Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00715.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, 703
Length: 1172
ACGTcount: A:0.29, C:0.37, G:0.11, T:0.23
Found at i:386 original size:99 final size:99
Alignment explanation
Indices: 279--790 Score: 572
Period size: 99 Copynumber: 5.2 Consensus size: 99
269 AACTCCTGTT
* * *
279 TACAAGTCCCCACCACCTCCTCCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACC
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACC
*
344 TCCACCACCATCACCACCCAAGCATCCTTACAAG
66 TCCACCACCATCACCACCCAAGCACCCTTACAAG
* * * *
378 TACAAGTCCCCACCACCACCACCACCACCCTCACCACCCAAACACCCCTACAAGTACAAGTCCCC
1 TACAAGT--CC-CCACCACCACCACCA---TCACCACCCAAGCATCCTTACAAGTACAAGTCTCC
* * * *
443 ACCCCCACCCCCACCATCACCACCTAAGCACCCTTACAAG
60 ACCACCTCCACCACCATCACCACCCAAGCACCCTTACAAG
* * *
483 TACAAGTCTCCA-C-CC-CCACCAT---C-TCC-AG--T--TTACAAGTATAAGTCTCCACCACC
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACC
*
536 TCCACCGCCATCACCACCCAAGCACCCTTACAAG
66 TCCACCACCATCACCACCCAAGCACCCTTACAAG
*
570 TACAAGTCCCCACCACCTCCACCACCATCACCACCCAAGCACCCTTACAAGTACAAG--TCC-CC
1 TACAAGTCCCCACCA---CCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCACC
* *
632 ACCTCCACCACCATCACC-CCCAAAGCATCCTTATAAG
63 ACCTCCACCACCATCACCACCC-AAGCACCCTTACAAG
* *
669 TACAAGTCTCCACCACCACCACCATCACCACCCAAGCATTCC-TACAAGTACAAGTCTCCCCCAC
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCA-TCCTTACAAGTACAAGTCTCCACCAC
* * *
733 CACCACCTCCATCCCCACCCAAGCACCCTTACAAG
65 CTCCACCACCATCACCACCCAAGCACCCTTACAAG
* *
768 TACAAGTCTCCACCCCCACCACC
1 TACAAGTCCCCACCACCACCACC
791 TCCGGTTTAC
Statistics
Matches: 347, Mismatches: 39, Indels: 54
0.79 0.09 0.12
Matches are distributed among these distances:
87 61 0.18
88 1 0.00
91 1 0.00
92 4 0.01
93 8 0.02
96 37 0.11
97 4 0.01
98 8 0.02
99 111 0.32
100 8 0.02
101 3 0.01
102 28 0.08
103 1 0.00
105 72 0.21
ACGTcount: A:0.30, C:0.49, G:0.06, T:0.14
Consensus pattern (99 bp):
TACAAGTCCCCACCACCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCACCACC
TCCACCACCATCACCACCCAAGCACCCTTACAAG
Found at i:445 original size:48 final size:48
Alignment explanation
Indices: 279--790 Score: 503
Period size: 51 Copynumber: 10.5 Consensus size: 48
269 AACTCCTGTT
* * *
279 TACAAGTCCCCACCACCTCCTCCATCACCACCCAAGCATCCTTACAAG
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
* *
327 TACAAGTCTCCTCCACCTCCACCACCATCACCACCCAAGCATCCTTACAAG
1 TACAAG--TCC-CCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
* *
378 TACAAGTCCCCACCACCACCACCACCACCCTCACCACCCAAACACCCCTACAAG
1 TACAAGT--CC-CCACCACCACCACCA---TCACCACCCAAGCACCCTTACAAG
* *
432 TACAAGTCCCCACCCCCACCCCCACCATCACCACCTAAGCACCCTTACAAG
