Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001068.1 Corchorus capsularis cultivar CVL-1 contig01068, 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: 14957
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:229 original size:2 final size:2
Alignment explanation
Indices: 222--253 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
212 AATAGAAAAC
222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254 GAATACATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2455 original size:23 final size:23
Alignment explanation
Indices: 2406--2456 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2396 TATTTACTAC
* *
2406 TAATTTTTTTTTTGCATAAGTAA
1 TAATTTTTTTTTTCCATAAGCAA
2429 -AATTTTTTTTTTCC-TATAGCAA
1 TAATTTTTTTTTTCCATA-AGCAA
2451 TAATTT
1 TAATTT
2457 GGGAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (23 bp):
TAATTTTTTTTTTCCATAAGCAA
Found at i:12204 original size:322 final size:323
Alignment explanation
Indices: 10879--14212 Score: 2370
Period size: 322 Copynumber: 10.3 Consensus size: 323
10869 CAGTTTAAAG
* * *
10879 TTTTGCATGATTTTTTGCAGAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
10944 ACATTGTATTTAAGGATTT-TTTTTACGAGCATCTGAATCTTATTTTGATTTATAATTAAAAATA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA-TT-TAATTAGAAATA
* * ** *
11008 AATTCTGAAAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAATTCTTCAATTTCTGTTGGA
129 AATTC---AGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTT-TTTTGGA
* * * * * * * * * *
11073 GTTGAATTATATATATTTTTTTGGGTATTATGGCAAAAGATTGAAGAAGAACATTTAGGATCAGC
190 GTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGT
* * * * *
11138 TTTTGCAAAATTTTAGTCGAAATCGTGTAATAACCATCACAGTTTTCGGCTAAAAACGCGTTCCG
254 TTTTACAAAATTTTA--C----T--TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCG
* *
11203 GAGCCCTGACTCAT
311 G-GCCCCGACTCAA
* * * * * *
11217 TTTTGCATGATTTTTGGCGTAAAGACTACATGAAATATCTATATTTATCGAACCAAATTTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
11282 ACATTGAATATTAA-GATTTGTTTTTACGGGCATCTGAATCTTGTTTGGATTTAATTAGAAATTA
66 ACATTGGATA-TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
** * * * * *
11346 ATTC-G---GGAA---AAAAACCATTATTAGAAGCTTG-AAAAGCGTGTC-ATTCTTTTTGGCGT
130 ATTCAGAAAAAAATGGAAAAACGA-TATTAGAAGCGTGAAAAACCCT-TCAATT-TTTTTGGAGT
* * * * **
11402 TGAATCATATA-TTTTT-T---T-CT-T-----AATATTCA-GAAAAA-TTTTCCAGGTCAGTTT
192 TGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTT-TGGGTCAGTTT
* * * * * *
11453 TTAGCCGAAA---T-CATGTGCT--CCATCACGGTTTTTGGACTAAAAACGCGATTCGGACCCTG
256 TTA--CAAAATTTTACTTGTACTAACCATCACGGTTTTTGG-CTAAAAACGCGTTTCGGGCCCCG
11512 ACTCAA
318 ACTCAA
* * * * * *
11518 TTTTGTATGATTTTTGGCATAAAGACTTCTTGAAATAACTATATTCATCGAACCAAATCCCAGCT
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
11583 ACATTGGATATAAGAATTTGTTTCTACAAGCAT-TAAAATCTTGTTTCGATTTAATTAGAAATTA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCT-GAATCTTGTTTCGATTTAATTAGAAATAA
* * * * * *
11647 ATTCAGAAAAAAATGGAAGAACGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
130 ATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGAGTTGA
* * * * *
11712 ATTATATATTTTTTCTGATTATTGTGCCAAAAAATTCA-GAAAAACCTTTTCGGTC--TTTTT--
195 ATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTAC
* * * *
11772 ----TTTT--TAG-CCGAA--ATCGA-GGTTTCTTGGCT-AAAACTGTGTTTCGGGGCCCCGACT
260 AAAATTTTACTTGTACTAACCATC-ACGGTTT-TTGGCTAAAAAC-GCGTTTC-GGGCCCCGACT
* *
11826 TAG
321 CAA
* * * *
11829 TTTTGCATGATTTTTGGCAGAAAGACTTCTTAAAATATCTATATTTATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * *
11894 ATATTGGATTTAAGGATTT-TTTATTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAA
66 ACATTGGATATAAGGATTTGTTT-TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
* *
11958 ATTCAG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAACTTTTTTGGAGTTAA
130 ATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGAGTTGA
* * * * * *
12022 ATTAAATATTATTT-TAAGTATTGTGGCAAAAAATTGAGGATATATTTTTTGGGTCAGTTTTTAC
195 ATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTAC
** * * * *
12086 AAAATTTTACTTGTACTAACCATCACGGTTTTTGGCTAAAAACGCAATCCAGGGCCACGGCTCAG
260 AAAATTTTACTTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCCGACTCAA
* * * *
12151 TATTGCATGGTTTTTAGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGGC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* ** * * * * *
12216 AGATTGGATATTTAAGGATTTAATTTTGCGAGTATTTGAATCTTATTTTGATTTAATTAGAAATA
66 ACATTGGATA--TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATA
* ** * *
12281 AATTC-GAAAAAAATGAAAAAATAATATTACAAGCGTAAAAAACCCTTCAATTTTTTTTGGAGTT
129 AATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGAGTT
* * * *
12345 GAATTATATATTTTTTCTGAATATTGTGGCAAAAGATTGAGGAAAAACTTTTCGGGTCCGTTTTT
193 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTT
* * * *
12410 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCAAAAAACACGTTCCGGAG
258 ACAAAATTTTA--C----T--TGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGG-G
12475 CCCCGACTCAA
313 CCCCGACTCAA
* * * * * *
12486 TTTTGAATGA-TTTTAGCGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATCTCGGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
** * * *
12550 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATAATGTTTGGATTTAATAAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
* ** * * *
12615 TTCGGAAAAAAATTAAAAAAAAAACGATATTAGAAGCTTGAAAAGCCCGTC-ATTCTTTTTGGAG
131 TTCAGAAAAAAA-T---GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT-TTTTTGGAG
* * * * * * * * **
12679 TTGAATCATATATTTTTACTTAGTATTTTGCCAAAAAAAT-AGAAAAAAATTCAT--GTCAGTTT
191 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTT
* * * * *
12741 TTAGTCGAAA---T-CGTGTACT--TCATCATGGTTTTTGGGCTAAAAACAC-TATTCGAGGCCC
256 TTA--CAAAATTTTACTTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGT-TTCG-GGCCC
*
12799 CGACTCAG
316 CGACTCAA
* * ** * * * *
12807 TTTTGCGTTATTTTTGGCCGAAAAACTTCTTGAAATAACTATATTCATCGAACCAAATC-CTAGC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC-AGC
* * * *
12871 TACATTGGATATAAAGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTA
65 CACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
* * * * *
12936 ATTCGGAAAAAAAATGAAAAAAAAATGATATTAGAAGTGTGAAAAGCCCGTT-AATCTTTTTT-G
130 ATTCAG-AAAAAAATG---GAAAAACGATATTAGAAGCGTGAAAAACCC-TTCAAT-TTTTTTGG
* * * * ** * * *
12999 TGTTGGATTATATATTTTTTCTGAGTATTAT-CCAAAAAATTTCGGAAAAAACTTTTCGTGTTAG
189 AGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGG-AAAAACTTTTTGGGTCAG
* ** * * * * *
13063 TTTTTATCCTAAA--TCGCGTGTACTAACCATCAAAGTTTTTTAGTTAAAAACGCGTTTCGGGGC
253 TTTTTA--CAAAATTTTACTTGTACTAACCATC-ACGGTTTTTGGCTAAAAACGCGTTTC-GGGC
* *
13126 CCC-AGGTCAG
314 CCCGA-CTCAA
* * * *
13136 TTTTGCATGATTTTTGGCAGAAAGACTTCTTGACATATCTATATTCATCTAAGTC-AATCTCAGC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAA-CCAAATCTCAGC
* * *
13200 CACATTGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTTTTTCGATTTAATTAGAAATAA
65 CACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
** * *
13265 ATTTTGAAAGAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCATTTTTTTTTGCA-TT
130 ATTCAGAAA-AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA-ATTTTTTTGGAGTT
* * * * *
