Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022759.1 Corchorus olitorius cultivar O-4 contig22792, 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: 28489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3683 original size:20 final size:20
Alignment explanation
Indices: 3637--3687 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3627 ACAAACTAAC
*
3637 CATCAAAACGAAATCATCAT
1 CATCAAATCGAAATCATCAT
*
3657 CACCAAATCGAAATCGA-CAT
1 CATCAAATCGAAATC-ATCAT
*
3677 GATCAAATCGA
1 CATCAAATCGA
3688 CAAGAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.18
Consensus pattern (20 bp):
CATCAAATCGAAATCATCAT
Found at i:4625 original size:10 final size:10
Alignment explanation
Indices: 4610--4650 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
4600 TCTGGGCTTC
4610 ATGGGCCGAA
1 ATGGGCCGAA
4620 ATGGGCCTG--
1 ATGGGCC-GAA
*
4629 ATGGGCCAAA
1 ATGGGCCGAA
4639 ATGGGCCGAA
1 ATGGGCCGAA
4649 AT
1 AT
4651 CAGTAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 7 0.27
10 18 0.69
11 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.37, T:0.15
Consensus pattern (10 bp):
ATGGGCCGAA
Found at i:12180 original size:32 final size:31
Alignment explanation
Indices: 12144--12368 Score: 269
Period size: 32 Copynumber: 7.2 Consensus size: 31
12134 CTTAATTCAG
* *
12144 AGTAATTAAGTTCAAAAAGGAAAATGATAATC
1 AGTAATTAA-TTCAAAAAGTAAAATGGTAATC
* *
12176 AGTAATTAAATTCAAAGAGTAAAATGATAATC
1 AGTAATT-AATTCAAAAAGTAAAATGGTAATC
*
12208 AGTAATTGAATTTAAAAAGT--AATGGTAATC
1 AGTAATT-AATTCAAAAAGTAAAATGGTAATC
*
12238 AGTAATTGAATTTAAAAAGT--AATGGTAATC
1 AGTAATT-AATTCAAAAAGTAAAATGGTAATC
* *
12268 AGTAATTAAATTCAAATAGTAAAATAGTAATC
1 AGTAATT-AATTCAAAAAGTAAAATGGTAATC
*
12300 AGTAATTCAATTCAAAGAGTAAAATGGTAATC
1 AGTAATT-AATTCAAAAAGTAAAATGGTAATC
*
12332 AGTAATCTGATTCAAAAAGTAAAATGGTAATC
1 AGTAAT-TAATTCAAAAAGTAAAATGGTAATC
12364 AGTAA
1 AGTAA
12369 AAAATAAAAA
Statistics
Matches: 174, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
30 56 0.32
32 115 0.66
33 3 0.02
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (31 bp):
AGTAATTAATTCAAAAAGTAAAATGGTAATC
Found at i:12230 original size:17 final size:17
Alignment explanation
Indices: 12208--12260 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
12198 AATGATAATC
12208 AGTAATTGAATTTAAAA
1 AGTAATTGAATTTAAAA
* **
12225 AGTAA-TG---GTAATC
1 AGTAATTGAATTTAAAA
12238 AGTAATTGAATTTAAAA
1 AGTAATTGAATTTAAAA
12255 AGTAAT
1 AGTAAT
12261 GGTAATCAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 8 0.31
14 2 0.08
16 2 0.08
17 14 0.54
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (17 bp):
AGTAATTGAATTTAAAA
Found at i:12275 original size:92 final size:94
Alignment explanation
Indices: 12154--12368 Score: 294
Period size: 92 Copynumber: 2.3 Consensus size: 94
12144 AGTAATTAAG
* * *
12154 TTCAAAAAGGAAAATGATAATCAGTAATTAAATTCAAAGAGTAAAAT-GATAATCAGTAATTGAA
1 TTCAAAAA-GTAAATGGTAATCAGTAATTAAATTCAAAGAGTAAAATAG-TAATCAGTAATTCAA
*
12218 TTTAAAAAGT-AATGGTAATCAGTAAT-TGAA
64 TTCAAAAAGTAAATGGTAATCAGTAATCTG-A
* *
12248 TTTAAAAAGT-AATGGTAATCAGTAATTAAATTCAAATAGTAAAATAGTAATCAGTAATTCAATT
1 TTCAAAAAGTAAATGGTAATCAGTAATTAAATTCAAAGAGTAAAATAGTAATCAGTAATTCAATT
*
12312 CAAAGAGTAAAATGGTAATCAGTAATCTGA
66 CAAAAAGT-AAATGGTAATCAGTAATCTGA
12342 TTCAAAAAGTAAAATGGTAATCAGTAA
