Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010621.1 Corchorus capsularis cultivar CVL-1 contig10642, 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: 38630
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:139 original size:29 final size:29
Alignment explanation
Indices: 76--181 Score: 97
Period size: 30 Copynumber: 3.6 Consensus size: 29
66 CGGAGCCGTT
* * *
76 AAGTTGAGGGGACAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGT-CCAAGATTG
*
106 AAGTTCAGGGGGCAAAATGTCCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCAAGATTG
* * * **
135 AAGTT-TGGGGGCAAAACGTCTAAACGCTAC
1 AAGTTCAGGGGGCAAAACGTC-CAA-GATTG
165 AAGTTCAGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
182 TGGTTGTTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
28 13 0.21
29 15 0.24
30 24 0.39
31 10 0.16
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (29 bp):
AAGTTCAGGGGGCAAAACGTCCAAGATTG
Found at i:3817 original size:166 final size:166
Alignment explanation
Indices: 3543--3877 Score: 670
Period size: 166 Copynumber: 2.0 Consensus size: 166
3533 GCCTAAACTC
3543 TAAATGTACAAAATTCTGGCATAGTGGCATTTAAAGATAAATATGAACTGCACAATACTCAAATT
1 TAAATGTACAAAATTCTGGCATAGTGGCATTTAAAGATAAATATGAACTGCACAATACTCAAATT
3608 CTGCTTCTTGGCAAGATAATGTAACACCCTTTTAGAATTGCCCTGATGGCATGATAAATCATAAA
66 CTGCTTCTTGGCAAGATAATGTAACACCCTTTTAGAATTGCCCTGATGGCATGATAAATCATAAA
3673 CCATACTTAAGAAACACATGTGATGCTAGACATAAG
131 CCATACTTAAGAAACACATGTGATGCTAGACATAAG
3709 TAAATGTACAAAATTCTGGCATAGTGGCATTTAAAGATAAATATGAACTGCACAATACTCAAATT
1 TAAATGTACAAAATTCTGGCATAGTGGCATTTAAAGATAAATATGAACTGCACAATACTCAAATT
3774 CTGCTTCTTGGCAAGATAATGTAACACCCTTTTAGAATTGCCCTGATGGCATGATAAATCATAAA
66 CTGCTTCTTGGCAAGATAATGTAACACCCTTTTAGAATTGCCCTGATGGCATGATAAATCATAAA
3839 CCATACTTAAGAAACACATGTGATGCTAGACATAAG
131 CCATACTTAAGAAACACATGTGATGCTAGACATAAG
3875 TAA
1 TAA
3878 TCTACAGTGA
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 169 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (166 bp):
TAAATGTACAAAATTCTGGCATAGTGGCATTTAAAGATAAATATGAACTGCACAATACTCAAATT
CTGCTTCTTGGCAAGATAATGTAACACCCTTTTAGAATTGCCCTGATGGCATGATAAATCATAAA
CCATACTTAAGAAACACATGTGATGCTAGACATAAG
Found at i:7720 original size:2 final size:2
Alignment explanation
Indices: 7713--7742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7703 TAGATTTAAG
7713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7743 TGTTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12265 original size:6 final size:6
Alignment explanation
Indices: 12248--12297 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
12238 AAAGCAAAGC
12248 AAATCT -AATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
12295 AAA
1 AAA
12298 GCAAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:14753 original size:33 final size:32
Alignment explanation
Indices: 14710--14811 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
14700 TTAAAGGATC
*
14710 GTGTGGCCGGGCATGGCCGA-GTCATGTGGCCG
1 GTGTGGCCGGGCATGGCC-ATGTCACGTGGCCG
* *
14742 GTTGTGGCCGGGCATGGTCATGTCGCGTGGCCG
1 G-TGTGGCCGGGCATGGCCATGTCACGTGGCCG
** * *
14775 GTGATGGCCGGGCATCTCCAAGTCGCGTGGCCG
1 GTG-TGGCCGGGCATGGCCATGTCACGTGGCCG
14808 GTGT
1 GTGT
14812 TGCGCGGCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.08
33 55 0.92
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (32 bp):
GTGTGGCCGGGCATGGCCATGTCACGTGGCCG
Found at i:21316 original size:23 final size:23
Alignment explanation
Indices: 21267--21329 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
21257 AAAGGATCGT
*
21267 GTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGGGCATGGCCGAGTCAC
* *
21290 GTGGCCGGGCATGGTC-ATGTCGC
1 GTGGCCGGGCATGGCCGA-GTCAC
21313 GTGGCCGGTG-ATGGCCG
1 GTGGCCGG-GCATGGCCG
21330 GGCATCTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19
Consensus pattern (23 bp):
GTGGCCGGGCATGGCCGAGTCAC
Found at i:21329 original size:33 final size:33
Alignment explanation
Indices: 21291--21355 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
21281 CCGAGTCATG
* *
21291 TGGCCGGGCATGGT-CATGTCGCGTGGCCGGTGA
1 TGGCCGGGCAT-CTCCAAGTCGCGTGGCCGGTGA
21324 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTG
1 TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTG
