Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015285.1 Corchorus olitorius cultivar O-4 contig15318, 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: 55632
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Found at i:511 original size:32 final size:32
Alignment explanation
Indices: 455--547 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
445 TTTCAAGTTG
*
455 ACCCGAGC-T-TT-CGAGCCGAACTCGAGCTC
1 ACCCGAGCTTATTACGAGCCGAGCTCGAGCTC
* *
484 ACCCTAGCTTATTACGAGCCGAGCTCGAGTTC
1 ACCCGAGCTTATTACGAGCCGAGCTCGAGCTC
*
516 ACCCGAGCTTATTACGAGCCGAGCTTGAGCTC
1 ACCCGAGCTTATTACGAGCCGAGCTCGAGCTC
548 GGAATTAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 7 0.13
30 1 0.02
31 2 0.04
32 45 0.82
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.22
Consensus pattern (32 bp):
ACCCGAGCTTATTACGAGCCGAGCTCGAGCTC
Found at i:537 original size:16 final size:16
Alignment explanation
Indices: 489--541 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
479 AGCTCACCCT
489 AGCTTATTACGAGCCG
1 AGCTTATTACGAGCCG
* *
505 AGCTCGAGTT-C-ACCCG
1 AGCT-TA-TTACGAGCCG
521 AGCTTATTACGAGCCG
1 AGCTTATTACGAGCCG
537 AGCTT
1 AGCTT
542 GAGCTCGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 21 0.72
17 2 0.07
18 2 0.07
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (16 bp):
AGCTTATTACGAGCCG
Found at i:4286 original size:105 final size:106
Alignment explanation
Indices: 4092--4300 Score: 314
Period size: 105 Copynumber: 2.0 Consensus size: 106
4082 AAAAAAAAAG
* * *
4092 AAAAGAAAATCGCTTCCCCACCAATTATTGCCTTTTTTTTAAAAAAAAAAAAACAAAATCGCTTT
1 AAAAAAAAATCGCTTCCCCACCAATTATTGCC-TTTTTTAAAAAAAAAAAAAACAAAATCGCTCT
* * * *
4157 GGTTGAGAGATTAAAAATGGTCGTGAGTCTTTTTATTGCCTT
65 GGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTTTATTGCCTT
*
4199 AAAAAAAAATCGCTTCCCCA-CAATTATTGCC-TTTTTAAAATAAAAAAAAAAGAAAATCGCTCT
1 AAAAAAAAATCGCTTCCCCACCAATTATTGCCTTTTTTAAAA-AAAAAAAAAACAAAATCGCTCT
4262 GGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTTTATTGC
65 GGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTTTATTGC
4301 TTTTTTTTCA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
104 8 0.09
105 55 0.59
106 11 0.12
107 19 0.20
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (106 bp):
AAAAAAAAATCGCTTCCCCACCAATTATTGCCTTTTTTAAAAAAAAAAAAAACAAAATCGCTCTG
GTTAAGAGAGTAAAAAAGATCGTGAGTCTTTTTATTGCCTT
Found at i:4326 original size:73 final size:74
Alignment explanation
Indices: 4230--4369 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 74
4220 AATTATTGCC
4230 TTTTTAAAATAAAAAAAAAAGAAAATCGCTCTGGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTT
1 TTTTTAAAATAAAAAAAAAAGAAAATCGCTCTGGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTT
4295 TATTGCTTT
66 TATTGCTTT
* * * * * *
4304 TTTTTCAAA-AAAAAAAAAAGAAAATCGCTTTGGTTGAGAGATTAAAAATGGTCGTGAGTCTTTT
1 TTTTTAAAATAAAAAAAAAAGAAAATCGCTCTGGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTT
4368 TA
66 TA
4370 AATATAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 52 0.87
74 8 0.13
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (74 bp):
TTTTTAAAATAAAAAAAAAAGAAAATCGCTCTGGTTAAGAGAGTAAAAAAGATCGTGAGTCTTTT
TATTGCTTT
Found at i:4728 original size:20 final size:20
Alignment explanation
Indices: 4703--4743 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4693 AGTGGTAGGA
*
4703 AGTCCAATACGTTAATCATC
1 AGTCCAATACGTTAATAATC
4723 AGTCCAATACGTTAATAATC
1 AGTCCAATACGTTAATAATC
4743 A
1 A
4744 CGTTCAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (20 bp):
AGTCCAATACGTTAATAATC
Found at i:45157 original size:19 final size:19
Alignment explanation
Indices: 45132--45180 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
45122 CTGCACCTCA
*
45132 CACACACATATGAATATTC
1 CACACACATATAAATATTC
* *
45151 TACACACATACAAATATTC
1 CACACACATATAAATATTC
45170 CACACACATAT
1 CACACACATAT
45181 TCACATATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (19 bp):
CACACACATATAAATATTC
Found at i:45185 original size:27 final size:27
Alignment explanation
Indices: 45155--45206 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
45145 ATATTCTACA
45155 CACATACAAATATTCCACACACATATT
1 CACATACAAATATTCCACACACATATT
** *
45182 CACATATGAATATTCTACACACATA
1 CACATACAAATATTCCACACACATA
45207 CGGAGTACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (27 bp):
CACATACAAATATTCCACACACATATT
Found at i:45286 original size:16 final size:16
Alignment explanation
Indices: 45265--45297 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45255 TACACACATG
45265 AGTATTCCACAAATAA
1 AGTATTCCACAAATAA
*
45281 AGTATTCCACACATAA
1 AGTATTCCACAAATAA
45297 A
1 A
45298 AAAGGGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (16 bp):
AGTATTCCACAAATAA
Done.