Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016964.1 Corchorus olitorius cultivar O-4 contig16997, 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: 24131
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:8871 original size:19 final size:18
Alignment explanation
Indices: 8838--8879 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
8828 GTAACATAAA
*
8838 TAGTAGTAGAACTAGAAG
1 TAGTACTAGAACTAGAAG
*
8856 TAGTACTAGTAACTAGTAG
1 TAGTACTAG-AACTAGAAG
8875 TAGTA
1 TAGTA
8880 ATCACTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (18 bp):
TAGTACTAGAACTAGAAG
Found at i:13051 original size:25 final size:25
Alignment explanation
Indices: 13004--13054 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
12994 TATTTTGAAC
*
13004 TTATTATTTATTATTTAAAATATAT
1 TTATTATTTATTATATAAAATATAT
*
13029 TTATTATTTATT-TAATAATATATAT
1 TTATTATTTATTAT-ATAAAATATAT
13054 T
1 T
13055 ATATCTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTATTTATTATATAAAATATAT
Found at i:13054 original size:21 final size:21
Alignment explanation
Indices: 12974--13056 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
12964 CGTTTAGTAA
12974 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTA-TTATTTA-T
* *
12998 TTGAACT-TATTATT-TATTAT
1 TTAAAATATATTATTAT-TTAT
13018 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
13040 TTAATAATATA-TATTAT
1 TTAA-AATATATTATTAT
13057 ATCTAAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.14
21 13 0.26
22 18 0.36
23 8 0.16
24 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:13271 original size:21 final size:21
Alignment explanation
Indices: 13247--13288 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13237 ATTTTGTAAG
13247 CGGGCCTT-AAAATTTTGTCCA
1 CGGG-CTTCAAAATTTTGTCCA
*
13268 CGGGCTTCAAATTTTTGTCCA
1 CGGGCTTCAAAATTTTGTCCA
13289 AACCCTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (21 bp):
CGGGCTTCAAAATTTTGTCCA
Found at i:16369 original size:32 final size:32
Alignment explanation
Indices: 16320--16383 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
16310 ATAAATCACA
*
16320 TTAATTTGTAGTATATAACATAAAAAATATAT
1 TTAATTTATAGTATATAACATAAAAAATATAT
*
16352 TTAATTTATAGTCTATAACATAAAAAATATAT
1 TTAATTTATAGTATATAACATAAAAAATATAT
16384 AATCTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
TTAATTTATAGTATATAACATAAAAAATATAT
Found at i:19299 original size:340 final size:340
Alignment explanation
Indices: 18901--19531 Score: 810
Period size: 340 Copynumber: 1.8 Consensus size: 340
18891 AATATTGGTC
* * * *
18901 ACTGATTTTCTTATCTAGGATTACTTAAAAGGTTATAAAGGTTATGGGAAACATTATAGTACTAT
1 ACTGATTTTCTTATCTAAGATTACTTAAAAGGTTATAAAGATTACGGAAAACATTATAGTACTAT
* * * * * ** *
18966 CTAGATTCAAGTAATCTTACATTCTTATTATTTTTAACAA-TTTCTTATCAATAATGAAAGTTAA
66 CTAGATGCAAATAACCTTACATCCTTATAAACTTTAACAACTTT-TTATCAATAATAAAAGTT-A
* *
19030 TTACCAATTTTATTACTTCAACAATATACT-AAAAAGGCTATAAAAGTTATAAAAATTGTA-TT-
