Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2012
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: 27116
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Found at i:297 original size:13 final size:13
Alignment explanation
Indices: 279--303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269 AAACAAATAA
279 AAATTTTCACACG
1 AAATTTTCACACG
292 AAATTTTCACAC
1 AAATTTTCACAC
304 ATTCAATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:4353 original size:76 final size:80
Alignment explanation
Indices: 4234--4415 Score: 223
Period size: 76 Copynumber: 2.3 Consensus size: 80
4224 TTGAATGATG
*
4234 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAG-TCCCGAAGGCAT
4297 TTGTGCGAG-TACTA-A
64 TTGTGCGAGTTACTATA
* * * **
4312 TCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTT
4375 GTGCGAGTTACTATA
66 GTGCGAGTTACTATA
* *
4390 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
4416 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
75 1 0.01
76 43 0.48
77 12 0.13
78 21 0.23
80 13 0.14
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:4429 original size:40 final size:39
Alignment explanation
Indices: 4235--4415 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 39
4225 TGAATGATGT
* * * *
4235 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* *
4275 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAG-TACTAAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
4313 CCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
4350 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
4391 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
4416 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 9, Indels: 14
0.84 0.06 0.09
Matches are distributed among these distances:
36 19 0.15
37 6 0.05
38 20 0.16
39 3 0.02
40 67 0.54
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:4433 original size:80 final size:75
Alignment explanation
Indices: 4287--4448 Score: 200
Period size: 80 Copynumber: 2.1 Consensus size: 75
4277 GGACTAAGAT
* **
4287 CCGAAGGCATTTGTGCGAGTACTAATCCGGGCTAAGCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CCGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAATC
*
4352 CGGGTTAAGTC
66 C-GGTTAAATC
*
4363 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAG-TACTA-AACCGGGCTAAG--CCGAAGGCATTTGAACGAGTTA-CT
* *
4427 ATATCCGGTTAAATT
61 AAATCCGGTTAAATC
4442 CCGAAGG
1 CCGAAGG
4449 TACGTGATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
76 19 0.26
77 5 0.07
78 10 0.14
79 16 0.22
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (75 bp):
CCGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAATC
CGGTTAAATC
Found at i:14894 original size:77 final size:81
Alignment explanation
Indices: 14774--14956 Score: 243
Period size: 77 Copynumber: 2.3 Consensus size: 81
14764 TTGAATGATG
*
14774 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAG-TCCCGAAGGCAT
14837 TTGTGCGAGTTACTA-A
65 TTGTGCGAGTTACTATA
* * * **
14853 TCCGGG-TAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATT
14915 TGTGCGAGTTACTATA
66 TGTGCGAGTTACTATA
* *
14931 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
14957 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
76 1 0.01
77 50 0.55
78 17 0.19
79 9 0.10
80 14 0.15
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:14918 original size:40 final size:40
Alignment explanation
Indices: 14774--14956 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
14764 TTGAATGATG
* * * *
14774 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
14814 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
14853 TCCGGG-TAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
14891 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
14932 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
14957 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
37 24 0.19
38 12 0.09
39 10 0.08
40 72 0.56
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:14975 original size:80 final size:76
Alignment explanation
Indices: 14827--14989 Score: 211
Period size: 77 Copynumber: 2.1 Consensus size: 76
14817 GGACTAAGAT
* **
14827 CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTAAGCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGAAGGCATTTGTGCGAGTTACTAAACCGGGTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
*
14892 CCGGGTTAAGTC
66 CC-GGTTAAATC
*
14904 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AACCGGG-TAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
14968 ATATCCGGTTAAATT
62 AAATCCGGTTAAATC
14983 CCGAAGG
1 CCGAAGG
14990 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
77 25 0.33
78 6 0.08
79 19 0.25
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (76 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACCGGGTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
CCGGTTAAATC
Found at i:25353 original size:40 final size:40
Alignment explanation
Indices: 25296--25520 Score: 194
Period size: 40 Copynumber: 5.7 Consensus size: 40
25286 TTGAATGATG
* * *
25296 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGA-GTGACCAAA
* * *
25336 TCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
* *
25376 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
** * *
25416 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTGACCAAA
* * *
25456 TCCAGG-TTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTGACCA-AA
* *
25497 -CCGGGCTATG-TCCGAAGGCATTTG
1 TCCGGACTAAGATCCGAAGGCATTTG
25521 AACGAGTAGC
Statistics
Matches: 168, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
39 16 0.10
40 140 0.83
41 12 0.07
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:25433 original size:80 final size:79
Alignment explanation
Indices: 25300--25527 Score: 284
Period size: 80 Copynumber: 2.9 Consensus size: 79
25290 ATGATGTCCG
* * * * *
25300 GGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTA
1 GGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTATAACCGGGCTAAG-TCCGAAGGCATTTGTA
25364 CGAGTTACTAAATCC-
64 CGAGTTACTAAATCCA
*
25379 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTTG
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGT-CCGAAGGCATTTG
*
25442 TGCGAGTTACTAAATCCA
62 TACGAGTTACTAAATCCA
* * *
25460 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTGAACG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTGTACG
25525 AGT
66 AGT
25528 AGCTATATCC
Statistics
Matches: 129, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
79 23 0.18
80 93 0.72
81 13 0.10
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTGTACG
AGTTACTAAATCCA
Found at i:25550 original size:39 final size:40
Alignment explanation
Indices: 25348--25553 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
25338 CGGACTAAGA
* **
25348 TCCGAAGGCATTTGTACGAGTTACTAAATCCGGACTAAGA-
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAA-AT
*
25388 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
* * *
25428 CCCGAAGGCATTTGTGCGAGTTACTAAATCCAGGTTAAGT
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
* *
25468 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCT--AT
1 TCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAAT
** *
25506 GTCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAAT
1 -TCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAAT
25546 TCCGAAGG
1 TCCGAAGG
25554 TACGTGATTT
Statistics
Matches: 145, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
38 7 0.05
39 30 0.21
40 106 0.73
41 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAAT
Done.