Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015199.1 Corchorus olitorius cultivar O-4 contig15232, 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: 12466
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1081 original size:336 final size:329
Alignment explanation
Indices: 4--1151 Score: 1267
Period size: 336 Copynumber: 3.4 Consensus size: 329
1 CAC
* *
4 CAAAAAGATTGGAGGACTTTTTCACGCTTTTAATATC-ATTTTTTCATATTTTTCTTAATTAAAT
1 CAAAAAGATTGGAGGACTTTTT-ACGCTTTTAATATCTATTTCTT-AT-TTTTTCTAAATT-AAT
* * *
68 TTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCTA
62 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* ** *
133 AGATTTTATTAGATGAATATAGATATTTCAAGGAGTGACGGCGCCAAAAATCATGCAAAACTGAG
127 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAG
* * * * *
198 CCGGGGCCCCGAAACGCGTTTTTAAACAAAAAAC--ATGATGATTAGTACACGTTTTTGGCTAAA
192 -CGGGTCCCCGAAACGCGTTTTT-AGCCAAAAACTGATGATTATTAGTACACGATTTTGGCTAAA
* * * * * *
261 ATTTTCCAAAAAAATGGCATGAAATTTTTTTCCAT-AATTTTTGGATAATAAATACTCATAAAAT
255 ATTTTGC-AAAAATTGACACGAAA-TATTTTCC-TCAATTTTTGGCT-A-AAATACTCATAAAA-
* *
325 ATATATAATTTAATGC
314 ATATATAATTCAATGT
* * * * * *
341 CAAATAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAAGTTC
1 CAAAAAGATTGGAGGACTTTTTACGCTTTTAATATC-TATTTCTTATTTTTTCTAAATTAATTTC
* *
405 TAATTAAATCGAAACAAGATTAATCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGCTG
65 TAATTAAATCGAAACAAGA-T--TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * *
470 AGATATGATTAGATGAATAT-GAATATCTCAAGGAGTCTTGCCA-CCAAAAATCATGCAAAACTG
127 AGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTCG-GAGCCAAAAATCATGCAAAACTG
* * * * * *
533 AGCCGGTGCCCCAAAACTCTTTTTTAGCCAAAAACTG-TGATTGTTATTACACGATTTTGGCTAA
190 AGCGGGT-CCCCGAAACGCGTTTTTAGCCAAAAACTGATGATTATTAGTACACGATTTTGGCTAA
* * * * *
597 AATTTTGTAAAAATTGACCCGAAATATATTTCCTCAGTTTTTGGCTAAAATAGTCATCAAATATA
254 AATTTTGCAAAAATTGACACGAAATAT-TTTCCTCAATTTTTGGCTAAAATACTCAT-AAAAATA
*
662 TATAATTCAACGT
317 TATAATTCAATGT
* * * * * * * *
675 CAAAAAGATTGAAAGG-CTTTTGAC-ATTTCAAATATCTTTTTCCTATTTTTTCCAAATTAATCT
1 CAAAAAGATTG-GAGGACTTTTTACGCTTT-TAATATCTATTTCTTATTTTTTCTAAATTAATTT
738 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
64 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
** * * *
803 ATTTGATTAGATGAATATAGATATTTCAAGTTGTCTCGGAGCCAAAAAATCTTGCAAAATTGTGT
129 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCC-AAAAATCATGCAAAACTGAG-
** * *
868 CGGGTCCTTGGAACGCGTTTTTAGCCAAAAATCGTGATGATTTATTAGTACACGATTTCGGCTAA
192 CGGGTCCCCGAAACGCGTTTTTAGCCAAAAA-C-TGATGA-TTATTAGTACACGATTTTGGCTAA
* *
933 AATTTGGCAAAAATTGACACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAATAT
254 AATTTTGCAAAAATTGACACGAAATATTT-TCCTCAATTTTTGGCTAAAATACTCATAAAAATAT
998 ATAATTCAATGT
318 ATAATTCAATGT
* * * *
1010 CAAAAAGATTGGGGGGCTTTTTATGCTTTTAATATCGTATTTCTTATTTTTTCTAAATTAATTTA
1 CAAAAAGATTGGAGGACTTTTTACGCTTTTAATATC-TATTTCTTATTTTTTCTAAATTAATTTC
* * *
1075 TAATTAAATCGAAACAAGATTCAGAT-CTTCGT-AAAACAAATTCTTAAATCCAATATTGCTGAG
65 TAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* *
1138 ATTTGGTTAAATGA
129 ATTTGATTAGATGA
1152 TGTAAAGTAT
Statistics
Matches: 684, Mismatches: 98, Indels: 60
0.81 0.12 0.07
Matches are distributed among these distances:
330 1 0.00
331 75 0.11
332 38 0.06
333 17 0.02
334 106 0.15
335 109 0.16
336 177 0.26
337 157 0.23
338 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (329 bp):
CAAAAAGATTGGAGGACTTTTTACGCTTTTAATATCTATTTCTTATTTTTTCTAAATTAATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
TTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAGCGGG
TCCCCGAAACGCGTTTTTAGCCAAAAACTGATGATTATTAGTACACGATTTTGGCTAAAATTTTG
CAAAAATTGACACGAAATATTTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCA
ATGT
Found at i:4830 original size:29 final size:29
Alignment explanation
Indices: 4782--4842 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4772 GTTCTAATTA
*
4782 ATGTATACTAATAAATTATTCAATTTTATT
1 ATGTATAC-AATAAATTATTCAATTATATT
*
4812 ATGTATA-AATATAATTATTTAATTATATT
1 ATGTATACAATA-AATTATTCAATTATATT
4841 AT
1 AT
4843 ATTATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.61
30 7 0.25
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
ATGTATACAATAAATTATTCAATTATATT
Found at i:9371 original size:13 final size:13
Alignment explanation
Indices: 9353--9379 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9343 TAAACAAAAC
9353 AAGCTCAACAAAT
1 AAGCTCAACAAAT
9366 AAGCTCAACAAAT
1 AAGCTCAACAAAT
9379 A
1 A
9380 GTATCCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
AAGCTCAACAAAT
Found at i:12363 original size:334 final size:332
Alignment explanation
Indices: 11664--12454 Score: 997
Period size: 333 Copynumber: 2.4 Consensus size: 332
11654 TTCACAATTT
* * * *
11664 TAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCA
1 TAATATCGTTTTTCCTATTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAAATTTAGATGCT
* *
11729 CATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAAATGAATA-AAGATATTTCAA
66 CGTAAAAACAAAT-CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAA-ATATTTCAA
** * * * *
11793 GGAGTCTCGGTGCCAAAAATCATGCAAAACAGAGTCGTGGCCCTGTAACGCGTTTTTAGCCAAAA
129 GGAGTCTCGGCACCAAAAATCATGCAAAACAGAGACGTGCCCCCGGAACGCGTTTTTAGCCAAAA
* *
11858 ACCGTGATGATTAGTTCACGATTTCGGCTAAAACTTTGCAAAAATTGACACGAAAGATATTTCCT
194 ACCGTGATGATTAGTACACGATTTCGGCTAAAACTTTGCAAAAAATGACACGAAAGATATTTCCT
** * * * * *
11923 CAATTTTTGGCTAAAATTCTCATAAAAAAATATATAATTCGATATCAAAAAGATTGAAAGGCTTT
259 CAATTTTAAGCTAAAATACTCATAAAAAAATATATAATTCAATACCAAAAAAATTGAAAGCCTTT
11988 TAACGCTTC
324 TAACGCTTC
* * *
11997 TAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAAATTCAGATGC
1 TAATATCGTTTTTCCTATTTTTTCAGAATTAATTTCTAATTAAATCGAAAC-AAAATTTAGATGC
* * * *
12062 TCGTAAAAATAAATCATTAAATCTAATGTGGCTGAGATTTTGATAGATGAATATAAATATTTCAA
65 TCGTAAAAACAAATC-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAA
* * *
12127 GGAGTCTTGGCACCAAAAATCATGCAAAACTGA-ACG-GACCCCCGGAACGCGTTTTTAGCCGAA
129 GGAGTCTCGGCACCAAAAATCATGCAAAACAGAGACGTG-CCCCCGGAACGCGTTTTTAGCCAAA
* * *
12190 AACCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAAATGAC-CAGAAAGATTTTTC
193 AACCGTGATGATTAGTACACGATTTCGGCTAAAACTTTGCAAAAAATGACAC-GAAAGATATTTC
** *
12253 CT-TGTTTTCAAG-TGAAAATACTCATAAAAAACA-A-ATAATTCAATGCCAAAAAAATTGAAAG
257 CTCAATTTT-AAGCT-AAAATACTCATAAAAAA-ATATATAATTCAATACCAAAAAAATTGAAAG
*
12314 CCTTTTTCACGCTTC
319 CC-TTTTAACGCTTC
* * **
12329 TAATATCGTTTTTCCTATTTTATTTCAAAATTAATTTCTAATTAAATCGAAATAAAATTTAGAAA
1 TAATATCGTTTTTCCTA-TTT-TTTCAGAATTAATTTCTAATTAAATCGAAACAAAATTTAGATG
* * *
12394 CTCGTACAAACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATATATAT
64 CTCGTAAAAACAAA-TCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATAT
12455 ATATATATAT
Statistics
Matches: 395, Mismatches: 51, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
331 30 0.08
332 76 0.19
333 164 0.42
334 123 0.31
335 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (332 bp):
TAATATCGTTTTTCCTATTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAAATTTAGATGCT
CGTAAAAACAAATCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGG
AGTCTCGGCACCAAAAATCATGCAAAACAGAGACGTGCCCCCGGAACGCGTTTTTAGCCAAAAAC
CGTGATGATTAGTACACGATTTCGGCTAAAACTTTGCAAAAAATGACACGAAAGATATTTCCTCA
ATTTTAAGCTAAAATACTCATAAAAAAATATATAATTCAATACCAAAAAAATTGAAAGCCTTTTA
ACGCTTC
Done.