Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014123.1 Corchorus olitorius cultivar O-4 contig14156, 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: 60321
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1225 original size:332 final size:329
Alignment explanation
Indices: 276--2481 Score: 2071
Period size: 332 Copynumber: 6.6 Consensus size: 329
266 ACTAAAAACG
276 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAA-GATTTGTT
* * *
341 TTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCG---GAAAATGGGAAAACG
65 TTTACGAGCATCTGAAT-ATGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAT-GGAAAACG
* * * * *
403 ACATTAAAGGCGTGAAAACTCTTTAATTTTTTTGACGTTGAATTATATATTTTTTCTGAGTATTG
128 ATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG
* * *
468 TGGCAAAAAATTGTGTAAAACCTTTTCGGGTCAGTTTTTGAAAAATTTTAGCCGAAATCGTGTAC
193 TGGCAAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * ** ** *
533 TAACCATCACAG-TTTTTGGTTAAAAACGCGTTCCGTAGCCCCGGCTCA-AATTGCTTGATTTAT
258 TAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCATGATTT-T
* *
596 GTTGTA--A
322 -TGGCAGGA
* * ** * * * *
603 AGACTCATTGAAATATTTATATTCATAAAACCAAATCTTAGCCACATTGAATTTAAGGATTTATT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAA-GATTTGTT
* * * * * * * *
668 TTTACGAACATCTGAATTTTGTTTTGATTAAATTAGAAATGAATTCG-GAAAAAATAGAAAA-AA
65 TTTACGAGCATCTGAA-TATGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAACGA
* * * *
731 AATTAGAAGCCTGAAAAACCCATCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG
129 TATTAAAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG
* * * * ** *
796 TCGCAAAAAATTTA-GAAAA-ATTTT---GT---TTTGT-C-AGTTTTTAGCCGAAATCTTGTAC
193 TGGCAAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * *
851 TAACCATCAC-GGTTCTTGGCTAAAAACGCATTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTT
258 TAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTT
915 GGCAGGA
323 GGCAGGA
* *
922 ATACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGGCACAATGGATTTAATGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAA-GATTTGTT
* *
987 TTTACGGGCATCTGAATCATATTTCGATTTAATTAGAAATAAATTCGTAAAAAAAATGGGAAAAC
65 TTTACGAGCATCTGAAT-ATGTTTCGATTTAATTAGAAATAAATTCG-AAAAAAAAT-GGAAAAC
* * * * *
1052 GACATTAAAAGCGTGAAAATCCTTTAATTTTTTTGGCGTTGAATTTTCTATTTTTTCTGAGTATT
127 GATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATT
* * *
1117 GCGGCAAAAAATTGCGGAAAACCTTTTTGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
192 GTGGCAAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
* * * *
1182 CTAACCATCACAG-TTCTTGGCTAAAAACACATTTCGGGGCCCCGGCTCAGTTGTGCATAATTTT
257 CTAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCATGATTTT
1246 TGGCAGGA
322 TGGCAGGA
* *
1254 ATACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACAATGGATTTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAG-ATTTGTT
* * * * * * * *
1319 TATATGAGCATATGAATATTGTTTCGGTTTACTTGGAAATAAATTCGGGGAAAAAAAA-GTAAAG
65 TTTACGAGCATCTGAATA-TGTTTCGATTTAATTAGAAATAAATTC---GAAAAAAAATGGAAAA
* * * * *
1383 CGATACTAAAAACGAGAAAATCCCTTCAATTTTTTTGGCATTGATTTATATATTTTTTCTGAGTA
126 CGATATTAAAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
* *** * ** *
1448 TTGTTTGTGGCAAAGAATTGAGGAAAAAAAATTTCGGGGCAG-CATTGCAAAATTTTAGTCGAAA
190 ----TTGTGGCAAAAAATTGAGG-AAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAA
* * * ** * * * * * *
1512 TCATGCAATAACCATCATGGTTTTTTGGCTAAAACCGCGTTTCAGGGCCCCGACTCGGTTTTGCA
250 TCGTGTACTAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCA
*
1577 TGATTTTTGGGAGGA
315 TGATTTTTGGCAGGA
* * *
1592 ATACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACAATGGATTTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAG-ATTTGTT
* * * *
1657 TTTATGAGCATCTGAATATAGTTTCGATTTACTTAGAAATAAATCCGAAAAAAAAGTAGAAAACC
65 TTTACGAGCATCTGAATAT-GTTTCGATTTAATTAGAAATAAATTCGAAAAAAAA-TGGAAAA-C
* * *
1722 GATACTAGAAA-CGAGAAAATCCCTTCAATTTTTTTGTCGTTGATACATATATATATATATATAT
127 GATATTA-AAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTG--------A-AT-TATATAT-T
* * * * **
1786 ATTTTCTGAGTATTGTTTGTGGCAAAGAATTAAGGAAAA-ATTTTCGGGGCAG-CATTGCAAAAT
179 -TTTTCTGAGTA----TTGTGGCAAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAAT
* * ** * *
1849 TTTAGCCGAAATCATGCACTAACCATCATGGATTTTTGGCTAAAAACGCATTTTGGGGCCCCGAC
239 TTTAGCCGAAATCGTGTACTAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGC
*** * *
1914 TCAGTTTTGCATGATTTAAAGCTGAA
304 TCAGTTTTGCATGATTTTTGGCAGGA
*
1940 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTTTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAA-GA-TTTGT
* *
