Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013014.1 Corchorus olitorius cultivar O-4 contig13047, 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: 33376
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:11446 original size:24 final size:24
Alignment explanation
Indices: 11414--11477 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
11404 TGTATTAAGT
*
11414 AAATAAACACTTGTAAGT-CA-CC
1 AAATCAACACTTGTAAGTCCATCC
* *
11436 AATCATCAACACCTGTAAGTCCATGC
1 AA--ATCAACACTTGTAAGTCCATCC
11462 AAATCAACACTTGTAA
1 AAATCAACACTTGTAA
11478 AGCCCAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.06
24 27 0.79
25 2 0.06
26 3 0.09
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.23
Consensus pattern (24 bp):
AAATCAACACTTGTAAGTCCATCC
Found at i:13310 original size:439 final size:437
Alignment explanation
Indices: 12503--13448 Score: 1511
Period size: 439 Copynumber: 2.2 Consensus size: 437
12493 GCATTAAATG
* * * *
12503 GTCCAACCCA-TAATTATGAGGGATTAAATAGCATAAAGCATAAAAATCTAAGGATCATTTGATA
1 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCT-AGGATCATTTGATA
*
12567 AATAATCCACAAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCC
65 AAT-ATCCACAAAAAAAATATTTGTTTATGGAGAACAAACATAAAAATTCCCTCTTGAACCCTCC
* * * *
12632 ATGAAACTCATTAATCAAATTCAGCTTTGAGGCCCTTAACGAAAGTCGTATATCACCACAATAAC
129 ACGAAACTCATTAATCAAATTCAGCTTTGAAGCCCTTAACGAAAGTCGTAGATCAACACAATAAC
* * *
12697 CTTTTAACCGACACTTGAATAACCTTAATCAGACAAGTTGACCAAAAATTATACGATATCAAATA
194 CTTTTAACCGACACTTGAATAACCTCAATCAGACAAGTGGAACAAAAATTATACGATATCAAATA
** * * *
12762 GACCGGCAATCAAGACCACAAAAATTTTAAATCATTTTTTAAAATTAAAACACTAAAATTGGCTT
259 GACCAACAATCAAGACCACAAAAATTTAAAAGCATTTTTTAAAATCAAAACACTAAAATTGGCTT
* *
12827 TTGAGTCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTGA
324 TTAAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATCACCTTGA
* * *
12892 TCGGACAAGCAAAACAAATAATAAAAGAATTAAAGCCAAAACGTTTAGTC
389 TCAGACAAGCAAAACAAAAAATAAAAGAATTAAA-CCAAAACGTTCAGTC
12942 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTGAGGATCATTTGATA
1 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCT-AGGATCATTTGATA
*
13007 AATATCCATAAAAAAAATATTTGTTTATGGAGAACAAACATAAAAATTCCCTCTTGAACCCTCCA
65 AATATCCACAAAAAAAATATTTGTTTATGGAGAACAAACATAAAAATTCCCTCTTGAACCCTCCA
13072 CGAAACTCATTAATCAAATTCAGCTTTGAAGCCCTTTAACGAAAGTCGTAGAT-AACACAATAAC
130 CGAAACTCATTAATCAAATTCAGCTTTGAAGCCC-TTAACGAAAGTCGTAGATCAACACAATAAC
* *
13136 CTTTTAACTGACACTTGAATAACCTCAATCGGACAAGTGGAACAAAAATTATACGATATCAAATA
194 CTTTTAACCGACACTTGAATAACCTCAATCAGACAAGTGGAACAAAAATTATACGATATCAAATA
* *
13201 GACCAACAATCAAGACCAC-ACAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGGCT
259 GACCAACAATCAAGACCACAAAAATTT-AAAAGCATTTTTTAAAATCAAAACACTAAAATTGGCT
* *
13265 TTTAAGTTCTTCATGGAAGTTGTAGATCATAAAATTACGTTTTAATAGACACTTGAATCACCTTG
323 TTTAAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATCACCTTG
*
13330 ATCAGACAAGCAAAACAAAAAATAAAAGAATTAAACCGAAACGTTCAGTC
388 ATCAGACAAGCAAAACAAAAAATAAAAGAATTAAACCAAAACGTTCAGTC
* * *
13380 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGTATAAAAGTATATGGATCATTCGATA
1 GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTA-GGATCATTTGATA
13445 AATA
65 AATA
13449 AACCAACAAA
Statistics
Matches: 469, Mismatches: 34, Indels: 9
0.92 0.07 0.02
Matches are distributed among these distances:
