Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001978.1 Corchorus capsularis cultivar CVL-1 contig01981, 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: 2277
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:993 original size:17 final size:18
Alignment explanation
Indices: 968--1013 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
958 TTGCAAAATA
*
968 TTAGCCGAAAGCA-TACG
1 TTAGTCGAAAGCAGTACG
*
985 TTAGTCGAAATCATGTACG
1 TTAGTCGAAAGCA-GTACG
1004 TTAGTCGAAA
1 TTAGTCGAAA
1014 TCATGGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (18 bp):
TTAGTCGAAAGCAGTACG
Found at i:1005 original size:19 final size:19
Alignment explanation
Indices: 981--1018 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
971 GCCGAAAGCA
981 TACGTTAGTCGAAATCATG
1 TACGTTAGTCGAAATCATG
1000 TACGTTAGTCGAAATCATG
1 TACGTTAGTCGAAATCATG
1019 GTTTTTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (19 bp):
TACGTTAGTCGAAATCATG
Found at i:2099 original size:334 final size:330
Alignment explanation
Indices: 1059--2273 Score: 1102
Period size: 334 Copynumber: 3.7 Consensus size: 330
1049 CGGTTCAGTG
* * * *
1059 TTGCATGATTTTTGGCGCCGAGACTCCTTGAACTATCTATATTCATCTAACCAAATCTCAACCAC
1 TTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
* * *** * **
1124 ATTGGATTTAAGGATCTG-TAAAACAACCATCTGAATCATGTTTCAATTTAATTAGAAA-TTAAT
66 ATTGAATTTAAGGATTTGTTTTTACGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTTAA-
* * * * * * *
1187 TCGTAAAATAAGAGGAAAAATGATATTAGAAGCATGAAAAGCCCTTCAATATTTTTGACGTTGAA
130 TC--AAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTTG-CGTTGAA
* * * * * * * *
1252 TTACATA-ATTTTTATGAGTATTTTGGCTAAACATTGAGGAAATAA-CTTTCGAGTCATTTTTTG
192 TTATATATATATTTATGAGTATTTTGGCTAAAAATTGACGAAAAAATATTTCGGGTCAATTTTTG
* * * *
1315 CAAAATTCTAGCCGAAATCATGTAATAATCATCACGGTTTTTTGCTAAAAACGTG-TTCTGAGAC
257 CAAAATTTTAGCTGAAATC-TGT-ATAATCATCACGGTTTTTGGCTAAAAACGCGTTTC-GAGAC
1379 CCC-TGCTAAGTT
319 CCCGTG-TAAGTT
* * * * * * * *
1391 TTGCATGATTTTTGGCGCCAAAACTCTTTGAGATATCCATATTCATTTAATCAAATCTCAGCTAC
1 TTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
* ** * * * * *
1456 ATTGAATTTGATAATTTGTTTTTAC-A-AATCTGAATCCTGTTTCGATTTAATAAGAAATTCATT
66 ATTGAATTTAAGGATTTGTTTTTACGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTTAAT
* * * * * *
1519 CACAAAATTATG-AATACGATATTAAAAGCCTGAAAAGTCCTCCAATCTTTTTCGCGTT-AA-AA
131 CAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTT-GCGTTGAATTA
* * * * * * * *
1581 TATATATA-TTGTGAGTATTTTAGCCAAAAATTGACGGAAAATTTTTTCGGATCAATTTTTGTAA
195 TATATATATTTATGAGTATTTTGGCTAAAAATTGACGAAAAAATATTTCGGGTCAATTTTTG-CA
* * * * *
1645 AAATGTTAG-TCAAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCAAGA-CC
259 AAATTTTAGCT-GAAATC-TGTA-TAATCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCC
*
1708 CGTCTTAA-TT
321 CGT-GTAAGTT
* * * * *
1718 TTGTATGATTTTTGGTGCCGAGACTCCGTGAAATATCTATATTCATCTAATCAAATCTCAACCAC
1 TTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
* * * *
1783 ATTGAATTTAAGGATTTTTTTTTACGAGAATCTAAATCTTGTTTCTATTTAATTAGAAAATTTAA
66 ATTGAATTTAAGGATTTGTTTTTACGAGAATCTGAATCATGTTTCAATTTAATTAG-AAATTTAA
* * *
1848 ACAAAAAAAATATGAAAAACGATATTAAAAACGTGAAAAGTCCTCCAATATTTTTAGCGTTGAAC
130 TC-AAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTT-GCGTTGAA-
* * *
1913 TTTTTATATATATTTAATGAGTATTGTGGGTAAAAATTGA-GAAAAAATATTTCGGGTCAATTTT
192 -TTATATATATATTT-ATGAGTATTTTGGCTAAAAATTGACGAAAAAATATTTCGGGTCAATTTT
* *
1977 TGCAAAATTTTAGCTGAAAT-TGTAT-ATCATCACGGTCTTTTGGCTAATAACGCGTTTCGGGAC
255 TGCAAAATTTTAGCTGAAATCTGTATAATCATCACGGT-TTTTGGCTAAAAACGCGTTTCGAGAC
*
2040 CCCGTGTCAGTT
319 CCCGTGTAAGTT
** * * *
2052 TTGCATGATTTTTTATGGCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCAC
1 TTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
* * *
2117 ATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCAATTTAATTAGAAA-TTAAT
66 ATTGAATTTAAGGATTTGTTTTTACGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTTAA-
* * * * * *
2181 TTGGAAAAAAATAGGAAAAACGATA-T-----CA-G--AAGCCCTTCAATCTTTTTGGCGCTGAA
130 -T-CAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTT-GCGTTGAA
*
2237 TTATATATAT-TTTATGAGTATTGTGGCTAAAAATTGA
192 TTATATATATATTTATGAGTATTTTGGCTAAAAATTGA
2274 AAAA
Statistics
Matches: 713, Mismatches: 141, Indels: 69
0.77 0.15 0.07
Matches are distributed among these distances:
321 23 0.03
322 3 0.00
323 9 0.01
325 22 0.03
326 30 0.04
327 100 0.14
328 88 0.12
329 34 0.05
330 7 0.01
331 38 0.05
332 125 0.18
333 34 0.05
334 135 0.19
336 21 0.03
337 25 0.04
338 19 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
TTGCATGATTTTTGGTGCCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
ATTGAATTTAAGGATTTGTTTTTACGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTTAAT
CAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATATTTTTGCGTTGAATTAT
ATATATATTTATGAGTATTTTGGCTAAAAATTGACGAAAAAATATTTCGGGTCAATTTTTGCAAA
ATTTTAGCTGAAATCTGTATAATCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGTGT
AAGTT
Done.