Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014272.1 Corchorus capsularis cultivar CVL-1 contig14293, 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: 41257
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5992 original size:18 final size:19
Alignment explanation
Indices: 5969--6008 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5959 TGAAATGGTT
5969 TTTTGC-TTGGCGATTATC
1 TTTTGCTTTGGCGATTATC
*
5987 TTTTGCTTTTGGTGATTATC
1 TTTTGC-TTTGGCGATTATC
6007 TT
1 TT
6009 GAACCATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (19 bp):
TTTTGCTTTGGCGATTATC
Found at i:10304 original size:2 final size:2
Alignment explanation
Indices: 10297--10338 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
10287 ATAATTACCC
* *
10297 TA TA TA TA TA TA TA -A TA CA TA CA TA TA TA TA TA TA 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
10338 T
1 T
10339 GTAGCTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:32470 original size:67 final size:67
Alignment explanation
Indices: 32362--32534 Score: 294
Period size: 67 Copynumber: 2.6 Consensus size: 67
32352 ATGCTTCAAG
* *
32362 ATTTGCTTCAAGGGTCGAATGACTTGATCTTGAACTTGATGACAATTTGAGAACTTGATTTGATT
1 ATTTGATTCAAGAGTCGAATGACTTGATCTTGAACTTGATGACAATTTGAGAACTTGATTTGATT
32427 TT
66 TT
*
32429 ATTTGATTTAAGAGTCGAATGACTTGATCTTGAACTTGATGACAATTTGAGAACTTGATTTGATT
1 ATTTGATTCAAGAGTCGAATGACTTGATCTTGAACTTGATGACAATTTGAGAACTTGATTTGATT
32494 TT
66 TT
* *
32496 ATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGAT
1 ATTTGATTCAAGAGTCGAATGACTTGATCTTGAACTTGAT
32535 TATTTAATTC
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 5 0.05
67 95 0.95
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.40
Consensus pattern (67 bp):
ATTTGATTCAAGAGTCGAATGACTTGATCTTGAACTTGATGACAATTTGAGAACTTGATTTGATT
TT
Found at i:32589 original size:99 final size:101
Alignment explanation
Indices: 32486--32674 Score: 240
Period size: 104 Copynumber: 1.9 Consensus size: 101
32476 TGAGAACTTG
* * * * * *
32486 ATTTGATTTTATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGAT-T-ATTTAATTCAAG
1 ATTTGATTTGATTCGATTCAACGGTCTG-ATGACTTGATCTCGAATTGATATAATTTAACTCAAG
32548 GGTCTTGGCGACTTAATCTTGAATTGAAGACTTGGGA
65 GGTCTTGGCGACTTAATCTTGAATTGAAGACTTGGGA
* *
32585 ATTTGATTTGATTCGATTCGACGGTCTTTGATGACTTGATCTCGAATTGATGATAATTTGACTCA
1 ATTTGATTTGATTCGATTCAACGGTC--TGATGACTTGATCTCGAATTGAT-ATAATTTAACTCA
*
32650 AGGGTCTTGGCGACTTGATCTTGAA
63 AGGGTCTTGGCGACTTAATCTTGAA
32675 CAAACAAATT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
99 22 0.29
101 19 0.25
102 1 0.01
103 1 0.01
104 32 0.43
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (101 bp):
ATTTGATTTGATTCGATTCAACGGTCTGATGACTTGATCTCGAATTGATATAATTTAACTCAAGG
GTCTTGGCGACTTAATCTTGAATTGAAGACTTGGGA
Found at i:32914 original size:91 final size:91
Alignment explanation
Indices: 32759--32982 Score: 335
Period size: 91 Copynumber: 2.5 Consensus size: 91
32749 TCTTTGATAA
* * * *
32759 TTTGAAAGAAAAATCCTCCATATACGTGGATCTTCTTTCAATAATTTCCCAATAACTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
*
32824 AGTAATTCTGCAATAATTG-GATCTTC
66 AGTAATTCTCCAATAATTGAG-TCTTC
*
32850 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAA-CTCCCAAATAACTGGGTCTT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCC-AATAACTGGGTCTT
*
32914 CAGTAATTCTCCAATAATTGAGTTTTC
65 CAGTAATTCTCCAATAATTGAGTCTTC
**
32941 TTTGAAAGAAGAATTTTCCACATACGTGGATCTTCTTTCAAT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAAT
32983 CTTCTTAAAC
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
90 4 0.03
91 116 0.96
92 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (91 bp):
TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
AGTAATTCTCCAATAATTGAGTCTTC
Found at i:33048 original size:16 final size:16
Alignment explanation
Indices: 33027--33061 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
33017 ATCTGAAATA
33027 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
33043 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
33059 CTT
1 CTT
33062 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:35930 original size:2 final size:2
Alignment explanation
Indices: 35923--35958 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
35913 ATTGAATTAT
* *
