Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5271.1
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: 27756
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6320 original size:48 final size:48
Alignment explanation
Indices: 6264--6355 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
6254 TAAAAAGGGC
* *
6264 AAGAGATGGTTTGTTTTTGTTCGTCTTGAGCAAAAATCCTTATGGGGA
1 AAGAGATGGTTTGTTTTTGTACGTCTTGAACAAAAATCCTTATGGGGA
*
6312 AAGAGATGGTTTGTTTTTGTACGTCTTGAATAAAAATCCTTATG
1 AAGAGATGGTTTGTTTTTGTACGTCTTGAACAAAAATCCTTATG
6356 CTCCAAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (48 bp):
AAGAGATGGTTTGTTTTTGTACGTCTTGAACAAAAATCCTTATGGGGA
Found at i:7587 original size:13 final size:13
Alignment explanation
Indices: 7571--7602 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
7561 TTTTCAAAAT
7571 CACTTTTTTCCAA
1 CACTTTTTTCCAA
7584 CACTTTTTTCCAA
1 CACTTTTTTCCAA
7597 CACTTT
1 CACTTT
7603 CTCAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (13 bp):
CACTTTTTTCCAA
Found at i:9961 original size:40 final size:40
Alignment explanation
Indices: 9898--10077 Score: 174
Period size: 40 Copynumber: 4.5 Consensus size: 40
9888 TATTCGAATG
*
9898 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * *
9938 ATATCCGGACTAAGATCCAAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * * *
9978 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCTAGCGACG
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * **
10018 ATATCCGGGCTAAG-TCCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
10057 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGAT-CCGAAG
10078 ATACTTGGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 14 0.12
39 16 0.14
40 83 0.72
41 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:10031 original size:80 final size:79
Alignment explanation
Indices: 9898--10077 Score: 213
Period size: 80 Copynumber: 2.3 Consensus size: 79
9888 TATTCGAATG
* * *
9898 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCCGGACTAAGAT-CCAAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACGATATCCGGACTAAG-TCCCAAAGGC
* *
9962 ATTTGTGCAAGTTGCT
65 -CTTGTGCAAGTGGCT
* * * *
9978 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCTAGCGACGATATCCGGGCTAAGTCCCGAAGGCC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACGATATCCGGACTAAGTCCCAAAGGCC
* *
10043 TTGTGCGAGTGGTT
66 TTGTGCAAGTGGCT
10057 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
10078 ATACTTGGGT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
77 1 0.01
78 13 0.15
79 18 0.21
80 55 0.63
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACGATATCCGGACTAAGTCCCAAAGGCC
TTGTGCAAGTGGCT
Found at i:12007 original size:2 final size:2
Alignment explanation
Indices: 12000--12077 Score: 86
Period size: 2 Copynumber: 39.5 Consensus size: 2
11990 GAGTGTAAGA
12000 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * *
12042 -G GG GG AT AG AG GG AG AG AG GG AG AG GG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12078 TAGTGTATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.01
Consensus pattern (2 bp):
AG
Found at i:12262 original size:41 final size:41
Alignment explanation
Indices: 12195--12386 Score: 199
Period size: 41 Copynumber: 4.7 Consensus size: 41
12185 TTGAGTCCAA
* * *
12195 CAGGCTTCATGCCAATGCATTTTATCAGACTTTATGCCTAG
1 CAGGCTTCATGCCGATGTATTATATCAGACTTTATGCCTAG
* * *
12236 TAGGCTTCATGCTGATGTATTATATCAGGCTTTATGCCTAG
1 CAGGCTTCATGCCGATGTATTATATCAGACTTTATGCCTAG
* * ** *
12277 TAGGCTTCTTGCC-AGTGTATTATATCA-AGCTTTGCGCCTAA
1 CAGGCTTCATGCCGA-TGTATTATATCAGA-CTTTATGCCTAG
* * *
12318 CAGGCTTCGTGCCGATGTATTATATCAGGCTTTGTGCCTAG
1 CAGGCTTCATGCCGATGTATTATATCAGACTTTATGCCTAG
* * *
