Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2263
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: 48058
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4875 original size:27 final size:27
Alignment explanation
Indices: 4708--4885 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
4698 TAAATTGTAC
*
4708 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
4735 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
4761 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
4789 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
4817 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
4844 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
4871 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
4886 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:4876 original size:82 final size:81
Alignment explanation
Indices: 4705--4885 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
4695 GATTAAATTG
* * * *
4705 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
4770 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
4786 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
4850 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
4868 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
4886 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:12880 original size:27 final size:27
Alignment explanation
Indices: 12713--12890 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
12703 TAAATTGTAC
*
12713 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
12740 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
12766 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
12794 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
12822 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
12849 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
12876 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12891 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:12881 original size:82 final size:81
Alignment explanation
Indices: 12710--12890 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
12700 GATTAAATTG
* * * *
12710 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12775 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
12791 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12855 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
12873 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12891 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:20799 original size:11 final size:11
Alignment explanation
Indices: 20736--20799 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
20726 GGTACGGTTT
*
20736 TGATGTGGTGG
1 TGATATGGTGG
* *
20747 TGCTAAGGTGG
1 TGATATGGTGG
*
20758 TTGA-ATAGTGG
1 -TGATATGGTGG
20769 TGATATGGTGG
1 TGATATGGTGG
20780 TTG-TATGGTGG
1 -TGATATGGTGG
*
20791 TGATTTGGT
1 TGATATGGT
20800 TTGTAGTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 5 0.12
11 32 0.78
12 4 0.10
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.39
Consensus pattern (11 bp):
TGATATGGTGG
Found at i:20799 original size:22 final size:22
Alignment explanation
Indices: 20743--20799 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
20733 TTTTGATGTG
* *
20743 GTGGTGCTAAGGTGGTTGAATA
1 GTGGTGATATGGTGGTTGAATA
* *
20765 GTGGTGATATGGTGGTTGTATG
1 GTGGTGATATGGTGGTTGAATA
*
20787 GTGGTGATTTGGT
1 GTGGTGATATGGT
20800 TTGTAGTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.39
Consensus pattern (22 bp):
GTGGTGATATGGTGGTTGAATA
Found at i:32465 original size:27 final size:27
Alignment explanation
Indices: 32038--32481 Score: 286
Period size: 27 Copynumber: 16.4 Consensus size: 27
32028 TTTCACCCTA
* * ** *
32038 CAAGGGTGTTTTGGTAAATACACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** * *
32065 CAAGGGTATTTCAATAATTTTGCAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
32092 CAATGGTTTTTTTGTAATTTTTTA-AAAGT
1 CAAGGGTATTTTGGTAA--TTTTACAAA-T
*
32121 CAAAGGTATTTCT-GTAATTTT-CTAAAT
1 CAAGGGTATTT-TGGTAATTTTAC-AAAT
* * * *
32148 TAGGGGTATTTTTGTAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
32175 AAAGGGTATTTTAGTAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** *
32202 CAAGATTATTTTGATAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * **
32229 CGAGGTTATTTTAGTAATTTTACAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* ** * **
32256 CAATGGTATTTTAATAATTTTATAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
32283 CAAGGGTATTTCGATAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
32310 CGAGGGTATTTTGGTAATTTCT-CAAAT
1 CAAGGGTATTTTGGTAATTT-TACAAAT
* * *
32337 TAGGGGTA-TTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * * *
32363 CTGGGGTATTTTTGTAATTTTTCAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
32390 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * * *
32417 TAGGGGTATTTTGGTAACTTTGCTAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
32444 CGAGGGTATTTTGGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
32471 CAAGGTTATTT
1 CAAGGGTATTT
32482 AATATTCTAC
Statistics
Matches: 333, Mismatches: 73, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
25 1 0.00
26 22 0.07
27 284 0.85
28 8 0.02
29 17 0.05
30 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:32520 original size:27 final size:27
Alignment explanation
Indices: 32478--32551 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
32468 AATCAAGGTT
32478 ATTT-AAT-ATTCTACCCTACAAGGGC
1 ATTTCAATAATTCTACCCTACAAGGGC
*
32503 ATTTCAATAATTCTACCCTACAGGGGC
1 ATTTCAATAATTCTACCCTACAAGGGC
* * *
32530 ATTTCAGTAATACTAGCCTACA
1 ATTTCAATAATTCTACCCTACA
32552 GATATGAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.09
26 3 0.07
27 36 0.84
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (27 bp):
ATTTCAATAATTCTACCCTACAAGGGC
Found at i:33369 original size:34 final size:34
Alignment explanation
Indices: 33326--33396 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
33316 ACCACCAAAG
33326 AAAACATTTAATTGTGTCATTTACTTGCACAATT
1 AAAACATTTAATTGTGTCATTTACTTGCACAATT
33360 AAAACATTTAATTGTGTCATTTACTTGCACAATT
1 AAAACATTTAATTGTGTCATTTACTTGCACAATT
33394 AAA
1 AAA
33397 TGCTTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (34 bp):
AAAACATTTAATTGTGTCATTTACTTGCACAATT
Found at i:41867 original size:93 final size:93
Alignment explanation
Indices: 41755--41926 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
41745 CGCCCATAAG
*
41755 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAAATCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAAATCGGACTCAACTC
41819 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
* *
41848 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
41913 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41927 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:41921 original size:46 final size:46
Alignment explanation
Indices: 41748--41923 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
41738 TGTAACCCGC
* *
41748 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * *
41794 CCATAAGTGAAATCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
41844 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41887 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
41924 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.