Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_770 ID=scaffold_770-JGI_221_v2.0
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: 5033
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.21
Warning! 1161 characters in sequence are not A, C, G, or T
Found at i:150 original size:88 final size:88
Alignment explanation
Indices: 1--386 Score: 497
Period size: 88 Copynumber: 4.4 Consensus size: 88
* * * * * *
1 AACCAGCTCTATCATAACCGAGGGAGGCAAGGTTTGTGTCTTTGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGACAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
*
66 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTGTTGTCTTC
* * * *
89 AACCAGCTCCATCACAACCGAGAGAGATAAGGTTTGTGCCTTCGACCTGCTTCGTTGTCAATCCA
1 AACCAGCTCCATCACAACCGAGAGAGACAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
* * *
154 GGTATGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTGTTGTCTTC
* * * * *
177 AACCAGCTCTATCACAACCGAGAGAGGA-TAGGTTTGTGTATTCGACCTGCCTCACTGTCAATGC
1 AACCAGCTCCATCACAACCGAGAGA-GACAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGC
* *
241 AGCAAGGCAAGATCTGCTGTCTTC
65 AGGAAGGCAAGATCTGTTGTCTTC
* * * *
265 AACCAGCTCCATCACAACCCAGAGAGGC-AGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGAA
1 AACCAGCTCCATCACAACCGAGAGAGACAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
329 GGAAGGCAAGATCTGTTGTCTTC
66 GGAAGGCAAGATCTGTTGTCTTC
* * *
352 AACAAGCTCAATCACAACCGAGAGAGGCAAGGTTT
1 AACCAGCTCCATCACAACCGAGAGAGACAAGGTTT
387 NNNNNNNNNN
Statistics
Matches: 257, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
87 78 0.30
88 177 0.69
89 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAGAGAGACAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
GGAAGGCAAGATCTGTTGTCTTC
Found at i:306 original size:42 final size:42
Alignment explanation
Indices: 170--310 Score: 106
Period size: 44 Copynumber: 3.3 Consensus size: 42
160 CAAGATCTTT
* * *
170 TGTCTTCAACCAGCTCTATCACAACCGAGAGAGGATAGGTTTG
1 TGTCTTCAACCAGCTCCATCACAACCCAGAGAGG-CAGGTTTG
* * * ** ** * *
213 TGTATTCGACCTGC-CTCACTGTCAATGCAGCA-AGGCAAGATCTG
1 TGTCTTCAACCAGCTC-CA-TCACAACCCAG-AGAGGC-AGGTTTG
257 CTGTCTTCAACCAGCTCCATCACAACCCAGAGAGGCAGGTTTG
1 -TGTCTTCAACCAGCTCCATCACAACCCAGAGAGGCAGGTTTG
300 TGTCTTCAACC
1 TGTCTTCAACC
311 TGCTTCGCTG
Statistics
Matches: 70, Mismatches: 21, Indels: 15
0.66 0.20 0.14
Matches are distributed among these distances:
42 12 0.17
43 18 0.26
44 25 0.36
45 14 0.20
46 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (42 bp):
TGTCTTCAACCAGCTCCATCACAACCCAGAGAGGCAGGTTTG
Found at i:1661 original size:88 final size:88
Alignment explanation
Indices: 1383--3308 Score: 2397
Period size: 88 Copynumber: 21.8 Consensus size: 88
1373 CTGGTCTGGC
** * *
1383 CTGTCAATGCAGGAAGGCCAATTTTCTGTTGGTCTTAAACCAGCTCCATCAAAACCGGAGAGAGG
1 CTGTCAATGCAGGAAGG-CAA-GATCTGTT-GTCTTCAACCAGCTCCATCACAACC-GAGAGAGG
**
1448 C-AGGTTTGTGTCTTTAACCTGCTTTCG
62 CAAGGTTTGTGTCTTCGACCTGC-TTCG
* * * * *
1475 CTGTCAAAGAAGGAAGGCAAGATCTGTTGTCTTTTAACAAGCTCAATCACAACCGAGAGAGGCAA
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTC-TTCAACCAGCTCCATCACAACCGAGAGAGGCAA
* *
1540 GGTTTGTGTCTTTGACTTGCTTCG
65 GGTTTGTGTCTTCGACCTGCTTCG
* *
1564 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAGG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
* * *
1629 GCTTGTGTCTTCGATCTGATTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * * * *
1652 ATGTTAATGCAGGAAGGTAAGATTTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
