Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000303.1 Hibiscus syriacus cultivar Beakdansim tig00000562_pilon, whole genome shotgun sequence
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: 40922
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3536 original size:5 final size:5
Alignment explanation
Indices: 3517--3570 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
3507 GTCCGTCCGT
* * * *
3517 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
3567 CTCG
1 CTCG
3571 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:3579 original size:6 final size:6
Alignment explanation
Indices: 3568--3616 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
3558 TCGGCTCGGC
3568 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3616 T
1 T
3617 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:9464 original size:5 final size:5
Alignment explanation
Indices: 9454--9501 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
9444 GTCCGTCCGT
* * * *
9454 CTCGG CTCGG CACGG CACGG CACGG CACGG -TCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
9502 TGGTCGTGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 3 0.08
5 37 0.93
ACGTcount: A:0.08, C:0.40, G:0.40, T:0.12
Consensus pattern (5 bp):
CTCGG
Found at i:9510 original size:6 final size:6
Alignment explanation
Indices: 9499--9607 Score: 184
Period size: 6 Copynumber: 18.2 Consensus size: 6
9489 TCGGCTCGGC
9499 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
9547 TCGTGG TCGTGG TCGAGG TCGAGG TC-TAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGT-GG TCGTGG TCGTGG TCGTGG
9595 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
9608 AATACGTGTC
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
6 98 0.99
7 1 0.01
ACGTcount: A:0.03, C:0.17, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:10938 original size:24 final size:25
Alignment explanation
Indices: 10911--10970 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
10901 TAAGTTTCGA
10911 TATTTTTTTAATCTAA-TA-TTTACT
1 TATTTTTTTAAT-TAATTATTTTACT
* * *
10935 TATTTATTTAGTTAATTATTTTAGT
1 TATTTTTTTAATTAATTATTTTACT
*
10960 TATTATTTTAA
1 TATTTTTTTAA
10971 GTATATATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 3 0.11
24 12 0.43
25 13 0.46
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (25 bp):
TATTTTTTTAATTAATTATTTTACT
Found at i:10964 original size:12 final size:13
Alignment explanation
Indices: 10941--10969 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
10931 TACTTATTTA
10941 TTTAGTTAATTAT
1 TTTAGTTAATTAT
10954 TTTAGTT-ATTAT
1 TTTAGTTAATTAT
10966 TTTA
1 TTTA
10970 AGTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTAGTTAATTAT
Found at i:11034 original size:18 final size:17
Alignment explanation
Indices: 11002--11035 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
10992 GGGCGTAGGT
*
11002 ATTTTAATTAATATTTA
1 ATTTTAATAAATATTTA
11019 ATTTTCAATAAATATTT
1 ATTTT-AATAAATATTT
11036 TTTATTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATAAATATTTA
Found at i:11533 original size:29 final size:29
Alignment explanation
Indices: 11491--11577 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
11481 TCTGAGGTTG
11491 TTACACTAAGATAACTGGAGACCAAACAC
1 TTACACTAAGATAACTGGAGACCAAACAC
11520 TTACACTAAGATAACTGGAGACCAAACAC
1 TTACACTAAGATAACTGGAGACCAAACAC
11549 TTACACTAAGATAACTGGAGACCAAACAC
1 TTACACTAAGATAACTGGAGACCAAACAC
11578 ACATATTTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (29 bp):
TTACACTAAGATAACTGGAGACCAAACAC
Found at i:12733 original size:21 final size:21
Alignment explanation
Indices: 12700--12758 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
12690 GTACTTAAGA
**
12700 TGAGTATTGATACCCATGGGG
1 TGAGTATCAATACCCATGGGG
*
12721 TGAGTATCAATACTCGTAT-GGG
1 TGAGTATCAATAC-C-CATGGGG
12743 -G-GTATCAATACCCATG
1 TGAGTATCAATACCCATG
12759 AGATTTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 10 0.32
21 12 0.39
22 4 0.13
23 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
TGAGTATCAATACCCATGGGG
Found at i:18898 original size:12 final size:12
Alignment explanation
Indices: 18881--18928 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
18871 CTATCATTTA
18881 TTTATTTTTCTT
1 TTTATTTTTCTT
18893 TTTATTTTTCTT
1 TTTATTTTTCTT
* *
18905 CTTTTTCATTTTCTC
1 -TTTAT--TTTTCTT
18920 TTTATTTTT
1 TTTATTTTT
18929 TTCCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 4 0.13
15 6 0.20
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTCTT
Found at i:18908 original size:15 final size:15
Alignment explanation
Indices: 18877--18921 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
18867 ATTTCTATCA
*
18877 TTTATTTATTTTTCTT
1 TTTATTT-TTCTTCTT
18893 TTTATTTTTCTTCTT
1 TTTATTTTTCTTCTT
18908 TTTCATTTTCTCTT
1 TTT-ATTTT-TCTT
18922 TATTTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTTTCTTCTT
Found at i:18916 original size:27 final size:27
Alignment explanation
Indices: 18886--18937 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18876 ATTTATTTAT
*
18886 TTTTCTTTTTATTTTTCTT-CTTTTTCA
1 TTTTCTCTTTATTTTT-TTCCTTTTTCA
18913 TTTTCTCTTTATTTTTTTCCTTTTT
1 TTTTCTCTTTATTTTTTTCCTTTTT
18938 TCACCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTCTCTTTATTTTTTTCCTTTTTCA
Found at i:18999 original size:69 final size:69
Alignment explanation
Indices: 18877--19007 Score: 158
Period size: 69 Copynumber: 1.9 Consensus size: 69
18867 ATTTCTATCA
* * * * * *
18877 TTTATTTATTTTTCTTTTTATTTTTCTTCTTTTTCATTTTCTCTTTATTTTTTTCCTTTTTTCAC
