Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007013.1 Hibiscus syriacus cultivar Beakdansim tig00018104_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: 69691
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2557 original size:25 final size:25
Alignment explanation
Indices: 2528--2584 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
2518 GGTATAATCA
*
2528 AAATTGTGTAGCGAAGCAATCTGTC
1 AAATTGTGTAGCGAAACAATCTGTC
2553 AAATTGTGTAGCGAAACAATCTGTC
1 AAATTGTGTAGCGAAACAATCTGTC
2578 AAATTGT
1 AAATTGT
2585 TTGCTTCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (25 bp):
AAATTGTGTAGCGAAACAATCTGTC
Found at i:4663 original size:2 final size:2
Alignment explanation
Indices: 4656--4690 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4646 ATTATGATGC
4656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4691 CCCTAAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5516 original size:31 final size:31
Alignment explanation
Indices: 5466--5540 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
5456 ATTTTTATGA
* * *
5466 TATATCATCATCTAATTTATTAATTGTATAAAT
1 TATA-CATCAT-TAATTTATGAAATATATAAAT
5499 TATACATCATTAATTTATGAAATATATAAAT
1 TATACATCATTAATTTATGAAATATATAAAT
*
5530 TAAACATCATT
1 TATACATCATT
5541 TAACGTGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 28 0.74
32 6 0.16
33 4 0.11
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (31 bp):
TATACATCATTAATTTATGAAATATATAAAT
Found at i:8154 original size:38 final size:40
Alignment explanation
Indices: 8104--8207 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 40
8094 AAGAAAAAGA
*
8104 AAAGTA-ATAAAATCCTAAAATTTATTTA-AAAA-AATTAT
1 AAAGTATA-AAAATTCTAAAATTTATTTAGAAAAGAATTAT
*
8142 AAAGTATAAAAATTCT-AAATTT-TTTAGAAAAGTATTTAT
1 AAAGTATAAAAATTCTAAAATTTATTTAGAAAAG-AATTAT
* *
8181 AAAATATAAAAATTCTAACAAATTATT
1 AAAGTATAAAAATTCTAA-AATTTATT
8208 GATCCAGTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
36 4 0.07
37 10 0.18
38 13 0.24
39 21 0.38
40 1 0.02
41 4 0.07
42 2 0.04
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (40 bp):
AAAGTATAAAAATTCTAAAATTTATTTAGAAAAGAATTAT
Found at i:10460 original size:25 final size:25
Alignment explanation
Indices: 10432--10486 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
10422 AACGACCCGG
*
10432 CCATCCGTTTTCGACACCTCCCGCA
1 CCATCCATTTTCGACACCTCCCGCA
*
10457 CCATCCATTTTCTACACCTCCCGCA
1 CCATCCATTTTCGACACCTCCCGCA
10482 CCATC
1 CCATC
10487 GTGTTCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.18, C:0.49, G:0.07, T:0.25
Consensus pattern (25 bp):
CCATCCATTTTCGACACCTCCCGCA
Found at i:10899 original size:18 final size:17
Alignment explanation
Indices: 10861--10908 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
10851 GTGTAAAACT
*
10861 GTTGACCATTGACCGCC
1 GTTGACCGTTGACCGCC
10878 GTTGACCGTTGACCGACC
1 GTTGACCGTTGACCG-CC
*
10896 GTTGACTGTTGAC
1 GTTGACCGTTGAC
10909 TTTGATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (17 bp):
GTTGACCGTTGACCGCC
Found at i:13784 original size:30 final size:30
Alignment explanation
Indices: 13748--13809 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13738 TAATCCTTAC
13748 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
1 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
13778 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
1 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
13808 AG
1 AG
13810 GGTAAGCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.32, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
Found at i:13834 original size:74 final size:77
Alignment explanation
