Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00550.F1
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: 4241
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3467 original size:44 final size:44
Alignment explanation
Indices: 3196--3948 Score: 290
Period size: 44 Copynumber: 17.0 Consensus size: 44
3186 CCTACTGCAA
* * *
3196 TTGTAGCTT-GATCTGCTCCATTGCAACTTCAAGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
3239 CTGCTATCTTCAGTCTGCCCCACTGCAACTTTAGGGAGATAAGAC
1 TTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
3284 TTGTAACTTCAA-CTTGCCCCACTGCAACTTTAGGGGGGTAAGGT
1 TTGTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * ***
3328 TTGTGGCTTCAATCTACTCTACCATAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* ** * * * *
3372 TCACCATGATAGGTTTGAT-T-CAACCTACTACAACTTCAGAGG-TATAGGAT
1 T-----TG-TAGCTTCAATCTGC-TCC-ACTGCAACTTCAG-GGAGATAAGAT
* *
3422 TTGTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
3466 TTGCAACTTCAATCTGCTCCACTGTAACTTCAGAGAGACAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** ** * * *
3510 TTGCGGCTTTGATTTGCTCTACTGCAACTTCAGGGAGACAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*** * ** * * ** *
3554 CTACAATCTTCAGCCTACTCCACTACTGCTT-AGGGAGATAGGA-
1 -TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * **** *
3597 TGGTGGCTTAAATCTGCTCCACTATTGCTT-AGGGAGACAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
3640 TTGTTGTCTTCGATCTGCTCCATTGCAACTTCAGGGAGACAAGAT
1 TTGTAG-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*** * ** * * ** *
3685 CTACAATCTTCAGCCTACTCCACTACTGCTT-AGGGAGATAGGA-
1 -TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
3728 TGGTAGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
3772 TCGCCATCTTCGATCTGCTCCACTACAACTTCAGGGAGATAAGAT
1 TTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * ** * * * *
3817 TTGCA-ATCTCTAGCCTACTCCACTACAACTT-AAGGAGATAGGA-
1 TTGTAGCT-TC-AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * * *
3860 TGGTGGCTTAAATCTGCTTCACTGTAACTTCAGGAAGACAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
3904 TCGCTATCTTCGATCTGCTCTACTGCAACTTTAGGGAGACAAGAT
1 TTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
3949 CTGCAATCTT
Statistics
Matches: 510, Mismatches: 170, Indels: 58
0.69 0.23 0.08
Matches are distributed among these distances:
42 62 0.12
43 30 0.06
44 223 0.44
45 162 0.32
46 2 0.00
48 1 0.00
49 4 0.01
50 24 0.05
51 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:3667 original size:131 final size:132
Alignment explanation
Indices: 3476--3958 Score: 650
Period size: 132 Copynumber: 3.7 Consensus size: 132
3466 TTGCAACTTC
* ** * * *
3476 AATCTGCTCCACTGTAACTTCA-GAGAGACAAGATTTG-CGGCTTTGATTTGCTCTACTGCAACT
1 AATCTGCTCCACTGTAACTTCAGGA-AGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACT
3539 TCAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
65 TCAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
3604 TTA
130 TTA
* ** * * *** *
3607 AATCTGCTCCACTATTGCTT-AGGGAGACAAGATTTGTTGTCTTCGATCTGCTCCATTGCAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
*
3671 CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTAGCT
66 CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCT
3736 TA
131 TA
* * *
3738 AATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTACAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
* * * ** *
3803 CAGGGAGATAAGATTTGCAATC-TCTAGCCTACTCCACTACAACTTAAGGAGATAGGATGGTGGC
66 CAGGGAGACAAGATCTACAATCTTC-AGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGC
3867 TTA
130 TTA
* * *
3870 AATCTGCTTCACTGTAACTTCAGGAAGACAAGATTCGCTATCTTCGATCTGCTCTACTGCAACTT
1 AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
* *
3935 TAGGGAGACAAGATCTGCAATCTT
66 CAGGGAGACAAGATCTACAATCTT