1 TTTATTTATTTTTCTTTCTATTCTTCTTCTTTCTAATTTTCCCTTTATTTTTTTCATTTTTTCAC
18942 CATT
66 CATT
* *
18946 TTTATTTTTTTTTCTTTCT-TTCTT-TTCTTTCTAATTTTTCCCTTTTTTATTTTTCATTTTTT
1 TTTATTTATTTTTCTTTCTATTCTTCTTCTTTCTAA-TTTTCCCTTTATT-TTTTTCATTTTTT
19008 TTTGAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
67 8 0.15
68 15 0.29
69 29 0.56
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (69 bp):
TTTATTTATTTTTCTTTCTATTCTTCTTCTTTCTAATTTTCCCTTTATTTTTTTCATTTTTTCAC
CATT
Found at i:19010 original size:27 final size:25
Alignment explanation
Indices: 18881--19010 Score: 77
Period size: 28 Copynumber: 4.8 Consensus size: 25
18871 CTATCATTTA
18881 TTTATTTTTCTTTTTATTTTTCTTCTTT
1 TTTATTTTTCTTTTT-TTTTTC--CTTT
*
18909 TTCATTTTCTCTTTATTTTTTTCCTTT
1 TTTATTTT-TCTTT-TTTTTTTCCTTT
*
18936 TTTCACCATTTTT-ATTTTTTTTT-CTTT
1 TTT----ATTTTTCTTTTTTTTTTCCTTT
* *
18963 CTTT-CTTTTCTTTCTAATTTTTCCCTTT
1 -TTTATTTTTCTTT-T--TTTTTTCCTTT
*
18991 TTTATTTTTCATTTTTTTTT
1 TTTATTTTTCTTTTTTTTTT
19011 GAAATTTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 29
0.68 0.08 0.25
Matches are distributed among these distances:
23 4 0.05
24 2 0.03
25 6 0.08
27 19 0.24
28 28 0.35
29 13 0.16
30 3 0.04
31 5 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTATTTTTCTTTTTTTTTTCCTTT
Found at i:19707 original size:42 final size:42
Alignment explanation
Indices: 19637--19716 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
19627 CAAGGGACTT
* *
19637 ATCATCTTGCTCAAAAGACTAACAGATGACCCGAAGGATTTA
1 ATCATCATGCTCAAAAGACTAACAGATGACCCAAAGGATTTA
* * *
19679 ATCATCATGCTCAAATGACTTACTGATGACCCAAAGGA
1 ATCATCATGCTCAAAAGACTAACAGATGACCCAAAGGA
19717 CTTACCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24
Consensus pattern (42 bp):
ATCATCATGCTCAAAAGACTAACAGATGACCCAAAGGATTTA
Found at i:20438 original size:41 final size:41
Alignment explanation
Indices: 20393--20490 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
20383 TTATAGATGG
20393 CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
1 CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
*
20434 CGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACC
1 CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
* *
20475 TGAAGGATTTAATCAT
1 CGAAGGACTT-ATCAT
20491 AATTTCGAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 48 0.91
42 5 0.09
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (41 bp):
CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
Found at i:20499 original size:41 final size:40
Alignment explanation
Indices: 20393--20526 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 40
20383 TTATAGATGG
* *
20393 CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGACC
1 CGAAGGACTTATCATATT-CTCGAAAGAATGACAGATGACC
*
20434 CGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACC
1 CGAAGGACTTATCATATT-CTCGAAAGAATGACAGATGACC
* * * * * *
20475 TGAAGGATTTAATCATAATT-TCGAATGACTTACTGATGACC
1 CGAAGGACTT-ATCAT-ATTCTCGAAAGAATGACAGATGACC
*
20516 CAAAGGACTTA
1 CGAAGGACTTA
20527 CAAATTTTGG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 72 0.90
42 5 0.06
43 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (40 bp):
CGAAGGACTTATCATATTCTCGAAAGAATGACAGATGACC
Found at i:22098 original size:258 final size:258
Alignment explanation
Indices: 20426--25003 Score: 5156
Period size: 258 Copynumber: 17.8 Consensus size: 258
20416 AAAGAATGAC
* * *
20426 AGATGACCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACCTGAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * *
20491 AAT-TTCGAATGACTTACTGATGACCCAAAGGACTTACAAATTTTGGAAATAGTCTACTTGGTAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
* * * * * *
20555 GAAACTTTGGAGACCACTTTCTTACTTTTCAAAATGTTCATTTTCT-AAAATTCTTAAATTAGAA
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAA-TCCTAAATGAGAA
* * * * *
20619 ATTTTGAAAATCGCTTTCTCATTTTTTACAAATCATATGAAAACATCCTACACAAAGGTCTTAT
195 ACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * * *
20683 AGATGACCC-AAGGACTTATAATCTTGCTTGAAAGTCTGACAGATGA-CCAATAGTATTTAATCA
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA-AGGATTTAATCA
* ** *
20746 TCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAATAGTCTACTAGGTA
65 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* ** * * * *
20811 AGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAAATTTATTTTTTAAAAATACTAAATGAAAA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
* * *
20876 ACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTTGCCCGAAGGTCTTA
195 ACTTTGAAAATCGTTTTCTCATTTTTTAC-AA-ATCATATGAAAACATCCTGCCCGAAGGTCTTA
20941 T
258 T
* ** * * * *
20942 AGATGACCTTAAGAACTTATCATCTTGCTC-AATGACTGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * * *
21006 CATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAGTTTTGGAAATAGTCTACCTAGCAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
* * * * *
21071 GAAACTTTGGAAATCTCTTTCTTATTTTTCAAAAATTTTATTTTTATGAAAATCCTAAATGAGAT
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTA-TTTTCTGAAAATCCTAAATGAGAA
* * *
21136 ACTTTGAAAATCAG-TTTCTCATTTTTTACAAATCATATTAAAACATCCTGCCCGAATGTTTTAT
195 ACTTTGAAAATC-GTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * * * *
21200 ATATGGCCTGAAGGACTTGTCATTTTGCTCGAAAGAATGACATATGACCCGAAGGATTTAAACAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* *
21265 AATG-TC-AAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
66 CATGCTCGAAA-GACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* * *
