Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00298.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: 2375
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Found at i:1234 original size:54 final size:54
Alignment explanation
Indices: 1170--1543 Score: 466
Period size: 54 Copynumber: 6.9 Consensus size: 54
1160 TGAAAACAAT
* * * * ** *
1170 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* * * *
1224 AACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* * * ** *
1278 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* *
1332 AACAATGAGAATGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG
* *
1386 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAG
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGTAACACTGAG
* * *
1440 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
* *
1494 AACAATGAGAATGCAGGTCAGAACGAGAACAATGC-GACTCAGAGCAACAC
1 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTG-CTCAGAGTAACAC
1544 CGACGAAAAC
Statistics
Matches: 284, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 2 0.01
54 280 0.99
55 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (54 bp):
AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGTAACACTGAG
Found at i:1284 original size:108 final size:108
Alignment explanation
Indices: 1170--1614 Score: 482
Period size: 108 Copynumber: 4.0 Consensus size: 108
1160 TGAAAACAAT
* * * *
1170 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGACAACAATGAAAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
* * *
1235 TGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
66 TGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
* * * * *
1278 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAGAACAATGAGAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
* * * *
1343 TGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
66 TGCGGGTCAGAACGAGAACAATGCTGCT-CAGAGCAACACTGAC
* * * * * *
1386 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAGAACAATGAGA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT-CAGAGCAACACTGACAACAATGAAA
* * *
1450 ATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
65 ATGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
* * * *
1494 AACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACGAAAACAACAA
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACA-C--TG------ACAA
* *
1559 CAATGAAAATGCAGGTCAGAATGAGAACAATG-TGACTCAGAGCAACACTGAC
57 CAATGAAAATGCGGGTCAGAACGAGAACAATGCTG-CTCAGAGCAACACTGAC
1611 AACA
1 AACA
1615 GCAGCAACAA
Statistics
Matches: 284, Mismatches: 39, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
107 3 0.01
108 223 0.79
109 5 0.02
111 1 0.00
116 2 0.01
117 50 0.18
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.13
Consensus pattern (108 bp):
AACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACTCAGAGCAACACTGACAACAATGAAAA
TGCGGGTCAGAACGAGAACAATGCTGCTCAGAGCAACACTGAC
Found at i:1304 original size:27 final size:27
Alignment explanation
Indices: 1274--1365 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
1264 AGAGCAACAC
1274 TGAGAACAATGAAAATGCGGGTCAGAA
1 TGAGAACAATGAAAATGCGGGTCAGAA
* * * *
1301 TGAGAGCAATGCAACT-CAGAG-CA-ACA
1 TGAGAACAATGAAAATGC-GGGTCAGA-A
*
1327 CTGAGAACAATGAGAATGCGGGTCAGAA
1 -TGAGAACAATGAAAATGCGGGTCAGAA
* *
1355 CGAGAAAAATG
1 TGAGAACAATG
1366 CTGCTCCAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 38 0.79
28 4 0.08
29 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.13
Consensus pattern (27 bp):
TGAGAACAATGAAAATGCGGGTCAGAA
Found at i:1467 original size:27 final size:27
Alignment explanation
Indices: 1383--1527 Score: 91
Period size: 27 Copynumber: 5.4 Consensus size: 27
1373 AAGTAACGCT
*
1383 GAGAACAATGAGAATGTGGGTCAGAAC
1 GAGAACAATGAGAATGCGGGTCAGAAC
* * * **
1410 GAGAACAATGCCG-CTCCAAGT-A-ACAC
1 GAGAACAATG-AGAATGCGGGTCAGA-AC
1436 TGAGAACAATGAGAATGCGGGTCAGAAC
1 -GAGAACAATGAGAATGCGGGTCAGAAC
* * * * * * *
1464 GAGAACAATGCTG-CTCCGAGTAACACC
1 GAGAACAATG-AGAATGCGGGTCAGAAC
* *
1491 GACAACAATGAGAATGCAGGTCAGAAC
1 GAGAACAATGAGAATGCGGGTCAGAAC
1518 GAGAACAATG
1 GAGAACAATG
1528 CGACTCAGAG
Statistics
Matches: 82, Mismatches: 28, Indels: 16
0.65 0.22 0.13
Matches are distributed among these distances:
25 1 0.01
26 5 0.06
27 70 0.85
