Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Tc02v2_t007550.1
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, 1000
Length: 2809
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Found at i:1882 original size:33 final size:33
Alignment explanation
Indices: 1844--1923 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
1834 TATCAGGCCA
1844 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1877 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1 CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
1910 CCAGCACCTAAGAA
1 CCAGCACCTAAGAA
1924 GCCGACTCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.33, C:0.44, G:0.17, T:0.06
Consensus pattern (33 bp):
CCAGCACCTAAGAACCCAACTCGGGAGCCACCC
Found at i:2068 original size:21 final size:21
Alignment explanation
Indices: 2044--2380 Score: 183
Period size: 21 Copynumber: 14.8 Consensus size: 21
2034 GAGGGGTCCG
*
2044 CTCACCTCCACCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* *
2065 CTCACCACCCCCACCCGTGC-A
1 CTCACCACCACCACCAGT-CTA
* *
2086 CTCACCCCCGCCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* *
2107 TTCACCACCGCCACCACCAGTCCATT
1 CTCACCA---CCACCACCAGT-C-TA
*
2133 CTCCACCACCACCACCAGTTTA
1 CT-CACCACCACCACCAGTCTA
*
2155 TTCTCCACCACCACCTCCACCTGTCTA
1 --CT-CACCACCA---CCACCAGTCTA
*
2182 CTCACCACCCCCACCAGT-TCA
1 CTCACCACCACCACCAGTCT-A
* *
2203 CTCGCCACCTCCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
2224 CTCACCCCCACCACCACCACCTGTCTATTCA
1 CTCA---CCACCACCACCA---GTCT----A
*
2255 CCATCACCACCACCACCAGTCCA
1 -C-TCACCACCACCACCAGTCTA
* * *
2278 TTCACCACCACCTCCTGTCTA
1 CTCACCACCACCACCAGTCTA
*
2299 CTCCCCACCACCACCAGTCTA
1 CTCACCACCACCACCAGTCTA
* * * * *
2320 CTCCCCTCCACCACCTGCCCA
1 CTCACCACCACCACCAGTCTA
*
2341 TTCACCACCACCACCACCCGTCTA
1 CTCACCACCACCACCA---GTCTA
*
2365 CTCTCCACCACCACCA
1 CTCACCACCACCACCA
2381 CCACCACCCG
Statistics
Matches: 244, Mismatches: 42, Indels: 57
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.01
21 128 0.52
22 3 0.01
23 1 0.00
24 67 0.27
25 3 0.01
26 2 0.01
27 21 0.09
30 12 0.05
31 1 0.00
32 1 0.00
33 3 0.01
ACGTcount: A:0.22, C:0.55, G:0.05, T:0.17
Consensus pattern (21 bp):
CTCACCACCACCACCAGTCTA
Found at i:2147 original size:27 final size:27
Alignment explanation
Indices: 2109--2289 Score: 95
Period size: 27 Copynumber: 7.3 Consensus size: 27
2099 CCAGTCTATT
*
2109 CACCACCGCCACCACCAGTCCATTCT-
1 CACCACCACCACCACCAGTCCATTCTC
**
2135 --CCACCACCACCACCAGTTTATTCTC
1 CACCACCACCACCACCAGTCCATTCTC
* * *
2160 CACCACCACCTCCACCTGT-C-TACT-
1 CACCACCACCACCACCAGTCCATTCTC
*
2184 CACCA-C-CC-CCACCAGTTCA--CT-
1 CACCACCACCACCACCAGTCCATTCTC
* * * * *
2205 CGCCACC---TCCACCAGTCTACTCAC
1 CACCACCACCACCACCAGTCCATTCTC
* * * *
2229 CCCCACCACCACCACCTGTCTATTCAC
1 CACCACCACCACCACCAGTCCATTCTC
* *
2256 CATCACCACCACCACCAGTCCATTCAC
1 CACCACCACCACCACCAGTCCATTCTC
2283 CACCACC
1 CACCACC
2290 TCCTGTCTAC
Statistics
Matches: 121, Mismatches: 21, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
21 22 0.18
22 4 0.03
23 2 0.02
24 32 0.26
25 3 0.02
