Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g00336.F2
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: 2265
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Found at i:1508 original size:63 final size:62
Alignment explanation
Indices: 1460--1724 Score: 386
Period size: 63 Copynumber: 4.2 Consensus size: 62
1450 GTCCATTCAC
* * *
1460 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCA-CCCCACCGGTGCCCT
* * * *
1523 CACCACCACCACCAGTTTCTTCACCCCCACCGCCAGTAAAATCTCCACCTCTACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACC-CCACCGGTGCCCT
*
1586 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACC-CCACCGGTGCCCT
* * *
1649 CACCACCACCACCAGATCCTTCACCCTCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACC-CCACCGGTGCCCT
*
1712 CACCACCCCCACC
1 CACCACCACCACC
1725 TGTGCCATCT
Statistics
Matches: 185, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
62 2 0.01
63 183 0.99
ACGTcount: A:0.23, C:0.54, G:0.08, T:0.15
Consensus pattern (62 bp):
CACCACCACCACCAGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCACCGGTGCCCT
Found at i:1546 original size:21 final size:21
Alignment explanation
Indices: 1415--1685 Score: 116
Period size: 21 Copynumber: 12.8 Consensus size: 21
1405 ATCCAATCTC
* *
1415 CACCACCACCACCAATGCAC-T
1 CACCACCACCACCAGTTC-CTT
* *
1436 CACCACCACCGCCCG-TCCATT
1 CACCACCACCACCAGTTCC-TT
1457 CACCACCACCACCATCGGTTCCTT
1 CACCACCACCACCA---GTTCCTT
* ****
1481 CACCCCCACCACCAGTAAAAT
1 CACCACCACCACCAGTTCCTT
* * * * *
1502 CCCCACCCCCACCGGTACCCT
1 CACCACCACCACCAGTTCCTT
*
1523 CACCACCACCACCAGTTTCTT
1 CACCACCACCACCAGTTCCTT
* * ****
1544 CACCCCCACCGCCAGTAAAAT
1 CACCACCACCACCAGTTCCTT
* * * * * *
1565 CTCCACCTCTACCGGTGCCCT
1 CACCACCACCACCAGTTCCTT
1586 CACCACCACCACCAGTTCCTT
1 CACCACCACCACCAGTTCCTT
* * ****
1607 CACCCCCACCCCCAGTAAAAT
1 CACCACCACCACCAGTTCCTT
* * * * *
1628 CCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTT
*
1649 CACCACCACCACCAGATCCTT
1 CACCACCACCACCAGTTCCTT
1670 CACC-CTCACCACCAGT
1 CACCAC-CACCACCAGT
1686 AAAATCCCTA
Statistics
Matches: 175, Mismatches: 68, Indels: 14
0.68 0.26 0.05
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 153 0.87
24 16 0.09
25 3 0.02
ACGTcount: A:0.24, C:0.54, G:0.08, T:0.15
Consensus pattern (21 bp):
CACCACCACCACCAGTTCCTT
Found at i:1745 original size:63 final size:61
Alignment explanation
Indices: 1460--1849 Score: 343
Period size: 63 Copynumber: 6.2 Consensus size: 61
1450 GTCCATTCAC
* * *
1460 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCCT
1 CACCACCACCACCAG-TCCTTCACCCCC-CCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* * * * *
1523 CACCACCACCACCAGTTTCTTCACCCCCACCGCCAGTAAAATCTCCACCTCTACCGGTGCCCT
1 CACCACCACCACCAG-TCCTTCACCCCC-CCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* *
1586 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAG-TCCTTCACCCCC-CCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* * *
1649 CACCACCACCACCAGATCCTTCACCCTCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCT
1 CACCACCACCACCAG-TCCTTCACCC-CCCCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* * * * * **** *
1712 CACCACCCCCACCTGTGCCATCTCCACCCCCACCCGTCCGCTCCCCACCCCCACCTGTGCCCT
1 CACCACCACCACCAGT-CCTTCACC-CCCCCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* * * * ** * * *
1775 CTCCACC-CCTACCCGTCCACTC-CCACCCCCACCTGTCCACTCTCCACCCCCACCTGTGCCCT
1 CACCACCACC-ACCAGTCC-TTCACC-CCCCCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
* *
1837 CTCCACCCCCACC
1 CACCACCACCACC
1850 TATCCTCTCT
Statistics
Matches: 286, Mismatches: 35, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
62 52 0.18
63 232 0.81
64 2 0.01
ACGTcount: A:0.20, C:0.57, G:0.08, T:0.16
Consensus pattern (61 bp):
CACCACCACCACCAGTCCTTCACCCCCCCACCAGTAAAATCCCCACCCCCACCGGTGCCCT
