Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014730.1 Corchorus capsularis cultivar CVL-1 contig14751, 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: 11534
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2908 original size:110 final size:111
Alignment explanation
Indices: 2702--2919 Score: 411
Period size: 110 Copynumber: 2.0 Consensus size: 111
2692 TTGTAAGATT
*
2702 CCATTGACAATCTTGATTCTGATTTGGTACGGTTGTTTAGAACTTATTGTAGTTTTGCTGGAATA
1 CCATTGACAATCTTGATTCTGATTTGGTACGGTTCTTTAGAACTTATTGTAGTTTTGCTGGAATA
*
2767 TGTGAATTTTGTGTATGATTAGTGCATTTTGAATATGTGAATTTTG
66 TGTGAATTTTGTGTATGATCAGTGCATTTTGAATATGTGAATTTTG
2813 CCATTGACAATCTTGATTCTGATTTGGTACGGTTCTTTAGAACTTATT-TAGTTTTGCTGGAATA
1 CCATTGACAATCTTGATTCTGATTTGGTACGGTTCTTTAGAACTTATTGTAGTTTTGCTGGAATA
2877 TGTGAATTTTGTGTATGATCAGTGCATTTTGAATATGTGAATT
66 TGTGAATTTTGTGTATGATCAGTGCATTTTGAATATGTGAATT
2920 GTGACAAGTT
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 58 0.55
111 47 0.45
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (111 bp):
CCATTGACAATCTTGATTCTGATTTGGTACGGTTCTTTAGAACTTATTGTAGTTTTGCTGGAATA
TGTGAATTTTGTGTATGATCAGTGCATTTTGAATATGTGAATTTTG
Found at i:3897 original size:21 final size:21
Alignment explanation
Indices: 3850--3932 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
3840 AGCAACGATT
* *
3850 GCTTATTTGCAT-GGCTACGA
1 GCTTATTTCCATATGCTACGA
* *
3870 ACATA-TTCCTATATGCTACGA
1 GCTTATTTCC-ATATGCTACGA
* *
3891 GCTTATTTGCATTTGCTACGA
1 GCTTATTTCCATATGCTACGA
* *
3912 GCTTTATTTACATTTGCTACG
1 GC-TTATTTCCATATGCTACG
3933 GACATTATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.06
20 5 0.10
21 22 0.44
22 20 0.40
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (21 bp):
GCTTATTTCCATATGCTACGA
Found at i:3925 original size:22 final size:21
Alignment explanation
Indices: 3883--3932 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
3873 TATTCCTATA
*
3883 TGCTACGAGCTTATTTGCATT
1 TGCTACGAGCTTATTTACATT
3904 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGC-TTATTTACATT
3926 TGCTACG
1 TGCTACG
3933 GACATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACATT
Found at i:3940 original size:22 final size:22
Alignment explanation
Indices: 3883--3942 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
3873 TATTCCTATA
*
3883 TGCTACGAGC-TTATTTGCATT
1 TGCTACGAGCATTATTTACATT
*
3904 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGCATTATTTACATT
3926 TGCTACG-GACATTATTT
1 TGCTACGAG-CATTATTT
3943 TAGGGTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (22 bp):
TGCTACGAGCATTATTTACATT
Found at i:9019 original size:155 final size:155
Alignment explanation
Indices: 8753--9071 Score: 622
Period size: 155 Copynumber: 2.1 Consensus size: 155
8743 AATATATTAA
8753 TTAAACTA-GAAAACAATTAAAAGAAATCTAAACTAAAGATTTAGAAGAGAATTTAGTAAAAACA
1 TTAAA-TACGAAAACAATTAAAAGAAATCTAAACTAAAGATTTAGAAGAGAATTTAGTAAAAACA
8817 ATGAATAAAAACATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATCTATGGTGGGACTTTTG
65 ATGAATAAAAACATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATCTATGGTGGGACTTTTG
8882 TTCTTAATAATTTGAGCTTTTTCTGT
130 TTCTTAATAATTTGAGCTTTTTCTGT
8908 TTAAATACGAAAACAATTAAAAGAAATCTAAACTAAAGATTTAGAAGAGAATTTAGTAAAAACAA
1 TTAAATACGAAAACAATTAAAAGAAATCTAAACTAAAGATTTAGAAGAGAATTTAGTAAAAACAA
8973 TGAATAAAAACATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATCTATGGTGGGACTTTTGT
66 TGAATAAAAACATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATCTATGGTGGGACTTTTGT
9038 TCTTAATAATTTGAGCTTTTTCTGT
131 TCTTAATAATTTGAGCTTTTTCTGT
9063 TTAAATACG
1 TTAAATACG
9072 TTTCTTATCT
Statistics
Matches: 163, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
154 2 0.01
155 161 0.99
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (155 bp):
TTAAATACGAAAACAATTAAAAGAAATCTAAACTAAAGATTTAGAAGAGAATTTAGTAAAAACAA
TGAATAAAAACATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATCTATGGTGGGACTTTTGT
TCTTAATAATTTGAGCTTTTTCTGT
Done.