Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024895.1 Corchorus olitorius cultivar O-4 contig24928, 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: 20585
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2286 original size:15 final size:15
Alignment explanation
Indices: 2266--2328 Score: 72
Period size: 15 Copynumber: 4.0 Consensus size: 15
2256 CACCAGATGA
2266 TGTTTCTGCAACGGT
1 TGTTTCTGCAACGGT
*
2281 TGTTTCTGAAACGGAT
1 TGTTTCTGCAACGG-T
*
2297 GATGTTTTTGCAACGGT
1 --TGTTTCTGCAACGGT
*
2314 TGTTTCTGGAACGGT
1 TGTTTCTGCAACGGT
2329 GCCAATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 26 0.65
16 1 0.03
17 1 0.03
18 12 0.30
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (15 bp):
TGTTTCTGCAACGGT
Found at i:2298 original size:33 final size:33
Alignment explanation
Indices: 2261--2327 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2251 TTCTGCACCA
2261 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG
1 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG
* *
2294 GATGATGTTTTTGCAACGGTTGTTTCTGGAACG
1 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG
2327 G
1 G
2328 TGCCAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.37
Consensus pattern (33 bp):
GATGATGTTTCTGCAACGGTTGTTTCTGAAACG
Found at i:2311 original size:18 final size:18
Alignment explanation
Indices: 2250--2312 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
2240 TATTTGCAAT
* *
2250 TTTCTGCACCAGATGATG
1 TTTCTGCAACGGATGATG
2268 TTTCTGCAACGG-T--TG
1 TTTCTGCAACGGATGATG
*
2283 TTTCTGAAACGGATGATG
1 TTTCTGCAACGGATGATG
*
2301 TTTTTGCAACGG
1 TTTCTGCAACGG
2313 TTGTTTCTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 13 0.35
16 1 0.03
17 1 0.03
18 22 0.59
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (18 bp):
TTTCTGCAACGGATGATG
Found at i:2426 original size:27 final size:27
Alignment explanation
Indices: 2395--2479 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
2385 CATTCAATTA
*
2395 GGGTTGCGGATGAAGCGCAGCTACTTG
1 GGGTTGCGGATGAAGCGCAGCCACTTG
2422 GGGTTGCGGATGAAGCGCAGCCACTTG
1 GGGTTGCGGATGAAGCGCAGCCACTTG
* *
2449 GGGTGGCGGATGAAGCGCAACCACTTG
1 GGGTTGCGGATGAAGCGCAGCCACTTG
2476 GGGT
1 GGGT
2480 GCCGCCACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.19, C:0.20, G:0.42, T:0.19
Consensus pattern (27 bp):
GGGTTGCGGATGAAGCGCAGCCACTTG
Found at i:3942 original size:25 final size:25
Alignment explanation
Indices: 3923--3993 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
3913 TAAACGCTCA
* *
3923 TGTGCTTGCGTTTGGAAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
3948 TGTGCTTGCGTTTAGCAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
3973 TGTGCTTGCGTTTAGCAAACG
1 TGTGCTTGCGTTTAGCAAACG
3994 CATGGGCTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (25 bp):
TGTGCTTGCGTTTAGCAAACGAGCC
Found at i:10184 original size:46 final size:46
Alignment explanation
Indices: 10131--10218 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
10121 TGCTTTAATC
*
10131 AGTTGTGTTTTTTGATTTTAAGAATGAAAGATGTGTGCATTGCTTT
1 AGTTGTGTTTTTTGATCTTAAGAATGAAAGATGTGTGCATTGCTTT
10177 AGTTGTGTTTTTTGATCTTAAGAATGAAAGATGTGTGCATTG
1 AGTTGTGTTTTTTGATCTTAAGAATGAAAGATGTGTGCATTG
10219 TTTTGTTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (46 bp):
AGTTGTGTTTTTTGATCTTAAGAATGAAAGATGTGTGCATTGCTTT
Found at i:11266 original size:1 final size:1
Alignment explanation
Indices: 11260--11288 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
11250 CAATGTGCTC
11260 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11289 GTGGCCAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14265 original size:28 final size:29
Alignment explanation
Indices: 14206--14268 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
14196 TGATATTATT
14206 AAAAAATATAAATAAAGACTTTGTGCCAA
1 AAAAAATATAAATAAAGACTTTGTGCCAA
* *
14235 AAAAAATATAAATAAATACTTTTTGCCAA
1 AAAAAATATAAATAAAGACTTTGTGCCAA
14264 AAAAA
1 AAAAA
14269 TAAATGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (29 bp):
AAAAAATATAAATAAAGACTTTGTGCCAA
