Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001489.1 Corchorus olitorius cultivar O-4 contig01489, 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: 18116
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1005 original size:316 final size:314
Alignment explanation
Indices: 99--1295 Score: 1236
Period size: 316 Copynumber: 3.8 Consensus size: 314
89 GTGTGTTAAC
* * ** * *
99 CATCACAGTTTTT-TGCTAAAAACGCG-TTCCCGGACCGCGGCTCAGTTTTGCATGATTTTTGGC
1 CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGGTCC-CGGCTAAGTTTTGCATGATTTTTGGC
* * ** * * * * * * *
162 -GTAAAGAATTGTTGATATATTTATATCCATCAAACCAAATCTCAACCACATTGAATTTAAGGAT
65 AG--ATGACTCCTTGAAAAATATATATTCATCAAACCAAATCTCAGCCACATTGGATATAAGGAT
* *
226 TTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAG-AATTAATTC--AAAAAAATGGAA
128 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAA
* * * * ** *
288 ATATGATATTAGATGCGTGAAAAACCTTTCAATCTTTTTGGCGTTGACTTATATATTTTTTATGA
193 AAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTA-ATATTTTTTATGA
* * *
353 GTATTGTGGC-AAAAAATTGAGAAATAA-TATTTCGGGTTTATTTTTGCAAAATTTTAGCCAAAA
257 GTATTGTGGCAAAAAAATTGAGAAAAAACT-TTTCGGG--------T-C-AATTTTTAGCCGAAA
416 TCGTGTACTAAT
311 -----T-C--AT
* *
428 CATCACGGTTTTT-GGCTAAAAACGCGTTCCGA-GTCCCCCGGCTCAA-TTTTGCATGATTTTTT
1 CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGGT--CCCGGCT-AAGTTTTGCATGATTTTTG
* * * * * * *
490 GCACAAAGACTCCTTGAAAGATATATATTCATCGAACCAAATCTCGGCTACGTTGGATATAAGGA
63 GCA-GATGACTCCTTGAAAAATATATATTCATCAAACCAAATCTCAGCCACATTGGATATAAGGA
*
555 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAGTAATTCGGAAAAAAAATTG
127 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAAA-TG
*
620 GAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATT-ATATTTTTTCT
190 GAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTAATATTTTTTAT
684 GAGTATTGTGGCAAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCAT
255 GAGTATTGTGGCAAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCAT
**
744 CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGGTCTTGGCTAAGTTTTGCATGATTTTTGGCA
1 CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGGTCCCGGCTAAGTTTTGCATGATTTTTGGCA
* * *
809 GATGGACTCCTTAAAAAATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
66 GAT-GACTCCTTGAAAAATATATATTCATCAAACCAAATCTCAGCCACATTGGATATAAGGATTT
* * * *
874 GTTTTTCCCAGCATCTGAATCTTGTTTCGATTTCATTAGAAATAAATTCG-AAAAAAATGGAAAA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGG-AAA
* *
938 AACGATATTAGAAGCATGAAAAGCCCATCAATC-TTTTGGCGTTGAATTAAATAATTCTTTT-TG
194 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATT-AAT-ATT-TTTTATG
* * **
1001 AGTATTGTTGG-AAAAAAATTGA-AAAAAACTTTTCGGGTCAGTTTTTAGTCGAAATTGT
256 AGTATTG-TGGCAAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCAT
* * * *
1059 -GT-AC-G---TTGGGCTAAAAACGCGTTTCG-GGACCCCGACTCAGTTTTGCATGATTTTTGGC
1 CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGG-TCCCGGCTAAGTTTTGCATGATTTTTGGC
** * * *
1117 AGAATGACTCCTTGAAGTATCTATATTTATCAAACCAAATTTCAGCCACATTGGATATAAGGATT
65 AG-ATGACTCCTTGAAAAATATATATTCATCAAACCAAATCTCAGCCACATTGGATATAAGGATT
* * **
1182 TGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAGTTAGAAATTAATTCGAAAAAAATATATAA
129 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-AAAAAA-A-ATGG
* *
1247 AAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCTTTGA
191 AAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
1296 TGTTCCCAAC
Statistics
Matches: 751, Mismatches: 87, Indels: 76
0.82 0.10 0.08
Matches are distributed among these distances:
308 2 0.00
309 144 0.19
310 2 0.00
311 5 0.01
312 35 0.05
313 33 0.04
314 42 0.06
315 38 0.05
316 159 0.21
317 25 0.03
318 3 0.00
319 1 0.00
324 13 0.02
325 1 0.00
326 1 0.00
329 25 0.03
330 110 0.15
331 11 0.01
333 22 0.03
334 30 0.04
335 49 0.07
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (314 bp):
CATCACGGTTTTTGGGCTAAAAACGCGTTTCGAGGTCCCGGCTAAGTTTTGCATGATTTTTGGCA
GATGACTCCTTGAAAAATATATATTCATCAAACCAAATCTCAGCCACATTGGATATAAGGATTTG
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTAATATTTTTTATGAGTAT
TGTGGCAAAAAAATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCAT
Found at i:10817 original size:377 final size:370
Alignment explanation
