Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010146.1 Corchorus olitorius cultivar O-4 contig10178, 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: 4056
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:81 original size:40 final size:41
Alignment explanation
Indices: 20--115 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 41
10 CATTTAAATA
* * *
20 ATCGGTCACTTTTTATTTAAATGTTTGGAGAGACAGCTCTC
1 ATCGGTCACGTTTTAATTAAATGTTTGGAGAAACAGCTCTC
* *
61 ATCGATCAC-TTTTAATTAAATGTTTGGAGAAATAGCTCTC
1 ATCGGTCACGTTTTAATTAAATGTTTGGAGAAACAGCTCTC
101 ATCGGTCACGTTTTA
1 ATCGGTCACGTTTTA
116 TTCCAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 36 0.73
41 13 0.27
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (41 bp):
ATCGGTCACGTTTTAATTAAATGTTTGGAGAAACAGCTCTC
Found at i:944 original size:324 final size:319
Alignment explanation
Indices: 212--2356 Score: 2218
Period size: 323 Copynumber: 6.7 Consensus size: 319
202 TGGAGTCCCT
* * * * * * * *
212 ACTCAATTTAGCATGAATTTTGG-TGCAAAGACTCCTTGAGATATATATATTCATCAAACCAAAT
1 ACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* * * *
276 CTTAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGCTTCGATTTAATTAG
65 CTCAGCGA-ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * *
341 AAATTAATTCGATAAAATGGAAAAACGATAATT-GAAGCGTGAAAAGCCTGTCAAT-TATTTTGG
129 AAATAAATTCGAAAAAATGGAAAAACGAT-ATTAGAAGCGTGAAAAGCCCGACAATCT-TTTTGG
* * **
404 CGTTGAATTATATATTTTTTCTGAG-ACTTAT-AGCAAAAGAATTCAAAAAAAATTTTCGGGTCA
192 CATTGAATTATATATTTTTTCTGAGTA-TTATGA-CAAAA-AATTGAAAAAAACCTTTCGGGTCA
* * * * * *
467 GTTTTTAGCTGAAATCATGTACTAACTATCATGGTTTTTTGGCTAAAAATGCGTTTCGGGATCCC
254 GTTTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCC
532 G
319 G
* *
533 ACGCAGTTTTGCATGATTCTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAATCAAAT
1 ACTCAGTTTTGCATGATT-TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* * *
598 CTCAGTCGAATCGGATTTAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTTGATTTAATTAG
65 CTCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* *
663 AAATAAAATCAGAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGCCCGACAATCTTTTTGGC
129 AAATAAATTC-GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGACAATCTTTTTGGC
*
728 ATTGAATTATATATTTTTTCTGAGTATTATGATAAAAAATTGACAAAAAACCTTTCGGGTCAGTT
193 ATTGAATTATATATTTTTTCTGAGTATTATGACAAAAAATTGA-AAAAAACCTTTCGGGTCAGTT
* * *
793 TTTAGCTGAAATCGTGTACTAACTATCACGGTTTTTGGGGATCAAAACGCGTTTCGGGACCCCG
257 TTTAGCCGAAATCGTGTACTAACTATCACGGTTTTT-GGGCTAAAAACGCGTTTCGGGACCCCG
*
857 ACTCAGTTTTGCATGATTCTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAATCAAAT
1 ACTCAGTTTTGCATGATT-TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
* *
922 CTCAGTCGAATCGGATTTAAGGATTTGTATTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
65 CTCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
** * *
987 AAATAAAATAAGAAAAAAATGGAAAAAACGATATTAGAAGCATGAAAAGCCCGTCAATCTTTTTG
129 AAAT-AAATTCG-AAAAAATGG-AAAAACGATATTAGAAGCGTGAAAAGCCCGACAATCTTTTTG
* * *
1052 GTATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGACAAAAAACCTTTCGGGTCAG
191 GCATTGAATTATATATTTTTTCTGAGTATTATGACAAAAAATTGA-AAAAAACCTTTCGGGTCAG
*
1117 TTTTTAGCCGAAATCGTGTACTAA-TCATCACGGTATTTGGGCTAAAAACGCGTTTCGGGACCCC
255 TTTTTAGCCGAAATCGTGTACTAACT-ATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCC
1181 G
319 G
* * * * * * * *
1182 ACTTAGTGTTGCATCATTTTTTGCAGATAGACTCCATG-AACATCTATATTCATCTAACCAAATC
1 ACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* ** * *
1246 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGATTATCTGAATCTTATTTTGATTTAATTAGA
66 TCAGCGA-ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * *** *
1311 AATAAATATGGAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAACCTTTCCAAT-TTTTTGGT
130 AATAAAT-TCGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCC-CGACAATCTTTTTGGC
* * * * * * *
1375 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAGCTTTTGGGGTCAGTT
193 ATTGAATTATATATTTTTTCTGAGTATTATGACAAAAAATTGA-AAAAAACCTTTCGGGTCAG--
* * * * *
1440 TTTGCAAAATTTAGCCGAAATCGTGTACTAACCATCAC-GATTTT-GGCTAAAAACGTGTTAC-A
255 -TT------TTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGG
* *
1502 GAGTCCCT
313 GA-CCCCG
* * * * * * *
1510 ACTCAATTTTGCATGAATTTTGGCACAAAGACTTCTTGAGATATCTATATTCATCGAACCAAATC
1 ACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * * *
1575 TTAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAA
66 TCAGCGA-ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * * * * * * * *
1640 AATTAATTCGGAAAAGTGGAAGAACGATATTTGATGTGTGAAAAGCCAGTCAATCATTTTGGCGT
130 AATAAATTCGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGACAATCTTTTTGGCAT
* * * * ** * * *
1705 TGAATTATATATTTTTTATGAGAATTGT-AGCAAAAAAGTG------ACCGAT-GAG--AG-CTC
195 TGAATTATATATTTTTTCTGAGTATTATGA-CAAAAAATTGAAAAAAACCTTTCGGGTCAGTTTT
* * * * *
1759 T--CC-AAA-CATTGAAATCA-TGT-AC-G--TTTGGGCTAAAAACGCGTTTCGGGACCCCG
259 TAGCCGAAATC-GTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCCG
* * *
1812 ACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATGTATATTCATCTAATCATATC
1 ACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * * * *
1877 TCAGCCGAATTGGATTTATGAATTTGTGTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGG
66 TCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* *
1942 AATAAATTCGAAAAAAATGGAAAAACGATATTTGAAGCGTGAAAAGCCC-ATCAATCATTTTGGC
130 AATAAATTCG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGA-CAATCTTTTTGGC
** * * ** * ** *
2006 ATTGGTTTTTATATTTTTTATGAGTATTATGGGAAAATATTGAAAAAAAATTTTCGGGTCAATTT
193 ATTGAATTATATATTTTTTCTGAGTATTATGACAAAAAATTGAAAAAAACCTTTCGGGTCAGTTT
* * * * * ** *
2071 TTAGCCGAAATCGTGTAATAACCATCACAG-TTTTGGCCTAAAAATG-GTTTCGGGGTCTCG
258 TTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCCG
* * *
2131 ACTCAGTTTTGCATGATTTTTGGCAGAATGACTCCTTGAAATATGTATATTCATCTAATCAAATA
1 ACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * * *
2196 TCAGCCGAATTGGATTTATGAATTTGTGTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGA
66 TCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* *
2261 AATAAATTCGGAAAAAATGGAAAAAGCGATATTTGAAGCGTGAAAAGGCC-ATCAATCTTTTTGG
130 AATAAATTC-GAAAAAATGGAAAAA-CGATATTAGAAGCGTGAAAAGCCCGA-CAATCTTTTTGG
* ** * *
2325 CATCGGTTTTTATATTTTTTATGAGTATTATG