21328 AGAAA-TTTGGAAACCACTTTCTTACTTTT-AAAATTTTCATTTTCT-AAAATTCTTAAATGAGA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAA-TCCTAAATGAGA
* * * * *
21390 AATTTTGAAAATCGTTTTCTCATTTTTTAGAAATCATATGAAAACATCCTACCCAAAGGTCTTAG
194 AACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * *
21455 AGATGGTCC-AAGGAC--ATAATCTTGCTCGAAAGTA-TAACAGATGA-CCAATAGTATTTAATC
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAG-ACTGACAGATGACCCGA-AGGATTTAATC
* ** * *
21515 ATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACATACCAATTTTGGAAATAGTCTACTAGGT
64 ATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGT
* * * * * *
21580 AAGAAACTTTGGAAAACGA-TTTCTTAATTTTCAAAAATTTTATTTT-TGTAAATACTAAATGAA
129 AAGAAACTTTGGAAATC-ACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAG
* * * *
21643 AAACTTTGAAAATCGTTTTCT-ATTTTTCACAAATATCACATGAAAACATCTTGCTCGAAGGTCT
193 AAACTTTGAAAATCGTTTTCTCATTTTTTAC-AA-ATCATATGAAAACATCCTGCCCGAAGGTCT
21707 TAT
256 TAT
** * * * * *
21710 AGATGATCCTAAGAAC-T-T-ATCTTG--CGAATGACTGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * *** * *
21770 CGTGCTCGAAAGACTTACTAATGGCTTGAAGGACTTACCAATTTTGGAAATATTCTACCTGGTAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
*
21835 GAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGAAAATCCTAAATGAGAA
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTA-TTTTCTGAAAATCCTAAATGAGAA
* * * *
21900 ACTTTGAAAATCGCTTTCTCATTTTCTACAAATCATATTAAAACATCCTGCCCGAATGTCTTAT
195 ACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * *
21964 AGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTGACAGATGACCAGAAGGATTTCATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * *
22029 AAT-ATTGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
* * * * *
22093 GAAACTTTGGAGACCACTTTCTTACTTTTC-AAA-TTTCATTTTCT-AAAATTCTTAAATGCGAA
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAA-TCCTAAATGAGAA
* ** * * * * * * *
22155 ATTTTGAAAATTATTTTCTTATATTTTACAAATCATATGAAATCATCCTACTCAAAGGTCTTCT
195 ACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * *
22219 AGATGGCCC-AAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGA-CCAATAGTATTCAATCA
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA-AGGATTTAATCA
* * * ** * *
22282 TCATGCTCGAAAGACTAACTAATAGCCTTAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
65 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
** * * * *
22347 AGAAACTTTGGAAAAAACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAAATACTAAATGAAAA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
* * * *
22412 ACTTTGAAAAGCGTTTTCTCATTTTTCACAAATATCACATGAAAACAT-CTTCCCGAAGGTCTTA
195 ACTTTGAAAATCGTTTTCTCATTTTTTAC-AA-ATCATATGAAAACATCCTGCCCGAAGGTCTTA
22476 T
258 T
* * * * * *
22477 AGATTGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * * * *
22542 CATGCTTGAAAGACTTATTGATGGCTCAAAGGACTTACCAGTTTTGGAAATAGTCTACCTAGCAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
*
22607 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTTATGAAAATCCTAAATGAGAA
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTA-TTTTCTGAAAATCCTAAATGAGAA
* *
22672 ACTTTGAAAATCAG-TTTCTCATTTTTTACAAATCATATTAAAACATCCTGCCCGAATGTCTTAT
195 ACTTTGAAAATC-GTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
** * *
22736 AGATGGCCTAAAGGACTTATCATCTTGCTCGAAAGAATGACATATGACCCGAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * *
22801 AATG-TC-AAATGACTTACTGATGACCCAAAAGACTTACCAATTTTGGAAATAGTAC-ACTTGGT
66 CATGCTCGAAA-GACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGT-CTACTTGGT
* * * *
22863 AAGAAATTTTGGAAACCACTTTCTTACTTTTCAAAATTTTCATTTTCT-AAAATTCTTAAATGAG
129 AAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAA-TCCTAAATGAG
* * *
22927 AAA-TTTTAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTACCCAAAGGTCTTA
193 AAACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTA
*
22991 G
258 T
* * * *
22992 AGATGGCCC-AAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGA-CCAATAGTATTTAATCA
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA-AGGATTTAATCA
* ** * *
23055 TCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGAAAATAGTCTACTAGGTA
65 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* * *
23120 AGAAACTTTGGAAAACACTTTCTTACTTTTCAAAA-TTTTATTTT-TGAAAATACTAAATGAAAA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
* * ** * * *
23183 ACTATGAAAATTGTTTTCTCATTTTTCCCATATATCACATGAAAACATCTTGCCCCAAGGTCTTA
195 ACTTTGAAAATCGTTTTCTCATTTTTTACA-A-ATCATATGAAAACATCCTGCCCGAAGGTCTTA
23248 T
258 T
* * * * * * *
23249 AGATGGCCCTATGAACTTATCATCTTACTCGAATGACTGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * ** * * *
23314 CGTGCTCGAAAGACTTATTGATGGCTTGAAA-AACTTACCAATTTTGGAAATAGTCTACCTGGCA
66 CATGCTCGAAAGACTTACTGATGGC-CCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* *
23378 AGAAACTTTGGAAATCTCTTTATTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
* * * * * *
23443 ACTTTTAAAATCGCTTTCTCATTTTTTACAAATCATATTAAAACATCTTGCCCAAATGTCTTAT
195 ACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * *
23507 AGATGGCCCGAAGGACTAATCATCTTACTCGAAAGAATGATATATGA-CCGAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * *
23571 AATG-TC---A-A-TTACTGATGACCCAAAAGACTTACCAATTTTGGAAATAGTCTACTAGGTAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
* * * *
23630 GAAACTTTGGAAAACGCTTTCTTACTTTTCAAAAATTTTATTTT-TGAAAATACTAAATGA-AGA
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGA-A
* * *
23693 ACTTTGAAAAGCGTTTTCTCATTTTTTCACAAATATCACATGAAAACAT-CTTCCCGAAGGTCTT
