Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013739.1 Corchorus olitorius cultivar O-4 contig13772, 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: 26707
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2087 original size:60 final size:59
Alignment explanation
Indices: 1958--2105 Score: 206
Period size: 60 Copynumber: 2.5 Consensus size: 59
1948 GATTAGTATA
* * * * *
1958 TATATGAAAATGCTCAAATAAGGACCTGATCTTTAATTTGGCCAAATAAGGGTCTAACGT
1 TATA-GAAAATGCTCAAATAAGGGCCCGATCTTTAAATTGGCCAAATAAGAGCCTAACGT
* *
2018 TATAAAAAATGCTCAAATAAGGGCCCGATCTTTTAAATTGGCCAAATAAGAGCCTAACTT
1 TATAGAAAATGCTCAAATAAGGGCCCGATC-TTTAAATTGGCCAAATAAGAGCCTAACGT
*
2078 TATCGAAAATGCTCAAATAAGGGCCCGA
1 TATAGAAAATGCTCAAATAAGGGCCCGA
2106 CGTCAGTTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 23 0.29
60 55 0.71
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (59 bp):
TATAGAAAATGCTCAAATAAGGGCCCGATCTTTAAATTGGCCAAATAAGAGCCTAACGT
Found at i:2183 original size:31 final size:30
Alignment explanation
Indices: 2145--2303 Score: 94
Period size: 31 Copynumber: 5.3 Consensus size: 30
2135 CGACGCCGGA
*
2145 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTCAGG
** * ** *
2176 CCCTTATTTG-GCCAAATT-AAAAAATCAGA
1 CCCTTATTTGAG-CATTTTGCAAACGTCAGG
* *
2205 CCCTTATTTGAGCATTTTGGTAAACATCAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTCAGG
** * *
2236 CCCTTATTTG-GCCAAATT--AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTGCAAACG-TCAGG
* *
2265 CCCTTATTTGAGCTTTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTG-CAAACGTCAGG
2296 CCCTTATT
1 CCCTTATT
2304 AAGCAATTAG
Statistics
Matches: 95, Mismatches: 23, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
28 3 0.03
29 37 0.39
30 4 0.04
31 47 0.49
32 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTCAGG
Found at i:2214 original size:29 final size:29
Alignment explanation
Indices: 2176--2274 Score: 110
Period size: 29 Copynumber: 3.3 Consensus size: 29
2166 AAACGTTAGG
2176 CCCTTATTTGGCCAAATTAAAAAATCAGA
1 CCCTTATTTGGCCAAATTAAAAAATCAGA
** * * *
2205 CCCTTATTTGAG-CATTTTGGTAAACATCAGG
1 CCCTTATTTG-GCCAAATT--AAAAAATCAGA
*
2236 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAAATCAGA
2265 CCCTTATTTG
1 CCCTTATTTG
2275 AGCTTTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
29 32 0.57
30 2 0.04
31 22 0.39
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAAATCAGA
Found at i:2237 original size:60 final size:60
Alignment explanation
Indices: 2143--2303 Score: 268
Period size: 60 Copynumber: 2.7 Consensus size: 60
2133 TTCGACGCCG
2143 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCA
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCA
* * * *
2203 GACCCTTATTTGAGCATTTTGGTAAACATCAGGCCCTTATTTGGCCAAATTAAAAGATCA
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCA
* *
2263 GACCCTTATTTGAGCTTTTTGACAAACGTTAGGCCCTTATT
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATT
2304 AAGCAATTAG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCA
Found at i:8262 original size:45 final size:45
Alignment explanation
Indices: 8148--8560 Score: 557
Period size: 46 Copynumber: 9.1 Consensus size: 45
8138 CGATTTTATT
* * * *
8148 ATTTTCCAAAATCTTCTTTTAG-ATTTCTTAAAGAGAAAACTTTT
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
* *
8192 ATTTTCCAAAATCTTCTTTTAGAAATACTTAAATAGAAAAACTTTC
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAG-AAAACTTTC
* * *
8238 ATTTTCCAAAATCTTCTTTTGAAATTACTTAAATAGCAAACATTC
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
8283 TATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAATAACTTTC
1 -ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAA-AACTTTC
* *
8330 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGCAAACATTC
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
*
8375 TATTTTCCAAAATCTTCTTTTGGAATTACTTAAATTGAAAA---T-
1 -ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
* * * *
8417 ATTTTACAAAATCTTCTTTTGGATTTACTTAAATGGAAAAAAACTTTT
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAAT---AGAAAACTTTC
*
8465 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTT
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
*
8510 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACATTC
1 ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
