Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00971.F3
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, 843
Length: 1406
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Found at i:477 original size:48 final size:48
Alignment explanation
Indices: 375--605 Score: 354
Period size: 48 Copynumber: 4.8 Consensus size: 48
365 AATCTATAAA
* * * *
375 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT---GAAAAACCACAT
* *
426 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTGAAAAACCACAT
* *
474 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTGAAAAACCACAT
*
522 CCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTGAAAAACCACAT
570 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT
606 CCAGTATATA
Statistics
Matches: 170, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
48 138 0.81
51 32 0.19
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.24
Consensus pattern (48 bp):
CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTGAAAAACCACAT
Found at i:610 original size:24 final size:24
Alignment explanation
Indices: 354--608 Score: 115
Period size: 24 Copynumber: 10.5 Consensus size: 24
344 TCCCGTAAAC
*
354 CCACCTGTTCCAATCTATAAACCT
1 CCACCAGTTCCAATCTATAAACCT
*
378 CCACCAGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTATAAACCT
* * *
402 CCTCCAGTTCC-A-GTAAAACCACTTCCT
1 CCACCAGTTCCAATCTATAA--A---CCT
* *
429 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTATAAACCT
** * * * *
453 CCACCAGTTGAAAAACCA-CATCCT
1 CCACCAGTT-CCAATCTATAAACCT
* *
477 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTATAAACCT
** * * * *
501 CCACCAGTTGAAAAACCA-CATCCT
1 CCACCAGTT-CCAATCTATAAACCT
* * *
525 CCACCTGTTCCAGTTTATAAACCT
1 CCACCAGTTCCAATCTATAAACCT
** * * * *
549 CCACCAGTTGAAAAACCA-CATCCT
1 CCACCAGTT-CCAATCTATAAACCT
* *
573 CCACCTGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTATAAACCT
597 CCACCAGTTCCA
1 CCACCAGTTCCA
609 GTATATAAGA
Statistics
Matches: 160, Mismatches: 58, Indels: 26
0.66 0.24 0.11
Matches are distributed among these distances:
22 4 0.03
23 9 0.06
24 119 0.74
25 10 0.06
27 13 0.08
28 1 0.01
29 4 0.03
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.24
Consensus pattern (24 bp):
CCACCAGTTCCAATCTATAAACCT
Found at i:636 original size:33 final size:33
Alignment explanation
Indices: 594--772 Score: 160
Period size: 33 Copynumber: 5.7 Consensus size: 33
584 AGTCTATAAA
* **
594 CCTCCACCAGTTCCAGTATATAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
627 CCTCCACCAGTTCCAGTCTAT-----A--A-AT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * *
652 -CTCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
*
684 CCTCCTCCAGTTCCAGTCTATAAGAAACCACAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * **
717 CCACCTCCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
750 CCTCCCCCAGTTCCAGTCTATAA
1 CCTCCTCCAGTTCCAGTATATAA
773 ATCTCCTCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
24 16 0.14
25 1 0.01
26 1 0.01
28 1 0.01
29 1 0.01
32 2 0.02
33 95 0.81
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.24
Consensus pattern (33 bp):
CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
Found at i:649 original size:57 final size:57
Alignment explanation
Indices: 569--933 Score: 295
Period size: 57 Copynumber: 6.4 Consensus size: 57
559 AAAAACCACA
* * *
569 TCCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * ***
626 TCCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAGAAACCGCA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
*
683 TCCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCAT
1 TCCTCCACCAGTTCCAGTCTAT---AAA-C-C-T---CCTCCAGTTCCAGTATACAAGAAACCAT
748 G
57 G
* * **
749 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------G-AACCACA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * * *
797 TCCTCCACCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-G
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * * * * * * *
853 TCCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACT-
1 T-CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCA-TG
* *
911 ACCTCC-CCAGGTTCCAGTGTATA
1 TCCTCCACCA-GTTCCAGTCTATA
934 CGAAGCCACT
Statistics
Matches: 248, Mismatches: 38, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
48 40 0.16
49 2 0.01
56 5 0.02
57 145 0.58
60 4 0.02
61 1 0.00
