Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010763.1 Corchorus capsularis cultivar CVL-1 contig10784, 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: 31785
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:532 original size:46 final size:46
Alignment explanation
Indices: 480--629 Score: 212
Period size: 46 Copynumber: 3.3 Consensus size: 46
470 TATAATATAT
480 ATTTAAAATATATTATATATGTTTTTAATATATATAAATAAATAAA
1 ATTTAAAATATATTATATATGTTTTTAATATATATAAATAAATAAA
* * * * * * *
526 ATTTAAAATATATTATATATATTATAAATTTATTTTATATAAAT-AT
1 ATTTAAAATATATTATATATGTTTTTAATATA-TATAAATAAATAAA
*
572 ATTTAAAATATATTATATATGTTTTTATTATATATAAATAAATAAA
1 ATTTAAAATATATTATATATGTTTTTAATATATATAAATAAATAAA
618 ATTTAAAATATA
1 ATTTAAAATATA
630 GTTTAAATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
45 9 0.10
46 69 0.79
47 9 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (46 bp):
ATTTAAAATATATTATATATGTTTTTAATATATATAAATAAATAAA
Found at i:580 original size:26 final size:28
Alignment explanation
Indices: 540--591 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
530 AAAATATATT
* *
540 ATATATATTATAAATTTATTTTATATAA
1 ATATATATTATAAATATATTATATATAA
568 ATATAT-TTA-AAATATATTATATAT
1 ATATATATTATAAATATATTATATAT
592 GTTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 3 0.14
28 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATATATTATAAATATATTATATATAA
Found at i:629 original size:39 final size:40
Alignment explanation
Indices: 554--633 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 40
544 ATATTATAAA
* * **
554 TTTATTTTATATAAATATATTTAAAATATATTATATATGTT
1 TTTATTATATATAAATATATATAAAATATAAAATATA-GTT
*
595 TTTATTATATATAAATA-A-ATAAAATTTAAAATATAGTT
1 TTTATTATATATAAATATATATAAAATATAAAATATAGTT
633 T
1 T
634 AAATATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.12
39 13 0.38
40 1 0.03
41 16 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (40 bp):
TTTATTATATATAAATATATATAAAATATAAAATATAGTT
Found at i:2893 original size:32 final size:30
Alignment explanation
Indices: 2849--3020 Score: 118
Period size: 32 Copynumber: 5.8 Consensus size: 30
2839 GAGCATTCAT
2849 AAGTCCCTAAACACAGAGGCATCTCTATCAAA
1 AAGTCCCTAAACACAG-GGCAT-TCTATCAAA
*
2881 AAGT-CCTCAAACACCTGGGCATTC-AT----
1 AAGTCCCT-AAACA-CAGGGCATTCTATCAAA
2907 AAGTCCCTAAACACAGAGGCATCTCTATCAAA
1 AAGTCCCTAAACACAG-GGCAT-TCTATCAAA
*
2939 AAGT-CCTCAAACACCTGGGCATTC-AT----
1 AAGTCCCT-AAACA-CAGGGCATTCTATCAAA
*
2965 AAGTCCCTAAATACAGCGGCATTTCTATCAAA
1 AAGTCCCTAAACACAG-GGCA-TTCTATCAAA
2997 AAGT-CCTCAAACACATGGGCATTC
1 AAGTCCCT-AAACACA-GGGCATTC
3021 ATAAGTCCCT
Statistics
Matches: 112, Mismatches: 6, Indels: 45
0.69 0.04 0.28
Matches are distributed among these distances:
25 4 0.04
26 26 0.23
27 11 0.10
28 4 0.04
30 4 0.04
31 16 0.14
32 42 0.38
33 5 0.04
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (30 bp):
AAGTCCCTAAACACAGGGCATTCTATCAAA
Found at i:2912 original size:58 final size:58
Alignment explanation
Indices: 2822--3099 Score: 427
Period size: 58 Copynumber: 4.8 Consensus size: 58
2812 CCCAATAATT
* *
2822 AAAGTCCTCAAACACCAGAGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
2880 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
* * *
2938 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAATACAGCGGCATTTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
* * *
2996 AAAGTCCTCAAACACATGGGCATTCATAAGTCCCTAAACACTGAGACATCTC--TC-A
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
* **
3051 GAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCA
1 AAAGTCCTCAAACACCTGGGC-ATTCATAAGTCCCTAAACACAGAGGCA
3100 ATTTTTCTTC
Statistics
Matches: 204, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
55 20 0.10
56 27 0.13
58 157 0.77
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.20
Consensus pattern (58 bp):
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
Found at i:3090 original size:27 final size:27
Alignment explanation
Indices: 2823--3102 Score: 106
Period size: 26 Copynumber: 9.9 Consensus size: 27
2813 CCAATAATTA
2823 AAGTCCTCAAACACCAGA-GC-ATTCAT
1 AAGTCCTCAAACA-CAGAGGCAATTCAT
2849 AAGTCC-CTAAACACAGAGGC-ATCTCTAT
1 AAGTCCTC-AAACACAGAGGCAAT-TC-AT
*
2877 CAAAAAGTCCTCAAACACCTG-GGC-ATTCAT
1 ----AAGTCCTCAAACA-CAGAGGCAATTCAT
2907 AAGTCC-CTAAACACAGAGGC-ATCTCTAT
1 AAGTCCTC-AAACACAGAGGCAAT-TC-AT
*
2935 CAAAAAGTCCTCAAACACCTG-GGC-ATTCAT
1 ----AAGTCCTCAAACA-CAGAGGCAATTCAT
* * *
