Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold838
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: 44507
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6261 original size:80 final size:79
Alignment explanation
Indices: 6116--6287 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 79
6106 ATGTCTGGGC
* **
6116 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
6181 TTA-CTAAATCCGGGT
66 -TAGCTAAATCC-GGT
* * * * *
6196 TAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTGAACG
*
6259 AGTAGCTATATCCGGT
64 AGTAGCTAAATCCGGT
* *
6275 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
6288 TATGTGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 17 0.22
80 55 0.71
81 6 0.08
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
TAGCTAAATCCGGT
Found at i:6268 original size:40 final size:40
Alignment explanation
Indices: 6112--6254 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
6102 AATGATGTCT
* * * *
6112 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
*
6152 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
* *
6192 GGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
6232 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
6255 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 76 0.86
41 10 0.11
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:6547 original size:47 final size:47
Alignment explanation
Indices: 6478--6645 Score: 255
Period size: 47 Copynumber: 3.6 Consensus size: 47
6468 AAGGGTTGGT
*
6478 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
6525 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
6572 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
6619 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
6646 TCCCGAAGGG
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:8149 original size:40 final size:40
Alignment explanation
Indices: 8100--8484 Score: 513
Period size: 40 Copynumber: 9.7 Consensus size: 40
8090 ATTGAGAGTG
8100 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
*
8140 ATATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* * * * *
8179 GTATCCGGGCTAAATTCCAAAGAGCATTCATGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* * **
8219 GTATCCGGGCTAAATTTCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
*
8259 ATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* * *
8299 GTATCCAGGCTGAA-TTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGGCT-AAGTCCCGAAGAGCATTCGTGCTAGTGAT
* *
8339 ATATCCGGGCTAAGTCCGGAAGAGCATTCATGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* * *
8379 GTATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* ** * *
8419 ATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
* *
8459 ATGTCCGGGCTAGGTCCCGAAGAGCA
1 ATATCCGGGCTAAGTCCCGAAGAGCA
8485 ATCATGCTGG
Statistics
Matches: 305, Mismatches: 37, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
39 38 0.12
40 265 0.87
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
Found at i:12511 original size:80 final size:79
Alignment explanation
Indices: 12366--12537 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 79
12356 ATGTCTGGGC
* **
12366 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
12431 TTA-CTAAATCCGGGT
66 -TAGCTAAATCC-GGT
* * * * *
12446 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCTGAAGGCATTTGAACG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGATCC-GAAGGCATTTGAACG
*
12509 AGTAGCTATATCCGGT
64 AGTAGCTAAATCCGGT
* *
12525 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
12538 TATGTGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 19 0.24
80 52 0.67
81 7 0.09
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
TAGCTAAATCCGGT
Found at i:12518 original size:40 final size:40
Alignment explanation
Indices: 12362--12504 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
12352 AATGATGTCT
* * * *
12362 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
*
12402 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
*
12442 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
* *
12482 GGGCTATGTCCTGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
12505 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 76 0.86
41 10 0.11
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:12860 original size:49 final size:47
Alignment explanation
Indices: 12729--13184 Score: 750
Period size: 47 Copynumber: 9.6 Consensus size: 47
12719 AAGGGTTGGT
*
12729 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
12776 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
12823 AATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
12872 AATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
12921 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
12968 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
13017 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
13064 AATGTGAAAGTGTATATATGCGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
13111 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
13158 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
13185 TCCCGAAGGG
Statistics
Matches: 390, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 248 0.64
49 142 0.36
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:12937 original size:96 final size:96
Alignment explanation
Indices: 12729--13184 Score: 753
Period size: 96 Copynumber: 4.8 Consensus size: 96
12719 AAGGGTTGGT
*
12729 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
12792 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
12823 AATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
12888 TATATGTGATAAGGTCTAATGGCCGATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
12921 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
12986 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
13017 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
13080 TATGCGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
13111 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
13175 -ATGTGATAAG
66 TATGTGATAAG
13185 TCCCGAAGGG
Statistics
Matches: 344, Mismatches: 12, Indels: 12
0.93 0.03 0.03
Matches are distributed among these distances:
94 107 0.31
95 1 0.00
96 190 0.55
98 46 0.13
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:35720 original size:40 final size:40
Alignment explanation
Indices: 35617--35802 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
35607 AGCTACTCTT
*
35617 CAAATGCCTTCGGGACATAGCCCAGG--TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATTTAGTAACTCGCA
*
35656 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCG-CA
* * * *
35697 CCAATGCCTTCGGG-CTTAGCCCGGAATTAATATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
35736 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
35777 CAAAAGCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35803 CATCATTCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.03
39 33 0.27
40 43 0.35
41 39 0.32
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:43713 original size:41 final size:40
Alignment explanation
Indices: 43626--43810 Score: 182
Period size: 41 Copynumber: 4.7 Consensus size: 40
43616 GCTACTCGTT
* *
43626 CAAATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
43666 CAAATGCCTTCGGGACTTAAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-AGCCCGGATTTAGTAACTCGCA
* * *
43707 CCAATGCCTTCGGG-CTTAGCCCGGAATT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
43745 CAAATGCCTTC-GGATCTTAGTCCGAATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
43786 CAAAAG-CTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43811 CATCATTCGA
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
37 2 0.02
38 19 0.16
39 19 0.16
40 36 0.30
41 42 0.35
42 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Done.