Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014584.1 Corchorus olitorius cultivar O-4 contig14617, 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: 46630
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3419 original size:28 final size:27
Alignment explanation
Indices: 3385--3453 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
3375 TAATAAATAA
*
3385 ATAAATAAAAAGATAAGTAGGTATAGAG
1 ATAAATAAAAAGATAAGTAGGTA-AAAG
* *
3413 ATAAATAGATAA-ATAGGTAGGTAAAAG
1 ATAAATA-AAAAGATAAGTAGGTAAAAG
3440 A-AAA-AAAAAGATAA
1 ATAAATAAAAAGATAA
3454 TAATAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 3 0.09
27 4 0.12
28 17 0.50
29 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (27 bp):
ATAAATAAAAAGATAAGTAGGTAAAAG
Found at i:3462 original size:4 final size:4
Alignment explanation
Indices: 3455--3569 Score: 66
Period size: 4 Copynumber: 30.0 Consensus size: 4
3445 AAAAGATAAT
* ** *
3455 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * *
3501 AGTA AATA AATA GA-A AATA ACTA AACT- AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AATA A-ATA AATA
* *
3547 AGTA AATA AAT- AATA GATA AATA
1 AATA AATA AATA AATA AATA AATA
3570 GCTATAAAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
3 16 0.20
4 61 0.74
5 5 0.06
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3484 original size:27 final size:27
Alignment explanation
Indices: 3454--3559 Score: 95
Period size: 27 Copynumber: 4.2 Consensus size: 27
3444 AAAAAGATAA
*
3454 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
3481 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* * *
3505 -AATAAATAGAAA-AT--A-ACTAAAC
1 TAATAAATAAAAAGATAAATAGTAAAT
3527 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
3554 AAATAA
1 TAATAA
3560 TAGATAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.03
20 1 0.02
21 1 0.02
22 2 0.03
23 22 0.35
24 2 0.03
25 1 0.02
26 1 0.02
27 26 0.41
28 5 0.08
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.25
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:3506 original size:19 final size:19
Alignment explanation
Indices: 3484--3570 Score: 57
Period size: 22 Copynumber: 4.0 Consensus size: 19
3474 GCTAAATTAA
3484 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
3503 TAAATAAATAGAAAATAACTAAACTAA
1 ----TAAATA-AAAA-GA-TAAA-TAG
3530 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
3549 TAAATAAATAATAGATAAATAG
1 TAAAT-AA-AA-AGATAAATAG
3571 CTATAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
19 7 0.13
20 6 0.11
21 3 0.06
22 14 0.26
23 12 0.23
24 4 0.08
25 1 0.02
26 4 0.08
27 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:3507 original size:46 final size:46
Alignment explanation
Indices: 3444--3558 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
3434 TAAAAGAAAA
* * * *
3444 AAAAAGAT-AATAATAAATAAATAGATAATAGCTAAATTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGAAAATAACTAAACTAATAAAT
