Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015208.1 Corchorus capsularis cultivar CVL-1 contig15229, 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: 45230
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4609 original size:15 final size:14
Alignment explanation
Indices: 4557--4636 Score: 71
Period size: 14 Copynumber: 5.9 Consensus size: 14
4547 TTGATGATTA
4557 ATTTTAATTAGTTT
1 ATTTTAATTAGTTT
**
4571 ATTAAAATTAGTTT
1 ATTTTAATTAGTTT
*
4585 -GTTT-ATTAGTTT
1 ATTTTAATTAGTTT
4597 ATGTTTAATTAG--T
1 AT-TTTAATTAGTTT
4610 A-TTTAATTAGTTT
1 ATTTTAATTAGTTT
*
4623 ATAATTAATTAGTT
1 AT-TTTAATTAGTT
4637 CATTATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
11 9 0.17
12 8 0.15
13 5 0.10
14 15 0.29
15 15 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
ATTTTAATTAGTTT
Found at i:4630 original size:26 final size:26
Alignment explanation
Indices: 4559--4635 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
4549 GATGATTAAT
*
4559 TTTAATTAGTTTATTAA--AATTAGTT
1 TTTAATTAGTTTA-TAATTAATTAGTA
* **
4584 TGTTTATTAGTTTATGTTTAATTAGTA
1 T-TTAATTAGTTTATAATTAATTAGTA
4611 TTTAATTAGTTTATAATTAATTAGT
1 TTTAATTAGTTTATAATTAATTAGT
4636 TCATTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.05
26 32 0.76
27 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTAATTAGTTTATAATTAATTAGTA
Found at i:4685 original size:18 final size:18
Alignment explanation
Indices: 4553--4685 Score: 67
Period size: 18 Copynumber: 7.9 Consensus size: 18
4543 AATTTTGATG
4553 ATTAATTTTAATTAGTTT
1 ATTAATTTTAATTAGTTT
** * *
4571 ATTAAAATTAGTTTGTTT
1 ATTAATTTTAATTAGTTT
*
4589 ATT-AGTTT-A-T-GTTT
1 ATTAATTTTAATTAGTTT
*
4603 AATTAGTATTTAATTAGTTT
1 -ATTAAT-TTTAATTAGTTT
*
4623 A-TAA--TTAATTAGTTC
1 ATTAATTTTAATTAGTTT
4638 ATT-A-TTT--TT--TTT
1 ATTAATTTTAATTAGTTT
*
4650 ATTAATTATTACTTAGTTT
1 ATTAATT-TTAATTAGTTT
*
4669 ATTAGTTTTAATTAGTT
1 ATTAATTTTAATTAGTT
4686 AATTTATGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
12 5 0.06
13 1 0.01
14 7 0.08
15 18 0.21
16 3 0.03
17 8 0.09
18 29 0.34
19 11 0.13
20 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (18 bp):
ATTAATTTTAATTAGTTT
Found at i:4929 original size:24 final size:28
Alignment explanation
Indices: 4896--4961 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
4886 CTCCGCCCGT
*
4896 AGGGACAGAGAGG-AGCAG-T-TG-CAG
1 AGGGAGAGAGAGGCAGCAGCTCTGCCAG
4920 AGGGAGAGAGAGGCAGCAGCTGCTGCTCAG
1 AGGGAGAGAGAGGCAGCAGCT-CTGC-CAG
4950 AGGGAGAGAGAG
1 AGGGAGAGAGAG
4962 CTTGCTGCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 12 0.34
25 5 0.14
26 1 0.03
28 2 0.06
30 15 0.43
ACGTcount: A:0.32, C:0.14, G:0.47, T:0.08
Consensus pattern (28 bp):
AGGGAGAGAGAGGCAGCAGCTCTGCCAG
Found at i:9174 original size:15 final size:14
Alignment explanation
Indices: 9156--9226 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 14
9146 TATCATTAAT
9156 TAATTAATCATAAAC
1 TAATTAA-CATAAAC
9171 TAATTAA-AT--AC
1 TAATTAACATAAAC
9182 TAATTAATCATAAAC
1 TAATTAA-CATAAAC
9197 TAATTAA-AT--AC
1 TAATTAACATAAAC
9208 TAATTAAACATAAAC
1 TAATT-AACATAAAC
9223 TAAT
1 TAAT
9227 AAACTAAGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
11 16 0.33
12 2 0.04
13 8 0.17
15 22 0.46
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATTAACATAAAC
Found at i:9183 original size:11 final size:11
Alignment explanation
Indices: 9169--9215 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
9159 TTAATCATAA
9169 ACTAATTAAAT
1 ACTAATTAAAT
9180 ACTAATTAATCAT
1 ACTAATTAA--AT