27 58 0.48
ACGTcount: A:0.24, C:0.54, G:0.05, T:0.17
Consensus pattern (27 bp):
CACCACCACCACCACCAGTCCATTCTC
Found at i:2235 original size:96 final size:96
Alignment explanation
Indices: 2067--2334 Score: 258
Period size: 96 Copynumber: 2.8 Consensus size: 96
2057 CCAGTCTACT
* * * * * * * *
2067 CACCACCCCCACCCGTGCACTCACCCCCGCCACCAGTCTATTCACCACCGCCACCACCAGTCCA-
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTA--CTCC-CCACCACCACCAGTCTAC
* * *
2131 T--TCTCCACCACCACCACCAGTTTATTCTCCAC
63 TCCCCTCCACCACCACCACCAGTCTATTCACCAC
* * * * * *
2163 CACCACCTCCACCTGTCTACTCACCACCCCCACCAGT-TCACTCGCCACCTCCACCAGTCTACTC
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCT-ACTCCCCACCACCACCAGTCTACTC
* *
2227 ACCC-CCACCACCACCACCTGTCTATTCACCAT
65 -CCCTCCACCACCACCACCAGTCTATTCACCAC
* * *
2259 CACCACCACCACCAGTCCATTCACCACCACCTCCTGTCTACTCCCCACCACCACCAGTCTACTCC
1 CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTACTCCCCACCACCACCAGTCTACTCC
2324 CCTCCACCACC
66 CCTCCACCACC
2335 TGCCCATTCA
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
93 14 0.10
94 3 0.02
95 4 0.03
96 117 0.84
97 2 0.01
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.17
Consensus pattern (96 bp):
CACCACCACCACCAGTCCACTCACCACCACCACCAGTCTACTCCCCACCACCACCAGTCTACTCC
CCTCCACCACCACCACCAGTCTATTCACCAC
Found at i:2265 original size:69 final size:69
Alignment explanation
Indices: 2138--2430 Score: 197
Period size: 75 Copynumber: 4.2 Consensus size: 69
2128 CCATTCTCCA
* * * * *
2138 CCACCACCACCAGTTTATTCTCCACCACCACCTCCACCTGTCTACTCACCACCCCCACCAGTTCA
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAGTTCA
2203 CTCG
66 CTCG
* *
2207 CCACCTCCACCAGTCTACTCACCCCCACCACCACCACCTGTCTATTCACCATCACCACCACCACC
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTC---T-A-C-TCACCACCACCACC
* * *
2272 AGTCCATTCA
60 AGTTCACTCG
* * * * *
2282 CCACCACCTCCTGTCTACT--CC-CCACCACCACCA---GTCTACTCCCCTCCACCACCTGCCCA
1 CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAG----
*
2341 TTCAC-CA
62 TTCACTCG
* * * * *
2348 CCACCACCACCCGTCTACTCTCCACCACCACCACCACCACCCGTCCACTCTCCACCTCCACC-GC
1 CCACCACCACCAGTCTA--CT-CACCACCACCACCACCACCTGTCTACTCACCACCACCACCAG-
* *
2412 TTTACTCA
62 TTCACTCG
2420 CCACCACCACC
1 CCACCACCACC
2431 TGTACGATCC
Statistics
Matches: 178, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
63 13 0.07
64 1 0.01
65 1 0.01
66 18 0.10
67 3 0.02
68 2 0.01
69 39 0.22
71 6 0.03
72 38 0.21
73 3 0.02
74 2 0.01
75 52 0.29
ACGTcount: A:0.22, C:0.56, G:0.04, T:0.17
Consensus pattern (69 bp):
CCACCACCACCAGTCTACTCACCACCACCACCACCACCTGTCTACTCACCACCACCACCAGTTCA
CTCG
Found at i:2418 original size:21 final size:21
Alignment explanation
Indices: 2376--2472 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
2366 TCTCCACCAC
**
2376 CACCACCACCACC-CGTCCACT
1 CACCACCACCACCGC-TTTACT
* *
2397 CTCCACCTCCACCGCTTTACT
1 CACCACCACCACCGCTTTACT
*
2418 CACCACCACCA-C-CTGTACGAT
1 CACCACCACCACCGCTTTAC--T
* *
2439 CCCCACCTCCACCGCTTTACT
1 CACCACCACCACCGCTTTACT
2460 CACCACCACCACC
1 CACCACCACCACC
