Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014239.1 Corchorus olitorius cultivar O-4 contig14272, 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: 3050
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:225 original size:12 final size:13
Alignment explanation
Indices: 207--236 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
197 GTTTTCTTTA
207 ATTTTCTTGATTG
1 ATTTTCTTGATTG
220 -TTTTCTTGATTG
1 ATTTTCTTGATTG
232 ATTTT
1 ATTTT
237 AATTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:1439 original size:324 final size:323
Alignment explanation
Indices: 418--1496 Score: 987
Period size: 324 Copynumber: 3.3 Consensus size: 323
408 CGATCAATAT
* * * * * * * **
418 TTCAAGGAGTCTTTGTGCAAAAAAACCTGCAAAATTGAGCCAGCACTCCGGAACGTGTTTTTAGC
1 TTCAAAGAGTCTTTGCGCAAAAAATCATGCAAAATTAAGCCGGCACTCCAGAACCCGTTTTTAGC
* * *
483 CAAAAACCGTGATTGTTAGTACACGATTTCCGCTAAAATTGACCCGAAAAGTTTTTCCTCAATTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAACTGACCCGAAAAGTTTTTCCTCAACTT
* * * *
548 TTTGTCACAATGCTCAGAAAAAATATATAATTCAACGCCAAAAATAAT-GTAGAGGTTTTTCACG
131 TTTGTCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-AATCGAAGAGGCTTTTCACG
* * * *
612 CTTCTAATATCGTTTTTCCATTTAT-TTTCCGAATTTATTTCTAATTAAATCGAAACAAGGTTCA
195 CTTCTAATATCGTTTTTCCATTT-TGTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGA
* * * * * * * * * *
676 GATGCTCGTAAAAATAAATCCTTAGATACAATGT-GACAGAGA--T-ATTCGATGACTATAGATA
259 GATGCTCATAAAAACAAATCTTTATATACAATGTGGA-TGACATTTGGTTCCATGAATAAAGATA
*
737 T
323 A
* * * * * * * * * **
738 TTCAAGGAGTCTTTACGCCAAAAATCATGAAAAATTGAGCCGGGAATCCGGAACGCGTTTTTTTC
1 TTCAAAGAGTCTTTGCGCAAAAAATCATGCAAAATTAAGCCGGCACTCCAGAACCCGTTTTTAGC
*
803 CAAAAACCGTGATAATTAGTACACGATTTCGTTGGCAAAAAAAAAGTACACGATTTCGGCTAAAA
66 CAAAAACCGTG------A-T----G-----GTT-----------AGTACACGATTTCCGCTAAAA
* *
868 TTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCATAATACTCAGAAAAAATATATAATTCAACGC
104 CTGACCCGAAAAGTTTTTCCTCAACTTTTTGTCATAATACTCAGAAAAAATATATAATTCAACGC
* *
933 CAAAAAAATCGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTGTTTTTTTCCGAATTAA
169 CAAAAAAATCGAAGAGGCTTTTCACGCTTCTAATATCGTTTTTCCA-T-TTTGTTTCCGAATTAA
* * * * *
998 TTTCTAATTAAATCGAAACTAGATTTAGATGCTCATAAAAACAAATTTTTATATACAATGTGGCT
232 TTTCTAATTAAATCAAAACAAGATTGAGATGCTCATAAAAACAAATCTTTATATACAATGTGGAT
* ** *
1063 GAGATTTGGTTTGATGAATATAGATAA
297 GACATTTGGTTCCATGAATAAAGATAA
* *
1090 TTCAAAGAGTCTTTGCGCCAAAAATCATGCAAAATTAAGCCGAG-ACTCCGGAACCCGTTTTTAT
1 TTCAAAGAGTCTTTGCGCAAAAAATCATGCAAAATTAAGCCG-GCACTCCAGAACCCGTTTTTA-
*
1154 GCCAAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAACTGACCCGAAAAGTTTTTTTCTC
64 GCC-AAAAACCGTGATGGTTAGTACACGATTTCCGCT-AAAACTGACCCGAAAAG-TTTTTCCTC
* * * * * *
1219 AACTTTTTG-CGA-AATATTTAGAAAAAATATATAATTCAATGTCAAAAAGAGT-GACG-GGCTT
126 AACTTTTTGTC-ATAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-AATCGAAGAGGCTT
* *
1280 TTCACGCTTCTAATATCGTTTTTCCA-TTTGTTTCTGAATTAATTTTTAATTAAATCAAAACAAG
189 TTCACGCTTCTAATATCGTTTTTCCATTTTGTTTCCGAATTAATTTCTAATTAAATCAAAACAAG
* * *
1344 ATTGAGATGCTCGTAAAAAGAAATCCTTT-TATCCAATGTGGATGACATTTGGTTCCATGAATAA
254 ATTGAGATGCTCATAAAAACAAAT-CTTTATATACAATGTGGATGACATTTGGTTCCATGAATAA
*
1408 AGATAT
318 AGATAA
* ** * * * * *
1414 TTCAAGGTTTCTTTGTGCAAAAAATCCTGCAAAATTGAGCCGGCACTCTAGAACGCGTTTTTAGC
1 TTCAAAGAGTCTTTGCGCAAAAAATCATGCAAAATTAAGCCGGCACTCCAGAACCCGTTTTTAGC
*
1479 CAAAATCCGTGATGGTTA