Indices: 9994--10850 Score: 1328
Period size: 377 Copynumber: 2.3 Consensus size: 370
9984 GTGGGGAAAG
* * * *
9994 GGGA-CATGAGCCTTCAAGATGGTCCATATTTCATTGCACAATAAAAGTGCCAGGTATTAAAGTA
1 GGGAGCATGAGCCTTCAAGATTGTTCATA-TTCATTGCACAATAAAAGTTCCAGGTA-T--ATTA
* * *
10058 TATAACAC-GGCACCACTATACCTTTATGTATAGTAGGAATG---CCACCACAAAGAATTCTAAC
62 CACAA-ACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATCCTAAC
*
10119 CAACCTTTATTCGATGCACCATTATACCATGATGTATAATAGGAATGCCACTGTTGTGCCTTTAA
126 CAACCTTTATTCGATGCACCATTATACCATGATGTATAATAGGAATGCCACTGTTGTACCTTTAA
*
10184 GCATTAAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAAATCA
191 GCATTAAAAAAAATGCCATGTAACAAAAGAACTTGCATCATTTGAAAATAGATAGAACAAAATCA
10249 AAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAACAGTCAAAAAAAACTGAGTA
256 AAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAACAGTCAAAAAAAACTGAGTA
* *
10314 TAAAACTTAAATTGCTCATGGTGGTGTACCAAAAGAAATGGAGTGGACGA
321 TAAAACTTAAATTGCTCATGGTGGTGAACCAAAAGAAATGGAGTGGACAA
* *
10364 GGGAGCATGAGCCTTCAAGATTGTTCATAATTCATTGCACAATGAGAGTTCCAGGTATATTACAC
1 GGGAGCATGAGCCTTCAAGATTGTTCAT-ATTCATTGCACAATAAAAGTTCCAGGTATATTACAC
* *
10429 GAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATCCTTACCAAC
65 AAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATCCTAACCAAC
* * * *
10494 CTTTATTTGGTGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTGTACCTTTTAGCAT
130 CTTTATTCGATGCACCATTATACCATGATGTATAATAGGAATGCCACTGTTGTACCTTTAAGCAT
*
10559 TCAAAAAAAATGCCATGTACCAAAAGAACTTGCATCATTTGAAAATAGATAGAACAAAATCAAAA
195 T-AAAAAAAATGCCATGTAACAAAAGAACTTGCATCATTTGAAAATAGATAGAACAAAATCAAAA
10624 CAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAAACAACTTTGAG
259 CAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACT-AACAGTC-AAAAAA-AAC--TGAG
* * * *
10689 TATAAAGCTTAAATTGCTCATGGTGGTGAATCAGAAGAAATGGAGTGGGCAA
319 TATAAAACTTAAATTGCTCATGGTGGTGAACCAAAAGAAATGGAGTGGACAA
* *
10741 GGGAGCATGAGCCTTCAAGATTGTTCATATTCCATTGCACTATAAAATTTCCAGGTATATTACAC
1 GGGAGCATGAGCCTTCAAGATTGTTCATATT-CATTGCACAATAAAAGTTCCAGGTATATTACAC
10806 AAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCAC
65 AAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCAC
10851 ATTGTGGCTT
Statistics
Matches: 445, Mismatches: 29, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
367 2 0.00
368 38 0.09
370 5 0.01
371 128 0.29
372 102 0.23
373 7 0.02
374 6 0.01
375 3 0.01
376 3 0.01
377 151 0.34
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (370 bp):
GGGAGCATGAGCCTTCAAGATTGTTCATATTCATTGCACAATAAAAGTTCCAGGTATATTACACA
AACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATCCTAACCAACC
TTTATTCGATGCACCATTATACCATGATGTATAATAGGAATGCCACTGTTGTACCTTTAAGCATT
AAAAAAAATGCCATGTAACAAAAGAACTTGCATCATTTGAAAATAGATAGAACAAAATCAAAACA
AGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAACAGTCAAAAAAAACTGAGTATAAAA
CTTAAATTGCTCATGGTGGTGAACCAAAAGAAATGGAGTGGACAA
Found at i:11010 original size:87 final size:85
Alignment explanation
Indices: 10901--11110 Score: 375
Period size: 87 Copynumber: 2.4 Consensus size: 85
10891 CCTTTATTTG
10901 GATGCACCATTATACCTTGATGTATAATAGGAATGCCATCTCTTTTGCTGCAAATAGAAATTCCC
1 GATGCACCATTATACCTTGATGTATAATAGGAATGCCATCTCTTTTGCTGCAAATAGAAATTCCC
*
10966 GTCACCAACTTTTATTCAGA
66 GTCACCAACTTTAATTCAGA
10986 GATGCACACCATTATACCTTGATGTATAATAGGAATGCCATCTCTTTTGCTGCAAATAGAAATTC
1 GATG--CACCATTATACCTTGATGTATAATAGGAATGCCATCTCTTTTGCTGCAAATAGAAATTC
11051 CCGTCACCAACTTTAATTCAGA
64 CCGTCACCAACTTTAATTCAGA
* *
11073 GATGCACCATTATACCTTGACGTATAATAGGAGTGCCA
1 GATGCACCATTATACCTTGATGTATAATAGGAATGCCA
11111 CTGTTGTGCC
Statistics
Matches: 120, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
85 36 0.30
87 84 0.70
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (85 bp):
GATGCACCATTATACCTTGATGTATAATAGGAATGCCATCTCTTTTGCTGCAAATAGAAATTCCC
GTCACCAACTTTAATTCAGA
Found at i:12473 original size:25 final size:25
Alignment explanation
Indices: 12445--12493 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
12435 CCCGCGCTGT
*
12445 AGCCCTCTTTTTCTTTTCGTCGAAA
1 AGCCCTCTTTCTCTTTTCGTCGAAA
12470 AGCCCTCTTTCTCTTTTCGTCGAA
1 AGCCCTCTTTCTCTTTTCGTCGAA
12494 CTTAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.12, T:0.43
Consensus pattern (25 bp):
AGCCCTCTTTCTCTTTTCGTCGAAA
Done.