Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014192.1 Corchorus capsularis cultivar CVL-1 contig14213, 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: 8818
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Found at i:259 original size:51 final size:51
Alignment explanation
Indices: 76--453 Score: 380
Period size: 51 Copynumber: 7.5 Consensus size: 51
66 AGATTTCATT
* * * * * *
76 TTTATTT-CACATTA-TTCAAAGATTTCATCTTTTACTTAAAAGATTTAATC
1 TTTATTTACAAATTACTTAAAAGATTTAATCTTTCAATTAAAA-ATTCAATC
* * * * * *
126 TTTATTTACAAAAATTACTTAAAAG-TTCAATCTTTTAATCAAAGATTACATTT
1 TTTATTTAC--AAATTACTTAAAAGATTTAATCTTTCAATTAAAAATT-CAATC
*
179 TTTATTTACAAACTTACTTAAAAG-CTTAATCTTTCAATTAAAAATTCAATC
1 TTTATTTACAAA-TTACTTAAAAGATTTAATCTTTCAATTAAAAATTCAATC
* *
230 TTTATTCACAAATTACTTAAAAGATTTAATCTTTCACTTAAAAATTCAATC
1 TTTATTTACAAATTACTTAAAAGATTTAATCTTTCAATTAAAAATTCAATC
*
281 TTTATTTACAAATTACTTAAAAG-CTTAATCTTTCAATTAAAAATTC-ATC
1 TTTATTTACAAATTACTTAAAAGATTTAATCTTTCAATTAAAAATTCAATC
* * * * *
330 TCTATTTACAAATTACTTGAAAGA-TTCATC-TTCTAATTAAAAATCCCA-C
1 TTTATTTACAAATTACTTAAAAGATTTAATCTTTC-AATTAAAAATTCAATC
* * * *
379 TTTCATTTACAAATCACTTTAAAA-ATTCAATCTTTTACTTAAAAATTCAATC
1 TTT-ATTTACAAATTAC-TTAAAAGATTTAATCTTTCAATTAAAAATTCAATC
*
431 TTTATATACAAATTACTTAAAAG
1 TTTATTTACAAATTACTTAAAAG
454 CTTAAACTTT
Statistics
Matches: 274, Mismatches: 38, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
48 3 0.01
49 43 0.16
50 59 0.22
51 96 0.35
52 37 0.14
53 30 0.11
54 6 0.02
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (51 bp):
TTTATTTACAAATTACTTAAAAGATTTAATCTTTCAATTAAAAATTCAATC
Found at i:282 original size:20 final size:21
Alignment explanation
Indices: 244--283 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
234 TTCACAAATT
*
244 ACTTAAAAGATTTAATCTTTC
1 ACTTAAAAGATTCAATCTTTC
265 ACTTAAAA-ATTCAATCTTT
1 ACTTAAAAGATTCAATCTTT
284 ATTTACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
ACTTAAAAGATTCAATCTTTC
Found at i:392 original size:150 final size:154
Alignment explanation
Indices: 93--463 Score: 470
Period size: 150 Copynumber: 2.4 Consensus size: 154
83 CACATTATTC
* *
93 AAAGATTTCATCTTTTACTTAAAAGATTTAATCTTTATTTACAAAAATTACTTAAAAG-TTCAAT
1 AAAGATTTAATCTTTTACTTAAAA-ATTCAATCTTTATTTAC--AAATTACTTAAAAGCTT-AAT
* * * * *
157 CTTTTAATCAAAGATTACATTTTTTATTTACAAACTTACTTAAAAGCTTAATCTTTCAATTAAAA
62 CTTTCAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAA
* *
222 ATTCAATCTTTATTCACAAATTAC-TTA
127 ATCCAATCTTTATTCACAAATCACTTTA
*
249 AAAGATTTAATCTTTCACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
1 AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
* * *
314 CAATTAAAAATT-CA-TCTCTATTTACAAA-TTACTTGAAAGATTCATC-TTCTAATTAAAAATC
66 CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTC-AATTAAAAATC
* *
375 CCA-CTTTCATTTACAAATCACTTTA
130 CAATCTTT-ATTCACAAATCACTTTA
* * *
400 AAA-ATTCAATCTTTTACTTAAAAATTCAATCTTTATATACAAATTACTTAAAAGCTTAAACTTT
1 AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
464 GTACCAGATT
Statistics
Matches: 192, Mismatches: 19, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
149 7 0.04
150 95 0.49
151 18 0.09
152 2 0.01
153 30 0.16
154 2 0.01
155 16 0.08
156 22 0.11
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (154 bp):
AAAGATTTAATCTTTTACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAAATCC
AATCTTTATTCACAAATCACTTTA
Found at i:1900 original size:71 final size:71
Alignment explanation
Indices: 1791--1923 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 71
1781 TAAAATAAGT
** *
1791 AACTGAAGAAGGACCACCTTAGATCATTCCGATGCTAACTTAAGGAA-GACCACCCTGAGTCAAC
1 AACTGAAGAACAACCACCTTAGATCATTCCGATGCTAACTGAA-GAAGGACCACCCTGAGTCAAC
1855 TAAAATA
65 TAAAATA
*
1862 AACTGAAGAACAACCACCCTT-GATCATTCCGACT-CTAACTGAAGAAGGACCACCCTGGGTCA
1 AACTGAAGAACAACCA-CCTTAGATCATTCCGA-TGCTAACTGAAGAAGGACCACCCTGAGTCA
1924 TTGAAGTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 3 0.05