192 CATTGAATTATATATTTTTTCTGAGTATTATG
2357 GCATTGGGCT
Statistics
Matches: 1558, Mismatches: 208, Indels: 117
0.83 0.11 0.06
Matches are distributed among these distances:
301 3 0.00
302 137 0.09
303 83 0.05
304 2 0.00
305 8 0.01
306 2 0.00
308 2 0.00
309 2 0.00
310 2 0.00
312 1 0.00
313 2 0.00
315 2 0.00
316 9 0.01
317 2 0.00
318 4 0.00
319 160 0.10
320 83 0.05
321 104 0.07
322 129 0.08
323 213 0.14
324 175 0.11
325 53 0.03
326 136 0.09
327 6 0.00
328 120 0.08
329 91 0.06
330 27 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (319 bp):
ACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
TCAGCGAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
ATAAATTCGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGACAATCTTTTTGGCATT
GAATTATATATTTTTTCTGAGTATTATGACAAAAAATTGAAAAAAACCTTTCGGGTCAGTTTTTA
GCCGAAATCGTGTACTAACTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGACCCCG
Found at i:3086 original size:324 final size:318
Alignment explanation
Indices: 2360--4056 Score: 1625
Period size: 322 Copynumber: 5.3 Consensus size: 318
2350 TATTATGGCA
* * * * *
2360 TTGGGCTAAAAACGTGCTTCGGGGCCCCGACTCAGTTTTGCATAATTTTTGGCAGAATGACTCCT
1 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * * * * * *
2425 TGAAGTTTGTATATTCATCTAATCAAATATCAGCCGAATTGGAGTTATGAATTTGTGTTTACGAG
66 TGAA-TATCTATATTCATCTAATCAAATCTCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAG
* * * * *
2490 CATCTAAATCTTGTTTCGATTTAATTAGGAATAAATTCGGAAAAAATGGAAAATCGATATTTGAA
129 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATACGGAAAAAATGGAAAAACGATATTAGAA
*** * ** * * *
2555 GCGTGAAAAGCTTATTAATCTTTTTGGCATTGGTTTTTATA-TTTTTATGAGTATTATGGGAAAA
194 GCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAA
* *
2619 AATTGA-CAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAAATCGTGTATTAACCATCACGGTTT
259 AATTGAGC-AAAAAATTTTCGGGTCAGTTTTTAGCCG-AAATCGTGTA--CATCATCACGGTTT
* ** *
2682 TTGGGCTAAAAACGCGTTTTGGGGTCTCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
1 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * *
2747 TGAAATATTTATATTCATCTAATCAAATCTCAGTCGAATCGGATTTAAGGATTTGTATTTACGAG
66 TG-AATATCTATATTCATCTAATCAAATCTCAG-CGAATTGGATTTAAGGATTTGTTTTTACGAG
* *
2812 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAAATAAGAAAAAAAATGGAAAAAACGATATTA
129 CATCTGAATCTTGTTTCGATTTAATTAGAAAT-AAATACG-GAAAAAATGG-AAAAACGATATTA
* * *
2877 GAAGCATGAAAAAGCCCGTCAATCTTTTTGGTATTGAATAATATA-TTTTTCTGAGTATTATGGC
191 GAAGCGTG-AAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGC
**
2941 -AAAAATTGA-CAAAAACCTTTCGGGTCAGTTTTTGAGCCGAAATCGTGTACTAATCATCACGGT
255 AAAAAATTGAGCAAAAAATTTTCGGGTCAGTTTTT-AGCCGAAATCGTGTAC--ATCATCACGGT
*
3004 AT
317 TT
* * * * *
3006 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTTAGTGTTGCATCATTTTTTTGCAGATAGACTCC
1 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGA-TTTTTGGCAGAAAGACTCC
* * * * *
3071 ATGAACATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAT
65 TTGAATATCTATATTCATCTAATCAAATCTCAGCGA-ATTGGATTTAAGGATTTGTTTTTACGAG
* * * * *
3136 TATCTGAATCTTATTTTGATTTAATTAGAAATAAATATGGAAAAAATGGAAAAACAATATTAGAA
