Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010125.1 Corchorus olitorius cultivar O-4 contig10157, 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: 1787
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1655 original size:321 final size:320
Alignment explanation
Indices: 1--1783 Score: 2132
Period size: 322 Copynumber: 5.6 Consensus size: 320
* * * * *
1 ACAAGATTCACATTCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGACTTGGTT-GAAGG
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAG-ACG
** * * *
65 AATATAGATATTTCAAGGAGTCAATCTGTCAAAAATCATGCAAATCTGAGTCGGGGCGCCGAAAT
65 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAAT
* * ** * *
130 GTGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCAACTAAAATCTGACTCGGAAAATT
130 GCGATTTTAGCCAAAAACCGTGATAG-TAGTACACGATTTCGGCCAAAATCTGACTCGAAAAATT
* * *
195 TTTTCACAATTTTTTTCAATAATACTCAGAAAAAATATATAATTCAACGCTAAAAAAAATTGAAG
194 TTTTCTCAATTTTTTTCCATAATACTCAGAAAAAATATATAATTCAACGC--CAAAAAATTGAAG
* * * *
260 GGTTTTTCACGCTTCTAGTATCGTTTTTGC-ATTTTTCCTGAATTTATTTCTATTTAACTGTAA
257 GGTTTTTCACGCTTCTAATATCGTTTTTGCTTTTTTTCCCGAATTTATTTCTATTTAACTCTAA
* * * * * *
323 ACAAGATTTAGATGCTCGTAAACACAAATTCTTAAATCCGTTGTGGTTGAGATTTGGTTCGACGA
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGACGA
* *
388 ATATAGAAATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGCGCCGAAATG
66 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATG
* * * * *
453 C-ATTTTTCGCCAAAAACCGTAATAGTTAGTACACAATTTCGGCCAAAATCTGAATCGAAAAGTT
131 CGA-TTTTAGCCAAAAACCGTGATAG-TAGTACACGATTTCGGCCAAAATCTGACTCGAAAAATT
* * **
517 TTTTCTCAATTTTTTGCCATAATACTCAGAAAAAATATATATTTCAACGCCAAAAAATTTGAAAA
194 TTTTCTCAATTTTTTTCCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAAA-TTGAAGG
* * * * *
582 GTTTTTCACGTTTCTGATATCGTTTTTGCATTTTTATCCCGAAATTATTTCTATTTAACTGTAA
258 GTTTTTCACGCTTCTAATATCGTTTTTGC-TTTTTTTCCCGAATTTATTTCTATTTAACTCTAA
* * * * * *
646 ACAAGATTTAGATGCTCGTAAACACAACTTCTTAAATCAATTGTGGCTGAGATTTGGTTTGACGA
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGACGA
* * *
711 ATATTGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCTAAACTGAGCTGGGGCGCCGAAATG
66 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATG
* * * * *
776 CGTTTTTAGCCAGAAACCGTGATA--AGTACACGATTTCTGCTAAAATCTGACT-AAAAATATTT
131 CGATTTTAGCCAAAAACCGTGATAGTAGTACACGATTTCGGCCAAAATCTGACTCGAAAA-ATTT
** * * *
838 TTTCTCAATATTTTTATTAATAATGCTCAGAAAAAATATATAATTCAACACCAAAAAAATTGTAG
195 TTTCTCAAT-TTTTT-TCCATAATACTCAGAAAAAATATATAATTCAACGCC-AAAAAATTGAAG
* * *
903 GG-TTTTCACGCTTCTAATATCATTTGTCAT-TTTTTTTTCCCGAATTTACTTCTATTTAACTCT
257 GGTTTTTCACGCTTCTAATATCGTTT-T--TGCTTTTTTTCCCGAATTTATTTCTATTTAACTCT
966 AA
319 AA
*** * *
968 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATATTTTGTGGTTGAGATTTGGTTCA-AGG
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTT-AGACG
* * * * *
1032 ATTACAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTAAGTCGGGGCGCCGAAAT
65 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAAT
* * * *
1097 GC-ATTTTTAGCCAAAAACC------GT-GTACACGATTTTGGCTAAAATCTGACTCGGAAATTT
130 GCGA-TTTTAGCCAAAAACCGTGATAGTAGTACACGATTTCGGCCAAAATCTGACTCGAAAAATT
* *
1154 TTTTCACAATTTTTTTCCATTAATACTAAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGG
194 TTTTCTCAATTTTTTTCCA-TAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGG
* * *
1219 GTTTTTCACGCTTCTAATATCG-TTTTGCATTTTTTGCCGAATTTATTTCTATTTAACTTTAA
258 GTTTTTCACGCTTCTAATATCGTTTTTGCTTTTTTTCCCGAATTTATTTCTATTTAACTCTAA
* * * *
1281 AAAAGATTAAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGACGA
* * * * *
1346 ATGTAGATATTTCAAGGAGTTTTTCCGCCAAAAATCATGCAAAACTAAGCCGGGGCGTCGAAATG
66 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATG
* * * *
1411 CGATTTTAGCCAAAAACCGTGATAGTTAATACACGATTTCGGCCAAAATCTTATTTGAAAAATTT
131 CGATTTTAGCCAAAAACCGTGATAG-TAGTACACGATTTCGGCCAAAATCTGACTCGAAAAATTT
* * * *
1476 TTTCTCAATTTTTTTTCCACAAGAGTC-GAAAAAATATATAATTCAACGCCAAAAAATTGATGGG
195 TTTCTCAA-TTTTTTTCCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGG
* * * *
1540 TTTTTCACGCTTCTAATATCGTTTTTACTTTTTTTCCCTAATTTATTTCTATTTAACACCAA
259 TTTTTCACGCTTCTAATATCGTTTTTGCTTTTTTTCCCGAATTTATTTCTATTTAACTCTAA
* * * * * * * *
1602 ACAAAATTCAGATTCTCGTAAACACAAATTCTTAAATCCATTGTGGATGAGATTTAGTTCGATGA
1 ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGACGA
* * *
1667 ATATAGATATTTCATA-GAGTCTTTTTGCCAAAAATCATGCAAAACTGAGCCGGGGCACCAAAAT
66 ATATAGATATTTCA-AGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAAT
* * *
1731 GCGATTTTAGCCAAAATCCGTGATA-AACATACACGATTTCGGCCAAAATCTGA
130 GCGATTTTAGCCAAAAACCGTGATAGTA-GTACACGATTTCGGCCAAAATCTGA
1784 TTCG
Statistics
Matches: 1252, Mismatches: 174, Indels: 72
0.84 0.12 0.05
Matches are distributed among these distances:
312 2 0.00
313 158 0.13
314 2 0.00
315 17 0.01
316 53 0.04
317 36 0.03
318 3 0.00
319 6 0.00
320 124 0.10
321 263 0.21
322 412 0.33
323 175 0.14
324 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (320 bp):
ACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGACGA
ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATG
CGATTTTAGCCAAAAACCGTGATAGTAGTACACGATTTCGGCCAAAATCTGACTCGAAAAATTTT
TTCTCAATTTTTTTCCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTT
TTTCACGCTTCTAATATCGTTTTTGCTTTTTTTCCCGAATTTATTTCTATTTAACTCTAA
Done.