Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010251.1 Corchorus capsularis cultivar CVL-1 contig10272, 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: 66905
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:372 original size:16 final size:15
Alignment explanation
Indices: 351--386 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
341 CCTAGCCGCT
351 CCTCTCCCCCCTTCTC
1 CCTCT-CCCCCTTCTC
367 CCTCT-CCCCTTCTC
1 CCTCTCCCCCTTCTC
381 CCTCTC
1 CCTCTC
387 TAATTCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.74
16 5 0.26
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (15 bp):
CCTCTCCCCCTTCTC
Found at i:377 original size:14 final size:14
Alignment explanation
Indices: 358--386 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
348 GCTCCTCTCC
358 CCCCTTCTCCCTCT
1 CCCCTTCTCCCTCT
372 CCCCTTCTCCCTCT
1 CCCCTTCTCCCTCT
386 C
1 C
387 TAATTCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (14 bp):
CCCCTTCTCCCTCT
Found at i:533 original size:15 final size:16
Alignment explanation
Indices: 515--550 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
505 GTTTTATTTG
515 AGTTTG-TTTTGAGTC
1 AGTTTGTTTTTGAGTC
*
530 AGTTTGTTTTTTAGTC
1 AGTTTGTTTTTGAGTC
546 AGTTT
1 AGTTT
551 CGAGTCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.14, C:0.06, G:0.22, T:0.58
Consensus pattern (16 bp):
AGTTTGTTTTTGAGTC
Found at i:9819 original size:18 final size:18
Alignment explanation
Indices: 9791--9825 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9781 AAAACAATTG
9791 CCTTCTATTCT-CATGAA
1 CCTTCTATTCTGCATGAA
9808 CCTTCATATTCTGCATGA
1 CCTTC-TATTCTGCATGA
9826 GTACACGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (18 bp):
CCTTCTATTCTGCATGAA
Found at i:15589 original size:227 final size:225
Alignment explanation
Indices: 15184--15613 Score: 662
Period size: 227 Copynumber: 1.9 Consensus size: 225
15174 AATATAACAT
* * *
15184 GGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGACA
1 GGGTGATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGCTTCTGAAGTTGACA
* *
15249 CATGTCCCTTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAGGGACACATATC
66 CATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAAGGACACATATC
* * * * *
15314 ACCCTTTAGGACCCGCTTGTGTAATTTTCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCAT
131 ACCCTTTAGAACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTATATAATTTGCCAT
15379 ATAACATTATGTAAGTTTAGCCAATAAACTTA
196 A-AAC-TTATGTAAGTTTAGCCAATAAACTTA
*
15411 GGGTGATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGGTTCTGAAGTTGACA
1 GGGTGATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGCTTCTGAAGTTGACA
* ** * *
15476 CATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTCAATCTGGTCCTTAAAGGACACATGTC
66 CATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAAGGACACATATC
* ** *
15541 ACCCTTTAGAACCCGCTTGTGTAGTCTGCTAAACTCCAGTGACGGTGTATTATATAATTTGTCAT
131 ACCCTTTAGAACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTATATAATTTGCCAT
15606 AAACTTAT
196 AAACTTAT
15614 TGATAGCCAC
Statistics
Matches: 183, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
225 4 0.02
226 3 0.02
227 176 0.96
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (225 bp):
GGGTGATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGCTTCTGAAGTTGACA
CATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAAGGACACATATC
ACCCTTTAGAACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTATATAATTTGCCAT
AAACTTATGTAAGTTTAGCCAATAAACTTA
Found at i:20810 original size:2 final size:2
Alignment explanation
Indices: 20803--20855 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
20793 ATCCTTTCTT
20803 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20845 GA GA GA GA GA G
1 GA GA GA GA GA G
20856 CAGTTGGCCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22473 original size:14 final size:14
Alignment explanation
Indices: 22454--22481 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22444 CACTCTACTA
22454 AATGCAGCCTAAAT
1 AATGCAGCCTAAAT
22468 AATGCAGCCTAAAT
1 AATGCAGCCTAAAT
22482 TGGTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AATGCAGCCTAAAT
Found at i:22902 original size:17 final size:18
Alignment explanation
Indices: 22877--22914 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
22867 CAGATTAAAT
22877 AAGAAGAAGAA-AAAAAA
1 AAGAAGAAGAACAAAAAA
*
22894 AAGATGAAGAAGCAAAAAA
1 AAGAAGAAGAA-CAAAAAA
22913 AA
1 AA
22915 ATCTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAGAAGAAGAACAAAAAA
Found at i:26228 original size:12 final size:12
Alignment explanation
Indices: 26211--26245 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
26201 AACCATTCCA
*
26211 TTTGATTTTGAT
1 TTTGATGTTGAT
26223 TTTGATGTTGAT
1 TTTGATGTTGAT
*
26235 ATTGATGTTGA
1 TTTGATGTTGA
26246 ACCCACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (12 bp):
TTTGATGTTGAT
Found at i:32544 original size:15 final size:15
Alignment explanation
Indices: 32520--32550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32510 GACTATGACT
32520 TTTGTCAGAAAGGAA
1 TTTGTCAGAAAGGAA
*
32535 TTTGTTAGAAAGGAA
1 TTTGTCAGAAAGGAA
32550 T
1 T
32551 GTGAAATAAA
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:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (15 bp):
TTTGTCAGAAAGGAA
Found at i:45439 original size:78 final size:78
Alignment explanation
Indices: 45357--45514 Score: 289
Period size: 78 Copynumber: 2.0 Consensus size: 78
45347 GAGAATCACC
* *
45357 CATGTTGGGTTGATTAGATTGAGAGTTTGCGAGAGAGATTGTTATGATTGTTGATTGTAATTTAT
1 CATGTTGGGTTGATTAGAATGAGAGTTTGCGAGAGAGATTGTTATGATTGTTGATTGTAATTGAT
45422 TGATTTGATAGTG
66 TGATTTGATAGTG
*
45435 CATGTTGGGTTGATTAGAATGAGAGTTTGCGAGAGGGATTGTTATGATTGTTGATTGTAATTGAT
1 CATGTTGGGTTGATTAGAATGAGAGTTTGCGAGAGAGATTGTTATGATTGTTGATTGTAATTGAT
45500 TGATTTGATAGTG
66 TGATTTGATAGTG
45513 CA
1 CA
45515 GATTTGTGAC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.42
Consensus pattern (78 bp):
CATGTTGGGTTGATTAGAATGAGAGTTTGCGAGAGAGATTGTTATGATTGTTGATTGTAATTGAT
TGATTTGATAGTG
Found at i:45623 original size:13 final size:13
Alignment explanation
Indices: 45607--45637 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
45597 AAGTTACAAC
45607 AATAAGTACATCA
1 AATAAGTACATCA
45620 AATAAGTACATCA
1 AATAAGTACATCA
45633 AATAA
1 AATAA
45638 AATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (13 bp):
AATAAGTACATCA
Found at i:45975 original size:31 final size:31
Alignment explanation
Indices: 45936--46006 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
45926 ATAAACCTTT
45936 GAAA-TCATAATTCTTCTTAATAAATAAATG
1 GAAACTCATAATTCTTCTTAATAAATAAATG
45966 GAAACTCATAATTCTTCTTAATAAATAAATG
1 GAAACTCATAATTCTTCTTAATAAATAAATG
