Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3319
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: 28581
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:2101 original size:36 final size:39
Alignment explanation
Indices: 2008--2183 Score: 161
Period size: 41 Copynumber: 4.6 Consensus size: 39
1998 TGAATGATGT
* * *
2008 CGGGCTATGTCCCGAAGGC-TTTGTGCTAAGTGAC-ATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-ATC
* * *
2047 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATC
2086 C-GGCT-AG-CCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATC
* *
2123 CGGGTTAAGTTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA-ATC
*
2164 CGGGCTATGT--CGAAGGCATT
1 CGGGCTAAGTCCCGAAGGCATT
2184 GGAACACGAG
Statistics
Matches: 114, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
36 23 0.20
37 6 0.05
38 16 0.14
39 24 0.21
40 11 0.10
41 34 0.30
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATC
Found at i:9972 original size:79 final size:81
Alignment explanation
Indices: 9836--10020 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
9826 TTGAATGATG
*
9836 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
9900 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9915 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9977 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
9995 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10021 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:10034 original size:40 final size:40
Alignment explanation
Indices: 9837--10020 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
9827 TGAATGATGT
* * * *
9837 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
9877 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
9917 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9955 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9996 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
10021 AACGAGGAGC
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:10042 original size:79 final size:79
Alignment explanation
Indices: 9837--10053 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
9827 TGAATGATGT
** * * * **
9837 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
9900 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
9917 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
9982 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
9996 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
10054 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:13958 original size:40 final size:40
Alignment explanation
Indices: 13748--13949 Score: 297
Period size: 40 Copynumber: 5.1 Consensus size: 40
13738 AACCCAAGTA
*
13748 CCTTCGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACT-AGCACAAATG
* *
13787 CCTTTGGGA--TAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
13825 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
13865 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
13905 CCTTTGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
13945 CCTTC
1 CCTTC
13950 AGATCTTAGT
Statistics
Matches: 149, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
37 4 0.03
38 28 0.19
39 9 0.06
40 108 0.72
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:15185 original size:13 final size:13
Alignment explanation
Indices: 15167--15192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15157 ATTTTTATTT
15167 TTAACATAAAATA
1 TTAACATAAAATA
15180 TTAACATAAAATA
1 TTAACATAAAATA
15193 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:22178 original size:39 final size:40
Alignment explanation
Indices: 22133--22300 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
22123 CGGGGTTTAG
* * *
22133 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
22172 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
22212 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
22252 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
22293 CCGGATAT
1 CCGGATAT
22301 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:22283 original size:41 final size:40
Alignment explanation
Indices: 22156--22300 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
22146 CTCGCACAAG
* * * * *
22156 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
22196 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
22236 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
22277 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
22301 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:23528 original size:38 final size:38
Alignment explanation
Indices: 23486--23561 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
23476 CAAGAACTCC
23486 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
23524 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
23562 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Done.