Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Tc08v2_t012960.1
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, 682
Length: 1138
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Found at i:408 original size:75 final size:75
Alignment explanation
Indices: 280--743 Score: 347
Period size: 87 Copynumber: 5.8 Consensus size: 75
270 CCACCTTACG
* * *
280 AGTACAAGTCTCC-CCCTCCTCCTCCCCCAGTTTACAAGTACAAGTCTCCTCCACCTCCACCAAA
1 AGTACAAGTCTCCTCCC-CCACCTCCTCCAGTTTACAAGTACAAGTCCCCTCCACCTCCACCAAA
*
344 GCACCCCTACA
65 GCACCCATACA
* * *
355 AGTATAAGTCTCCTCCCCCACCACCTCCAGTTTACAAGTATAAGTCCCCTCCACCACCACCACCA
1 AGTACAAGTCTCCTCCCCCACCTCCTCCAGTTTACAAGTACAAGTCCCCT---------CCACC-
* *
420 TCACCACCCAAGCACCCATACC
56 T--CCACCAAAGCACCCATACA
* * * *
442 AGTACAAGTCTCCACCTCCACCACCCCCAGTTTACAAGTACAAGTCCCCTCCACCACCACCACCA
1 AGTACAAGTCTCCTCCCCCACCTCCTCCAGTTTACAAGTACAAGTCCCCT---------CCACC-
*
507 TCACCACCCAAGCACCCATACA
56 T--CCACCAAAGCACCCATACA
* * * * * * *
529 AGTACAAGTCTCCTCCACCACCTCCTCCAGTCTACAAATACAAGTCTCCTCCTCCTCCCCCTAAG
1 AGTACAAGTCTCCTCCCCCACCTCCTCCAGTTTACAAGTACAAGTCCCCTCCACCTCCACCAAAG
* * *
594 GAGCCTTACA
66 CACCCATACA
* * * *
604 AGTATAAGTCTCCTCCACCACCTCCTCCAGTTTACAAGTACAAGTCTCCTCCTCCTCCTCCTCCA
1 AGTACAAGTCTCCTCCCCCACCTCCTCCAGTTTACAAGTACAAG--TCC-CCTCCACCTCCACCA
* *
669 AAGGAGCCATACA
63 AAGCACCCATACA
* * * *
682 AGTACAAGTCTCC-CCCACCACCCCCTCCAGTCTACAAGTACAAGTCTCCTCCACCACCACCA
1 AGTACAAGTCTCCTCCC-CCACCTCCTCCAGTTTACAAGTACAAGTCCCCTCCACCTCCACCA
744 CCCCATTACG
Statistics
Matches: 329, Mismatches: 43, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
75 107 0.33
76 5 0.02
77 5 0.02
78 66 0.20
84 5 0.02
85 1 0.00
87 140 0.43
ACGTcount: A:0.27, C:0.45, G:0.08, T:0.19
Consensus pattern (75 bp):
AGTACAAGTCTCCTCCCCCACCTCCTCCAGTTTACAAGTACAAGTCCCCTCCACCTCCACCAAAG
CACCCATACA
Found at i:451 original size:87 final size:87
Alignment explanation
Indices: 336--745 Score: 403
Period size: 87 Copynumber: 5.0 Consensus size: 87
326 TCCTCCACCT
* * * * *
336 CCACCAAAGCACCCCTACAAGTATAAGTCTCCTCCCCCACCACCTCCAGTTTACAAGTATAAGTC
1 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
401 CCCTCCACCACCACCACCATCA
66 CCCTCCACCACCACCACCATCA
* * * *
423 CCACCCAAGCACCCATACCAGTACAAGTCTCCACCTCCACCACCCCCAGTTTACAAGTACAAGTC
1 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
488 CCCTCCACCACCACCACCATCA
66 CCCTCCACCACCACCACCATCA
* * *
510 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTCTACAAATACAAGT-
1 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
* *
574 --CT------CCTCCTCC-TC-
66 CCCTCCACCACCACCACCATCA
* * * * * *
586 CC-CCTAAGGAGCCTTACAAGTATAAGTCTCCTCCACCACCTCCTCCAGTTTACAAGTACAAGT-
