Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g00224.M1
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: 6672
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Found at i:4991 original size:48 final size:47
Alignment explanation
Indices: 4916--5414 Score: 192
Period size: 48 Copynumber: 10.4 Consensus size: 47
4906 CCAATTGGAG
* * * * *
4916 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCA-AACCAGGCA
* * *
4964 CTCCAATAGGAGCACCAACTCCAAGTGCACCAGCTGC-AACACACGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAAAC-CA-GGCA
* * * * * *
5012 CACCAGTAGGAGCAGCACCTCC-TGGGGAAGCAGCTGCAAAACAAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAA-CAGCTGC-AAACCAGGCA
* *** * *
5060 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * *
5108 TGCCAATAGGAGCACCACCTCC-TG-GCACAGCAGCTGCAACACCGGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
* *
5156 CACCAGTAGGAGCACCACCTCC---TGACACACCAACTGCAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTG-CA-A-CAGCTGCAA-ACCAGGCA
* * * *
5204 TGA-CAATGGGAGCACCACCTCC-TG-GCACACCAGCTGCAACAGCAGGCA
1 -CACCAATAGGAGCACCACCTCCAAGTGCA-A-CAGCTGCAA-ACCAGGCA
*** * * * ** * * *
5252 TGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGCA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
*** * * * * *
5300 TGGCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCAGACA
1 CACCAATAGGAGCACCACCTCCAAGTGCAACAGCTGCAA-ACCAGGCA
** * * * * * * *
5348 TGCCAATTGGAGCAACTCCTACC-AGTGCAGCAGCTCCAGCAGCAGGCA
1 CACCAATAGGAGCACCACCT-CCAAGTGCAACAGCTGCA-AACCAGGCA
* *
5396 CACCTATAGAAGCACCACC
1 CACCAATAGGAGCACCACC
5415 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:5176 original size:144 final size:142
Alignment explanation
Indices: 4916--5321 Score: 363
Period size: 144 Copynumber: 2.8 Consensus size: 142
4906 CCAATTGGAG
* ** * **
4916 CACCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCACT-CCAATAGGAGCACC
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCA-TGCCAATAGGAGCACC
* * ** *
4980 AACTCCAAGTGCAC-CAGCTGCAACACACGGCACACCAGTAGGAGCAGCACCTCCTGGGGA-AGC
64 AACTCC-TG-GCACACAGCTGCAACAC-CGGCACACCAGTAGGAGCACCACCTCCT-GACACACC
*
5043 AGCTGCAAAACAAGGCA-
125 AACTGCAAAACAAGGCAT
* *
5060 CACCAATAGGAGCACCATCTCTGGGTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCA
1 CACCAATAGGAGCACCATCTCT-GGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
*
5125 CCTCCTGGCACAGCAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCCTGACACACCAAC
* *
5190 TGCAACACCAGGCAT
128 TGCAAAACAAGGCAT
* * * ** * * * * *
5205 GA-CAATGGGAGCACCACCTCCTGGCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCA
1 CACCAATAGGAGCACCATCT-CTGGTGCAACAGCTGCAACACCAGGCATGCCAATAGGAGCACCA
* * * *** *
5269 TCTCCTGGTACATCAGCTGGAACACCAGGCATGGCAATAGGAGCACCACCTCC
65 ACTCCTGGCACA-CAGCTGCAACACC-GGCACACCAGTAGGAGCACCACCTCC
5322 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:5243 original size:96 final size:96
Alignment explanation
Indices: 4946--5344 Score: 304
Period size: 96 Copynumber: 4.2 Consensus size: 96
4936 CCCAGTGCAT
** * * * ** *
4946 CAGCTGCAGTACCAGGCACTCCAATAGGAGCACCAACTCC-AAGTGCACCAGCTGCAACA-CACG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGA-CACACCAACTGCAACACCA-G
* * * * *
5009 GCA-CACCAGTAGGAGCAGCACCTCCTGGGGA-AG
64 GCATGA-CAATAGGAGCACCACCTCCT-GGCACAC
* * * *** * * * *
5042 CAGCTGCAAAACAAGGCACACCAATAGGAGCACCATCT-CTGGGTGCAACAGCTGCAACATCGGG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCT-GACACACCAACTGCAACACCAGG
* *
5106 CATGCCAATAGGAGCACCACCTCCTGGCACAG
65 CATGACAATAGGAGCACCACCTCCTGGCACAC