3489 AAAAAGATAAATAGTAAATAAATAGAAAATAACTAAACTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGAAAATAACTAAACTAATAAAT
3535 AAAAAGATAAATAGTAAATAAATA
1 AAAAAGATAAATAGTAAATAAATA
3559 ATAGATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 8 0.12
46 57 0.88
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (46 bp):
AAAAAGATAAATAGTAAATAAATAGAAAATAACTAAACTAATAAAT
Found at i:4152 original size:16 final size:16
Alignment explanation
Indices: 4123--4181 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
4113 AAGCTATTAA
*
4123 AAATAAAATCAATTCTT
1 AAAT-AAATTAATTCTT
4140 AAATAAATTAATTCTT
1 AAATAAATTAATTCTT
**
4156 AAATCCATTAATATC-T
1 AAATAAATTAAT-TCTT
*
4172 AAACAAATTA
1 AAATAAATTA
4182 TGAAATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 29 0.83
17 6 0.17
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAAATTAATTCTT
Found at i:7909 original size:40 final size:39
Alignment explanation
Indices: 7847--7931 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
7837 ACTTGACCCT
* *
7847 CCTAATAATTAAGGAGACAAATTAAATTCAGATTTAGTCC
1 CCTAATAATTAAGGAAACAAATTAAATCCAGATTTAG-CC
* *
7887 CCTAATAATTAA-GATAAGAAATTAAATCCAGGTTTAGCC
1 CCTAATAATTAAGGA-AACAAATTAAATCCAGATTTAGCC
*
7926 TCTAAT
1 CCTAAT
7932 TATAAATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 9 0.23
40 30 0.77
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (39 bp):
CCTAATAATTAAGGAAACAAATTAAATCCAGATTTAGCC
Found at i:8045 original size:13 final size:13
Alignment explanation
Indices: 8027--8058 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
8017 TGACACGTCA
8027 GGAGGGACAAATT
1 GGAGGGACAAATT
*
8040 GGAGGGACAAGTT
1 GGAGGGACAAATT
8053 GGAGGG
1 GGAGGG
8059 TCATATAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.12
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:21303 original size:21 final size:21
Alignment explanation
Indices: 21277--21320 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21267 TTGGGCTGAC
21277 ATTTCCAGGACATGCCGTGTA
1 ATTTCCAGGACATGCCGTGTA
21298 ATTTCCAGGACATGCCGTGTA
1 ATTTCCAGGACATGCCGTGTA
21319 AT
1 AT
21321 GAAATGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
ATTTCCAGGACATGCCGTGTA
Found at i:29923 original size:18 final size:18
Alignment explanation
Indices: 29900--29939 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
29890 GTGGTAATAG
29900 GAATGATAA-GCAGAATGA
1 GAATGATAATG-AGAATGA
*
29918 GAATGATAATGAGAATGG
1 GAATGATAATGAGAATGA
29936 GAAT
1 GAAT
29940 CTGGTTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (18 bp):
GAATGATAATGAGAATGA
Found at i:46450 original size:338 final size:329
Alignment explanation
Indices: 45596--46630 Score: 1301
Period size: 329 Copynumber: 3.1 Consensus size: 329
45586 CGTTCAATGT
** * *
45596 TTGAATTATATATTTTTTACGAGTAT-G-GGTC-AAAAA-TGAA-AGAAATTCTTTCGAGTC-AT
1 TTGAATTATATATTTTTTATAAGTATCGTGG-CAAAAAATTGAAGA-AAATTCTTTCGGGGCAAT
* * **
45655 TTTTGTAAAATTTTAGCTGAAATTATGTACTGACCATCATGGTTGTTTAACT-TAAAACGCATTC
