Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005728.1 Corchorus capsularis cultivar CVL-1 contig05746, 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: 6313
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:546 original size:35 final size:35
Alignment explanation
Indices: 491--645 Score: 208
Period size: 35 Copynumber: 4.4 Consensus size: 35
481 TCAAATCTTG
*
491 AACTTCTT-AATTG-GATCAACTCTGATCATCGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATCGAA
* *
524 AACTTCTTGAAATGAGATCAACTCCGATCATGGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATCGAA
* *
559 AACTTCTTGAAATGAGATTC-ACTCTGATCGTGGAA
1 AACTTCTTGAAATGAGA-TCAACTCTGATCATCGAA
594 AACTTCTTGAAATGAGATCAACTCTGATCATCGAAAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATCG--AA
*
631 AACTTCTTAAAATGA
1 AACTTCTTGAAATGA
646 CCGCATTGGA
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
33 8 0.07
34 6 0.06
35 76 0.70
36 2 0.02
37 16 0.15
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (35 bp):
AACTTCTTGAAATGAGATCAACTCTGATCATCGAA
Found at i:707 original size:54 final size:52
Alignment explanation
Indices: 641--924 Score: 311
Period size: 54 Copynumber: 5.4 Consensus size: 52
631 AACTTCTTAA
* * *
641 AATGACCGCATTGGATCATCTGGTCGTCAACTCTGACGATTGAAAATTTCTTTG
1 AATGACCACACTGGATCATCTGG--GTCAACTCTGACCATTGAAAATTTCTTTG
* ** *
695 AATGACCACATTGGATCATCTTGGGTCAACTCTGACCATTGAAAACATCTTGG
1 AATGACCACACTGGATCATC-TGGGTCAACTCTGACCATTGAAAATTTCTTTG
* * *
748 AATGACTACACTAGATTATCTAGGGGTCAACTCTGACCATTGAAAATTTCTTTG
1 AATGACCACACTGGATCATCT--GGGTCAACTCTGACCATTGAAAATTTCTTTG
** * * * *
802 AATGACTGCACAGGATCATCTGGGTCAACTCT-CCCATTGAAAACTTCTTGG
1 AATGACCACACTGGATCATCTGGGTCAACTCTGACCATTGAAAATTTCTTTG
*
853 AATGACCTCACT-GATCATCTGGGGGTCAACTCTGACCATTGAAAATTTCTTTG
1 AATGACCACACTGGATCATCT--GGGTCAACTCTGACCATTGAAAATTTCTTTG
* * *
906 AATAACCGCACTAGATCAT
1 AATGACCACACTGGATCAT
925 TTTAAACACC
Statistics
Matches: 196, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
50 8 0.04
51 25 0.13
52 23 0.12
53 67 0.34
54 70 0.36
55 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (52 bp):
AATGACCACACTGGATCATCTGGGTCAACTCTGACCATTGAAAATTTCTTTG
Found at i:740 original size:107 final size:103
Alignment explanation
Indices: 611--908 Score: 366
Period size: 107 Copynumber: 2.8 Consensus size: 103
601 TGAAATGAGA
* * ** * * *
611 TCAACTCTGATCATCGAAAAAACTTCTTAAAATGACCGCATTGGATCATCTGGTCGTCAACTCTG
1 TCAACTCTGACCATTG--AAAACTTCTTGGAATGACCACACT-GATCATCTGG-GGTCAACTCTG
*
676 ACGATTGAAAATTTCTTTGAATGAC-CACATTGGATCATCTTGGG
62 ACCATTGAAAATTTCTTTGAATGACGCACA--GGATCATC-TGGG
* * *
720 TCAACTCTGACCATTGAAAACATCTTGGAATGACTACACTAGATTATCTAGGGGTCAACTCTGAC
1 TCAACTCTGACCATTGAAAACTTCTTGGAATGACCACACT-GATCATCT-GGGGTCAACTCTGAC
785 CATTGAAAATTTCTTTGAATGACTGCACAGGATCATCTGGG
64 CATTGAAAATTTCTTTGAATGAC-GCACAGGATCATCTGGG
* *
826 TCAACTCT-CCCATTGAAAACTTCTTGGAATGACCTCACTGATCATCTGGGGGTCAACTCTGACC
1 TCAACTCTGACCATTGAAAACTTCTTGGAATGACCACACTGATCATCT-GGGGTCAACTCTGACC
890 ATTGAAAATTTCTTTGAAT
65 ATTGAAAATTTCTTTGAAT
909 AACCGCACTA
Statistics
Matches: 168, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
104 42 0.25
105 27 0.16
106 12 0.07
107 67 0.40
108 2 0.01
109 18 0.11
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (103 bp):
TCAACTCTGACCATTGAAAACTTCTTGGAATGACCACACTGATCATCTGGGGTCAACTCTGACCA
TTGAAAATTTCTTTGAATGACGCACAGGATCATCTGGG