* *
5138 CAGCTGCAACACCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
*
5203 ATGACAATGGGAGCACCACCTCCTGGCACAC
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
* *** * * * ** * * *
5234 CAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGC
* ** * *
5299 ATGGCAATAGGAGCACCACCTCCCAGTACAT
66 ATGACAATAGGAGCACCACCTCCTGGCACAC
*
5330 CAGTTGCAACACCAG
1 CAGCTGCAACACCAG
5345 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:5382 original size:144 final size:143
Alignment explanation
Indices: 5084--5423 Score: 333
Period size: 144 Copynumber: 2.4 Consensus size: 143
5074 CCATCTCTGG
* *
5084 GTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAACA
* * * *
5149 CCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATGACAATGGG
66 CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATGGG
* *
5214 AGCACCACCTCCT
131 AGCAACACCTCCA
* * * * * * *
5227 G-GCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAA
1 GTGCA-A-CAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAA
*** * * ** *
5291 CACCAGGCATGGCAATAGGAGCACCACCTCCCAG-TACATCAGTTGCAACACCAGACATGCCAAT
64 CACCAGGCACACCAATAGGAGCACCACCT-CCAGACACACCAACTGCAACACCAGACATGACAAT
* *
5355 TGGAGCAACTCCTACCA
128 GGGAGCAACACCT-CCA
* * * ** * * *
5372 GTGCAGCAGCTCCAGCAGCAGGCACACCTATAGAAGCACCACCACCTGGCAC
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGGCAC
5424 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:5569 original size:39 final size:39
Alignment explanation
Indices: 5497--5591 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
5487 AGGCATGGCG
*
5497 ACAGGAGCACCACCTCCAGCAGCAAAGAAAGGCACAACA
1 ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
* * **
5536 ACAGGAGCATCACCTCCAGCAG-AAACATCAGGCATGACA
1 ACAGGAGCACCACCTCCAGCAGCAAACA-AAGGCACAACA
* *
5575 ACAAGAGCACCAACTCC
1 ACAGGAGCACCACCTCC
5592 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:5739 original size:48 final size:48
Alignment explanation
Indices: 5604--5742 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 48
5594 ATGCACCAGA
* * * *
5604 TGCACCAGATGCAACACCTGGCAAGCCAATAGAAGCACCACCTCCTGG
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * **
5652 TGCACCAGCTTCAAGACCAGGTACGCCAATAGGTTCACCACCTCCTGC
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCTCCTGC
* * * * *
5700 TGCGCTAGCTGCAACAACAGGCATGCCAGTAGGAGCACCACCT
1 TGCACCAGCTGCAACACCAGGCAAGCCAATAGGAGCACCACCT
5743 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:5961 original size:48 final size:48
Alignment explanation
Indices: 5909--6001 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
5899 TCAACTCCTG
* *
5909 GTGCACCAG-CAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTT
1 GTGCACCAGCCA-CAACACCAAGCACACCAATAGGAACACCACCTCTTT
* * *
5957 GTGCACCGGCCACAACACCAAGCACGCCAATAGGAGCACCACCTC
1 GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTC
6002 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:6021 original size:48 final size:48
Alignment explanation
Indices: 5910--6050 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
5900 CAACTCCTGG
** * * ****
5910 TGCACCAGCAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTTG
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
*
5958 TGCACCGGCCA-CAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
1 TGCACCAG-CAGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
* ** * * * *
6006 TGCACCAGCTGCAACAGTAGGAAAGCCAATTGGAGCACCACCTCC
1 TGCACCAGCAGCAACACCAAGCACGCCAATAGGAGCACCACCTCC
6051 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.