Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3457
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: 39648
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:4605 original size:49 final size:48
Alignment explanation
Indices: 4548--4641 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 48
4538 GGCTTCGTGC
*
4548 TGGAAATGT-ATCCGGGCTAAAAGTCCCACAGGCTTCGTGCGGAAATATA
1 TGGAAATGTAATCCGGACTAAAAGTCCCAC--GCTTCGTGCGGAAATATA
* *
4597 TGGAAATGTAATCCGGACTAAAAGTCCCGCGCTTCGTGTGGAAAT
1 TGGAAATGTAATCCGGACTAAAAGTCCCACGCTTCGTGCGGAAAT
4642 GTATCCGGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
48 14 0.34
49 9 0.22
50 18 0.44
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (48 bp):
TGGAAATGTAATCCGGACTAAAAGTCCCACGCTTCGTGCGGAAATATA
Found at i:4641 original size:87 final size:86
Alignment explanation
Indices: 4513--4680 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 86
4503 AAGACACTGA
4513 AAATGTATCCGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAAGTCCC-AC
1 AAATGTATCCGGCTAAAGTCCCGCA-GCTTCGTGCTGGAAATGTATCCGGGC-AAAAGTCCCGA-
4577 AGGCTTCGTGC-GGAAATATATGG
63 AGGCTTCGTGCTGGAAATATATGG
*
4600 AAATGTAATCCGGACTAAAAGTCCCGC-GCTTCGTG-TGGAAATGTATCCGGGCCAAAGTCCCGA
1 AAATGT-ATCCGG-CT-AAAGTCCCGCAGCTTCGTGCTGGAAATGTATCCGGGCAAAAGTCCCGA
4663 AGGCTTCGTGCTGGAAAT
63 AGGCTTCGTGCTGGAAAT
4681 TATCCGGCCA
Statistics
Matches: 75, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
86 19 0.25
87 30 0.40
88 14 0.19
89 2 0.03
90 10 0.13
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (86 bp):
AAATGTATCCGGCTAAAGTCCCGCAGCTTCGTGCTGGAAATGTATCCGGGCAAAAGTCCCGAAGG
CTTCGTGCTGGAAATATATGG
Found at i:4704 original size:37 final size:38
Alignment explanation
Indices: 4597--4750 Score: 181
Period size: 37 Copynumber: 4.1 Consensus size: 38
4587 CGGAAATATA
* *
4597 TGGAAATGTAATCCGGACTAAAAGTCCCGC-GCTTCGTG-
1 TGGAAATGT-ATCCGGGC-CAAAGTCCCGCAGCTTCGTGC
*
4635 TGGAAATGTATCCGGGCCAAAGTCCCGAAGGCTTCGTGC
1 TGGAAATGTATCCGGGCCAAAGTCCCGCA-GCTTCGTGC
*
4674 TGGAAAT-TATCC-GGCCAAAGTCCCGCAGGCTTCATGC
1 TGGAAATGTATCCGGGCCAAAGTCCCGCA-GCTTCGTGC
** *
4711 TGGAAATGTATCCGGGTTAAAGTCCCGCAGCTTTGTGC
1 TGGAAATGTATCCGGGCCAAAGTCCCGCAGCTTCGTGC
4749 TG
1 TG
4751 ATAATATAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
36 9 0.09
37 37 0.36
38 36 0.35
39 20 0.20
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (38 bp):
TGGAAATGTATCCGGGCCAAAGTCCCGCAGCTTCGTGC
Found at i:7162 original size:27 final size:27
Alignment explanation
Indices: 7132--7184 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
7122 TAGTAATAGT
*
7132 TGGGCCT-AGCCCATTAACAGAATCAGG
1 TGGGCCTAAGCCCAGT-ACAGAATCAGG
7159 TGGGCCTAAGCCCAGTACAGAATCAG
1 TGGGCCTAAGCCCAGTACAGAATCAG
7185 TATCAGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (27 bp):
TGGGCCTAAGCCCAGTACAGAATCAGG
Found at i:7414 original size:46 final size:46
Alignment explanation
Indices: 7362--7518 Score: 143
Period size: 46 Copynumber: 3.3 Consensus size: 46
7352 AAAGCTAAAG
*
7362 GCCATAAATATCGTAGCAACGCTACCAGTTAACAGAACGGCTATAA
1 GCCATAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAA
* ** ** * ** * * *
7408 GCCATAAGTATTACAAAAAGGCTAAAAGCCTTATACAGGACGGCTACAG
1 GCCATAAATATCGCAGCAACGCTACCAG--TTA-ACAGAACGGCTATAA
* * *
7457 GCCGTAAATATCGCAGCAACGCTGCCAGTTAACAGAATGGCTATAA
1 GCCATAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAA
*
7503 GCCATAAGTATCGCAG
1 GCCATAAATATCGCAG
7519 AAAGGCTGAA
Statistics
Matches: 80, Mismatches: 28, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
46 44 0.55
47 3 0.04
48 3 0.04
49 30 0.38
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (46 bp):
GCCATAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAA
Found at i:7523 original size:95 final size:95
Alignment explanation
Indices: 7355--7557 Score: 307
Period size: 95 Copynumber: 2.1 Consensus size: 95
7345 AGATAGGAAA
* * * *
7355 GCTAAAGGCCATAAATATCGTAGCAACGCTACCAGTTAACAGAACGGCTATAAGCCATAAGTATT
1 GCTACAGGCCGTAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAAGCCATAAGTATC
7420 ACAAAAAGGCTAAAAGCCTTATACAGGACG
66 ACAAAAAGGCTAAAAGCCTTATACAGGACG
* *
7450 GCTACAGGCCGTAAATATCGCAGCAACGCTGCCAGTTAACAGAATGGCTATAAGCCATAAGTATC
1 GCTACAGGCCGTAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAAGCCATAAGTATC
* * * **
7515 GCAGAAAGGCTGAAAGCCTTATACAGGATT
66 ACAAAAAGGCTAAAAGCCTTATACAGGACG
7545 GCTACAGGCCGTA
1 GCTACAGGCCGTA
7558 CACTTCCTCC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (95 bp):
GCTACAGGCCGTAAATATCGCAGCAACGCTACCAGTTAACAGAACGGCTATAAGCCATAAGTATC
ACAAAAAGGCTAAAAGCCTTATACAGGACG
Found at i:7756 original size:27 final size:27
Alignment explanation
Indices: 7708--7760 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7698 CATTCTACCA
* *
7708 TACAAGGGTATTATGGTCATTTTACAC
1 TACAAGGGTATTATAGTAATTTTACAC
7735 TACAAGGGTATT-TCAGTAATTTTACA
1 TACAAGGGTATTAT-AGTAATTTTACA
7761 AACCAAGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTATAGTAATTTTACAC
Found at i:10257 original size:17 final size:17
Alignment explanation
Indices: 10221--10258 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10211 TTAATTCTGT
*
10221 CATTACTTTGCTCATCA
1 CATTACTTTGCTCATAA
10238 CATTACTTTGCATC-TAA
1 CATTACTTTGC-TCATAA
10255 CATT
1 CATT
10259 TCTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (17 bp):
CATTACTTTGCTCATAA
Found at i:10522 original size:17 final size:17
Alignment explanation
Indices: 10500--10557 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
10490 ACACATTTTC
10500 AACAGAATAACAAAAAT
1 AACAGAATAACAAAAAT
* *
10517 AACAGAAT-A-TAAAGT
1 AACAGAATAACAAAAAT
10532 AACAGAATAACAAAAAT
1 AACAGAATAACAAAAAT
10549 AACAGAATA
1 AACAGAATA
10558 CTAAGTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.34
16 2 0.06
17 21 0.60
ACGTcount: A:0.67, C:0.10, G:0.09, T:0.14
Consensus pattern (17 bp):
AACAGAATAACAAAAAT
Found at i:10665 original size:28 final size:28
Alignment explanation
Indices: 10604--10681 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
10594 AATTTGGTTA
* *
10604 AATATTATATTAAACATAAT-TTAATTC
1 AATATTATATTAAATAAAATATTAATTC
*
10631 AATATTATTTTAAATAAAATATT-ATGTC
1 AATATTATATTAAATAAAATATTAAT-TC
* *
10659 AATATTATGTTGAATAAAATATT
1 AATATTATATTAAATAAAATATT
10682 GTGTTTTGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (28 bp):
AATATTATATTAAATAAAATATTAATTC
Found at i:13559 original size:22 final size:22
Alignment explanation
Indices: 13506--13569 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
13496 ACACTAAACT
* *
13506 TTTAAAAATA-TATTTTAAAAA
1 TTTATAAATATTATATTAAAAA
*
13527 -TTATATA-ATTATATTAAAAA
1 TTTATAAATATTATATTAAAAA
* *
13547 TTTATAAATATTAAATTATAAA
1 TTTATAAATATTATATTAAAAA
13569 T
1 T
13570 AAAAATGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 6 0.18
22 12 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTATAAATATTATATTAAAAA
Found at i:20018 original size:38 final size:38
Alignment explanation
Indices: 19976--20144 Score: 180
Period size: 38 Copynumber: 4.4 Consensus size: 38
19966 TAAAGACCCG
*
19976 CAGGC-TATGTGCTGGTATTATATCTGGGTTAAATCCCA
1 CAGGCTTA-GTGCTGGTATTATATCCGGGTTAAATCCCA
* * *
20014 CAGGCTTTGTGCTGGTAATATATCCGGGTTAAATCCCG
1 CAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCA
* * * *
20052 TAGGCTTCGTACTGGTATTATATCCGGGTTAAAT-CCT
1 CAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCA
* * *
20089 CAGGCTTAGTGCTGGTATTATATTCGAGCTTAAAGTCCCG
1 CAGGCTTAGTGCTGGTATTATATCCG-GGTTAAA-TCCCA
* *
20129 CAGGTTTTGTGCTGGT
1 CAGGCTTAGTGCTGGT
20145 GACTAGATTC
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
37 24 0.22
38 68 0.62
39 2 0.02
40 16 0.15
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (38 bp):
CAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCA
Found at i:20122 original size:76 final size:77
Alignment explanation
Indices: 19956--20128 Score: 217
Period size: 76 Copynumber: 2.2 Consensus size: 77
19946 ATTTTATGTG
* * * *
19956 TATCCAGGCTTAAAGACCCGCAGGCTAT-GTGCTGGTATTATATCTGGGTTAAATCCCACAGGCT
1 TATCC-GGCTTAAAGTCCCGTAGGCT-TCGTACTGGTATTATATCCGGGTTAAATCCCACAGGCT
