Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008900.1 Corchorus olitorius cultivar O-4 contig08927, 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: 4356
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:2167 original size:328 final size:322
Alignment explanation
Indices: 1322--2273 Score: 979
Period size: 328 Copynumber: 2.9 Consensus size: 322
1312 AGTTATGCGT
* * **
1322 AAAGACTTCTTGAAATATCTATATTCATCGAATTAAATCCCAGCCACATTGGATTTAACGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCCCAGCCACATTGGATTTAACGATTTG
* * * * *
1387 TTTTTACAAGCATCTTAATCTTGTTTCAATTTATTTAGAAATTAATTCGGAAAAAATGGAAAAAC
66 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-AGAAAAAC
* *
1452 GATATTAGAAACGTGAAAAACCCTAATT-TATTTTGGCGTTGAATTATAT-T-T-T-TTTCCTT-
130 GATATTAGAAGCGTGAAAAACCCTCATTCT-TTTTGGCGTTGAATTATATATATATATTT--TTG
* ** *
1511 AGTATTATG-GCAAAAATTGAGGTAAAACTTTTCGAGTCATTTTTTCAAAATTTTAGCCGAAATC
192 AGTATTTTGCG-AAAAATTGAGAAAAAACTTTTCGGGTCA----TT-----TTTTAGCCGAAATC
* * * * *
1575 GTGTACTAATCATCACGGTTTTTGGCTAAAACCGC-TTTATGGAGCCTCGACTTAATTTTGCATG
247 GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTACGGAGCCCCGACTCAATTTTGCATG
1639 ATTTTTAGGAC
312 ATTTTTAGGAC
** * *
1650 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCCACATTGGATATAATGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCCCAGCCACATTGGATTTAACGATTTG
* * * * *
1715 TATTTACGAGAATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTGTAAAAAAAAATTGAGA
66 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG--GAAAAAAA--GA-A
* * * *
1780 AAACGATATTAGAAGCGTGAAAAGTCCGTCAATCTTTTTGGCGTTGAATGATATATATATATTTT
126 AAACGATATTAGAAGCGTGAAAA-ACCCTCATTCTTTTTGGCGTTGAATTATATATATATATTTT
* **
1845 TGAATATTTTGCGAAAAATTGAGAAAAAAAGTTTCGGGTCATTTTTTAGCCGAAAATCGTGTACT
190 TGAGTATTTTGCGAAAAATTGAGAAAAAACTTTTCGGGTCATTTTTTAGCCG-AAATCGTGTACT
* * * * *
1910 AACCATCACAGATTTTGGCCAAAAACGCGTTT-CGGATCCCCGACTCAGTTTTGCATGATTTTT-
254 AACCATCACGGTTTTTGGCTAAAAACGCGTTTACGGAGCCCCGACTCAATTTTGCATGATTTTTA
*
1973 GGTAG
319 GG-AC
* * * * *
1978 AAAGACTCCTTGAAAGATCTATATTCATCTAACCAAATCCCAGGCACATTCGATTTAAGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCCCAGCCACATTGGATTTAACGATTTG
* * *
2043 TTTTTACGAGCATATGAATCTTCTTTCGATTTAATTAAAAATTAATTCGGAAAAAAAGAAAAACG
66 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGAAAAACG
* *
2108 ATATTAGAAGCGTGAAAAAACCCTTCCTTCTTTTTGGCTTTGATAAATATATATATATATATATA
131 ATATTAGAAGCGTG-AAAAACCC-TCATTCTTTTTGGCGTTG------A-AT-TATATATATATA
* * * ** * * *
2173 TTTTATGGGTATTGTGGCAAAAAATTGAGAAAAAACTTTTATGGTCAGTTTTTACCCGAAATCGG
186 TTTT-TGAGTATT-TTGCGAAAAATTGAGAAAAAACTTTTCGGGTCATTTTTTAGCCGAAATCGT
*
2238 GTACTAACCATCACGGTTTTTGTCTAAAAACGCGTT
249 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTT
2274 CCAAGACTCG
Statistics
Matches: 517, Mismatches: 79, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
