Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g00224.M2
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: 6607
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Found at i:4926 original size:48 final size:47
Alignment explanation
Indices: 4851--5349 Score: 192
Period size: 48 Copynumber: 10.4 Consensus size: 47
4841 CCAATTGGAG
* * * * *
4851 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCA-AACCAGGCA
* * *
4899 CTCCAATAGGAGCACCAACTCCAAGTGCACCAGCTGC-AACACACGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAAAC-CA-GGCA
* * * * * *
4947 CACCAGTAGGAGCAGCACCTCC-TGGGGAAGCAGCTGCAAAACAAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAA-CAGCTGC-AAACCAGGCA
* *** * *
4995 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * *
5043 TGCCAATAGGAGCACCACCTCC-TG-GCACAGCAGCTGCAACACCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
* *
5091 CACCAGTAGGAGCACCACCTCC---TGACACACCAACTGCAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTG-CA-A-CAGCTGCAA-ACCAGGCA
* * * *
5139 TGA-CAATGGGAGCACCACCTCC-TG-GCACACCAGCTGCAACAGCAGGCA
1 -CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
*** * * * ** * * *
5187 TGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
*** * * * * *
5235 TGGCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCAGACA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * * * * * * *
5283 TGCCAATTGGAGCAACTCCTACC-AGTGCAGCAGCTCCAGCAGCAGGCA
1 CACCAATAGGAGCACCACCT-CCAAGTGCAACAGCTGCA-AACCAGGCA
* *
5331 CACCTATAGAAGCACCACC
1 CACCAATAGGAGCACCACC
5350 ACCTGGCACT
Statistics
Matches: 353, Mismatches: 79, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
46 5 0.01
47 10 0.03
48 323 0.92
49 10 0.03
50 5 0.01
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (47 bp):
CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAAACCAGGCA
Found at i:5111 original size:144 final size:142
Alignment explanation
Indices: 4851--5256 Score: 363
Period size: 144 Copynumber: 2.8 Consensus size: 142
4841 CCAATTGGAG
* ** * **
4851 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCACT-CCAATAGGAGCACC
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCA-TGCCAATAGGAGCACC
* * ** *
4915 AACTCCAAGTGCAC-CAGCTGCAACACACGGCACACCAGTAGGAGCAGCACCTCCTGGGGA-AGC
64 AACTCC-TG-GCACACAGCTGCAACAC-CGGCACACCAGTAGGAGCACCACCTCCT-GACACACC
*
4978 AGCTGCAAAACAAGGCA-
125 AACTGCAAAACAAGGCAT
* *
4995 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCA
1 CACCAATAGGAGCACCATCTCT-GGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
*
5060 CCTCCTGGCACAGCAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
* *
5125 TGCAACACCAGGCAT
128 TGCAAAACAAGGCAT
* * * ** * * * * *
5140 GA-CAATGGGAGCACCACCTCCTGGCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCA
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
* * * *** *
5204 TCTCCTGGTACATCAGCTGGAACACCAGGCATGGCAATAGGAGCACCACCTCC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCC
5257 CAGTACATCA
Statistics
Matches: 217, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
142 4 0.02
143 6 0.03
144 204 0.94
145 3 0.01
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (142 bp):
CACCAATAGGAGCACCATCTCTGGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCAA
CTCCTGGCACACAGCTGCAACACCGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGC
AAAACAAGGCAT
Found at i:5178 original size:96 final size:96
Alignment explanation
Indices: 4881--5279 Score: 304
Period size: 96 Copynumber: 4.2 Consensus size: 96
4871 CCCAGTGCAT
** * * * ** *
4881 CAGCTGCAGTACCAGGCACTCCAATAGGAGCACCAACTCC-AAGTGCACCAGCTGCAACA-CACG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGA-CACACCAACTGCAACACCA-G
* * * * *
4944 GCA-CACCAGTAGGAGCAGCACCTCCTGGGGA-AG
64 GCATGA-CAATAGGAGCACCACCTCCT-GGCACAC
* * * *** * * * *
4977 CAGCTGCAAAACAAGGCACACCAATAGGAGCACCATCT-CTGGGTGCAACAGCTGCAACATCGGG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCT-GACACACCAACTGCAACACCAGG
* *
5041 CATGCCAATAGGAGCACCACCTCCTGGCACAG
65 CATGACAATAGGAGCACCACCTCCTGGCACAC
* *
5073 CAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
*
5138 ATGACAATGGGAGCACCACCTCCTGGCACAC
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
* *** * * * ** * * *
5169 CAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
* ** * *
5234 ATGGCAATAGGAGCACCACCTCCCAGTACAT
