Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013058.1 Corchorus capsularis cultivar CVL-1 contig13079, 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: 20883
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:248 original size:32 final size:31
Alignment explanation
Indices: 175--253 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
165 GCTCAGTTAA
* *
175 CTCCACTTTAGGGA-CTAAATTGCATATTTT
1 CTCCACTTGAGGGACCGAAATTGCATATTTT
*
205 CT-CACTTGAGGGACCGAATTTGC-TATTTT
1 CTCCACTTGAGGGACCGAAATTGCATATTTT
234 CGCTCCACTTGAGGGACCGA
1 --CTCCACTTGAGGGACCGA
254 TCTTGTACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 16 0.38
30 9 0.21
31 2 0.05
32 15 0.36
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (31 bp):
CTCCACTTGAGGGACCGAAATTGCATATTTT
Found at i:2399 original size:31 final size:30
Alignment explanation
Indices: 2326--2400 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
2316 GGGCACATGT
*
2326 GCAAATGGGTCCCTGAAGTGAACTTAGTGA
1 GCAATTGGGTCCCTGAAGTGAACTTAGTGA
* * *
2356 GCAATTGAGTCCCTGAAGTTG-AGTTAATTGA
1 GCAATTGGGTCCCTGAAG-TGAACTT-AGTGA
*
2387 GTAATTGGGTCCCT
1 GCAATTGGGTCCCT
2401 CATCAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (30 bp):
GCAATTGGGTCCCTGAAGTGAACTTAGTGA
Found at i:2448 original size:15 final size:16
Alignment explanation
Indices: 2428--2459 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2418 AAAATCATAT
2428 ATATTTTTTTAA-AAA
1 ATATTTTTTTAATAAA
2443 ATATTTTTTTAATAAA
1 ATATTTTTTTAATAAA
2459 A
1 A
2460 AAATATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTTTAATAAA
Found at i:3094 original size:20 final size:21
Alignment explanation
Indices: 3053--3095 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3043 AAGATTATAC
*
3053 ATGGTTCCCCACATGTATTTG
1 ATGGTTCACCACATGTATTTG
*
3074 ATGGTTCACCGCATG-ATTTG
1 ATGGTTCACCACATGTATTTG
3094 AT
1 AT
3096 TTTACTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (21 bp):
ATGGTTCACCACATGTATTTG
Found at i:7010 original size:10 final size:10
Alignment explanation
Indices: 6995--7019 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6985 GAGGACTTTA
6995 GAATTTTCTG
1 GAATTTTCTG
7005 GAATTTTCTG
1 GAATTTTCTG
7015 GAATT
1 GAATT
7020 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:9242 original size:21 final size:22
Alignment explanation
Indices: 9196--9242 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
9186 GTGACTTGGC
*
9196 ATGGCGCGGCATAGGCTCGTGG
1 ATGGCGCGGCATAGGCTCGCGG
9218 -TGGCGCGGCAT-GG-TGCGCGG
1 ATGGCGCGGCATAGGCT-CGCGG
9238 ATGGC
1 ATGGC
9243 TTGGCAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 1 0.05
20 6 0.27
