Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012304.1 Corchorus olitorius cultivar O-4 contig12337, 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: 8345
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Found at i:161 original size:21 final size:21
Alignment explanation
Indices: 136--181 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
126 AAAAAAGAGT
136 AAAAGTAAAGTTGGTAA-TTAA
1 AAAAG-AAAGTTGGTAATTTAA
* *
157 AAAAGGAATTTGGTAATTTAA
1 AAAAGAAAGTTGGTAATTTAA
178 AAAA
1 AAAA
182 AAATCGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGAAAGTTGGTAATTTAA
Found at i:224 original size:27 final size:27
Alignment explanation
Indices: 194--289 Score: 82
Period size: 27 Copynumber: 3.9 Consensus size: 27
184 ATCGATAAAT
* *
194 TAAAAATGAATTTGGTAATTAAAGGAG
1 TAAAAATAAAATTGGTAATTAAAGGAG
*
221 TAAAAGTAAAATTGGTAATTAAA--A-
1 TAAAAATAAAATTGGTAATTAAAGGAG
*
245 -AAGAAT----TTGGTAATTAAAGGAG
1 TAAAAATAAAATTGGTAATTAAAGGAG
* *
267 TGAAAGTAAAATTGGTAATTAAA
1 TAAAAATAAAATTGGTAATTAAA
290 AAAAGAATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
19 12 0.23
21 1 0.02
23 7 0.13
25 1 0.02
27 32 0.60
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (27 bp):
TAAAAATAAAATTGGTAATTAAAGGAG
Found at i:242 original size:46 final size:46
Alignment explanation
Indices: 191--298 Score: 189
Period size: 46 Copynumber: 2.3 Consensus size: 46
181 AAAATCGATA
*
191 AATTAAAAATGAATTTGGTAATTAAAGGAGTAAAAGTAAAATTGGT
1 AATTAAAAAAGAATTTGGTAATTAAAGGAGTAAAAGTAAAATTGGT
*
237 AATTAAAAAAGAATTTGGTAATTAAAGGAGTGAAAGTAAAATTGGT
1 AATTAAAAAAGAATTTGGTAATTAAAGGAGTAAAAGTAAAATTGGT
283 AATTAAAAAAAGAATT
1 AATT-AAAAAAGAATT
299 GTAAAATATA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
46 48 0.81
47 11 0.19
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.29
Consensus pattern (46 bp):
AATTAAAAAAGAATTTGGTAATTAAAGGAGTAAAAGTAAAATTGGT
Found at i:254 original size:19 final size:19
Alignment explanation
Indices: 146--434 Score: 154
Period size: 19 Copynumber: 14.6 Consensus size: 19
136 AAAAGTAAAG
146 TTGGTAATTAAAAAAGGAAT
1 TTGGTAATTAAAAAA-GAAT
*
166 TTGGTAATTTAAAAAA-AAA
1 TTGGTAA-TTAAAAAAGAAT
* * *
185 TCGATAAATTAAAAATGAAT
1 TTGGT-AATTAAAAAAGAAT
*
205 TTGGTAATTAAAGGAGTAAAAGTAAAA
1 TTGGTAATT--A--A--AAAAG--AAT
232 TTGGTAATTAAAAAAGAAT
1 TTGGTAATTAAAAAAGAAT
*
251 TTGGTAATTAAAGGAGTGAAAGTAAAA
1 TTGGTAATT-AA--A---AAAG--AAT
278 TTGGTAATTAAAAAAAGAA-
1 TTGGTAATT-AAAAAAGAAT
297 TT-GTAA--AATATAAAGAA-
1 TTGGTAATTAA-A-AAAGAAT
*
314 TTGGTAACT-AAAAAGAAT
1 TTGGTAATTAAAAAAGAAT
332 TTGGTAATT-AAAAAGAA-
1 TTGGTAATTAAAAAAGAAT
* * *
349 TCGATAAGT-AAAAAGAA-
1 TTGGTAATTAAAAAAGAAT
* *
366 TTGGTAACTATAAAAGAAT
1 TTGGTAATTAAAAAAGAAT
385 TTGGTAATT-AAAAAGAAAT
1 TTGGTAATTAAAAAAG-AAT
*
404 TTGGTAAAGT-AAAAAGAAT
1 TTGGT-AATTAAAAAAGAAT
423 TTGGTAATTAAA
1 TTGGTAATTAAA
435 GAATGAAAAT