9193 AAACTAATTAAAT
1 --ACTAATTAAAT
9206 ACTAATTAAA
1 ACTAATTAAA
9216 CATAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
13 4 0.12
15 9 0.28
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:9186 original size:26 final size:26
Alignment explanation
Indices: 9156--9226 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
9146 TATCATTAAT
9156 TAATTAATCATAAACTAATTAAATAC
1 TAATTAATCATAAACTAATTAAATAC
9182 TAATTAATCATAAACTAATTAAATAC
1 TAATTAATCATAAACTAATTAAATAC
*
9208 TAATTAAACATAAACTAAT
1 TAATTAATCATAAACTAAT
9227 AAACTAAGCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATTAATCATAAACTAATTAAATAC
Found at i:9321 original size:27 final size:26
Alignment explanation
Indices: 9266--9320 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
9256 AATTAATCAT
9266 AAACTAATTAATATTAAAAAAATTAAA
1 AAACTAATTAATA-TAAAAAAATTAAA
*
9293 AAACTAATTAGTA-AAAAAAATTAAA
1 AAACTAATTAATATAAAAAAATTAAA
9318 AAA
1 AAA
9321 ATCTGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
27 12 0.44
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (26 bp):
AAACTAATTAATATAAAAAAATTAAA
Found at i:9797 original size:28 final size:27
Alignment explanation
Indices: 9742--9799 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
9732 TGTTGATTTC
**
9742 TATTAATTATACTTTTTTTTTTGAAAT
1 TATTAATTATACTTTTTAATTTGAAAT
9769 TATTAATTATACATTTTTAAATTTG-AAT
1 TATTAATTATAC-TTTTT-AATTTGAAAT
9797 TAT
1 TAT
9800 AAGTTAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
28 11 0.41
29 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
TATTAATTATACTTTTTAATTTGAAAT
Found at i:9799 original size:21 final size:23
Alignment explanation
Indices: 9759--9800 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
9749 TATACTTTTT
*
9759 TTTTTGAAATTATTAATTATACA
1 TTTTTGAAATTATGAATTATACA
9782 TTTTT-AAATT-TGAATTATA
1 TTTTTGAAATTATGAATTATA
9801 AGTTAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTTGAAATTATGAATTATACA
Found at i:21909 original size:18 final size:19
Alignment explanation
Indices: 21875--21912 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
21865 GTCCATCGTT
*
21875 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
21894 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
21912 A
1 A
21913 GCCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:22864 original size:33 final size:33
Alignment explanation
Indices: 22754--22863 Score: 143
Period size: 33 Copynumber: 3.3 Consensus size: 33
22744 ACAAAGGGTT
* *
22754 GCGTGGCCGGTTGTGGCCGGGCATGGCCGA-GTC
1 GCGTGGCCGGTTGTGGCCGGACATGTCC-ATGTC
** *
22787 GTTTGGCCGGTTGTAGCCGGACATGTCCATGTC
1 GCGTGGCCGGTTGTGGCCGGACATGTCCATGTC
22820 GCGTGGCCGG-TGATGGCCGGACATGTCCATGTC
1 GCGTGGCCGGTTG-TGGCCGGACATGTCCATGTC
22853 GCGTGGCCGGT
1 GCGTGGCCGGT
22864 GTTGCGCGGC
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 3 0.05
33 63 0.95
ACGTcount: A:0.09, C:0.26, G:0.42, T:0.23
Consensus pattern (33 bp):
GCGTGGCCGGTTGTGGCCGGACATGTCCATGTC
Found at i:23013 original size:19 final size:19
Alignment explanation
Indices: 22985--23022 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22975 CTAAGTCATG
*
22985 ATAAGCCCTTGGCGCATCA
1 ATAAGCCCTTGACGCATCA
*
23004 ATAAGTCCTTGACGCATCA
1 ATAAGCCCTTGACGCATCA
23023 TTCCCTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (19 bp):
ATAAGCCCTTGACGCATCA
Found at i:27250 original size:30 final size:29
Alignment explanation
Indices: 27200--27261 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
27190 TAATCAATTG
* *