129 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATACGGAAAAAATGGAAAAACGATATTAGAA
* ** * * ** * *
3201 GCGTGAAAAACCTTTCCATTTTTTTGGTGTTGAATTATTTATTTTTTCTGAGTATTGTGGCAAAA
194 GCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAA
* **
3266 AATTGAGGAAAAGCTTTTCGGGTCAGTTTTTGCAAAATTTAGCCGAAATCGTG----T-ATCACG
259 AATTGAGCAAAAAATTTTCGGGTCAG---TT------TTTAGCCGAAATCGTGTACATCATCACG
*
3326 ATTT
315 GTTT
* * * * * * * *
3330 TT-GGCTAAAAATGTG-TCCCGGAGTCTCGACTCAATTTTGCATGAATTTTGGC-GCAAAGACTC
1 TTGGGCTAAAAACGCGTTTCGGGA-CCCCGACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTC
* * * * *
3392 CTTAAGATATCTATATTCAT-TAAACCAAATCTTAGCCACATTGGATATAAGGATTTGTTTTTAC
64 CTTGA-ATATCTATATTCATCT-AATCAAATCTCAGCGA-ATTGGATTTAAGGATTTGTTTTTAC
* * * * * *
3456 GAGCATCTGATTCTTTTTTCGATTTAATTAGAAATTAATTCGG-AAAAATGGAAGAACGATATTT
126 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATACGGAAAAAATGGAAAAACGATATTA
* * * *
3520 GAAGCGTGAAAAGCCCGTCAATCATTTTGGCATTGAATTATATATTTTTTCTGAGAATTGTAGCA
191 GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCA
* * * *
3585 AAAAATTCAGGAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCGTGTACGTCA-CA--GTTT
256 AAAAATTGAGCAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACATCATCACGGTTT
*
3645 TTGGGCTAAAAACGCGTTTCGGGAGCCCGACTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCC
1 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGA-TTTTTGGCAGAAAGACTCC
* *
3710 TTGAAATATGTATATTCATCTAATCAAATCTCAGCCGAATTGGATTTAAGGATTTGTTTTTATGA
65 TTG-AATATCTATATTCATCTAATCAAATCTCAG-CGAATTGGATTTAAGGATTTGTTTTTACGA
* * * * * * *
3775 GCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGG-AAAAGTGGAAGAACGATATTTGA
128 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATACGGAAAAAATGGAAAAACGATATTAGA
* * * * * * * * *
3839 TGTGTGAAAAGCCAGTCAATCATTTTGGCGTTGAATTATATATTTTTTATGAGAATTGTAGCAAA
193 AGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCAAA
* ** * * * * * *
3904 AAAGTGA-C---CGA---T-GAG--AG-CTCT--CC-AAA-CAATG-AAATCATGTAC-G--T
258 AAATTGAGCAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATC-GTGTACATCAT-CACGGTTT
*
3948 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAATTTTGCATGATTTTTGGCAGAAAGACTCCT
1 TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* *
4013 TGAAATATGTATATTCATCTAATCATATCTCAGCCGAATTGGAT
66 TG-AATATCTATATTCATCTAATCAAATCTCAG-CGAATTGGAT
Statistics
Matches: 1169, Mismatches: 164, Indels: 104
0.81 0.11 0.07
Matches are distributed among these distances:
302 68 0.06
303 49 0.04
304 2 0.00
305 1 0.00
306 2 0.00
307 2 0.00
309 2 0.00
310 1 0.00
313 16 0.01
315 5 0.00
316 29 0.02
317 199 0.17
318 6 0.01
319 2 0.00
320 28 0.02
321 38 0.03
322 279 0.24
323 145 0.12
324 180 0.15
325 53 0.05
326 46 0.04
331 13 0.01
332 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (318 bp):
TTGGGCTAAAAACGCGTTTCGGGACCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
TGAATATCTATATTCATCTAATCAAATCTCAGCGAATTGGATTTAAGGATTTGTTTTTACGAGCA
TCTGAATCTTGTTTCGATTTAATTAGAAATAAATACGGAAAAAATGGAAAAACGATATTAGAAGC
GTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAA
TTGAGCAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACATCATCACGGTTT
Done.