Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011374.1 Corchorus capsularis cultivar CVL-1 contig11395, 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: 7726
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:454 original size:22 final size:22
Alignment explanation
Indices: 429--472 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
419 CACTCACCTA
*
429 GTAGAAATTGAGTGGGTGATTT
1 GTAGAAATTGAATGGGTGATTT
451 GTAGAAATTGAATGGGTGATTT
1 GTAGAAATTGAATGGGTGATTT
473 CTTTTTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (22 bp):
GTAGAAATTGAATGGGTGATTT
Found at i:1176 original size:13 final size:15
Alignment explanation
Indices: 1146--1178 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1136 TTTAACCATT
1146 AAATTAATATTTCGA
1 AAATTAATATTTCGA
1161 AAATTAAT-TTTC-A
1 AAATTAATATTTCGA
1174 AAATT
1 AAATT
1179 TTAAGATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
AAATTAATATTTCGA
Found at i:3171 original size:17 final size:17
Alignment explanation
Indices: 3151--3189 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3141 CTTAATGAAA
3151 TTCTATACTAACTAAAC
1 TTCTATACTAACTAAAC
*
3168 TTCTATACTAACTTAAC
1 TTCTATACTAACTAAAC
3185 TTCTA
1 TTCTA
3190 ACACCAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCTATACTAACTAAAC
Found at i:4775 original size:56 final size:55
Alignment explanation
Indices: 4684--4794 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 55
4674 GTGAAATATT
4684 TACAAATACAAATGTAATATACATAAATTTATTTCTATGTATTTAA-GTA-CAAA
1 TACAAATACAAATGTAATATACATAAATTTATTTCTATGTATTTAATGTAGCAAA
*
4737 TACAAATACAAATGTAACATTTTACATAAATTTATTTCTATGTATTTAATGTAGCAAA
1 TACAAATACAAATGT-A-A-TATACATAAATTTATTTCTATGTATTTAATGTAGCAAA
4795 AAAAATTCTA
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
53 15 0.29
54 1 0.02
55 1 0.02
56 28 0.54
57 3 0.06
58 4 0.08
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (55 bp):
TACAAATACAAATGTAATATACATAAATTTATTTCTATGTATTTAATGTAGCAAA
Found at i:5153 original size:16 final size:15
Alignment explanation
Indices: 5105--5154 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
5095 CTAACCTTCA
5105 TTTTTAATTAATATT
1 TTTTTAATTAATATT
*
5120 TATTATTATTTAAATATT
1 T-TT-TTAATT-AATATT
5138 TTTTTAATTGAATATT
1 TTTTTAATT-AATATT
5154 T
1 T
5155 GTGATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 7 0.24
18 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTTAATTAATATT
Found at i:7025 original size:6 final size:6
Alignment explanation
Indices: 7014--7039 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7004 AAAAGATTAA
7014 ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC AC
7040 GTACAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTAAC
Found at i:7241 original size:44 final size:44
Alignment explanation
Indices: 7171--7376 Score: 159
Period size: 44 Copynumber: 4.6 Consensus size: 44
7161 TATCTCTATG
* ** *
7171 TGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTCCAT-AGGA
* *
7216 -GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
* * *
7259 TGGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATA-GA
1 TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
* * ** * * *
7302 GTGGCTAACAAAATTTCATAG-GATCAGGTTATTAAAATTTCTTAGGT
1 -TGGTTATCAAAATTTCATAGTG-T--GGTTACCAAAATTCCATAGGA
** *
7349 TGGTTATTGAAATTTCATAGGGTGGTTA
1 TGGTTATCAAAATTTCATAGTGTGGTTA
7377 ATTATCACAA
Statistics
Matches: 133, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
43 7 0.05
44 93 0.70
46 31 0.23
47 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
Found at i:7292 original size:66 final size:65
Alignment explanation
Indices: 7169--7322 Score: 177
Period size: 66 Copynumber: 2.3 Consensus size: 65
7159 CTTATCTCTA
* ** * *
