Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014449.1 Corchorus capsularis cultivar CVL-1 contig14470, 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: 38106
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2285 original size:333 final size:329
Alignment explanation
Indices: 1675--2468 Score: 808
Period size: 333 Copynumber: 2.4 Consensus size: 329
1665 GTTAGCTCAA
* * * * *
1675 CCACATTGGATTTAAAAATTTATTTTTACGAGCATCAGAAACCGGTTTCAATTTAATAAGAAAAT
1 CCACATTGGATTTAAAGATTTATTTTTACGAGCATCA-AATCC-TTTTC-ATTTAATTAGAAATT
* * * ** *
1740 AAGTCAAAAAAGAAAAAGAAAAACGATATTAGAAACGTGAAAAT-CCTTTCAATCATTTTGGCAC
63 AATTCAGAAAA-AATAAGAAAAACGATATTAGAAGTGTGAAAATCCCTTT-AATCATTTTGACAC
*
1804 TGAATTATATATTTTTTATGAGTATCGTGGCCAAAATTAAGGAAAAAATCATTCGGTTCAATTTT
126 TGAATTATATATTTTTTATGAGTATCGTGGCCAAAATTAAGGAAAAAATCATTCGATTCAATTTT
* * * * **
1869 TGCAAAATTTTAGTCTAAATCGTGTACTAATCATCACGGTTTTCGACTAAAAACGTGTTTCGAGC
191 TGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTCGACTAAAAACACGTTTCGAGC
* ** * * *
1934 CTCTGGCTCAGTTTTGCATGATTTTTGAGGCTAAGACTCCTTAAAATATCT-ATAT-TTATCAAA
256 CTCTGACTCAGTTTTGCATGATTTTTGACACCAAGACTCATTAAAATATCTCA-ATCCT-TCAAA
*
1997 TCAAATTTCAG
319 TCAAATATCAG
* * * * *
2008 TCATATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGCAATT
1 CCACATTGGATTTAAAGATTTATTTTTACGAGCATC-AAATCCT-TTTC-ATTTAATTAGAAATT
* **
2073 AATTCAGAAAAAATAAGGAAAACGATATTAGAAGTGTGAAAATCCCTTTAATCATTTTGACGTTG
63 AATTCAGAAAAAATAAGAAAAACGATATTAGAAGTGTGAAAATCCCTTTAATCATTTTGACACTG
* * * * * ** * *
2138 AATTGTATATTTTTTTATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTTCGATTTAGTTTT
128 AATTATATA-TTTTTTATGAGTATCGTGGCC-AAAATTAAGGAAAAAATCATTCGATTCAATTTT
* * *
2203 TGTAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTTG-CTAAAAACACGTTCTGGA
191 TGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG-TTTTCGACTAAAAACACGTT-TCGA
* * * * *
2267 TCC-C-GACTCAGTTTTGCATGATTTTTGACACCGAGACTTATTGAAATATCTCAATCCTTCTAA
254 GCCTCTGACTCAGTTTTGCATGATTTTTGACACCAAGACTCATTAAAATATCTCAATCCTTCAAA
*
2330 TCGAATATCAG
319 TCAAATATCAG
* * * *
2341 CCACATTTGATTTAAAGATTTATTTTTACGAGCATCAAAAAATCGGTTTTCATATAATTGGAAAT
1 CCACATTGGATTTAAAGATTTATTTTTACGAGCATC---AAATC-CTTTTCATTTAATTAGAAAT
* * * * * *
2406 TAATTCGGAAAAAAATATATGAAAAATGTTATTAGAAGTGTGAAAAGCTCTTCAATCATTTTG
62 TAATTCAG-AAAAAATA-A-GAAAAACGATATTAGAAGTGTGAAAATCCCTTTAATCATTTTG
2469 TTTATGAGTA
Statistics
Matches: 378, Mismatches: 68, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
332 49 0.13
333 171 0.45
334 92 0.24
335 27 0.07
336 2 0.01
337 37 0.10
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (329 bp):
CCACATTGGATTTAAAGATTTATTTTTACGAGCATCAAATCCTTTTCATTTAATTAGAAATTAAT
TCAGAAAAAATAAGAAAAACGATATTAGAAGTGTGAAAATCCCTTTAATCATTTTGACACTGAAT
TATATATTTTTTATGAGTATCGTGGCCAAAATTAAGGAAAAAATCATTCGATTCAATTTTTGCAA
AATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTCGACTAAAAACACGTTTCGAGCCTCTG
ACTCAGTTTTGCATGATTTTTGACACCAAGACTCATTAAAATATCTCAATCCTTCAAATCAAATA
TCAG
Found at i:2730 original size:318 final size:315
Alignment explanation
Indices: 2146--2738 Score: 668
Period size: 318 Copynumber: 1.9 Consensus size: 315
2136 TGAATTGTAT
