Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold677
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: 18889
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:441 original size:21 final size:20
Alignment explanation
Indices: 411--469 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
401 TTATATATTT
411 ATTAAATTTATATATAAAAA
1 ATTAAATTTATATATAAAAA
*
431 ATTAAATTTTATATTATATAAA
1 ATTAAA-TTTATA-TATAAAAA
453 A-TAAATTTATTATATAA
1 ATTAAATTTA-TATATAA
470 TTATTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 14 0.41
21 12 0.35
22 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAATTTATATATAAAAA
Found at i:446 original size:32 final size:33
Alignment explanation
Indices: 377--446 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
367 ATTTTACTTC
* *
377 ATATTAATTTTATAATAATAAAATTTATATATT
1 ATATTAAATTTATAATAATAAAATTTAAATATT
*
410 -TATTAAATTTATATATAA-AAAA-TTAAATTTT
1 ATATTAAATTTATA-ATAATAAAATTTAAATATT
441 ATATTA
1 ATATTA
447 TATAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
31 7 0.22
32 21 0.66
33 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
ATATTAAATTTATAATAATAAAATTTAAATATT
Found at i:454 original size:17 final size:18
Alignment explanation
Indices: 382--469 Score: 58
Period size: 17 Copynumber: 5.0 Consensus size: 18
372 ACTTCATATT
*
382 AATTT-TATAATA-ATAA
1 AATTTATATATTATATAA
*
398 AATTTATATATT-TATTA
1 AATTTATATATTATATAA
* * *
415 AATTTATATATAAAAAATTA
1 AATTTATATAT--TATATAA
435 AATTT-TATATTATATAA
1 AATTTATATATTATATAA
** *
452 AATAAATTTATTATATAA
1 AATTTATATATTATATAA
470 TTATTTTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
16 5 0.09
17 26 0.46
18 11 0.20
19 5 0.09
20 9 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTATATATTATATAA
Found at i:472 original size:26 final size:26
Alignment explanation
Indices: 418--473 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
408 TTTATTAAAT
*
418 TTATATATAAAAAATTAAATTTTATA
1 TTATATATAAAAAATTAAATTATATA
*
444 TTATATA-AAATAAATT-TATTATATAA
1 TTATATATAAA-AAATTAAATTATAT-A
470 TTAT
1 TTAT
474 TTTCAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATATATAAAAAATTAAATTATATA
Found at i:8443 original size:5 final size:5
Alignment explanation
Indices: 8433--8459 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
8423 AAAAAATAAA
8433 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
8460 AAAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:9894 original size:13 final size:14
Alignment explanation
Indices: 9835--9894 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
9825 ATTAAAATAA
9835 AAAAATATTAAATT
1 AAAAATATTAAATT
*
9849 AAAAATATTAAAAAT
1 AAAAATATT-AAATT
9864 AAAAAT-TT--ATT
1 AAAAATATTAAATT
9875 ATCAAAAT-TTAAATT
1 A--AAAATATTAAATT
9890 AAAAA
1 AAAAA
9895 CTGTTACGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.08
13 11 0.28
14 11 0.28
15 14 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATATTAAATT
Found at i:11322 original size:14 final size:14
Alignment explanation
Indices: 11303--11335 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11293 CCCCACCCCC
*
11303 AAAAAAA-AAAAGG
1 AAAAAAAGAAAAAG
11316 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
11330 AAAAAA
1 AAAAAA
11336 GCTACGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:12157 original size:33 final size:33