*
1717 GTTTGTGTCTTCGACCTGCTTCC
66 GTTTGTGTCTTCGACCTGCTTCG
* * * * *
1740 CTGTCAATACAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATCACAAACGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
1805 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * * *
1828 CTGTCAATGCAGGATGGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAACCGAGGGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
* **
1893 GTTTTTGTCTTCGATGTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * *
1916 CTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAT
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
1981 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * *
2004 CTGTCAATGCAGGATA-GCAAGATCTGTTCTCTTCAACCAGCTCTATCATAACCGAGGGAGGCAA
1 CTGTCAATGCAGGA-AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
*
2068 GGTTTGTGTCTTCGATCTGCTTCG
65 GGTTTGTGTCTTCGACCTGCTTCG
* * * *
2092 TTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
*
2157 GTTTGTGTCTTCGACCTGCTTCA
66 GTTTGTGTCTTCGACCTGCTTCG
* ** * *
2180 CTGTCAATGCAGGATA-GCAAGATCTGTTGTCTTCAACCAGCTCTATCAGGGACGGGAGGGAGGC
1 CTGTCAATGCAGGA-AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA-CAAC-CGAGAGAGGC
* ** *
2244 AAGGTTTGTGTGTGGGGAGCTGCTTCG
63 AAGGTTTGTGTCT-TCGACCTGCTTCG
* * *
2271 CTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
2336 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * * *
2359 CTGTCAATGCAGGATGGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAACCGAGGGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
*
2424 GTTTGTGTCTTCGATCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
2447 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
2512 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
2535 CTGTCAATACAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
*
2600 G-TTGTGTC-TAGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * **
2621 GTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCAATTCA-AAATGAGAGAGGCC
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCC-A-TCACAACCGAGAGAGG-C
* ** *
2685 AAGGTTTGCGTC-TCGTTCTGATTCG
63 AAGGTTTGTGTCTTCGACCTGCTTCG
* * * * ** * * *
2710 CTCTCAATGCAGGAAGGCAACGTTCTTTTGTCATACAA-CAGCTTTATCACAACCGGGGGATGGA
1 CTGTCAATGCAGGAAGGCAA-GATCTGTTGTC-TTCAACCAGCTCCATCACAACCGAGAGA-GGC
* *** * * * *
2774 AAGATACATGTCTTCCATCTGTTTCT
63 AAGGTTTGTGTCTTCGACCTGCTTCG
** * * *
2800 CTCACAACGCAGGAAGGCAAGAT-T-TTTTTTTCAACCAGCTCCATCACAACCGA-AGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
**
2862 GTTTGTGTCGCCGA-CTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
2884 CTGTC-ACGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAATCCGAGAGAGGCAA
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAA-CCGAGAGAGGCAA
* ** *
2948 GGTTTGTGTCTTCGATCTAATTCA
65 GGTTTGTGTCTTCGACCTGCTTCG
* *
2972 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAGAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
* **
3037 GTTTGTGTCTTTGAATTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * * *
3060 CTGTCAATACAGGAAGGGAGGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAA
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
3125 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * * *
3148 CTGTCAATGCAGGTACGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAGAGAGG-ATA
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-A
* *
3212 GGTTTGTGTATTCGACCTGCCTCG
65 GGTTTGTGTCTTCGACCTGCTTCG
*