8555 TATTTT
1 -ATTTT
8561 TGAAAATACT
Statistics
Matches: 331, Mismatches: 25, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
41 32 0.10
43 1 0.00
44 26 0.08
45 76 0.23
46 157 0.47
47 7 0.02
48 32 0.10
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (45 bp):
ATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACTTTC
Found at i:12034 original size:16 final size:16
Alignment explanation
Indices: 12013--12052 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
12003 CCAAACAACC
12013 AAAAAAAAAAGA-AAG
1 AAAAAAAAAAGAGAAG
12028 AAAAAAAAAAGAGAAG
1 AAAAAAAAAAGAGAAG
12044 AAAAAAAAA
1 AAAAAAAAA
12053 GGCCATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAGAAG
Found at i:12035 original size:17 final size:16
Alignment explanation
Indices: 12013--12052 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
12003 CCAAACAACC
12013 AAAAAAAAAAGAAAGAA
1 AAAAAAAAAAG-AAGAA
*
12030 AAAAAAAAGAGAAGAA
1 AAAAAAAAAAGAAGAA
12046 AAAAAAA
1 AAAAAAA
12053 GGCCATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAGAA
Found at i:13424 original size:28 final size:28
Alignment explanation
Indices: 13364--13416 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13354 CCTATCATGA
* *
13364 AAAATTACCGTTTTGCCCTTTGTCGAAT
1 AAAATTACCGTTTTGCCCTCTGTAGAAT
*
13392 AAAATTATCGTTTTGCCC-CTGTAGA
1 AAAATTACCGTTTTGCCCTCTGTAGA
13417 CCTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (28 bp):
AAAATTACCGTTTTGCCCTCTGTAGAAT
Found at i:15485 original size:212 final size:212
Alignment explanation
Indices: 15099--15515 Score: 649
Period size: 212 Copynumber: 2.0 Consensus size: 212
15089 TCCATGATGT
* * * * *
15099 AGTGCTATTGGGAGGGCGAGAATTAATGGTATAAGGGGGAATAGCAAAAGAGGGTTGTTTATAAT
1 AGTGCTATTGGGAGGGCGAGAATGAATGGCATAAGGGGGAACAACAAAAGAGGGTTGTTTATAAG
*
15164 TTAGAATGGTAAAAGAACCAGAGGTGGGAAGGAAGTACACTGATTCTAAGTGTTTTGCAAGATTG
66 TTAGAATGGTAAAAGAACCAGAGGTGGGAAGGAAGTACACTGATTCTAAGTGTTTTGCAAAATTG
* * * *
15229 ATTACTTCAAAGAAATCAGTGGGGTGCTCAGCCTGCACAGCTCTAGAAAGATCAGGTTTAATAAT
131 ATCACTTCAAACAAATCAGTGGGGTGCTCAGCCTGCAAAGCTCTAAAAAGATCAGGTTTAATAAT
15294 GGTCACAAAGATTTAAC
196 GGTCACAAAGATTTAAC
* *
15311 AGTGCTGTTGGGTGGGCGAGAATGAATGGCATAAGGGGGAACAACAAAAGAGGGTTGTTTATAAG
1 AGTGCTATTGGGAGGGCGAGAATGAATGGCATAAGGGGGAACAACAAAAGAGGGTTGTTTATAAG
* *
15376 TTGGAATGGTAGAAGAACCAGAGGTGGGAAGGAAGTACACTGATTCTAAGTGTTTTGCAAAATTG
66 TTAGAATGGTAAAAGAACCAGAGGTGGGAAGGAAGTACACTGATTCTAAGTGTTTTGCAAAATTG
* *
15441 A-CAGCTTTATACAAATCAGTGGGGTGCTCAGCAC-GCAAAGCTCTAAAAAGATCAGGTTTAATA
131 ATCA-CTTCAAACAAATCAGTGGGGTGCTCAGC-CTGCAAAGCTCTAAAAAGATCAGGTTTAATA
*
15504 GTGGTCACAAAG
194 ATGGTCACAAAG
15516 TCAATTGAGC
Statistics
Matches: 186, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
211 1 0.01
212 184 0.99
213 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.25
Consensus pattern (212 bp):
AGTGCTATTGGGAGGGCGAGAATGAATGGCATAAGGGGGAACAACAAAAGAGGGTTGTTTATAAG
TTAGAATGGTAAAAGAACCAGAGGTGGGAAGGAAGTACACTGATTCTAAGTGTTTTGCAAAATTG
ATCACTTCAAACAAATCAGTGGGGTGCTCAGCCTGCAAAGCTCTAAAAAGATCAGGTTTAATAAT
GGTCACAAAGATTTAAC
Found at i:17557 original size:19 final size:19
Alignment explanation
Indices: 17533--17572 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
17523 ATGATATCAA
17533 TGTGAAATACAAACTGAAT
1 TGTGAAATACAAACTGAAT
*
17552 TGTGAAATGCAAACTGAAT
1 TGTGAAATACAAACTGAAT
17571 TG
1 TG
17573 AATGTTGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (19 bp):
TGTGAAATACAAACTGAAT
Found at i:23403 original size:29 final size:30
Alignment explanation
Indices: 23359--23417 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
23349 ATTTGTGTTG
*
23359 TGTGTCTTGC-GTTTTTGAAAAAAAAAATT
1 TGTGTCTTGCGGTTTTAGAAAAAAAAAATT
*
23388 TGTGTTTTGCGGTTTTAGAAAAAAAAAATT
1 TGTGTCTTGCGGTTTTAGAAAAAAAAAATT
23418 CAATTTTGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (30 bp):
TGTGTCTTGCGGTTTTAGAAAAAAAAAATT
Found at i:23424 original size:29 final size:30
Alignment explanation
Indices: 23365--23427 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
23355 GTTGTGTGTC
* ***
23365 TTGC-GTTTTTGAAAAAAAAAATTTGTGTT
1 TTGCGGTTTTAGAAAAAAAAAATTTCAATT
23394 TTGCGGTTTTAGAAAAAAAAAA-TTCAATT
1 TTGCGGTTTTAGAAAAAAAAAATTTCAATT
23423 TTGCG
1 TTGCG
23428 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (30 bp):
TTGCGGTTTTAGAAAAAAAAAATTTCAATT
Done.