66 CAAAAACCGTGATGGTTA
1497 ACCTCCGAAG
Statistics
Matches: 637, Mismatches: 78, Indels: 86
0.80 0.10 0.11
Matches are distributed among these distances:
320 64 0.10
322 16 0.03
323 4 0.01
324 139 0.22
325 3 0.00
326 1 0.00
327 47 0.07
328 52 0.08
329 19 0.03
336 3 0.00
338 3 0.00
343 1 0.00
346 3 0.00
347 125 0.20
348 3 0.00
349 70 0.11
350 1 0.00
351 1 0.00
352 69 0.11
353 3 0.00
354 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (323 bp):
TTCAAAGAGTCTTTGCGCAAAAAATCATGCAAAATTAAGCCGGCACTCCAGAACCCGTTTTTAGC
CAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAACTGACCCGAAAAGTTTTTCCTCAACTT
TTTGTCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATCGAAGAGGCTTTTCACGC
TTCTAATATCGTTTTTCCATTTTGTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGA
TGCTCATAAAAACAAATCTTTATATACAATGTGGATGACATTTGGTTCCATGAATAAAGATAA
Found at i:2544 original size:353 final size:349
Alignment explanation
Indices: 1887--2560 Score: 820
Period size: 353 Copynumber: 1.9 Consensus size: 349
1877 GTGATGGTTA
* * *
1887 GTACACGATTTCGGCTAAAAACTAACCCGAAAAGTTTTTCTCATTTTTTTGCAAAATATTTAGAA
1 GTACACGATTTCGGCTAAAAACTAACCCGAAAAGTTTTTCTCAATTTTTTGCAAAATACTCAGAA
* * * *
1952 AAAATATATAATTCAACGCCGAAAAGATTGACGGCTTTTTCACGCTTCTAAATTCTAATATCGTT
66 AAAATATATAATTCAACACCAAAAAAATTGAAGGCTTTTTCACG--TC---ATTCTAATATCGTT
* * * *
2017 TTCCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGGTTCGGATGCTCATAAAAACAA
126 TTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCATAAAAACAA
* * * * *
2082 ATCCTTATATATAATGTGACAGAGATTTGGTTCGATGAATATAGATATTTCAAGGATTCTTTACG
191 ATCCTTAAATACAATGTGACAGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACC
* * *
2147 CCAAAAAACATGCAAAATTGAGTCAGGAATCCGGAACGCGTTTTTTGCCAAAAACCGTGATAGTT
256 CCAAAAAACATGCAAAACTGAGTCAGGAATCCGAAACGCGTTTTTAGCCAAAAACCGTGATAGTT
2212 AGTACATGATTTCGTTGGCAAAAAAAAAT
321 AGTACATGATTTCGTTGGCAAAAAAAAAT
* * *
2241 GTACACGATTTCGGCT-AAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAG
1 GTACACGATTTCGGCTAAAAACTAACCCGAAAAGTTTTT-CTCAATTTTTTG-CAAAATACTCAG
2305 AAAAAATATATAATTCAACACCAAAAAAATTGAAAAGG-TTTTTCACG-C-TTCTAATATCGTTT
64 AAAAAATATATAATTCAACACCAAAAAAATTG--AAGGCTTTTTCACGTCATTCTAATATCGTTT
* * **
2367 TTCAATTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAATAAAGATTCAGATGCTTGTAAAAA
127 TCCAA---TTTTTTCCGAATTAATTTCTAATTAAATCGAAA-AAAGATTCAGATGCTCATAAAAA
* * * * * *
2432 TAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATTAATATATATATTTCAAGGAATCTTT
188 CAAATCCTTAAATACAATGTGACAGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTT
* * * ** * *
2497 -CTCCCAAAAATCATTCAAAACTGAGT-TGGGGTCATGAAACTCGTTTTTAGCCAAAAACCGTGA
253 AC-CCCAAAAAACATGCAAAACTGAGTCAGGAATC-CGAAACGCGTTTTTAGCCAAAAACCGTGA
2560 T
316 T
2561 TATTAATACA
Statistics
Matches: 271, Mismatches: 39, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
349 17 0.06
352 37 0.14
353 140 0.52
354 27 0.10
355 38 0.14
356 9 0.03
357 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (349 bp):
GTACACGATTTCGGCTAAAAACTAACCCGAAAAGTTTTTCTCAATTTTTTGCAAAATACTCAGAA
AAAATATATAATTCAACACCAAAAAAATTGAAGGCTTTTTCACGTCATTCTAATATCGTTTTCCA
ATTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCATAAAAACAAATCCT
TAAATACAATGTGACAGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACCCCAAA
AAACATGCAAAACTGAGTCAGGAATCCGAAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTAC
ATGATTTCGTTGGCAAAAAAAAAT
Done.