27200 TTTATCTTTTAATTGTAATTATTTTGGAT
1 TTTATCTTTTAACTGCAATTATTTTGGAT
27229 TTTATCTTTTTAACTGCAATTATTTTGGAT
1 TTTATC-TTTTAACTGCAATTATTTTGGAT
27259 TTT
1 TTT
27262 TTACACTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.23, C:0.06, G:0.10, T:0.61
Consensus pattern (29 bp):
TTTATCTTTTAACTGCAATTATTTTGGAT
Found at i:29485 original size:33 final size:33
Alignment explanation
Indices: 29396--29496 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
29386 TTTGTCATTT
* * *
29396 GGCGGAGCCTCCCCACTAGGGCGACTCTGCTAC
1 GGCGGAGCCTCCCCACTAGGACGGCTCTGCCAC
*
29429 GGCGGAGCCTCCCCACTAGGACGGCTCTGCCCC
1 GGCGGAGCCTCCCCACTAGGACGGCTCTGCCAC
*
29462 GGCGGAGCCGCCCCACTAGGACGGCT-TAGCCAC
1 GGCGGAGCCTCCCCACTAGGACGGCTCT-GCCAC
29495 GG
1 GG
29497 AAGACTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.15, C:0.41, G:0.33, T:0.12
Consensus pattern (33 bp):
GGCGGAGCCTCCCCACTAGGACGGCTCTGCCAC
Found at i:29611 original size:33 final size:33
Alignment explanation
Indices: 29564--29627 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
29554 TAGGGTCGGT
*
29564 GCCGCCCCAAGAGGGCGGCTTGGCCATGGCTCA
1 GCCGCCCCAAGAGGGCGGCCTGGCCATGGCTCA
* *
29597 GCCGCCCTAGGAGGGCGGCCTGGCCATGGCT
1 GCCGCCCCAAGAGGGCGGCCTGGCCATGGCT
29628 AGGCCGTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.12, C:0.36, G:0.39, T:0.12
Consensus pattern (33 bp):
GCCGCCCCAAGAGGGCGGCCTGGCCATGGCTCA
Found at i:42470 original size:9 final size:9
Alignment explanation
Indices: 42456--42506 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
42446 AGATAATTAT
42456 CAAATTTAG
1 CAAATTTAG
*
42465 CAAATTTAA
1 CAAATTTAG
*
42474 CAAA-TTAT
1 CAAATTTAG
*
42482 CAAA-TTAT
1 CAAATTTAG
42490 CAAATTTAG
1 CAAATTTAG
*
42499 CAGATTTA
1 CAAATTTA
42507 ACAATTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
8 15 0.41
9 22 0.59
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (9 bp):
CAAATTTAG
Found at i:42487 original size:8 final size:8
Alignment explanation
Indices: 42450--42495 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
42440 ATTTGTAGAT
42450 AATTATCA
1 AATTATCA
*
42458 AATTTAGCA
1 AA-TTATCA
*
42467 AATTTAACA
1 AA-TTATCA
42476 AATTATCA
1 AATTATCA
42484 AATTATCA
1 AATTATCA
42492 AATT
1 AATT
42496 TAGCAGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 19 0.56
9 15 0.44
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (8 bp):
AATTATCA
Found at i:42488 original size:34 final size:33
Alignment explanation
Indices: 42450--42517 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 33
42440 ATTTGTAGAT
42450 AATTATCAAATTTAGCAAATTTAACAAATTATCA
1 AATTATCAAATTTAGCAAATTTAAC-AATTATCA
*
42484 AATTATCAAATTTAGCAGATTTAACAATTATCA
1 AATTATCAAATTTAGCAAATTTAACAATTATCA
42517 A
1 A
42518 TTTTACGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 9 0.27
34 24 0.73
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (33 bp):
AATTATCAAATTTAGCAAATTTAACAATTATCA
Found at i:44935 original size:28 final size:29
Alignment explanation
Indices: 44867--44940 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
44857 GGGTCATCCA
44867 GGGGCATTTTGGTCATTTTCACATCTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
** *
44896 GGGGCATTTTGGTCATTTTTGCATGTA-G
1 GGGGCATTTTGGTCATTTTCACATCTAGG
*
44924 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
44941 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 17 0.41
29 24 0.59
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.42
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATCTAGG
Done.