Found at i:1043 original size:37 final size:37
Alignment explanation
Indices: 998--1599 Score: 603
Period size: 37 Copynumber: 16.3 Consensus size: 37
988 ACCTTAAATA
* *
998 AAGA-TTTAATAAGAAACCTAAACAGGGATCTTGAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
** * *
1034 GTGATTTTAATGAGACACCTAAACAGGGATCTTGAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * *
1071 AATG-TTTTGATGAGACACCTAAACAGGGACCTTAAAC
1 AA-GATTTTGATAAGACACCTAAACAGGGATCTTGAAC
*
1108 AAGGA-TTTGATAAGACACCTAAACAAGGATCTTGAAC
1 AA-GATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * * * *
1145 AAGGTTTTGATGAGACACCTAAACATGGACCTTAAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* *
1182 AAGGA-TTTGATAAGACACCTAAAAAGGGATACTTGAAA
1 AA-GATTTTGATAAGACACCTAAACAGGGAT-CTTGAAC
* * * *
1220 AAGATTTTGATGAGACACCTAAATAGGGACCTT-AAGA
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAA-C
* *
1257 AAGAATTTGATAAGACAACTAAACAGGGATCTTGAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * * **
1294 AAGGTTTTGATGAGACACCTAAACAGGGACCTAAAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * *
1331 AAGGA-TTTGATAAGAGACCTAAAAAGGGATCTTGAAA
1 AA-GATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * *
1368 AAGATTTTGATGAGACACCTAAATAGGGACCTT-AAGC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAA-C
* *
1405 AAGAATTTGATAAGACACCTAAACAGGGAGCTTGAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
* * * * * *
1442 AAGGTTTCGATGAGACACCTAAACTGGGACCTTAAAC
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
*
1479 AAGGA-TTTGATAAGACACCTAAACATGGAT-TTGGAAC
1 AA-GATTTTGATAAGACACCTAAACAGGGATCTT-GAAC
* * * *
1516 AAGATTTTGATGAGACACCTAAACAGGGACCTTAAAT
1 AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
*
1553 AAGGA-TTTGATAAGACACCTAAACAGGGATCTTAAAC
1 AA-GATTTTGATAAGACACCTAAACAGGGATCTTGAAC
*
1590 AAGACTTTGA
1 AAGATTTTGA
1600 CACAATTTTG
Statistics
Matches: 466, Mismatches: 81, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
36 15 0.03
37 410 0.88
38 41 0.09
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (37 bp):
AAGATTTTGATAAGACACCTAAACAGGGATCTTGAAC
Found at i:1593 original size:74 final size:74
Alignment explanation
Indices: 1046--1599 Score: 835
Period size: 74 Copynumber: 7.5 Consensus size: 74
1036 GATTTTAATG
1046 AGACACCTAAACAGGGATCTTGAACAATG-TTTTGATGAGACACCTAAACAGGGACCTTAAACAA
1 AGACACCTAAACAGGGATCTTGAACAA-GATTTTGATGAGACACCTAAACAGGGACCTTAAACAA
1110 GGATTTGATA
65 GGATTTGATA
* * *
1120 AGACACCTAAACAAGGATCTTGAACAAGGTTTTGATGAGACACCTAAACATGGACCTTAAACAAG
1 AGACACCTAAACAGGGATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAG
1185 GATTTGATA
66 GATTTGATA
* * *
1194 AGACACCTAAAAAGGGATACTTGAAAAAGATTTTGATGAGACACCTAAATAGGGACCTTAAGA-A
1 AGACACCTAAACAGGGAT-CTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAA-ACA
*
1258 AGAATTTGATA
64 AGGATTTGATA
* * *
1269 AGACAACTAAACAGGGATCTTGAACAAGGTTTTGATGAGACACCTAAACAGGGACCTAAAACAAG
1 AGACACCTAAACAGGGATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAG
1334 GATTTGATA
66 GATTTGATA
* * * * *
1343 AGAGACCTAAAAAGGGATCTTGAAAAAGATTTTGATGAGACACCTAAATAGGGACCTTAAGCAAG
1 AGACACCTAAACAGGGATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAG
*
1408 AATTTGATA
66 GATTTGATA
* * * *
1417 AGACACCTAAACAGGGAGCTTGAACAAGGTTTCGATGAGACACCTAAACTGGGACCTTAAACAAG
1 AGACACCTAAACAGGGATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAG
1482 GATTTGATA
66 GATTTGATA
* *