3236 CTGTCAATGCAGGAAGGCAATATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGC-AG
1 CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
*
3300 GGTTGTGTC
66 GTTTGTGTC
3309 NNNNNNNNNN
Statistics
Matches: 1574, Mismatches: 233, Indels: 59
0.84 0.12 0.03
Matches are distributed among these distances:
83 17 0.01
84 10 0.01
85 34 0.02
86 62 0.04
87 68 0.04
88 1043 0.66
89 159 0.10
90 108 0.07
91 58 0.04
92 15 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (88 bp):
CTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
GTTTGTGTCTTCGACCTGCTTCG
Found at i:3691 original size:44 final size:43
Alignment explanation
Indices: 3641--3780 Score: 108
Period size: 44 Copynumber: 3.2 Consensus size: 43
3631 ACAACCGAGA
3641 GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTGTCAATGCAG
1 GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTGTCAATGCAG
* * * * ** * **
3684 GATGGCAAGATCTGTTCTCTTCAACCAGC-T--CTATCATAACCGAGG
1 GA-GGCAAGGTTTG-TGTCTTCGACTTGCTTCGCTGTCA-ATGC-A-G
3729 GAGGCAAGGTTTGTGTCTTCGA-TCTGCTTCGCTGTCAATGCAG
1 GAGGCAAGGTTTGTGTCTTCGACT-TGCTTCGCTGTCAATGCAG
3772 GAAGGCAAG
1 G-AGGCAAG
3781 ATATTTTGTC
Statistics
Matches: 69, Mismatches: 18, Indels: 19
0.65 0.17 0.18
Matches are distributed among these distances:
42 5 0.07
43 15 0.22
44 29 0.42
45 15 0.22
46 5 0.07
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (43 bp):
GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTGTCAATGCAG
Found at i:3741 original size:88 final size:88
Alignment explanation
Indices: 3581--4487 Score: 1179
Period size: 88 Copynumber: 10.4 Consensus size: 88
3571 NNNNNNNNNN
* * *
3581 GCTTCGCTGTCAATGCAGGATGGC-AGATCTGTTGTC-TC-ATCAGCTTCATCACAACCGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
3643 GGCAAGGTTTGTGTCTTCGACTT
66 GGCAAGGTTTGTGTCTTCGACTT
* * * * *
3666 GCTTCGCTGTCAATGCAGGATGGCAAGATCTGTTCTCTTCAACCAGCTCTATCATAACCGAGGGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
3731 GGCAAGGTTTGTGTCTTCGA-TCT
66 GGCAAGGTTTGTGTCTTCGACT-T
* *
3754 GCTTCGCTGTCAATGCAGGAAGGCAAGATATTTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
* * *
3819 GGTAAGGTTTGTGCCTTCGACCT
66 GGCAAGGTTTGTGTCTTCGACTT
* * * * * *
3842 GCTTCACTGTCAATCCAGGAACGTATGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
* *
3907 GGTAAGGCTTGTGTCTTCGACTT
66 GGCAAGGTTTGTGTCTTCGACTT
* * * *
3930 GCTTCGTTGTCAATGCAGGAAGGTAAGATCTGCTGTCTTCAACCAGCCCCATCACAACCGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
3995 GGCAAGGTTTGTGTCTTCGA-TCT
66 GGCAAGGTTTGTGTCTTCGACT-T
* * * **
4018 GATTCGCTATCAATGCAGGAAGCCAAGATCTGTTGTCTTCAACCAGCTTTATCACAACCG-GAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
*
4082 GGCAAGGTTTGTGTGTTCGA-TCT
66 GGCAAGGTTTGTGTCTTCGACT-T
* * * * *
4105 GATTCGCTGTCAACGCAGGTACGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAG-GA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAG-
* * *
4169 AGGCAAAGTTTGTGTCTTAGACCT
65 AGGCAAGGTTTGTGTCTTCGACTT
* * *
4193 GCTTCGCTGTCAATGCAGGTACGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG-
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
* * *
4257 GGGATAGGTTTGTGTATTCGACCT
66 GGCA-AGGTTTGTGTCTTCGACTT
* * *
4281 GCCTCGCTGTCCATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
* *
4346 GGC-AGGTTTGTGTCTTCAACCT
66 GGCAAGGTTTGTGTCTTCGACTT
* ** *
4368 GTTTCGCTGTCAATAAAGGAAGGCAAGATCCGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
*
4433 GGCAAGGTTTGTGTCGTCGAGC-T
66 GGCAAGGTTTGTGTCTTCGA-CTT
*
4456 GCTTCGCTGTCACTGCAGGAAGGCAAGATCTG
