Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015864.1 Corchorus olitorius cultivar O-4 contig15897, 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: 21966
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1431 original size:17 final size:18
Alignment explanation
Indices: 1397--1431 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1387 ACATTTAAAC
*
1397 TCATTTGTGGCCATTAAT
1 TCATTTGTGGCCAATAAT
1415 TCATTTGT-GCCAATAAT
1 TCATTTGTGGCCAATAAT
1432 CCAACGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (18 bp):
TCATTTGTGGCCAATAAT
Found at i:3082 original size:249 final size:249
Alignment explanation
Indices: 2644--3136 Score: 914
Period size: 249 Copynumber: 2.0 Consensus size: 249
2634 TTCTTATCAC
2644 ACTTCAGCATGCTTTCGTTGCTTCCTTTGTGCTGAAATCAACTAATTTGACCAAGAAATGGCCTT
1 ACTTCAGCATGCTTTCGTTGCTTCCTTTGTGCTGAAATCAACTAATTTGACCAAGAAATGGCCTT
2709 CTGACATTAGGACTTGGACTTTGATCATCAAGGCCACGAAATTCTTCATACTTAGTCATATTTTG
66 CTGACATTAGGACTTGGACTTTGATCATCAAGGCCACGAAATTCTTCATACTTAGTCATATTTTG
* *
2774 GTCTTCAAATCATGAAAATAACACTTAGTTAAGAAAATGGCTTAAACCGGGGTGAGAAAGCCATA
131 CTCTTCAAATCATGAAAATAACACTTAGTTAAGAAAATGGCTTAAACCGGGGTGAGAAAGCCACA
*
2839 TGTCCTTAACTGAAAAGGATGCAAAAGTTGCAAATGAAGTCGGAATAAGCCAAA
196 TGTCCTTAACTGAAAAGGATGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAA
*
2893 ACTTCAGCATGCTTTCGTTGCTTCCTTTGTGCTGAAATCAACTAATTTGACTAAGAAATGGCCTT
1 ACTTCAGCATGCTTTCGTTGCTTCCTTTGTGCTGAAATCAACTAATTTGACCAAGAAATGGCCTT
* *
2958 CTGACATTAGGACTTGGACTTTGATCATCAAGTCCATGAAATTCTTCATACTTAGTCATATTTTG
66 CTGACATTAGGACTTGGACTTTGATCATCAAGGCCACGAAATTCTTCATACTTAGTCATATTTTG
3023 CTCTTCAAATCATGAAAATAACACTTAGTTAAGAAAATGGCTTAAACCGGGGTGAGAAAGCCACA
131 CTCTTCAAATCATGAAAATAACACTTAGTTAAGAAAATGGCTTAAACCGGGGTGAGAAAGCCACA
* *
3088 TGTCCTTAACTGAAAATGATGCAAAAGTTGCAAACGAAGTTGGAATAAG
196 TGTCCTTAACTGAAAAGGATGCAAAAGTTGCAAACGAAGTCGGAATAAG
3137 GAATAAGCCA
Statistics
Matches: 236, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
249 236 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (249 bp):
ACTTCAGCATGCTTTCGTTGCTTCCTTTGTGCTGAAATCAACTAATTTGACCAAGAAATGGCCTT
CTGACATTAGGACTTGGACTTTGATCATCAAGGCCACGAAATTCTTCATACTTAGTCATATTTTG
CTCTTCAAATCATGAAAATAACACTTAGTTAAGAAAATGGCTTAAACCGGGGTGAGAAAGCCACA
TGTCCTTAACTGAAAAGGATGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAA
Found at i:6011 original size:41 final size:41
Alignment explanation
Indices: 5966--6058 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
5956 TTTTCGTGTT
* *
5966 CAATTTAGTCCCTAATTTAGGA-TTCTATTTATTATTTAATA
1 CAATTTAGTCCCTAATTCAGGATTTC-ATTTATTAATTAATA
* * * *
6007 CAATTTAGTCTCTAATTCAGTATTTCATTTATTAATTGATT
1 CAATTTAGTCCCTAATTCAGGATTTCATTTATTAATTAATA
*
6048 CAATTTGGTCC
1 CAATTTAGTCC
6059 TTATTTGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 40 0.93
42 3 0.07
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (41 bp):
CAATTTAGTCCCTAATTCAGGATTTCATTTATTAATTAATA
Found at i:8783 original size:31 final size:32
Alignment explanation
Indices: 8713--8783 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
8703 TCTATCAGCT
* *
8713 TTTAATTTGTTTAATTTAAGACTTTCATTTTA
1 TTTAATTTGTTTAATTTAAGACTTTAATTTGA
* *
8745 ATT-ATTTGTTTAATTTAATG-C-TTAATTTGC
1 TTTAATTTGTTTAATTTAA-GACTTTAATTTGA
8775 TTTAATTTG
1 TTTAATTTG
8784 CAATAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 8 0.25
31 21 0.66
32 3 0.09
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (32 bp):
TTTAATTTGTTTAATTTAAGACTTTAATTTGA
Found at i:9073 original size:13 final size:12
Alignment explanation
Indices: 9035--9083 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
9025 ATTCATTTTT
9035 TTATATATTGATA
1 TTATATATT-ATA
*
9048 ATA-ATATTTATA
1 TTATATA-TTATA
9060 TTATATTATTATA
1 TTATA-TATTATA
9073 TTATATATTAT
1 TTATATATTAT
9084 CAATAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 14 0.45
13 15 0.48
14 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTATATATTATA
Found at i:9306 original size:16 final size:16
Alignment explanation
Indices: 9257--9309 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
9247 GACACCGCCT
9257 GAAAATACCTGAACCC
1 GAAAATACCTGAACCC
* * **
9273 G-ATATAACCCGAGGCC
1 GAAAAT-ACCTGAACCC
9289 GAAAATACCTGAACCC
1 GAAAATACCTGAACCC
9305 GAAAA
1 GAAAA
9310 AACTCGAATC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.17, T:0.11
Consensus pattern (16 bp):
GAAAATACCTGAACCC
Found at i:13208 original size:26 final size:26
Alignment explanation
Indices: 13172--13223 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
13162 GCGGAGGGGC
13172 TGGAGACATGCTATGGGTGAATGGAT
1 TGGAGACATGCTATGGGTGAATGGAT
13198 TGGAGACATGCTATGGGTGAATGGAT
1 TGGAGACATGCTATGGGTGAATGGAT
13224 GTGCAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (26 bp):
TGGAGACATGCTATGGGTGAATGGAT
Found at i:20421 original size:1 final size:1
Alignment explanation
Indices: 20415--20453 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
20405 GTTCCTATGT
* *
20415 AAAAAAAAAAAAAAAAAAAAAAAAAAATAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20454 GGCGACAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Done.