Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018268.1 Corchorus olitorius cultivar O-4 contig18301, 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: 17545
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:3413 original size:30 final size:31
Alignment explanation
Indices: 3365--3424 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3355 TGGTTAATTA
* *
3365 AGTCCCAAACGTTGCAAAATCGGCTCAAATC
1 AGTCCCAAACGTTACAAAATCGACTCAAATC
3396 AGTCCC-AACGTTACAAAATCGACTCAAAT
1 AGTCCCAAACGTTACAAAATCGACTCAAAT
3425 ATAAGTCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.20
Consensus pattern (31 bp):
AGTCCCAAACGTTACAAAATCGACTCAAATC
Found at i:8905 original size:1 final size:1
Alignment explanation
Indices: 8899--8948 Score: 91
Period size: 1 Copynumber: 50.0 Consensus size: 1
8889 CCTCGTCTAT
*
8899 AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8949 CCCCAAGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:12159 original size:18 final size:18
Alignment explanation
Indices: 12136--12173 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12126 TCACGTTTCT
12136 TTTCTAGGTCTCTTTTTG
1 TTTCTAGGTCTCTTTTTG
12154 TTTCTAGGTCTCTTTTTG
1 TTTCTAGGTCTCTTTTTG
12172 TT
1 TT
12174 GGTTGCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.16, G:0.16, T:0.63
Consensus pattern (18 bp):
TTTCTAGGTCTCTTTTTG
Found at i:13391 original size:2 final size:2
Alignment explanation
Indices: 13384--13408 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13374 GCTCAAAGAC
13384 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13409 AGTGATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13575 original size:31 final size:29
Alignment explanation
Indices: 13534--13701 Score: 119
Period size: 31 Copynumber: 5.6 Consensus size: 29
13524 TTTGGCTAAT
13534 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-T-AAAA
* * * **
13565 TGATCAAATAAGGGTCCGATC-TTTTAATT
1 TGCTCAAATAAGGG-CCTAACGTTTTAAAA
13594 TGGC-CAAATAAGGGCCTAACGTTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TT-AAAA
* * * **
13625 TGCTCAAATAAGAGCTCGATC-TTTTAATT
1 TGCTCAAATAAGGGC-CTAACGTTTTAAAA
*
13654 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTT--TAAAA
13685 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
13702 GACATCAGTT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 7 0.07
29 31 0.30
30 12 0.12
31 47 0.45
32 7 0.07
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACGTTTTAAAA
Found at i:13632 original size:60 final size:59
Alignment explanation
Indices: 13538--13699 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 59
13528 GCTAATTGCT
* *
13538 CAAATAAGGGCCTAACGTTTGTCAAAATGATCAAATAAGGG-TCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTT-TGAAAATGCTCAAATAAGGGCT-CGATCTTTTAATTTGGC
*
13598 CAAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGAGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTT-TTGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
13658 CAAATAAGGGCCTAACG-TTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTTG--AAAATGCTCAAATAAGGGC
13700 CTGACATCAG
Statistics
Matches: 94, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 88 0.94
61 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTTGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:13665 original size:29 final size:28
Alignment explanation
Indices: 13569--13665 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
13559 TCAAAATGAT
*
13569 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGAG-CCGATCTTTTAATTTGGC
* * * **
13598 CAAATAAGGGCCTAACGTTATTGAAAAT-GC
1 CAAATAAGAGCCGATC-TT-TT-AATTTGGC
13628 TCAAATAAGAGCTCGATCTTTTAATTTGGC
1 -CAAATAAGAGC-CGATCTTTTAATTTGGC
13658 CAAATAAG
1 CAAATAAG
13666 GGCCTAACGT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.08
29 23 0.43
30 8 0.15
31 15 0.28
32 3 0.06
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (28 bp):
CAAATAAGAGCCGATCTTTTAATTTGGC
Found at i:13892 original size:59 final size:59
Alignment explanation
Indices: 13744--13907 Score: 267
Period size: 60 Copynumber: 2.7 Consensus size: 59
13734 GATGTCAAGC
* *
13744 CCTTATTTGAGCATTTTGATAAACGTTAGGCCCTTATTTGGGCAAATTAAAAGATCGGGT
1 CCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTT-GGCAAATTAAAAGATCAGGT
*
13804 CCTTATTTGAGCATTTTGGTAAACATTAGGCCCTTATTTGGCTAAATTAAAAGATCAGG-
1 CCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTGGC-AAATTAAAAGATCAGGT
13863 CCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTGAGCAA
1 CCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTG-GCAA
13908 TTAGCCATAA
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
59 44 0.45
60 54 0.55
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTGGCAAATTAAAAGATCAGGT
Found at i:15977 original size:2 final size:2
Alignment explanation
Indices: 15970--15997 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15960 CTTTCAATGT
15970 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
15998 GAGTTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.