71 47 0.85
72 5 0.09
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (71 bp):
AACTGAAGAACAACCACCTTAGATCATTCCGATGCTAACTGAAGAAGGACCACCCTGAGTCAACT
AAAATA
Found at i:1967 original size:16 final size:17
Alignment explanation
Indices: 1922--1967 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
1912 CACCCTGGGT
1922 CATTGAAGTAAATTGAAG
1 CATTGAAGT-AATTGAAG
1940 CATTGAAG-AATTGAAG
1 CATTGAAGTAATTGAAG
1956 CATTG-AGTAATT
1 CATTGAAGTAATT
1968 AAAGAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.07
16 17 0.63
18 8 0.30
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (17 bp):
CATTGAAGTAATTGAAG
Found at i:2051 original size:29 final size:29
Alignment explanation
Indices: 2018--2073 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2008 TTGAAGCATT
*
2018 GATCACCTTGGACCAATTAACTAAAGAAA
1 GATCACCCTGGACCAATTAACTAAAGAAA
* * *
2047 GATCACCCTGGATCAATTGACTTAAGA
1 GATCACCCTGGACCAATTAACTAAAGA
2074 TGGACCTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (29 bp):
GATCACCCTGGACCAATTAACTAAAGAAA
Found at i:2263 original size:100 final size:100
Alignment explanation
Indices: 2052--2238 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
2042 AGAAAGATCA
* * * * * * *
2052 CCCTGGATCAATTGACTTAAGATGGACCTCCCTGGGTCAGTTGAAATTCACTTGTGGAGAGATCA
1 CCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTTGTAGAAAGATCA
* *
2117 CCCTGGATCAACCGAAATTCACAAAACAAAAATCG
66 CCCTGGATCAACCGAAAATAACAAAACAAAAATCG
2152 CCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTT-TAGAAAGATCA
1 CCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTTGTAGAAAGATCA
* *
2216 CCCTGGATCGACTTGAAAATAAC
66 CCCTGGATCAAC-CGAAAATAAC
2239 TTAAGAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
99 20 0.27
100 55 0.73
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
CCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTTGTAGAAAGATCA
CCCTGGATCAACCGAAAATAACAAAACAAAAATCG
Found at i:2329 original size:29 final size:29
Alignment explanation
Indices: 2276--2355 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
2266 GAAACTATCT
*
2276 GAAAGACCATCCTAGG-TC-ATGTAACT-GA
1 GAAAGACCACCCT-GGATCAAT-TAACTGGA
*
2304 GGAAAGATCACCCTGGATCAATTAACTGGA
1 -GAAAGACCACCCTGGATCAATTAACTGGA
* *
2334 GATAGACCACCCTGGGTCAATT
1 GAAAGACCACCCTGGATCAATT
2356 TGAAAATCAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.05
29 37 0.86
30 4 0.09
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (29 bp):
GAAAGACCACCCTGGATCAATTAACTGGA
Found at i:3381 original size:18 final size:18
Alignment explanation
Indices: 3360--3393 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3350 CCCTAGAGCT
3360 TTTTTCT-TCTTTTTTTC
1 TTTTTCTCTCTTTTTTTC
3377 TTTTTCTCTCTTTTTTT
1 TTTTTCTCTCTTTTTTT
3394 ATGCACTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTCTCTTTTTTTC
Found at i:4189 original size:5 final size:5
Alignment explanation
Indices: 4181--4206 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4171 TTTTTTTTTC
4181 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
4207 GGATGGGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:4481 original size:2 final size:2
Alignment explanation
Indices: 4474--4506 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4464 ATGAACAGCA
4474 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 A
4507 CAAAAGCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8505 original size:44 final size:44
Alignment explanation
Indices: 8437--8540 Score: 172
Period size: 44 Copynumber: 2.4 Consensus size: 44
8427 AGAAATTGGA
* *
8437 TGGGAACTCTCCCTTCCGACCACTAAACTAGGAATTAAAACTAG
1 TGGGAACTCTCCCTTCCGACCACTAAACTAGAAACTAAAACTAG
* *
8481 TGGGAACTCTCCCTTTCGATCACTAAACTAGAAACTAAAACTAG
1 TGGGAACTCTCCCTTCCGACCACTAAACTAGAAACTAAAACTAG
8525 TGGGAACTCTCCCTTC
1 TGGGAACTCTCCCTTC
8541 TTTTGAAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (44 bp):
TGGGAACTCTCCCTTCCGACCACTAAACTAGAAACTAAAACTAG
Done.