Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020199.1 Corchorus olitorius cultivar O-4 contig20232, 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: 11055
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:318 original size:31 final size:31
Alignment explanation
Indices: 283--354 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
273 TAAATTATTG
*
283 CAAATTAAAACAAAT-TAAG-CGTTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
314 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
345 CAAATTAAAA
1 CAAATTAAAA
355 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:833 original size:17 final size:17
Alignment explanation
Indices: 811--848 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
801 TTCGGGTTCA
*
811 GGCTCGGGTTGGGATCG
1 GGCTCGGGTCGGGATCG
*
828 GGCTCGGGTCGGGTTCG
1 GGCTCGGGTCGGGATCG
845 GGCT
1 GGCT
849 GCCTCGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.21, G:0.53, T:0.24
Consensus pattern (17 bp):
GGCTCGGGTCGGGATCG
Found at i:893 original size:16 final size:16
Alignment explanation
Indices: 852--894 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
842 TCGGGCTGCC
852 TCGGGTTCGGGTATAT
1 TCGGGTTCGGGTATAT
* *
868 TCAGGCTCGGGTA-ATT
1 TCGGGTTCGGGTATA-T
884 TCGGGTTCGGG
1 TCGGGTTCGGG
895 CGGGTTCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.12, C:0.16, G:0.40, T:0.33
Consensus pattern (16 bp):
TCGGGTTCGGGTATAT
Found at i:5071 original size:22 final size:22
Alignment explanation
Indices: 5021--5072 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5011 GGGGTCAACT
* *
5021 AAATTTT-ATAGATAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
*
5042 AAAATTTCATAAAGAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
5064 AAATTTTCA
1 AAATTTTCA
5073 AAATGTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTTCATAAAGAGGTTATC
Found at i:5291 original size:22 final size:22
Alignment explanation
Indices: 5178--5669 Score: 202
Period size: 22 Copynumber: 22.5 Consensus size: 22
5168 TCATGGAGTA
* *
5178 ATCAAAATTTC--AGGCAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* ***
5198 ATCAAAATTTCACATTAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
5220 TTCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
5242 TTCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
5264 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
5286 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
5308 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
5330 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5346 ATCAAGATTTCATAAGGAGCTT
1 ATCAAAATTTCATAGGGAGGTT
*
5368 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
5391 ATCAAAATTTTATAGCTAGGAAGGTTT
1 ATCAAAATTTCATAG---GG-AGG-TT
* * *
5418 ATCAAAGTTTAATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
5440 ATTACAATTT-ATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
5461 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
5483 A-CTAACAA-TTCATATGAAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
5505 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
5527 ATGAATATATCATATTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
5549 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
5572 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
5594 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
5617 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5638 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
5660 AAAAAAATTT
1 ATCAAAATTT
5670 TATAAAAAGG
Statistics
Matches: 356, Mismatches: 91, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 13 0.04
21 24 0.07
22 238 0.67
23 44 0.12
24 1 0.00
26 2 0.01
27 19 0.05
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:5396 original size:23 final size:23
Alignment explanation
Indices: 5344--5439 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
5334 AAATTTGTAG
* * * *
5344 TTATCAAGATTTCATAAGGA-GC
1 TTATCAAAATTTTATAGGGAGGT
5366 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
5389 TTATCAAAATTTTATAGCTAGGAAGGT
1 TTATCAAAATTTTATAG---GG-AGGT
* * *
5416 TTATCAAAGTTTAATAGCGAGGT
1 TTATCAAAATTTTATAGGGAGGT
5439 T
1 T
5440 ATTACAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
22 17 0.27
23 23 0.37
24 1 0.02
26 2 0.03
27 19 0.31
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:5418 original size:27 final size:24
Alignment explanation
Indices: 5366--5439 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 24
5356 CATAAGGAGC
5366 TTATCAAAATTTTATAG-GGAGGT
1 TTATCAAAATTTTATAGCGGAGGT
5389 TTATCAAAATTTTATAGCTAGGAAGGT
1 TTATCAAAATTTTATAGC--GG-AGGT
* *
5416 TTATCAAAGTTTAATAGC-GAGGT
1 TTATCAAAATTTTATAGCGGAGGT
5439 T
1 T
5440 ATTACAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
23 22 0.49
24 1 0.02
26 2 0.04
27 20 0.44
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (24 bp):
TTATCAAAATTTTATAGCGGAGGT
Found at i:5732 original size:22 final size:22
Alignment explanation
Indices: 5112--5739 Score: 155
Period size: 22 Copynumber: 28.9 Consensus size: 22
5102 ATTTCTGTGG
*
5112 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
