Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009253.1 Corchorus capsularis cultivar CVL-1 contig09274, 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: 37211
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2137 original size:159 final size:162
Alignment explanation
Indices: 1845--2170 Score: 552
Period size: 159 Copynumber: 2.0 Consensus size: 162
1835 AGATGATAGA
* *
1845 ATAATTTACCTTTCTAAACTCCATAGATGTGCTCAATATAATAATAATCAATTTAATTTTCTAGG
1 ATAATTTACCTTTCTAAACACCATAGATGTGCTCAATATAATAAT-ATCAATTTAATTTTCTAGA
*
1910 CTATTTGATAGGGAATGGATATTAAAATAAAGATTCCAGAACTGCAGCTGCCCAAGGTAGCATGC
65 CTATTTGACAGGGAATGGATATTAAAATAAAGATTCCAGAACTGCAGCTGCCCAAGGTAGCATGC
1975 AGAATTGA-ATTTTTTT-TTTCTAAAAAAAAAAC
130 AGAATTGATATTTTTTTGTTTCT-AAAAAAAAAC
*
2007 ATAATTTACCTTTCTAAACACCATAGATGTGCTCGATATAATAAT-T-AATTTAATTTTCTAGAC
1 ATAATTTACCTTTCTAAACACCATAGATGTGCTCAATATAATAATATCAATTTAATTTTCTAGAC
2070 TATTTGACAGGGAATGGATATTAAAATAAAGATTCCAGAACTGCAGCTGCCCAAGGTAGCATGCA
66 TATTTGACAGGGAATGGATATTAAAATAAAGATTCCAGAACTGCAGCTGCCCAAGGTAGCATGCA
*
2135 GAATTGATTTTTTTTTTGTTTCTAAAAAAAAAC
131 GAATTGA-TATTTTTTTGTTTCTAAAAAAAAAC
2168 ATA
1 ATA
2171 CTTGTATTAT
Statistics
Matches: 156, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
159 87 0.56
160 1 0.01
161 20 0.13
162 48 0.31
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (162 bp):
ATAATTTACCTTTCTAAACACCATAGATGTGCTCAATATAATAATATCAATTTAATTTTCTAGAC
TATTTGACAGGGAATGGATATTAAAATAAAGATTCCAGAACTGCAGCTGCCCAAGGTAGCATGCA
GAATTGATATTTTTTTGTTTCTAAAAAAAAAC
Found at i:6622 original size:16 final size:16
Alignment explanation
Indices: 6603--6654 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
6593 TTGATCCATG
6603 TCTCATTTCATCTCAA
1 TCTCATTTCATCTCAA
* * ***
6619 TCTCATTTTCTTTTTTG
1 TCTCA-TTTCATCTCAA
6636 TCTCATTTCATCTCAA
1 TCTCATTTCATCTCAA
6652 TCT
1 TCT
6655 AAAAAAGCTG
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.54
Consensus pattern (16 bp):
TCTCATTTCATCTCAA
Found at i:6952 original size:14 final size:15
Alignment explanation
Indices: 6928--6956 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6918 TAAACTGCAA
6928 TTTCAAAAAGCACTT
1 TTTCAAAAAGCACTT
6943 TTTC-AAAAGCACTT
1 TTTCAAAAAGCACTT
6957 CTTCCAGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (15 bp):
TTTCAAAAAGCACTT
Found at i:7262 original size:87 final size:87
Alignment explanation
Indices: 7116--7279 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
7106 TAAATTCTAA
* * *
7116 CTTTTAACCATTTCGATTACGAATGTATAAATATGTGATTTTGTCGAGTTGTAGTCAAGATGGTT
1 CTTTTAACCATTTCGATTACGAATGCATAAACATGTGATTTTGTCGAGTTGTAATCAAGATGGTT
7181 AGAAGTTTGAATTTGTCAAGAT
66 AGAAGTTTGAATTTGTCAAGAT
*
7203 CTTTTAACCATTTCGATTACGAATGCATAAACATGTGATTTTGTTGAGTTGTAATCAAGATGGTT
1 CTTTTAACCATTTCGATTACGAATGCATAAACATGTGATTTTGTCGAGTTGTAATCAAGATGGTT
7268 AGAAGTTTGAAT
66 AGAAGTTTGAAT
7280 AATGAATTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (87 bp):
CTTTTAACCATTTCGATTACGAATGCATAAACATGTGATTTTGTCGAGTTGTAATCAAGATGGTT
AGAAGTTTGAATTTGTCAAGAT
Found at i:9893 original size:13 final size:14
Alignment explanation
