Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011014.1 Corchorus capsularis cultivar CVL-1 contig11035, 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: 27025
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:524 original size:31 final size:29
Alignment explanation
Indices: 486--684 Score: 163
Period size: 31 Copynumber: 6.6 Consensus size: 29
476 TTAGACTAAT
*
486 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT--TAAAA
* * **
517 TGCTCAAATAAGGGTCCGATC-TTTTAATT
1 TGCTCAAATAAGGG-CCTAACGTTTTAAAA
546 TGGC-CAAATAAGGGCCTAACGTTATCTAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-T-TAAAA
* **
577 TGCTCAAATAAGGGCCTGATC-TTTTAATT
1 TGCTCAAATAAGGGCCT-AACGTTTTAAAA
*
606 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-T-TAAAA
* *
637 TACTCAAATAAGGGCCTAATGTTATTGAAAA
1 TGCTCAAATAAGGGCCTAACGTT-TT-AAAA
668 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
685 GGTGTCAGTT
Statistics
Matches: 135, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
28 6 0.04
29 34 0.25
30 10 0.07
31 79 0.59
32 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACGTTTTAAAA
Found at i:555 original size:60 final size:60
Alignment explanation
Indices: 490--653 Score: 269
Period size: 60 Copynumber: 2.7 Consensus size: 60
480 ACTAATTGCT
490 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGTCC-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CCAAAATGCTCAAATAAGGG-CCTGATCTTTTAATTTGGC
*
550 CAAATAAGGGCCTAACGTTATCTAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
* *
610 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCCT
1 CAAATAAGGGCCTAACGTTATCCAAAATGCTCAAATAAGGGCCT
654 AATGTTATTG
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
59 2 0.02
60 96 0.97
61 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:622 original size:29 final size:29
Alignment explanation
Indices: 521--622 Score: 111
Period size: 29 Copynumber: 3.4 Consensus size: 29
511 CCAAAATGCT
521 CAAATAAGGGTCC-GATCTTTTAATTTGGC
1 CAAATAAGGG-CCTGATCTTTTAATTTGGC
* **
550 CAAATAAGGGCCT-AACGTTATCTAAAAT-GC
1 CAAATAAGGGCCTGATC-TT-T-TAATTTGGC
580 TCAAATAAGGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTTGGC
610 CAAATAAGGGCCT
1 CAAATAAGGGCCT
623 AACGTTATCG
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
28 4 0.07
29 29 0.48
30 6 0.10
31 19 0.32
32 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:805 original size:59 final size:60
Alignment explanation
Indices: 711--875 Score: 253
Period size: 59 Copynumber: 2.8 Consensus size: 60
701 ACGCATGAGA
* *
711 CAGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTCAAAGAT
1 CAGGCCCTTATTTAAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
* * *
771 -GGGCCCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTAAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
*
830 CAGACCCTTATTTGAA-CATTTTGACAAACGTTAGGCCCTTATTTGA
1 CAGGCCCTTATTT-AAGCATTTTGACAAACGTTAGGCCCTTATTTGA
876 GCAATTAGCC
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 54 0.57
60 38 0.40
61 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
CAGGCCCTTATTTAAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
Found at i:1683 original size:17 final size:18
Alignment explanation
Indices: 1649--1683 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1639 AACTCAATTA
*
1649 GAAATTAATTTAGGAAAT
1 GAAATTAATTTAGAAAAT
1667 GAAATTAA-TTAGAAAAT
1 GAAATTAATTTAGAAAAT
1684 AATTTAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GAAATTAATTTAGAAAAT
Found at i:2501 original size:17 final size:19
Alignment explanation
Indices: 2479--2520 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2469 ATTGTTTTTG
2479 AAAAACATGA-AA-TATAA
1 AAAAACATGATAATTATAA
2496 AAAAACATGATAATTATAA
1 AAAAACATGATAATTATAA
2515 ATAAAA
1 A-AAAA
2521 GACTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 2 0.09
19 6 0.27
20 4 0.18
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAACATGATAATTATAA
Found at i:3005 original size:81 final size:81
Alignment explanation
Indices: 2870--3032 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
2860 TAGTATTTAT
*
2870 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAATACA
1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
*
2935 ACAATTAGGGAGAAAA
66 ACAATTAAGGAGAAAA
2951 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
3016 ACAATTAAGGAGAAAA
66 ACAATTAAGGAGAAAA
3032 T
1 T
3033 TTTGGATCTA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (81 bp):
TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
ACAATTAAGGAGAAAA
Found at i:18756 original size:30 final size:30
Alignment explanation
Indices: 18720--18781 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
18710 AAAAACTTTT
18720 TTTTTTGGGTGGATAAATTCAAATTATAAA
1 TTTTTTGGGTGGATAAATTCAAATTATAAA
18750 TTTTTTGGGTGGATAAATTCAAATTATAAA
1 TTTTTTGGGTGGATAAATTCAAATTATAAA
18780 TT
1 TT
18782 GACTCATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (30 bp):
TTTTTTGGGTGGATAAATTCAAATTATAAA
Found at i:25725 original size:20 final size:18
Alignment explanation
Indices: 25696--25738 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
25686 AAGACTAAAT
*
25696 TCTTTCTCTTTCTTTCTTTA
1 TCTTTATCTTT-TTT-TTTA
*
25716 TCTTTATCTTTTTTTTTT
1 TCTTTATCTTTTTTTTTA
25734 TCTTT
1 TCTTT
25739 TCTCTCTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
20 10 0.48
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (18 bp):
TCTTTATCTTTTTTTTTA
Found at i:25894 original size:17 final size:16
Alignment explanation
Indices: 25869--25912 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
25859 CTCTTTGTGT
*
25869 TTCTCCTTCTTCTCTTC
1 TTCTTCTTCTT-TCTTC
25886 TTCTTCTTCATTTCTTC
1 TTCTTCTTC-TTTCTTC
*
25903 TGCTTCTTCT
1 TTCTTCTTCT
25913 CCATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.61
Consensus pattern (16 bp):
TTCTTCTTCTTTCTTC
Done.