Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2868
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: 11206
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Found at i:487 original size:46 final size:46
Alignment explanation
Indices: 385--699 Score: 400
Period size: 46 Copynumber: 6.8 Consensus size: 46
375 GAGTGTGCTC
* *
385 CCTGAAATGAAATATGTAAGACCATGGTTG-AAGATACC-TGGCAA
1 CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
429 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATCCCATGGCAA
1 CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * *
475 CATGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
521 CCTGATATGAAATGTGTAAGACCATGGTTGAAAAGATTACTATGGCAA
1 CCTGACATGAAATGTGTAAGACCATGGTTG-AAAGA-TACCATGGCAA
** *
569 CCTGACATGAAATGAATAAGACCAGGGTTGAAAGATACCAATGGCAA
1 CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACC-ATGGCAA
* ** **
616 CATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGACATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* **
663 CGTGACATGAAATGAATAAGACCATGGTTGAAAGATA
1 CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATA
700 TTTATGGCAT
Statistics
Matches: 244, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
44 28 0.11
45 7 0.03
46 108 0.44
47 36 0.15
48 65 0.27
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CCTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:660 original size:94 final size:92
Alignment explanation
Indices: 401--699 Score: 370
Period size: 94 Copynumber: 3.2 Consensus size: 92
391 ATGAAATATG
* * * **
401 TAAGACCATGGTTG-AAGATACC-TGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGA
* * *
464 TCCCATGGCAACATGATATGAAAT-ATG
66 TACCATGGCAACATGACATGAAATGA-A
* * * **
491 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTG-AAAG
* *
556 ATTACTATGGCAACCTGACATGAAATGAA
65 A-TACCATGGCAACATGACATGAAATGAA
* *
585 TAAGACCAGGGTTGAAAGATACCAATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAA
1 TAAGACCATGGTTGAAAGATACC-ATGGCAACATGACAGG-AAATGAATAAGACCATGGTTGAAA
*
650 GATACCATGGCAACGTGACATGAAATGAA
64 GATACCATGGCAACATGACATGAAATGAA
679 TAAGACCATGGTTGAAAGATA
1 TAAGACCATGGTTGAAAGATA
700 TTTATGGCAT
Statistics
Matches: 187, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
90 14 0.07
91 8 0.04
92 36 0.19
93 5 0.03
94 87 0.47
95 18 0.10
96 19 0.10
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACATGAAATGAA
Found at i:2361 original size:93 final size:95
Alignment explanation
Indices: 2229--2403 Score: 293
Period size: 93 Copynumber: 1.9 Consensus size: 95
2219 CGCCCATAAG
*
2229 CGAACTCGACGACTCAAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAAC
1 CGAACTCGA-GACTCAAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAAC
2294 TCAACGAGTTCGGATGCCTAGTTACATCTCA
65 TCAACGAGTTCGGATGCCTAGTTACATCTCA
*
2325 CGAACTCG-GACTC-AACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAAC
1 CGAACTCGAGACTCAAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAAC
2387 TCAACGAGTTCGGATGC
65 TCAACGAGTTCGGATGC
2404 TCAACATCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
92 2 0.03
93 61 0.80
94 5 0.07
96 8 0.11
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (95 bp):
CGAACTCGAGACTCAAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACT
CAACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:2393 original size:46 final size:46
Alignment explanation
Indices: 2222--2400 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 46
2212 TGTAACCCGC
* *
2222 CCATAAGCGAACTCGACGACTCAAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCG--GACTC-AACTCAACGAGTTC-GGACATTCGCAT
* *
2271 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
2321 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
2364 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
2401 TGCTCAACAT
Statistics
Matches: 111, Mismatches: 9, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 42 0.38
47 34 0.31
48 2 0.02
49 16 0.14
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:2853 original size:30 final size:30
Alignment explanation
Indices: 2818--2874 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2808 TTAACTCAAA
2818 TTTTGCAAAATTACAATTTTACCCCTAAAC
1 TTTTGCAAAATTACAATTTTACCCCTAAAC
* * * *
2848 TTTTGCATATTTACATTTTTGCCCCTA
1 TTTTGCAAAATTACAATTTTACCCCTA
2875 GGCTCGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTACCCCTAAAC
Found at i:9869 original size:93 final size:93
Alignment explanation
Indices: 9757--9928 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
9747 CGCCCATAAG
*
9757 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
9821 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
9850 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9915 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9929 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:9923 original size:46 final size:46
Alignment explanation
Indices: 9750--9925 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
9740 TGTAACCCGC
* *
9750 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
9796 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
9846 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
9889 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
9926 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 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 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.