* * * * * * * *
2146 ATTTTTTTATGAGTATTGTGGCCAAAAATTGAGTAAAAATTTTTTCGATTTAGTTTTTGTAAAAT
1 ATTTTTTTATGAGTATTGTGGCAAAAAAATGAGGAAAAATTTTTCCAATTCAATTTTTGAAAAAT
* *
2211 TTTAGCCGAAATCATGTACTAACCATCACGGTTTTTTGCTAAAAACACGTTCTGGATCCCGACTC
66 TTTAGCCGAAATCATGTACTAAACATCACGGTTTTTTGCTAAAAACACATTCTGGATCCCGACTC
* * * * *
2276 AGTTTTGCATGATTTTTGACACCGAGACTTATTGAAATATCTCAATCCTTCTAATCGAATATCAG
131 AGTTTTGCATGATTTTTGACA-C-AAACTCATTGAAATATCTCAATCCATCTAAACAAATATCAG
* *
2341 CCACATTTGATTTAAAGATTTATTTTTACGAGCATCAAAAAATCGGTTTTCATATAATTGGAAAT
194 CCACATTTGATTTAAAGATTTATTTTTACGAGCATCAAAAAATCAGTTTTCATATAATTGGAAAA
2406 TAATTCGGAAAAAAATATATGAAAAATGTTATTAGAAGTGTGAAAAGCTCTTCAATC
259 TAATTCGGAAAAAAATATATGAAAAATGTTATTAGAAGTGTGAAAAGCTCTTCAATC
2463 ATTTTGTTTATGAGTATTGTGGCAAAAAAAATGAGGAAAAA-TTTTCCAATTCAATTTTAT-AAA
1 ATTTT-TTTATGAGTATTGTGGC-AAAAAAATGAGGAAAAATTTTTCCAATTCAATTTT-TGAAA
* * * *
2526 AATTTTAGCCGAAATCGTGTACTAAACATCACGG-TTTTTGATTAAAAATGA-ATTCTGGGTCCC
63 AATTTTAGCCGAAATCATGTACTAAACATCACGGTTTTTTG-CTAAAAA-CACATTCTGGATCCC
* * ** * *
2589 GGCTTAGTTTTGCATGATTTTTTGTGTA-AAACTCATTGAAATTATC-GATATTCATCTAAACAA
126 GACTCAGTTTTGCATGA-TTTTTG-ACACAAACTCATTGAAA-TATCTCA-ATCCATCTAAACAA
* * * * * *
2652 ATCTCAGTCACA-TTGAATTTAAGGATTTGTTTTTACGAGTATC-AAAAATCTAG-TTTCGATGT
187 ATATCAGCCACATTTG-ATTTAAAGATTTATTTTTACGAGCATCAAAAAATC-AGTTTTC-ATAT
2714 AA-T-GATTAAATAATTCGGAAAAAAA
249 AATTGGA--AAATAATTCGGAAAAAAA
2739 ATGATATTAG
Statistics
Matches: 229, Mismatches: 33, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
316 2 0.01
317 38 0.17
318 166 0.72
319 22 0.10
320 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (315 bp):
ATTTTTTTATGAGTATTGTGGCAAAAAAATGAGGAAAAATTTTTCCAATTCAATTTTTGAAAAAT
TTTAGCCGAAATCATGTACTAAACATCACGGTTTTTTGCTAAAAACACATTCTGGATCCCGACTC
AGTTTTGCATGATTTTTGACACAAACTCATTGAAATATCTCAATCCATCTAAACAAATATCAGCC
ACATTTGATTTAAAGATTTATTTTTACGAGCATCAAAAAATCAGTTTTCATATAATTGGAAAATA
ATTCGGAAAAAAATATATGAAAAATGTTATTAGAAGTGTGAAAAGCTCTTCAATC
Found at i:3886 original size:47 final size:47
Alignment explanation
Indices: 3834--3927 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
3824 TGGTTCCGTG
* *
3834 ACAAAAAGGTACCAACAATGAAGGAGTTCACGGGAGTTGGATTGATT
1 ACAAAAAGGTACCAACAATGAAGGAATTCACGGAAGTTGGATTGATT
* * *
3881 ACAAAAAGGTACCAACAATTAATGAATTCATGGAAGTTGGATTGATT
1 ACAAAAAGGTACCAACAATGAAGGAATTCACGGAAGTTGGATTGATT
3928 GCCTCAGGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.24
Consensus pattern (47 bp):
ACAAAAAGGTACCAACAATGAAGGAATTCACGGAAGTTGGATTGATT
Found at i:7882 original size:22 final size:22
Alignment explanation
Indices: 7854--7895 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7844 GACATGTGTC
*
7854 ACTTTTTGGTACATGTGGCACG
1 ACTTTTTAGTACATGTGGCACG
7876 ACTTTTTAGTACATGTGGCA
1 ACTTTTTAGTACATGTGGCA
7896 TGCCACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (22 bp):
ACTTTTTAGTACATGTGGCACG
Found at i:12485 original size:26 final size:26
Alignment explanation
Indices: 12449--12503 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
12439 TGGGAAAAAC
*
12449 AGGTAAGAGTAGGACTAGTAGTTCAA
1 AGGTAAAAGTAGGACTAGTAGTTCAA
*
12475 AGGTAAAAGTAGGACTAGTAGTTGAA
1 AGGTAAAAGTAGGACTAGTAGTTCAA