195 ACTTTGAAAATCGTTTTCTCATTTTTT-AC-AA-ATCATATGAAAACATCCTGCCCGAAGGTCTT
23757 AT
257 AT
* * * * * * *
23759 AGATGACCCTAAGAACTTCTCATCTTGCTCGAATGACTGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * * * * *
23824 CATGCTCGAAATAATTATTGATGGCTCAAAGGACTTACCAGTTTTGGAAATAGT-TACCTAGCAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
*
23888 GAAACTTTGGAAAT-ATCTTTCTTACTTTTCAAAATTTTTATTTTTATGAAAATCCTAAATGAGA
131 GAAACTTTGGAAATCA-CTTTCTTACTTTTCAAAATTTTTA-TTTTCTGAAAATCCTAAATGAGA
* *
23952 AACTTTGAAAATCAG-TTTCTCATTTTTTACAAATCATATTAAAACATCCTGCCCGAATGTCTTA
194 AACTTTGAAAATC-GTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTA
24016 T
258 T
* * * * *
24017 AGATGGCCCGAAGGACTTATCATCTTACTCAAAAGAATGACATAAGACCCGAAGGA-TTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * * * *
24081 AATG-TC-AAATGACTTACTGATGACCCAAAAGACTTAGCAATTTTAGAAATAGTCTACTTGGTA
66 CATGCTCGAAA-GACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* * * *
24144 AGAAATTTTGGAAACCACTTTCTTACTTTTCAAAATTTTCATTTTCT-AAAATTCTTAAATGAGA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAA-TCCTAAATGAGA
* * * * * * *
24208 AATTTTGAAAATC-ATTTCTCATTTTTTATAAATCATATGAAAACATCTTACCCAAAGGTCTTAG
194 AACTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
* * * * * * *
24272 AGATGGTCC-AATGATTTATAATCTTGCTCGAAAGTCTGACAGATGA-CCAATAGTA-TTAATCA
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA-AGGATTTAATCA
* ** *
24334 TCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAATAGTCTACTAGGTA
65 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTA
* * * * *
24399 AGAAACTTTGGAAAACGCTTTCTTACTTTTCAAAA-TTTTATTTTTTGAAAATACTAAATGAAAA
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAA
* * ** * *
24463 ACTTTGATAATCGTTTTCTCGTTTTTCCCAAATATCACATGAAAACATCTTGCCCGAAGGTCTTA
195 ACTTTGAAAATCGTTTTCTCATTTTTTAC-AA-ATCATATGAAAACATCCTGCCCGAAGGTCTTA
24528 T
258 T
* * * * * * *
24529 AGATGGCCCTAAGAACTTATCATCTTGCTGGAATGACAGAAAGATGACCCTAAGGATTTAATCAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* *** * * *
24594 CGTGCTCGAAAGACTTACTGATGGCTTGAAGGACATACCAATTTTGGAAATAGTCTACCTGGCAA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
* * * *
24659 GAAACTTTGGAAATCTCTTTATTAATTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAAT
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAAA
* * *
24724 CTTTGAAAATC-TCTTTCTCATTTTTTACAAATCATATTAAAACATCCTGCTCGAATGTCTTAT
196 CTTTGAAAATCGT-TTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
** *
24787 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACAGGAAGGATTTAATAAT
1 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
* * ** * *
24852 CTTGCTCGAAGGACTTACTGATGGCCTGAA-GACTTGCCAATTTTGGAAATAGTCTA-TCAGGTA
66 CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACT-TGGTA
* * * *
24915 AGAAAATTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA-TTTCT-AAACATCTTAAATGA-A
130 AGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAA-ATCCTAAATGAGA
* * *
24977 AATGTTTGAAAATTGTTTTCTCGTTTT
194 AA-CTTTGAAAATCGTTTTCTCATTTT
25004 ACGAAAATTA
Statistics
Matches: 3628, Mismatches: 588, Indels: 211
0.82 0.13 0.05
Matches are distributed among these distances:
249 1 0.00
250 43 0.01
251 84 0.02
252 90 0.02
253 218 0.06
254 251 0.07
255 567 0.16
256 327 0.09
257 456 0.13
258 749 0.21
259 595 0.16
260 243 0.07
261 4 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (258 bp):
AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCAT
CATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAA
GAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTCTGAAAATCCTAAATGAGAAA
CTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCCTGCCCGAAGGTCTTAT
Found at i:22722 original size:772 final size:774
Alignment explanation
Indices: 19012--24958 Score: 7188
Period size: 772 Copynumber: 7.7 Consensus size: 774
19002 TTTTTTTTTG
* * ****
19012 AAATTTTTAAATGAGAAACTTTGAAAAAAAATTTCTCACTTTTTTACAAATCATATGAAAACATC
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCA-TTTTTTACAAATCATATGAAAACATC
* * * * * *
19077 CT-GCCAGAAGGTCTTATAGATGGCCCGAGGGACTTATCATCTTGCTCGAAAGCCTAACAAAT-A
65 CTACCCA-AAGGTCTTATAGATGGCCC-AAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGA
* * * * * ** *
19140 GCCTGCAT-G-ATTTAATTATCATGCTCGAAAGACTTATTGATAGCCCGAATGACTTACCAATTT
128 -CC--AATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTT
* * * * * *
19203 TGGAAAATAGTCTATTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAATTCATTT
190 TGG-AAATAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTT
* * * * ** ** *
19268 TCTAAAAAT-CTTAAATGAGAAACTTTGAAAACCACTTTCTCATATTTTTTTCAAATATCATATG
254 TTTGAAAATAC-TAAATGAAAAACTTTGAAAATCGTTTTCTC--ATTTTTCACAAATATCACATG
* * * * * * * * * *
19332 GAAACATCTTACTCGAAGGTATTATAGGTGG-CATGAGGGACTTATCATCTTTCTCGAAAGACTG
316 AAAACATCTTGCCCGAAGGTCTTATAGATGGCCCT-AAGAACTTATCATCTTGCTCGAATGACTG
* * *
19396 ATAGATGACCCAAAGGATTTTAATCATCATGCTTGAAAGACTTATTGATGGCTCGAAA-GACTTA
380 AAAGATGACCCTAAGGA-TTTAATCATCATGCTCGAAAGACTTATTGATGGCTC-AAAGGACTTA
* * * * * * *
19460 GCAATTTTGGAAATAGTCTA-CTGGGTAAAAAACTTTAGAAATC-GTTTCTTACTTTTTAGAAA-
443 CCAATTTTGGAAATAGTCTACCT-AGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCA-AAAT
* * * * *
19522 -TTTAATTTTCTGAAAATCATAAATGAGAAACTTTGACACTC-GCTTTCTCATTTTTTTTTCAAA
506 TTTTATTTTTCTGAAAATCCTAAATGAGAAACTTTGAAAATCAG-TTTCTCA--TTTTTTAC-AA
** * * * * * *
19585 TATCATATGGAAATATCATGCCAGAAGGTTTTATAGATAGCCC-AAGGGACTTATCATCTTGCTC
567 -ATCATATTAAAACATCCTGCCCGAATGTCTTATAGATGGCCCGAA-GGACTTATCATCTTGCTC
