Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012629.1 Corchorus capsularis cultivar CVL-1 contig12650, 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: 11742
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:831 original size:27 final size:28
Alignment explanation
Indices: 794--850 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
784 ATAATATTAC
794 TCCCTCTGTTCCTTT-TTAATTGTCCTTT
1 TCCCTCTGTT-CTTTATTAATTGTCCTTT
822 TCCCT-TGTTCTTTATTAATTGTCCTTT
1 TCCCTCTGTTCTTTATTAATTGTCCTTT
849 TC
1 TC
851 ACTTATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 4 0.14
27 19 0.68
28 5 0.18
ACGTcount: A:0.09, C:0.26, G:0.07, T:0.58
Consensus pattern (28 bp):
TCCCTCTGTTCTTTATTAATTGTCCTTT
Found at i:3509 original size:17 final size:17
Alignment explanation
Indices: 3484--3527 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
3474 GGGCAACCAC
*
3484 AAAGATATATTGTGGTA
1 AAAGTTATATTGTGGTA
3501 AAAGTTATATTGTGGTA
1 AAAGTTATATTGTGGTA
3518 AAAGTTATAT
1 AAAGTTATAT
3528 AAAGGGCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (17 bp):
AAAGTTATATTGTGGTA
Found at i:5349 original size:22 final size:21
Alignment explanation
Indices: 5324--5375 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
5314 TTAATATACA
5324 ATTTTATTCTAATAAAAATTC-T
1 ATTTTATT-TAAT-AAAATTCAT
*
5346 ATTTTCATTTAATTAAATTCAAT
1 ATTTT-ATTTAATAAAATTC-AT
5369 ATTTTAT
1 ATTTTAT
5376 AATTATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.23
22 11 0.42
23 9 0.35
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTATTTAATAAAATTCAT
Found at i:6658 original size:22 final size:22
Alignment explanation
Indices: 6630--7252 Score: 135
Period size: 22 Copynumber: 27.9 Consensus size: 22
6620 TATCTCTATG
6630 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
6652 TGGTTATTATGATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
6675 -GGTTATCAAAA-TTCA-ATAGTG
1 TGGTTATCAAAATTTCATA-AG-A
* *
6696 TGGTTA-CCAAATTCTCATATGGA
1 TGGTTATCAAAATT-TCATA-AGA
* *
6719 -AGTTATCAAAATTTCATACTG-
1 TGGTTATCAAAATTTCATA-AGA
* * *
6740 TGGTTACCAAAATTTCTTAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
6762 TCATGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
6786 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
* *
6808 TGGTTAATTATCACAATTTTAT-AGAA
1 TGG----TTATCAAAATTTCATAAG-A
* * *
6834 AGGTTATCAAAATGTCATAGCGA
1 TGGTTATCAAAATTTCATA-AGA
* *
6857 -GG-TACTAAAAATCTCAT-AGTA
1 TGGTTA-TCAAAATTTCATAAG-A
* *
6878 TGGTTAACAAAATTTCATCAGGA
1 TGGTTATCAAAATTTCAT-AAGA
**
6901 -GGTTAT-AAATATTTCATGGGGA
1 TGGTTATCAAA-ATTTCAT-AAGA
*
6923 -GGTTATCAAAATTTTAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
6942 TGTGATTATCAAAATTTCATATGA
1 TG-G-TTATCAAAATTTCATAAGA
* *
6966 AGGTTATAAAAGTCTCATTTTCATAAG-
1 TGGTTATCAAA-----A-TTTCATAAGA
* *
6993 -GAG-TACCAAAATTTGAT-AGA
1 TG-GTTATCAAAATTTCATAAGA
* *
7013 AGGTTATC-AAATCTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* *
7033 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCATA-AGA
7057 TCGGATTATCAAAATTT-AT-AGAA
1 T-GG-TTATCAAAATTTCATAAG-A
* *
7080 AGATTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
7100 TGTTGTTATCAAAATTTCA-AAGCGA
1 TG--GTTATCAAAATTTCATAA--GA
*
7125 -GGTTATCAAAATTACATAATG-
1 TGGTTATCAAAATTTCATAA-GA
*
7146 TGATTATCAGAAA-TTCAT-AGA
1 TGGTTATCA-AAATTTCATAAGA
* * * * *
7167 GGGGTCAACAAAATTTTATAAAA
1 -TGGTTATCAAAATTTCATAAGA
*
7190 AGGTTATCAAAATTTCATAAAGA
1 TGGTTATCAAAATTTCAT-AAGA
*
7213 -GGTTATCAAATTTTCA-AA-A
1 TGGTTATCAAAATTTCATAAGA
7232 TGTGATTA-CAAAAATTTCATA
1 TG-G-TTATC-AAAATTTCATA
7253 GTGGTATTTC
Statistics
Matches: 444, Mismatches: 88, Indels: 137
0.66 0.13 0.20
Matches are distributed among these distances:
19 4 0.01
20 25 0.06
21 45 0.10
22 263 0.59
23 34 0.08
24 32 0.07
25 12 0.03
26 19 0.04
27 2 0.00
28 8 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:7153 original size:44 final size:44
Alignment explanation
Indices: 7060--7250 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 44
7050 ATAGAGATCG