2965 AAGTCC-CTAAATACAGCGGCATTTCTAT
1 AAGTCCTC-AAACACAGAGGCAATTC-AT
2993 CAAAAAGTCCTCAAACACATG-GGC-ATTCAT
1 ----AAGTCCTCAAACACA-GAGGCAATTCAT
* * * *
3023 AAGTCC-CTAAACACTGAGACATCTCTCAG
1 AAGTCCTC-AAACACAGAGGCA-AT-TCAT
3052 AAGTCCTCAAACACA-AGGGCAATTCAT
1 AAGTCCTCAAACACAGA-GGCAATTCAT
3079 AAGTCC-CTAAACACAGAGGCAATT
1 AAGTCCTC-AAACACAGAGGCAATT
3103 TTTCTTCTCT
Statistics
Matches: 199, Mismatches: 16, Indels: 77
0.68 0.05 0.26
Matches are distributed among these distances:
25 13 0.07
26 59 0.30
27 30 0.15
28 10 0.05
29 18 0.09
30 7 0.04
31 7 0.04
32 47 0.24
33 8 0.04
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (27 bp):
AAGTCCTCAAACACAGAGGCAATTCAT
Found at i:6839 original size:14 final size:14
Alignment explanation
Indices: 6820--6849 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6810 TCATGTCCAT
6820 GTATACTAAATTTA
1 GTATACTAAATTTA
6834 GTATACTAAATTTA
1 GTATACTAAATTTA
6848 GT
1 GT
6850 GAAAATACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (14 bp):
GTATACTAAATTTA
Found at i:6929 original size:19 final size:21
Alignment explanation
Indices: 6891--6929 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6881 TTCACACTAT
*
6891 ACAAAAGTGAATATATTAATA
1 ACAAAAGTGAATAAATTAATA
6912 ACAAAA-TGAA-AAATTAAT
1 ACAAAAGTGAATAAATTAAT
6930 TTTCCAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (21 bp):
ACAAAAGTGAATAAATTAATA
Found at i:7361 original size:32 final size:32
Alignment explanation
Indices: 7320--7383 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
7310 AGATTTAAGT
7320 ATAATTCTAAATGTAAGGCATAAATAGGCAAA
1 ATAATTCTAAATGTAAGGCATAAATAGGCAAA
*
7352 ATAATTCTAAATGTAAGGTATAAATAGGCAAA
1 ATAATTCTAAATGTAAGGCATAAATAGGCAAA
7384 TTTTTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.27
Consensus pattern (32 bp):
ATAATTCTAAATGTAAGGCATAAATAGGCAAA
Found at i:10855 original size:18 final size:18
Alignment explanation
Indices: 10834--10872 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
10824 AGGAGCTCAC
* *
10834 GGTGGTGGATATGGCGGT
1 GGTGGGGGATATGGAGGT
*
10852 GGTGGGGGTTATGGAGGT
1 GGTGGGGGATATGGAGGT
10870 GGT
1 GGT
10873 TATGGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.03, G:0.59, T:0.28
Consensus pattern (18 bp):
GGTGGGGGATATGGAGGT
Found at i:10897 original size:27 final size:27
Alignment explanation
Indices: 10849--10907 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
10839 TGGATATGGC
* * *
10849 GGTGGTGGGGGTTATGGAGGTGGTTAT
1 GGTGGTGGGGCTGATGGAGGTGGCTAT
* * *
10876 GGTGGTGGGGCTGGTGGTGGTGGCTCT
1 GGTGGTGGGGCTGATGGAGGTGGCTAT
10903 GGTGG
1 GGTGG
10908 CGGCAGTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.05, C:0.05, G:0.59, T:0.31
Consensus pattern (27 bp):
GGTGGTGGGGCTGATGGAGGTGGCTAT
Found at i:13805 original size:63 final size:63
Alignment explanation
Indices: 13706--13891 Score: 336
Period size: 63 Copynumber: 3.0 Consensus size: 63
13696 AATGCGAGGG
13706 CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAAGGC
1 CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAAGGC
* *
13769 CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTGCTTTTCCTGCATTTGGTGAAGGG
1 CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAAGGC
**
13832 CTGACCCTTTTAAAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAA
1 CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAA
13892 TTCCGCAAGG
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 118 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (63 bp):
CTGACCCTTTTGCAAGGAGATGATCCTGTTCTCTTCTTTCCTTTTCCTGCATTTGGTGAAGGC
Found at i:14964 original size:2 final size:2
Alignment explanation
Indices: 14957--14985 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14947 TGAAAAAGGA
14957 AT AT 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 AT AT A
14986 ATTAAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29991 original size:2 final size:2
Alignment explanation
Indices: 29984--30013 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29974 GAAGCTGATA
29984 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
30014 GTAAAGTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31602 original size:2 final size:2
Alignment explanation
Indices: 31595--31629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31585 TAATGACATA
31595 AT AT AT AT AT 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 AT AT AT AT AT A
31630 ACCTCAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.