Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1413
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: 31129
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:4774 original size:17 final size:18
Alignment explanation
Indices: 4752--4803 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
4742 AAGTGTACAG
4752 ATTAATTTTTTAAAAAA-
1 ATTAATTTTTTAAAAAAT
**
4769 ATTAATTTAAATAATAAAAT
1 ATTAATTT-TTTAA-AAAAT
4789 ATTAATTTTTTAAAA
1 ATTAATTTTTTAAAA
4804 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 8 0.29
18 5 0.18
19 7 0.25
20 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATTTTTTAAAAAAT
Found at i:12190 original size:21 final size:20
Alignment explanation
Indices: 12166--12225 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
12156 TTTTTTATTA
12166 TATATTATTAAACTATAATTT
1 TATATTATTAAA-TATAATTT
* * *
12187 TATATTAAT-ATTAAAATTT
1 TATATTATTAAATATAATTT
12206 T-TATTATTAAATAATAATTT
1 TATATTATTAAAT-ATAATTT
12226 AAACGAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 6 0.19
19 10 0.32
20 7 0.23
21 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTATTAAATATAATTT
Found at i:13107 original size:21 final size:23
Alignment explanation
Indices: 13082--13123 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13072 ATTCGAGTTA
13082 ATATC-AAG-CATAAATATTTAT
1 ATATCAAAGACATAAATATTTAT
*
13103 ATATCAAAGATATAAATATTT
1 ATATCAAAGACATAAATATTT
13124 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (23 bp):
ATATCAAAGACATAAATATTTAT
Found at i:14395 original size:47 final size:47
Alignment explanation
Indices: 14335--14427 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
14325 AAAACATTAT
*
14335 ATTATATATAATGTGTACACATGACTTGGAATAAATACTTCAACAAC
1 ATTATATATAATGTGTACACATAACTTGGAATAAATACTTCAACAAC
14382 ATTATATATAATGTGTACACATAACTTGGAATAAATACTTCAACAA
1 ATTATATATAATGTGTACACATAACTTGGAATAAATACTTCAACAA
14428 TTGGTTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (47 bp):
ATTATATATAATGTGTACACATAACTTGGAATAAATACTTCAACAAC
Found at i:14889 original size:20 final size:19
Alignment explanation
Indices: 14854--14892 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
14844 TAATTAAATT
14854 TTAATAATATATATTTATA
1 TTAATAATATATATTTATA
14873 TTAATAA-ATAATAATTTATA
1 TTAATAATAT-AT-ATTTATA
14893 CTAAATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 9 0.50
20 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAATATATATTTATA
Found at i:15362 original size:11 final size:13
Alignment explanation
Indices: 15345--15376 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
15335 TATATAAAAA
15345 AATAAAATTT-TT
1 AATAAAATTTATT
15357 AA-AAAATTTATT
1 AATAAAATTTATT
15369 AATAAAAT
1 AATAAAAT
15377 AATAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.39
12 6 0.33
13 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAAAATTTATT
Found at i:17225 original size:2 final size:2
Alignment explanation
Indices: 17212--17244 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17202 AATTGCAGAA
*
17212 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17245 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18659 original size:24 final size:25
Alignment explanation
Indices: 18609--18668 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
18599 ATGCATCTCA
*
18609 TTAA-TTTTAAGAAAATATATAAGT
1 TTAATTTTTAAGAAAATACATAAGT
*
18633 TT-ATTTTTAATAAAATAGCATAA-T
1 TTAATTTTTAAGAAAATA-CATAAGT
18657 TTAATTTATTAA
1 TTAATTT-TTAA
18669 AATTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 17 0.57
25 8 0.27
26 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (25 bp):
TTAATTTTTAAGAAAATACATAAGT
Found at i:21968 original size:29 final size:29
Alignment explanation
Indices: 21936--21991 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
21926 TATTTTAAAT
* *
21936 AATAAA-ATTTATATTTATATTAAATAATA
1 AATAAAGATTTAAATTT-TAATAAATAATA
21965 AATAAAGATTTAAATTTTAATAAATAA
1 AATAAAGATTTAAATTTTAATAAATAA
21992 ATTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
AATAAAGATTTAAATTTTAATAAATAATA
Found at i:22008 original size:13 final size:14
Alignment explanation
Indices: 21975--22008 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21965 AATAAAGATT
21975 TAAATTTTAATAAA
1 TAAATTTTAATAAA
21989 TAAATTTTAATAAA
1 TAAATTTTAATAAA
22003 -AAATTT
1 TAAATTT
22009 GTTAAAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATTTTAATAAA
Found at i:22649 original size:21 final size:18
Alignment explanation
Indices: 22619--22687 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 18
22609 TATTTTTATT
22619 TAAATTTAATTATAAACATA
1 TAAATTTAA-TATAAA-ATA
22639 TAAATATTAATATAAAATA
1 TAAAT-TTAATATAAAATA
**
22658 TATTTTTAATATAATAAATA
1 TAAATTTAATAT-A-AAATA
22678 GTAAATTTAA
1 -TAAATTTAA
22688 ATTTATTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 16 0.39
21 11 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATTTAATATAAAATA
Found at i:26232 original size:45 final size:45
Alignment explanation
Indices: 26161--26247 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
26151 GATTCCAGTG
* * * *
26161 CCAATCAAGATGGCGACAAGGGCTATCCACGATGGGCTATAAGTA
1 CCAATCAAGATGGCGAAAAGGACTATCAACGAGGGGCTATAAGTA
26206 CCAATCAAGATGGCGAAAAGGACTATCAACGAGGGGCTATAA
1 CCAATCAAGATGGCGAAAAGGACTATCAACGAGGGGCTATAA
26248 AATGGACCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (45 bp):
CCAATCAAGATGGCGAAAAGGACTATCAACGAGGGGCTATAAGTA
Done.