 TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAATAT
* * * *
759 TATTTTCTTAATATAATTTCATTAAATTTATAATTTCTGAATAT
1 TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAATAT
* *
803 TATTTTCTAAATATAATTTC-TAAACATATAT-ATTCCTAAATAT
1 TATTTTCTAAATATAATTTCAT-TACATATATAATTTCTAAATAT
*
846 TGTTTTCTAAATA-ATATTTCATTACATA
1 TATTTTCTAAATATA-ATTTCATTACATA
874 AAAGTGATTT
Statistics
Matches: 283, Mismatches: 41, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
42 12 0.04
43 68 0.24
44 199 0.70
45 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (44 bp):
TATTTTCTAAATATAATTTCATTACATATATAATTTCTAAATAT
Found at i:1066 original size:7 final size:7
Alignment explanation
Indices: 1054--1081 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1044 TTTTCTAAGA
1054 CTTCTCC
1 CTTCTCC
1061 CTTCTCC
1 CTTCTCC
1068 CTTCTCC
1 CTTCTCC
1075 CTTCTCC
1 CTTCTCC
1082 ACTTGCACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTCTCC
Found at i:3083 original size:18 final size:18
Alignment explanation
Indices: 3062--3114 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3052 AAACTAACTT
3062 TGAATGGGGAACTGACTC
1 TGAATGGGGAACTGACTC
*
3080 TGAATGGGGAACT-AGCTT
1 TGAATGGGGAACTGA-CTC
* *
3098 TGAATGGAGAATTGACT
1 TGAATGGGGAACTGACT
3115 TGGAATGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.26
Consensus pattern (18 bp):
TGAATGGGGAACTGACTC
Found at i:3140 original size:18 final size:19
Alignment explanation
Indices: 3095--3140 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
3085 GGGGAACTAG
3095 CTTTGAATG-GAGAATTGA
1 CTTTGAATGAGAGAATTGA
*
3113 CTTGGAATGAGAG-ATTGA
1 CTTTGAATGAGAGAATTGA
3131 CTTTGAATGA
1 CTTTGAATGA
3141 TCCTTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (19 bp):
CTTTGAATGAGAGAATTGA
Found at i:4867 original size:57 final size:57
Alignment explanation
Indices: 4786--4972 Score: 356
Period size: 57 Copynumber: 3.3 Consensus size: 57
4776 TCAGTGGAGC
* *
4786 TAGTGGCACTAAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
1 TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
4843 TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
1 TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
4900 TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
1 TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
4957 TAGTGCCACTGAAGAA
1 TAGTGCCACTGAAGAA
4973 GTCTGTGGAG
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 128 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (57 bp):
TAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAAT
Found at i:5038 original size:84 final size:84
Alignment explanation
Indices: 4891--5055 Score: 206
Period size: 84 Copynumber: 2.0 Consensus size: 84
4881 AACAATTGTC
* * ** * *
4891 CTGTGGAATTAGTGCCACTGAAGAACCATGAGTGGTTAGAGAATTAGAACAATTGTCCTGTGGAA
1 CTGTGGAACTAGTGCCACTAAAGAACCATGAGTGGCCAGAGAATCAGAACAATTGTCCAGTGGAA
4956 T-TAGTGCCACTGAAGAAGT
66 TGTA-TGCCACTGAAGAAGT
* * * * *
4975 CTGTGGAGCTAGTGGCACTAAATAACCATGAGTGGCCAGAGAATCAGAACGATTTTCCAGTGGAA
1 CTGTGGAACTAGTGCCACTAAAGAACCATGAGTGGCCAGAGAATCAGAACAATTGTCCAGTGGAA
*
5040 TGTATGGCACTGAAGA
66 TGTATGCCACTGAAGA
5056 GGAAGTATTA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 66 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (84 bp):
CTGTGGAACTAGTGCCACTAAAGAACCATGAGTGGCCAGAGAATCAGAACAATTGTCCAGTGGAA
TGTATGCCACTGAAGAAGT
Found at i:7675 original size:18 final size:18
Alignment explanation
Indices: 7652--7706 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
7642 GTCAATCCTA
7652 GGGAACTAACTTTGAATG
1 GGGAACTAACTTTGAATG
* *
7670 GGGAACTGACTTTAAATG
1 GGGAACTAACTTTGAATG
* *
7688 GGGAATTAGCTTTGAATG
1 GGGAACTAACTTTGAATG
7706 G
1 G
7707 AGAATTGACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (18 bp):
GGGAACTAACTTTGAATG
Found at i:7711 original size:18 final size:18
Alignment explanation
Indices: 7660--7741 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
7650 TAGGGAACTA
*
7660 ACTTTGAATGGGGAACTG
1 ACTTTGAATGGGGAATTG
*
7678 ACTTTAAATGGGGAATT-
1 ACTTTGAATGGGGAATTG
*
7695 AGCTTTGAATGGAGAATTG
1 A-CTTTGAATGGGGAATTG
* * *
7714 ACTTGGAAT-GAGAGACTG
1 ACTTTGAATGGGGA-ATTG
7732 ACTTTGAATG
1 ACTTTGAATG
7742 ATTCTTAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 5 0.09
18 47 0.89
