Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024175.1 Corchorus olitorius cultivar O-4 contig24208, 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: 18101
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7261 original size:2 final size:2
Alignment explanation
Indices: 7254--7284 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7244 CTGATCATTC
7254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7285 ATTAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12349 original size:6 final size:6
Alignment explanation
Indices: 12329--12368 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
12319 GCTTAAAATT
* *
12329 AAAAAG AAATA- AAAAAG AAAAAG GAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
12369 TCTCCTTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:12356 original size:12 final size:11
Alignment explanation
Indices: 12330--12367 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
12320 CTTAAAATTA
12330 AAAAGAAATAA-
1 AAAAGAAA-AAG
12341 AAAAGAAAAAGG
1 AAAAGAAAAA-G
12353 AAAAGAAAAAG
1 AAAAGAAAAAG
12364 AAAA
1 AAAA
12368 ATCTCCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:12830 original size:12 final size:12
Alignment explanation
Indices: 12813--12844 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12803 ATAGTTGTAA
12813 AGTTTTTTTTTT
1 AGTTTTTTTTTT
12825 AGTTTTTTTTTT
1 AGTTTTTTTTTT
12837 --TTTTTTTT
1 AGTTTTTTTT
12845 AAATGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (12 bp):
AGTTTTTTTTTT
Found at i:14728 original size:163 final size:164
Alignment explanation
Indices: 14205--14880 Score: 1012
Period size: 162 Copynumber: 4.2 Consensus size: 164
14195 CGATAGAAAG
* * * *
14205 ACGCCGCCATATTAATATATGGA-GG-GAGATATTTTTTTCTCTTTTCTGT-AGGGAAAAATTCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGAGGGAAAAATTCC
*
14267 CTCCCCCC-AAAACAAAGAAAGTTTCCAACTCTATGCCTATAATATATAGCGGCGTTTGGACATC
66 CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATC
14331 AGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
131 AGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
* * * * *
14365 ACGCTGTCATTTTAATATATGGAGGGAGAGATTTTTTTTTTCC-TTTTTTTGAGGG-AAAATCCC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGAGGGAAAAATTCC
* *
14428 CTCCCCCCTAAAACAAAAAAAGTTTTCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATC
66 CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATC
14493 AGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
131 AGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
* * *
14527 ACGCCACTATTTTAATATATGGAGGGAGAGA-ATTTTTTTCCCTTTTTTTTAGAGGGAAAAATTT
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTT-GAGGGAAAAATTC
14591 CCT-CCCCCTAAAACAAAGAAA-TGTTCCAACTCTACGCCTATAATATATAGCGGCG-TTGGACA
65 CCTCCCCCCTAAAACAAAGAAAGT-TTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACA
14653 TCAGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
129 TCAGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
* **
14689 ACGCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTTTTCTTTTTTTTGGAGGGAAAAATTC
1 ACGCCGCCATTTTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTT-GAGGGAAAAATTC
***
14754 CCTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCTCAT
65 CCTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACAT
* * * *
14819 CAGACGCCGCTAATTAGTGGTGTCTAGGAAAGGAA
130 CAGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
* *
