Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021392.1 Corchorus olitorius cultivar O-4 contig21425, 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: 19267
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:814 original size:15 final size:15
Alignment explanation
Indices: 794--822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
784 TGGAAGTTCG
794 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
809 AAATCAACAAGCTC
1 AAATCAACAAGCTC
823 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:2057 original size:21 final size:21
Alignment explanation
Indices: 2031--2101 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
2021 TGCTAGGAGA
2031 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
2052 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
2073 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2094 TCATTGGA
1 TCATTGGA
2102 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:6968 original size:2 final size:2
Alignment explanation
Indices: 6961--6994 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6951 TGTTTAGGTT
*
6961 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6995 AGATAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:7107 original size:73 final size:73
Alignment explanation
Indices: 6988--7133 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
6978 GTGTGTATGT
6988 GTGTGTGAGATAGAAAGGTTTATGTTGTTGTGAGAGAATCACCTTTGGGTGTTATGGATTTTAGG
1 GTGTGTGAGATAGAAAGGTTTATGTTGTTGTGAGAGAATCACCTTTGGGTGTTATGGATTTTAGG
7053 TTGATAAG
66 TTGATAAG
* * * * *
7061 GTGTGTGAGATAGAAAGGTTTGTGTTGTTGTGTGAGAATCACCTTTGGTTGTTATGGGTTTTGGG
1 GTGTGTGAGATAGAAAGGTTTATGTTGTTGTGAGAGAATCACCTTTGGGTGTTATGGATTTTAGG
7126 TTGATAAG
66 TTGATAAG
7134 ATTAAGAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.22, C:0.04, G:0.34, T:0.40
Consensus pattern (73 bp):
GTGTGTGAGATAGAAAGGTTTATGTTGTTGTGAGAGAATCACCTTTGGGTGTTATGGATTTTAGG
TTGATAAG
Found at i:13406 original size:69 final size:69
Alignment explanation
Indices: 13320--13502 Score: 294
Period size: 69 Copynumber: 2.7 Consensus size: 69
13310 CTATGTGCAC
* ** *
13320 GAACTGACTCGTATGGAAACGAGTTTGACTCATGGAAAAGTCTATATGGCTTGGATGGAACCAAG
1 GAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAG
13385 ACTT
66 ACTT
* * *
13389 GAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGCAAAGCCCATATGGCTTGGATGGAACCAAG
1 GAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAG
*
13454 GCTT
66 ACTT
13458 GAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT
1 GAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT
13503 GTTGATAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 103 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (69 bp):
GAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAG
ACTT
Found at i:13518 original size:50 final size:50
Alignment explanation
Indices: 13462--13798 Score: 584
Period size: 50 Copynumber: 6.7 Consensus size: 50
13452 AGGCTTGAAC
13462 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
13512 TGACTCGTATGGAAACGTGTTTGGCTTATGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
13562 TTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
13612 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
13662 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
13712 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG-TTGATAAT
* * * *
13763 TAACTCGTATAGAAACGAGTTTGACTTATGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
13799 ACAAAGCATT
Statistics
Matches: 272, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
50 232 0.85
51 40 0.15
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:14559 original size:50 final size:50
Alignment explanation
Indices: 14413--14562 Score: 239
Period size: 50 Copynumber: 3.0 Consensus size: 50
14403 CTTCAATGTC
* * *
14413 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCGAA-CTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGC-AATTTTA
*
14463 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
14513 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
14563 TTGTAAAACT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 2 0.02
50 91 0.98
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:15207 original size:26 final size:25
Alignment explanation
Indices: 15172--15245 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 25
15162 ATCCTTTCTC
*
15172 TTTTGATTTTAATTTGATTTGATTTT
1 TTTTGTTTTTAATTT-ATTTGATTTT
**
15198 TTTTGTTTTTGTTGTTTATTT-ATTTT
1 TTTTG-TTTT-TAATTTATTTGATTTT
**
15224 TTTAATTTTTAATTT-TTTGATT
1 TTTTGTTTTTAATTTATTTGATT
15246 GATTGATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.08
24 7 0.18
25 4 0.11
26 13 0.34
27 7 0.18
28 4 0.11
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (25 bp):
TTTTGTTTTTAATTTATTTGATTTT
Found at i:17924 original size:19 final size:18
Alignment explanation
Indices: 17891--17926 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17881 TTGAAATTAT
17891 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
17909 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
17927 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.