Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2253
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: 50929
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:38 original size:22 final size:24
Alignment explanation
Indices: 3--80 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
1 TG
* *
3 TGAGCTACCTGATA-GG-TCTTTA
1 TGAGCTTCCCGATATGGTTCTTTA
*
25 TGAGCTTCCCGATATGGTTCTTTG
1 TGAGCTTCCCGATATGGTTCTTTA
* * * *
49 TGAACTTCTCGATTATGGCTC-ATA
1 TGAGCTTCCCGA-TATGGTTCTTTA
73 TGAGCTTC
1 TGAGCTTC
81 TCGTTATATA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 12 0.27
23 2 0.05
24 23 0.52
25 7 0.16
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (24 bp):
TGAGCTTCCCGATATGGTTCTTTA
Found at i:4914 original size:12 final size:11
Alignment explanation
Indices: 4894--4931 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
4884 TTCTTTTTTC
4894 TTTTT-TTTAT
1 TTTTTATTTAT
4904 TTTTTAATTTAT
1 TTTTT-ATTTAT
4916 TTATTTATTTAT
1 TT-TTTATTTAT
4928 TTTT
1 TTTT
4932 GGTTAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.20
11 2 0.08
12 15 0.60
13 3 0.12
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:5047 original size:96 final size:98
Alignment explanation
Indices: 4923--5119 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 98
4913 TATTTATTTA
* *
4923 TTTATTTTTGGTTAAGAATATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
*
4988 CCCCGGTTACTCAGCCCAACATACTCTTAA-TT
66 CCCCGATTACTCAGCCCAACATACTCTTAAGTT
* *
5020 TTTA-TTTTGCTTAAGAACATAAC-GAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTC
1 TTTATTTTTGCTTAAGAACAT-ACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCC
*
5083 ACCCCGATTACTCAGCCCAACATATTCTTAAGTT
65 ACCCCGATTACTCAGCCCAACATACTCTTAAGTT
5117 TTT
1 TTT
5120 TTATTTCCGA
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
96 81 0.88
97 11 0.12
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (98 bp):
TTTATTTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
CCCCGATTACTCAGCCCAACATACTCTTAAGTT
Found at i:7151 original size:16 final size:16
Alignment explanation
Indices: 7130--7164 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7120 CCGACAAATC
7130 CTGAAATG-CAGAAAAG
1 CTGAAATGCCA-AAAAG
7146 CTGAAATGCCAAAAAG
1 CTGAAATGCCAAAAAG
7162 CTG
1 CTG
7165 GAAGTTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (16 bp):
CTGAAATGCCAAAAAG
Found at i:7469 original size:27 final size:28
Alignment explanation
Indices: 7380--7481 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
7370 ATTTCATGAC
7380 TATGAATGTGATTGGGCCTGATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
* *
7408 TATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
*
7436 TATGAATGTGATTGTGCC-GATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
*
7463 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
7482 AAAGGGGCCA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.36
28 42 0.64
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATTGGCCA
Found at i:7490 original size:56 final size:56
Alignment explanation
Indices: 7380--7498 Score: 168
Period size: 56 Copynumber: 2.1 Consensus size: 56
7370 ATTTCATGAC
* * *
7380 TATGAATGTGATTGGGCCTGATTGGCCATATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCATATGAAAGAGATTGGGCCTAAGGGGCCA
* *
7436 TATGAATGTGATTGTGCC-GATTGGCCATATGAATGAGATTGGGCCTAAAGGGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCATATGAAAGAGATTGGGCCT-AAGGGGCCA
*
7492 AATGAAT
1 TATGAAT
7499 AAGTATGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 26 0.46
56 30 0.54
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (56 bp):
TATGAATGTGATTGGGCCTGATTGGCCATATGAAAGAGATTGGGCCTAAGGGGCCA
Found at i:16280 original size:16 final size:16
Alignment explanation
Indices: 16259--16289 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16249 CGACAAATCC
16259 TGAAATGCAGAAAAGT
1 TGAAATGCAGAAAAGT
*
16275 TGAAATGCCGAAAAG
1 TGAAATGCAGAAAAG