* * * *
7060 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
7104 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * ***
7147 GATTATCAGAAA-TTCATAGAGGGGTCAACAAAATTTTATAAAAA
1 GATTATCA-AAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
7191 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
7235 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
7251 TAGTGGTATT
Statistics
Matches: 113, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
43 18 0.16
44 91 0.81
45 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:7332 original size:28 final size:28
Alignment explanation
Indices: 7292--7347 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
7282 TCATAGTATG
7292 GTTACCAAATTAGGAAGGTTATTAAACT
1 GTTACCAAATTAGGAAGGTTATTAAACT
7320 GTTACCAAATTAGGAAGGTTATTAAACT
1 GTTACCAAATTAGGAAGGTTATTAAACT
7348 TTTATATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
GTTACCAAATTAGGAAGGTTATTAAACT
Found at i:7408 original size:22 final size:22
Alignment explanation
Indices: 7333--7608 Score: 146
Period size: 22 Copynumber: 13.0 Consensus size: 22
7323 ACCAAATTAG
* * *
7333 GAAGGTTATTAAACTTTTATAT
1 GAAGGTTATCAAAATTTCATAT
* *
7355 GGA-GTAATCAAAATTTCA-A-
1 GAAGGTTATCAAAATTTCATAT
* *
7374 GGAGGATATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
7396 GAAGGTTATCAAAATTTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
** * * *
7419 TTA-GTTTTCAAAATGTCATAA
1 GAAGGTTATCAAAATTTCATAT
*
7440 GAGGGTTATCAAAATTTCATA-
1 GAAGGTTATCAAAATTTCATAT
* * * *
7461 GTATGTAGATCAAAATTTCATAG
1 GAAGGT-TATCAAAATTTCATAT
* * *
7484 GGAGATTAACAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
* * *
7507 G-AGATTATCAAAA-ATCATAG
1 GAAGGTTATCAAAATTTCATAT
*
7527 GGAGGTTATCAAAA--T--T-T
1 GAAGGTTATCAAAATTTCATAT
* * *
7544 GTA-GTTATCAAGATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * *
7565 GAAAGTTATCAAAATTTTATAG
1 GAAGGTTATCAAAATTTCATAT
*
7587 GAAGATTTATCAAAATTTCATA
1 GAAG-GTTATCAAAATTTCATA
7609 GTGTGATAAT
Statistics
Matches: 194, Mismatches: 44, Indels: 31
0.72 0.16 0.12
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 2 0.01
19 3 0.02
20 18 0.09
21 32 0.16
22 106 0.55
23 22 0.11
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:7454 original size:66 final size:63
Alignment explanation
Indices: 7330--7628 Score: 227
Period size: 66 Copynumber: 4.7 Consensus size: 63
7320 GTTACCAAAT
* * * * * * *
7330 TAGGAAGGTTATTAAACTTTTATATGGAGTAATCAAAATTTCA-AGGAGGATATCAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCATA-GTAGTTATCAAAATTTCATAAGAGGTTATCAAAATTTCA
* * *
7393 TATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATGTCATAAGAGGGTTATCAAAATTTC
1 TAGGAAGGTTATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGA-GGTTATCAAAATTTC
7458 A
63 A
* * * * * * *
7459 TA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATTATCAAAA-AT
1 TAGGAAGGT-TATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAA-GAGGTTATCAAAATTT
7522 CA
62 CA
* * * *
7524 TAGGGAGGTTATCAAAA-TT--T-GTAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTA
1 TAGGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAG-AGGTTATCAAAATTTCA
*
7584 TAGGAAGATTTATCAAAATTTCATAGT-GTGATAATCAAAATTTCA
1 TAGGAAG-GTTATCAAAATTTCATAGTAGT--T-ATCAAAATTTCA
7629 GAGTGTGTGA
Statistics
Matches: 185, Mismatches: 32, Indels: 34
0.74 0.13 0.14
Matches are distributed among these distances:
58 1 0.01
59 25 0.14
60 11 0.06
61 9 0.05
62 4 0.02
63 20 0.11
64 18 0.10
65 23 0.12
66 60 0.32
67 14 0.08
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.35
Consensus pattern (63 bp):
TAGGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGTTATCAAAATTTCA
Found at i:7928 original size:22 final size:22
Alignment explanation
Indices: 7900--7943 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7890 GATCATAAAA
7900 AATAGTGTA-ATTATCATAATTT
1 AATAGTG-AGATTATCATAATTT
*
7922 AATAGTGAGGTTATCATAATTT
1 AATAGTGAGATTATCATAATTT
7944 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
AATAGTGAGATTATCATAATTT
Done.