Found at i:16781 original size:21 final size:21
Alignment explanation
Indices: 16737--16788 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
16727 TACTTCTGTT
* *
16737 AAAAAAAAATCTATATCCACC
1 AAAAAAAAATCTATATCAAAC
16758 AAAAAAAAATCTATGAT-AAAC
1 AAAAAAAAATCTAT-ATCAAAC
16779 AAAACAAAAA
1 AAAA-AAAAA
16789 GTTTTCCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.15
Consensus pattern (21 bp):
AAAAAAAAATCTATATCAAAC
Found at i:17139 original size:6 final size:6
Alignment explanation
Indices: 17123--17170 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
17113 TAGCTTTCGT
* *
17123 AAAAAA AAAAAC CAAAAC AAAAAC AAATAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC -AA-AAAC AAAAAC AAAAAC AAAA
17171 GTACGTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 29 0.78
7 4 0.11
8 4 0.11
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:17154 original size:14 final size:14
Alignment explanation
Indices: 17137--17163 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17127 AAAAAAACCA
17137 AAACAAAAACAAAT
1 AAACAAAAACAAAT
17151 AAACAAAAACAAA
1 AAACAAAAACAAA
17164 AACAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.15, G:0.00, T:0.04
Consensus pattern (14 bp):
AAACAAAAACAAAT
Found at i:17159 original size:20 final size:19
Alignment explanation
Indices: 17123--17170 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
17113 TAGCTTTCGT
*
17123 AAAAA-AAAAAACCAAAAC
1 AAAAACAAAAAACAAAAAC
17141 AAAAACAAATAAACAAAAAC
1 AAAAACAAA-AAACAAAAAC
17161 AAAAACAAAA
1 AAAAACAAAA
17171 GTACGTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 18 0.67
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAAACAAAAAC
Found at i:17985 original size:22 final size:22
Alignment explanation
Indices: 17936--18388 Score: 129
Period size: 22 Copynumber: 20.3 Consensus size: 22
17926 TGACAATCAA
* ** *
17936 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGTGAGGTT
* * *
17958 ATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
17980 ACCAAAATTTCATA-TAGAGGTT
1 ACCAAAATTTCATAGT-GAGGTT
* *
18002 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGTG-AGGTT
**
18024 ACCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
*
18046 ACCAAAATTTCATAGGCCGAGGGAGGTT
1 ACCAAAATTTCAT------AGTGAGGTT
* *
18074 ACCAAAA--T--T--TGCGCTT
1 ACCAAAATTTCATAGTGAGGTT
* * *
18090 ATCAAAATTTCCTAGAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
* * *
18112 AACAAAATTTTATAGGGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
** * * *
18134 ATGAAAATTTTATGGAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
* * * *
18156 ATCGAAAA-TACATAGAGAGGAT
1 A-CCAAAATTTCATAGTGAGGTT
* *
18178 ATCACAATTTCATTCTCATAGGGAGGTT
1 A-C-CAA---AATT-TCATAGTGAGGTT
* * * *
18206 ATCGAAATTTCATGGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
* *
18228 ATCAAAATTTTCATAGTGCGGTT
1 ACCAAAA-TTTCATAGTGAGGTT
* * *
18251 ACC--AATTTTATTTAGTGTGATT
1 ACCAAAATTTCA--TAGTGAGGTT
** * *
18273 ATTAAAATTTTATAG-GCAGATT
1 ACCAAAATTTCATAGTG-AGGTT
* * * *
18295 ATCAAAATTTCACACTGAGATT
1 ACCAAAATTTCATAGTGAGGTT
* * *
18317 ATCGAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
* * *
18339 ACCCAAATTTCACAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
* * *
18361 ATCAAATTTTCATAGGGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
*
18383 ATCAAA
1 ACCAAA
18389 TTTGCAAAAT
Statistics
Matches: 324, Mismatches: 77, Indels: 60
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.03
18 1 0.00
20 5 0.02
21 5 0.02
22 237 0.73
23 28 0.09
24 8 0.02
26 4 0.01
27 1 0.00
28 25 0.08
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGAGGTT
Found at i:18004 original size:44 final size:44
Alignment explanation
Indices: 17936--18060 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
17926 TGACAATCAA
* * * * * *
17936 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* *
17980 ACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
*
18024 ACCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAG
18061 GCCGAGGGAG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:18385 original size:88 final size:89
Alignment explanation
Indices: 18193--18388 Score: 211
Period size: 88 Copynumber: 2.2 Consensus size: 89
18183 AATTTCATTC
* *** * *
18193 TCATAGGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTCATAGTGCGGTTACCAATT
1 TCATAGGGAGGTTATCAAAATTTCACACTGAGATTATCAAAATTTTCATAGTGCGGTTACCAATT
* *
18258 TTATTTAGTGTGATTATTAAAATTT
66 TCA-TCAGTGTGATTATTAAAATTT
* * * *
18283 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TTTCATAGTGTGGTTACCCAAA
1 TCATAGGGAGGTTATCAAAATTTCACACTGAGATTATCAAAATTTTCATAGTGCGGTTA-CC-AA
* *
18346 TTTCA-CAGTGTGGTTA-TCAAATTT
64 TTTCATCAGTGTGATTATTAAAATTT
18370 TCATAGGGAGGTTATCAAA
1 TCATAGGGAGGTTATCAAA
18389 TTTGCAAAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
87 8 0.09
88 39 0.45
89 33 0.38
90 7 0.08
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (89 bp):
TCATAGGGAGGTTATCAAAATTTCACACTGAGATTATCAAAATTTTCATAGTGCGGTTACCAATT
TCATCAGTGTGATTATTAAAATTT
Found at i:18402 original size:44 final size:43
Alignment explanation
Indices: 18193--18414 Score: 162
Period size: 44 Copynumber: 5.0 Consensus size: 43
18183 AATTTCATTC
**
18193 TCATAGGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATAGGGAGGTTATC-AAATTTCACAGTGTGGTTATC-AAATTT
* * * * * * *
18238 TCATAGTGCGGTTA-CCAATTTTATTTAGTGTGATTATTAAAATTT
1 TCATAGGGAGGTTATCAAATTTCA--CAGTGTGGTTA-TCAAATTT
* * * * *
18283 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TT
1 TCATAGGGAGGTTATC-AAATTTCACAGTGTGGTTATC-AAATTT
* * *
18326 TCATAGTGTGGTTACCCAAATTTCACAGTGTGGTTATCAAATTT
1 TCATAGGGAGGTTA-TCAAATTTCACAGTGTGGTTATCAAATTT
* *
18370 TCATAGGGAGGTTATCAAATTTGCAAAATGTGGTTATCAATATTT
1 TCATAGGGAGGTTATCAAATTT-CACAGTGTGGTTATCAA-ATTT
18415 CTACATTGGA
Statistics
Matches: 136, Mismatches: 30, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
43 20 0.15
44 75 0.55
45 34 0.25
46 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (43 bp):
TCATAGGGAGGTTATCAAATTTCACAGTGTGGTTATCAAATTT
Found at i:18404 original size:22 final size:21
Alignment explanation
Indices: 18193--18415 Score: 126
Period size: 22 Copynumber: 10.1 Consensus size: 21
18183 AATTTCATTC
* *
18193 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATC-AAATT
*
18215 TCATGGTGTGGTTATCAAAATTT
1 TCATAGTGTGGTTATC-AAA-TT
* *
18238 TCATAGTGCGGTTA-CCAATT
1 TCATAGTGTGGTTATCAAATT
* * *
18258 TTATTTAGTGTGATTATTAAAATT
1 TCA--TAGTGTGGTTA-TCAAATT
* * *
18282 TTATAG-GCAGATTATCAAAATT
1 TCATAGTG-TGGTTATC-AAATT
* * * *
18304 TCACACTGAGATTATCGAAATT
1 TCATAGTGTGGTTATC-AAATT
*
18326 TCATAGTGTGGTTACCCAAATT
1 TCATAGTGTGGTTA-TCAAATT
*
18348 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGTGGTTATCAAA-TT
* *
18370 TCATAGGGAGGTTATCAAATT
1 TCATAGTGTGGTTATCAAATT
* *
18391 TGCAAAATGTGGTTATCAATATT
1 T-CATAGTGTGGTTATCAA-ATT
18414 TC
1 TC
18416 TACATTGGAG
Statistics
Matches: 157, Mismatches: 32, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.03
21 11 0.07
22 115 0.73
23 20 0.13
24 7 0.04
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
TCATAGTGTGGTTATCAAATT
Found at i:20332 original size:22 final size:22
Alignment explanation
Indices: 20281--20332 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
20271 CATAAAAAAA
* *
20281 AAGGTTATCAAAATCTCTTATG
1 AAGGTTATCAAAATCTCATACG
* * *
20303 GAGATTATCAAAATTTCATACG
1 AAGGTTATCAAAATCTCATACG
20325 AAGGTTAT
1 AAGGTTAT
20333 TGAAATTTTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
AAGGTTATCAAAATCTCATACG
Found at i:20457 original size:22 final size:22
Alignment explanation
Indices: 20412--20493 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
20402 AAATTTGTTC
* *
20412 TTATCGAAATTTCCTA-GGATGG
1 TTATCAAAATTTCATAGGGA-GG
*
20434 TTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
*
20456 TTATGAAAATATT-AT-GGAGAGG
1 TTATCAAAAT-TTCATAGG-GAGG
*
20478 TTATCAAAATTACATA
1 TTATCAAAATTTCATA
20494 TAGAGAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.06
22 40 0.83
23 5 0.10
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Done.