323 22 0.04
324 21 0.04
326 7 0.01
327 11 0.02
328 259 0.50
329 3 0.01
330 7 0.01
331 4 0.01
332 40 0.08
333 67 0.13
334 38 0.07
335 3 0.01
336 31 0.06
337 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (322 bp):
AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCCCAGCCACATTGGATTTAACGATTTG
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGAAAAACG
ATATTAGAAGCGTGAAAAACCCTCATTCTTTTTGGCGTTGAATTATATATATATATTTTTGAGTA
TTTTGCGAAAAATTGAGAAAAAACTTTTCGGGTCATTTTTTAGCCGAAATCGTGTACTAACCATC
ACGGTTTTTGGCTAAAAACGCGTTTACGGAGCCCCGACTCAATTTTGCATGATTTTTAGGAC
Found at i:3003 original size:328 final size:329
Alignment explanation
Indices: 2413--3036 Score: 800
Period size: 328 Copynumber: 1.9 Consensus size: 329
2403 ACGTATCACA
* *
2413 GTTTTTGGCTAAAAACGCGTTTCAGGACCTGACTTAGTTTTGCATGAGTTTTGGCAGAAAGACTC
1 GTTTTTAGCTAAAAACGCGTTTCAGGACCTGACTCAGTTTTGCATGAGTTTTGGCAGAAAGACTC
** * * * * * *
2478 CTTGGAATATCTATATTCATCTGACCATATCTCAGCAACAATGGATTTAAGGATTGTTTTTACGA
66 CTTAAAATATATATATTCATCTGACCAAATCCCAGCAACAATGGATTTAACGATTGGTTTGACGA
* *
2543 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCTAGAAGAAAAAAAAGGAAAAACGATA
131 GCATCTGAATCTTATTTCGATTTAATTAAAAATAAATTC-AGAAGAAAAAAAAGGAAAAACGATA
* * *
2608 TTAGAAGCATGAAAACCCCTTCAATTTTTTGGCATTGAATTAAATACTTTTTCTGAGTATTGTGG
195 TTAGAAGCATGAAAAACCCTTCAATTTTTAGGCATTGAATTAAATACTTTTTATGAGTATTGTGG
* *
2673 CAAAGAATTGAGAAATAAATTTTCGGA-TAAGTTTTTCCAAAATTTTAGTCGAAATCGTTTACTC
260 CAAAAAATTGAGAAAAAAATTTT-GGAGTAAGTTTTTCCAAAATTTTAGTCGAAATCGTTTACTC
2737 ATTATG
324 ATTATG
* * * *
2743 GTTTTTAGCTAAAAACGTG-TTCTGGGTCCTCGACTCAGTTTTGCATGA-TTATTGG-ATTAAAG
1 GTTTTTAGCTAAAAACGCGTTTC-AGGACCT-GACTCAGTTTTGCATGAGTT-TTGGCA-GAAAG
* *
2805 ACTCCTTAAAATATATATATTCATC-GAAGCAAATCCCAG-ACACATTGGATTTAACGATTTGGT
62 ACTCCTTAAAATATATATATTCATCTG-ACCAAATCCCAGCA-ACAATGGATTTAACGA-TTGGT
* *
2868 TTGACGAGCATCTGAATCTTATTTCTATTTAATTAAAAATTAATTC-G-A-AAAAAAAAGGAAAA
124 TTGACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATAAATTCAGAAGAAAAAAAAGGAAAA
** * * * *
2930 ACGATATTAGAAGTGTGAAAAAGCTTTCAATCTTTTAGGCTTTGAATTATATA-TTTTTATGAGT
189 ACGATATTAGAAGCATGAAAAACCCTTCAAT-TTTTAGGCATTGAATTAAATACTTTTTATGAGT
*
2994 ATTGTGGCAAAAAATTGAGAAAAAAATTTTTGAGTAAGTTTTT
253 ATTGTGGCAAAAAATTGAGAAAAAAATTTTGGAGTAAGTTTTT
3037 AGCCGAAATC
Statistics
Matches: 253, Mismatches: 32, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
327 2 0.01
328 87 0.34
329 22 0.09
330 28 0.11
331 69 0.27
332 45 0.18
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (329 bp):
GTTTTTAGCTAAAAACGCGTTTCAGGACCTGACTCAGTTTTGCATGAGTTTTGGCAGAAAGACTC
CTTAAAATATATATATTCATCTGACCAAATCCCAGCAACAATGGATTTAACGATTGGTTTGACGA
GCATCTGAATCTTATTTCGATTTAATTAAAAATAAATTCAGAAGAAAAAAAAGGAAAAACGATAT
TAGAAGCATGAAAAACCCTTCAATTTTTAGGCATTGAATTAAATACTTTTTATGAGTATTGTGGC
AAAAAATTGAGAAAAAAATTTTGGAGTAAGTTTTTCCAAAATTTTAGTCGAAATCGTTTACTCAT
TATG
Done.