Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010059.1 Corchorus capsularis cultivar CVL-1 contig10080, 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: 17319
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:510 original size:75 final size:75
Alignment explanation
Indices: 384--649 Score: 437
Period size: 75 Copynumber: 3.5 Consensus size: 75
374 ATAATAATGT
384 GAATATTTTCTAAATCTTGCCAAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATAAT
1 GAATATTTTCTAAATCTTGCC-AAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATAAT
449 AATAAAGTTGA
65 AATAAAGTTGA
*
460 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAATAAAATAATA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATAATA
525 ATAAAGTTGA
66 ATAAAGTTGA
*
535 GAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAT-AAATAAAT
1 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAT-AAT
*
599 AATAAAGAATGA
65 AATAAAG-TTGA
* *
611 GAATATTTCTCTAAATCTTGCTAGATTGTGGG-GATTTAG
1 GAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAG
650 AAAATATTAA
Statistics
Matches: 180, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
74 4 0.02
75 117 0.65
76 39 0.22
77 20 0.11
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (75 bp):
GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATAATA
ATAAAGTTGA
Found at i:1471 original size:45 final size:46
Alignment explanation
Indices: 1402--1504 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 46
1392 TTTCATCACG
*
1402 ATCGT-TTGGCGGGTTGATTTTTTTATCGCCCTATACCTTTGCATC
1 ATCGTCTTGGCGGGTTGATTTTTTTATCGCCCTATACCTCTGCATC
* * * *
1447 ATCGTCTTGGTGGGTTGA-TTTTTTATTGCCCTCTACCTCTGTATC
1 ATCGTCTTGGCGGGTTGATTTTTTTATCGCCCTATACCTCTGCATC
1492 AGT-GTCTTGGCGG
1 A-TCGTCTTGGCGG
1505 CGATCTTCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 38 0.76
46 12 0.24
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (46 bp):
ATCGTCTTGGCGGGTTGATTTTTTTATCGCCCTATACCTCTGCATC
Found at i:1896 original size:188 final size:188
Alignment explanation
Indices: 1579--2103 Score: 1007
Period size: 188 Copynumber: 2.8 Consensus size: 188
1569 ATTTTTTTTC
*
1579 ATTTTTTTTCACTCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTA-CCGCCCTCTACCATGC
1 ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTATCC-CCCTCTACCATGC
*
1643 ATTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGTGTGACTGAATTTAGCTTAAGATTTG
65 ATTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTG
1708 TCCTACGTACCTCCTTGGGATTATCACGCCAACCTCCTACCTCTGAATCGGCGGGGTTG
130 TCCTACGTACCTCCTTGGGATTATCACGCCAACCTCCTACCTCTGAATCGGCGGGGTTG
*
1767 ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGAGGTTGATTTTTTATCCCCCTCTACCATGCA
1 ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTATCCCCCTCTACCATGCA
1832 TTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTGT
66 TTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTGT
1897 CCTACGTACCTCCTTGGGATTATCACGCCAACCTCCTACCTCTGAATCGGCGGGGTTG
131 CCTACGTACCTCCTTGGGATTATCACGCCAACCTCCTACCTCTGAATCGGCGGGGTTG
1955 ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTATCCCCCTCTACCATGCA
1 ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTATCCCCCTCTACCATGCA
2020 TTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTGT
66 TTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTGT
2085 CCTACGTACCTCCTTGGGA
131 CCTACGTACCTCCTTGGGA
2104 GAAGGATCAA
Statistics
Matches: 332, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 330 0.99
189 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.39
Consensus pattern (188 bp):
ATTTTTTTTCACCCTCTACCTCGACGTCTTGGCGGGGTTGATTTTTTATCCCCCTCTACCATGCA
TTGGCGTTTTGGCCATGAGTGTCATTTGTTTTTTGTTGCGTGACTGAATTTAGCTTAAGATTTGT
CCTACGTACCTCCTTGGGATTATCACGCCAACCTCCTACCTCTGAATCGGCGGGGTTG
Found at i:2514 original size:15 final size:15
Alignment explanation
Indices: 2494--2525 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2484 TCATTTTTCC
2494 ATTCATCCTTAAGCA
1 ATTCATCCTTAAGCA
*
2509 ATTCATCTTTAAGCA
1 ATTCATCCTTAAGCA
2524 AT
1 AT
2526 GTTTTTGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (15 bp):
ATTCATCCTTAAGCA
Found at i:3700 original size:7 final size:7