45997 GAAACTCATA
1 GAAACTCATA
46007 TAGAAATCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (31 bp):
GAAACTCATAATTCTTCTTAATAAATAAATG
Found at i:54795 original size:339 final size:334
Alignment explanation
Indices: 54353--55039 Score: 762
Period size: 339 Copynumber: 2.0 Consensus size: 334
54343 AAACATTTTA
* * * * **
54353 AAATCCAATGTGACTGAGATTTGATTAGATGAATATGGATATCTCAAGGATTCTTGGCGTAAAAA
1 AAATCCAATGTAACTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCACAAAAA
* * * * *
54418 ATCATGCAAAAGTGAACCGGGGCCCCAGAACGCGTTTTTAGACGAAAA-CCGTGATGGTTAATAC
66 ATCATGCAAAACTGAACCCGGGCCCCAGAACACGTTTTTA-ACCAAAAGCCGTGATGATT--TAC
* * *
54482 ACGATTTCGGCTAAAATTTTAC-AAAAATTAAACCAAAATATATTTTC-TAAATTTTTGGCTAAA
128 ACAATTTCGGCTAAAATTTTACAAAAAATGAAACCAAAAT-T-TTTTCATAAATTTTTGACTAAA
* * * * *
54545 ATACTCATTATATATATATATTTATAATTTAATGCCAAAAAGATT-GAAGGACTTCTCAAGCTTT
191 ATACTCA-TA-A-AAATATATATATAATTTAACGCC-AAAAGATTAG-AGGACTTCTCAAGATTC
* *
54609 TAATATCGTTTTTTGATATTTTAT-CTAAATTAATTTCTAATTAAATCGAAACA-A-GATTCAAA
251 TAATATCG-TTTTTCAT-TTTTATCCCAAATTAATTTCTAATTAAATCGAAACACACGATTCAAA
54671 TACTT-GTAAAAACAAATCCTT
314 T-CTTCGTAAAAACAAATCCTT
* * * *
54692 AAATCCAATGTAACTGAGATTTGATTAGTTGAATCTAGATATTTTAAGGAGTCTCGGCACAAAAA
1 AAATCCAATGTAACTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCACAAAAA
* * * * * * *
54757 CTCATGCAAAACTGAGCCCGGGTCTC-GAATCACGTTTTTATCCAAAAGCCTTGATGATTTACCC
66 ATCATGCAAAACTGAACCCGGGCCCCAGAA-CACGTTTTTAACCAAAAGCCGTGATGATTTACAC
* ** * *
54821 AATTTCGGTTAAAATTTTACAAAAAATGAGTCGAAAATTTTTTCATTAATTTTTGACTAAAATAC
130 AATTTCGGCTAAAATTTTACAAAAAATGAAACCAAAATTTTTTCATAAATTTTTGACTAAAATAC
* * * *
54886 TCATAAAAATATATATATAATTTAACGTCAAAATATTAGAGGACTTTTCATGATTCTAATATCGT
195 TCATAAAAATATATATATAATTTAACGCCAAAAGATTAGAGGACTTCTCAAGATTCTAATATCGT
* * * *
54951 TTTTCCTTTTTTTCCCAAATTAATTTCTAATTAAATCGAAACACGATCGATTCAGATGTTCGTAA
260 TTTTCATTTTTATCCCAAATTAATTTCTAATTAAATCGAAACAC-A-CGATTCAAATCTTCGTAA
55016 AAACAAATCCTT
323 AAACAAATCCTT
55028 AAATCCAATGTA
1 AAATCCAATGTA
55040 TAATCCTGGA
Statistics
Matches: 292, Mismatches: 45, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
331 5 0.02
332 34 0.12
333 28 0.10
334 21 0.07
335 3 0.01
336 43 0.15
337 44 0.15
338 21 0.07
339 93 0.32
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (334 bp):
AAATCCAATGTAACTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGCACAAAAA
ATCATGCAAAACTGAACCCGGGCCCCAGAACACGTTTTTAACCAAAAGCCGTGATGATTTACACA
ATTTCGGCTAAAATTTTACAAAAAATGAAACCAAAATTTTTTCATAAATTTTTGACTAAAATACT
CATAAAAATATATATATAATTTAACGCCAAAAGATTAGAGGACTTCTCAAGATTCTAATATCGTT
TTTCATTTTTATCCCAAATTAATTTCTAATTAAATCGAAACACACGATTCAAATCTTCGTAAAAA
CAAATCCTT
Found at i:55830 original size:30 final size:28
Alignment explanation
Indices: 55759--55836 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
55749 GAACTTACAC
*
55759 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
55787 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
55818 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
55837 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:66310 original size:1 final size:1
Alignment explanation
Indices: 66304--66330 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
66294 AGAGATAGAG
66304 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
66331 AAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.