1491 AGACACCTAAACATGGAT-TTGGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAA
1 AGACACCTAAACAGGGATCTT-GAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAA
1555 GGATTTGATA
65 GGATTTGATA
* *
1565 AGACACCTAAACAGGGATCTTAAACAAGACTTTGA
1 AGACACCTAAACAGGGATCTTGAACAAGATTTTGA
1600 CACAATTTTG
Statistics
Matches: 430, Mismatches: 44, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
73 4 0.01
74 358 0.83
75 67 0.16
76 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (74 bp):
AGACACCTAAACAGGGATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAG
GATTTGATA
Found at i:4554 original size:22 final size:22
Alignment explanation
Indices: 4529--4575 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4519 ATTTGTTCAT
*
4529 TATTAATTAACTATTAATTCGA
1 TATTAATTAACTATTAATTAGA
*
4551 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
4573 TAT
1 TAT
4576 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:4571 original size:11 final size:11
Alignment explanation
Indices: 4529--4571 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
4519 ATTTGTTCAT
*
4529 TATTAATTAAC
1 TATTAATTAGC
* *
4540 TATTAATTCGA
1 TATTAATTAGC
4551 TATTAATTAGC
1 TATTAATTAGC
4562 TATTAATTAG
1 TATTAATTAG
4572 ATATAGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:5562 original size:35 final size:35
Alignment explanation
Indices: 5507--5689 Score: 253
Period size: 35 Copynumber: 5.2 Consensus size: 35
5497 TCAAATCTTG
* *
5507 AACTTCTT-AACTG-GATCAACTCTGATCATCGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
* *
5540 AACTTCTTGAAATGAGATCAACTTTGATCGTGGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
* *
5575 AACTTCTTGAAATGAGAGCAACTATGATCATGGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
5610 AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
1 AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
* * *
5645 AACTTCTTGAATTGAGATCAAATCTAATCATCGGAGA
1 AACTTCTTGAAATGAGATCAACTCTGATCAT-GGA-A
5682 AACTTCTT
1 AACTTCTT
5690 AAACTGACCG
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
33 8 0.06
34 4 0.03
35 110 0.82
36 3 0.02
37 9 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (35 bp):
AACTTCTTGAAATGAGATCAACTCTGATCATGGAA
Found at i:5758 original size:54 final size:54
Alignment explanation
Indices: 5694--5975 Score: 331
Period size: 53 Copynumber: 5.3 Consensus size: 54
5684 CTTCTTAAAC
* * * *
5694 TGACCGCATTGGATCAACTGGTGGTCAACTCTAACGATTGAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
* * * * * *
5748 TGACCACATTGGATAATCT-GGGGTCAACTCTGACCATTGAAAACTTCTTGGAA
1 TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
* *
5801 TGACTGCAATGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
* * * * * *
5855 TGACTGCACTAGATCATCT--AGGTCAACTCT-GCCATTGAAAACTTCTTGGAA
1 TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
* * * *
5906 TGACCTCACT-GATCATCTGGGGGTCAACTATGACCATTAAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
5959 TGACCGCACTGGATCAT
1 TGACCGCACTGGATCAT
5976 TTTAAACACC
Statistics
Matches: 193, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
50 8 0.04
51 26 0.13
52 19 0.10
53 70 0.36
54 70 0.36
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (54 bp):
TGACCGCACTGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
Found at i:5790 original size:53 final size:53
Alignment explanation
Indices: 5694--5975 Score: 336
