Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010795.1 Corchorus olitorius cultivar O-4 contig10827, 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: 10248
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Found at i:5984 original size:109 final size:109
Alignment explanation
Indices: 5787--5985 Score: 362
Period size: 109 Copynumber: 1.8 Consensus size: 109
5777 TCAAAATTGC
5787 GTTTAAGTTTCAAAAAACCTTGCTCAAGGTCTCTCTTCAAAGTTTGCATTTGTAAGACCTCCAGG
1 GTTTAAGTTTCAAAAAACCTTGCTCAAGGTCTCTCTTCAAAGTTTGCATTTGTAAGACCTCCAGG
*
5852 CACAATTTCAGAAACTTCCGGGTATCACTTCATTTCATCATGTT
66 CACAATTTCAGAAACCTCCGGGTATCACTTCATTTCATCATGTT
*
5896 GTTTAAGTTTCAAAAAACCTTGCTCAAGGTCTCTCTTCAAAGTTTGCATTTGTAAGACCTCCGGG
1 GTTTAAGTTTCAAAAAACCTTGCTCAAGGTCTCTCTTCAAAGTTTGCATTTGTAAGACCTCCAGG
* *
5961 CACATTTTCAGAAACCTCTGGGTAT
66 CACAATTTCAGAAACCTCCGGGTAT
5986 TAATTCTGAT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (109 bp):
GTTTAAGTTTCAAAAAACCTTGCTCAAGGTCTCTCTTCAAAGTTTGCATTTGTAAGACCTCCAGG
CACAATTTCAGAAACCTCCGGGTATCACTTCATTTCATCATGTT
Found at i:6119 original size:142 final size:144
Alignment explanation
Indices: 5936--6284 Score: 549
Period size: 142 Copynumber: 2.4 Consensus size: 144
5926 CTCTCTTCAA
*
5936 AGTTTGCATTTGTAAGACCTCCGGGCACATTTTCAGAAACCTCTGGGTATTAATTCTGATAAATC
1 AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATC
* * *
6001 CTCTGGGTATCACCTCATTTCATCAAATTGTTAATCAAAGTTGCGTTTAAG-T-TTCAAAAAAAC
66 CTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAATTGCGTTTAAGTTATTAAAAAAAAC
*
6064 CTTGCTCAAGGTCG
131 CTTACTCAAGGTCG
*
6078 AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTTTGATAAATC
1 AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATC
*
6143 CTCCGGGTATCACCTCATTTCATCAAGTTGTTAATCAAAATTGCGTTTAAGTTTTTTATTAAAAA
66 CTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAATTGCGTTTAAG----TTATTAAAAA
6208 AAACCTTACTCAAGGTCG
127 AAACCTTACTCAAGGTCG
* * * *
6226 AGTTTGCATTTGTAAGACCTCCGGGTACGATTTCAGAAATCTCCGGGTATTAATTCTGA
1 AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGA
6285 CAAGTCTCCC
Statistics
Matches: 189, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
142 111 0.59
147 1 0.01
148 77 0.41
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (144 bp):
AGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATC
CTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAATTGCGTTTAAGTTATTAAAAAAAAC
CTTACTCAAGGTCG
Found at i:6360 original size:37 final size:37
Alignment explanation
Indices: 6310--6380 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
6300 TCTGACAAAT
* *
6310 CCTGTTCAGGATCATTGCTTTATCACTCAGTTTCAGA
1 CCTGTTCAGGATCATTGCTTCATCAATCAGTTTCAGA
*
6347 CCTGTTCAGGATCATTGCTTCATCAATTAGTTTC
1 CCTGTTCAGGATCATTGCTTCATCAATCAGTTTC
6381 GGAGTTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (37 bp):
CCTGTTCAGGATCATTGCTTCATCAATCAGTTTCAGA
Found at i:6447 original size:76 final size:78
Alignment explanation
Indices: 6358--6619 Score: 179
Period size: 71 Copynumber: 3.4 Consensus size: 78
6348 CTGTTCAGGA
* ** * * * *
6358 TCATTGCTTCATCAATTAGTTTCGGAGTTCTATTCAAGGTCATTCCTTTATCAA-TCAACTTCAT
1 TCATTGC-TCATCAATTAATTTCAAAATCCTATTCAAGGTCATGCCTTTATCAAGTCAACTTCAA
6422 AATCCTATTCAGAG
65 AATCCTATTCAGAG
* * * * *
6436 TCATTGC-CATCAATTAATTTCAAAATCCTATTCAGGGTTATGGCTTTATCAAGTTAATTTCAAA
1 TCATTGCTCATCAATTAATTTCAAAATCCTATTCAAGGTCATGCCTTTATCAAGTCAACTTCAAA
6500 ATCCTATTCAG-G
66 ATCCTATTCAGAG
