Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3395
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: 37668
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:4500 original size:90 final size:91
Alignment explanation
Indices: 4389--4555 Score: 293
Period size: 90 Copynumber: 1.8 Consensus size: 91
4379 GCCCCTAAGT
*
4389 GAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCATAA-TGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
4452 CGAGTTCGGATGCCTAGTTACATTCAC
65 CGAGTTCGGATGCCTAGTTACATTCAC
*
4479 GAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTGCATCCATAAGTGAACTCGGACTCAACTCAAC
4544 GAGTTCGGATGC
66 GAGTTCGGATGC
4556 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
90 37 0.51
91 36 0.49
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTCAC
Found at i:4543 original size:45 final size:44
Alignment explanation
Indices: 4388--4552 Score: 199
Period size: 45 Copynumber: 3.7 Consensus size: 44
4378 CGCCCCTAAG
* *
4388 TGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCATAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAA
* * * * *
4432 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA--CATTGCATCCA-TAA
*
4478 CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCATAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCATAA
4522 GTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -TGAACTCGGACTCAACTCAACGAGTTCGGA
4553 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
44 33 0.32
45 35 0.34
46 32 0.31
47 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (44 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCATAA
Found at i:12015 original size:93 final size:93
Alignment explanation
Indices: 11901--12071 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
11891 GCCCATAAGT
* *
11901 GAACTCAGACTCAACTCAACGAGCTCGGGCATTCACATCCATAAGTTAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
11966 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * *
11994 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
12059 CGAGTTCGGATGC
66 CGAGTTCGGATGC
12072 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:12068 original size:46 final size:46
Alignment explanation
Indices: 11893--12068 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
11883 TGTAACCCGC
* * *
11893 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
11939 CCATAAGTTAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* * * *
11989 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
12032 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12069 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:12525 original size:30 final size:30
Alignment explanation
Indices: 12502--12580 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
12492 ACTTTAAAAA
12502 AATTACACTTTTGCCCCTAAACTTTTGCAT
1 AATTACACTTTTGCCCCTAAACTTTTGCAT
12532 AATTACACTTTTGCCCCTAAACTTTTGCAT
1 AATTACACTTTTGCCCCTAAACTTTTGCAT
12562 AATTACACTTTTGCCCCTA
1 AATTACACTTTTGCCCCTA
12581 GGCTCGGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (30 bp):
AATTACACTTTTGCCCCTAAACTTTTGCAT
Found at i:12527 original size:14 final size:14
Alignment explanation
Indices: 12508--12559 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
12498 AAAAAATTAC
12508 ACTTTTGCCCCTAA
1 ACTTTTGCCCCTAA
*** *
12522 ACTTTTGCATAATTAC
1 ACTTTTGC--CCCTAA
12538 ACTTTTGCCCCTAA
1 ACTTTTGCCCCTAA
12552 ACTTTTGC
1 ACTTTTGC
12560 ATAATTACAC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 18 0.64
16 10 0.36
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (14 bp):
ACTTTTGCCCCTAA
Found at i:12543 original size:16 final size:16
Alignment explanation
Indices: 12522--12575 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
12512 TTGCCCCTAA
12522 ACTTTTGCATAATTAC
1 ACTTTTGCATAATTAC
*** *
12538 ACTTTTGC--CCCTAA
1 ACTTTTGCATAATTAC
12552 ACTTTTGCATAATTAC
1 ACTTTTGCATAATTAC
12568 ACTTTTGC
1 ACTTTTGC
12576 CCCTAGGCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 10 0.36
16 18 0.64
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (16 bp):
ACTTTTGCATAATTAC
Found at i:13744 original size:27 final size:26
Alignment explanation
Indices: 13706--13872 Score: 122
Period size: 27 Copynumber: 6.2 Consensus size: 26
13696 GGGCCGAAAT
*
13706 AATGACCAAAATACCCTTATAGAGTAA
1 AATGACCGAAATACCCTTATAG-GTAA
*
13733 AATGACCGAAATACCCTCATAGGATAA
1 AATGACCGAAATACCCTTATAGG-TAA
* * *
13760 AATGATCAAAATACCC-CATAGGGTAA
1 AATGACCGAAATACCCTTATA-GGTAA
* * *
13786 AATCAACGAAATACCCCTATAAGGTAA
1 AATGACCGAAATACCCTTAT-AGGTAA
* * * * *
13813 AATAACTGTAATACCCCTGTAGGGTAA
1 AATGACCGAAATACCCTTATA-GGTAA
* *
13840 AATGACTGTAATACCCCTGTA-AGGTAA
1 AATGACCGAAATA-CCCT-TATAGGTAA
13867 AATGAC
1 AATGAC
13873 TGATTTGCCC
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
26 22 0.19
27 89 0.76
28 5 0.04
29 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (26 bp):
AATGACCGAAATACCCTTATAGGTAA
Found at i:13854 original size:54 final size:53
Alignment explanation
Indices: 13769--13874 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 53
13759 AAATGATCAA
13769 AATACCCCATAGGGTAAAATCAACGAAATACCCCTATAAGGTAAAATAACTGT
1 AATACCCCATAGGGTAAAATCAACGAAATACCCCTATAAGGTAAAATAACTGT
* * * * *
13822 AATACCCCTGTAGGGTAAAAT-GACTGTAATACCCCTGTAAGGTAAAATGACTG
1 AATACCCC-ATAGGGTAAAATCAAC-GAAATACCCCTATAAGGTAAAATAACTG
13875 ATTTGCCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
53 10 0.22
54 36 0.78
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (53 bp):
