Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021123.1 Corchorus olitorius cultivar O-4 contig21156, 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: 111522
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1225 original size:31 final size:31
Alignment explanation
Indices: 1182--1285 Score: 102
Period size: 32 Copynumber: 3.3 Consensus size: 31
1172 GGTAATTTTC
* *
1182 TCAGATCATTCGGGTTTCGACTCAT-CTGGAT
1 TCAGGTCATTCGGGTCTCGACTC-TGCTGGAT
**
1213 TCAGGTCATTCGGGTCTCGGGTCTGCTGGAT
1 TCAGGTCATTCGGGTCTCGACTCTGCTGGAT
* **
1244 TTAGGGTCATTCGGGTCTCGGGTCTGCTGGAT
1 TCA-GGTCATTCGGGTCTCGACTCTGCTGGAT
*
1276 TTAGGGTCAT
1 TCA-GGTCAT
1286 GCATGTTCGG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
30 1 0.02
31 27 0.41
32 38 0.58
ACGTcount: A:0.13, C:0.20, G:0.32, T:0.35
Consensus pattern (31 bp):
TCAGGTCATTCGGGTCTCGACTCTGCTGGAT
Found at i:1250 original size:16 final size:16
Alignment explanation
Indices: 1231--1283 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1221 TTCGGGTCTC
1231 GGGTCTGCTGGATTTA
1 GGGTCTGCTGGATTTA
* * * *
1247 GGGTCATTC-GGGTCTC
1 GGGTC-TGCTGGATTTA
1263 GGGTCTGCTGGATTTA
1 GGGTCTGCTGGATTTA
1279 GGGTC
1 GGGTC
1284 ATGCATGTTC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.09, C:0.17, G:0.40, T:0.34
Consensus pattern (16 bp):
GGGTCTGCTGGATTTA
Found at i:1257 original size:32 final size:32
Alignment explanation
Indices: 1207--1285 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
1197 TTCGACTCAT
*
1207 CTGGATTCA-GGTCATTCGGGTCTCGGGTCTG
1 CTGGATTTAGGGTCATTCGGGTCTCGGGTCTG
1238 CTGGATTTAGGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTTAGGGTCATTCGGGTCTCGGGTCTG
1270 CTGGATTTAGGGTCAT
1 CTGGATTTAGGGTCAT
1286 GCATGTTCGG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 8 0.17
32 38 0.83
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.34
Consensus pattern (32 bp):
CTGGATTTAGGGTCATTCGGGTCTCGGGTCTG
Found at i:1507 original size:21 final size:22
Alignment explanation
Indices: 1478--1519 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1468 GTTTATAATA
*
1478 TTCTTGGGTCA-TCGGGTTACC
1 TTCTCGGGTCATTCGGGTTACC
*
1499 TTCTCGGGTTATTCGGGTTAC
1 TTCTCGGGTCATTCGGGTTAC
1520 GAGTTTGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTACC
Found at i:9364 original size:6 final size:6
Alignment explanation
Indices: 9347--9394 Score: 87
Period size: 6 Copynumber: 7.8 Consensus size: 6
9337 GGCTTACCAC
9347 CACAATG CACAAG CACAAG CACAAG CACAAG CACAAG CACAAG CACAA
1 CACAA-G CACAAG CACAAG CACAAG CACAAG CACAAG CACAAG CACAA
9395 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.50, C:0.33, G:0.15, T:0.02
Consensus pattern (6 bp):
CACAAG
Found at i:39006 original size:12 final size:12
Alignment explanation
Indices: 38989--39013 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38979 TATCCAGTTT
38989 AATCTTAGTTAG
1 AATCTTAGTTAG
39001 AATCTTAGTTAG
1 AATCTTAGTTAG
39013 A
1 A
39014 GGATGTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
AATCTTAGTTAG
Found at i:39193 original size:40 final size:40
Alignment explanation
Indices: 39138--39219 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
39128 AGATAAAACC
* * *
39138 CAAGACCTCATGATTCAGGTATGAACTAAGATTCTACTAT
1 CAAGACCTCATGATTCAAGTATGAACTAAGACTCTACCAT
*
39178 CAAGACTTCATGATTCAAGTATGAACTAAGACTCTACCAT
1 CAAGACCTCATGATTCAAGTATGAACTAAGACTCTACCAT
39218 CA
1 CA
39220 GGCATTTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (40 bp):
CAAGACCTCATGATTCAAGTATGAACTAAGACTCTACCAT
Found at i:40809 original size:22 final size:23
Alignment explanation
Indices: 40784--40832 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
40774 AAATTAGTCC
*
40784 AATACAT-GTTTTGAGTTAGATT
1 AATACATACTTTTGAGTTAGATT
*
40806 AATATATACTTTTGAGTTAGATT
1 AATACATACTTTTGAGTTAGATT
40829 AATA
1 AATA
40833 TATATATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (23 bp):
AATACATACTTTTGAGTTAGATT
Found at i:40822 original size:23 final size:23
