Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008945.1 Corchorus capsularis cultivar CVL-1 contig08966, 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: 44093
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:375 original size:23 final size:23
Alignment explanation
Indices: 336--380 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
326 TGTGCTCTGT
* *
336 TTAGAGTTTATTCAATTTAGTCA
1 TTAGAGTTTATGCAATTAAGTCA
359 TTAGA-TTTATGCTAATTAAGTC
1 TTAGAGTTTATGC-AATTAAGTC
381 CAAGAGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (23 bp):
TTAGAGTTTATGCAATTAAGTCA
Found at i:4252 original size:27 final size:27
Alignment explanation
Indices: 4221--4275 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
4211 CAAGCCCACG
4221 TTCTTGTCTCATATCCT-TTTGATTCTT
1 TTCTTGTCTCATATCCTATTT-ATTCTT
*
4248 TTCTTGTCTCATATTCTATTTATTCTT
1 TTCTTGTCTCATATCCTATTTATTCTT
4275 T
1 T
4276 ATTCCTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.13, C:0.20, G:0.05, T:0.62
Consensus pattern (27 bp):
TTCTTGTCTCATATCCTATTTATTCTT
Found at i:16336 original size:23 final size:23
Alignment explanation
Indices: 16310--16406 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 23
16300 AATTCATTAC
16310 ACATAATTTTCCATATTAAGCAT
1 ACATAATTTTCCATATTAAGCAT
** *
16333 ACATAATTGACAACCTTATTTCAAGCAT
1 ACATAATT---TTCCATA-TT-AAGCAT
* *
16361 ATATAATTTTCCATATTAAGAAT
1 ACATAATTTTCCATATTAAGCAT
*
16384 ACATAA-TTCCCATATTAAGCAT
1 ACATAATTTTCCATATTAAGCAT
16406 A
1 A
16407 GCATTTCAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
22 15 0.26
23 18 0.31
24 2 0.03
25 4 0.07
26 4 0.07
27 2 0.03
28 13 0.22
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (23 bp):
ACATAATTTTCCATATTAAGCAT
Found at i:16865 original size:13 final size:14
Alignment explanation
Indices: 16847--16875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16837 TAAAGAGAAG
16847 AAAAAA-GCCAAAA
1 AAAAAATGCCAAAA
16860 AAAAAATGCCAAAA
1 AAAAAATGCCAAAA
16874 AA
1 AA
16876 TTTCTCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.76, C:0.14, G:0.07, T:0.03
Consensus pattern (14 bp):
AAAAAATGCCAAAA
Found at i:21151 original size:30 final size:29
Alignment explanation
Indices: 21115--21205 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 29
21105 GGCATCCGAT
*
21115 GTGGCATGCCACGTGTACCAAAAATGCCAC
1 GTGGCATGCCACATGT-CCAAAAATGCCAC
* *
21145 GTGGCATGCCACATGTCCAAAAAAGGACAC
1 GTGGCATGCCACATGTCC-AAAAATGCCAC
*
21175 ATGGCATGCCACATGT-CAAAAATGCCAC
1 GTGGCATGCCACATGTCCAAAAATGCCAC
21203 GTG
1 GTG
21206 CCACATGTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.21