Period size: 54 Copynumber: 5.3 Consensus size: 53
5684 CTTCTTAAAC
* * * *
5694 TGACCGCATTGGATCAACTGGTGGTCAACTCTAACGATTGAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCTGG-GGTCAACTCTGACCATTGAAAATTTCTTTGAA
* * * * *
5748 TGACCACATTGGATAATCTGGGGTCAACTCTGACCATTGAAAACTTCTTGGAA
1 TGACCGCACTGGATCATCTGGGGTCAACTCTGACCATTGAAAATTTCTTTGAA
* * *
5801 TGACTGCAATGGATCATCTGGGGGTCAACTCTAACCATTGAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCT-GGGGTCAACTCTGACCATTGAAAATTTCTTTGAA
* * * * *
5855 TGACTGCACTAGATCATCT-AGGTCAACTCTG-CCATTGAAAACTTCTTGGAA
1 TGACCGCACTGGATCATCTGGGGTCAACTCTGACCATTGAAAATTTCTTTGAA
* * *
5906 TGACCTCACT-GATCATCTGGGGGTCAACTATGACCATTAAAAATTTCTTTGAA
1 TGACCGCACTGGATCATCT-GGGGTCAACTCTGACCATTGAAAATTTCTTTGAA
5959 TGACCGCACTGGATCAT
1 TGACCGCACTGGATCAT
5976 TTTAAACACC
Statistics
Matches: 195, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
50 8 0.04
51 26 0.13
52 20 0.10
53 69 0.35
54 72 0.37
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (53 bp):
TGACCGCACTGGATCATCTGGGGTCAACTCTGACCATTGAAAATTTCTTTGAA
Found at i:6123 original size:37 final size:37
Alignment explanation
Indices: 6059--6313 Score: 271
Period size: 37 Copynumber: 6.9 Consensus size: 37
6049 GAAAAGAAAG
* ** * **
6059 CTAAACAGGGATCTTGAACGTGATTTTGACGAGACAC
1 CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
* *
6096 CTAAACAGGGATCTTGAACAAGGTTTTGATGAGACAC
1 CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
* * * *
6133 CTAAACAAGGACCTTAAACAAGGATTTGATAAGAGAC
1 CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
* *
6170 CTAAAAAGGGATCTTGAAA-AAGGTTTTGATGAGACAC
1 CTAAACAGGGATCTT-AAACAAGGTTTTGATAAGACAC
* *
6207 CTAAACAGGGACCTTAAACAAGGATTTGATAAGACAC
1 CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
* * *
6244 CTAAACATGGACCTTAAACAAGGATTTGATAAGACAC
1 CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
* * * *
6281 TTAAAAAGAGATCTTCAAA-AAGATTTTGATAAG
1 CTAAACAGGGATCTT-AAACAAGGTTTTGATAAG
Statistics
Matches: 187, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
36 3 0.02
37 178 0.95
38 6 0.03
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (37 bp):
CTAAACAGGGATCTTAAACAAGGTTTTGATAAGACAC
Found at i:6180 original size:111 final size:111
Alignment explanation
Indices: 6001--6309 Score: 377
Period size: 111 Copynumber: 2.8 Consensus size: 111
5991 AGTGATTTTG
* * * * * * * * * *
6001 AACAAGAATTTGACAAAAAACCTAAAC-AGGCACCTAAAATAAAGATTTGAAAAGAAAGCTAAAC
1 AACAAGGATTTGATAAGACACCTAAACAAGG-ACCTTAAACAAGGATTTGATAAGAAACCTAAAA
*** * *
6065 AGGGATCTTGAACGTGATTTTGACGAGACACCTAAACAGGGATCTTG
65 AGGGATCTTGAAAAAGATTTTGACGAGACACCTAAACAGGGACCTTA
* * *
6112 AACAAGGTTTTGATGAGACACCTAAACAAGGACCTTAAACAAGGATTTGATAAGAGACCTAAAAA
1 AACAAGGATTTGATAAGACACCTAAACAAGGACCTTAAACAAGGATTTGATAAGAAACCTAAAAA
* *
6177 GGGATCTTGAAAAAGGTTTTGATGAGACACCTAAACAGGGACCTTA
66 GGGATCTTGAAAAAGATTTTGACGAGACACCTAAACAGGGACCTTA
* * *
6223 AACAAGGATTTGATAAGACACCTAAACATGGACCTTAAACAAGGATTTGATAAGACACTTAAAAA
1 AACAAGGATTTGATAAGACACCTAAACAAGGACCTTAAACAAGGATTTGATAAGAAACCTAAAAA
* *
6288 GAGATCTTCAAAAAGATTTTGA
66 GGGATCTTGAAAAAGATTTTGA
6310 TAAG
Statistics
Matches: 169, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
111 166 0.98
112 3 0.02
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (111 bp):
AACAAGGATTTGATAAGACACCTAAACAAGGACCTTAAACAAGGATTTGATAAGAAACCTAAAAA
GGGATCTTGAAAAAGATTTTGACGAGACACCTAAACAGGGACCTTA
Done.