Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2260
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: 15985
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Found at i:1896 original size:10 final size:10
Alignment explanation
Indices: 1881--1910 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1871 AATCCCCTGT
1881 TTATAAATCA
1 TTATAAATCA
1891 TTATAAATCA
1 TTATAAATCA
1901 TTATAAATCA
1 TTATAAATCA
1911 CACAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATAAATCA
Found at i:2396 original size:48 final size:48
Alignment explanation
Indices: 2325--2430 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
2315 AGATAAATAT
* * *
2325 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
2373 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
2421 ATGTGTATAT
1 ATATGTATAT
2431 ATTGTGGCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:4816 original size:104 final size:104
Alignment explanation
Indices: 4636--4859 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
4626 TGTATATAAA
** * *
4636 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
4701 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
4740 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
4804 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
4844 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
4860 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:4909 original size:70 final size:71
Alignment explanation
Indices: 4778--4928 Score: 241
Period size: 70 Copynumber: 2.1 Consensus size: 71
4768 TCATTGGTGG
* *
4778 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAA-GTGAAAAGGGGTTGCTATGTGCTGATTCCCCC
4843 GAGGGGT
65 GAGGGGT
***
4850 TGCTAAGTGCGATATCCATTGTATATTTGAAA-TGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
4914 AGGGGT
66 AGGGGT
4920 TGCTAAGTG
1 TGCTAAGTG
4929 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 46 0.62
72 28 0.38
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:4933 original size:27 final size:27
Alignment explanation
Indices: 4887--4938 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4877 TGAAATGAAA
* *
4887 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGATGATTCCCCCG
4914 AGGGGTTGCTAAGTGATGATTCCCC
1 AGGGGTTGCTAAGTGATGATTCCCC
4939 GATTCAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGATGATTCCCCCG
Found at i:12367 original size:104 final size:104
Alignment explanation
Indices: 12187--12410 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
12177 TGTATATAAA
** * *
12187 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
12252 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
12291 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
12355 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
12395 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
12411 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:12462 original size:71 final size:72
Alignment explanation
Indices: 12329--12480 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
12319 TCATTGGTGG
* *
12329 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12394 GAGGGGT
66 GAGGGGT
***
12401 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
12465 GAGGGGT
66 GAGGGGT
12472 TGCTAAGTG
1 TGCTAAGTG
12481 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Done.