Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_969
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: 39969
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1785 original size:20 final size:20
Alignment explanation
Indices: 1760--1802 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1750 TTTTATTATG
1760 TTTAATGACTTGCTGATCAT
1 TTTAATGACTTGCTGATCAT
1780 TTTAATGACTTGCTGATCAT
1 TTTAATGACTTGCTGATCAT
1800 TTT
1 TTT
1803 TCCCTTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTAATGACTTGCTGATCAT
Found at i:2755 original size:43 final size:42
Alignment explanation
Indices: 2708--2825 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
2698 TGGGATCACG
** * *
2708 TATCGACGCCAATAGCCCAGTTATGGTCTTATACGAAGTCTCA
1 TATCGACGCC-ATAGCCCAAATATGGTCTTACACAAAGTCTCA
* *
2751 TATCGATGCCATATCCCAAATATGGTCTTACACAAAGTCTCA
1 TATCGACGCCATAGCCCAAATATGGTCTTACACAAAGTCTCA
* * * *
2793 TA-CTGATGCCATATCCTAGATATGGTCTTACAC
1 TATC-GACGCCATAGCCCAAATATGGTCTTACAC
2826 GTAGTCTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 56 0.85
43 9 0.14
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
TATCGACGCCATAGCCCAAATATGGTCTTACACAAAGTCTCA
Found at i:2832 original size:42 final size:42
Alignment explanation
Indices: 2729--2832 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
2719 ATAGCCCAGT
*
2729 TATGGTCTTATACGAAGTCTCATATCGATGCCATATCCCAAA
1 TATGGTCTTACACGAAGTCTCATATCGATGCCATATCCCAAA
* * *
2771 TATGGTCTTACACAAAGTCTCATA-CTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAGTCTCATATC-GATGCCATATCCCAAA
*
2813 TATGGTCTTACACGTAGTCT
1 TATGGTCTTACACGAAGTCT
2833 TATAACCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 54 0.98
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (42 bp):
TATGGTCTTACACGAAGTCTCATATCGATGCCATATCCCAAA
Found at i:15446 original size:47 final size:47
Alignment explanation
Indices: 15377--15543 Score: 209
Period size: 47 Copynumber: 3.6 Consensus size: 47
15367 ATTTGAGTTT
*
15377 CGAACTCATTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
* * *
15424 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC-T-
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
*
15470 CGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
*
15517 TGAACTCGTTGAGTTGAGTCCGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
15544 ACTTATGGAT
Statistics
Matches: 101, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 4 0.04
46 27 0.27
47 52 0.51
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
Found at i:15492 original size:46 final size:46
Alignment explanation
Indices: 15428--15598 Score: 233
Period size: 46 Copynumber: 3.7 Consensus size: 46
15418 GGCATCCGAA
15428 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
* * * *
15474 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC-TC-GAG
15521 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
15567 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGA
15599 CAGGTTACAT
Statistics
Matches: 108, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 4 0.04
46 59 0.55
47 27 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
Found at i:15543 original size:93 final size:93
Alignment explanation
Indices: 15376--15589 Score: 401
Period size: 93 Copynumber: 2.3 Consensus size: 93
15366 TATTTGAGTT
* *
15376 TCGAACTCATTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGA
1 TCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGA
15441 GTCCGAGTTCACTTATGGATGCGAACGC
66 GTCCGAGTTCACTTATGGATGCGAACGC
*
15469 TCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCTGAACTCGTTGAGTTGA
1 TCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGA
15534 GTCCGAGTTCACTTATGGATGCGAACGC
66 GTCCGAGTTCACTTATGGATGCGAACGC
15562 TCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCGAGCTCGTTGAGTTGAGTCCGAGTTC
15590 ACTTATGGAC
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 118 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
TCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGA
GTCCGAGTTCACTTATGGATGCGAACGC
Found at i:20316 original size:40 final size:40
Alignment explanation
Indices: 20271--20462 Score: 244
Period size: 40 Copynumber: 4.8 Consensus size: 40
20261 ATAACCACAA
* * *
20271 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
*
20311 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
* * *
20351 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* * *
20391 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATC-GCTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* *
20431 GCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT
20463 CATTCAAATG
Statistics
Matches: 140, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 135 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
Found at i:28716 original size:40 final size:40
Alignment explanation
Indices: 28671--28862 Score: 244
Period size: 40 Copynumber: 4.8 Consensus size: 40
28661 ATAACCACAA
* * *
28671 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
*
28711 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
* * *
28751 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* * *
28791 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATC-GCTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* *
28831 GCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT
28863 CATTCAAATG
Statistics
Matches: 140, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 135 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
Found at i:36391 original size:42 final size:42
Alignment explanation
Indices: 36267--36427 Score: 180
Period size: 42 Copynumber: 3.8 Consensus size: 42
36257 CACACAGTAC
*
36267 CATACCAATGCCATATCCCAGATATGGTCTTACATG-GGATCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGAAG-TCT
* * * * * *
36309 CATACCGATGCCAATAGCCCAGCTATGGCCTTATACGAAGTCT
1 CATACCAATGCC-ATATCCCAGATATGGTCTTACATGAAGTCT
* * *
36352 CATATCAATGTCATATCCTAGATATGGTCTTACATGAAGTCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGAAGTCT
** *
36394 CATACTGATGCCATATCCTAGATATGGTCTTACA
1 CATACCAATGCCATATCCCAGATATGGTCTTACA
36428 CGTAGTCTTA
Statistics
Matches: 97, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 65 0.67
43 31 0.32
44 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
CATACCAATGCCATATCCCAGATATGGTCTTACATGAAGTCT
Found at i:39709 original size:63 final size:63
Alignment explanation
Indices: 39622--39751 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 63
39612 CAACCTAATT
* * *
39622 TATAACTTTAAATTTGGTAATTCAAGCTCAATTAAGATGCGCCTCATTCTTGATGTGATAAGGA
1 TATAACTTTAAATTTGGTAATTCAAACTCAATTAAGATGCCCCTCATTC-TGATGTGATAAGAA
* *
39686 TATAAC-TTAAATTTGGTATTTCAAACTCTATTAAGATGCCCCTCATTCTGATGTGATAAGAA
1 TATAACTTTAAATTTGGTAATTCAAACTCAATTAAGATGCCCCTCATTCTGATGTGATAAGAA
39748 TATA
1 TATA
39752 TCCATGTGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 17 0.28
63 38 0.62
64 6 0.10
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (63 bp):
TATAACTTTAAATTTGGTAATTCAAACTCAATTAAGATGCCCCTCATTCTGATGTGATAAGAA
Done.