Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020585.1 Corchorus olitorius cultivar O-4 contig20618, 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: 46962
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:764 original size:20 final size:21
Alignment explanation
Indices: 727--765 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
717 ACCCGGAAAC
**
727 TAAAGCGTGTTATTCGTGTTT
1 TAAAGCGTGTTAAACGTGTTT
748 TAAA-CGTGTTAAACGTGT
1 TAAAGCGTGTTAAACGTGT
766 CTTCGACACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (21 bp):
TAAAGCGTGTTAAACGTGTTT
Found at i:2768 original size:28 final size:28
Alignment explanation
Indices: 2728--2790 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
2718 TATTTCGCCT
2728 ATACCTAGGTTCTTAATTTGTTGGAAAA
1 ATACCTAGGTTCTTAATTTGTTGGAAAA
2756 ATACCTAGGTTCTTAATTTGTTGGAAAA
1 ATACCTAGGTTCTTAATTTGTTGGAAAA
2784 ATACCTA
1 ATACCTA
2791 AAGACTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (28 bp):
ATACCTAGGTTCTTAATTTGTTGGAAAA
Found at i:18956 original size:3 final size:3
Alignment explanation
Indices: 18950--18974 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18940 ATATCATACC
18950 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
18975 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:19694 original size:31 final size:31
Alignment explanation
Indices: 19658--19717 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
19648 AAAACCCTAA
19658 CCTAAACCCCAGAAATCCAACC-AAGCCAAGC
1 CCTAAACCCCAG-AATCCAACCGAAGCCAAGC
*
19689 CCTAAACCCCAGAATCCAGCCGAAGCCAA
1 CCTAAACCCCAGAATCCAACCGAAGCCAA
19718 CGGTAGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.40, C:0.42, G:0.12, T:0.07
Consensus pattern (31 bp):
CCTAAACCCCAGAATCCAACCGAAGCCAAGC
Found at i:36329 original size:22 final size:22
Alignment explanation
Indices: 36284--36330 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
36274 AAAATATTTC
**
36284 TAAATTGCCATTACTTTTTTTT
1 TAAATTGCCATTACTTTTGATT
36306 TAAATTGCCATTA-TTTATGATT
1 TAAATTGCCATTACTTT-TGATT
36328 TAA
1 TAA
36331 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (22 bp):
TAAATTGCCATTACTTTTGATT
Found at i:38402 original size:22 final size:22
Alignment explanation
Indices: 38358--38433 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
38348 TTATCACTAT
* *
38358 AAAATTTTATA-GGTAATTATC
1 AAAATTTCATAGGGTAGTTATC
* *
38379 AAAATTTCATATGGTGGTTATC
1 AAAATTTCATAGGGTAGTTATC
* * *
38401 AAAATTTAATAGGGTATTTATG
1 AAAATTTCATAGGGTAGTTATC
38423 AAAATTTCATA
1 AAAATTTCATA
38434 AAAATATTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 10 0.22
22 35 0.78
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (22 bp):
AAAATTTCATAGGGTAGTTATC
Found at i:40342 original size:15 final size:16
Alignment explanation
Indices: 40305--40342 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40295 ATATTTAAGA
40305 ATATATTTTTTAAAGG
1 ATATATTTTTTAAAGG
*
40321 ATTTATTTTTTAAA-G
1 ATATATTTTTTAAAGG
40336 ATATATT
1 ATATATT
40343 ATGATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (16 bp):
ATATATTTTTTAAAGG
Found at i:40690 original size:27 final size:27
Alignment explanation
Indices: 40592--40690 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
40582 GACCATCAGG
*
40592 TCAGGTCAATGGCAGAATACAGGACCA
1 TCAGGTCAAGGGCAGAATACAGGACCA
* * *
40619 TCAAGTCAAGGGTAGAATACGGGACCA
1 TCAGGTCAAGGGCAGAATACAGGACCA
* * * * *
40646 TCACGTTAAGGGTAGAATATAGGATCA
1 TCAGGTCAAGGGCAGAATACAGGACCA
*
40673 TCAGGTCAAGGGCGGAAT
1 TCAGGTCAAGGGCAGAAT
40691 TCAGAATCGG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.18
Consensus pattern (27 bp):
TCAGGTCAAGGGCAGAATACAGGACCA
Found at i:40860 original size:14 final size:13
Alignment explanation
Indices: 40841--40875 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
40831 TTACTCGCGG
40841 AGTCAACGGTCAA
1 AGTCAACGGTCAA
*
