Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012556.1 Corchorus olitorius cultivar O-4 contig12589, 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: 4553
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:489 original size:22 final size:22
Alignment explanation
Indices: 461--505 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
451 GTGATATTAA
461 ATGTCAACATTAAGTAATTTAT
1 ATGTCAACATTAAGTAATTTAT
483 ATGTCAACATTAAGTAATTTAT
1 ATGTCAACATTAAGTAATTTAT
505 A
1 A
506 CTAAGGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATGTCAACATTAAGTAATTTAT
Found at i:974 original size:15 final size:15
Alignment explanation
Indices: 954--990 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
944 AGGAATGTGA
954 GTTTGTTCGTAATTT
1 GTTTGTTCGTAATTT
969 GTTTGTTCGTAATTT
1 GTTTGTTCGTAATTT
984 GTTTGTT
1 GTTTGTT
991 TGTGTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.11, C:0.05, G:0.22, T:0.62
Consensus pattern (15 bp):
GTTTGTTCGTAATTT
Found at i:1088 original size:30 final size:30
Alignment explanation
Indices: 1052--1109 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1042 CATAGAGATT
1052 TATTTGAATTGTAATGAGATTTCATTGGGC
1 TATTTGAATTGTAATGAGATTTCATTGGGC
1082 TATTTGAATTGTAATGAGATTTCATTGG
1 TATTTGAATTGTAATGAGATTTCATTGG
1110 CTTTGTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (30 bp):
TATTTGAATTGTAATGAGATTTCATTGGGC
Found at i:2693 original size:108 final size:106
Alignment explanation
Indices: 2480--2701 Score: 234
Period size: 107 Copynumber: 2.1 Consensus size: 106
2470 TAATTTTCTA
* ** *
2480 ACCCTTAAAATAAAATTTTAATCTTAATTTGAGTTAAAATTAGTCAATTAGTTATATATTTTTAT
1 ACCCTTAAAATAAAACTAAAATCTTAATTTGAGCTAAAATTAGTCAATTAGTTATATATTTTTAT
* * ** *
2545 TTCTAAAACCCTATAACAATAAGTTATTAATTATGAAATTT
66 TTCTAAAACCCTATAAAAAAAACCTATTAATTATCAAATTT
* * * * *
2586 ACCCTTAAAATAAAACTAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTAGTTTTATA-TTTT
1 ACCCTTAAAATAAAACTAAAATCTTAATTT-GAGCTAAAATTAGT-CAATTAGTTATATATTTTT
*
2650 ATTTCTAAAACTCTATAATAAAAAAACCT-TTAATT-TCATAATTT
64 ATTTCTAAAACCCTAT-A-AAAAAAACCTATTAATTATCA-AATTT
*
2694 ACTCTTAA
1 ACCCTTAA
2702 CAATCAAATT
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
106 26 0.27
107 32 0.34
108 31 0.33
109 6 0.06
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (106 bp):
ACCCTTAAAATAAAACTAAAATCTTAATTTGAGCTAAAATTAGTCAATTAGTTATATATTTTTAT
TTCTAAAACCCTATAAAAAAAACCTATTAATTATCAAATTT
Found at i:3247 original size:16 final size:16
Alignment explanation
Indices: 3222--3254 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3212 GGCATAAAAA
3222 TTAAATA-TTTTTATT
1 TTAAATATTTTTTATT
3237 TTAATATATTTTTTATT
1 TTAA-ATATTTTTTATT
3254 T
1 T
3255 GATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAAATATTTTTTATT
Found at i:3966 original size:47 final size:47
Alignment explanation
Indices: 3912--4006 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
3902 TTTCCTATTT
3912 TTTCCATTTATGTAATTAGGAAGAAAAGTTAAAGAAAATAGCTATAA
1 TTTCCATTTATGTAATTAGGAAGAAAAGTTAAAGAAAATAGCTATAA
3959 TTTCCATTTATGTAATTAGGAAGAAAAGTTAAAGAAAATAGCTATAA
1 TTTCCATTTATGTAATTAGGAAGAAAAGTTAAAGAAAATAGCTATAA
4006 T
1 T
4007 CAACTTTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (47 bp):
TTTCCATTTATGTAATTAGGAAGAAAAGTTAAAGAAAATAGCTATAA
Found at i:4139 original size:16 final size:16
Alignment explanation
Indices: 4102--4145 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4092 ATTTTTTATT
4102 ATAAAAA-A-ATT-AA
1 ATAAAAATATATTAAA
4115 ATAAAAAATATATTAAA
1 AT-AAAAATATATTAAA
4132 ATAAAAATAT-TTAA
1 ATAAAAATATATTAA
4146 TTTTTATGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.07
14 5 0.19
15 5 0.19
16 11 0.41
17 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATATATTAAA
Found at i:4141 original size:14 final size:15
Alignment explanation
Indices: 4101--4142 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4091 GATTTTTTAT
*
4101 TATAAAAAAATTAAA
1 TATAAAAATATTAAA
*
4116 TAAAAAATATATTAAA
1 TATAAAA-ATATTAAA
4132 -ATAAAAATATT
1 TATAAAAATATT
4143 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 11 0.48
16 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TATAAAAATATTAAA
Done.