*
20020 TTGTGCTGGTAATA
64 TAGTGCTGGTAATA
* *
20034 TATCCGGGTTAAA-TCCCGTAGGCTTCGTACTGGTATTATATCCGGGTTAAAT-CCTCAGGCTTA
1 TATCCGGCTTAAAGTCCCGTAGGCTTCGTACTGGTATTATATCCGGGTTAAATCCCACAGGCTTA
*
20097 GTGCTGGTATTA
66 GTGCTGGTAATA
*
20109 TATTCGAGCTTAAAGTCCCG
1 TATCCG-GCTTAAAGTCCCG
20129 CAGGTTTTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
75 26 0.32
76 39 0.48
77 12 0.15
78 5 0.06
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (77 bp):
TATCCGGCTTAAAGTCCCGTAGGCTTCGTACTGGTATTATATCCGGGTTAAATCCCACAGGCTTA
GTGCTGGTAATA
Found at i:26334 original size:43 final size:43
Alignment explanation
Indices: 26258--26343 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
26248 TATGTGATTC
*
26258 CGATATGTGTTTACGAGTAAGACCCTGTCTGGGACAG-TGGCAT
1 CGATATGTGGTTACGAGTAAGACCCTGTCTGGGAC-GTTGGCAT
*
26301 CGATATGTGGTTAC-ATGTAAGACCAC-GTTTGGGACGTTGGCAT
1 CGATATGTGGTTACGA-GTAAGACC-CTGTCTGGGACGTTGGCAT
26344 TGTATGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
42 2 0.05
43 35 0.92
44 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (43 bp):
CGATATGTGGTTACGAGTAAGACCCTGTCTGGGACGTTGGCAT
Found at i:30615 original size:46 final size:46
Alignment explanation
Indices: 30565--30693 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
30555 ATGTTGAGCA
*
30565 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
30611 TCCGAACTCGTTAAGTTGAGTCCGATTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * ** *
30657 CCCGAGCTCGTTGAGTTGAGTCTAAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30694 GCGGGTTATA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:36057 original size:44 final size:46
Alignment explanation
Indices: 35953--36125 Score: 287
Period size: 46 Copynumber: 3.8 Consensus size: 46
35943 TGGTTGAGCA
35953 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
35999 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATG-AAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
36043 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
36089 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
36126 GCGGTTACAT
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
44 38 0.32
45 10 0.08
46 71 0.60
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:36106 original size:90 final size:90
Alignment explanation
Indices: 35953--36122 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 90
35943 TGGTTGAGCA
* * *
35953 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGTTGA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGTTGA
36018 GTCCGAGTTCACTTAGGATGAAATG
66 GTCCGAGTTCACTTAGGATGAAATG
* *
36043 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGTTGA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGTTGA
36108 GTCCGAGTTCACTTA
66 GTCCGAGTTCACTTA
36123 TGGGCGGTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (90 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGTTGA
GTCCGAGTTCACTTAGGATGAAATG
Found at i:38151 original size:27 final size:27
Alignment explanation
Indices: 38134--38201 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
38124 ATATTCAGTC
38134 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
38161 CGCACACTTAGTGCTATATAAT-AACT
1 CGCACACTCAGTGCTATATAATCAACT
*
38187 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
38202 GTACAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:38193 original size:26 final size:27
Alignment explanation
Indices: 38134--38229 Score: 122
Period size: 26 Copynumber: 3.5 Consensus size: 27
38124 ATATTCAGTC
* *
38134 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATAAACT
38161 CGCACACTTAGTGCTATATAAT-AACT
1 CGCACACTTAGTGCTATATAATAAACT
* * *
38187 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA--TAAACT
38216 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38230 CAATCTCATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
26 23 0.37
27 21 0.34
28 1 0.02
29 17 0.27
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATAAACT
Done.