28 5 0.06
29 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (27 bp):
GAGAACAATGAGAATGCGGGTCAGAAC
Found at i:1544 original size:54 final size:53
Alignment explanation
Indices: 1170--1614 Score: 426
Period size: 54 Copynumber: 8.1 Consensus size: 53
1160 TGAAAACAAT
* * * * *
1170 AACAATGAAAATGCGGGTCAGGACGGGAAGAATGCCACTCAGAGTAACACTGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATG-CGCTCAGAGCAACACTGAC
* * *
1224 AACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * * *
1278 AACAATGAAAATGCGGGTCAGAATGAGAGCAATGCAACTCAGAGCAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * * * *
1332 AACAATGAGAATGCGGGTCAGAACGAGAAAAATGCTGCTCCA-AGTAACGCTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCT-CAGAGCAACACTGAC
* * * *
1386 AACAATGAGAATGTGGGTCAGAACGAGAACAATGCCGCTCCA-AGTAACACTGAG
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATG-CGCT-CAGAGCAACACTGAC
* * * *
1440 AACAATGAGAATGCGGGTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGC-GCTCAGAGCAACACTGAC
* * *
1494 AACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACGAAAACAAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCG-CTCAGAGCAACA-C--TG------AC
* * *
1557 AACAATGAAAATGCAGGTCAGAATGAGAACAATGTGACTCAGAGCAACACTGAC
1 AACAATGAAAATGCGGGTCAGAACGAGAACAATGCG-CTCAGAGCAACACTGAC
1611 AACA
1 AACA
1615 GCAGCAACAA
Statistics
Matches: 342, Mismatches: 34, Indels: 30
0.84 0.08 0.07
Matches are distributed among these distances:
53 4 0.01
54 282 0.82
55 4 0.01
57 2 0.01
60 1 0.00
62 1 0.00
63 48 0.14
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.13
Consensus pattern (53 bp):
AACAATGAAAATGCGGGTCAGAACGAGAACAATGCGCTCAGAGCAACACTGAC
Found at i:1708 original size:51 final size:51
Alignment explanation
Indices: 1626--1724 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
1616 CAGCAACAAC
*
1626 AACAACAACGAAAATGCTAGTCAAAACGAGAACAATGC-TGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCAT-CTCAGAGCAGT
* ** *
1677 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGC
1725 TTCACCGACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAAAACGAGAACAATGCATCTCAGAGCAGT
Found at i:1776 original size:63 final size:63
Alignment explanation
Indices: 1677--1871 Score: 309
Period size: 63 Copynumber: 3.1 Consensus size: 63
1667 TCAGAGCAGT
1677 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* *
1740 AACAACAATGAAAATGCAAGTCAGGATGGGAACAATGCATCTCAAAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
* * * * * *
1803 AACAACAACGAAAATGCAAGTCAGAACGAAAACAATGCTTCTCAGAGCTACACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
*
1866 ACCAAC
1 AACAAC
1872 GAGAGCAACG
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 121 1.00
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.13
Consensus pattern (63 bp):
AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
Found at i:1811 original size:186 final size:189
Alignment explanation
Indices: 1456--1811 Score: 427
Period size: 186 Copynumber: 1.9 Consensus size: 189
1446 GAGAATGCGG
* * * *
1456 GTCAGAACGAGAACAATGCTGCTCCGAGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAG
1 GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
*
1521 AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAGGTCAGAATGAGAA
66 AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAAGTCAGAATGAGAA
* * * * *
1586 CAATGTGACTCAGAGCAACACTGACAACAGCAGCAACAACAACAACAACGAAAATGCTA
131 CAATGTCACTCAAAGCAACACCGACAACACCAACAACAACAACAACAACGAAAATGCTA
* ** * *
1645 GTCAAAACGAGAACAATGCTGCT-C-AG-AGCAGTAACAACAATGAAAATGCAAGTCAGGATGAG
1 GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
** * * * *
1707 AACAATGC-ATCTCAGAGCTTCACCGAC-ACCACCAACAACAATGAAAATGCAAGTCAGGATGGG
66 AACAATGCGA-CTCAGAGCAACACCGACGA-AAACAACAACAATGAAAATGCAAGTCAGAATGAG
** *
1770 AACAATG-CATCTCAAAGCTTCACCGACACCACCAACAACAAC
129 AACAATGTCA-CTCAAAGCAACACCGACAACACCAACAACAAC
1812 GAAAATGCAA
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
185 3 0.02
186 112 0.80
187 2 0.01
188 1 0.01
189 22 0.16
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (189 bp):
GTCAAAACGAGAACAATGCTGCTCCGAGTAACACCAACAACAATGAAAATGCAAGTCAGAACGAG
AACAATGCGACTCAGAGCAACACCGACGAAAACAACAACAATGAAAATGCAAGTCAGAATGAGAA
CAATGTCACTCAAAGCAACACCGACAACACCAACAACAACAACAACAACGAAAATGCTA
Done.