29 3 0.06
30 39 0.74
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.16
Consensus pattern (29 bp):
GTGGCATGCCACATGTCCAAAAATGCCAC
Found at i:21327 original size:410 final size:405
Alignment explanation
Indices: 20560--21338 Score: 940
Period size: 410 Copynumber: 1.9 Consensus size: 405
20550 AGGTTGCCTG
*
20560 TCGGCATAAATGCCATTTTGCACCCTTAAGTTTATACGGACTGCAACTTTGCACCCAACTTTTTT
1 TCGGCATAAATACCATTTTGCACCCTTAAGTTTATACGGACTGCAACTTTGCACCCAACTTTTTT
* *
20625 TTTTGACCAAAACGCACCCAAAAGTTTTATTTTTGTGCCGCTTTACACCCTCCATCACGTTAGGA
66 TTTTGACCAAAACGCACCCAAAAGTTTTATTTTTGTGCCACTTTACACCCTCCATCACGATAGGA
* * * ****
20690 CAAACGGACGTCCGACATGGCATGCCACGTGGACAAAAATGACATGTGGCACATGGCATTTTGAC
131 CAAACGGACATCCGACATGGCATGCCACGTGGACAAAAATGACATGTGCCACATGCCAAAAGGAC
* ** * ***** * *
20755 ACGTGGTGTGCCATGAGTCCTTTTTGTACACATGGCGTGCCACGTGGCATTTTTTGGTACACATT
196 ACATGGCATGCCATCAGTCAAAAATG-ACACA--GCGTGCCACATGGCATTTTTTGGTACACATG
** * *
20820 GCATGCCACGTCGGATGCCCGTTTATCCTATCATGACAGAGGGTGCAAAGTGGCATAAAAATAAA
258 GCATGCCACGTCGGACACCCGTTTATCCTACCATGACAGAGGGTGCAAAGTGGCACAAAAATAAA
*
20885 ACTTTAGGGTACGTTTTGGTCAAAATAAAAAAGTTGGGTGCAAAATGGTATTTATGCCGTTGCCG
323 ACTTTAGGGTACGTTTCGGTCAAAATAAAAAAGTTGGGTGCAAAATGGTATTTATGCCGTTGCCG
20950 ATCTGATTAGGAATGAGA
388 ATCTGATTAGGAATGAGA
* * *
20968 TCGGCATAAATACCATTTTGCACCCTTAAGTTTGTACGGACTGCCATTTTGCACCCAACTTTTTT
1 TCGGCATAAATACCATTTTGCACCCTTAAGTTTATACGGACTGCAACTTTGCACCCAACTTTTTT
* * * * * *
21033 ATTTTGACCAAAATGCACCCTAAAGTTTTATTTTTGTGTCATTTTGCACCCTCCATCATGATAGG
66 -TTTTGACCAAAACGCACCCAAAAGTTTTATTTTTGTGCCACTTTACACCCTCCATCACGATAGG
* ** * *
21098 ACAAACGGGCATCCGATGTGGCATGCCACGTGTACCAAAAATGCCACGTGGCATGCCACATGTCC
130 ACAAACGGACATCCGACATGGCATGCCACGTGGA-CAAAAATG--ACAT-G--TGCCACATG-CC
**
21163 AAAAAAGGACACATGGCATGCCA-CATGTCAAAAATG-C-CA-CGTGCCACATGTTA-TTTTT-G
188 --AAAAGGACACATGGCATGCCATCA-GTCAAAAATGACACAGCGTGCCACATGGCATTTTTTGG
* * * * * * *
21222 TCCACGTGGCATGCCATGTCGGACATCCGTTTTTCCTACCATGACGGAGGGTGTAAAGTGGCACA
250 TACACATGGCATGCCACGTCGGACACCCGTTTATCCTACCATGACAGAGGGTGCAAAGTGGCACA
*
21287 AAAATAAAACTTTAGGGTGCGTTTCGGTCAAAATAAAAAAGTTGGGTGCAAA
315 AAAATAAAACTTTAGGGTACGTTTCGGTCAAAATAAAAAAGTTGGGTGCAAA
21339 GTGACAGTCC
Statistics
Matches: 310, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
408 61 0.20
409 85 0.27
410 112 0.36
411 5 0.02
412 14 0.05
413 1 0.00
415 10 0.03
416 2 0.01
417 1 0.00
418 19 0.06
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (405 bp):
TCGGCATAAATACCATTTTGCACCCTTAAGTTTATACGGACTGCAACTTTGCACCCAACTTTTTT