1 TTCAAAAAGT-AAATGGTAATCAGTAA
12369 AAAATAAAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
92 55 0.51
93 2 0.02
94 33 0.31
95 2 0.02
96 15 0.14
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (94 bp):
TTCAAAAAGTAAATGGTAATCAGTAATTAAATTCAAAGAGTAAAATAGTAATCAGTAATTCAATT
CAAAAAGTAAATGGTAATCAGTAATCTGA
Found at i:12376 original size:22 final size:22
Alignment explanation
Indices: 12345--12387 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12335 AATCTGATTC
* *
12345 AAAAAGTAAAATGGTAATCAGT
1 AAAAAATAAAAAGGTAATCAGT
12367 AAAAAATAAAAAGGTAATCAG
1 AAAAAATAAAAAGGTAATCAG
12388 CAATTTGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (22 bp):
AAAAAATAAAAAGGTAATCAGT
Found at i:12384 original size:124 final size:122
Alignment explanation
Indices: 12144--12384 Score: 326
Period size: 124 Copynumber: 1.9 Consensus size: 122
12134 CTTAATTCAG
*
12144 AGTAATTAAGTTCAAAAAGGAAAATGATAATCAGTAATTAAATTCAAAGAGTAAAATGATAATCA
1 AGTAATTAAATTCAAAAAGGAAAATGATAATCAGTAATTAAATTCAAAGAGTAAAATGATAATCA
* **
12209 GTAATTGAATTTAAAAAGTAATGGTAATCAGTAATTGAATTTAAAAAGTAATGGTAATC
66 GTAATTGAATTCAAAAAGTAATGGTAATCAGTAA-T-AAAATAAAAAGTAATGGTAATC
* * * *
12268 AGTAATTAAATTCAAATAGTAAAAT-AGTAATCAGTAATTCAATTCAAAGAGTAAAATGGTAATC
1 AGTAATTAAATTCAAAAAGGAAAATGA-TAATCAGTAATTAAATTCAAAGAGTAAAATGATAATC
12332 AGTAATCTG-ATTCAAAAAGTAAAATGGTAATCAGTAA-AAAATAAAAAGGTAAT
65 AGTAAT-TGAATTCAAAAAGT--AATGGTAATCAGTAATAAAATAAAAA-GTAAT
12385 CAGCAATTTG
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
123 9 0.09
124 78 0.75
125 2 0.02
126 15 0.14
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.29
Consensus pattern (122 bp):
AGTAATTAAATTCAAAAAGGAAAATGATAATCAGTAATTAAATTCAAAGAGTAAAATGATAATCA
GTAATTGAATTCAAAAAGTAATGGTAATCAGTAATAAAATAAAAAGTAATGGTAATC
Found at i:12429 original size:73 final size:73
Alignment explanation
Indices: 12341--12520 Score: 189
Period size: 80 Copynumber: 2.4 Consensus size: 73
12331 CAGTAATCTG
* * * *
12341 ATTCAAAAAGTAAAATGGTAATCAGTAAAAAATAAAAAGGTAATCAGCAATTTGCTTAATTCAGA
1 ATTCAATAAGGAAAATGGTAATCAGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTAATTCAAA
12406 GTAATTAA
66 GTAATTAA
* * *
12414 ATTCAATAAGGAAAATGGTAATCGTAATTAAGTAAAAAGTAAAATGGTAATCAGTAATTGGCTTA
1 ATTCAATAAGGAAAATGGTAATC-------AGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTA
12479 ATTCAAAGTAATTAA
59 ATTCAAAGTAATTAA
* * * * *
12494 GTCCACTAAGGAAATTAGTAATCAGTA
1 ATTCAATAAGGAAAATGGTAATCAGTA
12521 TCTTAAACGT
Statistics
Matches: 88, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
73 25 0.28
80 63 0.72
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (73 bp):
ATTCAATAAGGAAAATGGTAATCAGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTAATTCAAA
GTAATTAA
Found at i:12457 original size:80 final size:80
Alignment explanation
Indices: 12364--12516 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 80
12354 AATGGTAATC
* * *
12364 AGTAAAAAATAAAAAGGTAATCAGCAATTTGCTTAATTCAGAGTAATTAAATTCAATAAGGAAAA
1 AGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTAATTCAAAGTAATTAAATCCAATAAGGAAAA
*
12429 TGGTAATCGTAATTA
66 TAGTAATCGTAATTA
* * * * * *
12444 AGTAAAAAGTAAAATGGTAATCAGTAATTGGCTTAATTCAAAGTAATTAAGTCCACTAAGGAAAT
1 AGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTAATTCAAAGTAATTAAATCCAATAAGGAAAA
