Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019419.1 Corchorus olitorius cultivar O-4 contig19452, 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: 2159
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:1462 original size:320 final size:320
Alignment explanation
Indices: 161--1466 Score: 1283
Period size: 320 Copynumber: 4.0 Consensus size: 320
151 ATACTCATAA
*
161 AAAATATATAATTCAACGCCAAAAAGATTGAACAGCTTTTCACGCTTTGAATATCGTTTTTCATA
1 AAAATATATAATTCAACGCCAAAAAGATTGAA-AGCTTTTCACGCTTTTAATATCGTTTTTCATA
* * *
226 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAGAAATCCTT
65 TTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * *
291 AAATGCAATATGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAA
130 AAATTCAATGTGGCTAAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAA
* * * * *
356 ATCATGTAAAACTGAGCTGGGTCCCCGAAACGCGTTTTTAGCCAAAAAATCGTGATGGTTAGTAC
195 ATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCGAAAAACCGTGATGGTTAGTAC
* * * ** * * * *
421 ACGATTT-AGCTAAAACTTTGCAGAAATTTTTTTCCC--CTA--TTTCTTGATACAATACTCAT
260 ACGATTTCGGCTAAAATTTTGCA-AAA--ATTGACCCAAATATTTTTCTAGATAAAATATTCAT
* * *
480 AATATATATATAATTTAACACCAAAAGGATTAGAGAA-CTTTTCACGCTTTTAATATCGTTTTTC
1 AA-A-ATATATAATTCAACGCCAAAAAGATT-GA-AAGCTTTTCACGCTTTTAATATCGTTTTTC
* * * *
544 ATA-TTTTTCTAAATTAATTTCTAATAAAAACAAAACAAGATTCAGATGCTTGTAAAAACAAAAT
62 ATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAAT
* * * * * * *
608 TCTTAAATTCAATGTGGCTGAGATTTGATTAA-ATGAATATGGATATCTCAAGGAGCCTTGGCGC
126 CCTTAAATTCAATGTGGCTAAGATTTGA-TAAGATGAATATAGATATTTCAAGGAGTCTCGGCAC
* * *
672 CAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAACGCTTTTTTAGCC-AAAAACTGTGATGGTT
190 CAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCGAAAAACCGTGATGGTT
* * ** ***
736 ATTACACGATTTCGACTAAAATTTTGTTAAAATTGAATTAAAAAAATATTTTCTCAATTTTAGGA
255 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTG----ACCCAAATATTTT-TC-----TA-GA
801 TAAAATACTT-AT
309 TAAAATA-TTCAT
* * * *
813 AAAAAATATATATAATTCAATGCTAAAAAGATTGAAGGGCTTTTGACG-TTTTCAATATCGTTTT
1 ---AAA-ATATATAATTCAACGCCAAAAAGATTGAA-AGCTTTTCACGCTTTT-AATATCGTTTT
*
877 TCGTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
60 TCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * *
942 TCCTTAAATAT-AATGTGGTTAAGATTTTG-TTAGATGAATATAGATATTTCAAGGAGTGTTGGC
125 TCCTTAAAT-TCAATGTGGCTAAGA-TTTGATAAGATGAATATAGATATTTCAAGGAGTCTCGGC
* * * *
1005 ACCAAAAATCATGCAAAACTAAGCC-AGGCCCCGGAACGCGGTTTTAGCCG-AAAACCGTGATGG
188 ACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCGAAAAACCGTGATGG
* * * * *** **
1068 TTAGTACATGATTTCGGCAAAAATTGACT-CGAAAATTTTTTCCTCA-A--TTTCTAG-TGAAAA
253 TTAGTACACGATTTCGGCTAAAATT--TTGC-AAAAATTGACCCAAATATTTTTCTAGAT-AAAA
*
1128 TAATCAATT
314 TATTC-A-T
* * *
1137 AAAATATATAATTCAACGTCAAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATTGTTTTTCAT
1 AAAATATATAATTCAACGCCAAAAAGATTGAAAG-C-TTTTCACGCTTTTAATATCGTTTTTCAT
* *
1202 A-TTTTTCTGAATTAATTTCTTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
64 ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * *
1266 TAAATTCAATGTGGCTCAGATTTGATAAGATGAATATAAATATTTCAAGGAGTCTCGACACAAAA
129 TAAATTCAATGTGGCTAAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAA
* * * * * *
1331 AATCATGCAAAACTGAGTC-GGGACCCGGAATGCGTTTTTAGCCGTAAGACCGTGATGGTTAGTA
194 AATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCGAAAAACCGTGATGGTTAGTA
* * *
1395 CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCT-G-TCAAATTTTGCAT
259 CACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-AAATATTTTTCTAGATAAAATATT-CAT
1457 AAAATATATA
1 AAAATATATA
1467 CAATTTTTCT
Statistics
Matches: 808, Mismatches: 126, Indels: 105
0.78 0.12 0.10
Matches are distributed among these distances:
318 2 0.00
319 17 0.02
320 266 0.33
321 227 0.28
322 19 0.02
323 9 0.01
324 3 0.00
326 2 0.00
327 2 0.00
328 2 0.00
329 2 0.00
331 1 0.00
332 2 0.00
333 11 0.01
334 61 0.08
335 117 0.14
336 65 0.08
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (320 bp):
AAAATATATAATTCAACGCCAAAAAGATTGAAAGCTTTTCACGCTTTTAATATCGTTTTTCATAT
TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
AATTCAATGTGGCTAAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAA
TCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCGAAAAACCGTGATGGTTAGTACA
CGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAATATTTTTCTAGATAAAATATTCAT
Found at i:1677 original size:267 final size:267
Alignment explanation
Indices: 1202--1693 Score: 700
Period size: 267 Copynumber: 1.8 Consensus size: 267
1192 TGTTTTTCAT
* *
1202 ATTTTTCTGAATTAATTTCTTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
1 ATTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
*
1267 AAATTCAATGTGGCTCAGATTTGATAAGATGAATATAAATATTTCAAGGAGTCTCGACACAAAAA
66 AAATTCAATGTGGCTCAGATTTGATAAGATGAATATAAATATCTCAAGGAGTCTCGACACAAAAA
* ** * * * *
1332 ATCATGCAAAACTGAGTCGGGACCCGGAATGCGTTTTTAGCCGTAAGACCGTGATGGTTAGTACA
131 ATCAAGCAAAACTGAGTCGGGACCCAAAACGCGTTTTTAGCCGAAAAACCGTGATGCTTAGTACA
1397 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCTGTCAAATTTTGCATAAAAT
196 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCTGTCAAATTTTGCATAAAAT
1462 ATATACA
261 ATATACA
* *
1469 ATTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTT
1 ATTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * ** * * * * *
1534 AAATTCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTGTTGGCGCCAAAA
66 AAATTCAATGTGGCTCAGATTTGATAAGATGAATATAAATATCTCAAGGAGTCTCGACACAAAAA
* * * * *
1599 ATCAAGCAAAGCTGAGCTGGGGCCCCAAAACGC-TATTTTAGCC-AAAAACTGTGATGCTTATTA
131 ATCAAGCAAAACTGAG-TCGGGACCCAAAACGCGT-TTTTAGCCGAAAAACCGTGATGCTTAGTA
* *
1662 CACGATTTCGGCTAAACTTTTGTAAAAATTGA
194 CACGATTTCGGCTAAAATTTTGCAAAAATTGA
1694 TTAGAAAAAT
Statistics
Matches: 195, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
267 176 0.90
268 19 0.10
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (267 bp):
ATTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATTCAATGTGGCTCAGATTTGATAAGATGAATATAAATATCTCAAGGAGTCTCGACACAAAAA
ATCAAGCAAAACTGAGTCGGGACCCAAAACGCGTTTTTAGCCGAAAAACCGTGATGCTTAGTACA
CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCTGTCAAATTTTGCATAAAAT
ATATACA
Done.