Indices: 9869--9898 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9859 AAAATTTATT
9869 AATTTAATTAAATA
1 AATTTAATTAAATA
9883 AATTTAA-TAAATA
1 AATTTAATTAAATA
9896 AAT
1 AAT
9899 CCCAAGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTAATTAAATA
Found at i:10904 original size:1 final size:1
Alignment explanation
Indices: 10898--10923 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10888 GCAGTTATAG
10898 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
10924 GGGATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15404 original size:2 final size:2
Alignment explanation
Indices: 15397--15427 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15387 TCCCCTAGGA
15397 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15428 TGCTCGATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:22543 original size:37 final size:37
Alignment explanation
Indices: 22492--22565 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
22482 CTCAATCCGT
* *
22492 TTGTGGAGTCCAAATTACATCGTCAGTGTATCAAATA
1 TTGTGGAGTCCAAATTACACCGTCAGTGCATCAAATA
*
22529 TTGTGGAGTTCAAATTACACCGTCAGTGCATCAAATA
1 TTGTGGAGTCCAAATTACACCGTCAGTGCATCAAATA
22566 ATTATTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (37 bp):
TTGTGGAGTCCAAATTACACCGTCAGTGCATCAAATA
Found at i:23790 original size:13 final size:13
Alignment explanation
Indices: 23768--23798 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23758 TACCCTAATA
23768 AAAAACAAAGATG
1 AAAAACAAAGATG
*
23781 AAAAATAAAGATG
1 AAAAACAAAGATG
23794 AAAAA
1 AAAAA
23799 AAGAATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAAACAAAGATG
Found at i:25861 original size:100 final size:96
Alignment explanation
Indices: 25679--25873 Score: 293
Period size: 100 Copynumber: 2.0 Consensus size: 96
25669 AACATCGTTT
* *
25679 AAAGGCTCCAAGCTTTAATTATTCATAAATCAAACAAAGATACCCAAAAGACGTCAAACTTGTGA
1 AAAGGCTCCAAGCTTTAATTAATCATAAATCAAACAAAGATACCAAAAAGACGTCAAACTTGTGA
*
25744 AATCAATATTGAAATTAGTATAGATTAACAG
66 AATCAATATTAAAATTAGTATAGATTAACAG
*
25775 AAAGGCTCCAAGCTTTAATTAATCATAAATCATACAAAGGATAGCCAAAAAAAGACGTCAAACTT
1 AAAGGCTCCAAGCTTTAATTAATCATAAATCAAACAAA-GATA-CC--AAAAAGACGTCAAACTT
*
25840 GTGAAATCAGT-TATAAAATTAGTATAGATTAACA
62 GTGAAATCAATAT-TAAAATTAGTATAGATTAACA
25874 AAGAAAAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
96 36 0.40
97 4 0.04
98 2 0.02
99 1 0.01
100 46 0.52
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.26
Consensus pattern (96 bp):
AAAGGCTCCAAGCTTTAATTAATCATAAATCAAACAAAGATACCAAAAAGACGTCAAACTTGTGA
AATCAATATTAAAATTAGTATAGATTAACAG
Found at i:27162 original size:178 final size:180
Alignment explanation
Indices: 26832--27179 Score: 549
Period size: 178 Copynumber: 1.9 Consensus size: 180
26822 TTGGCTTTTG
* * *
26832 AATTACCTTTAAATACACACTTGAATCACCTTGATCGGTTAAATAGAAAAAAAATAAAAGAATTA
1 AATTACCTTTAAATACACACATGAATCACCTTGATCGGTCAAATAG-AAAAAAATAAAACAATTA
* ** *
26897 AAGCCGAAATATCCAATCATCCAACCCATAATTCTAAGTGATTAAATAGTATAAATTATAAAAGT
65 AAGCCGAAACATCCAATCATCCAACAAATAATTCTAAGTGATTAAATAGCATAAATTATAAAAGT
26962 ATGAGGATCATTTAATAAATAATCCAACAAAAAAAATGATTGTAGATCATGA