14854 ACGCCGCAATTGTAATATATGGAGGGA
1 ACGCCGCCATTTTAATATATGGAGGGA
14881 AAAAGTTCCC
Statistics
Matches: 466, Mismatches: 38, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
160 20 0.04
161 31 0.07
162 211 0.45
163 84 0.18
164 58 0.12
165 62 0.13
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (164 bp):
ACGCCGCCATTTTAATATATGGAGGGAGAGATATTTTTTTCCCTTTTTTTTGAGGGAAAAATTCC
CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATC
AGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAA
Found at i:14857 original size:327 final size:322
Alignment explanation
Indices: 14216--14880 Score: 1046
Period size: 327 Copynumber: 2.0 Consensus size: 322
14206 CGCCGCCATA
* *
14216 TTAATATATGGAGGGAGATATTTTTTTCTCTTTTCTGTAGGGAAAAATTCCCTCCCCCCAAAACA
1 TTAATATATGGAGGGAGAAATTTTTTTCCCTTTTCTGTAGGGAAAAATTCCCTCCCCCCAAAACA
*
14281 AAGAAAGTTTCCAACTCTATGCCTATAATATATAGCGGCGTTTGGACATCAGACGCCGCTAAGTA
66 AAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATCAGACGCCGCTAAGTA
* *
14346 GTGGCGTCTAGAAAATGAAACGCTGTCATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTT
131 GTGGCGTCTAGAAAATGAAACGCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTT
*
14411 TTTTGAGGGAAAATCCCCTCCCCCCTAAAACAAAAAAAGTTTTCAACTCTACGCCTATAATATAT
196 TTTTGAGGGAAAATCCCCTCCCCCCTAAAACAAAAAAAGTTTCCAACTCTACGCCTATAATATAT
* * *
14476 AGCGGCGTTTGGACATCAGACGCCGCTAAGTAGTGGCGTCTAGAAAATGAAACGCCACTATT
261 AGCGGCGTTTGCACATCAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCACAATT
* * * *
14538 TTAATATATGGAGGGAGAGAATTTTTTTCCCTTTTTTTTAGAGGGAAAAATTTCCTCCCCCTAAA
1 TTAATATATGGAGGGAGA-AATTTTTTTCCCTTTTCTGT--AGGGAAAAATTCCCTCCCCCCAAA
14603 ACAAAGAAA-TGTTCCAACTCTACGCCTATAATATATAGCGGCG-TTGGACATCAGACGCCGCTA
63 ACAAAGAAAGT-TTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATCAGACGCCGCTA
14666 AGTAGTGGCGTCTAGAAAATGAAACGCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTTTT
127 AGTAGTGGCGTCTAGAAAATGAAACGCCGCCATTTTAATATATGGAGGGAGAGA-TTTTTTTTTT
* * *
14731 CTTTTTTTTGGAGGGAAAAATTCCCTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTAT
191 CCTTTTTTT-GAGGG-AAAATCCCCTCCCCCCTAAAACAAAAAAAGTTTCCAACTCTACGCCTAT
* * * * * *
14796 AATATATAGCGGCGTTTTCTCATCAGACGCCGCTAATTAGTGGTGTCTAGGAAAGGAAACGCCGC
254 AATATATAGCGGCGTTTGCACATCAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCAC
14861 AATT
319 AATT
*
14865 GTAATATATGGAGGGA
1 TTAATATATGGAGGGA
14881 AAAAGTTCCC
Statistics
Matches: 313, Mismatches: 23, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
322 18 0.06
323 16 0.05
324 73 0.23
325 80 0.26
326 5 0.02
327 121 0.39
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (322 bp):
TTAATATATGGAGGGAGAAATTTTTTTCCCTTTTCTGTAGGGAAAAATTCCCTCCCCCCAAAACA
AAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTGGACATCAGACGCCGCTAAGTA
GTGGCGTCTAGAAAATGAAACGCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTT
TTTTGAGGGAAAATCCCCTCCCCCCTAAAACAAAAAAAGTTTCCAACTCTACGCCTATAATATAT
AGCGGCGTTTGCACATCAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCACAATT
Found at i:15454 original size:23 final size:20
Alignment explanation
Indices: 15416--15459 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
15406 TTTAGTTGTT
15416 TGATTTTTGTTGACTTTCATG
1 TGATTTTTGTTGACTTT-ATG
*
15437 TGATTTTGGTGTTTACTTTATG
1 TGATTTT--TGTTGACTTTATG
15459 T
1 T
15460 CTAGCTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.14, C:0.07, G:0.20, T:0.59
Consensus pattern (20 bp):
TGATTTTTGTTGACTTTATG
Done.