Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017551.1 Corchorus olitorius cultivar O-4 contig17584, 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: 1902
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:673 original size:27 final size:27
Alignment explanation
Indices: 619--673 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
609 ACGATTTTGG
* * * *
619 CTGAAAACGCGTTCTAGGGCCTCGGCT
1 CTGAAAACGCATTCCAGGGCCCCAGCT
646 CTGAAAACGCATTCCAGGGCCCCAGCT
1 CTGAAAACGCATTCCAGGGCCCCAGCT
673 C
1 C
674 AGTTTTGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (27 bp):
CTGAAAACGCATTCCAGGGCCCCAGCT
Found at i:1470 original size:254 final size:257
Alignment explanation
Indices: 1015--1523 Score: 817
Period size: 254 Copynumber: 2.0 Consensus size: 257
1005 TTCCGCCAAG
* * *
1015 ACTCATTGAAGTATCTATATTCATCATCCCTAATCTCAGCCACATTGGATTTAAGTATTTGATTT
1 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
* * * * *
1080 TACGAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAATTTTAAAAAATGAT
66 TACGAGCATTCGAATCATGATTCAATTTAATCAGAAATTAATTCAGAAAAA--TTAAAAAAAGAT
* * * *
1145 ATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGC
129 ATTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTGC
* *
1210 GGTTAAAAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAGTTTTTGCC-AAATCGTCAAT
194 GGTTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTCAAT
1273 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
1 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
* * *
1338 TATGAGCATTTGAATCAT-ATTCAATTTAATCAGAAATTGATTCAGAAAAA-TAAAAAAAGATAT
66 TACGAGCATTCGAATCATGATTCAATTTAATCAGAAATTAATTCAGAAAAATTAAAAAAAGATAT
1401 TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTGCGG
131 TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTGCGG
*
1466 TTAAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGT
196 TTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATCGT
1524 GTACTAACCA
Statistics
Matches: 232, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
254 120 0.52
255 7 0.03
257 27 0.12
258 78 0.34
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (257 bp):
ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
TACGAGCATTCGAATCATGATTCAATTTAATCAGAAATTAATTCAGAAAAATTAAAAAAAGATAT
TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTGCGG
TTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTCAAT
Found at i:1828 original size:585 final size:573
Alignment explanation
Indices: 700--1854 Score: 1746
Period size: 585 Copynumber: 2.0 Consensus size: 573
690 TTGCTCCACG
* * *
700 ACTCATTGAAATATTTATATTCATCAGCCCCAATCTCAGCCACATTGTATTTAAGAATTTGATTT
1 ACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAATTTGATTT
*
765 TACGAGCATTTGAATCATATTTCAATTTAATCAGAAATTAATTCGGAAAAATAAAAAAAAAGATA
66 TACGAGCATTTGAATCATATTTCAATTTAATCAGAAATTAATTCAGAAAAAT-AAAAAAAAGATA
* * *
830 TTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGTCATTGAATTATATATTTTTAACAATTATTGCG
130 TTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTAACAAGTATTGCG
* *
895 ATTAACAATTGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTTGCCGAACACGATTCTTG
195 ATTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAACACGATTCTTG
*
960 GCTGAAAACGCATTCCAAAGCCCCGGCTCAGTTTTGCATGATTATTTCCGCCAAGACTCATTGAA
260 GCTGAAAACGCATTCCAAAGCCCCGGCTCAGTTTTGCATGATTATTTCCGCCAAAACTCATTGAA
* *
1025 GTATCTATATTCATCATCCCTAATCTCAGCCACATTGGATTTAAGTATTTGATTTTACGAGCATT
325 ATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGTATTTGATTTTACGAGCATT
* * * ** *
1090 CGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAATTTTAAAAAATGATATTAGAAGCG
390 CGAATCATGATTCAATTTAATCAGAAATTAATTCGGAAAAATTAGAAAAAATGATATTACAAGCG
* * *
1155 TGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAAT
455 TGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTACGGTTAAAAAT
* *
1220 TGAGGAAAAATCTTTCAGGTCAATTTTTGCAAAGTTTTTGCC-AAATCGTCAAT
520 TGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTCAAT
* *
1273 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
1 ACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAATTTGATTT
* *
1338 TATGAGCATTTGAATCATA-TTCAATTTAATCAGAAATTGATTCAGAAAAAT-AAAAAAAGATAT
