Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021301.1 Corchorus olitorius cultivar O-4 contig21334, 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: 33514
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1489 original size:30 final size:29
Alignment explanation
Indices: 1426--1495 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
1416 ACCGAACCGT
* ****
1426 CAAATAAGCCCCTGAACTTTTATTTCAGC
1 CAAATAAGCCCCTGAACTCTTAAAAAAGC
1455 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTCTTAAAAAA-GC
1485 CAAATAAGCCC
1 CAAATAAGCCC
1496 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTTAAAAAAGC
Found at i:9680 original size:14 final size:15
Alignment explanation
Indices: 9663--9697 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9653 CAGCTCTTCA
*
9663 CTTTTT-CCTTCTCT
1 CTTTTTCCCTTCTAT
9677 CTTTTTCCCTTCTAT
1 CTTTTTCCCTTCTAT
9692 CTTTTT
1 CTTTTT
9698 TTTTAATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTTTCCCTTCTAT
Found at i:13303 original size:2 final size:2
Alignment explanation
Indices: 13296--13328 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13286 TACTATTTAG
13296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13329 TAGTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16230 original size:17 final size:17
Alignment explanation
Indices: 16208--16240 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16198 AATCTAATTC
16208 AACATT-TTGCCAACTAA
1 AACATTATTG-CAACTAA
16225 AACATTATTGCAACTA
1 AACATTATTGCAACTA
16241 TGTGGAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (17 bp):
AACATTATTGCAACTAA
Found at i:24178 original size:483 final size:483
Alignment explanation
Indices: 23268--24237 Score: 1825
Period size: 483 Copynumber: 2.0 Consensus size: 483
23258 TGCTTTTATT
*
23268 TATAAGTAATAGAAAGTGCAAAGAAGTAATAGAATATGCTGTTAATTGGATAATAATAGACGCAT
1 TATAAGTAATAGAAAGTGCAAAGAAGTAATAGAATATGCAGTTAATTGGATAATAATAGACGCAT
*
23333 TGAAGAAAGAGTGGTTTAACTCAAAAGGGAAAAATATTGAACGATCCATGGTGAAGGGATGGGGA
66 TGAAGAAAGAGTGGTTTAACTCAAAAGGGAAAAACATTGAACGATCCATGGTGAAGGGATGGGGA
*
23398 ATGAGAAGAAAGAGGAAAGAGATGTGAAGGTGAAAACAGAGGGGAGTGATGAAAGGTTTGATTTT
131 AGGAGAAGAAAGAGGAAAGAGATGTGAAGGTGAAAACAGAGGGGAGTGATGAAAGGTTTGATTTT
23463 TGGCAAACCTGAAGATTGATCAGCACCGGGGAGTTGAAAGGAAGCAGCAACTGAGTTGGTAAGAG
196 TGGCAAACCTGAAGATTGATCAGCACCGGGGAGTTGAAAGGAAGCAGCAACTGAGTTGGTAAGAG
23528 GAAAAAAGAAAACAGGGGGAGAAACATTAATTAAAAGCAATTAAGGAAGGGATCAAATGGGTAAT
261 GAAAAAAGAAAACAGGGGGAGAAACATTAATTAAAAGCAATTAAGGAAGGGATCAAATGGGTAAT
23593 TACAAAAAAGGGTAGCAGGGAAAAGGAAGGGGGGAAAAACGTAGAGGGGCTTTTTAGTCATCCGA
326 TACAAAAAAGGGTAGCAGGGAAAAGGAAGGGGGGAAAAACGTAGAGGGGCTTTTTAGTCATCCGA
*
23658 AAAATGAGAACAGACCAAAAAAAGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTA
391 AAAATGAGAAAAGACCAAAAAAAGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTA
23723 GTAATTT-CTTGGGTACTAAAAATAATA
456 GTAATTTCCTTGGGTACTAAAAATAATA
23750 TATATAGTAATAGAAAGTGCAAAGAAGTAATAGAATATGCAGTTAATTGGATAATAATAGACGCA
1 TATA-AGTAATAGAAAGTGCAAAGAAGTAATAGAATATGCAGTTAATTGGATAATAATAGACGCA
* *
23815 TTGAAGAAAGCGTGGTTTAATTCAAAAGGGAAAAACATTGAACGATCCATGGTGAAGGGATGGGG
65 TTGAAGAAAGAGTGGTTTAACTCAAAAGGGAAAAACATTGAACGATCCATGGTGAAGGGATGGGG
*
23880 AAGGAGAAGAAAGAGGAAAGAGATGTGAAGGTGAAAACAGAGGGGAGTGATGAAATGTTTGATTT
130 AAGGAGAAGAAAGAGGAAAGAGATGTGAAGGTGAAAACAGAGGGGAGTGATGAAAGGTTTGATTT
