Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3589
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: 27179
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:9258 original size:77 final size:78
Alignment explanation
Indices: 9157--9379 Score: 247
Period size: 77 Copynumber: 2.8 Consensus size: 78
9147 GCTCCTCGTT
* * *
9157 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
9222 -TT-TAAACTCGCA
66 CTTGT-AACTCGCA
* * * *
9234 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG
*
9298 AACTTGTATCTCGCA
65 -ACTTGTAACTCGCA
* * * * * *
9313 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG
9377 GAC
64 GAC
9380 AGCATTCAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
77 47 0.39
78 13 0.11
79 45 0.37
80 16 0.13
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
CTTGTAACTCGCA
Found at i:9283 original size:40 final size:40
Alignment explanation
Indices: 9157--9378 Score: 224
Period size: 39 Copynumber: 5.7 Consensus size: 40
9147 GCTCCTCGTT
* * * *
9157 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
9197 C-AATGCCTTCGGGACTTAACCCGGATTTA--AACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
9234 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
9274 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
9313 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9354 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9379 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
37 8 0.05
38 30 0.19
39 57 0.37
40 49 0.32
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9387 original size:41 final size:41
Alignment explanation
Indices: 9310--9387 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
9300 CTTGTATCTC
* * *
9310 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
9351 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
9388 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:17185 original size:40 final size:39
Alignment explanation
Indices: 17025--17279 Score: 234
Period size: 39 Copynumber: 6.5 Consensus size: 39
17015 AAATCACGTA
* * * **
17025 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
17064 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
17103 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
17142 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
*
17182 CCTTCGGG-CTTAACCCGGAATT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
** * * *
17220 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
17260 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
17280 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.01
38 27 0.15
39 91 0.51
40 48 0.27
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:17288 original size:41 final size:41
Alignment explanation
Indices: 17211--17288 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
17201 ATTGTATCTC
* * *
17211 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
17252 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
17289 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19908 original size:22 final size:24
Alignment explanation
Indices: 19880--19924 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
19870 TTGGCCGTTG
19880 GTTGGCTT-TGCCA-TTTCTGGCT
1 GTTGGCTTATGCCAGTTTCTGGCT
*
19902 GTTGGCTTATGGCAGTTTCTGGC
1 GTTGGCTTATGCCAGTTTCTGGC
19925 CATTGGACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.07, C:0.20, G:0.31, T:0.42
Consensus pattern (24 bp):
GTTGGCTTATGCCAGTTTCTGGCT
Found at i:19930 original size:24 final size:22
Alignment explanation
Indices: 19881--19930 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
19871 TGGCCGTTGG
**
19881 TTGGCTTTGCCATTTCTGGCTG
1 TTGGCTTTGCCATTTCTGGCCA
*
19903 TTGGCTTATGGCAGTTTCTGGCCA
1 TTGGCTT-TGCCA-TTTCTGGCCA
19927 TTGG
1 TTGG
19931 ACTAACCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.08, C:0.20, G:0.30, T:0.42
Consensus pattern (22 bp):
TTGGCTTTGCCATTTCTGGCCA
Found at i:24118 original size:27 final size:26
Alignment explanation
Indices: 24088--24307 Score: 147
Period size: 27 Copynumber: 8.2 Consensus size: 26
24078 GCAAAATGGC
* *
24088 AATTTTACCCCACAAGGGCATCTTGGT
1 AATTTTACCCTACAAGGGTAT-TTGGT
* * *
24115 AATTCTACCCTATAAGGGTATTTTG-
1 AATTTTACCCTACAAGGGTATTTGGT
24140 ATATTTCTACCCTACAAGGGTATTTCGGT
1 A-ATTT-TACCCTACAAGGGTATTT-GGT
* *
24169 AATTTTATCCTACAGGGGTATTTCGGT
1 AATTTTACCCTACAAGGGTATTT-GGT
* * **
24196 AATTCTACCTTAC-AGAGGTATTTCAAT
1 AATTTTACCCTACAAG-GGTATTT-GGT
* * *
24223 AATTCTACCCTACAGGGGTATTTGAAT
1 AATTTTACCCTACAAGGGTATTTG-GT
* * * *
24250 AATTCTACCCTATAGGGGTGTTTCGGT
1 AATTTTACCCTACAAGGGTATTT-GGT
* * *
24277 AATTCTACCTTACAGGGGTATTTCGGT
1 AATTTTACCCTACAAGGGTATTT-GGT
24304 AATT
1 AATT
24308 CTACAACTTA
Statistics
Matches: 160, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.01
26 7 0.04
27 144 0.90
28 7 0.04
29 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
AATTTTACCCTACAAGGGTATTTGGT
Found at i:24157 original size:54 final size:54
Alignment explanation
Indices: 24088--24311 Score: 229
Period size: 54 Copynumber: 4.1 Consensus size: 54
24078 GCAAAATGGC
* * * * *
24088 AATTTTACCCCACAAGGGCATCTT-GGTAATTCTACCCTATAAGGGTATTTTGAT
1 AATTCTACCCTACAAGGGTAT-TTCGGTAATTCTACCCTACAGGGGTATTTTGAT
* * * * *
24142 ATTTCTACCCTACAAGGGTATTTCGGTAATTTTATCCTACAGGGGTATTTCGGT
1 AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTGAT
* **
24196 AATTCTACCTTAC-AGAGGTATTTCAATAATTCTACCCTACAGGGGTA-TTTGAAT
1 AATTCTACCCTACAAG-GGTATTTCGGTAATTCTACCCTACAGGGGTATTTTG-AT
* * * * * *
24250 AATTCTACCCTATAGGGGTGTTTCGGTAATTCTACCTTACAGGGGTATTTCGGT
1 AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTGAT
24304 AATTCTAC
1 AATTCTAC
24312 AACTTATTCA
Statistics
Matches: 138, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
53 7 0.05
54 127 0.92
55 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (54 bp):
AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTGAT
Found at i:24308 original size:27 final size:27
Alignment explanation
Indices: 24112--24311 Score: 240
Period size: 27 Copynumber: 7.4 Consensus size: 27
24102 AGGGCATCTT
* * *
24112 GGTAATTCTACCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
24139 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
24166 GGTAATTTTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
24193 GGTAATTCTACCTTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
24220 AATAATTCTACCCTACAGGGGTATTT-
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
24246 GAATAATTCTACCCTATAGGGGTGTTTC
1 G-GTAATTCTACCCTACAGGGGTATTTC
*
24274 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
24301 GGTAATTCTAC
1 GGTAATTCTAC
24312 AACTTATTCA
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
27 146 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Done.