Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019244.1 Corchorus olitorius cultivar O-4 contig19277, 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: 4348
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:1014 original size:15 final size:16
Alignment explanation
Indices: 989--1018 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
979 AATAATTATT
989 TTTAGATTATAATATA
1 TTTAGATTATAATATA
1005 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
1019 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:2160 original size:333 final size:331
Alignment explanation
Indices: 1405--3388 Score: 1489
Period size: 333 Copynumber: 6.0 Consensus size: 331
1395 ACAACATTGG
*
1405 ATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TCTAGA
1 ATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGA
* * *
1469 AAAAATAAGAAATACGATATTAAAAGCGTAAAAAACCCTCCAATCTTTTTGGCGTTG-A--AT-T
65 AAAAAT-AGAAA-ACGATATTAAAAGCGTGAAAAGCCCT-CAATATTTTTGGCGTTGAATTATAT
* * *
1530 ATATAT-TTTTATGAGTATTTTAGCCAAAAGTTGAGGAGAA-ATCTTTCGTGTC-ATTTATTGCA
127 ATATATATTTTATGAGTATTATAGCCAAAAATTGAGGA-AATATCTTTCGGGTCAATTT-TTGCA
* * * * *
1592 AAATATTAGCCGAAATAGTGTACTAACAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCAAGG
190 AAATTTTAGCCAAAATCGTG---TAATAAA-CATCACGGTTTTTGGCTAAAAACGGGTT-C-AGG
* *
1657 ACCCGGCTCAATTTTGCATTATTTTTGGCTCCAAGACTACTTGAAATATCTATATTCATCTAATC
249 ACCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTACTTGAAATATCTATATTCATCTAATC
* *
1722 AAATCTCAGACACATTAG
314 AAATCTCAGGCACATTAC
* * *
1740 ATTTAAGGATAATTTGTTTTTACGAGCATATGAGTCTTGTTTCGATTTAATTAGAAATTAATT-T
1 ATTTAA-G--AATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA
* *
1804 GAAAAAAATAGGAAAATGATATTAGAAA-CGTCAAAAGCCCATCAATATTTTTGGCGTTGAATTA
63 G-AAAAAATA-GAAAACGATATTA-AAAGCGTGAAAAGCCC-TCAATATTTTTGGCGTTGAATTA
* * * *
1868 TATAT-T-T-TTTTATGAGAATTTTAGCC-AAATTTGAGGAAATATCTTTCGGGTCAATTTTTAC
124 TATATATATATTTTATGAGTATTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGC
* * * * * *
1929 AAAATTTTAGCCGAAATCGTGTAATAAACATCACAGTTTTTGGATAAAAAAGGGTTCTGGAGGCC
189 AAAATTTTAGCCAAAATCGTGTAATAAACATCACGGTTTTTGGCTAAAAACGGGTTCAGGA-CCC
* * * * *
1994 GGCTCAGTTTTGCATTACTTTTGGCGCCAAGACTCCTTGAGAAATTTTTGTATTCATCTAATCAA
253 GGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTACTT--GAAATATCTATATTCATCTAATCAA
* *
2059 ATCTCAGCTTGCCATATTAT
316 ATCTCAG---G-CACATTAC
* * * * * *
2079 ATTTAAGAATTTATTTTTACAAGTATTTGAATATTGTTTCGTTTTAATTAGAAATTAATTCA-CA
1 ATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
* * ** * *
2143 AAAATA-TAAACGATATTAAAAGCATGAAAATTCCTC-CT-TTTTT-GCGTTAAATTATATATAT
66 AAAATAGAAAACGATATTAAAAGCGTGAAAAGCCCTCAATATTTTTGGCGTT-GA--AT-TATAT
* * * * *
2204 ATATATATATTATATGAGTATTATATCCAAAAATTGAGGAAAAAT-TCTTCAGCTCATTTTTTTG
127 ATATATAT-TT-TATGAGTATTATAGCCAAAAATTGAGGAAATATCT-TTCGGGTCA-ATTTTTG
* * ** * *
2268 CAAAATTTTAGTCAAAATCGTGTACTAATTATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACC
188 CAAAATTTTAGCCAAAATCGTGTAATAAACATCACGGTTTTTGGCTAAAAACG-GGTTCAGGACC
* * *
2333 CGACTCAGTTTTGCA-TATTTTTGGCGCCAACACTTA-TTGAAATATCTATATTCATCTAATAAA
252 CGGCTCAGTTTTGCATTATTTTTGGCGCCAAGAC-TACTTGAAATATCTATATTCATCTAATCAA
* *
2396 ATCTTAGGCACATTGC
316 ATCTCAGGCACATTAC
* * * * *
2412 ATTTAAGGATTTGTCTTTACGAGGATTTGAATCTTATTTCAATTTAATTAGAAATTAATTCAGAA
1 ATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
* **
2477 AAAATATGGAAAGCGATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTTACGTTGAATTATATA
66 AAAATA--GAAAACGATATTAAAAGCGTGAAAAGCCC-TCAATATTTTTGGCGTTGAATTATATA
* * * *
2542 TATATCTTTTATGAGTATTAT-GGCTAAAATTGAGGAAATATCTTTCGGGTCAACTTTTGCAAAA
128 TATATATTTTATGAGTATTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAA
* * * * * **
2606 TTTTATCCAAAATCGTGTAGTAATCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCGATT
193 TTTTAGCCAAAATCGTGTAATAAACATCACGGTTTTTGGCTAAAAACGGGTT-CAGGACCCGGCT
* * * * * * *
2671 AAGTTTTGAATGATTTTTGGCGCCCAGAATCCTTGAAATATCTATATTCATCTAACCAAA--T--
257 CAGTTTTGCATTATTTTTGGCGCCAAGACTACTTGAAATATCTATATTCATCTAATCAAATCTCA
2732 --CACA--AC
322 GGCACATTAC
* * * * * *
2738 -------CA-TTGTTTTTACAAGCATCTT-AATCATGTTTCGTTTTGATTAGAAATTAGTTCAGA
1 ATTTAAGAATTTGTTTTTACGAGCAT-TTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-
* * ** *
2794 AAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCCTTTCGGCGTT-AA--AT-
64 AAAAAATA-G-AAAACGATATTAAAAGCGTGAAAAGCCC-TCAATATTTTTGGCGTTGAATTATA
* * * * * * *
2855 TATATATTTTTTATAAGTATTATGGCTAAAAATTGAGGAAAAATATTTCCGGTCAATTTTTGCAA
126 TATATATATTTTATGAGTATTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAA
* * * * * ***** * * * *
2920 AATATTAGCCGAAATCGTGTAACATCACTTTTTTTTTTTTTTGCTAAAAACGCGTTCTGGGGCTC
191 AATTTTAGCCAAAATCGTGTAATA-AAC-ATCACGGTTTTTGGCTAAAAACGGGTTC-AGGAC-C
* * * * *
2985 CGAG-TCAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGAAATGTCTATATTCATCTAATCAA
252 CG-GCTCAGTTTTGCATTATTTTTGGCGCCAAGACTACTTGAAATATCTATATTCATCTAATCAA
3049 ATCTCA-GC-CA-T--
316 ATCTCAGGCACATTAC
* * *
3060 A-TT--G-----G-ATTTACGAGACATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-GA
1 ATTTAAGAATTTGTTTTTACGAG-CATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
* ** * * *
3115 AAAAAGTTAGGAAAAAAAGATATTAGGAGCGTAAAAAAATCCCTTCAATATTTTTGGCG-TGGA-
65 AAAAA--TA-G--AAAACGATATTAAAAGCGT--GAAAAGCCC-TCAATATTTTTGGCGTTGAAT
* * * * *
3178 -AT-TATATATCTTTTATGATTATTTTAGTC-AAAATTGAGGAAATATCTTTCCGGTCAATTTTT
122 TATATATATATATTTTATGAGTATTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTT
* * * *
3240 ACAAAATTTTA-CCTGAAATCGTGTAAT--A-ATCACGATTTTTGGCTAAAAACGCGTTCCAGGG
187 GCAAAATTTTAGCC-AAAATCGTGTAATAAACATCACGGTTTTTGGCTAAAAACGGGTT-CA-GG
* * * * * * * *
3301 CCCCAGG-TCAGTTTTGCATGATTTTCGGCACTAAGACTCCTTGAGATATCCATATTCATCTAAT
249 ACCC-GGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTACTTGAAATATCTATATTCATCTAAT
** *
3365 CAAATCTCATCCACATTGC
313 CAAATCTCAGGCACATTAC
3384 ATTTA
1 ATTTA
3389 GGGGGCGTTT
Statistics
Matches: 1344, Mismatches: 218, Indels: 183
0.77 0.12 0.10
Matches are distributed among these distances:
315 21 0.02
316 55 0.04
317 2 0.00
318 69 0.05
319 188 0.14
320 12 0.01
321 13 0.01
322 36 0.03
323 22 0.02
324 55 0.04
325 45 0.03
326 1 0.00
328 4 0.00
329 5 0.00
330 6 0.00
331 1 0.00
332 13 0.01
333 194 0.14
334 96 0.07
335 62 0.05
336 50 0.04
337 102 0.08
338 127 0.09
339 76 0.06
340 75 0.06
341 14 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (331 bp):
ATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
AAAATAGAAAACGATATTAAAAGCGTGAAAAGCCCTCAATATTTTTGGCGTTGAATTATATATAT
ATATTTTATGAGTATTATAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTT
TAGCCAAAATCGTGTAATAAACATCACGGTTTTTGGCTAAAAACGGGTTCAGGACCCGGCTCAGT
TTTGCATTATTTTTGGCGCCAAGACTACTTGAAATATCTATATTCATCTAATCAAATCTCAGGCA
CATTAC
Found at i:3036 original size:319 final size:312
Alignment explanation
Indices: 2448--3388 Score: 996
