Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018521.1 Corchorus olitorius cultivar O-4 contig18554, 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: 24461
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:321 original size:2 final size:2
Alignment explanation
Indices: 314--366 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
304 AAACCACTCA
314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
356 AT AT AT AT AT A
1 AT AT AT AT AT A
367 CTCCAGTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7404 original size:12 final size:12
Alignment explanation
Indices: 7387--7414 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7377 GAATTAAAAG
7387 TTATTTTTTATT
1 TTATTTTTTATT
7399 TTATTTTTTATT
1 TTATTTTTTATT
7411 TTAT
1 TTAT
7415 GTTAGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:11422 original size:139 final size:139
Alignment explanation
Indices: 11172--11451 Score: 488
Period size: 139 Copynumber: 2.0 Consensus size: 139
11162 AGGGCTTTTT
* *
11172 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCATATGTCCTAGTAATTGAATAGAAATAA
1 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCATATATCCTAGTAATTAAATAGAAATAA
* *
11237 AGAAGCCAGCCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGTTGAAAAAGG
66 AGAAGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGG
11302 GATGATTAA
131 GATGATTAA
11311 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCATATATCCTAGTAATTAAATAGAAATAA
1 TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCATATATCCTAGTAATTAAATAGAAATAA
* * * *
11376 AGAGGCCAACCTAGGAAGACCAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAGAGG
66 AGAAGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGG
11441 GATGATTAA
131 GATGATTAA
11450 TA
1 TA
11452 GAATCCAGCT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 133 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (139 bp):
TAAAATTATCTGTTAAGTTATGATTCAATAATGTTGCATATATCCTAGTAATTAAATAGAAATAA
AGAAGCCAACCAAGGAAGAACAAGCAGTATTTGAAGAGTCCGAGTTTTCTTGAAGGTGAAAAAGG
GATGATTAA
Found at i:16003 original size:33 final size:33
Alignment explanation
Indices: 15978--16423 Score: 487
Period size: 33 Copynumber: 13.5 Consensus size: 33
15968 GCCACCTGCT
* * * *
15978 AATCCTTATGGCCAACCTGGACAGCCAAGTGCT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * * *
16011 AATCCTTACGGTCAACCTGGACAGCCAAGTGCT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * **
16044 AATCCTTACGGCCAACCTGGACAGCCAAGTGTT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * *
16077 AATCCATACGGCCAGCCTGCACAGCCAACTGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* *
16110 AATCCATACGGCCAGCCTGCACAGCCAAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * **
16143 AATCCCTACGGCCAGCCTGCATTGCCAAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* *
16176 AATCCCTACGGCCAGCCTGCACAGCCAAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * *
16209 AATCCGTACGGCCAACCTGCGCAGCCCAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * *
16242 AATCCATATGGCCAACCTGCGCAGCCAAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
16275 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * * *
16308 AATCCTTATGGCCAACCTGCACAGCCGAGTGCT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * * * *
16341 AATCCTTATGGCCAACCTGCACACCCCAGTGCT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* * * * *
16374 AATCCTTATGGCCAACCTGCCCAGCCGAGTGCT
1 AATCCTTACGGCCAACCTGCACAGCCAAATGCC
* *
16407 AATCCATATGGCCAACC
1 AATCCTTACGGCCAACC
16424 CACACAACCA
Statistics
Matches: 377, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 377 1.00
ACGTcount: A:0.27, C:0.37, G:0.19, T:0.17
Consensus pattern (33 bp):
AATCCTTACGGCCAACCTGCACAGCCAAATGCC
Found at i:17134 original size:18 final size:18
Alignment explanation
Indices: 17092--17135 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17082 GATGGGTTCT
* *
17092 GGAATGGGTATGGGTATA
1 GGAATGGGCATGGGGATA
* *
17110 GGCATGGGCATGGGGATG
1 GGAATGGGCATGGGGATA
17128 GGAATGGG
1 GGAATGGG
17136 TGGCGCTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.52, T:0.20
Consensus pattern (18 bp):
GGAATGGGCATGGGGATA
Done.