AATACCCCATAGGGTAAAATCAACGAAATACCCCTATAAGGTAAAATAACTGT
Found at i:13873 original size:27 final size:27
Alignment explanation
Indices: 13795--13874 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
13785 AAATCAACGA
* *
13795 AATACCCCTATAAGGTAAAATAACTGT
1 AATACCCCTGTAAGGTAAAATGACTGT
*
13822 AATACCCCTGTAGGGTAAAATGACTGT
1 AATACCCCTGTAAGGTAAAATGACTGT
13849 AATACCCCTGTAAGGTAAAATGACTG
1 AATACCCCTGTAAGGTAAAATGACTG
13875 ATTTGCCCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (27 bp):
AATACCCCTGTAAGGTAAAATGACTGT
Found at i:17146 original size:27 final size:27
Alignment explanation
Indices: 17110--17225 Score: 112
Period size: 27 Copynumber: 4.3 Consensus size: 27
17100 GGCCGAAATG
*
17110 ATGACTGAAATACCCTC-ATAGGGTAAA
1 ATGACTGAAATACCC-CGATAAGGTAAA
*
17137 ATGACCGAAATACCCCGATAAGGTAAA
1 ATGACTGAAATACCCCGATAAGGTAAA
* * *
17164 ATGACTGTAATACCCCTG-CAGGGTAAA
1 ATGACTGAAATACCCC-GATAAGGTAAA
* *
17191 ATAACTGTAATACCCCTG-TAAGGTAAA
1 ATGACTGAAATACCCC-GATAAGGTAAA
*
17218 GTGACTGA
1 ATGACTGA
17226 TTTTCCCTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 73 0.97
28 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
ATGACTGAAATACCCCGATAAGGTAAA
Found at i:22602 original size:39 final size:39
Alignment explanation
Indices: 22559--22739 Score: 245
Period size: 39 Copynumber: 4.6 Consensus size: 39
22549 ACGTGGCTTG
* *
22559 CGGACTTCAAGTCCGGATATATTTCCAGCATATAGCCTA
1 CGGACCTCATGTCCGGATATATTTCCAGCATATAGCCTA
* *
22598 CGGACCTCATGTCTGGATATATTCCCAGCATATAGCCTA
1 CGGACCTCATGTCCGGATATATTTCCAGCATATAGCCTA
* * * *
22637 TGGACTTCATGTTCGGATATATTTCCAGTATATAGCCTA
1 CGGACCTCATGTCCGGATATATTTCCAGCATATAGCCTA
* *
22676 CGGACCTCATGTCCGAATATATTTCCAGCATATAGCCTG
1 CGGACCTCATGTCCGGATATATTTCCAGCATATAGCCTA
** *
22715 TAGACCTCATGTCCAGATATATTTC
1 CGGACCTCATGTCCGGATATATTTC
22740 AAATACCATG
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 122 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (39 bp):
CGGACCTCATGTCCGGATATATTTCCAGCATATAGCCTA
Found at i:22673 original size:78 final size:78
Alignment explanation
Indices: 22560--22739 Score: 270
Period size: 78 Copynumber: 2.3 Consensus size: 78
22550 CGTGGCTTGC
* * *
22560 GGACTTCAAGTCCGGATATATTTCCAGCATATAGCCTACGGACCTCATGTCTGGATATATTCCCA
1 GGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACGGACCTCATGTCCGAATATATTCCCA
22625 GCATATAGCCTAT
66 GCATATAGCCTAT
* * *
22638 GGACTTCATGTTCGGATATATTTCCAGTATATAGCCTACGGACCTCATGTCCGAATATATTTCCA
1 GGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACGGACCTCATGTCCGAATATATTCCCA
*
22703 GCATATAGCCTGT
66 GCATATAGCCTAT
* * *
22716 AGACCTCATGTCCAGATATATTTC
1 GGACTTCATGTCCGGATATATTTC
22740 AAATACCATG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 91 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (78 bp):
GGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACGGACCTCATGTCCGAATATATTCCCA
GCATATAGCCTAT
Found at i:28405 original size:39 final size:39
Alignment explanation
Indices: 28201--28422 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
28191 TTGAATGCTG
* * * * * *
28201 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
28241 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
28281 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
28321 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
28361 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
28400 ACCGGGCTATGT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28423 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 22, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
38 11 0.07
39 26 0.17
40 106 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:36229 original size:40 final size:40
Alignment explanation
Indices: 36094--36317 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
36084 TTGAATGCTG
* * *
36094 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
36134 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
36173 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * * *
36213 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
36253 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
36292 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
36318 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 65 0.41
40 81 0.52
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:36230 original size:79 final size:79
Alignment explanation
Indices: 36147--36317 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 79
36137 GGACTAAGAT
* *
36147 CCGAAGGCATTTGTGCGAGATA-CAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTA
* *
36211 AATCCGGGTTAAGTC
65 AAACCGGGCTAAGTC
* * * * * *
36226 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
36291 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
36305 CCGAAGGCATTTG
1 CCGAAGGCATTTG
36318 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
79 58 0.73
80 21 0.27
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:36335 original size:79 final size:80
Alignment explanation
Indices: 36173--36350 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
36163 GAGATACAAT
* * * *
36173 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
36238 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
36253 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
36317 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
36332 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
36351 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Done.