Indices: 13713--13941 Score: 266
Period size: 74 Copynumber: 2.9 Consensus size: 77
13703 ACCGTTACAG
* * *
13713 CAGGTTCCTTTGCTGTGTGCAAAGGTAATCCTTACAGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
13778 AG-TTT-C-CCC
66 AGCTTTACTCCC
* *
13787 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTACA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGCTGTGTGC-
13852 AGGGTATGCTTTACAGTTTCCC
65 A----A-GCTTTAC----TCCC
* * *
13874 CAGGTCCCTTTTGTTTTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGTCCCTTTGCTGTGTGC
1 CAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGCTGTGTGC
13939 AAG
65 AAG
13942 GGTAAGCCTT
Statistics
Matches: 131, Mismatches: 10, Indels: 20
0.81 0.06 0.12
Matches are distributed among these distances:
74 59 0.45
75 1 0.01
79 1 0.01
80 1 0.01
81 3 0.02
82 2 0.02
83 1 0.01
87 12 0.09
88 51 0.39
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.34
Consensus pattern (77 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGCTGTGTGCA
AGCTTTACTCCC
Found at i:13841 original size:44 final size:44
Alignment explanation
Indices: 13778--14082 Score: 381
Period size: 44 Copynumber: 7.0 Consensus size: 44
13768 GCTGTGTGCA
13778 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* * * *
13822 AGTTTCCCCCAGGTCCCTTTGTTGTGTACAAGGGTATGCTTTAC
1 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* *
13866 AGTTT-CCCCAGGTCCCTTTTGTTTTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCCCAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTAC
*
13910 AGTTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
** *
13954 AG-TTCCCCTCAGGTCTATTTG-TGTGTACAAGGGTAAGCCTTAC
1 AGTTTCCCC-CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* *
13997 AGTTT-CCCTACGTTCCC-TTGCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCCCA-GGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* * *
14040 AGTTT-CCCCAGG-CTCTTTTGCTATGTGCAAGGATAAGACCTTA
1 AGTTTCCCCCAGGTC-CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
14083 TCGTTTTTGC
Statistics
Matches: 227, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.00
42 6 0.03
43 94 0.41
44 116 0.51
45 10 0.04
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (44 bp):
AGTTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
Found at i:17473 original size:22 final size:21
Alignment explanation
Indices: 17436--17484 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
17426 TTTATTATTC
17436 GTTGAA-TTTTATCAAACTAT
1 GTTGAATTTTTATCAAACTAT
17456 GTTGAATTTTGTATCAAACTAT
1 GTTGAATTTT-TATCAAACTAT
*
17478 TTTGAAT
1 GTTGAAT
17485 GTGATAGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 17 0.65
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (21 bp):
GTTGAATTTTTATCAAACTAT
Found at i:19750 original size:20 final size:21
Alignment explanation
Indices: 19720--19797 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 21
19710 AAATGACCAA
*
19720 CAAAATCGCAACGCGAACTT-
1 CAAATTCGCAACGCGAACTTC
* * **
19740 CAATTTCGCAACAC-AGGTTC
1 CAAATTCGCAACGCGAACTTC
**
19760 CAAATTCGCAACGCGATTTTC
1 CAAATTCGCAACGCGAACTTC
19781 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
19798 TAGGTAAATC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 3 0.07
20 23 0.50
21 20 0.43
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (21 bp):
CAAATTCGCAACGCGAACTTC
Found at i:19781 original size:21 final size:21
Alignment explanation
Indices: 19757--19796 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19747 GCAACACAGG
19757 TTCCAAATTCGCAACGCGATT
1 TTCCAAATTCGCAACGCGATT
19778 TTCCAAATTCGCAACGCGA
1 TTCCAAATTCGCAACGCGA
