Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1661
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: 28150
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:1054 original size:18 final size:17
Alignment explanation
Indices: 1021--1059 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1011 TTGTATAAAT
1021 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1039 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1056 TGTG
1 TGTG
1060 GAAGGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1176 original size:8 final size:8
Alignment explanation
Indices: 1163--1191 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1153 CACTAGAGAC
1163 CAGTGTTA
1 CAGTGTTA
1171 CAGTGTTA
1 CAGTGTTA
1179 CAGTGTTA
1 CAGTGTTA
1187 CAGTG
1 CAGTG
1192 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:1305 original size:23 final size:23
Alignment explanation
Indices: 1278--1353 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
1268 AGTGTTATTG
1278 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1301 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1324 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1347 ATCAGTG
1 ATCAGTG
1354 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:8376 original size:18 final size:17
Alignment explanation
Indices: 8343--8381 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
8333 TTGTATAAAT
8343 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
8361 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
8378 TGTG
1 TGTG
8382 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:8499 original size:8 final size:8
Alignment explanation
Indices: 8486--8514 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
8476 CACTAGAGAC
8486 CAGTGTTA
1 CAGTGTTA
8494 CAGTGTTA
1 CAGTGTTA
8502 CAGTGTTA
1 CAGTGTTA
8510 CAGTG
1 CAGTG
8515 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:8628 original size:23 final size:23
Alignment explanation
Indices: 8601--8676 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
8591 AGTGTTATTG
8601 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
8624 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
8647 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
8670 ATCAGTG
1 ATCAGTG
8677 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:12633 original size:72 final size:72
Alignment explanation
Indices: 12546--13065 Score: 601
Period size: 72 Copynumber: 7.2 Consensus size: 72
12536 TTTGATTAAA
12546 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
1 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
12611 GGTTATT
66 GGTTATT
* * * * * ** *
12618 GGATATGTCCAACTGTT-TCAAACT-CTTCATGTTCCCCCAGTCTA-G-GGGATAGGACCACGAA
1 GGATAAGTCCAACTGTTCT-AAATTGGTT-AAGTTGCCTAAG-GTAGGAGGGATAGGACCACGAA
12679 TTTGGTTATT
63 TTTGGTTATT
*
12689 GGAGAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
1 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
12754 GGTTATT
66 GGTTATT
* * * * * ** *
12761 GGATATGTCCAACTGTT-TCAAACT-CTTCATGTTCCCCCAGTCTAGG-GGGATAGGACCACGAA
1 GGATAAGTCCAACTGTTCT-AAATTGGTT-AAGTTGCCTAAG-GTAGGAGGGATAGGACCACGAA
12823 TTTGGTTATT
63 TTTGGTTATT
* *
12833 GGAGAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGAACCACGAATTT
1 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
12898 GGTTATT
66 GGTTATT
* * * * * ** * * **
12905 GGATAGGTCCAACTGTT-TCAAACT-CTTCATGTTCCCCCAGTCTAAG-GGGATAATACCACGAA
1 GGATAAGTCCAACTGTTCT-AAATTGGTT-AAGTTGCCTAAG-GTAGGAGGGATAGGACCACGAA
12967 TTTGGTTATT
63 TTTGGTTATT
12977 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
1 GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
13042 GGTTATT
66 GGTTATT
* *
13049 GGATAGGTCTAACTGTT
1 GGATAAGTCCAACTGTT
13066 TCAAACTCTT
Statistics
Matches: 368, Mismatches: 61, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
70 2 0.01
71 70 0.19
72 281 0.76
73 15 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (72 bp):
GGATAAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTT
GGTTATT
Found at i:12922 original size:144 final size:144
Alignment explanation
Indices: 12550--13101 Score: 1025
Period size: 144 Copynumber: 3.8 Consensus size: 144
12540 ATTAAAGGAT
12550 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
1 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
*
12615 ATTGGATATGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTA-GGGGATAGGACCACGAA
66 ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAGGACCACGAA
12679 TTTGGTTATTGGAG
131 TTTGGTTATTGGAG
12693 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
1 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
*
12758 ATTGGATATGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAGGACCACGAA
66 ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAGGACCACGAA
12823 TTTGGTTATTGGAG
131 TTTGGTTATTGGAG
*
12837 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGAACCACGAATTTGGTT
1 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
* **
12902 ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAAGGGGATAATACCACGAA
66 ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAGGACCACGAA
*
12967 TTTGGTTATTGGAT
131 TTTGGTTATTGGAG
12981 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
1 AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
*
13046 ATTGGATAGGTCTAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAG
66 ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAG
13102 AACCGGTAAT
Statistics
Matches: 398, Mismatches: 10, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
143 112 0.28
144 286 0.72
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (144 bp):
AAGTCCAACTGTTCTAAATTGGTTAAGTTGCCTAAGGTAGGAGGGATAGGACCACGAATTTGGTT
ATTGGATAGGTCCAACTGTTTCAAACTCTTCATGTTCCCCCAGTCTAGGGGGATAGGACCACGAA
TTTGGTTATTGGAG
Found at i:13907 original size:16 final size:15
Alignment explanation
Indices: 13876--13905 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13866 GAGTTTTCAT
*
13876 TTTTTTATTAAAAAA
1 TTTTCTATTAAAAAA
13891 TTTTCTATTAAAAAA
1 TTTTCTATTAAAAAA
13906 ATAAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTCTATTAAAAAA
Found at i:15418 original size:22 final size:21
Alignment explanation
Indices: 15374--15416 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
15364 CAAGGTAAAA
15374 ATTAATTTACAATTAAATTTT
1 ATTAATTTACAATTAAATTTT
15395 ATTAATTATACAAATTAAATTT
1 ATTAATT-TAC-AATTAAATTT
15417 ATGATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATTTACAATTAAATTTT
Done.