Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008728.1 Corchorus capsularis cultivar CVL-1 contig08749, 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: 38112
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2619 original size:30 final size:32
Alignment explanation
Indices: 2565--2629 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
2555 AACTTTATGT
*
2565 TTTTCGATTGTACCCTTATTTTTAAAAT-ATA
1 TTTTCAATTGTACCCTTATTTTTAAAATCATA
*
2596 TTTTCAATTGTA-CCTTTTTTTTAAAATCATA
1 TTTTCAATTGTACCCTTATTTTTAAAATCATA
2627 TTT
1 TTT
2630 CTAGATTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (32 bp):
TTTTCAATTGTACCCTTATTTTTAAAATCATA
Found at i:2982 original size:38 final size:38
Alignment explanation
Indices: 2940--3012 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
2930 ACATAATGTG
*
2940 ATTATCAAAAAATCATAGGGAGGTTATCAAAATTTGTA
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
* **
2978 ATTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 ATTATCAAAAAATCATAAGGAGGTTATCAAAATTT
3013 TATAGGGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (38 bp):
ATTATCAAAAAATCATAAGGAGGTTATCAAAATTTGTA
Found at i:2995 original size:60 final size:61
Alignment explanation
Indices: 2919--3035 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
2909 CAAAGCGAGG
* *
2919 TTATCAAAATTACATAATGTGATTATCAAAAAATCATAGGGAG-GTTATCAAAATTTGTAA
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
* * * ** * *
2979 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGATTTATCAAAATTT
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTT
3036 CATAGGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (61 bp):
TTATCAAAATTACATAAGGAGATTATCAAAAAATCATAGGGAGAGTTATCAAAATTTGTAA
Found at i:3007 original size:22 final size:21
Alignment explanation
Indices: 2904--3451 Score: 131
Period size: 22 Copynumber: 25.4 Consensus size: 21
2894 CCTATTTCAG
*
2904 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAG-GAGGTTATCAA
* * * *
2926 AATTACATAATGTGATTATCAA
1 AATTTCAT-AGGAGGTTATCAA
**
2948 AAAATCATAGGGAGGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
*
2970 AATTT-GTA--A--TTATCAA
1 AATTTCATAGGAGGTTATCAA
*
2986 GATTTCATAAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTATCAA
* *
3008 AATTTTATAGGGAGATTTATCAA
1 AATTTCATA-GGAG-GTTATCAA
3031 AATTTCATAGGAAGGTTTATCAA
1 AATTTCATAGG-AGG-TTATCAA
* *
3054 AATGTCATAGCGAGGTTATCAC
1 AATTTCATAG-GAGGTTATCAA
* * * * * *
3076 AATTTTATAGTGTGATAATTGAC
1 AATTTCATAG-GAGGTTA-TCAA
** * *
3099 AA-TTCATATGTTGGTTTTTAA
1 AATTTCATA-GGAGGTTATCAA
* * * *
3120 ATTTTTATAACGCGGTTATCAA
1 AATTTCAT-AGGAGGTTATCAA
* *
3142 TATATCATATGGAGGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
* * *
3164 CATCTT-ATAGTGTTGATTATCAA
1 AAT-TTCATAG-G-AGGTTATCAA
*
3187 AATTTCATAGTGAGATCT-TC-A
1 AATTTCATAG-GAGGT-TATCAA
* *
3208 AATTTCCTTAGGGAGGTTAACAA
1 AATTT-CATA-GGAGGTTATCAA
*
3231 AATTTCATAAGAAGGTTAAAT-AA
1 AATTTCAT-AGGAGGTT--ATCAA
** * *
3254 AATTT-ATAAAAAGGTTCTCGA
1 AATTTCAT-AGGAGGTTATCAA
* * * *
3275 AATTGCATAGTATCGTTATTAA
1 AATTTCATAGGA-GGTTATCAA
* *
3297 AATTTTATTGGAAGGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
* *
3319 AATTTCATAAGGACGTCAT-AA
1 AATTTCAT-AGGAGGTTATCAA
** * * * *
3340 AAAATAAT-GTA-ATTATCAT
1 AATTTCATAGGAGGTTATCAA
3359 AATTTCATAGGAAGGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
* *
3381 AATTTCATAAGGACGTCAT-AA
1 AATTTCAT-AGGAGGTTATCAA
** * * * *
3402 AAAATAAT-GTA-ATTATCAT
1 AATTTCATAGGAGGTTATCAA
*
3421 AATTTCATAGGAATGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
3443 AATTTCATA
1 AATTTCATA
3452 AGGACGTCGT
Statistics
Matches: 372, Mismatches: 110, Indels: 88
0.65 0.19 0.15