* * * * * *
19649 AAAAGACTAACAGATGACCCGAAGGATTTAATCATCATGCTCAAATGACTTACTGATGACCCAAA
630 GAAAGAATGACAGATGACCCGAAGGATTTAATCATAAT-ATCGAATGACTTACTGATGACCCAAA
*
19714 GGACTTACCAATTTTGGGAAATAGTTTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTT
694 GGACTTACCAATTTT-GGAAATAGTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTT
*
19779 CAAAATTTAATTTTCTA
758 CAAAATTTCATTTTCTA
* * * * *
19796 AAAATCTTAAATGAAAAATTTTGAAAATCGTTTTCTCATTTTTTTTACAGATCATATGAAAATAA
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCA--TTTTTTACAAATCATATGAAAACAT
** * *
19861 CCTACCCAAAACTCATATAGATGGCCCAAGGAC-----A----GCTCGAAAGACT-ACAGATGAC
64 CCTACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGAC
* * *
19916 CAATAGTATTTAATCATCATGCTCGAAAAACTTAGTAATGGCCTTAAGGACTTACTAATTTTGGA
129 CAATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGA
* *
19981 AATAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTCATTTTCTGA
194 AATAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTTTTGA
* * * *
20046 AAATCCTAAATTAAAAACTTTGAAAATCGTTTTCTTATTTTTCACAAATATCACGTGAAAACATC
259 AAATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATC
* * * * * * *
20111 TTACCCGTAGGTCTTATAGATGGCCCAAAGGACATATCATCTTACTCGAATGACTGAAACATGAC
324 TTGCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGAC
*
20176 CCTAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAGTTTTGGA
389 CCTAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAATTTTGGA
* *
20241 AATAGTCTACCTAGCAAGAAACTTTTGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTA
454 AATAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTG
* *
20306 AAAATCCTAAATGAGAAACTTTGAAAAT-AGGTTTCACATTTTTTAGAAATCATATTAAAACATC
519 AAAATCCTAAATGAGAAACTTTGAAAATCA-GTTTCTCATTTTTTACAAATCATATTAAAACATC
* *
20370 CTGCCTGAATGTCTTATAGATGG--CGAAGGACTTATCATCTTGCTCAAAAGAATGACAGATGAC
583 CTGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGAC
20433 CCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACCTGAAGGATTTAATCATAATTTCG
648 CCGAAGG-------A--TT--T------AAT--C-----A--T--A--A--T-ATC--------G
*
20498 AATGACTTACTGATGACCCAAAGGACTTACAAATTTTGGAAATAGTCTACTTGGTAAGAAACTTT
672 AATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATAGTCTACTTGGTAAGAAACTTT
*
20563 GGAGACCACTTTCTTACTTTTCAAAATGTTCATTTTCTA
737 GGAAACCACTTTCTTACTTTTCAAAAT-TTCATTTTCTA
* *
20602 AAATTCTTAAATTAGAAATTTTGAAAATCGCTTTCTCATTTTTTACAAATCATATGAAAACATCC
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
* * *
20667 TACACAAAGGTCTTATAGATGACCCAAGGACTTATAATCTTGCTTGAAAGTCTGACAGATGACCA
66 TACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
20732 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
131 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
* *
20797 TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAAATTTATTTTTTAAAA
196 TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAA
20862 ATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
261 ATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
* *
20927 GCCCGAAGGTCTTATAGATGACCTTAAGAACTTATCATCTTGCTC-AATGACTGAAAGATGACCC
326 GCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCC
*
20991 TAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAGTTTTGGAAA
391 TAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAATTTTGGAAA
* * *
21056 TAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTATTTTTCAAAAATTTTATTTTTATGAA
456 TAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGAA
*
21121 AATCCTAAATGAGATACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATATTAAAACATCCTG
521 AATCCTAAATGAGAAACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATATTAAAACATCCTG
* * * * * *
21186 CCCGAATGTTTTATATATGGCCTGAAGGACTTGTCATTTTGCTCGAAAGAATGACATATGACCCG
586 CCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCG
* * *
21251 AAGGATTTAAACATAATGTCAAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATA
651 AAGGATTTAATCATAATATCGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATA
21316 GTCTACTTGGTAAGAAA-TTTGGAAACCACTTTCTTACTTTT-AAAATTTTCATTTTCTA
716 GTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAA-TTTCATTTTCTA
*
21374 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTAGAAATCATATGAAAACATCC
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
* * * *
21439 TACCCAAAGGTCTTAGAGATGGTCCAAGGAC--ATAATCTTGCTCGAAAGTATAACAGATGACCA
66 TACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
*
21502 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACATACCAATTTTGGAAA
131 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
* *
21567 TAGTCTACTAGGTAAGAAACTTTGGAAAACGA-TTTCTTAATTTTCAAAAATTTTA-TTTTTGTA
196 TAGTCTACTAGGTAAGAAACTTTGGAAAAC-ACTTTCTTACTTTTCAAAAATTTTATTTTTTGAA
21630 AATACTAAATGAAAAACTTTGAAAATCGTTTTCT-ATTTTTCACAAATATCACATGAAAACATCT
260 AATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCT
* **
21694 TGCTCGAAGGTCTTATAGATGATCCTAAGAAC-T-T-ATCTTG--CGAATGACTGAAAGATGACC
325 TGCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACC
* * * **
21754 CTAAGGATTTAATCATCGTGCTCGAAAGACTTACTAATGGCTTGAAGGACTTACCAATTTTGGAA
390 CTAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAATTTTGGAA
* * *
21819 ATATTCTACCTGGTAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGA
455 ATAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGA
*
21884 AAATCCTAAATGAGAAACTTTGAAAATC-GCTTTCTCATTTTCTACAAATCATATTAAAACATCC
520 AAATCCTAAATGAGAAACTTTGAAAATCAG-TTTCTCATTTTTTACAAATCATATTAAAACATCC
* *
21948 TGCCCGAATGTCTTATAGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTGACAGATGACC
584 TGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACC
* * *
22013 AGAAGGATTTCATCATAATATTGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAA
649 CGAAGGATTTAATCATAATATCGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAA
*
22078 TAGTCTACTTGGTAAGAAACTTTGGAGACCACTTTCTTACTTTTC-AAATTTCATTTTCTA
714 TAGTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAATTTCATTTTCTA
* ** * * *
22138 AAATTCTTAAATGCGAAATTTTGAAAATTATTTTCTTATATTTTACAAATCATATGAAATCATCC
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
* *
22203 TACTCAAAGGTCTTCTAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
66 TACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
* * *
22268 ATAGTATTCAATCATCATGCTCGAAAGACTAACTAATAGCCTTAAGGACTTACCAATTTTGGAAA
131 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
* *
22333 TAGTTTACTAGGTAAGAAACTTTGGAAAAAACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAA
196 TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAA
*
22398 ATACTAAATGAAAAACTTTGAAAAGCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
261 ATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
*
22463 -CCCGAAGGTCTTATAGATTGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCC
326 GCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCC
* *
22527 TAAGGATTTAATCATCATGCTTGAAAGACTTATTGATGGCTCAAAGGACTTACCAGTTTTGGAAA
391 TAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAATTTTGGAAA
* *
22592 TAGTCTACCTAGCAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTTTATTTTTATGAA
456 TAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGAA
22657 AATCCTAAATGAGAAACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATATTAAAACATCCTG
521 AATCCTAAATGAGAAACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATATTAAAACATCCTG
** *
22722 CCCGAATGTCTTATAGATGGCCTAAAGGACTTATCATCTTGCTCGAAAGAATGACATATGACCCG
586 CCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCG
* * *
22787 AAGGATTTAATCATAATGTCAAATGACTTACTGATGACCCAAAAGACTTACCAATTTTGGAAATA
651 AAGGATTTAATCATAATATCGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATA
*
22852 GTAC-ACTTGGTAAGAAATTTTGGAAACCACTTTCTTACTTTTCAAAATTTTCATTTTCTA
716 GT-CTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAA-TTTCATTTTCTA
22912 AAATTCTTAAATGAGAAATTTT-AAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
*
22976 TACCCAAAGGTCTTAGAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
66 TACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
*
23041 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGAAAA
131 ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
23106 TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTC-AAAATTTTA-TTTTTGAAA
196 TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAA
* * * *
23169 ATACTAAATGAAAAACTATGAAAATTGTTTTCTCATTTTTCCCATATATCACATGAAAACATCTT
261 ATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
* * *
23234 GCCCCAAGGTCTTATAGATGGCCCTATGAACTTATCATCTTACTCGAATGACTGAAAGATGACCC
326 GCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCC
* * *
23299 TAAGGATTTAATCATCGTGCTCGAAAGACTTATTGATGGCTTGAAA-AACTTACCAATTTTGGAA
391 TAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGC-TCAAAGGACTTACCAATTTTGGAA
* *
23363 ATAGTCTACCTGGCAAGAAACTTTGGAAATCTCTTTATTACTTTTCAAAATTTTTA-TTTTCTGA
455 ATAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGA
* *
23427 AAATCCTAAATGAGAAACTTTTAAAATC-GCTTTCTCATTTTTTACAAATCATATTAAAACATCT
520 AAATCCTAAATGAGAAACTTTGAAAATCAG-TTTCTCATTTTTTACAAATCATATTAAAACATCC
* * * * *
23491 TGCCCAAATGTCTTATAGATGGCCCGAAGGACTAATCATCTTACTCGAAAGAATGATATATGA-C
584 TGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACC
* *
23555 CGAAGGATTTAATCATAATGTC--A--A-TTACTGATGACCCAAAAGACTTACCAATTTTGGAAA
649 CGAAGGATTTAATCATAATATCGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAA
* * * *
23615 TAGTCTACTAGGTAAGAAACTTTGGAAAACGCTTTCTTACTTTTCAAAAATTTTATTTT-TGA
714 TAGTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTC-AAAATTTCATTTTCT-A
* * * *
23677 AAATAC-TAAATGA-AGAACTTTGAAAAGCGTTTTCTCATTTTTTCACAAATATCACATGAAAAC
1 AAATTCTTAAATGAGA-AATTTTGAAAATCGTTTTCTCATTTTTT-AC-AA-ATCATATGAAAAC
* * * * * * * * *
23740 AT-CTTCCCGAAGGTCTTATAGATGACCCTAAGAACTTCTCATCTTGCTCGAATGACTGAAAGAT
62 ATCCTACCCAAAGGTCTTATAGATGGCCC-AAGGACTTATAATCTTGCTCGAAAGTCTGACAGAT
* * * * * * * *
23804 GACC-CTAAGGATTTAATCATCATGCTCGAAATAATTATTGATGG-CTCAAAGGACTTACCAGTT
126 GACCAAT-AGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCT-TAAGGACTTACCAATT
* * *
23867 TTGGAAATAGT-TACCTA-GCAAGAAACTTTGGAAATA-TCTTTCTTACTTTTCAAAATTTTTAT
189 TTGGAAATAGTCTA-CTAGGTAAGAAACTTTGGAAA-ACACTTTCTTACTTTTCAAAAATTTTAT
* * * *
23929 TTTTATGAAAATCCTAAATGAGAAACTTTGAAAATCAG-TTTCTCATTTTTTAC-AA-ATCATAT
252 TTTT-TGAAAATACTAAATGAAAAACTTTGAAAATC-GTTTTCTCATTTTTCACAAATATCACAT
* * * * * * * * *
23991 TAAAACATCCTGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTACTCAAAAGAATG
315 GAAAACATCTTGCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTG
* * * * * * * * * *
24056 ACATAAGACCCGAAGGA-TTAATCATAATG-TC-AAATGACTTACTGATGACCCAAAAGACTTAG
380 AAAGATGACCCTAAGGATTTAATCATCATGCTCGAAA-GACTTATTGATGGCTCAAAGGACTTAC
* * * * * * *
24118 CAATTTTAGAAATAGTCTACTTGGTAAGAAATTTTGGAAACCACTTTCTTACTTTTCAAAATTTT
444 CAATTTTGGAAATAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTT
* * * *
24183 CA-TTTTCT-AAAATTCTTAAATGAGAAATTTTGAAAATCA-TTTCTCATTTTTTATAAATCATA
509 TATTTTTCTGAAAA-TCCTAAATGAGAAACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATA
* * * * * * * * * * **
24245 TGAAAACATCTTACCCAAAGGTCTTAGAGATGGTCC-AATGATTTATAATCTTGCTCGAAAGTCT
573 TTAAAACATCCTGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAAT
* * * * * * * **
24309 GACAGATGA-CCAATAGTA-TTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTA
638 GACAGATGACCCGA-AGGATTTAATCATAAT-ATCGAATGACTTACTGATGACCCAAAGGACTTA
* * *
24372 CCAATTTTGGAAATAGTCTACTAGGTAAGAAACTTTGGAAAACGCTTTCTTACTTTTCAAAATTT
701 CCAATTTTGGAAATAGTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAATTT
* *
24437 TATTTTTTGA
766 CATTTTCT-A
* * * * * ** *
24447 AAATAC-TAAATGAAAAACTTTGATAATCGTTTTCTCGTTTTTCCCAAATATCACATGAAAACAT
1 AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTAC-AA-ATCATATGAAAACAT
* * * * * * * * * *
24511 CTTGCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTGGAATGACAGAAAGATGA
64 CCTACCCAAAGGTCTTATAGATGGCCC-AAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGA
* * * * *
24576 CC-CTAAGGATTTAATCATCGTGCTCGAAAGACTTACTGATGG-CTTGAAGGACATACCAATTTT
128 CCAAT-AGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTT-AAGGACTTACCAATTTT
* * * * * *
24639 GGAAATAGTCTACCT-GGCAAGAAACTTTGGAAATCTCTTTATTAATTTTCAAAATTTTTATTTT
191 GGAAATAGTCTA-CTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTT
* * * * * * *
24703 CTGAAAATCCTAAATGAGAATCTTTGAAAATC-TCTTTCTCATTTTTTAC-AA-ATCATATTAAA
255 TTGAAAATACTAAATGAAAAACTTTGAAAATCGT-TTTCTCATTTTTCACAAATATCACATGAAA
* * * * * * *
24765 ACATCCTGCTCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAG
319 ACATCTTGCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAG
*** * * * * * *
24830 ATGACAGGAAGGATTTAATAATCTTGCTCGAAGGACTTACTGATGGC-CTGAA-GACTTGCCAAT
384 ATGACCCTAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTC-AAAGGACTTACCAAT
* * * * * *
24893 TTTGGAAATAGTCTATC-AGGTAAGAAAATTTGGAAATCACTTTCTTACTTTTCAAAAATTTCAT
448 TTTGGAAATAGTCTACCTA-GCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTAT
24957 TT
512 TT
24959 CTAAACATCT
Statistics
Matches: 4597, Mismatches: 431, Indels: 282
0.87 0.08 0.05
Matches are distributed among these distances:
763 3 0.00
764 483 0.11
765 210 0.05
766 297 0.06
767 139 0.03
768 312 0.07
769 85 0.02
770 664 0.14
771 416 0.09
772 702 0.15
773 329 0.07
774 149 0.03
775 14 0.00
777 1 0.00
779 1 0.00
782 2 0.00
783 4 0.00
784 35 0.01
785 43 0.01
786 3 0.00
787 1 0.00
789 1 0.00
790 1 0.00
791 1 0.00
792 1 0.00
796 2 0.00
798 5 0.00
804 51 0.01
805 53 0.01
806 82 0.02
808 1 0.00
809 1 0.00
813 230 0.05
814 233 0.05
815 42 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (774 bp):
AAATTCTTAAATGAGAAATTTTGAAAATCGTTTTCTCATTTTTTACAAATCATATGAAAACATCC
TACCCAAAGGTCTTATAGATGGCCCAAGGACTTATAATCTTGCTCGAAAGTCTGACAGATGACCA
ATAGTATTTAATCATCATGCTCGAAAGACTTACTAATGGCCTTAAGGACTTACCAATTTTGGAAA
TAGTCTACTAGGTAAGAAACTTTGGAAAACACTTTCTTACTTTTCAAAAATTTTATTTTTTGAAA
ATACTAAATGAAAAACTTTGAAAATCGTTTTCTCATTTTTCACAAATATCACATGAAAACATCTT
GCCCGAAGGTCTTATAGATGGCCCTAAGAACTTATCATCTTGCTCGAATGACTGAAAGATGACCC
TAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTCAAAGGACTTACCAATTTTGGAAA
TAGTCTACCTAGCAAGAAACTTTGGAAATCTCTTTCTTACTTTTCAAAATTTTTATTTTTCTGAA
AATCCTAAATGAGAAACTTTGAAAATCAGTTTCTCATTTTTTACAAATCATATTAAAACATCCTG
CCCGAATGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCG
AAGGATTTAATCATAATATCGAATGACTTACTGATGACCCAAAGGACTTACCAATTTTGGAAATA
GTCTACTTGGTAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAATTTCATTTTCTA
Found at i:24832 original size:41 final size:42
Alignment explanation
Indices: 24787--24886 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
24777 AATGTCTTAT
*
24787 AGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTAATAATCTTGCTCGAAAGACTGAC
* ** * * *
24828 AGATGACAGGAAGGATTTAATAATCTTGCTCGAAGGACTTAC
1 AGATGGCCCGAAGGACTTAATAATCTTGCTCGAAAGACTGAC
* *
24870 TGATGGCCTGAA-GACTT
1 AGATGGCCCGAAGGACTT
24887 GCCAATTTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 18 0.39
42 28 0.61
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (42 bp):
AGATGGCCCGAAGGACTTAATAATCTTGCTCGAAAGACTGAC
Found at i:28390 original size:24 final size:24
Alignment explanation
Indices: 28363--28433 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
28353 AAACATAATT
28363 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
28387 CAGGTTATGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * *
28411 CAGGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
28434 TCAAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:31641 original size:365 final size:361
Alignment explanation
Indices: 30990--31687 Score: 920
Period size: 365 Copynumber: 1.9 Consensus size: 361
30980 TGAACTGTAG
* * * *
30990 GAGTTGGAAGAGCAAATTGGGGATGTTTGCGCGGGACTAAATGAGGAAACTATTATGGTCAATAT
1 GAGTTGGAAGAGCAAATTGGGGATGTTTGAGCGGGACTAAACGAGGAAACTATTATCGCCAATAT
* * * * *
31055 GAGAAGACGAAAATCAGTCTATAATAATTAAAATATTAATGTATGAATATGAAGGAAATCAATGC
66 AAGAAGACGAAAATCAGTCCATAACAACTAAAATATCAATGTATGAATATGAAGGAAATCAATGC
* * * *
31120 TAATCTTATCAATGTTTAACACTAGTTTTGCACCAACATGGAATATAAGGCAGGATGTGATTGTA
131 TAATATTATCAATGTTTAACACTAGTTTCGCACCAACATAGAATATAAGGCAGGATGTGATGGTA
* ** * * *
31185 ATCAGTCATTCCTTTTTGTAAGGCATTCCTGAGGATCCTCATATTATTGAGGATATGTACCTAGA
196 ATCAATCATTAATATTTGTAAGGCATACCTGAGGATCCTCATATTATTGAGGATATGCACCTAGA
* * *
31250 TGTAGATAACATATCTTATGAGGTAACACTTAAATATTTTGAGTAT-AATGGGAATTACTT-GGA
261 TGTAGATAACATATCTTATAAGGTAACA-ATAAATATTTTGAGT-TCAATGGAAATTACTTAGG-
31313 GTTTTAAAAGCTCGTGTCACTTATTTTGTCGGAATTGTTT
323 G-TTTAAAAGCTCGTGTCACTTATTTTGTCGGAATTGTTT