21 15 0.68
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (22 bp):
ATGGCGCGGCATAGGCTCGCGG
Found at i:12100 original size:13 final size:13
Alignment explanation
Indices: 12084--12110 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12074 TCTAAAGTAG
12084 ATTAATAAAGCAA
1 ATTAATAAAGCAA
12097 ATTAATAAAGCAA
1 ATTAATAAAGCAA
12110 A
1 A
12111 CAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTAATAAAGCAA
Found at i:13041 original size:10 final size:10
Alignment explanation
Indices: 13026--13050 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13016 GAGGACTCTA
13026 GAATTTTCTG
1 GAATTTTCTG
13036 GAATTTTCTG
1 GAATTTTCTG
13046 GAATT
1 GAATT
13051 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:14359 original size:12 final size:12
Alignment explanation
Indices: 14342--14374 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
14332 GCAGATCTAG
14342 GAGAACTTGGTT
1 GAGAACTTGGTT
14354 GAGAACTTGGTT
1 GAGAACTTGGTT
14366 GAGAACTTG
1 GAGAACTTG
14375 AATCGGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (12 bp):
GAGAACTTGGTT
Found at i:17576 original size:936 final size:927
Alignment explanation
Indices: 15753--17619 Score: 2574
Period size: 936 Copynumber: 2.0 Consensus size: 927
15743 CCCTAGGGAC
* *
15753 GTCGCACCCTCTATTGCTAGAGAGGGTGTCAACTTCTCCCTCTTTTAAAACTAGAGAAAAACCTA
1 GTCGCACCCTCTATGGCTAGAGAGGGTGTCAACTTCTCCCTCTTCTAAAACTAGAGAAAAACCT-
* * * *
15818 AAAAGTAAAGAAAGGTAGAAAAAGAATAAAACTATATGAGAGATTAATTGTGTAGTATTGTGTTA
65 AAAACTAAAGAAAAGTAGAAAAAGAATAAAACTATATGAGAAAGTAATTGTGTAG-ATTGTGTTA
* *
15883 TGTGTGTGATTTGTGATACAGGAGGTGGCTATTTATAGTGGAGGAATAGGCTAGGACGGTTTAGG
129 TGTGTGTGATTTGTGATACAGGAGGTGGCTACTTATAGTGGAGGAATAGGCTAGGACGGTTTAGC
* * * *
15948 CTTGACTTGGTCTCCAAGTTGGATTAGGTGTCATCCTAGAGTAGAATCCAAGTTAGATGAGACTC
194 CTTGACTTGGACTCCAAGTTGGATTAGATGTCATCCTAGAGTAGAATCCAAGTAAAATGAGACTC
* * ** * *
16013 TAGAATTTTCTGGAATTGTGCAGCAACTTCGACGTCGATTTCGGGCTTGAATATGGCAGATTTGG
259 TAGAATTTTCTGGAATTCTGCAGAAACTTCGACGTCGATTTAAGGCTTGAAGATGGCAGATCTGG
16078 GCTTTGCACTTCGAAAGAAAGTTGTAGAGCTCGGAGTTAGCTTTCCAACGGCTACTCATGCGCTT
324 GCTTTGCACTTCGAAAGAAAGTTGTAGAGCTCGGAGTTAGCTTTCCAACGGCTACTCATGCGCTT
* ** * *
16143 AAAACGGACATCTGAGCAGAAAGTTATGGCCTTTCTACGAAGACTGCGTTGAAACCGGGCTTATA
389 AAAACGGACATCTGAGCAGAAAGGTATGGCCTTTCTACGAAGACTGCGTCCAAACAGGAC-T-TA
* * * ** *
16208 TCGCAAATCTTCGGGATTATTGCGGGATTTGGATATTCTTTTGGATATTAGGCCTACAAATTGGA
452 -CG---ATCTACGGGATAATTACGGGATTTGGATATTCTTGAGGATAATAGGCCTACAAATTGGA
* * * *
16273 ATTTAAACTCCAATTATAGGTTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAATCC
513 ATTTAAACTCCAATTATAGGCTTATATGGGCTGAATATAATCACATATAAATAATCCAAAAATCC
