Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019357.1 Corchorus olitorius cultivar O-4 contig19390, 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: 1949
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:77 original size:51 final size:51
Alignment explanation
Indices: 4--102 Score: 198
Period size: 51 Copynumber: 1.9 Consensus size: 51
1 AAA
4 ATATATATATATATATATATTCATCTAATCAAATCTCAGCCACATTGGTAT
1 ATATATATATATATATATATTCATCTAATCAAATCTCAGCCACATTGGTAT
55 ATATATATATATATATATATTCATCTAATCAAATCTCAGCCACATTGG
1 ATATATATATATATATATATTCATCTAATCAAATCTCAGCCACATTGG
103 ATTTAAGGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.38
Consensus pattern (51 bp):
ATATATATATATATATATATTCATCTAATCAAATCTCAGCCACATTGGTAT
Found at i:1232 original size:321 final size:319
Alignment explanation
Indices: 310--1394 Score: 1160
Period size: 321 Copynumber: 3.4 Consensus size: 319
300 CGAAATCGTG
* *
310 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAATAAATGGAAAAACGATATT-GAAAGCGTGAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAG-AAGCGTGAA
* * *
374 AACCCTTCAACCTTTTTGGCGTTGAATTATAT-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
65 AACCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGA
* * **
438 AAAAAATTTT-GTGTCAGTTTTTAGCCGAAATCGTGTACACCATCATTGTTTTTGGCTAAAAACG
130 AAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTATA-CATCACGGTTTTTGGCTAAAAACG
* * * *
502 AG-TTC-CGAGACCTGCACTCAGTTTTGCATGGTTTTTGGCATAGAA-ACTCCTTGAAATATCTA
194 AGTTTCGCGAGACCCG-GCTCAGTTTTGCATGATTTTTGGCAGA-AAGACTCCTTGAAATATCTA
* * * *
564 GACTCATGTAACCAAATCTCAGCTACATTAGATTTAAAGATTTGTTTTTACGGGCATCTGAATC
257 TATTCATCTAACCAAATCTCAGCTACATTAGATTT-AAGATTTGTTTTTACGAGCATCTGAATC
* * * * *
628 TTGTTTTGATTTTATTAGAAATAAATTC---AGAAAAA---AAAAACGATATTAAAAGTGTGAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* *
687 ACCCCTTCAAAT-TTTTTGGCGTTGAATTATA-AATTTTTTCTGAGTACTGTGGCAAAAAATTGA
66 A-CCCTTC-AATCTTTTTGGCGTTGAATTATATAA-TTTTTATGAGTATTGTGGCAAAAAATTGA
* *
750 GGAAAAACTTTTCGGGTCAGTTCTTTTTACAAAATTTTAGCCGAAATCGTGTGATAACTATCACG
128 GAAAAAAATTTTCGGGTCAG-------T------TTTTAGCCGAAATCGTGT-AT-AC-ATCACG
* * * * * * ** *
815 GTTTTTGGCTAAAAACGTGTTCCG-GAGTCACGGCTCAATATTATATGATTTTTGGC-GCAAAGT
177 GTTTTTGGCTAAAAACGAGTTTCGCGAGACCCGGCTCAGTTTTGCATGATTTTTGGCAG-AAAGA
* * * *
878 CTCCTTGAAATATCTATATTAATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
241 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCTACATTAGATTTAA-GATTTGTTTTT
** *
943 ACGAGTTTCTGAATT
305 ACGAGCATCTGAATC
* * * * * **
958 TTGTGTCGATTTAATTAGAAATTAATTTGGAAAAAAAATGGAGAACCGATATTAGAAGCCCGAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* **
1023 AGCCCATCAATCTTTTTGGAATTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGA
66 A-CCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGA
* *
1088 AAAAAATTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTATACATTACGGTTTTTGGCTAAAAACG
130 AAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGTGTATACATCACGGTTTTTGGCTAAAAACG
* * * *
1153 CGTTTCGCG-GCCCCGGTTCAGTTTTGCATGATTTTTGGCAGAAAGAATCCTTGAAATATCTATA
194 AGTTTCGCGAGACCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATA
* *
1217 TTCATCTAACCAAATCTCAGCTACATTAGATTCACAGATTTGTTTTTACGAGCGTCTGAATC
259 TTCATCTAACCAAATCTCAGCTACATTAGATTTA-AGATTTGTTTTTACGAGCATCTGAATC
* **
1279 TTGTTTCAATTTAATTAGAAATAAATTCGGGAAAAAAAAAAAGAAAAACGATATTAGAAGCGTGA
1 TTGTTTCGATTTAATTAGAAATAAATTC-GG-AAAAAAAATGGAAAAACGATATTAGAAGCGTG-
* * *
1344 AAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTACTGAGTATT
63 AAAACCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTA-TGAGTATT
1395 CTCTCGAAAT
Statistics
Matches: 627, Mismatches: 97, Indels: 80
0.78 0.12 0.10
Matches are distributed among these distances:
312 22 0.04
313 25 0.04
314 40 0.06
315 11 0.02
318 25 0.04
321 147 0.23
322 8 0.01
323 60 0.10
324 30 0.05
328 18 0.03
329 6 0.01
330 132 0.21
331 7 0.01
333 6 0.01
335 3 0.00
336 74 0.12
337 13 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (319 bp):
TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
ACCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGAA
AAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTATACATCACGGTTTTTGGCTAAAAACGAG
TTTCGCGAGACCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATT
CATCTAACCAAATCTCAGCTACATTAGATTTAAGATTTGTTTTTACGAGCATCTGAATC
Done.