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 8 0.02
19 16 0.04
20 4 0.01
21 39 0.10
22 208 0.56
23 83 0.22
24 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:3031 original size:23 final size:22
Alignment explanation
Indices: 2904--3389 Score: 133
Period size: 22 Copynumber: 22.4 Consensus size: 22
2894 CCTATTTCAG
* *
2904 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* ** * *
2926 AATTACATAATGTGATTATCAA
1 AATTTCATAGGGAGGTTATCAA
**
2948 AAAATCATAGGGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
*
2970 AATTT-GTA---A--TTATCAA
1 AATTTCATAGGGAGGTTATCAA
* *
2986 GATTTCATAAGGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* *
3008 AATTTTATAGGGAGATTTATCAA
1 AATTTCATAGGGAG-GTTATCAA
*
3031 AATTTCATAGGAAGGTTTATCAA
1 AATTTCATAGGGAGG-TTATCAA
* * *
3054 AATGTCATAGCGAGGTTATCAC
1 AATTTCATAGGGAGGTTATCAA
* * * * * * *
3076 AATTTTATAGTGTGATAATTGAC
1 AATTTCATAGGGAGGTTA-TCAA
* ** * *
3099 AA-TTCATATGTTGGTTTTTAA
1 AATTTCATAGGGAGGTTATCAA
* * ** *
3120 ATTTTTATAACGCGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* * *
3142 TATATCATATGGAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* ** *
3164 CATCTT-ATAGTGTTGATTATCAA
1 AAT-TTCATAG-GGAGGTTATCAA
* *
3187 AATTTCATAGTGAGATCT-TC-A
1 AATTTCATAGGGAGGT-TATCAA
* *
3208 AATTTCCTTAGGGAGGTTAACAA
1 AATTT-CATAGGGAGGTTATCAA
* *
3231 AATTTCATAAGAAGGTTAAAT-AA
1 AATTTCATAGGGAGGTT--ATCAA
*** * *
3254 AATTT-ATAAAAAGGTTCTCGA
1 AATTTCATAGGGAGGTTATCAA
* * * *
3275 AATTGCATA-GTATCGTTATTAA
1 AATTTCATAGGGA-GGTTATCAA
* * *
3297 AATTTTATTGGAAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
* * *
3319 AATTTCATAAGGACGTCAT-AA
1 AATTTCATAGGGAGGTTATCAA
** * * * *
3340 AAAAT-A-ATGTA-ATTATCAT
1 AATTTCATAGGGAGGTTATCAA
*
3359 AATTTCATAGGAAGGTTATCAA
1 AATTTCATAGGGAGGTTATCAA
3381 AATTTCATA
1 AATTTCATA
3390 AGGACGTCAT
Statistics
Matches: 324, Mismatches: 113, Indels: 54
0.66 0.23 0.11
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 4 0.01
19 7 0.02
20 4 0.01
21 26 0.08
22 194 0.60
23 75 0.23
24 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AATTTCATAGGGAGGTTATCAA
Found at i:3073 original size:45 final size:44
Alignment explanation
Indices: 2979--3085 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 44
2969 AAATTTGTAA
* * * * *
2979 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATGTCATAGCGAGAG
3024 TTATCAAAATTTCATAGGAAGGTTTATCAAAATGTCATAGCGAG-G
1 TTATCAAAATTTCATAGG-AGG-TTATCAAAATGTCATAGCGAGAG
* *
3069 TTATCACAATTTTATAG
1 TTATCAAAATTTCATAG
3086 TGTGATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 3 0.06
45 32 0.60
46 18 0.34
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATGTCATAGCGAGAG
Found at i:3372 original size:62 final size:62
Alignment explanation
Indices: 3297--3510 Score: 356
Period size: 62 Copynumber: 3.5 Consensus size: 62
3287 TCGTTATTAA
* *
3297 AATTTTATTGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
3359 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
* * *
3421 AATTTCATAGGAATGTTATCAAAATTTCATAAGGACGTCGTAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
* * *
3483 AATTTAATAGGAATGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
3511 GTATGAATAT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 145 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAATGTAATTATCAT
Found at i:16256 original size:27 final size:27
Alignment explanation
Indices: 16219--16272 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
16209 TAAGCTCCTG
16219 TGGTGGAGTGGTGAAGATGTAAAGACC
1 TGGTGGAGTGGTGAAGATGTAAAGACC
*
16246 TGGTGGAGTGGTGAAGATGTGAAGACC
1 TGGTGGAGTGGTGAAGATGTAAAGACC
16273 CAGTGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.43, T:0.22