62 1 0.00
63 4 0.02
66 46 0.19
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (57 bp):
TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
Found at i:802 original size:24 final size:24
Alignment explanation
Indices: 775--837 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
765 GTCTATAAAT
* *
775 CTCCTCCAGTTCCGGAACCA-CATC
1 CTCCTCCAGTTCCGG-ACCATAAGC
* * *
799 CTCCACCAGTTCCAGTCCATAAGC
1 CTCCTCCAGTTCCGGACCATAAGC
823 CTCCTCCAGTTCCGG
1 CTCCTCCAGTTCCGG
838 TATACAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.19, C:0.44, G:0.14, T:0.22
Consensus pattern (24 bp):
CTCCTCCAGTTCCGGACCATAAGC
Found at i:803 original size:228 final size:228
Alignment explanation
Indices: 521--959 Score: 533
Period size: 228 Copynumber: 1.9 Consensus size: 228
511 AAAAACCACA
* * * *
521 TCCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACATCCTCCACCTGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * *
586 TCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATGT-CCTCCACCAGTTCCAGTCTATAA
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCA-GTCCCTCCACCAGTTCCAATCTACAA
* * * * *
650 ATCTCCTCCGGTTCCAGTATACAAGAAACCGC-ATCCTCCTCCA-GTTCCAGTCTATAAGAAACC
130 ACCCCCTCCAGTTCCAGTATACAACAAACCACTA-CCTCC-CCAGGTTCCAGTCTATAAGAAACC
*
713 ACATCCACCTCCAGTTCCAGTATACAAGAAACCATG
193 ACATCCACCACCAGTTCCAGTATACAAGAAACCATG
* * * ***
749 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGGAACCACATCCTCCACCAGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * * * * *
814 TCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGAGTCCCTCCTCCGGTTCCAATCTACAAG
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCAGTCCCTCCACCAGTTCCAATCTACAAA
* * * * *
879 CCCCCTCCAGTTCCTGTATACAACAAACCACTACCTCCCCAGGTTCCAGTGTATACGAAGCCACT
131 CCCCCTCCAGTTCCAGTATACAACAAACCACTACCTCCCCAGGTTCCAGTCTATAAGAAACCACA
*
944 TCCACCACCTGTTCCA
196 TCCACCACCAGTTCCA
960 ACCTACAATC
Statistics
Matches: 175, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
227 5 0.03
228 169 0.97
229 1 0.01
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.24
Consensus pattern (228 bp):
TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCAGTCCCTCCACCAGTTCCAATCTACAAA
CCCCCTCCAGTTCCAGTATACAACAAACCACTACCTCCCCAGGTTCCAGTCTATAAGAAACCACA
TCCACCACCAGTTCCAGTATACAAGAAACCATG
Found at i:1026 original size:18 final size:18
Alignment explanation
Indices: 1003--1038 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
993 TACAAGCCAC
1003 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
1021 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
1039 AGCCATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (18 bp):
TCCCTCCATTCCCTAAGA
Found at i:1110 original size:60 final size:60
Alignment explanation
Indices: 1046--1168 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 60
1036 AGAAGCCATG
1046 CCCTCCCCTTCCTAAGCTACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
* *
1106 CCCTCCTCTTCCTAAGCTGCCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1166 CCC
1 CCC
1169 CAAGTTCGGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 4 0.07
60 56 0.93
ACGTcount: A:0.19, C:0.49, G:0.06, T:0.27
Consensus pattern (60 bp):
CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
Found at i:1146 original size:18 final size:18
Alignment explanation
Indices: 1107--1147 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1097 CCACCACCAC
* *
1107 CCTCCTCTTCCTAAGCTG
1 CCTCCTCTCCCTAAGATG
*
1125 CCTCCTCTCCCTAAGATT
1 CCTCCTCTCCCTAAGATG
1143 CCTCC
1 CCTCC
1148 CAAGTATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.49, G:0.07, T:0.32
Consensus pattern (18 bp):
CCTCCTCTCCCTAAGATG
Found at i:1188 original size:60 final size:60
Alignment explanation
Indices: 1065--1190 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
1055 TCCTAAGCTA
** * **
1065 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCCTCTTCCTAAGCTG
1 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
* *
1125 CCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC-CAAGTTCGGAAAATGG
1 CCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAAT-G
1185 CCTCCT
1 CCTCCT
1191 TTGCCACCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 11 0.19
60 46 0.81
ACGTcount: A:0.21, C:0.44, G:0.09, T:0.26
Consensus pattern (60 bp):
CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
Done.