Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3857
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: 16938
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:3153 original size:23 final size:24
Alignment explanation
Indices: 3127--3171 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3117 GAAGAATAAG
*
3127 TTTA-TTAAAAATCATGTTTAATT
1 TTTATTTAAAAATCAAGTTTAATT
*
3150 TTTATTTCAAAATCAAGTTTAA
1 TTTATTTAAAAATCAAGTTTAA
3172 GAATTGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTATTTAAAAATCAAGTTTAATT
Found at i:3433 original size:21 final size:22
Alignment explanation
Indices: 3407--3447 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3397 AGAACCTAGT
3407 ATTAACTTAATCA-GCAGCAGA
1 ATTAACTTAATCAGGCAGCAGA
3428 ATTAACTTAATCAGGCAGCA
1 ATTAACTTAATCAGGCAGCA
3448 ACATGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
ATTAACTTAATCAGGCAGCAGA
Found at i:6752 original size:22 final size:21
Alignment explanation
Indices: 6727--6787 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
6717 TTCCTTTCTT
6727 TATTTATTTCATTTACTTATTA
1 TATTTATTT-ATTTACTTATTA
6749 TATTATATTTATTTTA-TTATTA
1 TATT-TATTTA-TTTACTTATTA
*
6771 TA-TTATATATTTACTTA
1 TATTTATTTATTTACTTA
6788 AATATTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.11
20 8 0.23
21 1 0.03
22 13 0.37
23 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTATTTATTTACTTATTA
Found at i:6793 original size:24 final size:22
Alignment explanation
Indices: 6744--6794 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
6734 TTCATTTACT
* * *
6744 TATTATATTATATTTATTTTAT
1 TATTATATTATATTTACTTAAA
6766 TATTATATTATATATTTACTTAAA
1 TATTATA-T-TATATTTACTTAAA
6790 TATTA
1 TATTA
6795 AGTAATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 1 0.04
24 16 0.67
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATATTATATTTACTTAAA
Found at i:6813 original size:18 final size:18
Alignment explanation
Indices: 6790--6824 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6780 TTTACTTAAA
6790 TATTAAGTA-ATACATATT
1 TATTAA-TATATACATATT
6808 TATTAATATATACATAT
1 TATTAATATATACATAT
6825 GTATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTAATATATACATATT
Found at i:7780 original size:58 final size:58
Alignment explanation
Indices: 7630--7782 Score: 225
Period size: 58 Copynumber: 2.6 Consensus size: 58
7620 ATTCATCGGA
* * * *
7630 ATTAAACTCTAAACTTAACGCCAATTAACTTGAACTTACTAGCAATATCATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
* * * *
7688 ATTAAACTTTGAATTTAACGCCAATCAACTTGAATTTACCATCAATATGATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
*
7746 ATTAAACTCTGAACTTAATGCCAATCAACTTGAATTT
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTT
7783 TCCAATATCT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 84 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.33
Consensus pattern (58 bp):
ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
Found at i:11782 original size:3 final size:3
Alignment explanation
Indices: 11776--11800 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11766 ATTGTCTGGT
11776 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
11801 AAATCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11867 original size:14 final size:16
Alignment explanation
Indices: 11837--11868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11827 TGTTATCAAC
11837 TAGTTAGACATAAATT
1 TAGTTAGACATAAATT
11853 TAGTTAGA-A-AAATT
1 TAGTTAGACATAAATT
11867 TA
1 TA
11869 AAATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGTTAGACATAAATT
Found at i:12972 original size:29 final size:30
Alignment explanation
Indices: 12920--12988 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
12910 AGCCTCTATC
*
12920 TTTATAATTTTTAAAGGATTAAAT-CAAATT
1 TTTATAATTTTTAAAGGATAAAATAC-AATT
* *
12950 TTTATTATTTTT-AGGGATAAAATACAA-T
1 TTTATAATTTTTAAAGGATAAAATACAATT
12978 TTTACTAATTT
1 TTTA-TAATTT
12989 AAAATTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 5 0.15
29 16 0.48
30 12 0.36
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGATAAAATACAATT
Found at i:13338 original size:29 final size:29
Alignment explanation
Indices: 13286--13341 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
13276 TATAGAGACG
** * *
13286 GATTAATTTAGTCTTTTTATTATTAAATA
1 GATTAATTTAGTCACTGTAATATTAAATA
13315 GATTAATTTAGTCACTGTAATATTAAA
1 GATTAATTTAGTCACTGTAATATTAAA
13342 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
GATTAATTTAGTCACTGTAATATTAAATA
Done.