Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022189.1 Corchorus olitorius cultivar O-4 contig22222, 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: 22378
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:6011 original size:31 final size:31
Alignment explanation
Indices: 5973--6031 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5963 GAGCAACTGC
5973 ACTTAGCAAGACCTGTCCTATATCATTTTGA
1 ACTTAGCAAGACCTGTCCTATATCATTTTGA
6004 ACTTAGCAAGACCTGTCCTATATCATTT
1 ACTTAGCAAGACCTGTCCTATATCATTT
6032 CGAAATACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (31 bp):
ACTTAGCAAGACCTGTCCTATATCATTTTGA
Found at i:9356 original size:16 final size:16
Alignment explanation
Indices: 9335--9394 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
9325 ATCTTAGCTT
9335 TCTCTCCCACACACAA
1 TCTCTCCCACACACAA
*
9351 TCTCTCCCACACGCAA
1 TCTCTCCCACACACAA
9367 TCTCTCCCACACACAA
1 TCTCTCCCACACACAA
*
9383 TCTCACCCACAC
1 TCTCTCCCACAC
9395 TAAAAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.28, C:0.52, G:0.02, T:0.18
Consensus pattern (16 bp):
TCTCTCCCACACACAA
Found at i:11078 original size:13 final size:14
Alignment explanation
Indices: 11053--11086 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
11043 TCCACTATCA
11053 AATCAATCAATTAT
1 AATCAATCAATTAT
11067 AATCAA-CAATTAT
1 AATCAATCAATTAT
11080 AA-CAATC
1 AATCAATC
11087 TCTCAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 10 0.53
14 6 0.32
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (14 bp):
AATCAATCAATTAT
Found at i:12314 original size:46 final size:46
Alignment explanation
Indices: 12256--12348 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
12246 CTTATTTTTC
*
12256 CCTTTATTAAGAACAATTACTACTGTTCTTAAAAACATTTTAAACA
1 CCTTTATTAAGAACAAATACTACTGTTCTTAAAAACATTTTAAACA
*
12302 CCTTT-TTCAAGAACAAATACTACTGTTTTTAAAAACATTTTAAACA
1 CCTTTATT-AAGAACAAATACTACTGTTCTTAAAAACATTTTAAACA
12348 C
1 C
12349 ACATCCGAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (46 bp):
CCTTTATTAAGAACAAATACTACTGTTCTTAAAAACATTTTAAACA
Found at i:15592 original size:21 final size:20
Alignment explanation
Indices: 15560--15603 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
15550 TCGGGTCATT
*
15560 TTTCGGTTGGGTAGTTTCGG
1 TTTCGGTTGGGTAGATTCGG
*
15580 TTTCGGATTGGGTGGATTCGG
1 TTTCGG-TTGGGTAGATTCGG
15601 TTT
1 TTT
15604 GTTGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.07, C:0.09, G:0.39, T:0.45
Consensus pattern (20 bp):
TTTCGGTTGGGTAGATTCGG
Found at i:20659 original size:6 final size:6
Alignment explanation
Indices: 20650--20696 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
20640 AAAAAAACAA
*
20650 AAAAAC AAAAGAC -AAAA- AAAAAC AAAAAC AAAAAC AAAAAC CAAAAC
1 AAAAAC AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
20697 TAGGTAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.14
6 30 0.81
7 2 0.05
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:20666 original size:12 final size:11
Alignment explanation
Indices: 20638--20696 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
20628 TAGCTTTCGT
20638 AAAA-AAAAAC
1 AAAACAAAAAC
20648 AAAA-AAACAA-
1 AAAACAAA-AAC
*
20658 AAGACAAAAA-
1 AAAACAAAAAC
20668 AAAACAAAAAC
1 AAAACAAAAAC
20679 AAAAACAAAAACC
1 -AAAACAAAAA-C
20692 AAAAC
1 AAAAC
20697 TAGGTAGCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 21 0.50
11 5 0.12
12 15 0.36
13 1 0.02
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:20668 original size:17 final size:16
Alignment explanation
Indices: 20648--20688 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
20638 AAAAAAAAAC
20648 AAAAAAACAAAAGACAA
1 AAAAAAACAAAA-ACAA
20665 AAAAAAACAAAAACAA
1 AAAAAAACAAAAACAA
20681 AAACAAAA
1 AAA-AAAA
20689 ACCAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAACAA
Found at i:21523 original size:44 final size:44
Alignment explanation
Indices: 21460--21584 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
21450 TGACAATCAA
* * * * *
21460 ACCAAAATTACATAGAGAGATTATCAAAATTTCGTAGTGTTGTT
1 ACCAAAATTTCACACAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
21504 ACCAAATTTTCACATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCACACAGAGATTATCAAAATTTCATAGTGTAGTT
* * * *
21548 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCACACAGAGATTATCAAAATTTCATAG
21585 GGAGGGAGGT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCACACAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:21589 original size:22 final size:22
Alignment explanation
Indices: 21460--21605 Score: 96
Period size: 22 Copynumber: 6.5 Consensus size: 22
21450 TGACAATCAA
* *
21460 ACCAAAATTACATAGAGAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * * **
21482 ATCAAAATTTCGTAGTGTTGTT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
21504 ACCAAATTTTCACATAGAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * *
21526 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGAG-AGGTT
* *
21548 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
21570 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
21596 ACCAAAATTT
1 ACCAAAATTT
21606 GTGCTTATCA
Statistics
Matches: 90, Mismatches: 28, Indels: 8
0.71 0.22 0.06
Matches are distributed among these distances:
21 1 0.01
22 71 0.79
23 1 0.01
24 1 0.01
26 16 0.18
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:21674 original size:22 final size:23
Alignment explanation
Indices: 21627--21684 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
21617 ATTCCTAAAG
* *
21627 AGGTTAAC-AAAATTTTATAGGG
1 AGGTTATCGAAAATTTTATAGGA
21649 AGGTTAT-GAAAATTTTAT-GGAA
1 AGGTTATCGAAAATTTTATAGG-A
21671 AGGTTATCGAAAAT
1 AGGTTATCGAAAAT
21685 ACATATAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 23 0.74
23 6 0.19
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.33
Consensus pattern (23 bp):
AGGTTATCGAAAATTTTATAGGA
Found at i:21747 original size:22 final size:22
Alignment explanation
Indices: 21713--21956 Score: 149
Period size: 22 Copynumber: 11.1 Consensus size: 22
21703 AGTTTCATTC
* *
21713 TCATAGGGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
*
21735 TCATGGTGTGGTTATCAAAATTT
1 TCATAGTGTGGTTATCAAAA-TT
* * *
21758 TCATACTGCGGTTA-C-CAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
21778 TTATTTAGTGTGATTATTAAAATT
1 TCA--TAGTGTGGTTATCAAAATT
* * *
21802 TTATAG-GCAGATTATCAAAATT
1 TCATAGTG-TGGTTATCAAAATT
* * * * *
21824 TCACACTGAGATTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
21846 TCATAGTGTGGTTACCCAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
21868 TCATAGTGTGGTTATCGAATTT
1 TCATAGTGTGGTTATCAAAATT
* * *
21890 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
21912 TCATA-T-TAGGTTATC-AAATT
1 TCATAGTGT-GGTTATCAAAATT
* * *
21932 TGCAAAATGTGGTTATCAATATT
1 T-CATAGTGTGGTTATCAAAATT
21955 TC
1 TC
21957 TACGCTGGAG
Statistics
Matches: 175, Mismatches: 35, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
20 10 0.06
21 13 0.07
22 125 0.71
23 20 0.11
24 7 0.04
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:21915 original size:44 final size:44
Alignment explanation
Indices: 21713--21932 Score: 164
Period size: 44 Copynumber: 5.0 Consensus size: 44
21703 AGTTTCATTC
*
21713 TCATAGGGAGGTTATCAAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATC-AAATTT
** * * * * *
21758 TCATACTGCGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAATTT
1 TCATAGGGAGGTTATCAAAATTTCA--TAGTGTGGTTA-TCAAATTT
* * * * * *
21803 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TT
1 TCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATC-AAATTT
* * * * *
21846 TCATAGTGTGGTTACCCAAATTTCATAGTGTGGTTATCGAATTT
1 TCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAATTT
*
21890 TCATAGGGAGGTTATCGAAATTTCATA-T-TAGGTTATCAAATTT
1 TCATAGGGAGGTTATCAAAATTTCATAGTGT-GGTTATCAAATTT
21933 GCAAAATGTG
Statistics
Matches: 131, Mismatches: 35, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
42 1 0.01
43 25 0.19
44 70 0.53
45 28 0.21
46 7 0.05
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (44 bp):
TCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAATTT
Done.