Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2184
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: 7516
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Found at i:3536 original size:49 final size:47
Alignment explanation
Indices: 3446--3904 Score: 739
Period size: 47 Copynumber: 9.7 Consensus size: 47
3436 TTAGGATTCT
* *
3446 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
3493 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
3542 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
3591 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
3638 ATGTGATGAATGTGAAAGTGTATA-A--T-ATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
3681 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
3728 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
3775 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
3822 ATGTGATGAATGTGAAAGTGTAATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGT-ATATATGTGATAAGGCCTAATGGCCG
* * *
3870 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
3905 TCCCGAAGGG
Statistics
Matches: 392, Mismatches: 12, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
43 41 0.10
44 2 0.01
46 3 0.01
47 211 0.54
48 40 0.10
49 95 0.24
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:3801 original size:184 final size:187
Alignment explanation
Indices: 3476--3904 Score: 720
Period size: 184 Copynumber: 2.3 Consensus size: 187
3466 CATATATGTG
3476 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC
1 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCC
3541 GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
64 GATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
3606 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-ATA-AT
128 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATAT
3664 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
1 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
3729 TGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 TGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
3793 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATAT
131 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATAT
* * * * * * *
3850 GTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 AT-A-A-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
3905 TCCCGAAGGG
Statistics
Matches: 229, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
184 95 0.41
185 3 0.01
186 50 0.22
187 1 0.00
188 38 0.17
189 42 0.18
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (187 bp):
ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
TGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATAT
Found at i:4718 original size:25 final size:25
Alignment explanation
Indices: 4689--4737 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4679 CCTGGCTGTG
4689 CTTAGTACTTATCTAAATGAATGAT
1 CTTAGTACTTATCTAAATGAATGAT
4714 CTTAGTACTTATCTAAATGAATGA
1 CTTAGTACTTATCTAAATGAATGA
4738 CCTTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
CTTAGTACTTATCTAAATGAATGAT
Found at i:5890 original size:39 final size:39
Alignment explanation
Indices: 5844--5948 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 39
5834 AATTTTTATT
* *
5844 TATTTTTATATTTTTATATAATTTTTTGATAATCTTTTAA
1 TATTTTTATATTTTTATATAATTTTTTAATAAT-TCTTAA
*
5884 T-TTTTTATTTTTTTACATATTTAA-TTTTTAATAATTCTTAA
1 TATTTTTATATTTTT--ATA--TAATTTTTTAATAATTCTTAA
5925 TATTTTTA-ATTTATT-TATAATTTT
1 TATTTTTATATTT-TTATATAATTTT
5949 GTACTCATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
37 3 0.06
38 3 0.06
39 14 0.26
40 1 0.02
41 12 0.22
42 18 0.33
43 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (39 bp):
TATTTTTATATTTTTATATAATTTTTTAATAATTCTTAA
Found at i:6447 original size:22 final size:22
Alignment explanation
Indices: 6395--6471 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
6385 CAAATAAATC
6395 ATTTCTCT-AATATT-CTCTCTAA
1 ATTTCTCTCAAT-TTCCTCTC-AA
6417 GA-TTCTCTCAATTTCCTCTC-A
1 -ATTTCTCTCAATTTCCTCTCAA
*
6438 ATTTGCTCTCAATTTCCTTTCAA
1 ATTT-CTCTCAATTTCCTCTCAA
6461 ATTTCTCTCAA
1 ATTTCTCTCAA
6472 ATCCCTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 30 0.62
23 14 0.29
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTCTCAA
Found at i:6473 original size:11 final size:11
Alignment explanation
Indices: 6421--6471 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
6411 CTCTAAGATT
6421 CTCTCAATTTC
1 CTCTCAATTTC
*
6432 CTCTCAATTTG
1 CTCTCAATTTC
6443 CTCTCAATTTC
1 CTCTCAATTTC
*
6454 CTTTCAAATTT-
1 CTCTC-AATTTC
6465 CTCTCAA
1 CTCTCAA
6472 ATCCCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 2 0.06
11 28 0.80
12 5 0.14
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:6932 original size:7 final size:7
Alignment explanation
Indices: 6920--6945 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6910 TAGTCGATTG
6920 GTATTTA
1 GTATTTA
6927 GTATTTA
1 GTATTTA
6934 GTATTTA
1 GTATTTA
6941 GTATT
1 GTATT
6946 ATGTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Done.