66 TACGAGCATTTGAATCATATTTCAATTTAATCAGAAATTAATTCAGAAAAATAAAAAAAAGATAT
*
1401 TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTT-ACGAGTATTGCG
131 TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATA-TTTTTAACAAGTATTGCG
* *
1465 GTTAAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTA
195 ATTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTG-C-----C--G-----
* ** * * *
1530 ACCATCACGATTCTTGGCTGAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATGATTTTTTGC
247 A--A-CACGATTCTTGGCTGAAAACGCATTCCAAAGCCCCGGCTCAGTTTTGCATGATTATTTCC
1595 GCCAAAACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGTATT
309 GCCAAAACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGTATT
* *
1660 TGATTTTACGAGCATTTGAATCAT-ATTCAATTTAATCAGAAATTGATTCGGAAAAA-TAGAAGA
374 TGATTTTACGAGCATTCGAATCATGATTCAATTTAATCAGAAATTAATTCGGAAAAATTAGAA-A
1723 AAATGATATTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGA
438 AAATGATATTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGA
*
1788 GTATTACGGTTAAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATC
503 GTATTACGGTTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATC
1853 GT
568 GT
1855 GTACTAACCA
Statistics
Matches: 524, Mismatches: 39, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
570 111 0.21
571 6 0.01
572 30 0.06
573 78 0.15
576 1 0.00
578 1 0.00
583 1 0.00
584 3 0.01
585 147 0.28
586 146 0.28
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (573 bp):
ACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAATTTGATTT
TACGAGCATTTGAATCATATTTCAATTTAATCAGAAATTAATTCAGAAAAATAAAAAAAAGATAT
TACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTAACAAGTATTGCGA
TTAAAAATTGAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAACACGATTCTTGG
CTGAAAACGCATTCCAAAGCCCCGGCTCAGTTTTGCATGATTATTTCCGCCAAAACTCATTGAAA
TATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGTATTTGATTTTACGAGCATTC
GAATCATGATTCAATTTAATCAGAAATTAATTCGGAAAAATTAGAAAAAATGATATTACAAGCGT
GCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTACGGTTAAAAATT
GAGGAAAAATCTCTCAGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTCAAT
Found at i:1872 original size:331 final size:328
Alignment explanation
Indices: 1273--1902 Score: 1170
Period size: 331 Copynumber: 1.9 Consensus size: 328
1263 AATCGTCAAT
1273 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
1 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
*
1338 TATGAGCATTTGAATCATATTCAATTTAATCAGAAATTGATTCAGAAAAATAAAAAAAGATATTA
66 TACGAGCATTTGAATCATATTCAATTTAATCAGAAATTGATTCAGAAAAATAAAAAAAGATATTA
*
1403 CAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTGCGGTT
131 CAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTACGGTT
1468 AAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACC
196 AAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACC
*
1533 ATCACGATTCTTGGCTGAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATGATTTTTTGCGCC
261 ATCACGATTCTTGGCTGAAAACACGTTCCAGGGCCCCGGCTCAGTTTTGTATGATTTTTTGCGCC
1598 AAA
326 AAA
*
1601 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGTATTTGATTT
1 ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
*
1666 TACGAGCATTTGAATCATATTCAATTTAATCAGAAATTGATTCGGAAAAATAGAAGAAAATGATA
66 TACGAGCATTTGAATCATATTCAATTTAATCAGAAATTGATTCAGAAAAATA-AA-AAAA-GATA
*
1731 TTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTACG
128 TTACAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTACG
1796 GTTAAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTA
193 GTTAAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTA
*
1861 ACCATCACGATTTTTGGCTGAAAACACGTTCCAGGGCCCCGG
258 ACCATCACGATTCTTGGCTGAAAACACGTTCCAGGGCCCCGG
Statistics
Matches: 292, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
328 114 0.39
329 2 0.01
330 4 0.01
331 172 0.59
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (328 bp):
ACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTT
TACGAGCATTTGAATCATATTCAATTTAATCAGAAATTGATTCAGAAAAATAAAAAAAGATATTA
CAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTGAATTATATACTTTTTACGAGTATTACGGTT
AAAAATTGAGGAAAAATCTCTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACC
ATCACGATTCTTGGCTGAAAACACGTTCCAGGGCCCCGGCTCAGTTTTGTATGATTTTTTGCGCC
AAA
Done.