Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01599.P4
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: 26749
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:8516 original size:21 final size:21
Alignment explanation
Indices: 8490--8531 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
8480 ACATTCCTTA
8490 AGTGCCAAGCCAAACAAATAT
1 AGTGCCAAGCCAAACAAATAT
8511 AGTGCCAAGCCAAACAAATAT
1 AGTGCCAAGCCAAACAAATAT
8532 TAACTATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (21 bp):
AGTGCCAAGCCAAACAAATAT
Found at i:9228 original size:73 final size:73
Alignment explanation
Indices: 9142--9286 Score: 254
Period size: 73 Copynumber: 2.0 Consensus size: 73
9132 ATAACCTTTT
* *
9142 CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTTATTCAACATCTATTCATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACAATTCATTCAACATCTATTCATTTA
9207 ACATTTCA
66 ACATTTCA
* *
9215 CATGTTATAAAACATATACAAGTAATCACATTAGATATACAATTCATTCAACATCTATTCATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACAATTCATTCAACATCTATTCATTTA
9280 ACATTTC
66 ACATTTC
9287 CCATTTTAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (73 bp):
CATGTTATAAAACATATACAAGTAAACACATTAGACATACAATTCATTCAACATCTATTCATTTA
ACATTTCA
Found at i:9390 original size:13 final size:13
Alignment explanation
Indices: 9333--9403 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
9323 AGATCTATCT
*
9333 ATATAAACATTTC
1 ATATAATCATTTC
* *
9346 GTATAAACACTTT-
1 ATATAATCA-TTTC
*
9359 ATATAATTATTTCC
1 ATATAATCATTT-C
9373 ATATAATCGA-TTC
1 ATATAATC-ATTTC
9386 ATATAATCATTTC
1 ATATAATCATTTC
9399 ATATA
1 ATATA
9404 TTATTTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.08
13 31 0.65
14 12 0.25
15 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATAATCATTTC
Found at i:9838 original size:44 final size:44
Alignment explanation
Indices: 9785--9895 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 44
9775 CATAATGTCA
* *
9785 TTCAACTATGATCTTACACATTAAATCATGATGCCATAGCGTCT
1 TTCAGCTATGATCTTACTCATTAAATCATGATGCCATAGCGTCT
* * ** *
9829 TTTAGCTATGGTCTTACTTGTTTGAATCATGATGCCATAGCGTCT
1 TTCAGCTATGATCTTAC-TCATTAAATCATGATGCCATAGCGTCT
9874 TTCAGCTATGATCTTACTCATT
1 TTCAGCTATGATCTTACTCATT
9896 TCCAGTATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 17 0.31
45 38 0.69
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (44 bp):
TTCAGCTATGATCTTACTCATTAAATCATGATGCCATAGCGTCT
Found at i:11433 original size:13 final size:14
Alignment explanation
Indices: 11410--11441 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11400 ATATTCGACC
11410 ACATA-GTGATG-T
1 ACATATGTGATGAT
11422 ACATATGTGATGAT
1 ACATATGTGATGAT
11436 ACATAT
1 ACATAT
11442 TGAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 6 0.33
14 7 0.39
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (14 bp):
ACATATGTGATGAT
Found at i:12630 original size:2 final size:2
Alignment explanation
Indices: 12623--12653 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12613 AGTGTATACG
12623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12654 GATGCTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18404 original size:50 final size:51
Alignment explanation
Indices: 18322--18430 Score: 202
Period size: 50 Copynumber: 2.2 Consensus size: 51
18312 GACCATGGCA
*
18322 ACAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
18373 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
18423 ACAAGTGA
1 ACAAGTGA
18431 AAAGAGGTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 49 0.88
51 7 0.12
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:18464 original size:31 final size:31
Alignment explanation
Indices: 18426--18543 Score: 182
Period size: 31 Copynumber: 3.8 Consensus size: 31
18416 ACAAATGACA
* ** *
18426 AGTGAAAAGAGGTAGCTTTTGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
18457 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
18488 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
18519 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
18544 AAGTGACAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:18717 original size:49 final size:48
Alignment explanation
Indices: 18565--18768 Score: 218
Period size: 49 Copynumber: 4.3 Consensus size: 48
18555 GATTTCCGTA
* * * * * * *
18565 TAAGACCATATCTGGGATATGGCATCG--GTGTGATATATGCTACTGTA
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGAT-TTGTG
* * * * * *
18612 TAAGACCATATCTGGGATATGACATC-A-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTTGTG
18658 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATT-TGTG
*
18707 TAAGATCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTT-GTG
*
18756 TAAGGCCATAGCT
1 TAAGACCATAGCT
18769 ATAACACCCT
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
46 25 0.18
47 37 0.27
48 14 0.10
49 60 0.44
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (48 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTTGTG
Found at i:21490 original size:46 final size:46
Alignment explanation
Indices: 21438--21706 Score: 385
Period size: 46 Copynumber: 5.8 Consensus size: 46
21428 GCTTTCTGAA
21438 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
21484 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
21530 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
21576 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * * *
21622 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGACAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * * *
21668 AAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
21707 TCTTGTCACA
Statistics
Matches: 202, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 202 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:22563 original size:42 final size:43
Alignment explanation
Indices: 22511--22614 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
22501 GGGTGTTACA
*
22511 ATAGCT-GGCTATGGCATCGA-TATATGAATATGTGTAAGACC
1 ATAGCTGGGCTATGGCATCGATTATATGAAGATGTGTAAGACC
*
22552 ATAGCTGGGCTATGGCATC-ATTATGTGAAGATGTGTAAGACC
1 ATAGCTGGGCTATGGCATCGATTATATGAAGATGTGTAAGACC
* **
22594 ATAGTTGAACTATGGCATCGA
1 ATAGCTGGGCTATGGCATCGA
22615 GAAAACGAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
41 7 0.13
42 47 0.85
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (43 bp):
ATAGCTGGGCTATGGCATCGATTATATGAAGATGTGTAAGACC
Done.