1 TACAAGTCCCCA---CCACCACCACCATCACCACCCAAGCACCCTTACAAG
* * *
483 TACAAGTCTCCA-C-CC-CCACCAT---C-TCC-AG----TTTACAAG
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
* * *
519 TATAAGTCTCCACCACCTCCACCGCCATCACCACCCAAGCACCCTTACAAG
1 TACAAG--TCC-CCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
570 TACAAGTCCCCACCACCTCCACCACCATCACCACCCAAGCACCCTTACAAG
1 TACAAGTCCCCACCA---CCACCACCATCACCACCCAAGCACCCTTACAAG
* * *
621 TACAAGTCCCCACCTCCACCACCATCACC-CCCAAAGCATCCTTATAAG
1 TACAAGTCCCCACCACCACCACCATCACCACCC-AAGCACCCTTACAAG
* *
669 TACAAGTCTCCACCACCACCACCATCACCACCCAAGCATTCC-TACAAG
1 TACAAGTCCCCACCACCACCACCATCACCACCCAAGCA-CCCTTACAAG
* *
717 TACAAGTCTCCCCCACCACCACCTCCATCCCCACCCAAGCACCCTTACAAG
1 TACAAG--T-CCCCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
* *
768 TACAAGTCTCCACCCCCACCACC
1 TACAAGTCCCCACCACCACCACC
791 TCCGGTTTAC
Statistics
Matches: 391, Mismatches: 37, Indels: 72
0.78 0.07 0.14
Matches are distributed among these distances:
36 12 0.03
38 2 0.01
39 3 0.01
40 3 0.01
41 3 0.01
42 7 0.02
45 8 0.02
46 4 0.01
47 6 0.02
48 94 0.24
49 11 0.03
50 6 0.02
51 191 0.49
52 2 0.01
54 39 0.10
ACGTcount: A:0.30, C:0.49, G:0.06, T:0.14
Consensus pattern (48 bp):
TACAAGTCCCCACCACCACCACCATCACCACCCAAGCACCCTTACAAG
Found at i:457 original size:105 final size:105
Alignment explanation
Indices: 288--503 Score: 297
Period size: 105 Copynumber: 2.1 Consensus size: 105
278 TTACAAGTCC
* * * * * * * *
288 CCACCACCTCCTCCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACCTCCACCACC
1 CCACCACCACCACCATCACCACCCAAACACCCCTACAAGTACAAGTCCCCACCACCACCACCACC
*
353 ATCACCACCCAAGCATCCTTACAAGTACAAGTCCCCACCA
66 ATCACCACCCAAGCACCCTTACAAGTACAAGTCCCCACCA
* * *
393 CCACCACCACCACCCTCACCACCCAAACACCCCTACAAGTACAAGTCCCCACCCCCACCCCCACC
1 CCACCACCACCACCATCACCACCCAAACACCCCTACAAGTACAAGTCCCCACCACCACCACCACC
* * *
458 ATCACCACCTAAGCACCCTTACAAGTACAAGTCTCCACCC
66 ATCACCACCCAAGCACCCTTACAAGTACAAGTCCCCACCA
498 CCACCA
1 CCACCA
504 TCTCCAGTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.30, C:0.52, G:0.05, T:0.13
Consensus pattern (105 bp):
CCACCACCACCACCATCACCACCCAAACACCCCTACAAGTACAAGTCCCCACCACCACCACCACC
ATCACCACCCAAGCACCCTTACAAGTACAAGTCCCCACCA
Found at i:788 original size:285 final size:286
Alignment explanation
Indices: 279--823 Score: 832
Period size: 285 Copynumber: 1.9 Consensus size: 286
269 AACTCCTGTT
* *
279 TACAAGTCCCCACCACCTCCTCCATCACCACCCAAGCATCCTTACAAGTACAAGTCTCCTCCACC
1 TACAAGTCCCCACCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAG-CTCCTCCACC
344 TCCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCCCCACCACCACCACCACCACCCT
65 TCCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGT--CCACCACCACCACCACCA--CT
* * *
