Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.D02G014500.1.v1.1
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, 871
Length: 1452
ACGTcount: A:0.28, C:0.40, G:0.10, T:0.22
Found at i:360 original size:48 final size:45
Alignment explanation
Indices: 308--793 Score: 225
Period size: 48 Copynumber: 10.6 Consensus size: 45
298 CTCCACCACC
* * * *
308 GCCTTATGTGTATAAATCTCCACCACCACCACCTAAACATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC--AACA-AAGGAGAA
* *
356 GCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * ******* *
401 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC--AAAGGAGA-A
* * * * * ***** * *
449 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * *
497 TCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
545 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
587 GCCTTATGAATACAAGTCTCCACCACCACCACC--GAAA-GAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * * ***** * *
629 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * * *
677 TCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
725 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
*
767 GCCTTATGAATACAAGTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACC
794 TCCATCTCCA
Statistics
Matches: 343, Mismatches: 78, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
42 108 0.31
43 5 0.01
45 40 0.12
46 4 0.01
47 6 0.02
48 172 0.50
49 4 0.01
50 4 0.01
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (45 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
Found at i:476 original size:27 final size:26
Alignment explanation
Indices: 438--526 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
428 ACCATCACCT
*
438 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
465 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
486 TCTCCACCACCTCCTTATGTGTATAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
513 TCTCCACCACCTCC
1 TCTCCACCACCTCC
527 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
25 2 0.04
26 1 0.02
27 27 0.56
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.28
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:584 original size:42 final size:42
Alignment explanation
Indices: 538--793 Score: 269
Period size: 42 Copynumber: 5.8 Consensus size: 42
528 CCAAAGCATG
538 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
580 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
* * **
622 AAGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCA---CCACCACC-GA
*** * ** ** * * *
668 TCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCA
1 AGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC---G-A
716 TGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 --AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
760 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
794 TCCATCTCCA
Statistics
Matches: 173, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
42 107 0.62
44 1 0.01
45 14 0.08
46 1 0.01
47 1 0.01
48 47 0.27
49 1 0.01
50 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.18
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:686 original size:180 final size:182
Alignment explanation
Indices: 260--901 Score: 772
Period size: 180 Copynumber: 3.5 Consensus size: 182
250 CACCCCCTCC
* * * * * * *
260 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
325 CTCCACCACCACCACCTAAA-CATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
66 CTCCACCACCTCCACC-AAAGCATGAGGAGAAGCCTTATGAATACAAGTCT---CCACCACCACC
* * * ***** *
389 ACCAAAGGAGAAGCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
127 ACCGAAGGAGAAGCCTTATGAATACAAGTCTCCA---CCACCACCACC-TCAAAGACACA
* *
449 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
514 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
* *
579 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC-GAAAGAGA-A
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGACACA
*
629 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
694 CTCCTCCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
* * * ** *
759 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCTCCATCACCACC
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGA-CACA
* * * * * * * * ** *
812 TCCATACT-ACTATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACT-ACTACAA
1 GCCTTA-TGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA-TGTGTATAA
* *
875 GTCCCCACCACCACCACCAAAGCATGA
64 GTCTCCACCACCTCCACCAAAGCATGA
902 AGAACAACCA
Statistics
Matches: 400, Mismatches: 47, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
180 165 0.41
181 3 0.01
182 1 0.00
183 82 0.20
184 2 0.00
186 43 0.11
188 3 0.01
189 101 0.25
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (182 bp):
GCCTTATGAGTACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTCAAAGACACA
Found at i:848 original size:138 final size:137
Alignment explanation
Indices: 580--842 Score: 415
Period size: 138 Copynumber: 1.9 Consensus size: 137
570 CCACCACCGA
580 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
* * ** * *
645 TCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACC
66 TCTCCACCACCTCCATCACC-TATCCACCACCTCCATATGACTATAAATCTCCACCACCTCCACC
710 AAAGCATG