13329 GAATTATATAATTTTTCCTGAGTATTATGGCAAAAAATTGAGGACAAATTTTTTGGGTAAGTTTT
193 GAATTATAT-ATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTT
* * * ** * * *
13394 TGA-AAAATTTTACATGTA-T----ATCATGGGTTTTAACTAAAAACACGTTTCGGGGCCTCGGC
257 T-ACAAAATTTTACTTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCCGAC
13453 TCAA
320 TCAA
* * * * *
13457 TATTGCATGGTTTTTAGCATAAAGACTCCTTGAAATATTTATATTCATTTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * ** * *
13522 ATATTGGATTTAACGATTTAATTTTATGAGCATCTGAATCTTGTTAT-AATTTAATTAGAAATAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATAA
* * * * **
13586 ATT-TGGAAAAAATGGAAAAAACGATATTAGAAACGTGAAAAACCCTTAAATTTTTTATGCCGTT
130 ATTCAGAAAAAAATGG-AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTT-TGGAGTT
* * * *
13650 TAATTACATATTTTTTTTTCTGAGTTTTGTGGCAAAAAAATTGAGGAAAAACTTTTCGGGTCAGT
193 GAATT--ATA-TATTTTTTCTGAGTATTGTGGC-AAAAAATTGAGGAAAAACTTTTTGGGTCAGT
* **** * * * * *
13715 TTTTACTAAATTTTAGCCAAAATCGTGTACGATCA-TGATTTTGGCTAAAAACGCGTTCCGGAGC
254 TTTTACAAAATTTTA-CTTGTA-C-T-AACCATCACGGTTTTTGGCTAAAAACGCGTTTCGG-GC
13779 CCCGACTCAA
314 CCCGACTCAA
** * * *
13789 TTTCACATGATTTTTGGTGCA-GAA-ACTCCTTAAAATATCTATATTAAT-TGAACCAAATCTCA
1 TTTTGCATGATTTTT-G-GCATAAAGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTCA
* * * * *
13851 GCCACATTAGATATAAGGATTTATTTTTACGAGCATCTAAAACTTGTTTCGATTTAATTAGAATT
63 GCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * * * ** *
13916 TAATTCGGAAAAAAAAT-GAAAAATGATATTAGAAGCTTGATAAGCCAATCAATCTTTTTT-TAT
128 AAATTCAG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT-TTTTTTGGA-
* * * * *** * * *
13979 GTTGAATTATATATTTTTTCTTAGTAGTGTTGCAAAAAATTCG-GAAAAAAAAAATTCGAGTTAG
190 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAG-GAAAAACTTTTTGGGTCAG
* ** * * * * * * * *
14043 GTTTTAGCCGAA----ACAGTGTATTAAACATCACGTTTTTTGGCCAAAAACGTGTTCCGGAGGC
253 TTTTTA-CAAAATTTTAC-TTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGG-GCC
* *
14104 CCGGCTTAA
315 CCGACTCAA
* * * * * * *
14113 TTTTGCATGATTTTTTGCGTAAAGACTCCTTAAAATATCTATATTTATCGAAACAAATGTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * *
14178 ACATTGGATATATGGATTTATTTTTATGAGCATCT
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCT
14213 ATAATCTCAT
Statistics
Matches: 2397, Mismatches: 443, Indels: 326
0.76 0.14 0.10
Matches are distributed among these distances:
300 4 0.00
301 135 0.06
302 16 0.01
303 4 0.00
305 2 0.00
307 33 0.01
308 17 0.01
309 26 0.01
310 93 0.04
311 129 0.05
312 12 0.01
313 15 0.01
314 7 0.00
315 4 0.00
317 5 0.00
318 4 0.00
319 31 0.01
320 51 0.02
321 200 0.08
322 255 0.11
323 70 0.03
324 241 0.10
325 54 0.02
326 96 0.04
327 82 0.03
328 42 0.02
329 183 0.08
330 19 0.01
331 4 0.00
332 213 0.09
333 30 0.01
334 88 0.04
335 49 0.02
336 42 0.02
337 41 0.02
338 71 0.03
339 29 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (323 bp):
TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
TTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGAGTTGAA
TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTACA
AAATTTTACTTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTCAA
Found at i:14613 original size:20 final size:20
Alignment explanation
Indices: 14588--14628 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
14578 GCTAAGTGGA
*
14588 TTACTAAATACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
**
14608 TTACTAGCCACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
14628 T
1 T
14629 GGACTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.44, G:0.07, T:0.29
Consensus pattern (20 bp):
TTACTAAACACCGCCCCCTT
Done.