1 GCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
4488 CTTCACTGTC
Statistics
Matches: 722, Mismatches: 86, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
85 24 0.03
86 11 0.02
87 164 0.23
88 519 0.72
89 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
GCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGA
GGCAAGGTTTGTGTCTTCGACTT
Found at i:4232 original size:263 final size:264
Alignment explanation
Indices: 3583--4487 Score: 1214
Period size: 263 Copynumber: 3.4 Consensus size: 264
3573 NNNNNNNNGC
* ** * *
3583 TTCGCTGTCAATGCAGGATGGC-AGATCTGTTGTC-TC-ATCAGCTTCATCACAACCGAGAGAGG
1 TTCGCTGTCAACGCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
* * *
3645 CAAGGTTTGTGTCTTCGACTTGCTTCGCTGTCAATGCAGGATGGCAAGATCTGTTCTCTTCAACC
66 CAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACC
* * *
3710 AGCTCTATCATAACCGAGGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
131 AGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
* * * *
3775 GGCAAGATATTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTTGTGCCTTCGAC
196 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGAC
*
3840 CTGC
261 CTGA
* * * *
3844 TTCACTGTCAATC-CAGGAACGTATGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAG
1 TTCGCTGTCAA-CGCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAG
* * * * * *
3908 GTAAGGCTTGTGTCTTCGACTTGCTTCGTTGTCAATGCAGGAAGGTAAGATCTGCTGTCTTCAAC
65 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
* * *
3973 CAGCCCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGATTCGCTATCAATGCAGGA
130 CAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* ** *
4038 AGCCAAGATCTGTTGTCTTCAACCAGCTTTATCACAACCG-GAGAGGCAAGGTTTGTGTGTTCGA
195 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
*
4102 TCTGA
260 CCTGA
* *
4107 TTCGCTGTCAACGCAGGTACGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAG-GAAG
1 TTCGCTGTCAACGCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAG-AG
* * * * *
4171 GCAAAGTTTGTGTCTTAGACCTGCTTCGCTGTCAATGCAGGTACGCAAGATCTTTTGTCTTCAAC
65 GCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAAC
* * * * *
4236 CAGCTCCATCACAACCGAGAG-GGGATAGGTTTGTGTATTCGACCTGCCTCGCTGTCCATGCAGG
130 CAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGG
* *
4300 AAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAGAGGC-AGGTTTGTGTCTTCA
194 AAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCG
*
4364 ACCTGT
259 ACCTGA
*** * *
4370 TTCGCTGTCAATAAAGGAAGGCAAGATCCGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
1 TTCGCTGTCAACGCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
* * *
4435 CAAGGTTTGTGTCGTCGAGCTGCTTCGCTGTCACTGCAGGAAGGCAAGATCTG
66 CAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
4488 CTTCACTGTC
Statistics
Matches: 557, Mismatches: 78, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
261 16 0.03
262 15 0.03
263 343 0.62
264 183 0.33
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (264 bp):
TTCGCTGTCAACGCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
CAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACC
AGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGAC
CTGA
Found at i:4497 original size:31 final size:31
Alignment explanation
Indices: 4454--4517 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
4444 TGTCGTCGAG
* * * *
4454 CTGCTTCGCTGTCACTGCAGGAAGGCAAGAT
1 CTGCTTCACTGTCAATCCAGGAACGCAAGAT
*
4485 CTGCTTCACTGTCAATCCAGGAACGCATGAT