Period size: 319 Copynumber: 2.9 Consensus size: 312
2438 TTGAATCTTA
* * * *
2448 TTTCAATTTAATTAGAAATTAATTCAGAAAAAATATGG-AAAGCGATATTAAAAGCGTGAAAAGC
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGC
**
2512 CCTTCAATATTTTTTACGTTGAATTATATATATATCTTTTATGAGTATTATGGCTAAAATTGAGG
66 CCTTCAATATTTTTGGCGTT-AA--AT-TATATATCTTTTATGAGTATTATGGCTAAAATTGAGG
* * * * *
2577 AAATATCTTTCGGGTCAACTTTTGCAAAATTTTATCCAAAATCGTGTAGTAATCATCACGGTTTT
127 AAATATCTTTCCGGTCAATTTTTGCAAAATTTTA-CCGAAATCGTGTA--AATCA-C-TGATTTT
* * * * * *
2642 TGGCTAAAAACGCGTTCCGGGACCCGATTAAGTTTTGAATGATTTTTGGCGCCCAGAA-TCCTTG
187 TGGCTAAAAACGCGTTCCGGGGCCCGAGTCAGTTTTGCATGATTTTTGGC-ACCAAAACTCCTTG
* ** *
2706 AAATATCTATATTCATCTAACCAAATCACAACC-ATTGTTTTTACAAG-CATCTTAATCATG
251 AAATATCTATATTCATCTAATCAAATCACAACCAATTGGATTTACAAGACATCTAAATCATG
* * * *
2766 TTTCGTTTTGATTAGAAATTAGTTCAGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGC
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGC
** * * *
2831 CCTTCAATCCTTTCGGCGTTAAATTATATATTTTTTATAAGTATTATGGCTAAAAATTGAGGAAA
66 CCTTCAATATTTTTGGCGTTAAATTATATATCTTTTATGAGTATTATGGCT-AAAATTGAGGAAA
* * * **
2896 AATATTTCCGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAACATCACTTTTTTTTTTTTT
130 TATCTTTCCGGTCAATTTTTGCAAAATTTTA-CCGAAATCGTGTAA-ATCAC-----TGATTTTT
* *
2961 TGCTAAAAACGCGTTCTGGGGCTCCGAGTCAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGA
188 GGCTAAAAACGCGTTCCGGGGC-CCGAGTCAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGA
* * * * *
3026 AATGTCTATATTCATCTAATCAAATCTCAGCCATATTGGATTTACGAGACATCTAAATCTTG
252 AATATCTATATTCATCTAATCAAATCACAACCA-ATTGGATTTACAAGACATCTAAATCATG
* * * *
3088 TTTCGATTTAATTAGAAATTAATTC-GAAAAAAGTTAGGAAAAAAAGATATTAGGAGCGTAAAAA
1 TTTCGATTTAATTAGAAATTAATTCAGAAAAAA-TAAGG-AAAAACGATATTAGAAGCGT--GAA
* ** * * *
3152 AATCCCTTCAATATTTTTGGCGTGGAATTATATATCTTTTATGATTATTTTAG-TCAAAATTGAG
62 AAGCCCTTCAATATTTTTGGCGTTAAATTATATATCTTTTATGAGTATTATGGCT-AAAATTGAG
*
3216 GAAATATCTTTCCGGTCAATTTTTACAAAATTTTACCTGAAATCGTGTAATAATCAC-GATTTTT
126 GAAATATCTTTCCGGTCAATTTTTGCAAAATTTTACC-GAAATCGTGT-A-AATCACTGATTTTT
* * * * *
3280 GGCTAAAAACGCGTTCCAGGGCCCCAGGTCAGTTTTGCATGATTTTCGGCACTAAGACTCCTTGA
188 GGCTAAAAACGCGTTCCGGGGCCCGA-GTCAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGA
* * * * *
3345 GATATCCATATTCATCTAATCAAATCTCATCCACATTGCATTTA
252 AATATCTATATTCATCTAATCAAATCACAACCA-ATTGGATTTA
3389 GGGGGCGTTT
Statistics
Matches: 521, Mismatches: 82, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
314 2 0.00
315 29 0.06
316 53 0.10
318 66 0.13
319 195 0.37
321 18 0.03
322 36 0.07
323 20 0.04
324 51 0.10
325 50 0.10
326 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (312 bp):
TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGC
CCTTCAATATTTTTGGCGTTAAATTATATATCTTTTATGAGTATTATGGCTAAAATTGAGGAAAT
ATCTTTCCGGTCAATTTTTGCAAAATTTTACCGAAATCGTGTAAATCACTGATTTTTGGCTAAAA
ACGCGTTCCGGGGCCCGAGTCAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGAAATATCTAT
ATTCATCTAATCAAATCACAACCAATTGGATTTACAAGACATCTAAATCATG
Found at i:3505 original size:11 final size:11
Alignment explanation
Indices: 3489--3522 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3479 GTGTGGTAAT
3489 CCGGATTACCC
1 CCGGATTACCC
3500 CCGGATTACCC
1 CCGGATTACCC
* *
3511 CCTGATCACCC
1 CCGGATTACCC
3522 C
1 C
3523 TTTAAGGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.50, G:0.15, T:0.18
Consensus pattern (11 bp):
CCGGATTACCC
Done.