21356 TTGCGCGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (33 bp):
TGGCCGGGCATCTCCAAGTCGCGTGGCCGGTGA
Found at i:25776 original size:15 final size:15
Alignment explanation
Indices: 25758--25813 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
25748 GATTACCATT
25758 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
25773 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
25786 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
25801 TTACTCTTTTACT
1 TTACTCTTTTACT
25814 TCTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:25840 original size:21 final size:21
Alignment explanation
Indices: 25794--25881 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
25784 TGCTCCTTTT
* *
25794 TTACTGATTACTCTTTTACTTC
1 TTACTGATTACTATTTGAC-TC
25816 TTACTGATTACTATTTGACTC
1 TTACTGATTACTATTTGACTC
* *
25837 TTACTAATTACCACTTTG-CTC
1 TTACTGATTACTA-TTTGACTC
* * * *
25858 TCACTGGTTACTGTTTTACTC
1 TTACTGATTACTATTTGACTC
25879 TTA
1 TTA
25882 ATGACTACCT
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.06
21 29 0.55
22 21 0.40
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (21 bp):
TTACTGATTACTATTTGACTC
Found at i:25910 original size:35 final size:35
Alignment explanation
Indices: 25871--25950 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
25861 CTGGTTACTG
25871 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
1 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
* ** * * *
25906 TTTTACTCTTAATGGCTGTCTTTTGCTGATTACTA
1 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
25941 TTTTACTCTT
1 TTTTACTCTT
25951 TACTGATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.50
Consensus pattern (35 bp):
TTTTACTCTTAATGACTACCTTCTACTGATCACTA
Found at i:25987 original size:21 final size:22
Alignment explanation
Indices: 25941--25989 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
25931 CTGATTACTA
*
25941 TTTTACTCTTTACTGATTATTC
1 TTTTACTCTTTACTCATTATTC
*
25963 -TTTACTCTTTAC-CATTTTTC
1 TTTTACTCTTTACTCATTATTC
25983 TTTTACT
1 TTTTACT
25990 GATTACTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTACTCTTTACTCATTATTC
Found at i:26161 original size:31 final size:31
Alignment explanation
Indices: 26107--26172 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
26097 AATTACTGAT
*
26107 TTACTGATTACTATTTTTACCTTGACTTTTAA
1 TTACTGATTAC-ATTTTTACCTTGACTCTTAA
26139 TTACTGATTA-ATTTCTTACCTTGACTCTTAA
1 TTACTGATTACATTT-TTACCTTGACTCTTAA
26170 TTA
1 TTA
26173 TCAATTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 18 0.56
32 10 0.31
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (31 bp):
TTACTGATTACATTTTTACCTTGACTCTTAA
Found at i:26298 original size:47 final size:47
Alignment explanation
Indices: 26204--26409 Score: 301
Period size: 47 Copynumber: 4.4 Consensus size: 47
26194 TTTTACTTGA
* *
26204 TTACTGATTTACTGA-TACTATTACCTTGACTTTTGATTAATCT-TTT
1 TTACTGATTTACTGATTACCATCACCTTGAC-TTTGATTAATCTCTTT
* *
26250 TTACTGATTTACTAATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
* *
26297 TTACTGATTTACTGATTACTATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
* * *
26344 TTACTGATTTACTGATTACCATCACCTTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
26391 TTACTGA-TTACTGATTACC
1 TTACTGATTTACTGATTACC
26410 CCTTTTTACT
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
46 38 0.26
47 109 0.74
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.49
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
Found at i:26313 original size:26 final size:26
Alignment explanation
Indices: 26283--26361 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
26273 ACTTTGACTT
26283 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
* * ** *
26309 TGATTACTATC-ACTT--TGACTT--
1 TGATTAATCTCTTTTTACTGATTTAC
26330 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
26356 TGATTA
1 TGATTA
26362 CCATCACCTT
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
21 9 0.24
22 2 0.05
23 5 0.13
24 5 0.13
25 2 0.05
26 15 0.39
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (26 bp):
TGATTAATCTCTTTTTACTGATTTAC
Found at i:27147 original size:51 final size:51
Alignment explanation
Indices: 27064--27319 Score: 211
Period size: 51 Copynumber: 5.1 Consensus size: 51