12501 AGG
1 AGG
12504 AATGGTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (26 bp):
AGGTAAAAGTAGGACTAGTAGTTCAA
Found at i:15742 original size:3 final size:3
Alignment explanation
Indices: 15734--15765 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
15724 GTACTTTCTT
*
15734 GAA GAA GAA GAG GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
15766 GAGGGTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17698 original size:21 final size:21
Alignment explanation
Indices: 17669--17710 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17659 TTGCTCTATA
17669 ATCCATTTTGACAAAGTTTAT
1 ATCCATTTTGACAAAGTTTAT
* *
17690 ATCCTTTTTGGCAAAGTTTAT
1 ATCCATTTTGACAAAGTTTAT
17711 GATTGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (21 bp):
ATCCATTTTGACAAAGTTTAT
Found at i:20487 original size:50 final size:50
Alignment explanation
Indices: 20412--20514 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
20402 TCGTTAATTT
20412 ATTAGCTTCTCAAGGACAGGAGTAGAAGTGATTAGTATTTGTGATTTCTG
1 ATTAGCTTCTCAAGGACAGGAGTAGAAGTGATTAGTATTTGTGATTTCTG
* * * *
20462 ATTAGCTTCTCAAGTATATGAGTAGACGTGATTAGTATTTGTGATTTCTG
1 ATTAGCTTCTCAAGGACAGGAGTAGAAGTGATTAGTATTTGTGATTTCTG
20512 ATT
1 ATT
20515 GAATTGTTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (50 bp):
ATTAGCTTCTCAAGGACAGGAGTAGAAGTGATTAGTATTTGTGATTTCTG
Found at i:28603 original size:32 final size:30
Alignment explanation
Indices: 28555--28616 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
28545 TAAAGTCATG
28555 ATTAAATTTATATATTTATTTATTTATATA
1 ATTAAATTTATATATTTATTTATTTATATA
* *
28585 ATTACATTTAATAGTATTTATTTATTTCTATA
1 ATTAAATTT-ATA-TATTTATTTATTTATATA
28617 TCATAGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.29
31 3 0.11
32 17 0.61
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (30 bp):
ATTAAATTTATATATTTATTTATTTATATA
Found at i:33773 original size:28 final size:28
Alignment explanation
Indices: 33720--33773 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
33710 TATAGTGCTA
* ***
33720 GATTAATTCTTTTAGTTTTTTTTTTAGG
1 GATTAATTCTTTTAGTTATAAGTTTAGG
33748 GATTAATTCTTTTAGTTATAAGTTTA
1 GATTAATTCTTTTAGTTATAAGTTTA
33774 AAATTCTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.59
Consensus pattern (28 bp):
GATTAATTCTTTTAGTTATAAGTTTAGG
Found at i:34073 original size:18 final size:18
Alignment explanation
Indices: 34039--34077 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
34029 TATTTCAAAA
34039 TTTAACTTCTATATTTTC
1 TTTAACTTCTATATTTTC
34057 TTTAA-TTCTATATTTT-
1 TTTAACTTCTATATTTTC
34073 TTTAA
1 TTTAA
34078 AAATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAACTTCTATATTTTC
Found at i:37804 original size:30 final size:30
Alignment explanation
Indices: 37737--37808 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
37727 ACACCGAACC
****
37737 GTCAAATAAGCCCCTGAACTATTATTTCAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAAA
* *
37767 -CCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAAA
37796 GTCAAATAAGCCC
1 GTCAAATAAGCCC
37809 TGTTGCCAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (30 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAAA
Done.