*
23945 TTGGCAAACCTGAAGATTGATCAGCACCGGGGAGTTGAAAGGAAGCAGCAACTGAGTTGTTAAGA
195 TTGGCAAACCTGAAGATTGATCAGCACCGGGGAGTTGAAAGGAAGCAGCAACTGAGTTGGTAAGA
24010 GGAAAAAAGAAAACAGGGGGAGAAACATTAATTAAAAGCAATTAAGGAAGGGATCAAATGGGTAA
260 GGAAAAAAGAAAACAGGGGGAGAAACATTAATTAAAAGCAATTAAGGAAGGGATCAAATGGGTAA
* * *
24075 TTACGAAAAAGGGTAGCAGGGAAAAGGAAGGGGGGAAACACGTAGAGGTGCTTTTTAGTCATCCG
325 TTACAAAAAAGGGTAGCAGGGAAAAGGAAGGGGGGAAAAACGTAGAGGGGCTTTTTAGTCATCCG
24140 AAAAATGAGAAAAGACCAAAAAAAGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTT
390 AAAAATGAGAAAAGACCAAAAAAAGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTT
24205 AGTAATTTCCTTGGGTACTAAAAATAATA
455 AGTAATTTCCTTGGGTACTAAAAATAATA
24234 TATA
1 TATA
24238 GTATATATTA
Statistics
Matches: 475, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
482 4 0.01
483 447 0.94
484 24 0.05
ACGTcount: A:0.42, C:0.10, G:0.28, T:0.21
Consensus pattern (483 bp):
TATAAGTAATAGAAAGTGCAAAGAAGTAATAGAATATGCAGTTAATTGGATAATAATAGACGCAT
TGAAGAAAGAGTGGTTTAACTCAAAAGGGAAAAACATTGAACGATCCATGGTGAAGGGATGGGGA
AGGAGAAGAAAGAGGAAAGAGATGTGAAGGTGAAAACAGAGGGGAGTGATGAAAGGTTTGATTTT
TGGCAAACCTGAAGATTGATCAGCACCGGGGAGTTGAAAGGAAGCAGCAACTGAGTTGGTAAGAG
GAAAAAAGAAAACAGGGGGAGAAACATTAATTAAAAGCAATTAAGGAAGGGATCAAATGGGTAAT
TACAAAAAAGGGTAGCAGGGAAAAGGAAGGGGGGAAAAACGTAGAGGGGCTTTTTAGTCATCCGA
AAAATGAGAAAAGACCAAAAAAAGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTA
GTAATTTCCTTGGGTACTAAAAATAATA
Found at i:32575 original size:271 final size:272
Alignment explanation
Indices: 32085--32575 Score: 693
Period size: 272 Copynumber: 1.8 Consensus size: 272
32075 TGATTTACAA
** * *
32085 CTTTCATGAAGGACTCAAAAGTTAGTTTTTATGTTTCAATTCAAAAAAATGCTTCCGAAATTTGG
1 CTTTCATGAAGGACTCAAAAGGCAGATTTTATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGG
* * * **
32150 TGATTTTGATTGCCGGTCTATTAAATATCATATAATTTTCGATCCACAAGTCTGATTAATGTTAT
66 TGATTTCGATTGCCGGTCTATTAAATACCATATAATTTTCGATCCACAAGTCCGATTAAAATTAT
* * * *
32215 TCAAGTGTCGGTTAAAAGGTTATTGCATGATCTGCGACTTTCATGAAGGACCCGAAAGCTAAATT
131 TCAAGTGTCGGTTAAAAGGTTATGGCATGATATACGACTTTCATGAAGGACCAGAAAGCTAAATT
** * *
32280 TGATCTATGAGTTTCATTAAGGGTTTTTTTTTGCCAAACATTAAGGGTTCAAAAGGGTTAAAAGG
196 TGATCTACAAGGTTCATGAAGGGTTTTTTTTTGCCAAACATTAAGGGTTCAAAAGGGTTAAAAGG
32345 TAATTATATGAT
261 TAATTATATGAT
* *
32357 CTTTCATGAAGGACTTAAAAGGCA-ATTTTATGTTTCAATTGGAAAAAAATGCTTCCCAAATTTG
1 CTTTCATGAAGGACTCAAAAGGCAGATTTTATGTTTCAATT-CAAAAAAATGCTTCCCAAATTTG
* * *
32421 GT-AGTTTCGATTGCCGGTCTATTTAATACCATATAATTTTGGATCCACAGGTCCGATTAAAATT
65 GTGA-TTTCGATTGCCGGTCTATTAAATACCATATAATTTTCGATCCACAAGTCCGATTAAAATT
* * * *
32485 -TTTAAGTGTCGGTTAAAAGGTTATGGCGTGATATACGACTTTCATGGA-GTCTCAGAAAGCTAA
129 ATTCAAGTGTCGGTTAAAAGGTTATGGCATGATATACGACTTTCATGAAGGAC-CAGAAAGCTAA
32548 ATTTGATCTACAAGGTTCATGAAGGGTT
193 ATTTGATCTACAAGGTTCATGAAGGGTT
32576 CAAACGGGAA
Statistics
Matches: 190, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
270 2 0.01
271 92 0.48
272 96 0.51
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (272 bp):
CTTTCATGAAGGACTCAAAAGGCAGATTTTATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGG
TGATTTCGATTGCCGGTCTATTAAATACCATATAATTTTCGATCCACAAGTCCGATTAAAATTAT
TCAAGTGTCGGTTAAAAGGTTATGGCATGATATACGACTTTCATGAAGGACCAGAAAGCTAAATT
TGATCTACAAGGTTCATGAAGGGTTTTTTTTTGCCAAACATTAAGGGTTCAAAAGGGTTAAAAGG
TAATTATATGAT
Done.