Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006086.1 Corchorus capsularis cultivar CVL-1 contig06104, 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: 13781
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:651 original size:7 final size:7
Alignment explanation
Indices: 639--705 Score: 53
Period size: 7 Copynumber: 8.7 Consensus size: 7
629 AATTAAATAT
639 AATATAA
1 AATATAA
646 AATATAA
1 AATATAA
653 ATATATAA
1 A-ATATAA
661 TATATATAA
1 -A-ATATAA
*
670 CATATAA
1 AATATAA
*
677 ATTATAA
1 AATATAA
*
684 TATATATAT
1 -A-ATATAA
693 AATATATA
1 AATATA-A
701 AATAT
1 AATAT
706 CTTTAGTCGG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
7 24 0.49
8 13 0.27
9 12 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (7 bp):
AATATAA
Found at i:682 original size:25 final size:24
Alignment explanation
Indices: 632--703 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
622 ATAAACAAAT
632 TAAATATAATATAAAATATAAA-TA
1 TAAATAT-ATATAAAATATAAATTA
*
656 TATAATATATATAACATATAAATTA
1 TA-AATATATATAAAATATAAATTA
*
681 TAATATATATATAATATATAAAT
1 TAA-ATATATATAAAATATAAAT
704 ATCTTTAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 16 0.37
25 27 0.63
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATATATAAAATATAAATTA
Found at i:686 original size:23 final size:23
Alignment explanation
Indices: 615--703 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
605 ATTCTAATAT
* *
615 TATATATATAA-ACAAATTA-AA
1 TATATATAAAATATAAATTATAA
636 TATAATATAAAATATAAATATATAA
1 TAT-ATATAAAATATAAAT-TATAA
*
661 TATATATAACATATAAATTATAA
1 TATATATAAAATATAAATTATAA
684 TATATATATAATATATAAAT
1 TATATATA-AA-ATATAAAT
704 ATCTTTAGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
21 3 0.05
22 7 0.12
23 18 0.31
24 17 0.29
25 13 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATATAAAATATAAATTATAA
Found at i:1805 original size:55 final size:55
Alignment explanation
Indices: 1738--1851 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
1728 CAGGTGCGGC
* ** *
1738 TAAATCTAAATTGGGTTTGTGAGTTGCTGGTACTATTTTCATTCTTTCTATTCAA
1 TAAATATAAATTGGGTTTGCAAGTTGCTGGTACTAGTTTCATTCTTTCTATTCAA
*
1793 TAAATATAAATTGGGTTTGCAAGTTGTTGGTACTAGTTTCATTCTTTCTATTCAA
1 TAAATATAAATTGGGTTTGCAAGTTGCTGGTACTAGTTTCATTCTTTCTATTCAA
1848 TAAA
1 TAAA
1852 ATTTTCGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (55 bp):
TAAATATAAATTGGGTTTGCAAGTTGCTGGTACTAGTTTCATTCTTTCTATTCAA
Found at i:2222 original size:30 final size:30
Alignment explanation
Indices: 2150--2223 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
2140 AAGTTCATTT
* * *
2150 TATCCTGAATTGACACAATCCGATAATGTTA
1 TATCCTGAATTGACACAAT-CAATAACGATA
* *
2181 TATCCTCAATTGACACAAAT-AATAACGATG
1 TATCCTGAATTGACAC-AATCAATAACGATA
2211 TATCCTGAATTGA
1 TATCCTGAATTGA
2224 ATTTTGGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 18 0.50
31 15 0.42
32 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (30 bp):
TATCCTGAATTGACACAATCAATAACGATA
Found at i:10499 original size:59 final size:61
Alignment explanation
Indices: 10405--10520 Score: 173
Period size: 59 Copynumber: 1.9 Consensus size: 61
10395 TGAAAAGTGG
**
10405 TGACAATTGATTTCTTTTATGGTCTAACATATATCAG-A-AACAAAGTTCCAAAAAGACAA
1 TGACAATTGATTTCGATTATGGTCTAACATATATCAGAACAACAAAGTTCCAAAAAGACAA
* *
10464 TGACAATTGATTTCGATTATGGTCTAACTTGTATCAGAACCAACAAAGTTCCAAAAA
1 TGACAATTGATTTCGATTATGGTCTAACATATATCAGAA-CAACAAAGTTCCAAAAA
10521 TATCAGAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 33 0.66
60 1 0.02
62 16 0.32
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (61 bp):
TGACAATTGATTTCGATTATGGTCTAACATATATCAGAACAACAAAGTTCCAAAAAGACAA
Found at i:13482 original size:2 final size:2
Alignment explanation
Indices: 13475--13513 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
13465 CTGCTAAAGC
*
13475 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13514 AACTTTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Done.