Alignment explanation
Indices: 40792--40836 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
40782 CCAATACATG
40792 TTTTGAGTTAGATTAATATATAC
1 TTTTGAGTTAGATTAATATATAC
40815 TTTTGAGTTAGATTAATATATA
1 TTTTGAGTTAGATTAATATATA
40837 TATGTATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTTGAGTTAGATTAATATATAC
Found at i:42835 original size:14 final size:14
Alignment explanation
Indices: 42816--42844 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42806 AATCTACGTC
42816 TATTCCTTTTAACT
1 TATTCCTTTTAACT
42830 TATTCCTTTTAACT
1 TATTCCTTTTAACT
42844 T
1 T
42845 TTGCAAGACT
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:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTCCTTTTAACT
Found at i:44456 original size:9 final size:9
Alignment explanation
Indices: 44444--44487 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
44434 CCGCCCCAGC
44444 CGCCCCCGT
1 CGCCCCCGT
*
44453 CGCCCCCGC
1 CGCCCCCGT
* *
44462 CTCCTCCGT
1 CGCCCCCGT
44471 CGCCCCCGT
1 CGCCCCCGT
*
44480 CTCCCCCG
1 CGCCCCCG
44488 CCTCCGTCGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.18, T:0.14
Consensus pattern (9 bp):
CGCCCCCGT
Found at i:44477 original size:18 final size:18
Alignment explanation
Indices: 44435--44487 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
44425 CCGTCGCCTC
* *
44435 CGCCCCAGCCGCCCCCGT
1 CGCCCCCGCCTCCCCCGT
*
44453 CGCCCCCGCCTCCTCCGT
1 CGCCCCCGCCTCCCCCGT
*
44471 CGCCCCCGTCTCCCCCG
1 CGCCCCCGCCTCCCCCG
44488 CCTCCGTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.02, C:0.68, G:0.19, T:0.11
Consensus pattern (18 bp):
CGCCCCCGCCTCCCCCGT
Found at i:44480 original size:27 final size:27
Alignment explanation
Indices: 44420--44516 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
44410 CCCCCGCCAC
* * *
44420 CGCCCCCGTCGCCTCCG-C-CC-CAGC
1 CGCCCCCGTCGCCCCCGCCTCCTCCGT
44444 CGCCCCCGTCGCCCCCGCCTCCTCCGT
1 CGCCCCCGTCGCCCCCGCCTCCTCCGT
*
44471 CGCCCCCGTCTCCCCCGCCTCCGT-CGT
1 CGCCCCCGTCGCCCCCGCCTCC-TCCGT
* * *
44498 CGTCCGCGTCGCCGCCGCC
1 CGCCCCCGTCGCCCCCGCC
44517 CCCCGACCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
24 16 0.26
25 1 0.02
26 2 0.03
27 41 0.67
28 1 0.02
ACGTcount: A:0.01, C:0.64, G:0.22, T:0.13
Consensus pattern (27 bp):
CGCCCCCGTCGCCCCCGCCTCCTCCGT
Found at i:44496 original size:24 final size:24
Alignment explanation
Indices: 44420--44496 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
44410 CCCCCGCCAC
* *
44420 CGCCCCCGTCGCCTCCGCC-CCAGC
1 CGCCCCCGTCGCCCCCGCCTCC-GT
44444 CGCCCCCGTCGCCCCCGCCTCCTCCGT
1 CGCCCCCGTCGCCCCCG---CCTCCGT
*
44471 CGCCCCCGTCTCCCCCGCCTCCGT
1 CGCCCCCGTCGCCCCCGCCTCCGT
44495 CG
1 CG
44497 TCGTCCGCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 25 0.54
27 19 0.41
28 2 0.04
ACGTcount: A:0.01, C:0.66, G:0.19, T:0.13
Consensus pattern (24 bp):
CGCCCCCGTCGCCCCCGCCTCCGT
Found at i:45581 original size:40 final size:40
Alignment explanation
Indices: 45536--45668 Score: 266
Period size: 40 Copynumber: 3.3 Consensus size: 40
45526 CTTTGACTCT
45536 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
1 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
45576 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
1 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
45616 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
1 TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
45656 TTGCCCATTGATT
1 TTGCCCATTGATT
45669 ATAATTACTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.13, C:0.16, G:0.15, T:0.56
Consensus pattern (40 bp):
TTGCCCATTGATTTATTTTATTTGTTTTTTGGCCGTATTC
Found at i:51629 original size:13 final size:13
Alignment explanation
Indices: 51611--51635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51601 CTAATAATCG
51611 TATATATCTAATA
1 TATATATCTAATA
51624 TATATATCTAAT
1 TATATATCTAAT
51636 TAATAAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATCTAATA
Found at i:53391 original size:19 final size:19
Alignment explanation