40854 TAGTCAACAGTCAA
1 -AGTCAACGGTCAA
40868 AGTCAACG
1 AGTCAACG
40876 CTGATATGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (13 bp):
AGTCAACGGTCAA
Found at i:41922 original size:19 final size:19
Alignment explanation
Indices: 41904--41940 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41894 TATTAATTAT
*
41904 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
41922 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
41941 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:43686 original size:251 final size:251
Alignment explanation
Indices: 43243--43745 Score: 952
Period size: 251 Copynumber: 2.0 Consensus size: 251
43233 AGCTTCTTCG
43243 ATTTTCTTACGATTGGCATCCCATTCTTCAATTGAAACATTGGATTCGAAATAATTCATACTTGA
1 ATTTTCTTACGATTGGCATCCCATTCTTCAATTGAAACATTGGATTCGAAATAATTCATACTTGA
* *
43308 CGAAACCTTTTTACCAACTTGTTTTGTTTGCTCAAGTCTTGATGAAAACCCAGCATTAATTCTTG
66 CGAAACCCTTTTACCAACTTGTTTTGCTTGCTCAAGTCTTGATGAAAACCCAGCATTAATTCTTG
43373 GTTTTCGATGAACTGCAGCCATAAGTAATCCTAGAGAAAATTGTCCAAGGAAAAAGGTTGTTATA
131 GTTTTCGATGAACTGCAGCCATAAGTAATCCTAGAGAAAATTGTCCAAGGAAAAAGGTTGTTATA
43438 AGAAGGAAAAATTAGAGAAATTAATGGGTGAATTATATAAAATTTAAATGGTTTAA
196 AGAAGGAAAAATTAGAGAAATTAATGGGTGAATTATATAAAATTTAAATGGTTTAA
*
43494 ATTTTCTTACGATTGGCATCCCATTCTTCAATTGAAACATTGGATTCGAAATAATTCATATTTGA
1 ATTTTCTTACGATTGGCATCCCATTCTTCAATTGAAACATTGGATTCGAAATAATTCATACTTGA
*
43559 CGAAACCCTTTTACCAACTTGTTTTGCTTGTTCAAGTCTTGATGAAAACCCAGCATTAATTCTTG
66 CGAAACCCTTTTACCAACTTGTTTTGCTTGCTCAAGTCTTGATGAAAACCCAGCATTAATTCTTG
* *
43624 GTTTTCGATGAACTGCAGCCATGATTAATCCTAGAGAAAATTGTCCAAGGAAAAAGGTTGTTATA
131 GTTTTCGATGAACTGCAGCCATAAGTAATCCTAGAGAAAATTGTCCAAGGAAAAAGGTTGTTATA
43689 AGAAGGAAAAATTAGAGAAATTAATGGGTGAATTATATAAAATTTAAATGGTTTAA
196 AGAAGGAAAAATTAGAGAAATTAATGGGTGAATTATATAAAATTTAAATGGTTTAA
43745 A
1 A
43746 AATCAAAGTG
Statistics
Matches: 246, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
251 246 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (251 bp):
ATTTTCTTACGATTGGCATCCCATTCTTCAATTGAAACATTGGATTCGAAATAATTCATACTTGA
CGAAACCCTTTTACCAACTTGTTTTGCTTGCTCAAGTCTTGATGAAAACCCAGCATTAATTCTTG
GTTTTCGATGAACTGCAGCCATAAGTAATCCTAGAGAAAATTGTCCAAGGAAAAAGGTTGTTATA
AGAAGGAAAAATTAGAGAAATTAATGGGTGAATTATATAAAATTTAAATGGTTTAA
Found at i:44187 original size:171 final size:171
Alignment explanation
Indices: 43902--44236 Score: 634
Period size: 171 Copynumber: 2.0 Consensus size: 171
43892 TAAGAATTAC
* *
43902 TTCTATTGAATACAATCGTTCGATGTTGAAAAAATATTTCAAAATTACAACATGATCTAAAATTT
1 TTCTATTGAATACAATCGCTCGATATTGAAAAAATATTTCAAAATTACAACATGATCTAAAATTT
43967 ATTATATTTCTAAATAGCAACTATTAATCTATAAATGGAAAACTGGATTTGCTTGAAACATATTA
66 ATTATATTTCTAAATAGCAACTATTAATCTATAAATGGAAAACTGGATTTGCTTGAAACATATTA
44032 TATCATCTAAATTGTAAAGTTTGCTTATATAATGTCTACTG
131 TATCATCTAAATTGTAAAGTTTGCTTATATAATGTCTACTG
44073 TTCTATTGAATACAATCGCTCGATATTGAAAAAATATTTCAAAATTACAACATGATCTAAAATTT
1 TTCTATTGAATACAATCGCTCGATATTGAAAAAATATTTCAAAATTACAACATGATCTAAAATTT
*
44138 ATTATCTTTCTAAATAGCAACTATTAATCTATAAATGGAAAACTGGATTTGCTTGAAACATATTA
66 ATTATATTTCTAAATAGCAACTATTAATCTATAAATGGAAAACTGGATTTGCTTGAAACATATTA
*
44203 TATCATCTAAATTGTAAAGTTTGTTTATATAATG
131 TATCATCTAAATTGTAAAGTTTGCTTATATAATG
44237 CTGTTTAAAA
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 160 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (171 bp):
TTCTATTGAATACAATCGCTCGATATTGAAAAAATATTTCAAAATTACAACATGATCTAAAATTT
ATTATATTTCTAAATAGCAACTATTAATCTATAAATGGAAAACTGGATTTGCTTGAAACATATTA
TATCATCTAAATTGTAAAGTTTGCTTATATAATGTCTACTG
Found at i:46596 original size:16 final size:16
Alignment explanation
Indices: 46575--46605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46565 TCAAGTTGTA
*
46575 TAGTAATCTTATTAAT
1 TAGTAACCTTATTAAT
46591 TAGTAACCTTATTAA
1 TAGTAACCTTATTAA
46606 CTGAGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
TAGTAACCTTATTAAT
Done.