Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012342.1 Corchorus capsularis cultivar CVL-1 contig12363, 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: 25414
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:51 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
32 ATAATCTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1134 original size:29 final size:29
Alignment explanation
Indices: 1101--1158 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1091 CTTAGGGTTT
1101 TCCTACCAACCATCAAAGCTCTAGTCACA
1 TCCTACCAACCATCAAAGCTCTAGTCACA
1130 TCCTACCAACCATCAAAGCTCTAGTCACA
1 TCCTACCAACCATCAAAGCTCTAGTCACA
1159 GGATCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.38, G:0.07, T:0.21
Consensus pattern (29 bp):
TCCTACCAACCATCAAAGCTCTAGTCACA
Found at i:19744 original size:29 final size:30
Alignment explanation
Indices: 19677--19747 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
19667 GAGAGTGGGA
* *
19677 AAAACTTCCAAAATTGAGAATTCAGGGGGC
1 AAAACGTCCAAAATTGAGAATTCAGGAGGC
* * * *
19707 AAAATGTCCAAAATTGA-AGTTCATGAGGT
1 AAAACGTCCAAAATTGAGAATTCAGGAGGC
19736 AAAACGTCCAAA
1 AAAACGTCCAAA
19748 TGCTACAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (30 bp):
AAAACGTCCAAAATTGAGAATTCAGGAGGC
Found at i:21526 original size:24 final size:25
Alignment explanation
Indices: 21494--21591 Score: 104
Period size: 25 Copynumber: 4.1 Consensus size: 25
21484 AAATGAAGGA
*
21494 AAATG-AGTTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
21517 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
21542 AAATGAAGTTT--AG-AG-T-TT-G
1 AAATGAAGTTTGAAGAAGTTGTTAG
21561 AAAGTTGAGAGTTTGAAGAAGTTGTTAG
1 AAA--TGA-AGTTTGAAGAAGTTGTTAG
21589 AAA
1 AAA
21592 GTTCAAAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
19 4 0.06
20 2 0.03
21 4 0.06
22 7 0.11
23 7 0.11
24 11 0.17
25 21 0.33
26 1 0.02
27 2 0.03
28 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.34
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:21565 original size:15 final size:15
Alignment explanation
Indices: 21547--21577 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21537 GTTAGAAATG
*
21547 AAGTTTAGAGTTTGA
1 AAGTTGAGAGTTTGA
21562 AAGTTGAGAGTTTGA
1 AAGTTGAGAGTTTGA
21577 A
1 A
21578 GAAGTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AAGTTGAGAGTTTGA
Found at i:24816 original size:31 final size:30
Alignment explanation
Indices: 24776--24944 Score: 141
Period size: 31 Copynumber: 5.6 Consensus size: 30
24766 ACTTGGCAAT
24776 TGCTCAAATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * * **
24807 TACTCAAATAAGGGCTTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCT-AACTTTGCCAAAA
*
24836 TGATCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * **
24867 TGCTCAAATAAGGGCCCGATCTTTG--AATT
1 TGCTCAAATAAGGG-CCTAACTTTGCCAAAA
*
24896 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGCCAAAA
24927 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
24945 TCTGATACGT
Statistics
Matches: 104, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
28 5 0.05
29 36 0.35
30 4 0.04
31 53 0.51
32 6 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:24873 original size:60 final size:60
Alignment explanation
Indices: 24779--24942 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
24769 TGGCAATTGC
* * ** *
24779 TCAAATAAGGGCCTAACATTTGCCAAAATACTCAAATAAGGGCTTGATCTTTTAATTTGA
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGA
*
24839 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGA
* *
24899 CCAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
24943 TATCTGATAC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGA
Found at i:25012 original size:31 final size:30
Alignment explanation
Indices: 24974--25169 Score: 152
Period size: 31 Copynumber: 6.5 Consensus size: 30
24964 TGAAACCAGA
24974 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGA-AACGTTAGG
* *
25005 CCCTTATTTGAGTATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGA-AACGTTAGG
** * **
25036 CCCTTATTTG-GTCAAATT--AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTCGAAACG-TTAGG
*
25065 CCCTTATTTGAGCATTTTCGATAATGTTAGG
1 CCCTTATTTGAGCATTTTCGA-AACGTTAGG
** * * *
25096 CCCTTATTTG-GCCAAATT--AAAAGATCATG
1 CCCTTATTTGAG-CATTTTCGAAACG-TTAGG
*
25125 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTCG-AAACGTTAGG
25156 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
25170 ATTAGCCTTC
Statistics
Matches: 130, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
28 6 0.05
29 36 0.28
30 4 0.03
31 77 0.59
32 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTCGAAACGTTAGG
Found at i:25072 original size:60 final size:59
Alignment explanation
Indices: 25002--25165 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 59
24992 CGATAACGTT
* *
25002 AGGCCCTTATTTGAGTATTTTCAATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* *
25062 GGGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
*
25122 ATGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
25166 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
60 92 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Done.