409 CACCACCCAAACACCCCTACAAGTACAAGTCCCCACCCCCACCCCCACCATCACCACCTAAGCAC
126 CACCACCCAAACACCCCTACAAGTACAAGTCCCCACCACCACCACCACCATCACCACCCAAGCAC
*
474 CCTTACAAGTACAAGTCTCCACCCCCACCATCTCCAGTTTACAAGTATAAGTCTCCACCACCTCC
191 CCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTATAAGTCTCCACCACCTCC
539 ACCGCCATCACCACCCAAGCACCCTTACAAG
256 ACCGCCATCACCACCCAAGCACCCTTACAAG
570 TACAAGTCCCCACCACCTCCACCACCATCACCACCCAAGCACCCTTACAAGTACAAG-TCC-CCA
1 TACAAGTCCCCACCACCT---CCACCATCACCACCCAAGCACCCTTACAAGTACAAGCTCCTCCA
* *
633 CCTCCACCACCATCACC-CCCAAAGCATCCTTATAAGTACAAGT-CTCCACCACCACCACCA-TC
63 CCTCCACCACCATCACCACCC-AAGCATCCTTACAAGTACAAGTCCACCACCACCACCACCACTC
* ** * *
695 ACCACCCAAGCATTCCTACAAGTACAAGTCTCCC-CCACCACCACCTCCATCCCCACCCAAGCAC
127 ACCACCCAAACACCCCTACAAGTACAAGTC-CCCACCACCACCACCACCATCACCACCCAAGCAC
*
759 CCTTACAAGTACAAGTCTCCACCCCCACCACCTCCGGTTTACAAGTATAAGTCTCCACCACCTCC
191 CCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTATAAGTCTCCACCACCTCC
824 TCCCGTTTAC
Statistics
Matches: 235, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
285 117 0.50
286 3 0.01
288 16 0.07
290 3 0.01
291 59 0.25
292 3 0.01
294 34 0.14
ACGTcount: A:0.30, C:0.49, G:0.06, T:0.15
Consensus pattern (286 bp):
TACAAGTCCCCACCACCTCCACCATCACCACCCAAGCACCCTTACAAGTACAAGCTCCTCCACCT
CCACCACCATCACCACCCAAGCATCCTTACAAGTACAAGTCCACCACCACCACCACCACTCACCA
CCCAAACACCCCTACAAGTACAAGTCCCCACCACCACCACCACCATCACCACCCAAGCACCCTTA
CAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTATAAGTCTCCACCACCTCCACCGC
CATCACCACCCAAGCACCCTTACAAG
Found at i:802 original size:30 final size:30
Alignment explanation
Indices: 768--853 Score: 75
Period size: 33 Copynumber: 2.8 Consensus size: 30
758 CCCTTACAAG
*
768 TACAAGTCTCCACCCCCACCACCTCCGGTT
1 TACAAGTCTCCACCCCCACCACCTCCCGTT
* * *
798 TACAAGTAT-AAGTCTCCACCACCTCCTCCCGTT
1 TACAAGTCTCCA--C-CC-CCACCACCTCCCGTT
* *
831 TACAAGTCTCCTCCTCCACCACC
1 TACAAGTCTCCACCCCCACCACC
854 ACCCCATTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
29 1 0.02
30 15 0.36
31 2 0.05
32 3 0.07
33 21 0.50
ACGTcount: A:0.22, C:0.47, G:0.08, T:0.23
Consensus pattern (30 bp):
TACAAGTCTCCACCCCCACCACCTCCCGTT
Found at i:826 original size:33 final size:34
Alignment explanation
Indices: 761--837 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 34
751 CCAAGCACCC
*
761 TTACAAGTACAAGTCTCCACCCCCACCACCTCCGGT
1 TTACAAGTACAAGTCTCCA--CCCACCACCTCCCGT
* *
797 TTACAAGTATAAGTCTCCA-CCACCTCCTCCCGT
1 TTACAAGTACAAGTCTCCACCCACCACCTCCCGT
830 TTACAAGT
1 TTACAAGT
838 CTCCTCCTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 20 0.53
36 18 0.47
ACGTcount: A:0.26, C:0.39, G:0.10, T:0.25
Consensus pattern (34 bp):
TTACAAGTACAAGTCTCCACCCACCACCTCCCGT
Done.