19 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (18 bp):
ACTTTGAATGGGGAATTG
Found at i:8255 original size:16 final size:16
Alignment explanation
Indices: 8227--8348 Score: 149
Period size: 16 Copynumber: 7.7 Consensus size: 16
8217 TAGTTTTCTA
*
8227 GGGTTATTCGGGTTTC
1 GGGTCATTCGGGTTTC
*
8243 GGGTCATTTGGG-TTC
1 GGGTCATTCGGGTTTC
*
8258 GGGTTATTCGGGTTTC
1 GGGTCATTCGGGTTTC
* *
8274 GGATCATTCGGGTCTC
1 GGGTCATTCGGGTTTC
8290 GGGTCATAT-GGGTTTC
1 GGGTCAT-TCGGGTTTC
* *
8306 GGGTCATTTGGGTCTC
1 GGGTCATTCGGGTTTC
*
8322 GGGTCATTCGGGTTGC
1 GGGTCATTCGGGTTTC
8338 GGGTCATTCGG
1 GGGTCATTCGG
8349 ACGGGTCTAC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
15 14 0.16
16 75 0.83
17 1 0.01
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
GGGTCATTCGGGTTTC
Found at i:8303 original size:32 final size:32
Alignment explanation
Indices: 8227--8348 Score: 167
Period size: 32 Copynumber: 3.8 Consensus size: 32
8217 TAGTTTTCTA
* *
8227 GGGTTATTCGGGTTTCGGGTCATTTGGGT-TC
1 GGGTCATTCGGGTTTCGGGTCATTCGGGTCTC
* *
8258 GGGTTATTCGGGTTTCGGATCATTCGGGTCTC
1 GGGTCATTCGGGTTTCGGGTCATTCGGGTCTC
*
8290 GGGTCATAT-GGGTTTCGGGTCATTTGGGTCTC
1 GGGTCAT-TCGGGTTTCGGGTCATTCGGGTCTC
*
8322 GGGTCATTCGGGTTGCGGGTCATTCGG
1 GGGTCATTCGGGTTTCGGGTCATTCGG
8349 ACGGGTCTAC
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
31 28 0.35
32 52 0.64
33 1 0.01
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (32 bp):
GGGTCATTCGGGTTTCGGGTCATTCGGGTCTC
Found at i:8617 original size:29 final size:29
Alignment explanation
Indices: 8575--8634 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
8565 ATACTTGATA
8575 TGTGTCTCCTTATCAGGTGAGGTAGGTTT
1 TGTGTCTCCTTATCAGGTGAGGTAGGTTT
8604 TGTGTCTCCTTATCAGGTGAGGTAGGTTT
1 TGTGTCTCCTTATCAGGTGAGGTAGGTTT
8633 TG
1 TG
8635 AATATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.13, G:0.32, T:0.42
Consensus pattern (29 bp):
TGTGTCTCCTTATCAGGTGAGGTAGGTTT
Found at i:9221 original size:16 final size:16
Alignment explanation
Indices: 9200--9302 Score: 100
Period size: 16 Copynumber: 6.4 Consensus size: 16
9190 GGTTAACTTC
*
9200 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
9216 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
* **
9232 TCGGGTCACTCGAATT
1 TCGGGTCATTCGGGTT
*
9248 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
9264 TCGGGTCA-TCTAGGTT
1 TCGGGTCATTC-GGGTT
* *
9280 GCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
9296 TCGGGTC
1 TCGGGTC
9303 GGACGGGTTC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
15 2 0.03
16 63 0.94
17 2 0.03
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:9236 original size:32 final size:31
Alignment explanation
Indices: 9198--9302 Score: 111
Period size: 32 Copynumber: 3.3 Consensus size: 31
9188 CGGGTTAACT
* * *
9198 TCTCGGGTTATTCGGGTTTCGGGTCATACGGG
1 TCTCGGGTCA-TCGGGTTACGGGTCATTCGGG
**
9230 TCTCGGGTCACTCGAATTACGGGTCATTCGGG
1 TCTCGGGTCA-TCGGGTTACGGGTCATTCGGG
* * *
9262 TTTCGGGTCATCTAGGTTGCGGGTCATTCGGG
1 TCTCGGGTCATC-GGGTTACGGGTCATTCGGG
9294 TCTCGGGTC
1 TCTCGGGTC
9303 GGACGGGTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 2 0.03
32 58 0.97
ACGTcount: A:0.10, C:0.22, G:0.35, T:0.32
Consensus pattern (31 bp):
TCTCGGGTCATCGGGTTACGGGTCATTCGGG
Found at i:9301 original size:48 final size:48
Alignment explanation
Indices: 9198--9302 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
9188 CGGGTTAACT
* *
9198 TCTCGGGTTATTCGGGTTTCGGGTCATACGGGTCTCGGGTCACTCGAA
1 TCTCGGGTCATTCGGGTTTCGGGTCATACAGGTCTCGGGTCACTCGAA
* **
9246 T-TACGGGTCATTCGGGTTTCGGGTCAT-CTAGGT-TGCGGGTCATTCGGG
1 TCT-CGGGTCATTCGGGTTTCGGGTCATAC-AGGTCT-CGGGTCACTCGAA
9294 TCTCGGGTC
1 TCTCGGGTC
9303 GGACGGGTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
47 3 0.06
48 44 0.92
49 1 0.02
ACGTcount: A:0.10, C:0.22, G:0.35, T:0.32
Consensus pattern (48 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATACAGGTCTCGGGTCACTCGAA
Found at i:9981 original size:15 final size:16
Alignment explanation
Indices: 9949--9982 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9939 AAAGAAGAAT
*
9949 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
9965 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
9980 TAA
1 TAA
9983 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Done.