Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016594.1 Corchorus olitorius cultivar O-4 contig16627, 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: 7829
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:942 original size:295 final size:293
Alignment explanation
Indices: 357--945 Score: 962
Period size: 294 Copynumber: 2.0 Consensus size: 293
347 TTTTTAGTGA
357 CTATGGAAATTACTTAAAGGCCAAATTAAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTTTGGT
1 CTATGGAAATTACTTAAAGGCCAAATTAAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTTTGGT
* * * * *
422 TTTTTCTCACTTTTCGGGTGAGTAAAGAGGCCCTTGATGAATTTCCTCCCTTACTTTTCCTCCTG
66 CTTTTCTCACTTTTCAGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCTG
* * **
487 CCTTTTTTTTGTAATTTACTATTTTTGTATTTATAATTAGTGTGTTTTAATTATGTATTAATTGT
131 CCTTTTTTTTATAATTTACTATTTTTATATTTATAATTAGTGTGTTTTAATTACATATTAATTGT
* *
552 GTGTGGATATTAGGATTTATCGATTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAA
196 GTGTGGATATTAGGATTTACCGATTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAAA
*
617 TGTATGTACCCGAGTTCATTAATTTAACAATTG
261 TGTATCTACCCGAGTTCATTAATTTAACAATTG
* *
650 CTATGGAAATTACTTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTTTTG
1 CTATGGAAATTACTT-AAAGGCCAAATTAAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTTTGG
*
715 TCTTTTCTCACTTTTCAGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
65 TCTTTTCTCACTTTTCAGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCT
* *
780 GCCTTTTTTTTATAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATT
130 GCCTTTTTTTTATAATTTACTATTTTTATATTTATAATT-AGTGTGTTTTAATTACATATTAATT
* * *
845 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTTTGCCGGAATTCCAAAGGATTAGTGCTGTA
194 GTGTGTGGATATTAGGATTTACCGATTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATA
* *
910 AATGTGTCTACTCGAGTTCATTAATTTAACAATTG
259 AATGTATCTACCCGAGTTCATTAATTTAACAATTG
945 C
1 C
946 AATCAAGATT
Statistics
Matches: 272, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
293 15 0.06
294 142 0.52
295 115 0.42
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (293 bp):
CTATGGAAATTACTTAAAGGCCAAATTAAGGATTAATGTGGTGCCTCCTTTTGCCTTTTTTTGGT
CTTTTCTCACTTTTCAGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCTG
CCTTTTTTTTATAATTTACTATTTTTATATTTATAATTAGTGTGTTTTAATTACATATTAATTGT
GTGTGGATATTAGGATTTACCGATTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAAA
TGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:1640 original size:6 final size:7
Alignment explanation
Indices: 1630--1654 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1620 AAAAAAGAAA
1630 AAAAAGT
1 AAAAAGT
1637 AAAAAGT
1 AAAAAGT
1644 AAAAAGT
1 AAAAAGT
1651 AAAA
1 AAAA
1655 TTGGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAAGT
Found at i:2076 original size:14 final size:14
Alignment explanation
Indices: 2057--2087 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2047 TTTAACTTGG
2057 AAACCCTAATTCCC
1 AAACCCTAATTCCC
2071 AAACCCTAATTCCC
1 AAACCCTAATTCCC
2085 AAA
1 AAA
2088 TTACCTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCCTAATTCCC
Found at i:2356 original size:165 final size:167
Alignment explanation
Indices: 2071--2388 Score: 385
Period size: 165 Copynumber: 1.9 Consensus size: 167
2061 CCTAATTCCC
* * * *
2071 AAACCCTAATTCCCAAATTACCTTATGAACAAGCCCTAAAATTTGCATAAAACTTCCCAAATACC
1 AAACACTAATTCCCAAATTACCTTATGAACAAACCCTAAAATTTGCAGAAAAC-TCCCAAAAACC
* * * * *
2136 CAGAAACAATTCATAGCAATAACTCATAATACAACACCTTTTTTCCAATACCCATAACAGATAAT
65 CAGAAACAATTCATAACAAAAAATCATAATACAACACCTTTTTTCCAAAACCCATAACAGAAAAT
*
2201 CTATTTTAACCCAAAAT-CACAATCATTTTAACTCAGA
130 CGATTTTAACCCAAAATCCACAATCATTTTAACTCAGA
* * *
2238 AAACACTAATTCCC-AATTCATCTTATGAACAAACCCTGAAATTT-CAGAAATA-TCGCAAAAAC
1 AAACACTAATTCCCAAATT-ACCTTATGAACAAACCCTAAAATTTGCAGAAA-ACTCCCAAAAAC
* * ** *
2300 CCATAAACAATTCA-AACAAAAAAATTATAATACAACATTTTTTTTCCAAAACCCATAACCGAAA
64 CCAGAAACAATTCATAAC-AAAAAATCATAATACAACACCTTTTTTCCAAAACCCATAACAGAAA
* *
2364 ATCGGTTTTTACCCAAAATCCACAA
128 ATCGATTTTAACCCAAAATCCACAA
2389 AAAAAAACCT
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
164 2 0.02
165 75 0.59
166 14 0.11
167 36 0.28
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.26
Consensus pattern (167 bp):
AAACACTAATTCCCAAATTACCTTATGAACAAACCCTAAAATTTGCAGAAAACTCCCAAAAACCC
AGAAACAATTCATAACAAAAAATCATAATACAACACCTTTTTTCCAAAACCCATAACAGAAAATC
GATTTTAACCCAAAATCCACAATCATTTTAACTCAGA
Found at i:2724 original size:16 final size:16
Alignment explanation
Indices: 2690--2722 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2680 TCTTTTTTTG
*
2690 TTAAATGAATTTAAAT
1 TTAAATGAAATTAAAT
2706 TTAAAT-AAATTAAAT
1 TTAAATGAAATTAAAT
2721 TT
1 TT
2723 TATTTCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATGAAATTAAAT
Found at i:6286 original size:6 final size:6
Alignment explanation
Indices: 6270--6304 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
6260 CATTCTGTTG
*
6270 CTTTTT TTTTTT CTTTTT CTTTTT -TTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
6305 TTTGAGCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
CTTTTT
Found at i:6294 original size:17 final size:17
Alignment explanation
Indices: 6272--6304 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6262 TTCTGTTGCT
6272 TTTTTTTTTTCTTTTTC
1 TTTTTTTTTTCTTTTTC
6289 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTCTTTTT
6305 TTTGAGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTTCTTTTTC
Done.