437 1 0.00
438 83 0.18
439 316 0.67
440 69 0.15
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (437 bp):
GTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTAGGATCATTTGATAA
ATATCCACAAAAAAAATATTTGTTTATGGAGAACAAACATAAAAATTCCCTCTTGAACCCTCCAC
GAAACTCATTAATCAAATTCAGCTTTGAAGCCCTTAACGAAAGTCGTAGATCAACACAATAACCT
TTTAACCGACACTTGAATAACCTCAATCAGACAAGTGGAACAAAAATTATACGATATCAAATAGA
CCAACAATCAAGACCACAAAAATTTAAAAGCATTTTTTAAAATCAAAACACTAAAATTGGCTTTT
AAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATCACCTTGATC
AGACAAGCAAAACAAAAAATAAAAGAATTAAACCAAAACGTTCAGTC
Found at i:17397 original size:23 final size:22
Alignment explanation
Indices: 17325--17406 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 22
17315 GACTTGGAGT
* *
17325 GGAGGCTCACTCAGCTTTTGCGC
1 GGAGGCTC-CCCAGCTCTTGCGC
* ** *
17348 GGA-GCATTCCCCTGCTCTCACGT
1 GGAGGC--TCCCCAGCTCTTGCGC
17371 GGAGGCTCACCCAGCTCTTGCGC
1 GGAGGCTC-CCCAGCTCTTGCGC
17394 GGAGCGCTCCCCA
1 GGAG-GCTCCCCA
17407 AAAAGCCCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
22 4 0.09
23 32 0.73
24 8 0.18
ACGTcount: A:0.13, C:0.38, G:0.28, T:0.21
Consensus pattern (22 bp):
GGAGGCTCCCCAGCTCTTGCGC
Found at i:17816 original size:16 final size:16
Alignment explanation
Indices: 17795--17856 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
17785 TTCCTACCCT
17795 ACTCACCCAATACAAC
1 ACTCACCCAATACAAC
*
17811 ACTCACCCAAAACAAC
1 ACTCACCCAATACAAC
* *
17827 ACTCACCCAGTACAAT
1 ACTCACCCAATACAAC
*
17843 ACTCACCCAGTACA
1 ACTCACCCAATACA
17857 TACTCACCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.42, C:0.42, G:0.03, T:0.13
Consensus pattern (16 bp):
ACTCACCCAATACAAC
Found at i:19936 original size:36 final size:36
Alignment explanation
Indices: 19882--20006 Score: 160
Period size: 36 Copynumber: 3.5 Consensus size: 36
19872 GTTGTAATGT
* * *
19882 CACTGGCCTTGGTCGCCCAATACTTGGGTATAACGC
1 CACTGGCCTTAGTCGCCCAATGCTTGGCTATAACGC
*
19918 CACTGGCCTTAGTTGCCCAATGCTTGGCTATAACGC
1 CACTGGCCTTAGTCGCCCAATGCTTGGCTATAACGC
* * *
19954 CGCTGGCCTTAGTCGCCCAATGTTTGGCTATAACGA
1 CACTGGCCTTAGTCGCCCAATGCTTGGCTATAACGC
** *
19990 CGTTGGCCTAAGTCGCC
1 CACTGGCCTTAGTCGCC
20007 TAATACATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.26
Consensus pattern (36 bp):
CACTGGCCTTAGTCGCCCAATGCTTGGCTATAACGC
Found at i:20272 original size:1 final size:1
Alignment explanation
Indices: 20266--20302 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
20256 GCTGAATTAT
20266 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20303 TCCTCCCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24221 original size:9 final size:11
Alignment explanation
Indices: 24198--24234 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
24188 GGTTTAATCG
24198 AAAAATATATA
1 AAAAATATATA
24209 AAAAATA-ATA
1 AAAAATATATA
24219 AAAATATATATA
1 AAAA-ATATATA
24231 AAAA
1 AAAA
24235 TTTTCGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 10 0.42
12 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATATATA
Found at i:30396 original size:12 final size:13
Alignment explanation
Indices: 30378--30407 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
30368 GTTTTCTTTA
30378 ATTTTCTTGATTG
1 ATTTTCTTGATTG
30391 -TTTTCTTGATTG
1 ATTTTCTTGATTG
30403 ATTTT
1 ATTTT
30408 AATTGCTAGT
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
Done.