Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1007
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: 34451
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:7570 original size:79 final size:79
Alignment explanation
Indices: 7430--7651 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 79
7420 TATTCGAATG
* * * **
7430 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGC
7495 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* *
7511 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGC
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGT-CCGAAGGC
7574 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* * * *
7590 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG
7652 TATGTGATTC
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
78 1 0.01
79 64 0.52
80 45 0.37
81 12 0.10
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:7632 original size:40 final size:40
Alignment explanation
Indices: 7430--7637 Score: 262
Period size: 40 Copynumber: 5.2 Consensus size: 40
7420 TATTCGAATG
* * *
7430 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
*
7471 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
7511 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
7550 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
7590 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
7630 ATATCCGG
1 ATATCCGG
7638 TTAAATTCCG
Statistics
Matches: 147, Mismatches: 14, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
39 37 0.25
40 81 0.55
41 28 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:10522 original size:47 final size:47
Alignment explanation
Indices: 10448--10603 Score: 249
Period size: 47 Copynumber: 3.3 Consensus size: 47
10438 TCCTTCGGGA
* * *
10448 CTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCAGCCATTAGGC
** *
10495 CTTATCACATATACACACTTTCACATTCATCACATTTGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCAGCCATTAGGC
*
10542 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATCAGCCATTAGGC
10589 CTTATCACATATACA
1 CTTATCACATATACA
10604 TATCTTGTAC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 99 1.00
ACGTcount: A:0.30, C:0.31, G:0.06, T:0.33
Consensus pattern (47 bp):
CTTATCACATATACACACTTTCACATTCATCACATCAGCCATTAGGC
Found at i:12455 original size:13 final size:13
Alignment explanation
Indices: 12437--12461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12427 TACTAAATTT
12437 TCATGGATTCAAA
1 TCATGGATTCAAA
12450 TCATGGATTCAA
1 TCATGGATTCAA
12462 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:17080 original size:27 final size:27
Alignment explanation
Indices: 17050--17105 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
17040 AAGTGTAGTG
17050 AATGAGAAATTTGACAAGTATGCGCTT
1 AATGAGAAATTTGACAAGTATGCGCTT
*
17077 AATGAGAAATTTGACAGGTATGCGCTT
1 AATGAGAAATTTGACAAGTATGCGCTT
17104 AA
1 AA
17106 ATCCTCAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (27 bp):
AATGAGAAATTTGACAAGTATGCGCTT
Found at i:18652 original size:30 final size:30
Alignment explanation
Indices: 18617--18673 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
18607 CCGAAGCTAA
*
18617 TTAAATCGCACACTTAGTGCCAAAGCTAGT
1 TTAAATCACACACTTAGTGCCAAAGCTAGT
18647 TTAAATCACACACTTAGTGCCAAAGCT
1 TTAAATCACACACTTAGTGCCAAAGCT
18674 TCCGATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (30 bp):
TTAAATCACACACTTAGTGCCAAAGCTAGT
Found at i:25479 original size:46 final size:45
Alignment explanation
Indices: 25421--25540 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 45
25411 TGTAACCCGC
* * * * *
25421 CCATAAGCGAACTCAGACTCAACTCAATGC-GCTCGGGCGTTCGCAT
1 CCATAAGTGAACTC-GACTCAACTCAA-CCAGCTCAGACATTCGCAT
* *
25467 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCAGACATTTGCAT
1 CCATAAGTGAACTC-GACTCAACTCAACCAGCTCAGACATTCGCAT
25513 CCATAAGTGAACTCGAACTCAACTCAAC
1 CCATAAGTGAACTCG-ACTCAACTCAAC
25541 GAGTTCGGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.03
46 62 0.97
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGACTCAACTCAACCAGCTCAGACATTCGCAT
Found at i:32998 original size:46 final size:46
Alignment explanation
Indices: 32906--33030 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 46
32896 TGTAACCCGC
* * * * * *
32906 CCATAAGCGAACTCAGACTC-ACTCAACGCAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAAC-CAGTTCAGACATTCGCAT
*
32952 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCAGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCAGACATTCGCAT
* *
32998 CCA-AAGTGAACTCGAACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACCAGTTC
33031 GGATGCTCAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 28 0.41
46 34 0.49
47 7 0.10
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACCAGTTCAGACATTCGCAT
Done.