Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2340
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: 223142
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:201111 original size:22 final size:21
Alignment explanation
Indices: 201086--201141 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
201076 TATTATCTAA
201086 TTAATAAAAAATTTATTTAAA-T
1 TTAATAAAAAA--TATTTAAATT
201108 TTAATTATAAAAATATTTAAATT
1 TTAA-TA-AAAAATATTTAAATT
*
201131 TTAAGAAAAAA
1 TTAATAAAAAA
201142 ATAGTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.17
22 13 0.43
23 7 0.23
24 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAATAAAAAATATTTAAATT
Found at i:207635 original size:18 final size:18
Alignment explanation
Indices: 207612--207653 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
207602 TATATTTATA
*
207612 TCATATTCATATTA-ATTT
1 TCATATT-ATAATATATTT
207630 TCATATTATAATATATTT
1 TCATATTATAATATATTT
207648 T-ATATT
1 TCATATT
207654 TTATTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATATTATAATATATTT
Found at i:207855 original size:17 final size:17
Alignment explanation
Indices: 207834--207895 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
207824 TATATTATAA
*
207834 AATTAAATTAAAAAAAT
1 AATTAAATTATAAAAAT
* *
207851 TATTAAATCGATAAAAAT
1 AATTAAAT-TATAAAAAT
*
207869 AAATAAATTATAAAAAT
1 AATTAAATTATAAAAAT
207886 AATTTAAATT
1 AA-TTAAATT
207896 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 17 0.47
18 19 0.53
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTAAATTATAAAAAT
Found at i:207875 original size:18 final size:17
Alignment explanation
Indices: 207854--207887 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
207844 AAAAAATTAT
207854 TAAATCGATAAAAATAAA
1 TAAAT-GATAAAAATAAA
*
207872 TAAATTATAAAAATAA
1 TAAATGATAAAAATAA
207888 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
TAAATGATAAAAATAAA
Found at i:208826 original size:73 final size:73
Alignment explanation
Indices: 208746--208882 Score: 247
Period size: 73 Copynumber: 1.9 Consensus size: 73
208736 TGATCTGGGT
*
208746 TTGGTTACTTTGCTTGTTTCTGATTGTTATCTTATTGTTTTCTTCTTTTTTCTTTTAATCTTTTA
1 TTGGTTACTTTGCTTGTTTCTGATTGTTATCTTATTGTTTTCTTCATTTTTCTTTTAATCTTTTA
208811 ATCTTTTC
66 ATCTTTTC
* *
208819 TTGGTTACTTTGCTTGTTTCTGATTGTTATCTTCTTGTTTTCTTCATTTTTCTTTTAGTCTTTT
1 TTGGTTACTTTGCTTGTTTCTGATTGTTATCTTATTGTTTTCTTCATTTTTCTTTTAATCTTTT
208883 CTTGGTAGAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.66
Consensus pattern (73 bp):
TTGGTTACTTTGCTTGTTTCTGATTGTTATCTTATTGTTTTCTTCATTTTTCTTTTAATCTTTTA
ATCTTTTC
Found at i:208881 original size:65 final size:63
Alignment explanation
Indices: 208769--208888 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 63
208759 TTGTTTCTGA
* *
208769 TTGTTATCTTATTGTTTTCTTCTTTTTTCTTTTAATCTTTTAATCTTTTCTTGGTTACTTTGC
1 TTGTTATCTGATTGTTATCTTCTTTTTTCTTTTAATCTTTTAATCTTTTCTTGGTTACTTTGC
** *
208832 TTGTT-TCTGATTGTTATCTTCTTGTTTTCTTCATTTTTCTTTTAGTCTTTTCTTGGT
1 TTGTTATCTGATTGTTATCTTCTT-TTTTCTT--TTAATCTTTTAATCTTTTCTTGGT
208889 AGAGGATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
62 16 0.33
63 12 0.24
65 21 0.43
ACGTcount: A:0.09, C:0.14, G:0.10, T:0.67
Consensus pattern (63 bp):
TTGTTATCTGATTGTTATCTTCTTTTTTCTTTTAATCTTTTAATCTTTTCTTGGTTACTTTGC
Found at i:214982 original size:24 final size:24
Alignment explanation
Indices: 214954--214999 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
214944 ATATTTATAT
214954 ATTTTATTATTAAAT-TTAAATAAA
1 ATTTT-TTATTAAATATTAAATAAA
* *
214978 ATTTTTTTTTAATTATTAAATA
1 ATTTTTTATTAAATATTAAATA
215000 TTAATTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTTATTAAATATTAAATAAA
Found at i:221432 original size:50 final size:50
Alignment explanation
Indices: 221355--221549 Score: 237
Period size: 50 Copynumber: 3.9 Consensus size: 50
221345 AAAGTCTCAT
* * * *
221355 TTTTACCTAGATGTATCGATACATTTTTTAATGTATTGATACATTCTGTA
1 TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTA
* * * * *
221405 TTTTACCCAAATGTATCGATACGTTTTTCAATTTATCTATATATTCTGTC
1 TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTA
* * *
221455 TTTTACCCGAATGTATCGATACATTTTTCAATGTATCGATGCATTCTGTCT
1 TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGT-A
* * * *
221506 TTTTATCCAAATGTATCAATACATTTTTTAATATATCGATACAT
1 TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACAT
221550 CTAGTTAAAA
Statistics
Matches: 122, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 84 0.69
51 38 0.31
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (50 bp):
TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTA
Done.