7169 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTCCATGAGGAGGTTATCAAAATTTCATA
1 TGTGGTTAACAAAATTTCAT-AGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAATTTCATA
7234 G
65 G
* *
7235 TGTGGTTACCAAAATTTCATAGTATGGTTACCAAAATTTCAT-AGTGTA-GTTACCAAAATTTCA
1 TGTGGTTAACAAAATTTCATAG-ATGGTTACCAAAATTCCATGAG-G-AGGTTACCAAAATTTCA
7298 TAG
63 TAG
* *
7301 AGTGGCTAACAAAATTTCATAG
1 TGTGGTTAACAAAATTTCATAG
7323 GATCAGGTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
65 4 0.05
66 71 0.93
67 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (65 bp):
TGTGGTTAACAAAATTTCATAGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAATTTCATAG
Found at i:7347 original size:24 final size:22
Alignment explanation
Indices: 7172--7369 Score: 129
Period size: 22 Copynumber: 8.9 Consensus size: 22
7162 ATCTCTATGT
* *
7172 GGTTATCAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
* *
7193 TGGTTATTATAATTCCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
*
7216 GGTTATCAAAATTTCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
7238 GGTTACCAAAATTTCATA-GTA
1 GGTTATTAAAATTTCATAGGTA
**
7259 TGGTTACCAAAATTTCATAGTGTA
1 -GGTTATTAAAATTTCATAG-GTA
**
7283 -GTTACCAAAATTTCATAGAGT-
1 GGTTATTAAAATTTCATAG-GTA
* **
7304 GGCTAACAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
7328 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
*
7350 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
7370 GTGGTTAATT
Statistics
Matches: 147, Mismatches: 18, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
20 2 0.01
21 3 0.02
22 119 0.81
23 4 0.03
24 19 0.13
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:7467 original size:22 final size:22
Alignment explanation
Indices: 7422--7546 Score: 76
Period size: 22 Copynumber: 5.6 Consensus size: 22
7412 TTCAAAATGC
*
7422 CATAGCGAGGTTATACAAAAATTT
1 CATAGTGAGGTTA-AC-AAAATTT
*
7446 CATAGTGTGGTTAACAAAATTT
1 CATAGTGAGGTTAACAAAATTT
* * * *
7468 CATTAG-AAGGTT-GCTAATACTT
1 CA-TAGTGAGGTTAAC-AAAATTT
* * *
7490 CATCGGGAGGTTATCAAAATTT
1 CATAGTGAGGTTAACAAAATTT
* * *
7512 GATAGTGTGGTTATCAAAATTT
1 CATAGTGAGGTTAACAAAATTT
7534 CATA-TGAAGGTTA
1 CATAGTG-AGGTTA
7547 TAAAAGTCTC
Statistics
Matches: 78, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 5 0.06
22 56 0.72
23 6 0.08
24 11 0.14
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (22 bp):
CATAGTGAGGTTAACAAAATTT
Found at i:7547 original size:22 final size:22
Alignment explanation
Indices: 7497--7710 Score: 81
Period size: 22 Copynumber: 9.5 Consensus size: 22
7487 CTTCATCGGG
*
7497 AGGTTATCAAAATTTGATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
7519 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
7541 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* *
7566 ATGAG-TACCAAAATTTGATA-GA
1 A-G-GTTATCAAAATTTCATATGA
*
7588 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* *
7607 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
*
7632 TATGATTATCAAAATTT-ATATGA
1 -A-GGTTATCAAAATTTCATATGA
**
7655 ATATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
7677 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
7699 AGGTTATCAAAA
1 AGGTTATCAAAA
7711 ATAATAATGT
Statistics
Matches: 149, Mismatches: 20, Indels: 46
0.69 0.09 0.21
Matches are distributed among these distances:
19 2 0.01
20 12 0.08
21 29 0.19
22 66 0.44
23 8 0.05
24 3 0.02
25 15 0.10
26 8 0.05
27 6 0.04
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:7654 original size:18 final size:19
Alignment explanation
Indices: 7631--7669 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
7621 TTTCATAAAG
7631 ATATG-ATTATCAAAATTT
1 ATATGAATTATCAAAATTT
7649 ATATGAATATTATCAAAATTT
1 ATATG-A-ATTATCAAAATTT
7670 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATGAATTATCAAAATTT
Done.