Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019200.1 Corchorus olitorius cultivar O-4 contig19233, 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, 841
Length: 1403
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:891 original size:333 final size:332
Alignment explanation
Indices: 1--1403 Score: 2068
Period size: 333 Copynumber: 4.3 Consensus size: 332
* *
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAATAACGATCACGGTTTTTGGCTAAAAACGCAT
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC-ATCACGGTTTTTGGCGAAAAACGCAT
* *
66 TTCGGAGCCTCGGCTCAGTTTTGCTTGACTTTTGACGTCAAAGATCCTTGGAATATCTATATTCA
65 TTCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCA
* *
131 TCAAACCAAATCTCAGCCAAAGTTGATTTAAAGATATGTTTTTACGAGCATCTGAATCTTGTTTC
130 TCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
* * *
196 GATTTAAATAAAAATTAATTAGGATAAAAATTGGAAAAATGATACTAGAATGGTTAGAAGCCGTT
195 GATTTAAATAAAAATTAATTAGGA-AAAAAATGGAAAAATGATACTAGAAAGGTTAGAAGCCCTT
*
261 CAATCTTTTTTGCGTTGAATTACATATTGTTTTATGACTATTTTGGCCAAAAATTGAGAAAAAAA
259 CAATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGAGAAAAAAA
326 TTTTCGGGT
324 TTTTCGGGT
* * *
335 CTGTTTTTGCAAAATTTGAGTCGAAATCGTGTACTGACCATCACGGTTTTTTTGGCGAAAAACGC
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACT-AACATCACGG--TTTTTGGCGAAAAACGC
* * * * *
400 ATTTCGAAGCCCCGGATCAGTTTTGCTTGACTTTTGGCGCCAATGATCCTTGAAATATCTATATT
63 ATTTCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATT
* * * *
465 CATCTACCCAAATCTCAGTCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTT
128 CATCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTT
* *
530 TCGATTTAAACAGAAATTAATTAGGAAAAAAATGGAAAAATGATACTAGAAAGGTTAGAAGCCCT
193 TCGATTTAAATAAAAATTAATTAGGAAAAAAATGGAAAAATGATACTAGAAAGGTTAGAAGCCCT
* * * *
595 TTAATCTTTTTTGCGTTTG-ATTATATATTTTTTTATGAGTATTTTGGCCAAAAATTGAGAAAAT
258 TCAATCTTTTTTGCG-TTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGAGAAAAA
659 AATTTTCGGGT
322 AATTTTCGGGT
*
670 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACGATCACGGTTTTTGGCTAAAAACGCAT
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC-ATCACGGTTTTTGGCGAAAAACGCAT
*
735 TTCGGAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCA
65 TTCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCA
* * *
800 TCAAACCATATCGCAGCCAAAGTTGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
130 TCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
*
865 GATTTAAATAAAAATTAATTAGGAAAAAATTGGAAAAATGATACTAGAAAGGTTAGAAGCCCTTC
195 GATTTAAATAAAAATTAATTAGGAAAAAAATGGAAAAATGATACTAGAAAGGTTAGAAGCCCTTC
*
930 AATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGTGAAAAAAAA
260 AATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGAG-AAAAAAA
995 TTTTCGGGT
324 TTTTCGGGT
1004 CAGTTTTTGCAAAA-TTT--T---AATC--G-----A-A--A--------GGCGAAAAACGCATT
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACATCACGGTTTTTGGCGAAAAACGCATT
* *
1045 TCGAAGGGC-CGGCTCTGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCA
66 TCGAA-GCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCA
1109 TCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
130 TCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTC
* *
1174 AATTTAAATAGAAATTAATTAGGAAAAAAATTGGAAAAATGATACTAGAAAGGTTAGAAGCCCTT
195 GATTTAAATAAAAATTAATTAGGAAAAAAA-TGGAAAAATGATACTAGAAAGGTTAGAAGCCCTT
* * *
