Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00971.F1
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: 1860
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Found at i:787 original size:24 final size:23
Alignment explanation
Indices: 760--1062 Score: 113
Period size: 24 Copynumber: 12.5 Consensus size: 23
750 TCCCGTAAAC
*
760 CCACCTGTTCCAATCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
*
784 CCACCAGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
* * *
808 CCTCCAGTTCCAGT-AAAACCACTTCCT
1 CCACCAGTTCCAATCTAAA--A---CCT
* *
835 CCACCTGTTCCGATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
859 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
*
883 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
907 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
*
931 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
955 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
* * *
979 CCACCTGTTCCAGTTTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
1003 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
* *
1027 CCACCTGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
1051 CCACCAGTTCCA
1 CCACCAGTTCCA
1063 GTATATAAGA
Statistics
Matches: 192, Mismatches: 72, Indels: 30
0.65 0.24 0.10
Matches are distributed among these distances:
22 2 0.01
23 14 0.07
24 146 0.76
25 13 0.07
27 14 0.07
28 1 0.01
29 2 0.01
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.23
Consensus pattern (23 bp):
CCACCAGTTCCAATCTAAAACCT
Found at i:883 original size:48 final size:48
Alignment explanation
Indices: 781--1059 Score: 425
Period size: 48 Copynumber: 5.8 Consensus size: 48
771 AATCTATAAA
* * * * *
781 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTT---GAAAAACCACAT
832 CCTCCACCTGTTCC-GATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAG-TCTACAAACCTCCACCAGTTGAAAAACCACAT
*
880 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
*
928 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
* *
976 CCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
*
1024 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTT
1060 CCAGTATATA
Statistics
Matches: 216, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
48 184 0.85
50 1 0.00
51 31 0.14
ACGTcount: A:0.30, C:0.39, G:0.08, T:0.23
Consensus pattern (48 bp):
CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
Found at i:1090 original size:33 final size:33
Alignment explanation
Indices: 1048--1226 Score: 160
Period size: 33 Copynumber: 5.7 Consensus size: 33
1038 AGTCTATAAA
* **
1048 CCTCCACCAGTTCCAGTATATAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
1081 CCTCCACCAGTTCCAGTCTAT-----A--A-AT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * *
1106 -CTCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
*
1138 CCTCCTCCAGTTCCAGTCTATAAGAAACCACAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * **
1171 CCACCTCCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
1204 CCTCCCCCAGTTCCAGTCTATAA
1 CCTCCTCCAGTTCCAGTATATAA
1227 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:1103 original size:57 final size:57
Alignment explanation
Indices: 1023--1387 Score: 295
Period size: 57 Copynumber: 6.4 Consensus size: 57
1013 AAAAACCACA
* * *
1023 TCCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * ***
1080 TCCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAGAAACCGCA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
*
1137 TCCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCAT
1 TCCTCCACCAGTTCCAGTCTAT---AAA-C-C-T---CCTCCAGTTCCAGTATACAAGAAACCAT
1202 G
57 G
* * **
1203 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------G-AACCACA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * * *
1251 TCCTCCACCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-G
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCATG
* * * * * * * *
1307 TCCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACT-
1 T-CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCA-TG
* *
1365 ACCTCC-CCAGGTTCCAGTGTATA
1 TCCTCCACCA-GTTCCAGTCTATA
1388 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:1256 original size:24 final size:24
Alignment explanation
Indices: 1229--1291 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
1219 GTCTATAAAT
* *
1229 CTCCTCCAGTTCCGGAACCA-CATC
1 CTCCTCCAGTTCCGG-ACCATAAGC
* * *
1253 CTCCACCAGTTCCAGTCCATAAGC
1 CTCCTCCAGTTCCGGACCATAAGC
1277 CTCCTCCAGTTCCGG
1 CTCCTCCAGTTCCGG
1292 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:1382 original size:228 final size:228
Alignment explanation
Indices: 975--1413 Score: 533
Period size: 228 Copynumber: 1.9 Consensus size: 228
965 AAAAACCACA
* * * *
975 TCCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACATCCTCCACCTGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * *
1040 TCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATGTCCTCCACCAGTTCCAGTCTATAAA
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGTCCTCCACCAGTTCCAATCTACAAA
* * * * *
1105 TCTCCTCCGGTTCCAGTATACAAGAAACCGCATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
131 CCCCCTCCAGTTCCAGTATACAACAAACCACATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
*
1170 TCCACCTCCAGTTCCAGTATACAAGAAACCATG
196 TCCACCACCAGTTCCAGTATACAAGAAACCATG
* * * ***
1203 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGGAACCACATCCTCCACCAGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * * * *
1268 TCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-GTCCCTCCTCCGGTTCCAATCTACAA
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT-CCTCCACCAGTTCCAATCTACAA
* * * * *
1332 GCCCCCTCCAGTTCCTGTATACAACAAACCAC-TACCTCC-CCAGGTTCCAGTGTATACGAAGCC
130 ACCCCCTCCAGTTCCAGTATACAACAAACCACAT-CCTCCTCCA-GTTCCAGTCTATAAGAAACC
* *
1395 ACTTCCACCACCTGTTCCA
193 ACATCCACCACCAGTTCCA
1414 ACCTACAATC
Statistics
Matches: 175, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
227 6 0.03
228 169 0.97
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.24
Consensus pattern (228 bp):
TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGTCCTCCACCAGTTCCAATCTACAAA
CCCCCTCCAGTTCCAGTATACAACAAACCACATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
TCCACCACCAGTTCCAGTATACAAGAAACCATG
Found at i:1480 original size:18 final size:18
Alignment explanation
Indices: 1457--1492 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1447 TACAAGCCAC
1457 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
1475 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
1493 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:1564 original size:60 final size:60
Alignment explanation
Indices: 1500--1622 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 60
1490 AGAAGCCATG
1500 CCCTCCCCTTCCTAAGCTACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
* *
1560 CCCTCCTCTTCCTAAGCTGCCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1620 CCC
1 CCC
1623 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:1600 original size:18 final size:18
Alignment explanation
Indices: 1561--1601 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1551 CCACCACCAC
* *
1561 CCTCCTCTTCCTAAGCTG
1 CCTCCTCTCCCTAAGATG
*
1579 CCTCCTCTCCCTAAGATT
1 CCTCCTCTCCCTAAGATG
1597 CCTCC
1 CCTCC
1602 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:1642 original size:60 final size:60
Alignment explanation
Indices: 1519--1644 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
1509 TCCTAAGCTA
** * **
1519 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCCTCTTCCTAAGCTG
1 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
* *
1579 CCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC-CAAGTTCGGAAAATGG
1 CCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAAT-G
1639 CCTCCT
1 CCTCCT
1645 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.