3959 TAGTCTGCTT
Statistics
Matches: 310, Mismatches: 37, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
130 13 0.04
131 122 0.39
132 174 0.56
133 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
AATCTGCTCCACTGTAACTTCAGGAAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTT
CAGGGAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCT
TA
Found at i:3793 original size:87 final size:88
Alignment explanation
Indices: 3608--3817 Score: 219
Period size: 87 Copynumber: 2.4 Consensus size: 88
3598 GGTGGCTTAA
* * * * ** *
3608 ATCTGCTCCACTATTGCTTAGGGAGACAAGATTTGTTGTCTTCGATCTGCTCCATTGCAACTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTCA
*
3673 GGGAGACAAGATCTACAATCTTC
66 GGAAGACAAGATCTACAATCTTC
* * * *
3696 AGCCTACTCCACTACTGCTTAGGGAGATAGGA-TGGTAG-CTTAAATCTGCTTCACTGCAACTTC
1 A-TCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTC
* *
3759 AGGAAGACAAGAT-TCGCCATCTTC
65 AGGAAGACAAGATCT-ACAATCTTC
**
3783 GATCTGCTCCACTACAACTTCAGGGAGATAAGATT
1 -ATCTGCTCCACTACTGCTT-AGGGAGATAAGATT
3818 TGCAATCTCT
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
86 1 0.01
87 54 0.55
88 17 0.17
89 26 0.27
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (88 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTGGTAGTCTTAAATCTGCTCCACTGCAACTTCA
GGAAGACAAGATCTACAATCTTC
Found at i:3958 original size:45 final size:45
Alignment explanation
Indices: 3432--3967 Score: 283
Period size: 45 Copynumber: 12.2 Consensus size: 45
3422 TTGTGGCTTT
*
3432 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAA-CTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * ** *
3476 AATCTGCTCCACTGTAACTTCAGAGAGACAAGATTTGC-GGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * * *
3520 GATTTGCTCTACTGCAACTTCAGGGAGACAAGATCTACAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * ** * * * * *
3565 AGCCTACTCCACTACTGCTT-AGGGAGATAGGATGGTG---GCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGAT-TTGCAATCTTC
**** ***
3607 AATCTGCTCCACTATTGCTT-AGGGAGACAAGATTTGTTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * *
3651 GATCTGCTCCATTGCAACTTCAGGGAGACAAGATCTACAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * ** * * ** * *
3696 AGCCTACTCCACTACTGCTT-AGGGAGATAGGA--TGGTAGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * *
3738 AATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * *
3783 GATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCAATC-TC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
** * * * * * * * *
3827 TAGCCTACTCCACTACAACTT-AAGGAGATAGGATGGTG---GCTTA
1 -AATCTGCTCCACTGCAACTTCAGGGAGACAAGAT-TTGCAATCTTC
* * * * *
3870 AATCTGCTTCACTGTAACTTCAGGAAGACAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
* * * * *
3915 GATCTGCTCTACTGCAACTTTAGGGAGACAAGATCTGCAATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
*
3960 AGTCTGCT
1 AATCTGCT
3968 TCCTCGCTAC
Statistics
Matches: 353, Mismatches: 122, Indels: 33
0.69 0.24 0.06
Matches are distributed among these distances:
41 2 0.01
42 64 0.18
43 19 0.05
44 120 0.34
45 148 0.42
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGACAAGATTTGCAATCTTC
Found at i:4221 original size:64 final size:64
Alignment explanation
Indices: 4105--4232 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
4095 TCATGTATCT
* * *
4105 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAAGGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAAGAAATCAAATACTCCTAACTAGATGTG
*
4169 ATGCTTATGTCAAATAATTAAGATGCTATGATCGAAATGAAAT-AAATACTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAA-GAAATCAAATACTCCTAACTAGATGTG
4233 TTATGAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 55 0.93
65 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAAGATGCTATGATCGAAAGAAATCAAATACTCCTAACTAGATGTG
Done.