TTTTGACCAAAACGCACCCAAAAGTTTTATTTTTGTGCCACTTTACACCCTCCATCACGATAGGA
CAAACGGACATCCGACATGGCATGCCACGTGGACAAAAATGACATGTGCCACATGCCAAAAGGAC
ACATGGCATGCCATCAGTCAAAAATGACACAGCGTGCCACATGGCATTTTTTGGTACACATGGCA
TGCCACGTCGGACACCCGTTTATCCTACCATGACAGAGGGTGCAAAGTGGCACAAAAATAAAACT
TTAGGGTACGTTTCGGTCAAAATAAAAAAGTTGGGTGCAAAATGGTATTTATGCCGTTGCCGATC
TGATTAGGAATGAGA
Found at i:43690 original size:30 final size:30
Alignment explanation
Indices: 43656--43719 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
43646 AATTTGTTGG
*
43656 TGTCGTGCCACCCCAAGGACTATGAAGTGA
1 TGTCGTACCACCCCAAGGACTATGAAGTGA
43686 TGTCGTACCACCCCAAGGACTATGAAGTGA
1 TGTCGTACCACCCCAAGGACTATGAAGTGA
43716 TGTC
1 TGTC
43720 TCGTATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (30 bp):
TGTCGTACCACCCCAAGGACTATGAAGTGA
Found at i:43851 original size:189 final size:189
Alignment explanation
Indices: 43531--43908 Score: 756
Period size: 189 Copynumber: 2.0 Consensus size: 189
43521 TAGTAAAAAT
43531 TCGTATTAATAACTAATGGTGCCATATGCCAAAATAGCCATGTTAATGGCGCCATGATTTTTCCT
1 TCGTATTAATAACTAATGGTGCCATATGCCAAAATAGCCATGTTAATGGCGCCATGATTTTTCCT
43596 TAGCCAAATATTTTGTTTCCAATCTAAGGCCAACAACGCCATGTTTCCTAAATTTGTTGGTGTCG
66 TAGCCAAATATTTTGTTTCCAATCTAAGGCCAACAACGCCATGTTTCCTAAATTTGTTGGTGTCG
43661 TGCCACCCCAAGGACTATGAAGTGATGTCGTACCACCCCAAGGACTATGAAGTGATGTC
131 TGCCACCCCAAGGACTATGAAGTGATGTCGTACCACCCCAAGGACTATGAAGTGATGTC
43720 TCGTATTAATAACTAATGGTGCCATATGCCAAAATAGCCATGTTAATGGCGCCATGATTTTTCCT
1 TCGTATTAATAACTAATGGTGCCATATGCCAAAATAGCCATGTTAATGGCGCCATGATTTTTCCT
43785 TAGCCAAATATTTTGTTTCCAATCTAAGGCCAACAACGCCATGTTTCCTAAATTTGTTGGTGTCG
66 TAGCCAAATATTTTGTTTCCAATCTAAGGCCAACAACGCCATGTTTCCTAAATTTGTTGGTGTCG
43850 TGCCACCCCAAGGACTATGAAGTGATGTCGTACCACCCCAAGGACTATGAAGTGATGTC
131 TGCCACCCCAAGGACTATGAAGTGATGTCGTACCACCCCAAGGACTATGAAGTGATGTC
43909 GTACCACCCA
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (189 bp):
TCGTATTAATAACTAATGGTGCCATATGCCAAAATAGCCATGTTAATGGCGCCATGATTTTTCCT
TAGCCAAATATTTTGTTTCCAATCTAAGGCCAACAACGCCATGTTTCCTAAATTTGTTGGTGTCG
TGCCACCCCAAGGACTATGAAGTGATGTCGTACCACCCCAAGGACTATGAAGTGATGTC
Found at i:43879 original size:30 final size:30
Alignment explanation
Indices: 43845--43923 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
43835 AATTTGTTGG
*
43845 TGTCGTGCCACCCCAAGGACTATGAAGTGA
1 TGTCGTACCACCCCAAGGACTATGAAGTGA
43875 TGTCGTACCACCCCAAGGACTATGAAGTGA
1 TGTCGTACCACCCCAAGGACTATGAAGTGA
*
43905 TGTCGTACCACCCAAAGGA
1 TGTCGTACCACCCCAAGGA
43924 ATGAGGAGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (30 bp):
TGTCGTACCACCCCAAGGACTATGAAGTGA
Done.