Consensus pattern (27 bp):
TGGTGGAGTGGTGAAGATGTAAAGACC
Found at i:19362 original size:16 final size:16
Alignment explanation
Indices: 19337--19367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19327 AACTTTCAGC
*
19337 GAAAGTGATGAAGCAT
1 GAAAGCGATGAAGCAT
19353 GAAAGCGATGAAGCA
1 GAAAGCGATGAAGCA
19368 AACGAAGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.32, T:0.13
Consensus pattern (16 bp):
GAAAGCGATGAAGCAT
Found at i:19710 original size:24 final size:24
Alignment explanation
Indices: 19683--19737 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
19673 CAAATTCCGT
*
19683 TTGCAAAATCCGTTTTTGATTCTA
1 TTGCAAAATCCGTTTTTGATTCCA
* *
19707 TTGCAAATTCCGTTTTTGATTCCG
1 TTGCAAAATCCGTTTTTGATTCCA
19731 TTGCAAA
1 TTGCAAA
19738 GTACTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (24 bp):
TTGCAAAATCCGTTTTTGATTCCA
Found at i:20412 original size:30 final size:28
Alignment explanation
Indices: 20371--20442 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
20361 GCCTTGGCAA
***
20371 CAGGGCTTATTTGGCCTTTTATAAGAGTT
1 CAGGGCTTATTTGGCC-GAAATAAGAGTT
*
20400 CAGGGACTTATTTGGCCGAAATAATAGTT
1 CAGGG-CTTATTTGGCCGAAATAAGAGTT
20429 CAGGGGCTTATTTG
1 CA-GGGCTTATTTG
20443 CCGGTTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (28 bp):
CAGGGCTTATTTGGCCGAAATAAGAGTT
Found at i:22856 original size:155 final size:156
Alignment explanation
Indices: 22615--22920 Score: 409
Period size: 155 Copynumber: 2.0 Consensus size: 156
22605 ATATTATTCG
* * *
22615 TTGTACAATATGTTTATCGAACTAATATTTTTACTAATATGATCGCAGATTAGAAGGTCTTATTG
1 TTGTACAATATGTTTATCAAACTAATATTTTTACTAATATGATCGCAGATCAAAAGGTCTTATTG
* ** * * * * *
22680 CCTTAGCTATAGTAACCTTCGGGGTAGTAGCAGCAATTATGTCAAGAGGACA-AACATCGCACTT
66 CCTTAGCTACAAAAACCTTCGGGGTAGCAGCAACAATTATGCCAAGAGGA-AGAACAACGCACTC
22744 GAGATTTGACATACCACTACAATCTCA
130 GAGATTTGACATACCACTACAATCTCA
* ** *
22771 TTGTACAATATGTTTATCAAACTAATA-TTTTACTAATATGATTGTGGATCAAAAGGTCTTATTT
1 TTGTACAATATGTTTATCAAACTAATATTTTTACTAATATGATCGCAGATCAAAAGGTCTTATTG
* * * * *
22835 CCTTAGTTACAAAAACTTTCGGGGTAGCGGCAATAATTATGCCAGGAGGAAGAACAACGCACTCG
66 CCTTAGCTACAAAAACCTTCGGGGTAGCAGCAACAATTATGCCAAGAGGAAGAACAACGCACTCG
22900 AGATTTGACATACCACTACAA
131 AGATTTGACATACCACTACAA
22921 CCGACGGAAA
Statistics
Matches: 129, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
154 1 0.01
155 102 0.79
156 26 0.20
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (156 bp):
TTGTACAATATGTTTATCAAACTAATATTTTTACTAATATGATCGCAGATCAAAAGGTCTTATTG
CCTTAGCTACAAAAACCTTCGGGGTAGCAGCAACAATTATGCCAAGAGGAAGAACAACGCACTCG
AGATTTGACATACCACTACAATCTCA
Found at i:24006 original size:15 final size:15
Alignment explanation
Indices: 23988--24021 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23978 AAAAGGGAAC
23988 ATATAAAAAAAAGTT
1 ATATAAAAAAAAGTT
* *
24003 ATATATAAAGAAGTT
1 ATATAAAAAAAAGTT
24018 ATAT
1 ATAT
24022 TTTCGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (15 bp):
ATATAAAAAAAAGTT
Found at i:26939 original size:22 final size:21
Alignment explanation
Indices: 26914--26955 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
26904 TAATTGGACA
* *
26914 AAATACAACTAATGAATAATTT
1 AAATAAAAATAATG-ATAATTT
26936 AAATAAAAATAATGATAATT
1 AAATAAAAATAATGATAATT
26956 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (21 bp):
AAATAAAAATAATGATAATTT
Found at i:36209 original size:22 final size:22
Alignment explanation
Indices: 36177--36219 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
36167 AAAATCCTAA
36177 AACAGAGTTCCT-TTAACCCATC
1 AACAGAGTTCCTATT-ACCCATC
*
36199 AACAGATTTCCTATTACCCAT
1 AACAGAGTTCCTATTACCCAT
36220 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
AACAGAGTTCCTATTACCCATC
Done.