130 ATGAGGATCATTTAATAAATAATCCAAC-AAAAAAATGATTGTAGATCATGA
*
27014 AATTACCTTTAAATAGACACATGAATCACCTTGATCGGTCAAATAG-AAAAAA-AAAACAATTAA
1 AATTACCTTTAAATACACACATGAATCACCTTGATCGGTCAAATAGAAAAAAATAAAACAATTAA
* * *
27077 AGCCGAAACATTCAATCGTCCAACAAATAATTGTAAG-GATTAAATAGCATAAATTATAAAAGTA
66 AGCCGAAACATCCAATCATCCAACAAATAATTCTAAGTGATTAAATAGCATAAATTATAAAAGTA
*
27141 TGATGATCATTTAATAAATAATCCAACAAAAAAATGATT
131 TGAGGATCATTTAATAAATAATCCAACAAAAAAATGATT
27180 TGTTTATGGA
Statistics
Matches: 154, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
177 12 0.08
178 52 0.34
179 41 0.27
180 6 0.04
182 43 0.28
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (180 bp):
AATTACCTTTAAATACACACATGAATCACCTTGATCGGTCAAATAGAAAAAAATAAAACAATTAA
AGCCGAAACATCCAATCATCCAACAAATAATTCTAAGTGATTAAATAGCATAAATTATAAAAGTA
TGAGGATCATTTAATAAATAATCCAACAAAAAAATGATTGTAGATCATGA
Found at i:27840 original size:53 final size:53
Alignment explanation
Indices: 27776--27879 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
27766 TTCTCAACTG
27776 TTTTTTTGGTACATTCAATTCTCTTTTTAATGTATGTTATAGATATACATATT
1 TTTTTTTGGTACATTCAATTCTCTTTTTAATGTATGTTATAGATATACATATT
27829 TTTTTTTGGTACATTCAATTCTCTTTTTAATGTATGTTATAGATATACATA
1 TTTTTTTGGTACATTCAATTCTCTTTTTAATGTATGTTATAGATATACATA
27880 ATAGATATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (53 bp):
TTTTTTTGGTACATTCAATTCTCTTTTTAATGTATGTTATAGATATACATATT
Found at i:27885 original size:13 final size:13
Alignment explanation
Indices: 27867--27892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27857 AATGTATGTT
27867 ATAGATATACATA
1 ATAGATATACATA
27880 ATAGATATACATA
1 ATAGATATACATA
27893 TTTGTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAGATATACATA
Found at i:34642 original size:12 final size:12
Alignment explanation
Indices: 34625--34650 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34615 AGGGTTAGAA
34625 AAAAATTCAAGT
1 AAAAATTCAAGT
34637 AAAAATTCAAGT
1 AAAAATTCAAGT
34649 AA
1 AA
34651 TAAACACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAATTCAAGT
Found at i:36834 original size:78 final size:75
Alignment explanation
Indices: 36696--36917 Score: 303
Period size: 70 Copynumber: 3.0 Consensus size: 75
36686 AGTTTTACTT
* * * *
36696 AACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAA---CTATTTT---ATTTTA
1 AACTAAAAACTCTATTTTTATATAA-TAAATCTAATATCCTTATAATTTATATTTTACCATTTTA
36755 CTATTTTAATC
65 CTATTTTAATC
*
36766 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTATCATTT
1 AACTAAAAACTCTATTTTTATATAA-TAAATCTAATATCCTTATAA-T-TTATATTTTACCATTT
*
36831 TACTATTTTACTC
63 TACTATTTTAATC
*
36844 AACTAAAAACTCTATTTTTATATAATAAATCTAATATCCTTATTATTTATATTTTACCATTTTAC
1 AACTAAAAACTCTATTTTTATATAATAAATCTAATATCCTTATAATTTATATTTTACCATTTTAC
36909 TATTTTAAT
66 TATTTTAAT
36918 TAAAAAACTG
Statistics
Matches: 136, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
70 43 0.32
75 32 0.24
76 1 0.01
77 19 0.14
78 41 0.30
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (75 bp):
AACTAAAAACTCTATTTTTATATAATAAATCTAATATCCTTATAATTTATATTTTACCATTTTAC
TATTTTAATC
Done.