2005 TTTTACGAGCATCTGAATATTGTTTCAATTTAATTAGAAATAAATTCGAAAAAAAAAATTGAAAA
64 TTTTACGAGCATCTGAATA-TGTTTCGATTTAATTAGAAATAAATTCG--AAAAAAAA-TGGAAA
* ** *
2070 ATGATATTAAAAGCGTGAAAAACCCTTCAAAATTTTTGGCATTGAATTATATA-TTTTT-TGAGT
125 ACGATATTAAAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGT
* ** *
2133 ATTGTGGCAAAAAAATTGAGGAAAACCTGTTCGGGTCTTTTTTTCCAAAATTTTAGCCGAAATCG
189 ATTGTGGC-AAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCG
* ** * ** **
2198 TGTACTAACCATCACAGATTTTT-GTTAAAAACGTGTTCCGAAGCCCCAGG-TCA-AATTGCATG
253 TGTACTAACCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCC-GGCTCAGTTTTGCATG
** **
2260 ATTTTTGTTATAA
317 ATTTTTGGCAGGA
* * * ** * *
2273 AGACTCTTTAAAATATTTATATTCATAAAACCAAATCTCAACCACATTGGATTTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAG-ATTTGTT
** * * * * * * **
2338 TTTACGAATATCTGAATCTTGTTTTGATTAAATCAGGAATGAATTCGGAAAAAAAATGGAAAAAA
65 TTTACGAGCATCTGAAT-ATGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAAATGGAAAACG
* * * * * *
2403 AAATTTAGAAGCCTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTTT
128 ATA-TTAAAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTAT
* *
2468 TGTCGTAAAAAATT
191 TGTGGCAAAAAATT
2482 TAGAAAAAAA
Statistics
Matches: 1566, Mismatches: 242, Indels: 137
0.81 0.12 0.07
Matches are distributed among these distances:
317 4 0.00
318 62 0.04
319 103 0.07
320 4 0.00
321 7 0.00
322 61 0.04
323 18 0.01
324 4 0.00
326 4 0.00
327 113 0.07
328 64 0.04
329 5 0.00
330 16 0.01
331 47 0.03
332 264 0.17
333 127 0.08
334 36 0.02
335 52 0.03
336 6 0.00
337 58 0.04
338 203 0.13
339 3 0.00
340 6 0.00
341 2 0.00
342 1 0.00
346 1 0.00
347 1 0.00
348 161 0.10
349 55 0.04
350 61 0.04
351 17 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (329 bp):
AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGATTTGTTT
TTACGAGCATCTGAATATGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAACGATA
TTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
CAAAAAATTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
CCATCACAGATTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
AGGA
Found at i:12715 original size:24 final size:24
Alignment explanation
Indices: 12683--12729 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12673 GACCCAAAGT
12683 AGTGTGTGTTTTTAATTTAGGGCC
1 AGTGTGTGTTTTTAATTTAGGGCC
12707 AGTGTGTGTTTTTAATTTAGGGC
1 AGTGTGTGTTTTTAATTTAGGGC
12730 TTTCTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.06, G:0.30, T:0.47
Consensus pattern (24 bp):
AGTGTGTGTTTTTAATTTAGGGCC
Found at i:17163 original size:117 final size:116
Alignment explanation
Indices: 16950--17185 Score: 400
Period size: 117 Copynumber: 2.0 Consensus size: 116
16940 CTAAGCTAAC
** *
16950 TGTCCTCAGCATACCTTCATGTGCATTTAAAGTTAAAGAAAATGCCAGTAAATATTATAAATTAT
1 TGTCCTCAGCATACCTTCACATGCATTTAAAGTTAAAGAAAATGCCAGAAAATATTATAAATTAT
* *
17015 CAGTGTTTATGTTTAGTAGAATCGAGAATGCATCAGAATGGTATGTAAAAT
66 CAGTGTTTATGTTTAGTAGAATCAAGAATGCATCAGAATGGCATGTAAAAT
* *
17066 TGTCCTCAGCATACCTTCACATGCTTTTAAAGTTAAAGAAAATGCCAGCAAAATGTTATAAATTA
1 TGTCCTCAGCATACCTTCACATGCATTTAAAGTTAAAGAAAATGCCAG-AAAATATTATAAATTA
17131 TCAGTGTTTATGTTTAGTAGAATCAAGAATGCATCAGAATGGCATGTAAAAT
65 TCAGTGTTTATGTTTAGTAGAATCAAGAATGCATCAGAATGGCATGTAAAAT
17183 TGT
1 TGT
17186 TCTGCACGCA
Statistics
Matches: 112, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
116 45 0.40
117 67 0.60
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (116 bp):
TGTCCTCAGCATACCTTCACATGCATTTAAAGTTAAAGAAAATGCCAGAAAATATTATAAATTAT
CAGTGTTTATGTTTAGTAGAATCAAGAATGCATCAGAATGGCATGTAAAAT
Found at i:18160 original size:14 final size:16
Alignment explanation
Indices: 18142--18184 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
18132 GAAAAGTAAA
18142 GTAAAAAAAAAAAC-T
1 GTAAAAAAAAAAACAT
*
18157 -TAAAAAAATAAACAT
1 GTAAAAAAAAAAACAT
18172 GTAAAAGAAAAAA
1 GTAAAA-AAAAAA
18185 GAAAGCCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 5 0.22
17 5 0.22
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (16 bp):
GTAAAAAAAAAAACAT
Found at i:30619 original size:18 final size:18
Alignment explanation
Indices: 30591--30625 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30581 CTTTCATATT
30591 TTAATATTCGGAGATTGAA
1 TTAATATTCGGA-ATTGAA
30610 TTAA-ATTCGGAATTGA
1 TTAATATTCGGAATTGA
30626 TACTCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (18 bp):
TTAATATTCGGAATTGAA
Found at i:60298 original size:2 final size:2
Alignment explanation
Indices: 60291--60321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60281 AATATAATTT
60291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.