Found at i:1757 original size:126 final size:125
Alignment explanation
Indices: 1460--1781 Score: 398
Period size: 126 Copynumber: 2.6 Consensus size: 125
1450 GTCCATTCAC
* * * *
1460 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCCTCA
1 CACCACCACCACCAGTGCCTTCACCCCCACC-CCAGTAAAATCCCCACCCCCACCGGTGCCCTCA
* * * *
1525 CCACCACCACCAGTTTCTTCACCCCCACCGCCAGTAAAATCTCCACCTCTACCGGTGCCCT
65 CCACCACCACCAGATCCTTCACCCCCACCACCAGTAAAATCTCCACCTCCACCGGTGCCCT
* *
1586 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCTCA
1 CACCACCACCACCAGTGCCTTCACCCCCA-CCCCAGTAAAATCCCCACCCCCACCGGTGCCCTCA
*
1651 CCACCACCACCAGATCCTTCACCCTCACCACCAGTAAAATC-CCTACCTCCACCGGTGCCCT
65 CCACCACCACCAGATCCTTCACCCCCACCACCAGTAAAATCTCC-ACCTCCACCGGTGCCCT
* * **** *
1712 CACCACCCCCACCTGTGCCATCTCCACCCCCA-CCC-GTCCGCTCCCCACCCCCACCTGTGCCCT
1 CACCACCACCACCAGTGCC-T-T-CACCCCCACCCCAGTAAAATCCCCACCCCCACCGGTGCCCT
*
1775 CTCCACC
63 CACCACC
1782 CCTACCCGTC
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
125 2 0.01
126 155 0.90
127 6 0.03
128 1 0.01
129 8 0.05
ACGTcount: A:0.21, C:0.55, G:0.08, T:0.16
Consensus pattern (125 bp):
CACCACCACCACCAGTGCCTTCACCCCCACCCCAGTAAAATCCCCACCCCCACCGGTGCCCTCAC
CACCACCACCAGATCCTTCACCCCCACCACCAGTAAAATCTCCACCTCCACCGGTGCCCT
Found at i:1826 original size:62 final size:63
Alignment explanation
Indices: 1690--1998 Score: 277
Period size: 62 Copynumber: 5.0 Consensus size: 63
1680 ACCAGTAAAA
* * * * * * *
1690 TCCCTACCTCCACCGGTGCCCTCACCACCCCCACCTGTGCCA-TCTCCACCCCCACCCGTCCGC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGT-CCACTCACCACCCCCACCCGTCCAC
* *
1753 TCCCCACCCCCACCTGTGCCCTCTCCACCCCTACCCGTCCACTC-CCACCCCCACCTGTCCAC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* ** * * * * *
1815 TCTCCACCCCCACCTGTGCCCTCTCCACCCCCACCTATCCTCTCTCCA-CCCCACCGGTGCGC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* * * * * * *
1877 TCACCA-CCCCACCCGT-CCTTTCTCCACCCCCACCAGTGCGCTCACCACCCCCACCCATCCAC
1 TCCCCACCCCCACCTGTGCC-CTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* * ** * * * *
1939 TCCCCACCCCCACCAGTACATTCACCACCACCACCCGTCTACTCACCACCTCCACCCGTC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTC
1999 AAGTCTCCAC
Statistics
Matches: 201, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
60 2 0.01
61 31 0.15
62 89 0.44
63 78 0.39
64 1 0.00
ACGTcount: A:0.15, C:0.61, G:0.08, T:0.16
Consensus pattern (63 bp):
TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
Found at i:1945 original size:21 final size:21
Alignment explanation
Indices: 1714--2015 Score: 238
Period size: 21 Copynumber: 14.5 Consensus size: 21
1704 GGTGCCCTCA
*
1714 CCACCCCCACCTGTGCCA-TCT
1 CCACCCCCACCCGT-CCACTCT
* *
1735 CCACCCCCACCCGTCCGCTCC
1 CCACCCCCACCCGTCCACTCT
*
1756 CCACCCCCACCTGTGCC-CTCT
1 CCACCCCCACCCGT-CCACTCT
*
1777 CCACCCCTACCCGTCCACTC-
1 CCACCCCCACCCGTCCACTCT
*
1797 CCACCCCCACCTGTCCACTCT
1 CCACCCCCACCCGTCCACTCT
*
1818 CCACCCCCACCTGTGCC-CTCT
1 CCACCCCCACCCGT-CCACTCT
** *
1839 CCACCCCCACCTATCCTCTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
1860 CCA-CCCCACCGGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
**
1880 CCA-CCCCACCCGTCCTTTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
1900 CCACCCCCACCAGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
* *
1921 CCACCCCCACCCATCCACTCC
1 CCACCCCCACCCGTCCACTCT
* * * *
1942 CCACCCCCACCAGTACATTCA
1 CCACCCCCACCCGTCCACTCT
* * *
1963 CCACCACCACCCGTCTACTCA
1 CCACCCCCACCCGTCCACTCT
* * *
1984 CCACCTCCACCCGTCAAGTCT
1 CCACCCCCACCCGTCCACTCT
*
2005 CCACCACCACC
1 CCACCCCCACC
2016 AGTAAAATCT
Statistics
Matches: 229, Mismatches: 45, Indels: 14
0.80 0.16 0.05
Matches are distributed among these distances:
20 54 0.24
21 171 0.75
22 4 0.02
ACGTcount: A:0.16, C:0.61, G:0.07, T:0.16
Consensus pattern (21 bp):
CCACCCCCACCCGTCCACTCT
Done.