Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013477.1 Corchorus olitorius cultivar O-4 contig13510, 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: 15403
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:531 original size:23 final size:23
Alignment explanation
Indices: 505--580 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
495 AAAAAACAAC
*
505 AACAACAACATTTTGATCATCAA
1 AACAACAACATTTTGAACATCAA
528 AACAACAACATTTTGAACATCAA
1 AACAACAACATTTTGAACATCAA
* * **
551 AACAGCAACATCTTGAACAGAAA
1 AACAACAACATTTTGAACATCAA
574 AACAACA
1 AACAACA
581 TCTTCAACAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.53, C:0.22, G:0.07, T:0.18
Consensus pattern (23 bp):
AACAACAACATTTTGAACATCAA
Found at i:582 original size:20 final size:20
Alignment explanation
Indices: 531--597 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
521 TCATCAAAAC
* *
531 AACAACATTTTGAACATCAAA
1 AACAACATCTTGAACA-GAAA
552 ACAGCAACATCTTGAACAGAAA
1 A-A-CAACATCTTGAACAGAAA
*
574 AACAACATCTTCAACAGAAA
1 AACAACATCTTGAACAGAAA
594 AACA
1 AACA
598 GTAACATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 21 0.51
21 2 0.05
22 5 0.12
23 13 0.32
ACGTcount: A:0.54, C:0.22, G:0.07, T:0.16
Consensus pattern (20 bp):
AACAACATCTTGAACAGAAA
Found at i:596 original size:43 final size:43
Alignment explanation
Indices: 531--618 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
521 TCATCAAAAC
* * ** *
531 AACAACATTTTGAACATCAAAACAGCAACATCTTGAACAGAAA
1 AACAACATCTTCAACAGAAAAACAGCAACATCTTCAACAGAAA
* *
574 AACAACATCTTCAACAGAAAAACAGTAACATTTTCAACAGAAA
1 AACAACATCTTCAACAGAAAAACAGCAACATCTTCAACAGAAA
617 AA
1 AA
619 ACAGCAGCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.18
Consensus pattern (43 bp):
AACAACATCTTCAACAGAAAAACAGCAACATCTTCAACAGAAA
Found at i:609 original size:23 final size:22
Alignment explanation
Indices: 549--618 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
539 TTTGAACATC
*
549 AAAACAGCAACATCTTGAACAGA
1 AAAACAG-AACATCTTCAACAGA
572 AAAAC--AACATCTTCAACAGA
1 AAAACAGAACATCTTCAACAGA
*
592 AAAACAGTAACATTTTCAACAGA
1 AAAACAG-AACATCTTCAACAGA
615 AAAA
1 AAAA
619 ACAGCAGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 19 0.45
23 23 0.55
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAACAGAACATCTTCAACAGA
Found at i:632 original size:24 final size:23
Alignment explanation
Indices: 526--633 Score: 73
Period size: 23 Copynumber: 4.8 Consensus size: 23
516 TTTGATCATC
* * * **
526 AAAACAACAACATTTTGAACATC
1 AAAACAGCAACAATTTCAACAGA
*
549 AAAACAGCAAC-ATCTTGAACAG-
1 AAAACAGCAACAAT-TTCAACAGA
571 AAAA-A-CAAC-ATCTTCAACAGA
1 AAAACAGCAACAAT-TTCAACAGA
* *
592 AAAACAGTAACATTTTCAACAGAA
1 AAAACAGCAACAATTTCAACAG-A
*
616 AAAACAGCAGCAATTTCA
1 AAAACAGCAACAATTTCA
634 GGGGATCTTC
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
20 14 0.20
21 5 0.07
22 6 0.09
23 28 0.40
24 17 0.24
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAACAGCAACAATTTCAACAGA
Found at i:2475 original size:13 final size:13
Alignment explanation
Indices: 2457--2483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2447 GGCTTTGGGC
2457 TTTGGGTTGGGTA
1 TTTGGGTTGGGTA
2470 TTTGGGTTGGGTA
1 TTTGGGTTGGGTA
2483 T
1 T
2484 ATCATAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.48
Consensus pattern (13 bp):
TTTGGGTTGGGTA
Found at i:2666 original size:42 final size:43
Alignment explanation
Indices: 2595--2678 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
2585 TTTAAACGTG
2595 TTAATCGTGTCAACGACACGATTATGACACGAAACACGATAATC
1 TTAATCGTGTC-ACGACACGATTATGACACGAAACACGATAATC
*
2639 TTAATCGTGTC-CGACACGATT-TCGACACGAGACACGATAA
1 TTAATCGTGTCACGACACGATTAT-GACACGAAACACGATAA
2679 GCCAAACACG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
41 1 0.03
42 26 0.68
44 11 0.29
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCACGACACGATTATGACACGAAACACGATAATC
Found at i:12123 original size:21 final size:21
Alignment explanation
Indices: 12082--12124 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12072 CCAATTTAGG
* *
12082 TTTAGATTTCAATTTCTTTTT
1 TTTAGATTTAAATTTCATTTT
12103 TTTAGATTTAAGATTT-ATTTT
1 TTTAGATTTAA-ATTTCATTTT
12124 T
1 T
12125 ATGCATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTAGATTTAAATTTCATTTT
Found at i:15020 original size:21 final size:21
Alignment explanation
Indices: 14994--15085 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
14984 TGCTAGGAGA
14994 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
15015 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
15036 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
15057 TCATTGGAGATGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
15078 TCATTGGA
1 TCATTGGA
15086 ATTGCCTAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 2 0.03
21 66 0.97
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.