12509 TAGTAATC
66 TAGTAATC
12517 AGTATCTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (80 bp):
AGTAAAAAATAAAAAGGTAATCAGCAATTGGCTTAATTCAAAGTAATTAAATCCAATAAGGAAAA
TAGTAATCGTAATTA
Found at i:12566 original size:77 final size:78
Alignment explanation
Indices: 12366--12572 Score: 206
Period size: 80 Copynumber: 2.6 Consensus size: 78
12356 TGGTAATCAG
* * ** * *
12366 TAAAAAATAAAAAGGTAATCAGCAATTTG-CTTAATTCAGAGTAATTAAATTCAATAAGGAAAAT
1 TAAAAAGTAAAATGGTAATCAATAA-TTGACTTAATTCAGAGTAATTAAGTCCAATAAGGAAAAT
*
12430 GGTAATCGTAATTAA
65 AGTAATCGTAATT-A
* * * * *
12445 GTAAAAAGTAAAATGGTAATCAGTAATTGGCTTAATTCAAAGTAATTAAGTCCACTAAGGAAATT
1 -TAAAAAGTAAAATGGTAATCAATAATTGACTTAATTCAGAGTAATTAAGTCCAATAAGGAAAAT
12510 AGTAATCAGT-ATCT-
65 AGTAATC-GTAAT-TA
* * *
12524 T-AAACGTAAAATGGTAATTAATTATTGACTTAATTCAGAGTAATTAAGT
1 TAAAAAGTAAAATGGTAATCAATAATTGACTTAATTCAGAGTAATTAAGT
12573 AAAAGGGTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
77 42 0.39
78 1 0.01
79 3 0.03
80 60 0.55
81 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (78 bp):
TAAAAAGTAAAATGGTAATCAATAATTGACTTAATTCAGAGTAATTAAGTCCAATAAGGAAAATA
GTAATCGTAATTA
Found at i:13742 original size:3 final size:3
Alignment explanation
Indices: 13734--13792 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
13724 GAAACTCAGT
*
13734 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13782 TAA TAA TAA TA
1 TAA TAA TAA TA
13793 TATGCTAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:14357 original size:3 final size:3
Alignment explanation
Indices: 14349--14496 Score: 235
Period size: 3 Copynumber: 49.0 Consensus size: 3
14339 GGTCCACTTG
14349 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
14397 TTA TTA TTA TTA TTA TTA TAA CTA -AA TTTA GTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
14443 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14491 TTA TTA
1 TTA TTA
14497 ATCACAAATT
Statistics
Matches: 135, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
2 1 0.01
3 131 0.97
4 3 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:20048 original size:20 final size:21
Alignment explanation
Indices: 20013--20065 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
20003 TTTTCTTCCT
20013 TTGCTTTGATTTGATTGATTA
1 TTGCTTTGATTTGATTGATTA
*
20034 TTGCTTTGA-TTGATTGTTTA
1 TTGCTTTGATTTGATTGATTA
*
20054 TT-CCTTGATTTG
1 TTGCTTTGATTTG
20066 GTTTAGTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 9 0.31
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (21 bp):
TTGCTTTGATTTGATTGATTA
Found at i:28345 original size:16 final size:18
Alignment explanation
Indices: 28314--28357 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
28304 TTGCCACGTC
28314 ATATTTTTTATAAAAAAA
1 ATATTTTTTATAAAAAAA
*
28332 ATATTTTTT-T-AAAAAT
1 ATATTTTTTATAAAAAAA
28348 ATATTTTTTA
1 ATATTTTTTA
28358 AATAAATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTTATAAAAAAA
Found at i:28347 original size:14 final size:15
Alignment explanation
Indices: 28328--28359 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28318 TTTTTATAAA
28328 AAAAATAT-TTTTTT
1 AAAAATATATTTTTT
28342 AAAAATATATTTTTT
1 AAAAATATATTTTTT
28357 AAA
1 AAA
28360 TAAATTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAAATATATTTTTT
Done.