Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015694.1 Corchorus capsularis cultivar CVL-1 contig15715, 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: 53692
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:21703 original size:13 final size:13
Alignment explanation
Indices: 21687--21727 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
21677 ATTTGAAAAT
21687 TTTGAAAAATCAA
1 TTTGAAAAATCAA
21700 TTTGAAAAATCAA
1 TTTGAAAAATCAA
21713 TTTGAAAAATCAA
1 TTTGAAAAATCAA
21726 TT
1 TT
21728 AATTTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (13 bp):
TTTGAAAAATCAA
Found at i:21927 original size:25 final size:25
Alignment explanation
Indices: 21898--21947 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21888 ATTGTTTATG
21898 GAAAGTGAATAATTATTGATTGATT
1 GAAAGTGAATAATTATTGATTGATT
21923 GAAAGTGAATAATTATTGATTGATT
1 GAAAGTGAATAATTATTGATTGATT
21948 ATTACTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (25 bp):
GAAAGTGAATAATTATTGATTGATT
Found at i:22769 original size:106 final size:107
Alignment explanation
Indices: 22567--22801 Score: 337
Period size: 106 Copynumber: 2.2 Consensus size: 107
22557 TTTAGAGTTC
* * *
22567 TAGAAATAGAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTCT
1 TAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATCTTTATTCT
** ** *
22632 AAGGGTAAATTTTAAAATTAATAATTTATTGTTATAGGGGTT
66 AAGGGTAAATTGCAAAATTAATAATACATTGTTATAAGGGTT
* *
22674 TAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACCCCAAATT-AAATTTTATCTTTATTTT
1 TAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATCTTTATTCT
* *
22738 AAGGGTAAATTGCATAATTAATAATACATTGTTATAAGGTTT
66 AAGGGTAAATTGCAAAATTAATAATACATTGTTATAAGGGTT
* *
22780 TATAAATAAAATATATAACTAA
1 TAGAAATAAAATATAAAACTAA
22802 ATCTTTACTT
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
106 70 0.62
107 43 0.38
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (107 bp):
TAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATCTTTATTCT
AAGGGTAAATTGCAAAATTAATAATACATTGTTATAAGGGTT
Found at i:23677 original size:23 final size:23
Alignment explanation
Indices: 23624--23685 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
23614 TAGAAATTTA
*
23624 AAATAAT-TATGAAAAAAATAAG
1 AAATAATATATAAAAAAAATAAG
*
23646 AAATGATATATAAAAAAAAGTAA-
1 AAATAATATATAAAAAAAA-TAAG
* *
23669 TAATAATATTTAAAAAA
1 AAATAATATATAAAAAA
23686 CATGAGAGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 6 0.18
23 24 0.73
24 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (23 bp):
AAATAATATATAAAAAAAATAAG
Found at i:31658 original size:2 final size:2
Alignment explanation
Indices: 31651--31682 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31641 CTACGGTTTA
31651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31683 GATAAGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31998 original size:31 final size:30
Alignment explanation
Indices: 31953--32042 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
31943 ATATATGGGT
31953 AAAAGTA-CACAATTGGTCCCTGAAGTGGAG
1 AAAAGTAGCA-AATTGGTCCCTGAAGTGGAG
* *
31983 CGAAAGTAGCAAATTGGTCCCTCAAGT-GA-
1 -AAAAGTAGCAAATTGGTCCCTGAAGTGGAG
*
32012 AAAAATGAGC-AATTGAGTCCCTGAAGTGGAG
1 AAAAGT-AGCAAATTG-GTCCCTGAAGTGGAG
32043 TTAACTGAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
28 9 0.18
29 13 0.27
30 4 0.08
31 21 0.43
32 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (30 bp):
AAAAGTAGCAAATTGGTCCCTGAAGTGGAG
Found at i:35001 original size:27 final size:28
Alignment explanation
Indices: 34971--35026 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
