Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005316.1 Corchorus capsularis cultivar CVL-1 contig05334, 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: 5490
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Found at i:971 original size:139 final size:141
Alignment explanation
Indices: 826--1157 Score: 544
Period size: 141 Copynumber: 2.4 Consensus size: 141
816 AAGTTAGTGA
* *
826 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
*
890 CGCTA-CAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
66 CGCCACCAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
954 TATTGAACATG
131 TATTGAACATG
965 TCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
1 TCGTTAGTTAATTTT-TCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
* * *
1029 TTGCCACCAAAAAGATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
65 TCGCCACCAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
1094 TTATTGAACATG
130 TTATTGAACATG
* * * *
1106 TTGTTAGTTAATTTTGCCAATCAAAATTGTAATTGATTGATGATTATCTAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAAT
1158 CAAAGTTGTA
Statistics
Matches: 179, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
139 56 0.31
140 8 0.04
141 115 0.64
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (141 bp):
TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
CGCCACCAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
TATTGAACATG
Found at i:1541 original size:19 final size:19
Alignment explanation
Indices: 1517--1557 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1507 GTAAAAGTAG
1517 TAATCAATAAATTGATAAT
1 TAATCAATAAATTGATAAT
*
1536 TAATCAGTAAATTGATAAT
1 TAATCAATAAATTGATAAT
1555 TAA
1 TAA
1558 AAGAGGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (19 bp):
TAATCAATAAATTGATAAT
Found at i:1595 original size:40 final size:40
Alignment explanation
Indices: 1536--1665 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
1526 AATTGATAAT
*
1536 TAATCAGTAAATTGATAATTAAAAGAGGAAGTAAAAGTAG
1 TAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAAGTAG
* * ** * * * *
1576 TAATCAGTAAA-TCAGTAATTAAGAGTCAAGGTAAAGGGAT
1 TAATCAGTAAATTGA-TAATTAAAAGAGAAAGTAAAAGTAG
* *
1616 TAATCAGTAAATTGATAATTAAGAGAGAAAGTAAAACTAG
1 TAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAAGTAG
*
1656 TAACCAGTAA
1 TAATCAGTAA
1666 TTAAGAAAGG
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 2 0.03
40 66 0.94
41 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (40 bp):
TAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAAGTAG
Found at i:1596 original size:59 final size:58
Alignment explanation
Indices: 1483--1597 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 58
1473 AGGATTAACT
* *
1483 AGTAAATTGATAATTAAGAGAGGAGTAAAAGTAGTAATCAATAAATTGATAATTAATC
1 AGTAAATTGATAATTAAAAGAGGAGTAAAAGTAGTAATCAATAAATAGATAATTAATC
*
1541 AGTAAATTGATAATTAAAAGAGGAAGTAAAAGTAGTAATCAGTAAATCAG-TAATTAA
1 AGTAAATTGATAATTAAAAGAGG-AGTAAAAGTAGTAATCAATAAAT-AGATAATTAA
1598 GAGTCAAGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 22 0.42
59 29 0.56
60 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.28
Consensus pattern (58 bp):
AGTAAATTGATAATTAAAAGAGGAGTAAAAGTAGTAATCAATAAATAGATAATTAATC
Found at i:1667 original size:32 final size:32
Alignment explanation
Indices: 1631--1715 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
1621 AGTAAATTGA
* * *
1631 TAATTAAGAGAGAAAGTAAAACTAGTAACCAG
1 TAATTAAGAAAGGAAGTAAAACGAGTAACCAG
* * *
1663 TAATTAAGAAAGGAAGTAAAAGGATTAATCAG
1 TAATTAAGAAAGGAAGTAAAACGAGTAACCAG
1695 TAATTAAGAAAGGAAGTAAAA
1 TAATTAAGAAAGGAAGTAAAA
1716 ATGACTAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (32 bp):
TAATTAAGAAAGGAAGTAAAACGAGTAACCAG
Found at i:2413 original size:7 final size:7
Alignment explanation
Indices: 2401--2431 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2391 TGCCTTAATC
2401 TATACTA
1 TATACTA
2408 TATACTA
1 TATACTA
2415 TATACTA
1 TATACTA
2422 TATA-TA
1 TATACTA
2428 TATA
1 TATA
2432 ACATAAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (7 bp):
TATACTA
Found at i:4199 original size:13 final size:13
Alignment explanation
Indices: 4181--4205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4171 TTTCCTTCTT
4181 CAGTCCATTTTTC
1 CAGTCCATTTTTC
4194 CAGTCCATTTTT
1 CAGTCCATTTTT
4206 GTTGGGTCCG
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Done.