Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012984.1 Corchorus olitorius cultivar O-4 contig13017, 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: 39472
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:669 original size:17 final size:18
Alignment explanation
Indices: 647--681 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
637 CTAGGCGTTT
*
647 TCAATTT-CTTGGTTTGA
1 TCAATTTCCTTGGCTTGA
664 TCAATTTCCTTGGCTTGA
1 TCAATTTCCTTGGCTTGA
682 GTATTCTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (18 bp):
TCAATTTCCTTGGCTTGA
Found at i:3002 original size:19 final size:18
Alignment explanation
Indices: 2978--3050 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 18
2968 ATTTCGGTTT
* *
2978 TTTTTTATTAAAAAACCAA
1 TTTTTT-TTAAAAAATCAC
2997 TTTTTTTTAAAACAATCAC
1 TTTTTTTTAAAA-AATCAC
3016 TTTTTTTTTGAAAAAATCAC
1 -TTTTTTTT-AAAAAATCAC
*
3036 TTTTTTTGAAAAAAT
1 TTTTTTTTAAAAAAT
3051 AAATTGAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.27
19 17 0.35
20 14 0.29
21 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTTTTTTAAAAAATCAC
Found at i:3002 original size:20 final size:19
Alignment explanation
Indices: 2977--3042 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
2967 GATTTCGGTT
*
2977 TTTTTTTATTAAAAAACCA-
1 TTTTTTT-TTAAAAAATCAC
*
2996 ATTTTTTTTAAAACAATCAC
1 TTTTTTTTTAAAA-AATCAC
3016 TTTTTTTTTGAAAAAATCAC
1 TTTTTTTTT-AAAAAATCAC
3036 TTTTTTT
1 TTTTTTT
3043 GAAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.15
19 10 0.24
20 21 0.51
21 4 0.10
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTTTTTTAAAAAATCAC
Found at i:9678 original size:29 final size:30
Alignment explanation
Indices: 9639--9699 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
9629 TATAAATAAT
* *
9639 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
9668 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
9698 AT
1 AT
9700 TAATTAGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:11425 original size:22 final size:22
Alignment explanation
Indices: 11399--11444 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11389 TTCACCAACA
11399 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
11421 TCTCCTTTCCTTCATGCTAAAC
1 TCTCCTTTCCTTCATGCTAAAC
11443 TC
1 TC
11445 AAAAGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.37, G:0.04, T:0.41
Consensus pattern (22 bp):
TCTCCTTTCCTTCATGCTAAAC
Found at i:23996 original size:2 final size:2
Alignment explanation
Indices: 23989--24022 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23979 TATATTTGTT
23989 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24023 AGAAATGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39146 original size:29 final size:30
Alignment explanation
Indices: 39086--39165 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
39076 GCTAAATACC
* *
39086 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTAGGGA
*
39117 CAAAATAATCTCTTATGTTTT-TTTAGGGA
1 CAAAATAATCCCTTATGTTTTCTTTAGGGA
* *
39146 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
39166 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTAGGGA
Found at i:39328 original size:31 final size:31
Alignment explanation
Indices: 39293--39386 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
39283 GACTGATTTG
39293 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
1 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
*
39324 TCCCAAAAGAAAAACATAAGGGATTTTTTTG
1 TCCCAAAAGAAAAACATAAGGGATTTTTTTA
* * *
39355 TCACAAAAGAAAAATATAAGAGAATTTTTTTA
1 TCCCAAAAGAAAAACATAAG-GGATTTTTTTA
39387 GTATTTAGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 48 0.84
32 9 0.16
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (31 bp):
TCCCAAAAGAAAAACATAAGGGATTTTTTTA
Done.