34961 TTCTTGAAAG
*
34971 TAGCTTCAT-AATTCAATACAGCAAGTT
1 TAGCTTCATAAATTCAATACAACAAGTT
34998 TAGCTTCATAAATTCAATACAACAAGTT
1 TAGCTTCATAAATTCAATACAACAAGTT
35026 T
1 T
35027 CCTCTTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (28 bp):
TAGCTTCATAAATTCAATACAACAAGTT
Found at i:35654 original size:18 final size:18
Alignment explanation
Indices: 35631--35671 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35621 TTTATGTATG
35631 TATATAT-ATATATCATGT
1 TATATATCA-ATATCATGT
*
35649 TATATATCAATTTCATGT
1 TATATATCAATATCATGT
35667 TATAT
1 TATAT
35672 CAATTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATATCAATATCATGT
Found at i:37116 original size:31 final size:29
Alignment explanation
Indices: 37041--37121 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 29
37031 TCTCAGTTAA
37041 TTCCACTTCAGGGACTCAATTGCTCACTTT
1 TTCCACTTCAGGGAC-CAATTGCTCACTTT
*
37071 TT-CACTTGAGGGACCAATATGCT-ACTTTT
1 TTCCACTTCAGGGACCAAT-TGCTCAC-TTT
*
37100 GTTCCAGTTCAGGGACCAATTG
1 -TTCCACTTCAGGGACCAATTG
37122 TGTAGTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.14
29 18 0.41
30 6 0.14
31 14 0.32
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (29 bp):
TTCCACTTCAGGGACCAATTGCTCACTTT
Found at i:42587 original size:36 final size:37
Alignment explanation
Indices: 42542--42625 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 37
42532 ATTTGTTTGA
*
42542 TTGCCTGTTCTTTTAATTTGTTTTTTGGGC-CATGTT
1 TTGCATGTTCTTTTAATTTGTTTTTTGGGCACATGTT
** * *
42578 TTGCATGTTCTTTTTCTTTTTTTTTTTGGCATCATGTT
1 TTGCATGTTCTTTTAATTTGTTTTTTGGGCA-CATGTT
42616 TTGCATGTTC
1 TTGCATGTTC
42626 CAACTTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
36 25 0.61
38 16 0.39
ACGTcount: A:0.08, C:0.14, G:0.17, T:0.61
Consensus pattern (37 bp):
TTGCATGTTCTTTTAATTTGTTTTTTGGGCACATGTT
Found at i:44200 original size:30 final size:30
Alignment explanation
Indices: 44164--44221 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
44154 GGGGCATGAC
*
44164 CCCCCAAAAATGGAAAAATTACATAGTAAT
1 CCCCCAAAAATGAAAAAATTACATAGTAAT
*
44194 CCCCCAAAAATGAAAAAATTGCATAGTA
1 CCCCCAAAAATGAAAAAATTACATAGTA
44222 GTCCATAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (30 bp):
CCCCCAAAAATGAAAAAATTACATAGTAAT
Found at i:47917 original size:22 final size:22
Alignment explanation
Indices: 47889--47933 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
47879 TGTATTTTTT
47889 GAGAAATTATTAGGTGGATCGG
1 GAGAAATTATTAGGTGGATCGG
47911 GAGAAATTATTAGGTGGATCGG
1 GAGAAATTATTAGGTGGATCGG
47933 G
1 G
47934 TCCACCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.27
Consensus pattern (22 bp):
GAGAAATTATTAGGTGGATCGG
Found at i:48984 original size:13 final size:13
Alignment explanation
Indices: 48966--48991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48956 CTAAAAAGTT
48966 TTAGTCTTATATA
1 TTAGTCTTATATA
48979 TTAGTCTTATATA
1 TTAGTCTTATATA
48992 GTACAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TTAGTCTTATATA
Found at i:52778 original size:20 final size:20
Alignment explanation
Indices: 52753--52793 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52743 TCTTGGGTTC
* *
52753 TACTCTCATGGAATGTGAGT
1 TACTCTCACGAAATGTGAGT
*
52773 TACTCTTACGAAATGTGAGT
1 TACTCTCACGAAATGTGAGT
52793 T
1 T
52794 TTCTTTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (20 bp):
TACTCTCACGAAATGTGAGT
Found at i:53659 original size:2 final size:2
Alignment explanation
Indices: 53652--53692 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
53642 CTGCCCCGAA
*
53652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.