35923 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35959 AGAGTTGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38142 original size:31 final size:31
Alignment explanation
Indices: 38104--38299 Score: 116
Period size: 31 Copynumber: 6.5 Consensus size: 31
38094 TATGACTAAT
38104 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
* * **
38135 TGTTCAAATAAGGGCCTGA--TCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGTTAAAA
38164 TGGC-CAAATAAGGGCCTAACGTTATCG--AAAA
1 T-GCTCAAATAAGGGCCTAACGTT-T-GTTAAAA
**
38195 TGCTCAAATAAGGGCC---CGATCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACG-T-TTGTTAAAA
38224 TGGC-CAAATAAGGGCCTAACGTTATCG--AAAA
1 T-GCTCAAATAAGGGCCTAACGTT-T-GTTAAAA
* *
38255 TACTCAAATAAGGGCCTAACGCTATCG--AAAA
1 TGCTCAAATAAGGGCCTAACG-T-TTGTTAAAA
38286 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
38300 TCTGGTGTCA
Statistics
Matches: 128, Mismatches: 15, Indels: 44
0.68 0.08 0.24
Matches are distributed among these distances:
28 2 0.02
29 37 0.29
30 11 0.09
31 74 0.58
32 3 0.02
33 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
Found at i:38172 original size:29 final size:29
Alignment explanation
Indices: 38139--38240 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
38129 TTAAAATGTT
38139 CAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTGATCTTTTAATTTGGC
* * **
38168 CAAATAAGGGCCT-AACGTTATCGAAAAT-GC
1 CAAATAAGGGCCTGATC-TT-T-TAATTTGGC
*
38198 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTTGGC
38228 CAAATAAGGGCCT
1 CAAATAAGGGCCT
38241 AACGTTATCG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.04
29 30 0.53
30 6 0.11
31 17 0.30
32 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:38176 original size:60 final size:60
Alignment explanation
Indices: 38108--38271 Score: 269
Period size: 60 Copynumber: 2.7 Consensus size: 60
38098 ACTAATTGCT
*
38108 CAAATAAGGGCCTAACGTT-T-GTTAAAATGTTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCG--AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
38168 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
38228 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCT
38272 AACGCTATCG
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
60 96 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:38368 original size:31 final size:30
Alignment explanation
Indices: 38333--38497 Score: 126
Period size: 31 Copynumber: 5.5 Consensus size: 30
38323 ATGAGACAGA
38333 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** *
38364 CCCTTATTTG-GCCAAATT-CAAA-GATTGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
38393 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * * *
38424 CCCTTATTTG-GCCAAATT--AAAAGATCATG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
* *
38453 ACCTTATTTGAGTATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGG
*
38484 TCCTTATTTGAGCA
1 CCCTTATTTGAGCA
38498 ATTAGCCATT
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 37 0.36
30 4 0.04
31 51 0.50
32 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:38395 original size:29 final size:29
Alignment explanation
Indices: 38359--38462 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
38349 TTGGCAAACG
38359 TTAGGCCCTTATTTGGCCAAATTCAAAGA
1 TTAGGCCCTTATTTGGCCAAATTCAAAGA
* **
38388 TTGGGCCCTTATTTGAG-CATTTTGGCAAACG-
1 TTAGGCCCTTATTTG-GCCAAATT--CAAA-GA
*
38419 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TTAGGCCCTTATTTGGCCAAATTCAAAGA
* * *
38448 TCATGACCTTATTTG
1 TTAGGCCCTTATTTG
38463 AGTATTTTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.02
29 33 0.56
30 2 0.03
31 22 0.37
32 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (29 bp):
TTAGGCCCTTATTTGGCCAAATTCAAAGA
Found at i:38405 original size:60 final size:60
Alignment explanation
Indices: 38333--38493 Score: 250
Period size: 60 Copynumber: 2.7 Consensus size: 60
38323 ATGAGACAGA
* **
38333 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATTGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
*
38393 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCATG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
* * * *
38453 ACCTTATTTGAGTATTTTGACAAACGTTAGGTCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
38494 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
Done.