1239 CAATCTTTTTTGAGTTGAATTATAGATTGTTTTATGACTATTTCGGCCAAAAATTGAGAAAAAAA
259 CAATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGAGAAAAAAA
1304 TTTTCGGGT
324 TTTTCGGGT
* * * *
1313 CACTTTTTGCAAAATTTTAGTCGAAATCATGTACTAATCATCCCAGTTTTTTGGCGAAAAACGCA
1 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAA-CATCAC-GGTTTTTGGCGAAAAACGCA
* *
1378 TTTCGAAG-CTCCGGATCAGGTTTGCT
64 TTTCGAAGCCT-CGGCTCAGTTTTGCT
Statistics
Matches: 960, Mismatches: 72, Indels: 73
0.87 0.07 0.07
Matches are distributed among these distances:
309 190 0.20
310 93 0.10
312 1 0.00
315 4 0.00
317 2 0.00
319 1 0.00
321 1 0.00
322 1 0.00
324 1 0.00
326 1 0.00
328 4 0.00
331 1 0.00
332 3 0.00
333 250 0.26
334 71 0.07
335 176 0.18
336 160 0.17
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (332 bp):
CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACATCACGGTTTTTGGCGAAAAACGCATT
TCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATATCTATATTCAT
CAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTTGTTTCG
ATTTAAATAAAAATTAATTAGGAAAAAAATGGAAAAATGATACTAGAAAGGTTAGAAGCCCTTCA
ATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTGAGAAAAAAATT
TTCGGGT
Found at i:1303 original size:309 final size:309
Alignment explanation
Indices: 725--1338 Score: 1070
Period size: 309 Copynumber: 2.0 Consensus size: 309
715 GTTTTTGGCT
*
725 AAAAACGCATTTCGGAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATA
1 AAAAACGCATTTCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATA
* *
790 TCTATATTCATCAAACCATATCGCAGCCAAAGTTGATTTAAGGATATGTTTTTACGAGCATCTGA
66 TCTATATTCATCAAACCAAATCGCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGA
*
855 ATCTTGTTTCGATTTAAATAAAAATTAATTAGGAAAAAATTGGAAAAATGATACTAGAAAGGTTA
131 ATCTTGTTTCAATTTAAATAAAAATTAATTAGGAAAAAATTGGAAAAATGATACTAGAAAGGTTA
* * *
920 GAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTGTTTTATGACTATTTTGGCCAAAAATTG
196 GAAGCCCTTCAATCTTTTTTGAGTTGAATTATAGATTGTTTTATGACTATTTCGGCCAAAAATTG
* *
985 TGAAAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAATCGAAAGGCG
261 AGAAAAAAAATTTTCGGGTCACTTTTTGCAAAATTTTAATCGAAAGGCG
* *
1034 AAAAACGCATTTCGAAGGGC-CGGCTCTGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAAT
1 AAAAACGCATTTCGAA-GCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAAT
*
1098 ATCTATATTCATCAAACCAAATCTCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTG
65 ATCTATATTCATCAAACCAAATCGCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTG
*
1163 AATCTTGTTTCAATTTAAATAGAAATTAATTAGGAAAAAAATTGGAAAAATGATACTAGAAAGGT
130 AATCTTGTTTCAATTTAAATAAAAATTAATTAGG-AAAAAATTGGAAAAATGATACTAGAAAGGT
1228 TAGAAGCCCTTCAATCTTTTTTGAGTTGAATTATAGATTGTTTTATGACTATTTCGGCCAAAAAT
194 TAGAAGCCCTTCAATCTTTTTTGAGTTGAATTATAGATTGTTTTATGACTATTTCGGCCAAAAAT
*
1293 TGAG-AAAAAAATTTTCGGGTCACTTTTTGCAAAATTTTAGTCGAAA
259 TGAGAAAAAAAATTTTCGGGTCACTTTTTGCAAAATTTTAATCGAAA
1339 TCATGTACTA
Statistics
Matches: 289, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
309 192 0.66
310 97 0.34
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (309 bp):
AAAAACGCATTTCGAAGCCTCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGGAATA
TCTATATTCATCAAACCAAATCGCAGCCAAAGTGGATTTAAGGATATGTTTTTACGAGCATCTGA
ATCTTGTTTCAATTTAAATAAAAATTAATTAGGAAAAAATTGGAAAAATGATACTAGAAAGGTTA
GAAGCCCTTCAATCTTTTTTGAGTTGAATTATAGATTGTTTTATGACTATTTCGGCCAAAAATTG
AGAAAAAAAATTTTCGGGTCACTTTTTGCAAAATTTTAATCGAAAGGCG
Done.