Indices: 53367--53403 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53357 TTATTTTGTA
*
53367 ACTGTACAGATAAGATTAC
1 ACTGTACAAATAAGATTAC
*
53386 ACTGTACAAATTAGATTA
1 ACTGTACAAATAAGATTA
53404 GGTACTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
ACTGTACAAATAAGATTAC
Found at i:64496 original size:2 final size:2
Alignment explanation
Indices: 64489--64523 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
64479 TAATATTTAG
* *
64489 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64524 GTTTAATAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68445 original size:13 final size:13
Alignment explanation
Indices: 68410--68437 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
68400 TATACTTTTC
68410 TTCCTACCATAAA
1 TTCCTACCATAAA
68423 TTCCTACCATAAA
1 TTCCTACCATAAA
68436 TT
1 TT
68438 GTACCCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (13 bp):
TTCCTACCATAAA
Found at i:71158 original size:2 final size:2
Alignment explanation
Indices: 71153--71177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71143 ATAGCATTTC
71153 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
71178 ATATGTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:75033 original size:4 final size:4
Alignment explanation
Indices: 75024--75052 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
75014 AAATTCCTTT
75024 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
75053 AAAATCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:89010 original size:11 final size:12
Alignment explanation
Indices: 88990--89015 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88980 TAGTTTCTTC
88990 TTTTATTTTTTT
1 TTTTATTTTTTT
89002 TTTTATTTTTTT
1 TTTTATTTTTTT
89014 TT
1 TT
89016 ATCCACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:97805 original size:2 final size:2
Alignment explanation
Indices: 97800--97828 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
97790 TTTTTTGTGT
97800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97829 TACAATTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99520 original size:27 final size:27
Alignment explanation
Indices: 99490--99544 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
99480 TTTTAATACG
99490 TTTTATCCAACAAATAAAATTGCTAAT
1 TTTTATCCAACAAATAAAATTGCTAAT
* ** *
99517 TTTTTTTGAAGAAATAAAATTGCTAAT
1 TTTTATCCAACAAATAAAATTGCTAAT
99544 T
1 T
99545 AAGTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (27 bp):
TTTTATCCAACAAATAAAATTGCTAAT
Found at i:106036 original size:123 final size:122
Alignment explanation
Indices: 105793--106037 Score: 280
Period size: 124 Copynumber: 2.0 Consensus size: 122
105783 CTTTTTAAAT
* *
105793 TAAAATGGTAAAGATAAAATAATTATAAAATATTGAATTTAATTAAATAAAAATAGAGGTTTTAA
1 TAAAATGGTAAAAATAAAATAATTATAAAATATTAAATTTAATTAAATAAAAATAGAGGTTTTAA
* ** * * *
105858 TAGAATAAAACTATATATTAAAAATTTTTAATATATCCAAATTTTTATTGAAAAATAG
66 TAGAATAAAACTAAATATTAAAAA-TTGGAATATATACAAATATGTATTGAAAAATAG
* * *
105916 TAAAATGGTAAAAATAAAGTAATTATAAAGATATTAAATTTAATTGAATAAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAA-ATATTAAATTTAATTAAATAAAAATAGAGGTTTTA
* * * * *
105981 GTAGGATAAAACTACAATAGTTAAACAA-TGGCATTTA-AGAAATATGT-TTGAAAAATA
65 ATAGAATAAAACTA-AATA-TTAAA-AATTGGAATATATACAAATATGTATTGAAAAATA
106038 AGGGTATAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
123 37 0.36
124 50 0.49
125 8 0.08
126 5 0.05
127 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (122 bp):
TAAAATGGTAAAAATAAAATAATTATAAAATATTAAATTTAATTAAATAAAAATAGAGGTTTTAA
TAGAATAAAACTAAATATTAAAAATTGGAATATATACAAATATGTATTGAAAAATAG
Found at i:109677 original size:21 final size:22
Alignment explanation
Indices: 109637--109677 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
109627 GACAAACTTG
*
109637 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
109659 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
109678 TATTATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Done.