Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6161.1
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: 13559
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.32
Warning! 662 characters in sequence are not A, C, G, or T
Found at i:705 original size:15 final size:15
Alignment explanation
Indices: 685--741 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
675 CGATGAATTT
*
685 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
700 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
715 ATTGAAATTATATTG
1 ATTGAAATTATATTG
730 ATTG-AATTATAT
1 ATTGAAATTATAT
742 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:1144 original size:23 final size:23
Alignment explanation
Indices: 1114--1200 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 23
1104 ACTTTATCGA
1114 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
1137 TCAGGCAC-CTAGTGTGTCGTA--
1 TCAGGCACTTTA-TGTGTCGTATT
* **
1158 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
1180 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
1201 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 31 0.60
22 4 0.08
23 17 0.33
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:2296 original size:23 final size:23
Alignment explanation
Indices: 2270--2347 Score: 57
Period size: 27 Copynumber: 3.2 Consensus size: 23
2260 CATGATAGAT
2270 TCATGCATTTATATAAGATAACA
1 TCATGCATTTATATAAGATAACA
* * * * *
2293 TCATCACATATCTATAACCATGATATA
1 TCAT-GCATTTATATAA-GAT-A-ACA
*
2320 TTCATGCATTTATATAAGATAACG
1 -TCATGCATTTATATAAGATAACA
2344 TCAT
1 TCAT
2348 CACATATCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
23 8 0.21
24 10 0.26
25 3 0.08
26 3 0.08
27 11 0.28
28 4 0.10
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (23 bp):
TCATGCATTTATATAAGATAACA
Found at i:2323 original size:51 final size:51
Alignment explanation
Indices: 2260--2360 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
2250 GACATATTTT
2260 CATGATAGATTCATGCATTTATATAAGATAACATCATCACATATCTATAAC
1 CATGATAGATTCATGCATTTATATAAGATAACATCATCACATATCTATAAC
* *
2311 CATGATATATTCATGCATTTATATAAGATAACGTCATCACATATCTATAA
1 CATGATAGATTCATGCATTTATATAAGATAACATCATCACATATCTATAA
2361 TCAGGTTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (51 bp):
CATGATAGATTCATGCATTTATATAAGATAACATCATCACATATCTATAAC
Found at i:2567 original size:32 final size:32
Alignment explanation
Indices: 2526--2588 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2516 GACCTCCGAG
*
2526 CTCTTAACACTACAAACAGGGAAAAATGAAAT
1 CTCTTAACACTACAAACAGGGAAAAAGGAAAT
2558 CTCTTAACACTACAAACAGGGAAAAAGGAAA
1 CTCTTAACACTACAAACAGGGAAAAAGGAAA
2589 CGGGGTAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (32 bp):
CTCTTAACACTACAAACAGGGAAAAAGGAAAT
Found at i:3689 original size:35 final size:35
Alignment explanation
Indices: 3643--3712 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3633 GATTTTTGGT
*
3643 TTAGCCAATCAGTACAGTTTATTCTTCAAAGTCAC
1 TTAGCCAATCAGTACAGTTTATTATTCAAAGTCAC
3678 TTAGCCAATCAGTACAGTTTATTATTCAAAGTCAC
1 TTAGCCAATCAGTACAGTTTATTATTCAAAGTCAC
3713 CCCTGTTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (35 bp):
TTAGCCAATCAGTACAGTTTATTATTCAAAGTCAC
Found at i:11170 original size:41 final size:41
Alignment explanation
Indices: 11125--11203 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
11115 TTCAAGATTT
11125 TTGGTTTAGCCAATCAGTACAGTTTATTATTCAAAGTCACC
1 TTGGTTTAGCCAATCAGTACAGTTTATTATTCAAAGTCACC
*
11166 TTGGTTTAGCCAATCAGTACAGTTTATTCTTCAAAGTC
1 TTGGTTTAGCCAATCAGTACAGTTTATTATTCAAAGTC
11204 TCTCCTGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (41 bp):
TTGGTTTAGCCAATCAGTACAGTTTATTATTCAAAGTCACC
Done.