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
*
5265 CAGTTGCAACACCAG
1 CAGCTGCAACACCAG
5280 ACATGCCAAT
Statistics
Matches: 246, Mismatches: 51, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
95 4 0.02
96 239 0.97
97 3 0.01
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.12
Consensus pattern (96 bp):
CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
ATGACAATAGGAGCACCACCTCCTGGCACAC
Found at i:5317 original size:144 final size:143
Alignment explanation
Indices: 5019--5358 Score: 333
Period size: 144 Copynumber: 2.4 Consensus size: 143
5009 CCATCTCTGG
* *
5019 GTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
* * * *
5084 CCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATGACAATGGG
66 CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATGGG
* *
5149 AGCACCACCTCCT
131 AGCAACACCTCCA
* * * * * * *
5162 G-GCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAA
1 GTGCA-A-CAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAA
*** * * ** *
5226 CACCAGGCATGGCAATAGGAGCACCACCTCCCAG-TACATCAGTTGCAACACCAGACATGCCAAT
64 CACCAGGCACACCAATAGGAGCACCACCT-CCAGACACACCAACTGCAACACCAGACATGACAAT
* *
5290 TGGAGCAACTCCTACCA
128 GGGAGCAACACCT-CCA
* * * ** * * *
5307 GTGCAGCAGCTCCAGCAGCAGGCACACCTATAGAAGCACCACCACCTGGCAC
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCAC
5359 TCAAGCTGAA
Statistics
Matches: 154, Mismatches: 38, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
142 3 0.02
143 2 0.01
144 140 0.91
145 6 0.04
146 3 0.02
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (143 bp):
GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATGGG
AGCAACACCTCCA
Found at i:5504 original size:39 final size:39
Alignment explanation
Indices: 5432--5526 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
5422 AGGCATGGCG
*
5432 ACAGGAGCACCACCTCCAGCAGCAAAGAAAGGCACAACA
1 ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
* * **
5471 ACAGGAGCATCACCTCCAGCAG-AAACATCAGGCATGACA
1 ACAGGAGCACCACCTCCAGCAGCAAACA-AAGGCACAACA
* *
5510 ACAAGAGCACCAACTCC
1 ACAGGAGCACCACCTCC
5527 TGATGCACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.41, C:0.34, G:0.19, T:0.06
Consensus pattern (39 bp):
ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
Found at i:5674 original size:48 final size:48
Alignment explanation
Indices: 5539--5677 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 48
5529 ATGCACCAGA
* * * *
5539 TGCACCAGATGCAACACCTGGCAAGCCAATAGAAGCACCACCTCCTGG
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * **
5587 TGCACCAGCTTCAAGACCAGGTACGCCAATAGGTTCACCACCTCCTGC
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * *
5635 TGCGCTAGCTGCAACAACAGGCATGCCAGTAGGAGCACCACCT
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCT
5678 ACCAGTGCAC
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.28, C:0.35, G:0.22, T:0.15
Consensus pattern (48 bp):
TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
Found at i:5896 original size:48 final size:48
Alignment explanation
Indices: 5844--5936 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
5834 TCAACTCCTG
* *
5844 GTGCACCAG-CAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTT
1 GTGCACCAGCCA-CAACACCAAGCACACCAATAGGAACACCACCTCTTT
* * *
5892 GTGCACCGGCCACAACACCAAGCACGCCAATAGGAGCACCACCTC
1 GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTC
5937 CCAATGCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.32, C:0.39, G:0.18, T:0.11
Consensus pattern (48 bp):
GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTCTTT
Found at i:5956 original size:48 final size:48
Alignment explanation
Indices: 5845--5985 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
5835 CAACTCCTGG
** * * ****
5845 TGCACCAGCAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTTG
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
*
5893 TGCACCGGCCA-CAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
1 TGCACCAG-CAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
* ** * * * *
5941 TGCACCAGCTGCAACAGTAGGAAAGCCAATTGGAGCACCACCTCC
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCC
5986 TGGTGCACCT
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
47 1 0.01
48 71 0.96
49 2 0.03
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.11
Consensus pattern (48 bp):
TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
Done.