*
16338 TCAACTTCAGGGCTTCTTCTAGGCTTGGCTTCAATCCTTTGCAAATAAAGCTCTAAATCTTGAAA
578 TCAACTTCAGGGCTTCTTCTAGGCTTGGCTTCAATCCTTTGCAAATAAAGCTCCAAATCTTGAAA
* *
16403 TTTTACTTCTTGAATTAATTCTTCAATTATCTTTAAATCTTCAAAATATCTTCAATCACGAACTT
643 TTTTACTTCTTGAACTAATTCTTCAATTATCTTCAAATCTTCAAAATATCTTCAATCACGAACTT
*
16468 CGTATCTTCAAATCTTCATTCCAAATGACTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGC
708 CGTATCTTCAAATCTTCATTCCAAATGACTAAATCCATAGTTGAATAAAAAGTCACTAAAATAGC
16533 TCCAAAAAGAGTGAAAAACAATAAGTTTTCACTTTTCTTGTCTTCAAGACCTAAAAACACAAATA
773 TCCAAAAAGAGTGAAAAACAATAAGTTTTCACTTTTCTTGTCTTCAAGACCTAAAAACACAAATA
*
16598 CTAACAAAATAGGGTAAAAAAACATATAAAAATAGTAAAAAGTATATAAAATAGCTATAAAAACA
838 CTAACAAAATAGAGTAAAAAAACATATAAAAATAGTAAAAAGTATATAAAATAGCTATAAAAACA
16663 TGCATAATTTGAGCTCGATCAGGTT
903 TGCATAATTTGAGCTCGATCAGGTT
*
16688 GTCGCACCCCTCTATGGCTAGAGAGGGTGTCGACTTC-CCC-CTTCTAAAACTAGAGAAAAAGAA
1 GTCGCA-CCCTCTATGGCTAGAGAGGGTGTCAACTTCTCCCTCTTCTAAAACTAGAG--AAA-AA
* *
16751 GCT-AAACTAAAGAAAAGTAGAAAAAGAGAATAAAACTATATCTATGTGAAAGTATATCTAGTGT
62 CCTAAAACTAAAGAAAAGTAG-AAAA-AGAATAAAAC--TA--TATGAGAAAGTA-AT-T-GTGT
16815 A-ATTGTGTAGTATTGTGTGTGATTTGTGATACAGGAGGTGGCTACTTATAGTGGAGGAATAAGG
118 AGATTGTGT--TA-TGTGTGTGATTTGTGATACAGGAGGTGGCTACTTATAGTGGAGGAAT-A-G
* *
16879 GGTAGGACGGTTTAGCCTTGACTTGGACTCCAAGTTGGATTAGATGTCTTCCTAGAGTAGAATCC
178 GCTAGGACGGTTTAGCCTTGACTTGGACTCCAAGTTGGATTAGATGTCATCCTAGAGTAGAATCC
* * *
16944 AAGTCAAAAT-AGGATTCTAGAATTTTCTGGATTTCTGCAGAAACTTCGAC-TTGATATTAAGGC
243 AAGT-AAAATGA-GACTCTAGAATTTTCTGGAATTCTGCAGAAACTTCGACGTCGAT-TTAAGGC
*
17007 TTGAAGATGGCAGATCTGGGGTTTGCACTTC-AAAGGAAAGTTGTAGAGCTCGGAGTTAGCTTTC
305 TTGAAGATGGCAGATCTGGGCTTTGCACTTCGAAA-GAAAGTTGTAGAGCTCGGAGTTAGCTTTC
* * * * *
17071 CAATGGCTACTCATGGGCTTAAAACGGATATCTGAGCAGAAAGGTATGGTCTTTTTACCG-AGAC
369 CAACGGCTACTCATGCGCTTAAAACGGACATCTGAGCAGAAAGGTATGGCCTTTCTA-CGAAGAC
* *
17135 TGC-TCCAAATAGGAC-TA-G-T-TACGGGA-AATTACGGGATTTGGATATT-TTGGAGGGTCCA
433 TGCGTCCAAACAGGACTTACGATCTACGGGATAATTACGGGATTTGGATATTCTT-GAGGAT--A
* ** * *
17193 ATCGG-C-ATTAATTGGGATCTT-AACTTCAATTAT-GGACTTATATGGGCTGAATATAATCACA
495 ATAGGCCTACAAATTGGAAT-TTAAACTCCAATTATAGG-CTTATATGGGCTGAATATAATCACA
* * * *
17254 TATAAATTATCCAAAAATTCTTAACTTCCGGGCTTCTTCT-GGACTTTGGCTTCAATCCTTTGCA
558 TATAAATAATCCAAAAATCCTCAACTTCAGGGCTTCTTCTAGG-C-TTGGCTTCAATCCTTTGCA
* *
17318 AATAAA-CTCCAAATCTT-CAATTCTTACTTCTTGAACTAATTCTTCAATTGTCTTCAAATCTTC
621 AATAAAGCTCCAAATCTTGAAATT-TTACTTCTTGAACTAATTCTTCAATTATCTTCAAATCTTC
* *
17381 AAAATATCTTCAATCACGAACTTCGTATCTTCAAATCTTCATTCCAAATGGCTAAGTCCATAGTT
685 AAAATATCTTCAATCACGAACTTCGTATCTTCAAATCTTCATTCCAAATGACTAAATCCATAGTT