5134 TGGTTAAC-AAA-TT--T-GGA
1 AGGTTATCAAAATTTCATAGGA
* * *
5151 AGGTTATTAAACTTTTATCATGG-
1 AGGTTATCAAAATTTCAT-A-GGA
* *
5174 A-GTAATCAAAATTTC--AGGC
1 AGGTTATCAAAATTTCATAGGA
* * **
5193 AGGATATCAAAATTTCACATTA
1 AGGTTATCAAAATTTCATAGGA
* **
5215 AGGTTTTCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* *
5238 A-GTTTTCAAAATTTCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * *
5258 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
5281 AGATTAACAAAATTTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
** *
5303 AGGTTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
5325 AGGTTATCAAAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
*
5342 A-GTTATCAAGATTTCATAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
5363 AGCTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
5385 AGGTTTATCAAAATTTTATAGCTAGGA
1 AGG-TTATCAAAA-TTT-CA--TAGGA
* *
5412 AGGTTTATCAAAGTTTAATAGCG-
1 AGG-TTATCAAAATTTCATAG-GA
* *
5435 AGGTTATTACAATTT-ATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
5456 TGATTATCAAAATTTCAGAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
5478 TGATTA-CTAACAA-TTCATATGA
1 AGGTTATC-AA-AATTTCATAGGA
* * * *
5500 AGGTTTTTAAATTTTCATAACG-
1 AGGTTATCAAAATTTCAT-AGGA
* * * * *
5522 TGGTTATGAATATATCATATTG-
1 AGGTTATCAAAATTTCATA-GGA
* * *
5544 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* *
5567 TGGTTATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
5590 A-GTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
5611 AGGTCT-TCAAAATTCCTTAGGG
1 AGGT-TATCAAAATTTCATAGGA
* *
5633 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
** * **
5655 AGGTTAAAAAAATTTTATAAAA
1 AGGTTATCAAAATTTCATAGGA
* ** * *
5677 AGGTTCTTGAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** * *
5699 TCGTTTTTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
5721 AGATTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
5740 AGTAGATCAT
Statistics
Matches: 449, Mismatches: 110, Indels: 94
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 11 0.02
18 5 0.01
19 6 0.01
20 16 0.04
21 38 0.08
22 291 0.65
23 43 0.10
24 8 0.02
25 3 0.01
26 3 0.01
27 16 0.04
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:5746 original size:22 final size:22
Alignment explanation
Indices: 5707--5754 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5697 TATCGTTTTT
* *
5707 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAAGAAGATCATC
*
5729 AAAATTTCATAAGTAGATCATC
1 AAAATTTCATAAGAAGATCATC
5751 AAAA
1 AAAA
5755 ATAGTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAGAAGATCATC
Found at i:9539 original size:22 final size:22
Alignment explanation
Indices: 9513--9570 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
9503 GTATCTATGT
* * *
9513 GGTTATCAAAATTTCATAAGTA
1 GGTTATAAAAATTTAATAAGGA
* * *
9535 TGTTATTATAATTTAATAAGGA
1 GGTTATAAAAATTTAATAAGGA
9557 GGTTATAAAAATTT
1 GGTTATAAAAATTT
9571 TACAATGTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (22 bp):
GGTTATAAAAATTTAATAAGGA
Found at i:10803 original size:177 final size:178
Alignment explanation
Indices: 10425--10878 Score: 479
Period size: 177 Copynumber: 2.6 Consensus size: 178
10415 TAACTTTTCA
* * * * * *
10425 GAAGCATTTTTGGTATTTGAAAAATAAAATTTAGCTTTCAAGTCCTACATGAAAGTTGA-AGATC
1 GAAGCTTTTTTGATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTT-ATAGATC
* * ** *
10489 ATGAGACAGCCTTTTAACAGACACTTAAATCACCTCAATCGGACATATGGAGCAGAAATTATGTA
65 ATGAAACAACCTTTTAACAGACACTTAAATCACCTCAATAAGACATATGGAGCAGAAATAATGTA
* * * * * *
10554 TTATTAAGTGGACGATTCATTCTCGCTAACCGAAAAAATTAATTTTTTG
130 TTACTAAGTGGACGATCCATTCCCGCTAACCGAAAAAACTAATTATTCG
* * *
10603 AAAGCATTTTTT-ATACTTGAAACATTAAATTTAGCTTTGGAGTCCTGCATGAAAGTTATAGATC
1 GAAGC-TTTTTTGATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTATAGATC
* * ** * * * *
10667 ATAAAAGAACCTTTTATGAGA-ACTTGATTCAGCTCAATAAGACATCTGGAGCA-AAAGTAATGT
65 ATGAAACAACCTTTTAACAGACACTTAAATCACCTCAATAAGACATATGGAGCAGAAA-TAATGT
* *
10730 -TATACTAAGTGGATCG-TCCATTCCCGTTAACCGAAACAACTAATTATTCG
129 AT-TACTAAGTGGA-CGATCCATTCCCGCTAACCGAAAAAACTAATTATTCG
* * * * * *
10780 GAAGCTTTTTTGATACTTGAAACATTAAATTTAGTTTTCGAATCTTTCATGAAAGCTGTAGATCA
1 GAAGCTTTTTTGATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTATAGATCA
* *
10845 TGAAACAACCTTTTAATAGACACTTGAATCACCT
66 TGAAACAACCTTTTAACAGACACTTAAATCACCT
10879 TGATCGTATA
Statistics
Matches: 225, Mismatches: 44, Indels: 14
0.80 0.16 0.05
Matches are distributed among these distances:
176 10 0.04
177 135 0.60
178 75 0.33
179 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (178 bp):
GAAGCTTTTTTGATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTATAGATCA
TGAAACAACCTTTTAACAGACACTTAAATCACCTCAATAAGACATATGGAGCAGAAATAATGTAT
TACTAAGTGGACGATCCATTCCCGCTAACCGAAAAAACTAATTATTCG
Found at i:10961 original size:12 final size:12
Alignment explanation
Indices: 10944--10970 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10934 CCATTTATAA
10944 ATATATTATATT
1 ATATATTATATT
10956 ATATATTATATT
1 ATATATTATATT
10968 ATA
1 ATA
10971 ATTTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATATTATATT
Done.