Alignment explanation
Indices: 12115--12182 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
12105 ACAGAACCCA
12115 AAGACTTTTGATTTCAAACAGGGAAACAAGCTC
1 AAGACTTTTGATTTCAAACAGGGAAACAAGCTC
12148 AAGACTTTTGATTTCAAACAGGGAAACAAGCTC
1 AAGACTTTTGATTTCAAACAGGGAAACAAGCTC
12181 AA
1 AA
12183 ACACGAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (33 bp):
AAGACTTTTGATTTCAAACAGGGAAACAAGCTC
Found at i:12808 original size:30 final size:30
Alignment explanation
Indices: 12752--12914 Score: 216
Period size: 30 Copynumber: 5.6 Consensus size: 30
12742 TGAGATAGTT
* *
12752 TGTCTTCTGATATTCGGC--CG-GGGGGGG
1 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
12779 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
1 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
*
12809 TGTCTTCTGATAATCGGC-----CGGGGGG
1 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
12834 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
1 TGTCTTCTGATAATCGGCGGGGTGGGGGGG
12864 TGTCTTCTGATAATCGGCGGGGTTGGGGAGGGG
1 TGTCTTCTGATAATCGGCGGGG-T-GGG-GGGG
12897 TGTCTTCTGATAATCGGC
1 TGTCTTCTGATAATCGGC
12915 CTGGGGGGGG
Statistics
Matches: 121, Mismatches: 4, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
25 24 0.20
27 17 0.14
29 1 0.01
30 53 0.44
31 1 0.01
32 3 0.02
33 22 0.18
ACGTcount: A:0.11, C:0.16, G:0.44, T:0.29
Consensus pattern (30 bp):
TGTCTTCTGATAATCGGCGGGGTGGGGGGG
Found at i:12851 original size:55 final size:55
Alignment explanation
Indices: 12752--12885 Score: 234
Period size: 55 Copynumber: 2.4 Consensus size: 55
12742 TGAGATAGTT
*
12752 TGTCTTCTGATATTCGGCCGGGGGGGGTGTCTTCTGATAATCGGCGGGGTGGGGGGG
1 TGTCTTCTGATAATCGGCC--GGGGGGTGTCTTCTGATAATCGGCGGGGTGGGGGGG
12809 TGTCTTCTGATAATCGGCCGGGGGGTGTCTTCTGATAATCGGCGGGGTGGGGGGG
1 TGTCTTCTGATAATCGGCCGGGGGGTGTCTTCTGATAATCGGCGGGGTGGGGGGG
12864 TGTCTTCTGATAATCGG-CGGGG
1 TGTCTTCTGATAATCGGCCGGGG
12886 TTGGGGAGGG
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
54 5 0.07
55 53 0.70
57 18 0.24
ACGTcount: A:0.10, C:0.16, G:0.45, T:0.28
Consensus pattern (55 bp):
TGTCTTCTGATAATCGGCCGGGGGGTGTCTTCTGATAATCGGCGGGGTGGGGGGG
Found at i:12873 original size:85 final size:86
Alignment explanation
Indices: 12752--12922 Score: 269
Period size: 85 Copynumber: 2.0 Consensus size: 86
12742 TGAGATAGTT
*
12752 TGTCTTCTGATATTCGGCCGGGGGGGGTGTCTTCTGATAATCGGCGGGG-T-GGG-GGGGTGTCT
1 TGTCTTCTGATAATCGGCCGGGGGGGGTGTCTTCTGATAATCGGCGGGGTTGGGGAGGGGTGTCT
12814 TCTGATAATCGGCC-GGGGGG
66 TCTGATAATCGGCCTGGGGGG
*
12834 TGTCTTCTGATAATCGGCGGGGTGGGGGGGTGTCTTCTGATAATCGGCGGGGTTGGGGAGGGGTG
1 TGTCTTCTGATAATCGGC--CG-GGGGGGGTGTCTTCTGATAATCGGCGGGGTTGGGGAGGGGTG
12899 TCTTCTGATAATCGGCCTGGGGGG
63 TCTTCTGATAATCGGCCTGGGGGG
12923 GGGGAGGGGA
Statistics
Matches: 80, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
82 17 0.21
84 1 0.01
85 29 0.36
86 1 0.01
87 3 0.04
88 23 0.29
89 6 0.08
ACGTcount: A:0.11, C:0.16, G:0.46, T:0.28
Consensus pattern (86 bp):
TGTCTTCTGATAATCGGCCGGGGGGGGTGTCTTCTGATAATCGGCGGGGTTGGGGAGGGGTGTCT
TCTGATAATCGGCCTGGGGGG
Found at i:13130 original size:19 final size:19
Alignment explanation
Indices: 13111--13148 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13101 ATTTTTTATT
13111 TTTA-AAAATA-TTATAAA
1 TTTATAAAATATTTATAAA
*
13128 TTTATATAATATTTATAAA