130 AAAGCATG
*
718 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
*
783 TCTCCACCACCTCCATCTCC-AT-CACCACCTCCATACT-ACTATAAATCTCCACCACCTCCA
66 TCTCCACCACCTCCATCACCTATCCACCACCTCCATA-TGACTATAAATCTCCACCACCTCCA
843 TCACCATCAC
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
135 31 0.27
136 2 0.02
138 83 0.72
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.20
Consensus pattern (137 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
TCTCCACCACCTCCATCACCTATCCACCACCTCCATATGACTATAAATCTCCACCACCTCCACCA
AAGCATG
Found at i:861 original size:48 final size:48
Alignment explanation
Indices: 777--1376 Score: 501
Period size: 48 Copynumber: 12.4 Consensus size: 48
767 GCCTTATGAA
* *
777 TACAAGTCTCCACCACCTCCATCTCCAT---CACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * *
822 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * ** * * *
870 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCACCATATTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * * *
921 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * *
969 TACAAGTCCCCACCACCTCCTTCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
** * * * *
1017 TACAAGTCTCCACCACCACCAAAACACGT-A-GAGCAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATCAC-CATCACCA-CCACCTCCATACTAC
* * * * *
1065 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * *
1113 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * *
1161 TACAAGTCCCCACCACCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* * * * ** * *
1209 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * *
1260 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
* ** * ** *
1308 TACAAATCTCCACCACCACCCCCA-CATTACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCAC-CACCTCCATACTAC
*
1356 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1377 GTGAAGTCTC
Statistics
Matches: 439, Mismatches: 102, Indels: 25
0.78 0.18 0.04
Matches are distributed among these distances:
45 25 0.06
47 9 0.02
48 322 0.73
49 10 0.02
50 7 0.02
51 66 0.15
ACGTcount: A:0.30, C:0.47, G:0.03, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCACCATCACCATCACCACCACCTCCATACTAC
Found at i:883 original size:27 final size:26
Alignment explanation
Indices: 805--886 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 26
795 CCATCTCCAT
* *
805 CACCACCTCCATACTACTATAAATCTC
1 CACCACCTCCATACTACTA-CAATCAC
832 CACCACCTCCAT-C-AC--C-ATCAC
1 CACCACCTCCATACTACTACAATCAC
*
853 CACCACCTCCATACTACTACAAGTCCC
1 CACCACCTCCATACTACTACAA-TCAC
880 CACCACC
1 CACCACC
887 ACCACCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.35
22 1 0.02
23 2 0.04
25 3 0.07
26 2 0.04
27 22 0.48
ACGTcount: A:0.30, C:0.50, G:0.01, T:0.18
Consensus pattern (26 bp):
CACCACCTCCATACTACTACAATCAC
Found at i:1204 original size:144 final size:143
Alignment explanation
Indices: 777--1372 Score: 518
Period size: 147 Copynumber: 4.1 Consensus size: 143
767 GCCTTATGAA
* * *
777 TACAAGTCTCCACCACCTCCATCTCCAT---CACCACCTCCATACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * *
839 TCCATCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCA--ACACCAT-AA-
* * * *
904 AACAACCACCATATTAC
127 AGCACCCCCCATACTAC
* * * * * * * *
921 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * * *
986 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCTCCACCACCACCAAAACACGTAGAGC
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACAC-CATAAAGC
*
1051 AACCCCCATACTAC
130 ACCCCCCATACTAC
* * * *
1065 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * * * * *
1130 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACCTCCATCTCCAT-CACCA
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAAGCA
1194 CCTCCTCCATACTAC
131 CC-CC-CCATACTAC
* * * * * ** * * *
1209 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTACTACAAGTCTCCACC
1 TACAAGTCTCCACCACCTCCATC--ACCAT-CACCACCACCACCATACTACTACAAATCTCCACC
* * * * * * ** * *
1274 ACCACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACCCCCA-CATTAC
63 ACCACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAA
* *
1338 GTCTCACCACCATACTAC
128 G-CAC-CCCCCATACTAC
*
1356 TACAAATCTCCACCACC
1 TACAAGTCTCCACCACC
1373 ACCAGTGAAG
Statistics
Matches: 376, Mismatches: 64, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
142 4 0.01
143 4 0.01
144 170 0.45
145 4 0.01
146 8 0.02
147 182 0.48
148 3 0.01
149 1 0.00
ACGTcount: A:0.30, C:0.47, G:0.03, T:0.19
Consensus pattern (143 bp):
TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
ACCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAACACCATAAAGCA
CCCCCCATACTAC
Found at i:1318 original size:24 final size:23
Alignment explanation
Indices: 1291--1372 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1281 TCACCATCTC
1291 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACC-TACTACTACAAAT
** * *
1315 CTCCACCACC-ACCCCCAC-ATT
1 CTCCACCACCTACTACTACAAAT
1336 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACC-TACTACTACAAAT
1363 CTCCACCACC
1 CTCCACCACC
1373 ACCAGTGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 2 0.05
24 24 0.55
25 2 0.05
26 6 0.14
27 2 0.05
ACGTcount: A:0.30, C:0.49, G:0.01, T:0.20
Consensus pattern (23 bp):
CTCCACCACCTACTACTACAAAT
Done.