1 CTGCTTCACTGTCAATCCAGGAACGCAAGAT
4516 CT
1 CT
4518 TTTGTCTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (31 bp):
CTGCTTCACTGTCAATCCAGGAACGCAAGAT
Found at i:4640 original size:88 final size:88
Alignment explanation
Indices: 4482--4998 Score: 613
Period size: 88 Copynumber: 5.8 Consensus size: 88
4472 AGGAAGGCAA
* * * * **
4482 GATCTGCTTCACTGTCAATCCAGGAACGCATGATCTTTTGTCTTCAACCAGCTCCATCACAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACCG
* * *
4547 GGAGAGGTAAGGCTTGTGTCTTC
66 AGAGAGGCAAGGTTTGTGTCTTC
* * *
4570 GA-CTTGCTTCGTTGTCAATGCAGGAAGGTAAGATCTGCTGTCTTCAACCAGCCCCATCACAACC
1 GATC-TGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACC
*
4634 GAGAGAGGCAAGGTTTGTGTCTTT
65 GAGAGAGGCAAGGTTTGTGTCTTC
* * **
4658 GATCTGATTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTTATCACAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACCG
* * * *
4723 AGGGAGGTAAGATTTGTGTTTTC
66 AGAGAGGCAAGGTTTGTGTCTTC
* *
4746 GATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTGTCTTCAACCAACTCCATCACAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACCG
4811 AGAGAGGCAAGGTTTGTGTCTTC
66 AGAGAGGCAAGGTTTGTGTCTTC
* * ** * *
4834 GATCTGATTCGCTGTCAATGCATGCATGAATGCAAGATCTTATGTCTTCAACCTGCTCCATCAGA
1 GATCTGCTTCGCTGTCAATGCA-G---GAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACA
* * *
4899 ACCGACAGAAGCAAGGTTTGTGGTCTTT
62 ACCGAGAGAGGCAAGGTTTGT-GTCTTC
* * * * * *
4927 GAACTGCTACGCTGTCTATACAGGAAGGCAGGATCTGTTGTCTTCAACCAGCTTCTCATCACAAC
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGC-TC-CATCACAAC
4992 CGAGAGA
64 CGAGAGA
4999 CGTAAAATTA
Statistics
Matches: 362, Mismatches: 58, Indels: 15
0.83 0.13 0.03
Matches are distributed among these distances:
87 1 0.00
88 245 0.68
89 26 0.07
90 2 0.01
91 14 0.04
92 52 0.14
93 22 0.06
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATCACAACCG
AGAGAGGCAAGGTTTGTGTCTTC
Found at i:4671 original size:207 final size:206
Alignment explanation
Indices: 4287--4694 Score: 591
Period size: 207 Copynumber: 2.0 Consensus size: 206
4277 ACCTGCCTCG
* * * * *
4287 CTGTCCATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAGAGGCAGG
1 CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGAAGG
* * * *
4352 TTTGTGTCTTCAACCTGTTTCGCTGTCAATAAAGGAAGGCAAGATCCGTTGTCTTCAACCAGCTC
66 CTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATCCGCTGTCTTCAACCAGCCC
* *
4417 CATCACAACCGAGAGAGGCAAGGTTTGTGTCGTCGAGCTGCTTCGCTGTCACTGCAGGAAGGCAA
131 CATCACAACCGAGAGAGGCAAGGTTTGTGTCGTCGAGCTGATTCGCTGTCAATGCAGGAAGGCAA
4482 GATCTGCTTCA
196 GATCTGCTTCA
* * *
4493 CTGTCAATCCAGGAACGCATGATCTTTTGTCTTCAACCAGCTCCATCACAACCGGGAGAGGTAAG
1 CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG-AAG
* * * ** * *
4558 GCTTGTGTCTTCGACTTGCTTCGTTGTCAATGCAGGAAGGTAAGATCTGCTGTCTTCAACCAGCC
65 GCTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATCCGCTGTCTTCAACCAGCC
* * *
4623 CCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGATCTGATTCGCTGTCAATGCAGGAAGGCA
130 CCATCACAACCGAGAGAGGCAAGGTTTGTGTCGTCGAGCTGATTCGCTGTCAATGCAGGAAGGCA
4688 AGATCTG
195 AGATCTG
4695 TTGTCTTCAA
Statistics
Matches: 177, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
206 54 0.31
207 123 0.69
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (206 bp):
CTGTCAATCCAGGAACGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGAAGG
CTTGTGTCTTCAACCTGCTTCGCTGTCAATAAAGGAAGGCAAGATCCGCTGTCTTCAACCAGCCC
CATCACAACCGAGAGAGGCAAGGTTTGTGTCGTCGAGCTGATTCGCTGTCAATGCAGGAAGGCAA
GATCTGCTTCA
Done.