1 TTTATAAAATATTTATAAA
13147 TT
1 TT
13149 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATAAAATATTTATAAA
Found at i:13400 original size:18 final size:17
Alignment explanation
Indices: 13368--13401 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13358 AAAATATTTT
13368 TTATATTTTTATTTTAA
1 TTATATTTTTATTTTAA
*
13385 TTATTTTTTATATTTTA
1 TTATATTTT-TATTTTA
13402 TTCATGTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATATTTTTATTTTAA
Found at i:13833 original size:17 final size:17
Alignment explanation
Indices: 13792--13827 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
13782 TTTTAACTTC
13792 AAATTTAATATCTATAA
1 AAATTTAATATCTATAA
13809 AAATTTAA-AT-TATAA
1 AAATTTAATATCTATAA
13824 AAAT
1 AAAT
13828 ATTTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTTAATATCTATAA
Found at i:13886 original size:27 final size:30
Alignment explanation
Indices: 13845--13910 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 30
13835 AGATAATAAT
13845 TATTTAATATAATTTAACTAAA-ATTTATA
1 TATTTAATATAATTTAACTAAATATTTATA
*
13874 TATTT-AT-TAATTTAATTAAATATTTATA
1 TATTTAATATAATTTAACTAAATATTTATA
*
13902 AATATTAAT
1 TAT-TTAAT
13911 TTTTTTAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 12 0.38
28 11 0.34
29 7 0.22
30 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTAATATAATTTAACTAAATATTTATA
Found at i:13898 original size:20 final size:21
Alignment explanation
Indices: 13873--13911 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
13863 TAAAATTTAT
*
13873 ATATTTATTAAT-TTAATTAA
1 ATATTTATAAATATTAATTAA
13893 ATATTTATAAATATTAATT
1 ATATTTATAAATATTAATT
13912 TTTTTAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTTATAAATATTAATTAA
Found at i:15049 original size:19 final size:20
Alignment explanation
Indices: 15027--15086 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 20
15017 TTATATATTT
15027 ATTAAA-TTATTATATAAAA
1 ATTAAATTTATTATATAAAA
15046 ATTAAATTTATATATTATATAAA
1 ATTAAATTTAT-TA-TATA-AAA
* *
15069 ATAAAATTTATTGTATAA
1 ATTAAATTTATTATATAA
15087 CTATTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 6 0.17
20 5 0.14
21 6 0.17
22 5 0.14
23 13 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTAAATTTATTATATAAAA
Found at i:15075 original size:23 final size:24
Alignment explanation
Indices: 15034--15079 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
15024 TTTATTAAAT
*
15034 TATTATATAAAAATTAAATTTATA
1 TATTATATAAAAATAAAATTTATA
15058 TATTATAT-AAAATAAAATTTAT
1 TATTATATAAAAATAAAATTTAT
15080 TGTATAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTATATAAAAATAAAATTTATA
Found at i:15350 original size:2 final size:2
Alignment explanation
Indices: 15338--15371 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
15328 TTCTCTTAGC
15338 AT AT CAT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15372 CGCAACCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16634 original size:14 final size:14
Alignment explanation
Indices: 16615--16652 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16605 TAAAAAAATG
16615 TTATTATTTTATTA
1 TTATTATTTTATTA
*
16629 TTATTATTTATTTTA
1 TTATTATTT-TATTA
16644 TT-TTATTTT
1 TTATTATTTT
16653 TTTGCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.68
15 6 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTATTTTATTA
Done.