Alignment explanation
Indices: 3688--3717 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3678 ACTAGTGTGT
3688 ATATATA
1 ATATATA
3695 ATATATA
1 ATATATA
3702 ATATATA
1 ATATATA
3709 ATATATA
1 ATATATA
3716 AT
1 AT
3718 TAAGTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:4818 original size:27 final size:27
Alignment explanation
Indices: 4780--4838 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
4770 AACAACCAAC
*
4780 CATATTTGGCAAAGGAGAATCTAGAGT
1 CATATTTGGCAAAGGAGAATCTACAGT
4807 CATATTTGGCAAAGGAGAATCTACAGT
1 CATATTTGGCAAAGGAGAATCTACAGT
*
4834 AATAT
1 CATAT
4839 GATAAGTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (27 bp):
CATATTTGGCAAAGGAGAATCTACAGT
Found at i:5540 original size:105 final size:106
Alignment explanation
Indices: 5381--5592 Score: 293
Period size: 105 Copynumber: 2.0 Consensus size: 106
5371 TATTATTAAT
* * * *
5381 ATTATTTTCGGAAGTAATTAATAGTATTATCTAGCAATCCTAACCTTTAAAGGGAAATCCTAACC
1 ATTATTATCGGAAGTAATTAATAATATTAACTAGCAATCCTAACCCTTAAAGGGAAATCCTAACC
*
5446 CTTCACCTACTAGGATTTGAAGACTATAAATATT-AAGTAG
66 CTTCACCTACTAGGATTTCAAGACTATAAATATTAAAGTAG
* * * **
5486 ATTATTATCGGAATTAATTAATTAATATTAACTAGCAATCCTAGCCCTT-GAGGGATTTCCTAAC
1 ATTATTATCGGAAGTAATTAA-TAATATTAACTAGCAATCCTAACCCTTAAAGGGAAATCCTAAC
* *
5550 CCTTCACTTACTGGGATTTCAAGACTATAAATATTAAAGTAG
65 CCTTCACCTACTAGGATTTCAAGACTATAAATATTAAAGTAG
5592 A
1 A
5593 GCCTATATAC
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 63 0.68
106 30 0.32
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (106 bp):
ATTATTATCGGAAGTAATTAATAATATTAACTAGCAATCCTAACCCTTAAAGGGAAATCCTAACC
CTTCACCTACTAGGATTTCAAGACTATAAATATTAAAGTAG
Found at i:6843 original size:215 final size:215
Alignment explanation
Indices: 6472--6901 Score: 860
Period size: 215 Copynumber: 2.0 Consensus size: 215
6462 ATGATGGCAA
6472 AAATGATTATATTCTTTTTAATGTTGGAACCTTGGAAAAAATTCAACTCCCGTTCGACATGGATG
1 AAATGATTATATTCTTTTTAATGTTGGAACCTTGGAAAAAATTCAACTCCCGTTCGACATGGATG
6537 ATCCGTATGCCGTCCTTATGACAGCAACTCCTCCTAATGGTCATATCGTGTTCATGAAAGCAAAG
66 ATCCGTATGCCGTCCTTATGACAGCAACTCCTCCTAATGGTCATATCGTGTTCATGAAAGCAAAG
6602 GGCAATCATGAAGAATGCATATTTCAGTTCTGTTGTCCAGGTGATTATACATTTTCTATTGAGAC
131 GGCAATCATGAAGAATGCATATTTCAGTTCTGTTGTCCAGGTGATTATACATTTTCTATTGAGAC
6667 CATCGACTCATTCCCTCAAG
196 CATCGACTCATTCCCTCAAG
6687 AAATGATTATATTCTTTTTAATGTTGGAACCTTGGAAAAAATTCAACTCCCGTTCGACATGGATG
1 AAATGATTATATTCTTTTTAATGTTGGAACCTTGGAAAAAATTCAACTCCCGTTCGACATGGATG
6752 ATCCGTATGCCGTCCTTATGACAGCAACTCCTCCTAATGGTCATATCGTGTTCATGAAAGCAAAG
66 ATCCGTATGCCGTCCTTATGACAGCAACTCCTCCTAATGGTCATATCGTGTTCATGAAAGCAAAG
6817 GGCAATCATGAAGAATGCATATTTCAGTTCTGTTGTCCAGGTGATTATACATTTTCTATTGAGAC
131 GGCAATCATGAAGAATGCATATTTCAGTTCTGTTGTCCAGGTGATTATACATTTTCTATTGAGAC
6882 CATCGACTCATTCCCTCAAG
196 CATCGACTCATTCCCTCAAG
6902 GCGTCGTAAC
Statistics
Matches: 215, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 215 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (215 bp):
AAATGATTATATTCTTTTTAATGTTGGAACCTTGGAAAAAATTCAACTCCCGTTCGACATGGATG
ATCCGTATGCCGTCCTTATGACAGCAACTCCTCCTAATGGTCATATCGTGTTCATGAAAGCAAAG
GGCAATCATGAAGAATGCATATTTCAGTTCTGTTGTCCAGGTGATTATACATTTTCTATTGAGAC
CATCGACTCATTCCCTCAAG
Found at i:15219 original size:4 final size:4
Alignment explanation
Indices: 15184--15229 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
15174 AAATCATTAA
* *
15184 AAAG AAAAG AAA- AAA- AAAG AAGG AAAG CAAG AAAG AAAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
15230 AGTTTGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
3 6 0.17
4 26 0.72
5 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:15488 original size:2 final size:2
Alignment explanation
Indices: 15471--15504 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
15461 AAGGTTTTAC
15471 TA TA TA T- TA TA T- TA TA 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
15505 ATCCAACCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17298 original size:2 final size:2
Alignment explanation
Indices: 17293--17319 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17283 ATGACTGATC
17293 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.