27054 AAGGTAACAT
* * * *
27064 TTTATTTACTAATTACT-TAAA-AGTTCAATCTTTCATTCAAAGGTTAAAGC
1 TTTATTTACCAATTACTCTAAAGA-TTCAATCTTTTATTCAAAAGTTAAATC
* * ** * * * *
27114 TTTATTTACCAATCACTCTAACGATTCAATCTTTTACCCGAACA-TGACATT
1 TTTATTTACCAATTACTCTAAAGATTCAATCTTTTATTC-AAAAGTTAAATC
* *
27165 TTTACTTACCAATTACT-TAAAAATTCAATCTTTTATTCAAAAGTTAAATC
1 TTTATTTACCAATTACTCTAAAGATTCAATCTTTTATTCAAAAGTTAAATC
* * * * *
27215 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTA-CCTAAACA-TGACATT
1 TTTATTTACCAATTACTCTAAAGATTCAATCTTTTATTC-AAA-AGTTAAATC
* * * *
27266 TTTGTTTACCAATTTACT-TAAAAATTCAATCTTTTATTCAGAGGTTAAATC
1 TTTATTTACCAA-TTACTCTAAAGATTCAATCTTTTATTCAAAAGTTAAATC
27317 TTT
1 TTT
27320 TAGCAAAAGG
Statistics
Matches: 158, Mismatches: 38, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
49 3 0.02
50 52 0.33
51 93 0.59
52 10 0.06
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (51 bp):
TTTATTTACCAATTACTCTAAAGATTCAATCTTTTATTCAAAAGTTAAATC
Found at i:27168 original size:101 final size:101
Alignment explanation
Indices: 27063--27319 Score: 388
Period size: 101 Copynumber: 2.5 Consensus size: 101
27053 AAAGGTAACA
* * * *
27063 TTTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAAGGTTAAAGCTTTATTTACCAATC
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACCAATC
* *
27128 ACTCTAACGATTCAATCTTTTACCCGAACATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCAAACATGACAT
* * * *
27164 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACTAATT
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACCAATC
*
27229 ACTCTAAAGATTCAATCTTTTACCTAAACATGACAT
66 ACTCTAAAGATTCAATCTTTTACCCAAACATGACAT
* *
27265 TTTTGTTTACCAATTTACTTAAAAATTCAATCTTTTATTCAGAGGTTAAATCTTT
1 TTTTATTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
27320 TAGCAAAAGG
Statistics
Matches: 140, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
101 101 0.72
102 39 0.28
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (101 bp):
TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACCAATC
ACTCTAAAGATTCAATCTTTTACCCAAACATGACAT
Found at i:30108 original size:27 final size:27
Alignment explanation
Indices: 30048--30127 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
30038 TGATCTTAAA
* *
30048 AAAAATGACTAAAATGCCCTCCTGAGTGC
1 AAAAATGACCAAAATG-CC-CCTGGGTGC
*
30077 AAAAATGACCGAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
*
30104 GAAAATGACCAAAATGCCCCTGGG
1 AAAAATGACCAAAATGCCCCTGGG
30128 CGACTCTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 30 0.65
28 2 0.04
29 14 0.30
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:31212 original size:28 final size:28
Alignment explanation
Indices: 31176--31236 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
31166 TAATCTCATA
31176 GGTCAAGGAGCTGGAAAGGAACAGATAG
1 GGTCAAGGAGCTGGAAAGGAACAGATAG
31204 GGTCAAGGAGCTGGAAAGGAACAGATAG
1 GGTCAAGGAGCTGGAAAGGAACAGATAG
31232 GGTCA
1 GGTCA
31237 TGAAGCCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.39, T:0.11
Consensus pattern (28 bp):
GGTCAAGGAGCTGGAAAGGAACAGATAG
Found at i:35155 original size:2 final size:2
Alignment explanation
Indices: 35150--35176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35140 CATAAGTGTG
35150 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35177 GTTAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35225 original size:27 final size:26
Alignment explanation
Indices: 35188--35241 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
35178 TTAAATAAAA
*
35188 TCACTAAATCACTAATCAGACTATAAG
1 TCACTAAATCACTAATCACAC-ATAAG
*
35215 TCACTATATCACTAATCACACATAAG
1 TCACTAAATCACTAATCACACATAAG
35241 T
1 T
35242 ATATATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.28
Consensus pattern (26 bp):
TCACTAAATCACTAATCACACATAAG
Found at i:35804 original size:36 final size:36
Alignment explanation
Indices: 35753--35828 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
35743 TCATGGCTAA
*
35753 TAAAGTGGCTCAACCAAATTCCGCATCAGGTTTGTT
1 TAAAGTGGCTCAACCAAATTCCGCATCAGGTTTGTC
*
35789 TAAAGTGGCTTAACCAAATTCCGCATCAGGTTTGTC
1 TAAAGTGGCTCAACCAAATTCCGCATCAGGTTTGTC
35825 TAAA
1 TAAA
35829 CCTTTACGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (36 bp):
TAAAGTGGCTCAACCAAATTCCGCATCAGGTTTGTC
Done.