16290 CTGGAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.16
Consensus pattern (16 bp):
TGAAATGCAGAAAAGT
Found at i:16556 original size:28 final size:27
Alignment explanation
Indices: 16512--16611 Score: 137
Period size: 28 Copynumber: 3.6 Consensus size: 27
16502 TCATGACTAC
16512 GAATGTGATTGGGCCTGACTGGCCATAT
1 GAATGTGATTGGGCCTGA-TGGCCATAT
*
16540 GAAAGTGATTGGGCCTGATGGGCCATAT
1 GAATGTGATTGGGCCTGAT-GGCCATAT
* *
16568 GAATGTGATTGTGCCCGATTGGCCATAT
1 GAATGTGATTGGGCCTGA-TGGCCATAT
*
16596 GAATGAGATTGGGCCT
1 GAATGTGATTGGGCCT
16612 AAAGGGGCCA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
27 1 0.02
28 61 0.97
29 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (27 bp):
GAATGTGATTGGGCCTGATGGCCATAT
Found at i:18345 original size:25 final size:27
Alignment explanation
Indices: 18320--18390 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 27
18310 CCCAAACAAA
18320 ATAAAGTAATAAATAAT-AA-AATAAA
1 ATAAAGTAATAAATAATAAATAATAAA
*
18345 ATAAAGTAATGAATAAATAAATAATAAA
1 ATAAAGTAATAAAT-AATAAATAATAAA
18373 ATAAAG-AA-AAATAA-AAAT
1 ATAAAGTAATAAATAATAAAT
18391 TGGGTTACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.10
25 15 0.37
26 6 0.15
27 4 0.10
28 12 0.29
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (27 bp):
ATAAAGTAATAAATAATAAATAATAAA
Found at i:18390 original size:16 final size:16
Alignment explanation
Indices: 18330--18388 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
18320 ATAAAGTAAT
*
18330 AAATAATAAAATAAAAT
1 AAATAATAAAAT-AAAG
* *
18347 AAAGTAAT-GAATAAAT
1 AAA-TAATAAAATAAAG
18363 AAATAATAAAATAAAG
1 AAATAATAAAATAAAG
18379 AAA-AATAAAA
1 AAATAATAAAA
18389 ATTGGGTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 11 0.30
16 16 0.43
17 6 0.16
18 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (16 bp):
AAATAATAAAATAAAG
Found at i:29104 original size:20 final size:20
Alignment explanation
Indices: 29030--29096 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
29020 GCATCATAGA
29030 TGCATAACAAAGGCACCGAAG
1 TGCA-AACAAAGGCACCGAAG
* *
29051 TGCAAACAAAGACACCAAAG
1 TGCAAACAAAGGCACCGAAG
* *
29071 TGTATACAAAGGCACCGAAG
1 TGCAAACAAAGGCACCGAAG
29091 TGCAAA
1 TGCAAA
29097 GATAGGCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.10
Consensus pattern (20 bp):
TGCAAACAAAGGCACCGAAG
Found at i:34832 original size:12 final size:12
Alignment explanation
Indices: 34817--34856 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
34807 TTCTTTTTTC
34817 TTTTTTT-TTTA
1 TTTTTTTATTTA
*
34828 TTTTTTAATTTA
1 TTTTTTTATTTA
*
34840 TTTATTTATTTA
1 TTTTTTTATTTA
34852 TTTTT
1 TTTTT
34857 GGTTAAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:34972 original size:96 final size:97
Alignment explanation
Indices: 34848--35049 Score: 300
Period size: 96 Copynumber: 2.1 Consensus size: 97
34838 TATTTATTTA
* *
34848 TTTATTTTTGGTTAAGAATATACTGAACCTTTTGACGCGAAGAGAGATGAAAGCCAAGCACCCCA
1 TTTA-TTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGAAAGCCAAGCACCCCA
*
34913 CCCCGGTTACTCAGCCCAACATACTCTTAA-TT
65 CCCCGATTACTCAGCCCAACATACTCTTAAGTT
* * *
34945 TTTATTTTGCTTAAGAACATAAC-GAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTGCTTAAGAACAT-ACTGAACCTTTTGACGCGAAGAGAGATGAAAGCCAAGCACCCCA
*
35009 CCCCGATTACTCAGCCCAACATATTCTTAAGTTT
65 CCCCGATTACTCAGCCCAACATACTCTTAAG-TT
35043 TTTATTT
1 TTTATTT
35050 CCGATTAGTG
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
96 80 0.84
97 6 0.06
98 9 0.09
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (97 bp):
TTTATTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGAAAGCCAAGCACCCCAC
CCCGATTACTCAGCCCAACATACTCTTAAGTT
Found at i:37077 original size:16 final size:16
Alignment explanation
Indices: 37056--37090 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37046 CCGACAAATC
37056 CTGAAATG-CAGAAAAG
1 CTGAAATGCCA-AAAAG
37072 CTGAAATGCCAAAAAG
1 CTGAAATGCCAAAAAG
37088 CTG
1 CTG
