Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017819.1 Corchorus olitorius cultivar O-4 contig17852, 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: 23666
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:747 original size:21 final size:21
Alignment explanation
Indices: 721--760 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
711 TGGTGTTCTT
721 GTGAGTTCATGACAAAAGGGA
1 GTGAGTTCATGACAAAAGGGA
*
742 GTGAGTTTATGACAAAAGG
1 GTGAGTTCATGACAAAAGG
761 AAATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.23
Consensus pattern (21 bp):
GTGAGTTCATGACAAAAGGGA
Found at i:9108 original size:25 final size:27
Alignment explanation
Indices: 9079--9128 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
9069 TTCACAACTA
*
9079 CTAATT-AATTACCA-TTTTCTTCTAC
1 CTAATTCAATTACCACTTCTCTTCTAC
*
9104 CTAATTCAATTCCCACTTCTCTTCT
1 CTAATTCAATTACCACTTCTCTTCT
9129 TTTGCTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 7 0.33
27 8 0.38
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (27 bp):
CTAATTCAATTACCACTTCTCTTCTAC
Found at i:10692 original size:33 final size:33
Alignment explanation
Indices: 10645--10740 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
10635 AAATGGTCGG
**
10645 TGCCGCCCTTGGTGGGCGGCGTGGCCATGGGGA
1 TGCCGCCCCCGGTGGGCGGCGTGGCCATGGGGA
10678 TGCCGCCCCCGGTGGGCGGCGTGGCCATGGGGA
1 TGCCGCCCCCGGTGGGCGGCGTGGCCATGGGGA
*
10711 TGTCGCCCCCGGTGGGCGGCGTGGCCATGG
1 TGCCGCCCCCGGTGGGCGGCGTGGCCATGG
10741 TCACCATGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.05, C:0.31, G:0.48, T:0.16
Consensus pattern (33 bp):
TGCCGCCCCCGGTGGGCGGCGTGGCCATGGGGA
Found at i:11759 original size:27 final size:27
Alignment explanation
Indices: 11729--11796 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
11719 AGCACCAGCG
11729 GCAGCCTC-CCTCTCCCTATACATCCGA
1 GCAGCCTCACC-CTCCCTATACATCCGA
*
11756 GCAGCCTCAGCCTCCCTATACATCCGA
1 GCAGCCTCACCCTCCCTATACATCCGA
*
11783 GCAGCCTCAGCCTC
1 GCAGCCTCACCCTC
11797 TTTATCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.47, G:0.15, T:0.19
Consensus pattern (27 bp):
GCAGCCTCACCCTCCCTATACATCCGA
Found at i:12464 original size:21 final size:21
Alignment explanation
Indices: 12438--12515 Score: 156
Period size: 21 Copynumber: 3.7 Consensus size: 21
12428 CAAAAGTGTA
12438 AAAAGGGGGGCGGTGATAAGT
1 AAAAGGGGGGCGGTGATAAGT
12459 AAAAGGGGGGCGGTGATAAGT
1 AAAAGGGGGGCGGTGATAAGT
