Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1603
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: 23970
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:735 original size:55 final size:56
Alignment explanation
Indices: 597--768 Score: 316
Period size: 55 Copynumber: 3.1 Consensus size: 56
587 ACAAGGGATG
597 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-A-AAT-AAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
650 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
706 ATGGGCAAAACATGTCATG-AACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
761 ATGGGCAA
1 ATGGGCAA
769 TAAACTAATA
Statistics
Matches: 116, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
53 38 0.33
54 1 0.01
55 47 0.41
56 30 0.26
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:2036 original size:40 final size:40
Alignment explanation
Indices: 1889--2070 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
1879 TCGAATGATG
* * * *
1889 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
1929 TCCGGACTAAGAT-ACGAAGGTATTTGTGTGA--TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1967 TCCGGGCTAAG-CCGGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
2005 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2046 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2071 AACGAGTAGC
Statistics
Matches: 113, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
36 7 0.06
37 6 0.05
38 28 0.25
39 9 0.08
40 54 0.48
41 9 0.08
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5507 original size:47 final size:47
Alignment explanation
Indices: 5453--5903 Score: 644
Period size: 47 Copynumber: 9.6 Consensus size: 47
5443 ATATTGAATA
5453 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
5500 AATGTGAAAGTGTATATATTGTTGATAA-GCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATA-TG-TGATAAGGCCTAATGGCCGATGTGATG
* * *
5548 AATGTGAAAGTGTGTATATGTGATAATGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAA-GGCCTAATGGCCGATGTGATG
*
5596 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
5645 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
5692 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
5741 AATGTGAAAGTG--TATATGTGATAAGGCCTAA--GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
5784 AATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCGATG-GATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
5830 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
5877 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
5904 TCCCGAAGGG
Statistics
Matches: 364, Mismatches: 27, Indels: 26
0.87 0.06 0.06
Matches are distributed among these distances:
43 24 0.07
45 38 0.10
46 45 0.12
47 100 0.27
48 64 0.18
49 77 0.21
50 16 0.04
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:5622 original size:96 final size:96
Alignment explanation
Indices: 5453--5903 Score: 654
Period size: 96 Copynumber: 4.8 Consensus size: 96
5443 ATATTGAATA
* * * *
5453 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATA
5518 T-TGTTGATAA-GCCTAATAGCCGATGTGATG
66 TATG-TGATAAGGCCTAATAGCCGATGTGATG
5548 AATGTGAAAGTGTGTATATGTGATAATGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTAT
1 AATGTGAAAGTGTGTATATGTGATAA-GGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTAT
5613 ATATGTGATAAGGCCTAATAGCCGATGTGATG
65 ATATGTGATAAGGCCTAATAGCCGATGTGATG
*
5645 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATA
*
5710 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATAGCCGATGTGATG
* *
5741 AATGTGAAA--GTGTATATGTGATAAGGCCTAA--GCCGATGTGATGAATGTGAAA--GTGTATA
1 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATA
**
5800 TATGTGATAAGGCCTAACGGCCGATG-GATG
66 TATGTGATAAGGCCTAATAGCCGATGTGATG
* * * * * *
5830 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAA--GTGTATA
1 AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATA
*
5893 AATGTGATAAG
66 TATGTGATAAG
5904 TCCCGAAGGG
Statistics
Matches: 330, Mismatches: 19, Indels: 16
0.90 0.05 0.04
Matches are distributed among these distances:
89 13 0.04
90 31 0.09
91 17 0.05
92 20 0.06
93 35 0.11
94 21 0.06
95 25 0.08
96 120 0.36
97 48 0.15
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
AATGTGAAAGTGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATA
TATGTGATAAGGCCTAATAGCCGATGTGATG
Found at i:5729 original size:145 final size:141
Alignment explanation
Indices: 5453--5903 Score: 662
Period size: 145 Copynumber: 3.2 Consensus size: 141
5443 ATATTGAATA
*
5453 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* *
5518 TTGTTGATAA-GCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTATATGTGATAATGGCCGAA
66 -TG-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA-GGCCGAA
5582 TGGCCAATGTGATG
128 TGGCCAATGTGATG
*
5596 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTA
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATA
* * *
5661 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGA
*
5726 ATGGCCGATGTGATG
127 ATGGCCAATGTGATG
5741 AATGTGAAAGTG--TATATGTGATAAGGCCT-A-AGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * * *
5802 TGTGATAAGGCCTAACGGCCGATG-GATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGG
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
*
5866 CCAACGTGATG
131 CCAATGTGATG
* *
5877 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
5904 TCCCGAAGGG
Statistics
Matches: 281, Mismatches: 20, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
136 40 0.14
138 28 0.10
139 51 0.18
140 1 0.00
141 17 0.06
143 18 0.06
144 31 0.11
145 82 0.29
146 13 0.05
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
CCAATGTGATG
Found at i:6103 original size:36 final size:37
Alignment explanation
Indices: 6024--6161 Score: 233
Period size: 37 Copynumber: 3.7 Consensus size: 37
6014 CCGAGCTCTA
6024 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
6061 AAGACCCGATGACTACGTGTGGAGATTATGT-CGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
*
6097 AAGACCCGATGACTACGTGTGGAGAATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAG-ATTATGTCCGGGT
* *
6135 AAGACCCGATAACTTCGTGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
6162 TCGTCTGAGC
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
36 29 0.30
37 40 0.42
38 27 0.28
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
Found at i:12870 original size:55 final size:56
Alignment explanation
Indices: 12807--12915 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 56
12797 AAATAAGAAG
12807 CATGTCATGAAACATGTTGTGTTAATGGAA-AATAAAATAAGAAGCATGGGCAAAA
1 CATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAA
12862 CATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAA
1 CATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAA
12916 TAAACTAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 30 0.57
56 23 0.43
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (56 bp):
CATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAA
Found at i:14180 original size:79 final size:81
Alignment explanation
Indices: 14044--14226 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
14034 TCGAATGATG
* *
14044 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
14108 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
14123 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
14185 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
14203 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
14227 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:14242 original size:40 final size:40
Alignment explanation
Indices: 14045--14228 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
14035 CGAATGATGT
* * * *
14045 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
14085 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
14125 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
14163 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
14204 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
14229 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:14250 original size:79 final size:79
Alignment explanation
Indices: 14097--14261 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
14087 GGACTAAGAT
* **
14097 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
14162 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
14176 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
14239 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
14255 CCGAAGG
1 CCGAAGG
14262 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:16281 original size:15 final size:16
Alignment explanation
Indices: 16245--16274 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16235 ACATATCATT
16245 TATTTCATTATATCAA
1 TATTTCATTATATCAA
16261 TATTTCA-TATATCA
1 TATTTCATTATATCA
16275 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:18150 original size:30 final size:30
Alignment explanation
Indices: 18116--18176 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18106 TCCTTAACTC
18116 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
18146 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
18176 A
1 A
18177 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.