37091 GAAGTTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (16 bp):
CTGAAATGCCAAAAAG
Found at i:37338 original size:28 final size:28
Alignment explanation
Indices: 37306--37408 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
37296 ATTTCATGAC
37306 TATGAATGTGATTGGGCCTGATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
* *
37334 TATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
* *
37362 TATGAATGTGATTGTGCCCGATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
*
37390 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
37409 AAAGGGGCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATTGGCCA
Found at i:43946 original size:16 final size:16
Alignment explanation
Indices: 43925--43959 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43915 GCAAATCCCA
* *
43925 AAATGCCGAAAAGTCG
1 AAATGCCAAAAAGCCG
43941 AAATGCCAAAAAGCCG
1 AAATGCCAAAAAGCCG
43957 AAA
1 AAA
43960 GTTAGGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.09
Consensus pattern (16 bp):
AAATGCCAAAAAGCCG
Found at i:45154 original size:16 final size:16
Alignment explanation
Indices: 45133--45163 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45123 CGACAAATCC
45133 TGAAATGCAGAAAAGT
1 TGAAATGCAGAAAAGT
*
45149 TGAAATGCCGAAAAG
1 TGAAATGCAGAAAAG
45164 CTGGAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.16
Consensus pattern (16 bp):
TGAAATGCAGAAAAGT
Found at i:45416 original size:28 final size:28
Alignment explanation
Indices: 45383--45457 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
45373 ATTTCATGAC
*
45383 TATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* * *
45411 TATGAATGTGATTGTGCCCGATTGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
45439 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
45458 AAAGGGGCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:47190 original size:25 final size:28
Alignment explanation
Indices: 47165--47242 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 28
47155 CCCAAACAAA
47165 ATAAAGTAATAAAT-AAT-AA-AATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
*
47190 ATAAAGTAATGAATAAATAAATAATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
*
47218 ATAAAG--A-AAATAAAGAAA-AATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
47242 A
1 A
47243 ATTGGGTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 7 0.15
25 22 0.47
26 4 0.09
27 2 0.04
28 12 0.26
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (28 bp):
ATAAAGTAATAAATAAATAAATAATAAA
Found at i:47209 original size:16 final size:15
Alignment explanation
Indices: 47172--47241 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 15
47162 AAAATAAAGT
*
47172 AATAAATAATAAAATAA
1 AATAAATAAT-GAAT-A
47189 AATAAAGTAATGAATA
1 AATAAA-TAATGAATA
*
47205 AATAAATAATAAAATA
1 AATAAATAAT-GAATA
* *
47221 AAGAAAATAAAGAA-A
1 AA-TAAATAATGAATA
47236 AATAAA
1 AATAAA
47242 AATTGGGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 15 0.34
17 15 0.34
18 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AATAAATAATGAATA
Found at i:50862 original size:20 final size:20
Alignment explanation
Indices: 50839--50898 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
50829 TTAAATTCTA
50839 AAAGATAAATACAA-ATAAAT
1 AAAGATAAATA-AATATAAAT
* *
50859 AAAGATAATTAAATATAATT
1 AAAGATAAATAAATATAAAT
50879 AAAGATAAATGAAAT-TAAAT
1 AAAGATAAAT-AAATATAAAT
50899 CTTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 28 0.82
21 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAATATAAAT
Found at i:50866 original size:10 final size:10
Alignment explanation
Indices: 50839--50888 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
50829 TTAAATTCTA
50839 AAAGATAAAT
1 AAAGATAAAT
50849 ACAA-ATAAAT
1 A-AAGATAAAT
*
50859 AAAGATAATT
1 AAAGATAAAT
* *
50869 AAATATAATT
1 AAAGATAAAT
50879 AAAGATAAAT
1 AAAGATAAAT
50889 GAAATTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAGATAAAT
Done.