Statistics
Matches: 216, Mismatches: 23, Indels: 61
0.72 0.08 0.20
Matches are distributed among these distances:
15 2 0.01
16 1 0.00
17 34 0.16
18 40 0.19
19 56 0.26
20 27 0.12
21 14 0.06
22 5 0.02
23 2 0.01
25 10 0.05
27 25 0.12
ACGTcount: A:0.53, C:0.01, G:0.17, T:0.29
Consensus pattern (19 bp):
TTGGTAATTAAAAAAGAAT
Found at i:320 original size:18 final size:18
Alignment explanation
Indices: 308--434 Score: 143
Period size: 18 Copynumber: 7.1 Consensus size: 18
298 TGTAAAATAT
308 AAAGAA-TTGGTAACTAA
1 AAAGAATTTGGTAACTAA
*
325 AAAGAATTTGGTAATTAA
1 AAAGAATTTGGTAACTAA
* * *
343 AAAGAA-TCGATAAGTAA
1 AAAGAATTTGGTAACTAA
360 AAAGAA-TTGGTAACTATA
1 AAAGAATTTGGTAACTA-A
*
378 AAAGAATTTGGTAATTAA
1 AAAGAATTTGGTAACTAA
*
396 AAAGAAATTTGGTAAAGTAA
1 AAAG-AATTTGGT-AACTAA
*
416 AAAGAATTTGGTAATTAA
1 AAAGAATTTGGTAACTAA
434 A
1 A
435 GAATGAAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
17 27 0.28
18 34 0.36
19 25 0.26
20 9 0.09
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (18 bp):
AAAGAATTTGGTAACTAA
Found at i:328 original size:17 final size:18
Alignment explanation
Indices: 278--434 Score: 153
Period size: 17 Copynumber: 8.7 Consensus size: 18
268 GAAAGTAAAA
278 TTGGTAATTAAAAAAAGAA-
1 TTGGTAATT--AAAAAGAAT
* *
297 TT-GTAAAATATAAAGAA-
1 TTGGT-AATTAAAAAGAAT
*
314 TTGGTAACTAAAAAGAAT
1 TTGGTAATTAAAAAGAAT
332 TTGGTAATTAAAAAGAA-
1 TTGGTAATTAAAAAGAAT
* * *
349 TCGATAAGTAAAAAGAA-
1 TTGGTAATTAAAAAGAAT
*
366 TTGGTAACTATAAAAGAAT
1 TTGGTAATTA-AAAAGAAT
385 TTGGTAATTAAAAAGAAAT
1 TTGGTAATTAAAAAG-AAT
*
404 TTGGTAAAGTAAAAAGAAT
1 TTGGT-AATTAAAAAGAAT
423 TTGGTAATTAAA
1 TTGGTAATTAAA
435 GAATGAAAAT
Statistics
Matches: 117, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
17 40 0.34
18 38 0.32
19 30 0.26
20 9 0.08
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.29
Consensus pattern (18 bp):
TTGGTAATTAAAAAGAAT
Found at i:387 original size:53 final size:55
Alignment explanation
Indices: 278--434 Score: 198
Period size: 53 Copynumber: 2.9 Consensus size: 55
268 GAAAGTAAAA
* * *
278 TTGGTAATTAAAAAAAGAATT-G-TAAAATATAAAGAATTGGTAACTAAAAAGAAT
1 TTGGTAATTAAAAAGA-AATTCGATAAAGTAAAAAGAATTGGTAACTAAAAAGAAT
332 TTGGTAATTAAAAAG-AA-TCGAT-AAGTAAAAAGAATTGGTAACTATAAAAGAAT
1 TTGGTAATTAAAAAGAAATTCGATAAAGTAAAAAGAATTGGTAACTA-AAAAGAAT
* * *
385 TTGGTAATTAAAAAGAAATTTGGTAAAGTAAAAAGAATTTGGTAATTAAA
1 TTGGTAATTAAAAAGAAATTCGATAAAGTAAAAAGAA-TTGGTAACTAAA
435 GAATGAAAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
51 1 0.01
52 23 0.26
53 24 0.27
54 16 0.18
55 3 0.03
56 14 0.16
57 9 0.10
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.29
Consensus pattern (55 bp):
TTGGTAATTAAAAAGAAATTCGATAAAGTAAAAAGAATTGGTAACTAAAAAGAAT
Found at i:770 original size:28 final size:27
Alignment explanation
Indices: 732--823 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