2473 ACCAGTTCCA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.08
20 1 0.02
21 46 0.78
22 2 0.03
23 5 0.08
ACGTcount: A:0.22, C:0.57, G:0.05, T:0.16
Consensus pattern (21 bp):
CACCACCACCACCGCTTTACT
Found at i:2421 original size:18 final size:18
Alignment explanation
Indices: 2400--2469 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
2390 GTCCACTCTC
*
2400 CACCTCCACCGCTTTACT
1 CACCACCACCGCTTTACT
* *
2418 CACCACCACCACCTGTACGAT
1 CACCACCACC-GCTTTAC--T
*
2439 CCCCACCTCCACCGCTTTACT
1 ---CACCACCACCGCTTTACT
2460 CACCACCACC
1 CACCACCACC
2470 ACCACCAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 18 0.46
19 5 0.13
21 2 0.05
23 5 0.13
24 9 0.23
ACGTcount: A:0.21, C:0.54, G:0.06, T:0.19
Consensus pattern (18 bp):
CACCACCACCGCTTTACT
Found at i:2445 original size:42 final size:42
Alignment explanation
Indices: 2376--2472 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
2366 TCTCCACCAC
*
2376 CACCACCACCACCCGTCCACTCTCCACCTCCACCGCTTTACT
1 CACCACCACCACCCGTCCACTCCCCACCTCCACCGCTTTACT
* *
2418 CACCACCACCACCTGTACGA-TCCCCACCTCCACCGCTTTACT
1 CACCACCACCACCCGT-CCACTCCCCACCTCCACCGCTTTACT
2460 CACCACCACCACC
1 CACCACCACCACC
2473 ACCAGTTCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.57, G:0.05, T:0.16
Consensus pattern (42 bp):
CACCACCACCACCCGTCCACTCCCCACCTCCACCGCTTTACT
Found at i:2488 original size:117 final size:117
Alignment explanation
Indices: 2039--2488 Score: 350
Period size: 117 Copynumber: 3.8 Consensus size: 117
2029 TGTTGGAGGG
* * * * * * *
2039 GTCCGCTCACCTCCACCACCAGTCTACTCACCACCCCCACCCGTGCACTCACCC-CCGCCACCAG
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGT-CACTC-CCCACCTCCACCAG
* * ** ** **
2103 -TCTATTCACCACCGCCACCACCAGTCCATTCTCCACCACCACCACCAGTTTATTC
64 CTCTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCA--CCACCC
* *
2158 -TCCAC-CACCACCTCCACCTGTCTACTCACCACCCCCACCAGTTCACTCGCCACCTCCACCAG-
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAG-TCACTCCCCACCTCCACCAGC
* * * * *
2220 TCTACTCACCCCCACCACCACCACCTGT-C-TA-TTCACCATCACCACCACCACCA
65 TCTACTCA---CCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
* * * * * * *
2273 GTCCATTCACCACCACCTCCTGTCTACTCCCCACCACCACCAGTCTACTCCCCTCCACCACCTGC
1 GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGTC-ACTCCCCACCTCCACCAGC
* * * * *
2338 -CCATTCACCACCACCACCACCCGTCTACTCTCCACCACCACCACCACCACCC
65 TCTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
* * *
2390 GTCCACTCTCCACCTCCACC-GCTTTACTCACCACCACCACCTGT-ACGATCCCCACCTCCACC-
1 GTCCACTCACCACCTCCACCTG-TCTACTCACCACCACCACCAGTCAC--TCCCCACCTCCACCA
*
2452 GCTTTACTCACCACCACCACCACCAGTTCCA-ACTCCA
63 GCTCTACTCACCACCACCACCACCAG-TCCACACTCCA
2489 TCTCTTCCTC
Statistics
Matches: 263, Mismatches: 51, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
114 16 0.06
115 3 0.01
116 11 0.04
117 208 0.79
118 9 0.03
119 1 0.00
120 15 0.06
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.17
Consensus pattern (117 bp):
GTCCACTCACCACCTCCACCTGTCTACTCACCACCACCACCAGTCACTCCCCACCTCCACCAGCT
CTACTCACCACCACCACCACCAGTCCACACTCCACCACCACCACCACCACCC
Done.