64 TTTTGCAAAATTTTAGCTGAAA-T-TGTA-T-ACCATCACGGTT-TTTGGCTATAAAACGCATTC
* * * * * *
45719 TAGGG-TACCGACTCAGTTTTGCTGGGTCTTTGGCGCCAAGACTCATTGACATATCTATATTAAT
124 TGGGGCT--CGGCTCAGTTTTGCTTGGTTTTTGGCGCCAAGACTCCTTGACATATCTATATTCAT
* * * * *
45783 CTAACCAAATATCAGCCACATTGGATTTAAGGATATC-TTTCTACGAGCATCTGAATTTTGTTTT
187 CTAACCAAATATCAGCCACATTGGATTTAAGAATTTCATTT-TACGAACATCTGAATCTTGTTTC
* * * *
45847 GATTTATTAAGAAATCAATTTGGAAAATAAAAATAAAAACGATATTAGAAGCGTGAAAAGCTTTT
251 GATTTATTAAGAAATCAATTTGGAGAATAATAATAAAAACGATATTAGAAGCGTGAAAGGCCTTT
*
45912 CAATATTTTTGGTG
316 CAATATTTTTGGAG
* * * * * *
45926 CTGAATTATATATTTTTTATTAGTATTGTGG-ACAAAAATTGAAGAAAATTCTTTTGGGTCAGTT
1 TTGAATTATATATTTTTTATAAGTATCGTGGCA-AAAAATTGAAGAAAATTCTTTCGGGGCAATT
* * *
45990 TTTGCAAAATTTTAGCTGAAATTGTATACGATCACGGTTTTTGGGTA-AAAACGCATTCCGGGGC
65 TTTGCAAAATTTTAGCTGAAATTGTATACCATCACGGTTTTTGGCTATAAAACGCATTCTGGGGC
46054 TCGGGCTCAGTTTTGCTTGGTTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
130 TC-GGCTCAGTTTTGCTTGGTTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
* *
46119 AATCA-CATCCACATTAGATTTAAGAATTTCATTTTACGAACATCTGAATCTTGTTTCGATTTAT
194 AAT-ATCAGCCACATTGGATTTAAGAATTTCATTTTACGAACATCTGAATCTTGTTTCGATTTAT
* *
46183 TTAGAAATCAATTTGGAGAATAATAATAAAAACGATATTAG-AGCTTGAAAGGCCTTTCAATATT
258 TAAGAAATCAATTTGGAGAATAATAATAAAAACGATATTAGAAGCGTGAAAGGCCTTTCAATATT
46247 TTTGGAG
323 TTTGGAG
* * *
46254 TTGAATTATAAATTTTTTATAAGTATCGTGGCAAAAAATTGGAGAAATTTCTTTCGGGGCAATTT
1 TTGAATTATATATTTTTTATAAGTATCGTGGCAAAAAATTGAAGAAAATTCTTTCGGGGCAATTT
*
46319 TTGCAAAATTTTAGCTGAAATCGTGTACTAACCATTACGGTTTTTGGCTAAAAAGTAAAACGCAT
66 TTGCAAAATTTTAGCTGAAAT--TGTA-T-ACCATCACGGTTTTTGGCT----A-TAAAACGCAT
*
46384 TCTGGGGCCTCGGCTCAGTTTTGCTTGGTTTTTGGCGCCAACACTCCTTGACATATCTATATTCA
122 TCTGGGG-CTCGGCTCAGTTTTGCTTGGTTTTTGGCGCCAAGACTCCTTGACATATCTATATTCA
* *
46449 TCTAACCAAATATCAGCCATATTGGATTTAAGAA-TTCGA-TTTACGAAGATCTGAATCTTGTTT
186 TCTAACCAAATATCAGCCACATTGGATTTAAGAATTTC-ATTTTACGAACATCTGAATCTTGTTT
* *
46512 CGATTTATTCAGAATTCAATTTGGAGAATAATAATAAAAACGATATTAGAAGCGTGAAAGGCCTT
250 CGATTTATTAAGAAATCAATTTGGAGAATAATAATAAAAACGATATTAGAAGCGTGAAAGGCCTT
46577 TCAATATTTTTGGAG
315 TCAATATTTTTGGAG
* * *
46592 TTGAATTATATA-TTTTTATGAGTATCGTAGCCAAAAATT
1 TTGAATTATATATTTTTTATAAGTATCGTGGCAAAAAATT
Statistics
Matches: 620, Mismatches: 58, Indels: 47
0.86 0.08 0.06
Matches are distributed among these distances:
328 102 0.16
329 165 0.27
330 42 0.07
331 3 0.00
332 27 0.04
333 18 0.03
334 23 0.04
336 1 0.00
337 98 0.16
338 138 0.22
339 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (329 bp):
TTGAATTATATATTTTTTATAAGTATCGTGGCAAAAAATTGAAGAAAATTCTTTCGGGGCAATTT
TTGCAAAATTTTAGCTGAAATTGTATACCATCACGGTTTTTGGCTATAAAACGCATTCTGGGGCT
CGGCTCAGTTTTGCTTGGTTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAA
TATCAGCCACATTGGATTTAAGAATTTCATTTTACGAACATCTGAATCTTGTTTCGATTTATTAA
GAAATCAATTTGGAGAATAATAATAAAAACGATATTAGAAGCGTGAAAGGCCTTTCAATATTTTT
GGAG
Done.