129 --A-CAATTTTATTACTT--A-AATATACTAAAAAAAGCAATAAAAGTTATAAAAATTGTATTTA
**
19092 TAA-C-A-ATCCTTAATAACATTAGTAAACTTTCATCAATGATGAAGATTTA-CCATTTTTTTCC
188 TAACCTATATCCTTAATAACATTAGTAAACTTTCATCAATGATGAAGATTTACCCATTTTTTTAA
* *
19153 TCGAAAGTTACTGAAAAACCTATAATAATCATAAAAAAGATATATTACTATCAACTAATTCAATG
253 ACAAAAGTTACTGAAAAACCTATAATAATCATAAAAAAGATATATTACTATCAACTAATTCAATG
19218 ACCTTACATTATAGAGGTATAAT
318 ACCTTACATTATAGAGGTATAAT
*
19241 ACTGATTTTCTTATTTAAGATTACTTAAAAGGTTATAAAGATTACGGAAAACATTATAGTACTAT
1 ACTGATTTTCTTATCTAAGATTACTTAAAAGGTTATAAAGATTACGGAAAACATTATAGTACTAT
* ** * *
19306 CTAGATGGAAATAACCTTACATCCTTATAAACTTTAGTAACTTTTTATTATTAATAAAAGTTAAC
66 CTAGATGCAAATAACCTTACATCCTTATAAACTTTAACAACTTTTTATCAATAATAAAAGTTAAC
* *
19371 AATTTTATTACTTAAATTTACTAAAAAAAGCAATAAAAGTTATTAAAATTGTATTTACTAATCCT
131 AATTTTATTACTTAAATATACTAAAAAAAGCAATAAAAGTTATAAAAATTGTATTTA-TAA-CCT
* * * * *
19436 ATTATTCTTAATATCATTAGTAAACTTTCATCAATGGTGAATATTTACCCCTTTTTTTAAACAAA
194 A-TATCCTTAATAACATTAGTAAACTTTCATCAATGATGAAGATTTACCCATTTTTTTAAACAAA
* *
19501 AGTTATTGAAAAACCTATAATGATCATAAAA
258 AGTTACTGAAAAACCTATAATAATCATAAAA
19532 GTTTGGCAAA
Statistics
Matches: 247, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
333 7 0.03
334 28 0.11
335 2 0.01
336 14 0.06
337 4 0.02
339 2 0.01
340 106 0.43
341 3 0.01
342 40 0.16
343 41 0.17
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (340 bp):
ACTGATTTTCTTATCTAAGATTACTTAAAAGGTTATAAAGATTACGGAAAACATTATAGTACTAT
CTAGATGCAAATAACCTTACATCCTTATAAACTTTAACAACTTTTTATCAATAATAAAAGTTAAC
AATTTTATTACTTAAATATACTAAAAAAAGCAATAAAAGTTATAAAAATTGTATTTATAACCTAT
ATCCTTAATAACATTAGTAAACTTTCATCAATGATGAAGATTTACCCATTTTTTTAAACAAAAGT
TACTGAAAAACCTATAATAATCATAAAAAAGATATATTACTATCAACTAATTCAATGACCTTACA
TTATAGAGGTATAAT
Found at i:21337 original size:20 final size:20
Alignment explanation
Indices: 21312--21353 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
21302 TCCAACACAA
21312 AAAGTGCATTGTTTTTAGCC
1 AAAGTGCATTGTTTTTAGCC
21332 AAAGTGCATTGTTTTTAGCC
1 AAAGTGCATTGTTTTTAGCC
21352 AA
1 AA
21354 TTTGGCTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (20 bp):
AAAGTGCATTGTTTTTAGCC
Found at i:22294 original size:20 final size:20
Alignment explanation
Indices: 22269--22308 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22259 AATTACGCCT
22269 TTTTTCTCTTTCATTT-TTTA
1 TTTTTCT-TTTCATTTATTTA
*
22289 TTTTTCTTTTGATTTATTTA
1 TTTTTCTTTTCATTTATTTA
22309 AGCCCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTTCTTTTCATTTATTTA
Found at i:22460 original size:21 final size:19
Alignment explanation
Indices: 22434--22489 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
22424 GCTGCTATAA
*
22434 TAATCTCATCTATACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
22455 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
22474 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
22490 ATTGCTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.