1 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
* * * *
649 --CTCCTCCTCCTCCTCC-T--
66 CCCTCCACCACCACCACCATCA
* * * * *
666 CCA---AAGGAGCCATACAAGTACAAGTCTCCCCCACCACCCCCTCCAGTCTACAAGTACAAGTC
1 CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
*
728 TCCTCCACCACCACCACC
66 CCCTCCACCACCACCACC
746 CCATTACGTC
Statistics
Matches: 280, Mismatches: 33, Indels: 26
0.83 0.10 0.08
Matches are distributed among these distances:
75 56 0.20
76 2 0.01
77 2 0.01
78 59 0.21
80 2 0.01
81 21 0.08
84 2 0.01
87 136 0.49
ACGTcount: A:0.28, C:0.46, G:0.08, T:0.18
Consensus pattern (87 bp):
CCACCCAAGCACCCATACAAGTACAAGTCTCCTCCACCACCACCTCCAGTTTACAAGTACAAGTC
CCCTCCACCACCACCACCATCA
Found at i:455 original size:48 final size:48
Alignment explanation
Indices: 403--550 Score: 140
Period size: 48 Copynumber: 3.3 Consensus size: 48
393 TATAAGTCCC
*
403 CTCCACCACCACCACCATCACCACCCAAGCACCCATACCAGTACAAGT
1 CTCCACCACCACCACCATCACCACCCAAGCACCCATACAAGTACAAGT
* **
451 CT---CCACCTCCA-C--CACC-CCC-AG----TTTACAAGTACAAGT
1 CTCCACCACCACCACCATCACCACCCAAGCACCCATACAAGTACAAGT
487 CCCCTCCACCACCACCACCATCACCACCCAAGCACCCATACAAGTACAAGT
1 ---CTCCACCACCACCACCATCACCACCCAAGCACCCATACAAGTACAAGT
*
538 CTCCTCCACCACC
1 CTCCACCACCACC
551 TCCTCCAGTC
Statistics
Matches: 77, Mismatches: 8, Indels: 30
0.67 0.07 0.26
Matches are distributed among these distances:
36 12 0.16
39 2 0.03
40 2 0.03
41 3 0.04
42 12 0.16
43 1 0.01
44 1 0.01
45 12 0.16
46 3 0.04
47 2 0.03
48 14 0.18
51 13 0.17
ACGTcount: A:0.30, C:0.51, G:0.06, T:0.13
Consensus pattern (48 bp):
CTCCACCACCACCACCATCACCACCCAAGCACCCATACAAGTACAAGT
Found at i:565 original size:36 final size:36
Alignment explanation
Indices: 525--739 Score: 223
Period size: 36 Copynumber: 5.7 Consensus size: 36
515 CAAGCACCCA
525 TACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTC
1 TACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTC
* * * * ** *
561 TACAAATACAAGTCTCCTCCTCCTCCCCCTAAGGAGCC
1 TACAAGTACAAGTCTCCTCCACCACCTCCT--CCAGTC
* *
599 TTACAAGTATAAGTCTCCTCCACCACCTCCTCCAGTT
1 -TACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTC
* * *
636 TACAAGTACAAGTCTCCTCCTCCTCCTCCTCCAAAGGAGCC
1 TACAAGTACAAGTCTCCTCCACCACCTCCTCC-----AGTC
* *
677 ATACAAGTACAAGTCTCCCCCACCACCCCCTCCAGTC
1 -TACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTC
714 TACAAGTACAAGTCTCCTCCACCACC
1 TACAAGTACAAGTCTCCTCCACCACC
740 ACCACCCCAT
Statistics
Matches: 143, Mismatches: 27, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
36 80 0.56
37 5 0.03
38 3 0.02
39 25 0.17
41 2 0.01
42 28 0.20
ACGTcount: A:0.26, C:0.43, G:0.09, T:0.22
Consensus pattern (36 bp):
TACAAGTACAAGTCTCCTCCACCACCTCCTCCAGTC
Done.