** * * * *
6512 -----G-TCATCGGTCAATTTCAAAATCCTATTC-AGGATCACTG-CTTTATCAACTTAATTTCA
1 TCATTGCTCATCAATTAATTTCAAAATCCTATTCAAGG-TCA-TGCCTTTATCAAGTCAACTTCA
*
6569 AAATCCTATTC-GGG
64 AAATCCTATTCAGAG
* *** *
6583 ATCATTGCCTTATCTGCTAATTTCAAGATCCTATTCA
1 -TCATTG-CTCATCAATTAATTTCAAAATCCTATTCA
6620 GGATCATTGG
Statistics
Matches: 147, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
70 3 0.02
71 56 0.38
72 2 0.01
76 37 0.25
77 20 0.14
78 7 0.05
79 22 0.15
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.38
Consensus pattern (78 bp):
TCATTGCTCATCAATTAATTTCAAAATCCTATTCAAGGTCATGCCTTTATCAAGTCAACTTCAAA
ATCCTATTCAGAG
Found at i:6500 original size:40 final size:37
Alignment explanation
Indices: 6417--6657 Score: 183
Period size: 40 Copynumber: 6.4 Consensus size: 37
6407 ATCAATCAAC
* * * *
6417 TTCATAATCCTATTCAGAGTCATTGC-CATCAATTAAT
1 TTCAAAATCCTATTCAGGGTCA-TGCTTATCAGTTAAT
*
6454 TTCAAAATCCTATTCAGGGTTATGGCTTTATCAAGTTAAT
1 TTCAAAATCCTATTCAGGGTCAT-GC-TTATC-AGTTAAT
* *
6494 TTCAAAATCCTATTCAGGG---T-C--ATCGGTCAAT
1 TTCAAAATCCTATTCAGGGTCATGCTTATCAGTTAAT
* *
6525 TTCAAAATCCTATTCAGGATCACTGCTTTATCAACTTAAT
1 TTCAAAATCCTATTCAGGGTCA-TGC-TTATC-AGTTAAT
* *
6565 TTCAAAATCCTATTC-GGGATCATTGCCTTATCTGCTAAT
1 TTCAAAATCCTATTCAGGG-TCA-TG-CTTATCAGTTAAT
* * *
6604 TTCAAGATCCTATTCAGGATCATTGGCTTATCAGTTGAT
1 TTCAAAATCCTATTCAGGGTCA-T-GCTTATCAGTTAAT
*
6643 TTCAACATCCTATTC
1 TTCAAAATCCTATTC
6658 GGGATCCTTA
Statistics
Matches: 165, Mismatches: 22, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
31 23 0.14
32 3 0.02
35 2 0.01
36 2 0.01
37 22 0.13
39 55 0.33
40 57 0.35
41 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
TTCAAAATCCTATTCAGGGTCATGCTTATCAGTTAAT
Found at i:6538 original size:71 final size:71
Alignment explanation
Indices: 6451--6587 Score: 215
Period size: 71 Copynumber: 1.9 Consensus size: 71
6441 GCCATCAATT
* * *
6451 AATTTCAAAATCCTATTCAGGGTTA-TGGCTTTATCAAGTTAATTTCAAAATCCTATTCAGGG-T
1 AATTTCAAAATCCTATTCAGGATCACT-GCTTTATCAACTTAATTTCAAAATCCTATTC-GGGAT
6514 CATCGGTC
64 CATCGGTC
6522 AATTTCAAAATCCTATTCAGGATCACTGCTTTATCAACTTAATTTCAAAATCCTATTCGGGATCA
1 AATTTCAAAATCCTATTCAGGATCACTGCTTTATCAACTTAATTTCAAAATCCTATTCGGGATCA
6587 T
66 T
6588 TGCCTTATCT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
70 3 0.05
71 57 0.93
72 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (71 bp):
AATTTCAAAATCCTATTCAGGATCACTGCTTTATCAACTTAATTTCAAAATCCTATTCGGGATCA
TCGGTC
Found at i:6615 original size:39 final size:39
Alignment explanation
Indices: 6522--6663 Score: 176
Period size: 39 Copynumber: 3.6 Consensus size: 39
6512 GTCATCGGTC
* * *
6522 AATTTCAAAATCCTATTCAGGATCACTGCTTTATCAACTT
1 AATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGC-T
* *
6562 AATTTCAAAATCCTATTCGGGATCATTGCCTTATCTGCT
1 AATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGCT
* * *
6601 AATTTCAAGATCCTATTCAGGATCATTGGCTTATCAGTT
1 AATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGCT
* * *
6640 GATTTCAACATCCTATTCGGGATC
1 AATTTCAAAATCCTATTCAGGATC
6664 CTTATTTGAG
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 56 0.63
40 33 0.37
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGCT
Found at i:8500 original size:11 final size:11
Alignment explanation
Indices: 8484--8508 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8474 AGACACAACC
8484 AAACAAAAAGA
1 AAACAAAAAGA
8495 AAACAAAAAGA
1 AAACAAAAAGA
8506 AAA
1 AAA
8509 TCAGGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAACAAAAAGA
Done.