722 TGGTCAACTT
732 GGTAATTAAAAAGTAAAAATGAAATTG
1 GGTAATTAAAAAGTAAAAATGAAATTG
*** *
759 GGTAATTAAAAAGTAATTGGTAAAATTG
1 GGTAATTAAAAAGTAA-AAATGAAATTG
* ** *
787 GATAATTAAAGAA-TGGAAATGAAATTT
1 GGTAATTAAA-AAGTAAAAATGAAATTG
814 GGTAATTAAA
1 GGTAATTAAA
824 GGGTAAAATT
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
27 31 0.62
28 17 0.34
29 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (27 bp):
GGTAATTAAAAAGTAAAAATGAAATTG
Found at i:793 original size:55 final size:55
Alignment explanation
Indices: 710--823 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 55
700 AATCAAAGAG
* *
710 TAAAAAGGAAATTGGTCAACTTGGTAATTAAA-AAGTAAAAATGAAATTGGGTAAT
1 TAAAAAGGAAATTGGTAAAATTGGTAATTAAAGAA-TAAAAATGAAATTGGGTAAT
* ** *
765 TAAAAA-GTAATTGGTAAAATTGGATAATTAAAGAATGGAAATGAAATTTGGTAAT
1 TAAAAAGGAAATTGGTAAAATTGG-TAATTAAAGAATAAAAATGAAATTGGGTAAT
820 TAAA
1 TAAA
824 GGGTAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
54 14 0.27
55 35 0.69
56 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (55 bp):
TAAAAAGGAAATTGGTAAAATTGGTAATTAAAGAATAAAAATGAAATTGGGTAAT
Found at i:2927 original size:17 final size:17
Alignment explanation
Indices: 2905--2940 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2895 TCCTTAAGTG
2905 GCGCATAAGGAGACTTA
1 GCGCATAAGGAGACTTA
2922 GCGCATAAGGAGACTTA
1 GCGCATAAGGAGACTTA
2939 GC
1 GC
2941 ATGTTCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (17 bp):
GCGCATAAGGAGACTTA
Found at i:5259 original size:3 final size:3
Alignment explanation
Indices: 5253--5285 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5243 TCTTTTTATT
5253 ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5286 CTATAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5275 original size:8 final size:8
Alignment explanation
Indices: 5252--5285 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
5242 CTCTTTTTAT
5252 TATAATAA
1 TATAATAA
5260 TAATAATAA
1 T-ATAATAA
5269 TATAATAA
1 TATAATAA
5277 TATAATAA
1 TATAATAA
5285 T
1 T
5286 CTATAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAATAA
Found at i:6936 original size:15 final size:16
Alignment explanation
Indices: 6916--6945 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6906 GTTGGGGATG
6916 ATGGT-GAGGAAAATT
1 ATGGTGGAGGAAAATT
6931 ATGGTGGAGGAAAAT
1 ATGGTGGAGGAAAAT
6946 GGGCAGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (16 bp):
ATGGTGGAGGAAAATT
Found at i:8315 original size:60 final size:60
Alignment explanation
Indices: 8221--8345 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
8211 GCTAATTGCT
8221 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * * *
8281 CAAATAAGGGCCTAACGTTAT-CGAAAATGTTCAAATAAGGGTCCGATCTTTTAATTTTGC
1 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
8341 CAAAT
1 CAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Done.