Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003748.1 Corchorus capsularis cultivar CVL-1 contig03756, 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: 2507
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:119 original size:20 final size:19
Alignment explanation
Indices: 89--133 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
79 TTCTTTTTTT
*
89 TAAAAAAAATA-AATTTCAA
1 TAAAAAAAATATAA-TGCAA
108 TAAAATAAAATATAATGCAA
1 TAAAA-AAAATATAATGCAA
128 TAAAAA
1 TAAAAA
134 TATTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAAAAATATAATGCAA
Found at i:737 original size:22 final size:22
Alignment explanation
Indices: 712--917 Score: 74
Period size: 22 Copynumber: 9.4 Consensus size: 22
702 GTTGTGAAAG
712 TTTGATAACCACACTATAAAAT
1 TTTGATAACCACACTATAAAAT
** * *
734 TTTGATAACGTTC-TTATGAAAT
1 TTTGATAAC-CACACTATAAAAT
** *
756 TTTGATAACTTC-CAATGAAAAT
1 TTTGATAACCACACTAT-AAAAT
* * * *
778 TTTGGTAATCACAGTATACAAT
1 TTTGATAACCACACTATAAAAT
* ** * *
800 TTTAATAACTTCCCTATGAAAT
1 TTTGATAACCACACTATAAAAT
* * *
822 TTTGATAACAACATTATGAAAT
1 TTTGATAACCACACTATAAAAT
** * * ***
844 TGCGATAATCACACAACCGAAT
1 TTTGATAACCACACTATAAAAT
* * * * *
866 TATGATAATCTCAGTATGAAAT
1 TTTGATAACCACACTATAAAAT
** *
888 TTTGATAAGAATACTATAAAAT
1 TTTGATAACCACACTATAAAAT
910 TTTGATAA
1 TTTGATAA
918 TTTCCTTAGG
Statistics
Matches: 129, Mismatches: 52, Indels: 6
0.69 0.28 0.03
Matches are distributed among these distances:
21 5 0.04
22 121 0.94
23 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTGATAACCACACTATAAAAT
Found at i:844 original size:66 final size:65
Alignment explanation
Indices: 706--844 Score: 147
Period size: 66 Copynumber: 2.1 Consensus size: 65
696 AAACTCGTTG
* * * **
706 TGAAAGTTTGATAACCACACTATAAAATTTTGATAACGTTCTTATGAAATTTTGATAACTTCCAA
1 TGAAATTTTGATAACCACACTATAAAATTTTAATAACGTTCCTATGAAATTTTGATAACTAACAA
* * * *
771 TGAAAATTTTGGTAATCACAGTATACAATTTTAATAAC-TTCCCTATGAAATTTTGATAAC-AAC
1 TG-AAATTTTGATAACCACACTATAAAATTTTAATAACGTT-CCTATGAAATTTTGATAACTAAC
834 ATTA
64 A--A
838 TGAAATT
1 TGAAATT
845 GCGATAATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
65 6 0.10
66 52 0.85
67 3 0.05
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (65 bp):
TGAAATTTTGATAACCACACTATAAAATTTTAATAACGTTCCTATGAAATTTTGATAACTAACAA
Found at i:1252 original size:16 final size:16
Alignment explanation
Indices: 1183--1245 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
1173 CGGGCTCGGG
*
1183 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
*
1198 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
1214 CGGGTTCGGGTAGTGT
1 CGGGTTCGGGTATTTT
1230 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
1246 TCGGTTCAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 11 0.28
16 29 0.73
ACGTcount: A:0.08, C:0.14, G:0.40, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:1252 original size:32 final size:31
Alignment explanation
Indices: 1183--1245 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
1173 CGGGCTCGGG
1183 CGGGTTCGGGTACTTCAGGTTCGGGTATTTT
1 CGGGTTCGGGTACTTCAGGTTCGGGTATTTT
* *
1214 CGGGTTCGGGTAGTGTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTACT-TCAGGTTCGGGTATTTT
1246 TCGGTTCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.08, C:0.14, G:0.40, T:0.38
Consensus pattern (31 bp):
CGGGTTCGGGTACTTCAGGTTCGGGTATTTT
Found at i:1291 original size:23 final size:22
Alignment explanation
Indices: 1256--1304 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1246 TCGGTTCAGT
1256 CTCGGTTCGGTCTC-AGGTCGGG
1 CTCGGTTCGGTCTCGA-GTCGGG
*
1278 CTCGGATTTGGTCTCGAGTCGGG
1 CTCGG-TTCGGTCTCGAGTCGGG
1301 -TCGG
1 CTCGG
1305 GCTCGGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 14 0.58
24 1 0.04
ACGTcount: A:0.06, C:0.24, G:0.41, T:0.29
Consensus pattern (22 bp):
CTCGGTTCGGTCTCGAGTCGGG
Found at i:1773 original size:31 final size:31
Alignment explanation
Indices: 1738--1809 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
1728 TAAGTTATTG
*
1738 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
1769 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
1800 CAAATTAAAA
1 CAAATTAAAA
1810 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:2042 original size:2 final size:2
Alignment explanation
Indices: 2035--2064 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2025 TTGCTTAAGT
2035 TA TA TA TA 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
2065 GTTGTTTAGC
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):
TA
Done.