*
17446 GAATAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAATAAGTTTTTACTTTTCTTGTC
750 GAATAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAATAAGTTTTCACTTTTCTTGTC
*
17511 TTCAAGACCTAAAAACACAAATACTAACAAAATAGAGTAAAAACACATATAAAAATA-TCAAAAA
815 TTCAAGACCTAAAAACACAAATACTAACAAAATAGAGTAAAAAAACATATAAAAATAGT-AAAAA
* *
17575 GTATATAAAGTAGCTATAAAAACATGCATAATTTTAGCTCGATCA
879 GTATATAAAATAGCTATAAAAACATGCATAATTTGAGCTCGATCA
17620 TATTTTCCCC
Statistics
Matches: 829, Mismatches: 71, Indels: 63
0.86 0.07 0.07
Matches are distributed among these distances:
934 14 0.02
935 35 0.04
936 410 0.49
937 48 0.06
938 5 0.01
939 2 0.00
941 9 0.01
942 10 0.01
943 1 0.00
944 9 0.01
945 46 0.06
946 1 0.00
947 80 0.10
948 157 0.19
949 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (927 bp):
GTCGCACCCTCTATGGCTAGAGAGGGTGTCAACTTCTCCCTCTTCTAAAACTAGAGAAAAACCTA
AAACTAAAGAAAAGTAGAAAAAGAATAAAACTATATGAGAAAGTAATTGTGTAGATTGTGTTATG
TGTGTGATTTGTGATACAGGAGGTGGCTACTTATAGTGGAGGAATAGGCTAGGACGGTTTAGCCT
TGACTTGGACTCCAAGTTGGATTAGATGTCATCCTAGAGTAGAATCCAAGTAAAATGAGACTCTA
GAATTTTCTGGAATTCTGCAGAAACTTCGACGTCGATTTAAGGCTTGAAGATGGCAGATCTGGGC
TTTGCACTTCGAAAGAAAGTTGTAGAGCTCGGAGTTAGCTTTCCAACGGCTACTCATGCGCTTAA
AACGGACATCTGAGCAGAAAGGTATGGCCTTTCTACGAAGACTGCGTCCAAACAGGACTTACGAT
CTACGGGATAATTACGGGATTTGGATATTCTTGAGGATAATAGGCCTACAAATTGGAATTTAAAC
TCCAATTATAGGCTTATATGGGCTGAATATAATCACATATAAATAATCCAAAAATCCTCAACTTC
AGGGCTTCTTCTAGGCTTGGCTTCAATCCTTTGCAAATAAAGCTCCAAATCTTGAAATTTTACTT
CTTGAACTAATTCTTCAATTATCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGTATCTT
CAAATCTTCATTCCAAATGACTAAATCCATAGTTGAATAAAAAGTCACTAAAATAGCTCCAAAAA
GAGTGAAAAACAATAAGTTTTCACTTTTCTTGTCTTCAAGACCTAAAAACACAAATACTAACAAA
ATAGAGTAAAAAAACATATAAAAATAGTAAAAAGTATATAAAATAGCTATAAAAACATGCATAAT
TTGAGCTCGATCAGGTT
Found at i:19293 original size:27 final size:27
Alignment explanation
Indices: 19252--19321 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
19242 AGGGTCTTCT
* * *
19252 AGGGGCATTTGGGTCATCTT-TACATTC
1 AGGGGCATTTAGGTCAT-TTGCACACTC
*
19279 AGGGGTATTTAGGTCATTTGCACACTC
1 AGGGGCATTTAGGTCATTTGCACACTC
*
19306 AGGGGCATTTTGGTCA
1 AGGGGCATTTAGGTCA
19322 CATTATTCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (27 bp):
AGGGGCATTTAGGTCATTTGCACACTC
Found at i:19621 original size:17 final size:17
Alignment explanation
Indices: 19599--19635 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19589 TGTCCTTTTA
19599 ATTTGCTAAGTTTACAT
1 ATTTGCTAAGTTTACAT
*
19616 ATTTGCTATGTTTACAT
1 ATTTGCTAAGTTTACAT
19633 ATT
1 ATT
19636 CCACAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTTGCTAAGTTTACAT
Done.