Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016497.1 Corchorus capsularis cultivar CVL-1 contig16518, 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: 3949
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Found at i:166 original size:46 final size:46
Alignment explanation
Indices: 116--210 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
106 CACAATTATC
116 TCATCAATTAATTGATTAATGAATTGATTAATTTCATTGTTAAATG
1 TCATCAATTAATTGATTAATGAATTGATTAATTTCATTGTTAAATG
162 TCATCAATTAATTGATTAATGAATTGATTAATTTCATTGTTAAATG
1 TCATCAATTAATTGATTAATGAATTGATTAATTTCATTGTTAAATG
208 TCA
1 TCA
211 ATCTCATTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (46 bp):
TCATCAATTAATTGATTAATGAATTGATTAATTTCATTGTTAAATG
Found at i:1351 original size:138 final size:137
Alignment explanation
Indices: 1113--1450 Score: 457
Period size: 138 Copynumber: 2.4 Consensus size: 137
1103 CCAAAAGCTA
* * * *
1113 ATGATTATTTAATTTTGCCACAAATAAATGAATCAATTAGTATTATGTTACAAAAAAATAAATTG
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTATTATGTTAC--CAAAA-AAATTG
* *
1178 ATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTT-AGTTAACTTT-TCCAATCAAAGT
63 ATTGAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGA-TCAACTTTGT-CAATCAAAGT
1241 TATAATTGATGG
126 TATAATTGATGG
* *
1253 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTATTTATATTACCAAAAAAATTGAT
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTA-TTATGTTACCAAAAAAATTGAT
* * *
1318 TGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTGATCAACTTTGTCAATCAAAGTTATA
65 TGAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGTCAATCAAAGTTATA
*
1383 ATTGATTG
130 ATTGATGG
* *
1391 ATGATTATTTGATTTTGT-CATAAATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAA
1 ATGATTATTT-ATTTTTTCCATAAATAAATGAATCAATTAGT-ATTATGTTACCAAAAAAA
1451 AAAATAGATT
Statistics
Matches: 177, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
138 118 0.67
139 13 0.07
140 38 0.21
141 8 0.05
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (137 bp):
ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTATTATGTTACCAAAAAAATTGATT
GAACATCCAAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGTCAATCAAAGTTATAA
TTGATGG
Found at i:1947 original size:141 final size:140
Alignment explanation
Indices: 1665--2137 Score: 779
Period size: 141 Copynumber: 3.4 Consensus size: 140
1655 AAGTTAGTGA
* * *
1665 TCGTTAGTTAATTTT-TCCAATCAAAGTTATAATTGATTGATAATTATTTAATTTTACCAT-AAA
1 TCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
* *
1728 TCGCTACAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
65 TCGCCACAAAAAAATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
1793 TATTGAACATG
130 TATTGAACATG
* * *
1804 TCGTTAGTTAATTTTGTCAATCAAAGTTTTAATTGAATAATGATTATATAATTTTACCATAAAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
*
1869 CGCCACAAAAAATATTACCATAAATAAATAAATCGATTAGTAATTATGTTACCAAAAAAATAAAT
66 CGCCACAAAAAA-ATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
1934 TATTGAACATG
130 TATTGAACATG
1945 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
*
2010 CGCCACCAAAAAGATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
66 CGCCA-CAAAAAAATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
2075 TATTGAACATG
130 TATTGAACATG
* * * *
2086 TTGTTAATTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATCTAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAAT
2138 CAAAGTTGTA
Statistics
Matches: 313, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
139 53 0.17
140 16 0.05
141 238 0.76
142 6 0.02
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (140 bp):
TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
CGCCACAAAAAAATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATT
ATTGAACATG
Found at i:3530 original size:13 final size:13
Alignment explanation
Indices: 3512--3536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3502 TAAAGGCATT
3512 TATTGCATTAATA
1 TATTGCATTAATA
3525 TATTGCATTAAT
1 TATTGCATTAAT
3537 TTTCCTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
TATTGCATTAATA
Found at i:3700 original size:32 final size:32
Alignment explanation
Indices: 3664--3765 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
3654 TTTCTTTCTA
3664 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT
1 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT
* * *
3696 CATTGTG-TTTCTCATTTACTTA-TTA--CT-AA
1 CATTGGGTTTTC-CATTT-CTTAGTTATGTTCAT
*
3725 C-TTGGATTTTCCATTTCTTAGTTATGTTCAT
1 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT
*
3756 CATTGTGTTT
1 CATTGGGTTT
3766 CTCATATACT
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
27 4 0.08
28 11 0.21
29 6 0.11
30 2 0.04
31 6 0.11
32 20 0.38
33 4 0.08
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.54
Consensus pattern (32 bp):
CATTGGGTTTTCCATTTCTTAGTTATGTTCAT
Found at i:3764 original size:60 final size:60
Alignment explanation
Indices: 3666--3788 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
3656 TCTTTCTACA
* *
3666 TTGGGTTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATTTACTTATTACTAAC
1 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC
*
3726 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTAGTAAC
1 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC
3786 TTG
1 TTG
3789 CAATTGATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (60 bp):
TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC
Done.