Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3720
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: 15865
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Found at i:3010 original size:40 final size:40
Alignment explanation
Indices: 2808--2996 Score: 324
Period size: 40 Copynumber: 4.7 Consensus size: 40
2798 ATTCGGATTG
2808 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
2848 ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
2888 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
2928 ATAACCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
2968 ATAACCGGGCTAAGTCCTGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
2997 AGCTAGTAGC
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:3029 original size:39 final size:39
Alignment explanation
Indices: 2808--3029 Score: 223
Period size: 40 Copynumber: 5.6 Consensus size: 39
2798 ATTCGGATTG
* *
2808 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACT-CCGAAGGCATTTGAGCGAGTTACT
* * * *
2848 ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAACT-CCGAAGGCATTTGAGCGAGTTACT
* * * *
2888 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT
1 ATAACCGGGCTAACT-CCGAAGGCATTTGAGCGAGTTACT
** *
2928 ATAACCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACT-CCGAAGGCATTTGAGCGAGTTACT
* *
2968 ATAACCGGGCTAAGTCCTGAAGGCATTTGAGCTAG-TAGCT
1 ATAACCGGGCTAACTCC-GAAGGCATTTGAGCGAGTTA-CT
*
3008 ATATCC-GGCTAAACTCCGAAGG
1 ATAACCGGGCT-AACTCCGAAGG
3030 TACTTGGTTT
Statistics
Matches: 165, Mismatches: 14, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
39 13 0.08
40 152 0.92
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATAACCGGGCTAACTCCGAAGGCATTTGAGCGAGTTACT
Found at i:5254 original size:40 final size:39
Alignment explanation
Indices: 5164--5426 Score: 282
Period size: 40 Copynumber: 6.6 Consensus size: 39
5154 TTGAATGATG
* * * *
5164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*** * *
5204 TCCAAACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
5244 TCCGAGCTAAGCCCGAAGGCA-TTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
5282 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
5322 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
*
5362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
5403 -CCGGGCTATGTCCCGAA-GCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
5427 AACGAGTAGC
Statistics
Matches: 194, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
38 23 0.12
39 26 0.13
40 135 0.70
41 10 0.05
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5390 original size:80 final size:80
Alignment explanation
Indices: 5164--5433 Score: 327
Period size: 80 Copynumber: 3.4 Consensus size: 80
5154 TTGAATGATG
* * * * * **
5164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCAAACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
* *
5228 TGTGCGAGATACTAAT
65 TGTGCGAGTTACTAAA
*
5244 TCCGAGCTAAG-CCCGAAGGCA-TTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
5307 GTGCGAGTTACTAAA
66 GTGCGAGTTACTAAA
* * **
5322 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATT
5386 TGTGCGAGTTACTATAA
65 TGTGCGAGTTACTA-AA
* *
5403 -CCGGGCTATGTCCCGAA-GCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
5434 AGCTATATTC
Statistics
Matches: 166, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
78 52 0.31
79 37 0.22
80 75 0.45
81 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:14140 original size:38 final size:40
Alignment explanation
Indices: 13990--14175 Score: 279
Period size: 40 Copynumber: 4.7 Consensus size: 40
13980 ATTCGGATTG
* *
13990 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
14030 ATAACCGGGCTAAGTACCGAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
14070 ATATCCGGACTAAGTCCCGAAGGCATTCGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
14110 ATAACCGGGCT-AGTCCCGAA-GCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
14148 ATAA-CGAGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
14176 AGCTAGTAGC
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
37 5 0.04
38 30 0.23
39 16 0.12
40 80 0.61
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:14197 original size:38 final size:38
Alignment explanation
Indices: 13997--14197 Score: 228
Period size: 40 Copynumber: 5.2 Consensus size: 38
13987 TTGATAACCG
* *
13997 GGCTAAGTCCTGAAGGCATTTGTGCAAGTTACTATAACC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ACC
* *
14036 GGGCTAAGTACCGAAGGCATTTGTGCGAGTTATTATATCC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-CC
*
14076 GGACTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAACC
1 GG-CTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ACC
*
14116 GGGCT-AGTCCCGAA-GCATTTGTGCGAGTTACTATAAC
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACC
* * *
14153 GAGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATATC
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATACC
14192 GGCTAA
1 GGCTAA
14198 ACTCCGAAGG
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
36 1 0.01
37 5 0.04
38 35 0.25
39 30 0.21
40 67 0.48
41 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (38 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATACC
Done.