12480 AAAAGGGGGGCGGTGATAAGT
1 AAAAGGGGGGCGGTGATAAGT
12501 AAAAGGGGGGCGGTG
1 AAAAGGGGGGCGGTG
12516 TTTAGCAATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.32, C:0.05, G:0.50, T:0.13
Consensus pattern (21 bp):
AAAAGGGGGGCGGTGATAAGT
Found at i:13748 original size:298 final size:290
Alignment explanation
Indices: 13085--13847 Score: 875
Period size: 298 Copynumber: 2.6 Consensus size: 290
13075 TTATAATTAA
* * * * *
13085 TGTGG-TACGCCCTTGGATTTTCCTCGAGCTTGGGAACAAGGTTTCAATAAATTTAACACTCTTA
1 TGTGGATAAGCCCTTGGATTTTCCTCGAGCTTGGAAACAAGGTTTCAGTGAATTTAACACTCTTG
* * *
13149 AAATCCAA-ATATTTACTTTGAAATTTGGATTAGGACA---TT-TTT--TTGTGACAGATA--AG
66 AAATCCAATA-ATTTACTTTGAAATTTGGATTCGAACATTTTTGTTTCCTTGAGACAGATATGAG
* *
13205 AACAATAATTTATGTAATTGTTACATATAAAATTCATTTTGCTA-TT-TAAAAAAAGAAGAAGAA
130 AACAATAAATTATGTAA--GTTACATATAAAATTCATTTTGCTACTTAAAAAAAAAGAAGAAGAA
*
13268 AATGGATTTGAAAGTTTGGATAACACCTACATATAGGTAAATTCAATGTTGACTTAGTAATTATA
193 AATGGATTTGAAAGTTTGGATAACA-C-ACATATAGGTAAATTCAATATTGACTTAGTAATTATA
*
13333 TAGGGCTTTAAGATCCCATCTGCCCCACTAGTCAT
256 TAGCGCTTTAAGATCCCATCTGCCCCACTAGTCAT
* * * *
13368 TATGGATATGCCCTTCGATTTTCCTCGAGGC-CGGAAACAAGGTTTCAGTGAATTTAACACTCTT
1 TGTGGATAAGCCCTTGGATTTTCCTCGA-GCTTGGAAACAAGGTTTCAGTGAATTTAACACTC-T
*
13432 TGAAATCCAGAT-ATTTACTTTGAAATTTAGATTCGAACATTTTTTGTTTCCTTGAGACAGATCA
64 TGAAATCCA-ATAATTTACTTTGAAATTTGGATTCGAACA-TTTTTGTTTCCTTGAGACAGAT-A
* *
13496 TGAGAACAA-AAATTATGTAGGTTACATATAAAATTAATTTTGCTACTTAAAAAAAACAAGAAGA
126 TGAGAACAATAAATTATGTAAGTTACATATAAAATTCATTTTGCTACTT-AAAAAAA-AAG-A-A
* *
13560 TGAAGATAAAGATGGATTTGAAAGTTTGTATAACA-A-TTATA-GTAAAATTCAATATTGACTTA
187 -GAAG--AAA-ATGGATTTGAAAGTTTGGATAACACACATATAGGT-AAATTCAATATTGACTTA
* * * *
13622 GTAATTATATAGCGCTTTAAGATTCCATCTGTCCTACTGGTCAT
247 GTAATTATATAGCGCTTTAAGATCCCATCTGCCCCACTAGTCAT
*
13666 TGTGGATAAGCCCTTGGATTTTCCTCGAGCTTGGAAACAAGGTTTCAGTGAATTTATC-CTCTTG
1 TGTGGATAAGCCCTTGGATTTTCCTCGAGCTTGGAAACAAGGTTTCAGTGAATTTAACACTCTTG
* * ** *
13730 AAATCGGAATAAATTTACTATGAAATTTGGATTCGAACATTTTTGTTTCCTTTCGGCAG--ATGA
66 AAATC-CAAT-AATTTACTTTGAAATTTGGATTCGAACATTTTTGTTTCCTTGAGACAGATATGA
* * **
13793 GAACAATAAATTATGTAAGTTATATATATAATTCATTTTGCTACTTTTAAAAAAA
129 GAACAATAAATTATGTAAGTTACATATAAAATTCATTTTGCTACTTAAAAAAAAA
13848 TACTCCCTCT
Statistics
Matches: 408, Mismatches: 41, Indels: 52
0.81 0.08 0.10
Matches are distributed among these distances:
283 4 0.01
