Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010051.1 Corchorus olitorius cultivar O-4 contig10083, 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: 8646
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:709 original size:178 final size:177
Alignment explanation
Indices: 400--894 Score: 789
Period size: 178 Copynumber: 2.8 Consensus size: 177
390 TCCACCATAA
* * * **
400 AAAAATTATGTAATATTAAGTAGACCGTCTATTCCCACTAACCGAAACAAC-TAATTCTTT-GGA
1 AAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAT-ATT-TTTCGGA
* *
463 AGCATTTGTTATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCAT
64 AGCATTT-TTATA-CTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCAT
*
527 GGAACAACCTTTCGAGAGACACTTGAATCACTTTAATCAGACATCTGGAAC
127 GGAACAACCTTTCGAGAGACACTTGAATCACTTCAATCAGACATCTGGAAC
** * *
578 AAAAGTTATATAATATTAAGTGGATTGTCTATTCCCGTTAACTGAAACAACATATTTTTCGGAAA
1 AAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAG
643 CATTTTTAATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGA
66 CATTTTT-ATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGA
*
708 ACAACCTTTCGAGAGACACTTGAATCACTTCAATCAGACATCTGGAGC
130 ACAACCTTTCGAGAGACACTTGAATCACTTCAATCAGACATCTGGAAC
756 AAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAG
1 AAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAG
821 CATTTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGA
66 CA-TTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGA
*
886 ACAATCTTT
130 ACAACCTTT
895 TAATAAACAC
Statistics
Matches: 294, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
177 9 0.03
178 279 0.95
179 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (177 bp):
AAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAG
CATTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGAA
CAACCTTTCGAGAGACACTTGAATCACTTCAATCAGACATCTGGAAC
Found at i:945 original size:178 final size:178
Alignment explanation
Indices: 401--952 Score: 758
Period size: 178 Copynumber: 3.1 Consensus size: 178
391 CCACCATAAA
* * **
401 AAAATTATGTAATATTAAGTAGACCGTCTATTCCCACTAACCGAAACAAC-TAATTCTTT-GGAA
1 AAAATTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAT-ATT-TTTCGGAA
* * *
464 GCATTTGTTATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATG
64 GCATTTTTTATA-CTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATG
*
528 GAACAACCTTTCGAGAGACACTTGAATCACTTTAATCAGACATCTGGAACA-
128 GAACAACCTTTCGAGAGACACTTGAATCACCTTAATCAGACATCTGGAA-AG
* ** * *
579 AAAGTTATATAATATTAAGTGGATTGTCTATTCCCGTTAACTGAAACAACATATTTTTCGGAAAC
1 AAAATTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAGC
*
644 ATTTTTAATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGAA
66 ATTTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGAA
709 CAACCTTTCGAGAGACACTTGAATCA-CTTCAATCAGACATCTGG--AG
131 CAACCTTTCGAGAGACACTTGAATCACCTT-AATCAGACATCTGGAAAG
755 CAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAA
1 -AAAA-TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAA
820 GCATTTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGG
64 GCATTTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGG
* ** * * * * * * * *
885 AACAATCTTTTAATAAACACTTAAATCACCTTGATCGGATAACCGGAAAG
129 AACAACCTTTCGAGAGACACTTGAATCACCTTAATCAGACATCTGGAAAG
*
935 AAAATTATATAATGTTAA
1 AAAATTATATAATATTAA
953 ATAGACCGAT
Statistics
Matches: 332, Mismatches: 32, Indels: 20
0.86 0.08 0.05
Matches are distributed among these distances:
175 1 0.00
177 12 0.04
178 309 0.93
179 8 0.02
180 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AAAATTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACATATTTTTCGGAAGC
ATTTTTTATACTTGAAACATTAAATTTAGTTTTCGATTCCTTCATGAAAGTTGTAGATCATGGAA
CAACCTTTCGAGAGACACTTGAATCACCTTAATCAGACATCTGGAAAG
Found at i:986 original size:36 final size:36
Alignment explanation
Indices: 940--1009 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
930 GAAAGAAAAT
940 TATATAATGTTAAATAGACCGATTAGCCAAACCACA
1 TATATAATGTTAAATAGACCGATTAGCCAAACCACA
976 TATATAATGTTAAATAGACCGATTAGCCAAACCA
1 TATATAATGTTAAATAGACCGATTAGCCAAACCA
1010 TTTATAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (36 bp):
TATATAATGTTAAATAGACCGATTAGCCAAACCACA
Found at i:8087 original size:105 final size:106
Alignment explanation
Indices: 7951--8222 Score: 415
Period size: 107 Copynumber: 2.6 Consensus size: 106
7941 AAATATTTTT
* *
7951 ATTTTAATTT-TGACTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAAAAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
*
8014 T-ATTATTAATTATGGAATTTACCCTTAAAATAAAAATAAA
66 TAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAA
* *
8054 ATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAAAAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
* *
8119 TAAATTATTAATTTTGAAATTTATCCTTAAAATAAAAATAAA
66 T-AATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAA
* * * *
8161 ATTTTAATTTGGGACTGAACTTAGCGAAATTATTTTTATATTTTATTTCTAAAACTCTATAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
8223 TAAAAAACCT
Statistics
Matches: 152, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
103 10 0.07
104 13 0.09
105 37 0.24
107 92 0.61
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (106 bp):
ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
TAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAA
Found at i:8248 original size:107 final size:104
Alignment explanation
Indices: 7951--8257 Score: 374
Period size: 107 Copynumber: 2.9 Consensus size: 104
7941 AAATATTTTT
* *
7951 ATTTTAATTT-TGACTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTAT-AAAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
*
8013 ATATTATTAA-TTATGGAATTTACCCTTAAAATAAAAATAAA
66 AAATTATTAATTTAT--AATTTA-CCTTAAAATAAAAATAAA
* *
8054 ATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAAAAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
8119 TAAATTATTAATTT-TGAAATTTATCCTTAAAATAAAAATAAA
66 -AAATTATTAATTTAT--AATTTA-CCTTAAAATAAAAATAAA
* * * *
8161 ATTTTAATTTGGGACTGAACTTAGCGAAATTATTTTTATATTTTATTTCTAAAACTCTATAATAA
1 ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA-AA
* *
8226 AAAACCT-TTAATTTCATTATTTACTCTTAAAA
65 AAAA-TTATTAATTT-ATAATTTAC-CTTAAAA
8258 ATTTAATTTC
Statistics
Matches: 179, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
103 10 0.06
104 13 0.07
105 31 0.17
106 5 0.03
107 113 0.63
108 6 0.03
109 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (104 bp):
ATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAA
AAATTATTAATTTATAATTTACCTTAAAATAAAAATAAA
Found at i:8579 original size:16 final size:15
Alignment explanation
Indices: 8552--8598 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
8542 GTCACCTTCT
* *
8552 TTATTAAAAAAATTA
1 TTATTTAAAAAATAA
*
8567 TTTTTTCAAAAAATAA
1 TTATTT-AAAAAATAA
8583 TTATTTAAAAAA-AA
1 TTATTTAAAAAATAA
8597 TT
1 TT
8599 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 13 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTTAAAAAATAA
Found at i:8606 original size:12 final size:12
Alignment explanation
Indices: 8589--8623 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
8579 ATAATTATTT
8589 AAAAAAAATTGA
1 AAAAAAAATTGA
8601 AAAAAAAATTGA
1 AAAAAAAATTGA
8613 ACTAAAAAAAT
1 A--AAAAAAAT
8624 AGATTTCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
14 8 0.38
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTGA
Done.