Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022195.1 Corchorus olitorius cultivar O-4 contig22228, 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: 14774
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Found at i:5331 original size:3 final size:3
Alignment explanation
Indices: 5323--5360 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5313 TTATGCCTAA
5323 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5361 CTTAACCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6464 original size:38 final size:38
Alignment explanation
Indices: 6376--6549 Score: 287
Period size: 38 Copynumber: 4.6 Consensus size: 38
6366 GAATTGCTAG
* *
6376 TTAAGTAAACCTTCTTAGGTCCT-TGTTTAGAATTTTAAT
1 TTAAGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCAT
*
6415 TTAAGTAAACCTACTTAGGTCTATGTTTAGAATTTCAT
1 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
6453 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
1 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
6491 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
1 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
*
6529 TTAAGAAAACCTGCTTAGGTC
1 TTAAGTAAACCTGCTTAGGTC
6550 CTTGTGTAGA
Statistics
Matches: 130, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
38 102 0.78
39 28 0.22
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (38 bp):
TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCAT
Found at i:6641 original size:27 final size:27
Alignment explanation
Indices: 6610--6681 Score: 144
Period size: 27 Copynumber: 2.7 Consensus size: 27
6600 GCTTTGATCA
6610 AGTAAACCTGCTTAGGTCCCCATTTCG
1 AGTAAACCTGCTTAGGTCCCCATTTCG
6637 AGTAAACCTGCTTAGGTCCCCATTTCG
1 AGTAAACCTGCTTAGGTCCCCATTTCG
6664 AGTAAACCTGCTTAGGTC
1 AGTAAACCTGCTTAGGTC
6682 TACGTTTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (27 bp):
AGTAAACCTGCTTAGGTCCCCATTTCG
Found at i:6711 original size:66 final size:66
Alignment explanation
Indices: 6637--6787 Score: 189
Period size: 67 Copynumber: 2.3 Consensus size: 66
6627 CCCCATTTCG
* * **
6637 AGTAAACCTGCTTAGGTCCCCA-TTTCGAGTAAACCTGCTTAGGT-CTACGTTTGGAATTTTCGT
1 AGTAAACCTGCTTAGGTCCCCATTTTCAAGAAAACCTGCTTAGGTCCTA--TTTAAAATTTTCGT
*
6700 TTA
64 TAA
*
6703 AGTAAACCTGCTTAGGTCCCCATTTTTAAGAAAACCTGCTTAGGTCCCTATTTAAAATTTTCGTT
1 AGTAAACCTGCTTAGGTCCCCATTTTCAAGAAAACCTGCTTAGGT-CCTATTTAAAATTTTCGTT
6768 AA
65 AA
* *
6770 AGTGAACCTGTTTAGGTC
1 AGTAAACCTGCTTAGGTC
6788 TCTGCTTAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
66 22 0.30
67 49 0.66
69 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (66 bp):
AGTAAACCTGCTTAGGTCCCCATTTTCAAGAAAACCTGCTTAGGTCCTATTTAAAATTTTCGTTA
A
Found at i:6739 original size:28 final size:28
Alignment explanation
Indices: 6699--6755 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
6689 GGAATTTTCG
*
6699 TTTAAGTAAACCTGCTTAGGTCCCCATT
1 TTTAAGAAAACCTGCTTAGGTCCCCATT
*
6727 TTTAAGAAAACCTGCTTAGGTCCCTATT
1 TTTAAGAAAACCTGCTTAGGTCCCCATT
6755 T
1 T
6756 AAAATTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (28 bp):
TTTAAGAAAACCTGCTTAGGTCCCCATT
Found at i:8814 original size:19 final size:18
Alignment explanation
Indices: 8781--8816 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8771 TGCAAATAAT
8781 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
8799 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
8817 TAAGTCTTCA
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
Found at i:10361 original size:30 final size:28
Alignment explanation
Indices: 10327--10387 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
10317 GATAGTTTAT
10327 TAAA-GAAACTTGAAAATTAAAGACATAAGA
1 TAAAGGAAA-TTGAAAATTAAAG-CATAA-A
10357 TAAAGGAAATTGAAAATTAAAGCATAAA
1 TAAAGGAAATTGAAAATTAAAGCATAAA
10385 TAA
1 TAA
10388 CTAATCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 4 0.13
29 5 0.17
30 17 0.57
31 4 0.13
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (28 bp):
TAAAGGAAATTGAAAATTAAAGCATAAA
Found at i:10428 original size:14 final size:14
Alignment explanation
Indices: 10411--10440 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10401 GCATAAAAAT
*
10411 AAATCTTAAATCTA
1 AAATCTTAAAACTA
10425 AAATCTTAAAACTA
1 AAATCTTAAAACTA
10439 AA
1 AA
10441 CCTAAATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATCTTAAAACTA
Found at i:11631 original size:12 final size:12
Alignment explanation
Indices: 11614--11638 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11604 TGCTCTCAAC
11614 CAAATTTTGCTT
1 CAAATTTTGCTT
11626 CAAATTTTGCTT
1 CAAATTTTGCTT
11638 C
1 C
11639 TTATGTTGTG
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:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (12 bp):
CAAATTTTGCTT
Found at i:12152 original size:13 final size:13
Alignment explanation
Indices: 12134--12159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12124 GATTAGTCAT
12134 GCGGCCTTGCGGG
1 GCGGCCTTGCGGG
12147 GCGGCCTTGCGGG
1 GCGGCCTTGCGGG
12160 TGCTCCAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.54, T:0.15
Consensus pattern (13 bp):
GCGGCCTTGCGGG
Done.