284 47 0.12
285 35 0.09
286 1 0.00
289 2 0.00
290 3 0.01
292 34 0.08
293 5 0.01
294 24 0.06
295 47 0.12
296 13 0.03
297 26 0.06
298 136 0.33
299 5 0.01
301 3 0.01
302 23 0.06
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (290 bp):
TGTGGATAAGCCCTTGGATTTTCCTCGAGCTTGGAAACAAGGTTTCAGTGAATTTAACACTCTTG
AAATCCAATAATTTACTTTGAAATTTGGATTCGAACATTTTTGTTTCCTTGAGACAGATATGAGA
ACAATAAATTATGTAAGTTACATATAAAATTCATTTTGCTACTTAAAAAAAAAGAAGAAGAAAAT
GGATTTGAAAGTTTGGATAACACACATATAGGTAAATTCAATATTGACTTAGTAATTATATAGCG
CTTTAAGATCCCATCTGCCCCACTAGTCAT
Found at i:14716 original size:3 final size:3
Alignment explanation
Indices: 14708--14738 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
14698 TTGCTACTTT
14708 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
14739 TGGATTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14947 original size:301 final size:294
Alignment explanation
Indices: 14142--15148 Score: 1195
Period size: 303 Copynumber: 3.3 Consensus size: 294
14132 AACAAGAAGA
* * *
14142 TGAAGTTTGGATAACAACTATAGTAAAATTCAATGTTGACTTAGTAATTATACAGGTCTTTAAGA
1 TGAAGTTTGGATAACAGCTATAGTAAAATTCAATGTTGACTTAGTAATTATATAGGACTTTAAGA
* * * * *
14207 TTCCATCGGCCCCACTTGTCATTGTGGATATGCCCTTGGATTTTCCTCGAGTCTGAAAACAAGGT
66 TCCCATCTGCCCCACTGGTCATTGTGGATACGCCCTTGGATTTTCCTC--GCCTG-AAACAAGGT
* * * *
14272 TTCATTGAATTTAACACTCTTGAAATACGAATATTTACTTTGAAATTTGGATTCAGACATTTTCC
128 TTCAGTGAATTTAACACTCTTAAAATCCGAATATTTACTTTGAAATTTGGATTCAGACATTTTTC
* *
14337 GTTTGCTTGTGGCAGATGAGAACAATAATTTATGTAATTGTTACATGTAAAATTCATTTTGCTAC
193 GTTTCCTTGTGGCAGATGAGAACAATAATTTATGTAATTGTTACATATAAAATTCATTTTGCTAC
** * *
14402 TAAAAAAAACAAAAAGCAAGAAGAA-CATAAGATGGATT
258 TTTAAAAAA-AAAAAG-AAGAAGAAGAAGAAGATGGATT
* *
14440 TGAAAGTTTAGATAACAGCTATA-TAGGTAAATTCAATGTTGACTTAGTAATTATGTAAGG-CTT
1 TG-AAGTTTGGATAACAGCTATAGTA---AAATTCAATGTTGACTTAGTAATTATAT-AGGACTT
* *
14503 TAAGATCCCATCTGCGCCCCACTGGTCATTGTGGATACACCCTTGGATTTTCCTCGATCATGGAA
61 TAAGATCCCATCT--GCCCCACTGGTCATTGTGGATACGCCCTTGGATTTTCCTCG--CCT-GAA
* * *
14568 ACAAGGTTTCAGTGAATTTAATACTCTTAAAATCTGAGTATTTACTTTGAAATTTGGATTCAGAC
121 ACAAGGTTTCAGTGAATTTAACACTCTTAAAATCCGAATATTTACTTTGAAATTTGGATTCAGAC
* * * *
14633 ATTTTTTGTTTCCTTGTGGCAAATGAGAACAATAATTTATGTAATTGTTACATATACAATTGATT
186 ATTTTTCGTTTCCTTGTGGCAGATGAGAACAATAATTTATGTAATTGTTACATATAAAATTCATT
*
14698 TTGCTACTTTAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGGATT
251 TTGCTACTTTAA-AA-AA-AAAAAGAAGAAGAAGAAGAAGATGGATT
* *
14745 TGAGAGTTTGGATAACAGCTATAGTAAAATTCAATGCTGACTTAGTAATTATTTAGGACATTATA
1 TGA-AGTTTGGATAACAGCTATAGTAAAATTCAATGTTGACTTAGTAATTATATAGGAC-TT-T-
* * * * *
14810 AAGATCCCATCTTCCCCATTGGTCATTGTGGATAGGTCATTGGATTTTCCTC-CCTAGAAACAAG
62 AAGATCCCATCTGCCCCACTGGTCATTGTGGATACGCCCTTGGATTTTCCTCGCCT-GAAACAAG
* * * **
14874 GTTTTAGTGAATTTAACACTCTTAAAATCCAAATATTTACTTTGAAATTTGGTTTTGGACATTTT
126 GTTTCAGTGAATTTAACACTCTTAAAATCCGAATATTTACTTTGAAATTTGGATTCAGACATTTT
* * *
14939 TCGTTTCCTCGTTTCCTCGTGGCAGATGATAATAATAATTTATGTAATTGTTTCATATAAAATTC
191 TCGTTT-C-C---T--T-GTGGCAGATGAGAACAATAATTTATGTAATTGTTACATATAAAATTC
*
15004 ATTTTGCTACTTT-ACAAAAAAAA-AAGAAGAAGAAGAAGATGGATT
248 ATTTTGCTACTTTAAAAAAAAAAAGAAGAAGAAGAAGAAGATGGATT
* * *
15049 TGAATGTTTTGATAGCAGATATAGTAAAATTCAATGTTGACTTAGTAATTATATA-GAGCTTTAA
1 TGAA-GTTTGGATAACAGCTATAGTAAAATTCAATGTTGACTTAGTAATTATATAGGA-CTTTAA
*
15113 GATCCCATCAT--CCCACTGGTCATTGTGGATATGCCC
64 GATCCCATC-TGCCCCACTGGTCATTGTGGATACGCCC
15149 CTTTAGTCTA
Statistics
Matches: 612, Mismatches: 67, Indels: 58
0.83 0.09 0.08
Matches are distributed among these distances:
298 4 0.01
299 18 0.03
300 21 0.03
301 124 0.20
302 9 0.01
303 200 0.33
304 119 0.19
305 43 0.07
306 17 0.03
307 1 0.00
308 2 0.00
309 54 0.09
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (294 bp):
TGAAGTTTGGATAACAGCTATAGTAAAATTCAATGTTGACTTAGTAATTATATAGGACTTTAAGA
TCCCATCTGCCCCACTGGTCATTGTGGATACGCCCTTGGATTTTCCTCGCCTGAAACAAGGTTTC
AGTGAATTTAACACTCTTAAAATCCGAATATTTACTTTGAAATTTGGATTCAGACATTTTTCGTT
TCCTTGTGGCAGATGAGAACAATAATTTATGTAATTGTTACATATAAAATTCATTTTGCTACTTT
AAAAAAAAAAAGAAGAAGAAGAAGAAGATGGATT
Found at i:17552 original size:19 final size:19
Alignment explanation
Indices: 17528--17567 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17518 TATGACTAAT
17528 ATGAAGAAATGGAGATAAG
1 ATGAAGAAATGGAGATAAG
17547 ATGAAGAAATGGAGATAAG
1 ATGAAGAAATGGAGATAAG
17566 AT
1 AT
17568 AGCAATAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (19 bp):
ATGAAGAAATGGAGATAAG
Found at i:19351 original size:13 final size:13
Alignment explanation
Indices: 19328--19363 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
19318 AAGTGGTCCT
*
19328 TATTA-TATATTC
1 TATTATTATATTA
19340 TATTATTATATTA
1 TATTATTATATTA
19353 TATTATTATAT
1 TATTATTATAT
19364 AATAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Done.