* * * *
31353 GAGTTGGAGGAGCAAATTGGGGATGTTTGTAG-TGGACTAAGCGAGGAAACTATTCTCGCCAATA
1 GAGTTGGAAGAGCAAATTGGGGATGTTTG-AGCGGGACTAAACGAGGAAACTATTATCGCCAATA
* * *
31417 TAAGAAGACGAAAACATTAGTCCATAACAACTAGAATATCAATGTTTGAATATGAAGGAAATCAA
65 TAAGAAGACG-AAA-ATCAGTCCATAACAACTAAAATATCAATGTATGAATATGAAGGAAATCAA
* *
31482 TGCTATTATTATCAATGTTTAACACT-GATTTCGCACCAACATAGAATATATGGCAGGATGTGAT
128 TGCTAATATTATCAATGTTTAACACTAG-TTTCGCACCAACATAGAATATAAGGCAGGATGTGAT
* * * * *
31546 GGTAATCAATCCTTAATATTTGTATGGCATA-CTCGAGGATCTTGATATTCTTGAGGATATGCAC
192 GGTAATCAATCATTAATATTTGTAAGGCATACCT-GAGGATCCTCATATTATTGAGGATATGCAC
* * * *
31610 CTTGATGTCGATAACTTATCTTATAAGGTAACAATCAATATTTTGAGTTCAATGGAAATTACTTA
256 CTAGATGTAGATAACATATCTTATAAGGTAACAATAAATATTTTGAGTTCAATGGAAATTACTTA
31675 GGGTTTAAAAGCT
321 GGGTTTAAAAGCT
31688 TGTTGGGGAT
Statistics
Matches: 288, Mismatches: 40, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
363 74 0.26
364 34 0.12
365 180 0.62
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (361 bp):
GAGTTGGAAGAGCAAATTGGGGATGTTTGAGCGGGACTAAACGAGGAAACTATTATCGCCAATAT
AAGAAGACGAAAATCAGTCCATAACAACTAAAATATCAATGTATGAATATGAAGGAAATCAATGC
TAATATTATCAATGTTTAACACTAGTTTCGCACCAACATAGAATATAAGGCAGGATGTGATGGTA
ATCAATCATTAATATTTGTAAGGCATACCTGAGGATCCTCATATTATTGAGGATATGCACCTAGA
TGTAGATAACATATCTTATAAGGTAACAATAAATATTTTGAGTTCAATGGAAATTACTTAGGGTT
TAAAAGCTCGTGTCACTTATTTTGTCGGAATTGTTT
Found at i:33181 original size:22 final size:22
Alignment explanation
Indices: 33153--33219 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
33143 GGCATGTGAA
*
33153 ATATGTCTCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
*
33175 ATTTGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
*
33197 ATATGTCCCGAAGGACATATGT
1 ATATGTCCCGAAGGACCTATGT
33219 A
1 A
33220 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATGT
Found at i:35836 original size:54 final size:54
Alignment explanation
Indices: 35756--36194 Score: 614
Period size: 54 Copynumber: 8.2 Consensus size: 54
35746 TGAATGGGCG
* * * *
35756 CTATGTATGC-ACCTAA-AAATACATAATAAGTTTATGAATTTCCGTATTGGCA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
* * * *
35808 CTATGTGTGCAACCTAAAAAATTCATAATTACTTTATGAATTTTCGTATTGGCA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
*
35862 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATCGACA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
* * * *
35916 CTATCTGTGTAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATCGGCA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
* *
35970 CTATTTGTGCAACCTAAG-AATTCATAATTAGTTTTTGAATTTCCGTATTGACA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
*
36023 CTATGTGTGCAACCTAAGAAATTCATAATTTGTTTATGAATTTCCGTATTGACA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
* *
36077 CTATGTGTGCAACCTATGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
* * * * * * * *
36131 CTATGTGTGCACCCCACGTAATTCATAATGAGTTTTTGAATTACCGTATCGACA
1 CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
*
36185 TTATGTGTGC
1 CTATGTGTGC
36195 GAAAACTAAT
Statistics
Matches: 350, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
52 9 0.03
53 55 0.16
54 286 0.82
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (54 bp):
CTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGACA
Found at i:36180 original size:215 final size:215
Alignment explanation
Indices: 35766--36181 Score: 634
Period size: 215 Copynumber: 1.9 Consensus size: 215
35756 CTATGTATGC
*
35766 ACCTAAAAATACATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAAAAAATT
1 ACCTAAAAATACATAATAAGTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAAAAATT
* *
35831 CATAATTACTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTT
66 CATAATTACTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATTAGTT
* * * *
35896 TATGAATTTCCGTATCGACACTATCTGTGTAACCTAAGAAATTCATAATTAGTTTATGAATTTCC
131 TATGAATTTCCGTATCGACACTATCTGTGCAACCCAAGAAATTCATAATGAGTTTATGAATTACC
35961 GTATCGGCACTATTTGTGCA
196 GTATCGGCACTATTTGTGCA
* * * * *
35981 ACCTAAGAATTCATAATTAGTTTTTGAATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATT
1 ACCTAAAAATACATAATAAGTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAAAAATT
** *
36046 CATAATTTGTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTATGAAATTCATAATTAGTT
66 CATAATTACTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATTAGTT
* * * * * * *
36111 TATGAATTTCCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTTTGAATTACC
131 TATGAATTTCCGTATCGACACTATCTGTGCAACCCAAGAAATTCATAATGAGTTTATGAATTACC
36176 GTATCG
196 GTATCG
36182 ACATTATGTG
Statistics
Matches: 179, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
215 179 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (215 bp):
ACCTAAAAATACATAATAAGTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAAAAATT
CATAATTACTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATTAGTT
TATGAATTTCCGTATCGACACTATCTGTGCAACCCAAGAAATTCATAATGAGTTTATGAATTACC
GTATCGGCACTATTTGTGCA
Found at i:40254 original size:39 final size:40
Alignment explanation
Indices: 40197--40276 Score: 153
Period size: 39 Copynumber: 2.0 Consensus size: 40
40187 TAATTATACT
40197 ATACTACATGTGTTCAAGTTATGACCATTCAAGTAAGATA
1 ATACTACATGTGTTCAAGTTATGACCATTCAAGTAAGATA
40237 ATACTACAT-TGTTCAAGTTATGACCATTCAAGTAAGATA
1 ATACTACATGTGTTCAAGTTATGACCATTCAAGTAAGATA
40276 A
1 A
40277 ATTATAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (40 bp):
ATACTACATGTGTTCAAGTTATGACCATTCAAGTAAGATA
Done.