Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold267
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: 2306539
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2295455 original size:13 final size:13
Alignment explanation
Indices: 2295437--2295461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2295427 AAAAGATCAG
2295437 TGTATCGATACAA
1 TGTATCGATACAA
2295450 TGTATCGATACA
1 TGTATCGATACA
2295462 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2295530 original size:19 final size:19
Alignment explanation
Indices: 2295506--2295583 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
2295496 AGCTTCGTAG
2295506 CGATACAACACTTATGTAT
1 CGATACAACACTTATGTAT
2295525 CGAT---ACA--T-TGTAT
1 CGATACAACACTTATGTAT
2295538 CGATACAACACTTATGTAT
1 CGATACAACACTTATGTAT
* *
2295557 CAATACATCACTTATGTAT
1 CGATACAACACTTATGTAT
*
2295576 TGATACAA
1 CGATACAA
2295584 TTTCTGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
13 9 0.19
14 1 0.02
16 6 0.12
18 1 0.02
19 31 0.65
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (19 bp):
CGATACAACACTTATGTAT
Found at i:2295538 original size:13 final size:13
Alignment explanation
Indices: 2295520--2295544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2295510 ACAACACTTA
2295520 TGTATCGATACAT
1 TGTATCGATACAT
2295533 TGTATCGATACA
1 TGTATCGATACA
2295545 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2304463 original size:88 final size:87
Alignment explanation
Indices: 2304316--2304730 Score: 422
Period size: 88 Copynumber: 4.7 Consensus size: 87
2304306 TGAAGGGTAA
** * * * * *
2304316 ATTTGAAATTTTTGGGAGAATAAGGTTAGAATATCCCCTAGAAGTA-TTGGAGATGGAGTTTCCC
1 ATTTG-AATTTTTGTTAGAACAAGGTTAGAGTAT-CCCTTGAAATAGTAGG-GATGGAGTTTCCC
* * *
2304380 TAAGGATAAAATTATGCAAAGAAAA
63 TAAGGATAAAGTTATACAAAGAAAG
* * * * *
2304405 ATTTGAATTTTTATTCA-AACAGGGTTAGAGTATCTCCTTGAAATAGTGGGGATAGAGTTTCTCT
1 ATTTGAATTTTTGTT-AGAACAAGGTTAGAGTATC-CCTTGAAATAGTAGGGATGGAGTTTCCCT
* *
2304469 AAGGATAAAGTTATACGAAGGAAG
64 AAGGATAAAGTTATACAAAGAAAG
* * * *
2304493 ATTTGAATTTTTGTTAGAATAAGGTTAGAGTATCCCCTCAGAATAGTTGGGATGGAGTTTCCCTA
1 ATTTGAATTTTTGTTAGAACAAGGTTAGAGTATCCCTTGA-AATAGTAGGGATGGAGTTTCCCTA
* *
2304558 AAGATAAAGTTATACAAAGGAAG
65 AGGATAAAGTTATACAAAGAAAG
** * * *
2304581 ATTTGAATTTTTGTTAGAA-TGGGTTTGAAGTATCCTCTCGAAATAGTAGAGATGGAGTTTCCCT
1 ATTTGAATTTTTGTTAGAACAAGGTTAG-AGTATCC-CTTGAAATAGTAGGGATGGAGTTTCCCT
*
2304645 AAGGATAAAGTTATACGAAGAAAG
64 AAGGATAAAGTTATACAAAGAAAG
* * * * *
2304669 ATTTAAATTTTTGTTAGAACAAGGTTAGAGTATCTTCTTGGAATAATAGGGATAGAGTTTCC
1 ATTTGAATTTTTGTTAGAACAAGGTTAGAGTATC-CCTTGAAATAGTAGGGATGGAGTTTCC
2304731 ACAAAATCGA
Statistics
Matches: 270, Mismatches: 47, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
87 11 0.04
88 243 0.90
89 16 0.06
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (87 bp):
ATTTGAATTTTTGTTAGAACAAGGTTAGAGTATCCCTTGAAATAGTAGGGATGGAGTTTCCCTAA
GGATAAAGTTATACAAAGAAAG
Found at i:2304626 original size:176 final size:176
Alignment explanation
Indices: 2304316--2304702 Score: 514
Period size: 176 Copynumber: 2.2 Consensus size: 176
2304306 TGAAGGGTAA
** *
2304316 ATTTGAAATTTTTGGGAGAATAAGGTTAGAATATCCCCTAGAAGTATTGGAGATGGAGTTTCCCT
1 ATTTG-AATTTTTGTTAGAATAAGGTTAGAGTATCCCCTAGAAGTATTGGAGATGGAGTTTCCCT
* * *
2304381 AAGGATAAAATTATGCAAAGAAAAATTTGAATTTTTATTCAAACAGGGTTAGAGTATCTCCTTGA
65 AAAGATAAAATTATACAAAGAAAAATTTGAATTTTTATTCAAACAGGGTTAGAGTATCTCCTCGA
* * * *
2304446 AATAGTGGGGATAGAGTTTCTCTAAGGATAAAGTTATACGAAGGAAG
130 AATAGTAGAGATAGAGTTTCCCTAAGGATAAAGTTATACGAAGAAAG
2304493 ATTTGAATTTTTGTTAGAATAAGGTTAGAGTATCCCCTCAGAA-TAGTTGG-GATGGAGTTTCCC
1 ATTTGAATTTTTGTTAGAATAAGGTTAGAGTATCCCCT-AGAAGTA-TTGGAGATGGAGTTTCCC
* * * * * *
2304556 TAAAGATAAAGTTATACAAAGGAAGATTTGAATTTTTGTT-AGAA-TGGGTTTGAAGTATC-CTC
64 TAAAGATAAAATTATACAAAGAAAAATTTGAATTTTTATTCA-AACAGGGTTAG-AGTATCTC-C
*
2304618 TCGAAATAGTAGAGATGGAGTTTCCCTAAGGATAAAGTTATACGAAGAAAG
126 TCGAAATAGTAGAGATAGAGTTTCCCTAAGGATAAAGTTATACGAAGAAAG
* *
2304669 ATTTAAATTTTTGTTAGAACAAGGTTAGAGTATC
1 ATTTGAATTTTTGTTAGAATAAGGTTAGAGTATC
2304703 TTCTTGGAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
175 8 0.04
176 165 0.89
177 13 0.07
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (176 bp):
ATTTGAATTTTTGTTAGAATAAGGTTAGAGTATCCCCTAGAAGTATTGGAGATGGAGTTTCCCTA
AAGATAAAATTATACAAAGAAAAATTTGAATTTTTATTCAAACAGGGTTAGAGTATCTCCTCGAA
ATAGTAGAGATAGAGTTTCCCTAAGGATAAAGTTATACGAAGAAAG
Done.