12359 CAGGCTTCGTGTCGATGTGTTATATCAG
1 CAGGCTTCATGCCGATGTATTATATCAG
12387 GTTTTGAGTC
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 126 0.98
42 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
CAGGCTTCATGCCGATGTATTATATCAGACTTTATGCCTAG
Found at i:12387 original size:41 final size:40
Alignment explanation
Indices: 12217--12427 Score: 217
Period size: 41 Copynumber: 5.2 Consensus size: 40
12207 CAATGCATTT
* * * *
12217 TATCAGACTTTATGCCTAGTAGGCTTCATGCTGATGTATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGC-GATGTATTA
* * * *
12258 TATCAGGCTTTATGCCTAGTAGGCTTCTTGCCAGTGTATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGCGA-TGTATTA
* * *
12299 TATCAAGCTTTGCGCCTAACAGGCTTCGTGCCGATGTATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTG-CGATGTATTA
*
12340 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCGATGTGTTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTG-CGATGTATTA
* * * * *
12381 TATCAGGTTTTGAGTCTAGCA-GCTTCGTGCCAGTGTATTG
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGCGA-TGTATTA
12421 TATCAGG
1 TATCAGG
12428 TAAGTTGTAC
Statistics
Matches: 146, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.01
40 21 0.14
41 121 0.83
42 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (40 bp):
TATCAGGCTTTGTGCCTAGCAGGCTTCGTGCGATGTATTA
Found at i:15130 original size:46 final size:46
Alignment explanation
Indices: 15080--15169 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
15070 TAGACAAAAA
15080 GAAAGAAAGTGTAAGTAAATCAAAACTTCAACGAAGCGTTGATATT
1 GAAAGAAAGTGTAAGTAAATCAAAACTTCAACGAAGCGTTGATATT
15126 GAAAGAAAGTGTAAGTAAATCAAAACTTCAACGAAGCGTTGATA
1 GAAAGAAAGTGTAAGTAAATCAAAACTTCAACGAAGCGTTGATA
15170 CCAAAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (46 bp):
GAAAGAAAGTGTAAGTAAATCAAAACTTCAACGAAGCGTTGATATT
Found at i:16809 original size:24 final size:24
Alignment explanation
Indices: 16782--16830 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16772 GAATTTTGTT
16782 GAAAAATTAATTTAGAAAATCTAA
1 GAAAAATTAATTTAGAAAATCTAA
16806 GAAAAATTAATTTAGAAAATCTAA
1 GAAAAATTAATTTAGAAAATCTAA
16830 G
1 G
16831 TGATTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (24 bp):
GAAAAATTAATTTAGAAAATCTAA
Found at i:21917 original size:55 final size:55
Alignment explanation
Indices: 21793--21931 Score: 154
Period size: 55 Copynumber: 2.5 Consensus size: 55
21783 CGTGCGACAT
* * **
21793 AACCGTGGGCGAACCTGCCAAAACAACACGGGCACGCGCCATGCCCATGCCTTGA
1 AACCGTGGGCGAACCTGCCAAAACAACACGGGCACGCGACACGCCCATGCCAAGA
* * ** ** * *
21848 AACTGT-GGCTGAACCTGTCAAATTAACACGGGCGTGCGACACGCCCGTGCCAAGC
1 AACCGTGGGC-GAACCTGCCAAAACAACACGGGCACGCGACACGCCCATGCCAAGA
21903 AACCGTGGGCGAACCTGCCAAAACAACAC
1 AACCGTGGGCGAACCTGCCAAAACAACAC
21932 AAGCGTGGAC
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
54 3 0.05
55 60 0.91
56 3 0.05
ACGTcount: A:0.29, C:0.34, G:0.25, T:0.12
Consensus pattern (55 bp):
AACCGTGGGCGAACCTGCCAAAACAACACGGGCACGCGACACGCCCATGCCAAGA
Found at i:27271 original size:84 final size:84
Alignment explanation
Indices: 27130--27297 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
27120 ACAGTCAGGG
27130 ATACAATTTAAACTTCTATAAGTAAACATTCAAAAGATGCCATTTTCGCATGGCTTATATACATT
1 ATACAATTTAAACTTCTATAAGTAAACATTCAAAAGATGCCATTTTCGCATGGCTTATATACATT
27195 AACCAAAATATCCTCTCAC
66 AACCAAAATATCCTCTCAC
*
27214 ATACAATTTAAACTTCTATAAGTACACATTCAAAAGATGCCATTTTCGCATGGCTTATATACATT
1 ATACAATTTAAACTTCTATAAGTAAACATTCAAAAGATGCCATTTTCGCATGGCTTATATACATT
27279 AACCAAAATATCCTCTCAC
66 AACCAAAATATCCTCTCAC
27298 TACTAGTCTA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (84 bp):
ATACAATTTAAACTTCTATAAGTAAACATTCAAAAGATGCCATTTTCGCATGGCTTATATACATT
AACCAAAATATCCTCTCAC
Done.