19797 ATAGGTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCCAAATTCGCAACGCGATT
Found at i:19874 original size:40 final size:40
Alignment explanation
Indices: 19781--19879 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
19771 CGCGATTTTC
*
19781 CAAATTCGCAACGCGAATAGGTAAATCGCAACGCGAAAAT
1 CAAATTCGCAACGCGAATAGGTAAATCGCAACGAGAAAAT
* * * * *
19821 CAAATTCGTAACGCAAATAGGTAAATCGTAACGATAATAT
1 CAAATTCGCAACGCGAATAGGTAAATCGCAACGAGAAAAT
*
19861 GTAAA-TCGCAACGCGAATA
1 -CAAATTCGCAACGCGAATA
19880 TTATTTTCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATAGGTAAATCGCAACGAGAAAAT
Found at i:19880 original size:20 final size:20
Alignment explanation
Indices: 19786--19880 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
19776 TTTTCCAAAT
*
19786 TCGCAACGCGAATAGGTAAA
1 TCGCAACGCGAATATGTAAA
* *
19806 TCGCAACGCGAAAAT-CAAA
1 TCGCAACGCGAATATGTAAA
* * *
19825 TTCGTAACGCAAATAGGTAAA
1 -TCGCAACGCGAATATGTAAA
* **
19846 TCGTAACGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
19866 TCGCAACGCGAATAT
1 TCGCAACGCGAATAT
19881 TATTTTCGAA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:20025 original size:22 final size:22
Alignment explanation
Indices: 20000--20050 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
19990 TCACTCTCTA
* *
20000 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCACATATC
*
20022 CGGCGAAATCCGTCCACATATC
1 CGGCGACATCCGTCCACATATC
20044 CGGCGAC
1 CGGCGAC
20051 CCCCTCTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCACATATC
Found at i:20477 original size:20 final size:18
Alignment explanation
Indices: 20432--20480 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
20422 GAAATTTGCA
*
20432 ATGCGATTTTCATTTCGC
1 ATGCGATTTTCATTTAGC
20450 ATTGCGATTTTCATTTTAGC
1 A-TGCGATTTTCA-TTTAGC
20470 GATGCGATTTT
1 -ATGCGATTTT
20481 AAGTTTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 14 0.52
21 1 0.04
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (18 bp):
ATGCGATTTTCATTTAGC
Found at i:22613 original size:21 final size:21
Alignment explanation
Indices: 22587--22681 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
22577 TTCACCTGTC
*
22587 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
22608 ATCGTTAAAGAGGCCCCTCC-
1 ATCGTTCAAGAGGCCCCTCCT
* *
22628 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
22648 CATCGTTCAAGAGGTCCATCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
22670 ACCGTTCAAGAG
1 ATCGTTCAAGAG
22682 CTCGATTCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.27
21 44 0.73
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:22634 original size:41 final size:42
Alignment explanation
Indices: 22589--22681 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 42
22579 CACCTGTCAT
* *
22589 CGTTCAAGAGGCCTCTC-CTATCGTTAAAGAGGCCCCT-CCAC
1 CGTTCAAGAGGCCCCTCTC-ATCGTTAAAGAGGCCCATCCCAC
* * *
22630 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCATCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGTTAAAGAGGCCCATCCCAC
22672 CGTTCAAGAG
1 CGTTCAAGAG
22682 CTCGATTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 30 0.67
42 15 0.33
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCGTTAAAGAGGCCCATCCCAC
Found at i:24057 original size:26 final size:27
Alignment explanation
Indices: 24021--24126 Score: 97
Period size: 27 Copynumber: 3.7 Consensus size: 27
24011 TTTTTTTTGC
24021 TTGTTTAATTGAT-TGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAAAGTTGAT
* * **
24047 TTGTTTAATTGATGAGGAATAAGATTTTTTTT
1 TTGTTTAATTGATGTGTAA-AAG----TTGAT
*
24079 GCTTGTTTAATTGATTTGTAAAAGTTGAT
1 --TTGTTTAATTGATGTGTAAAAGTTGAT
24108 TTGTTTAATTGATGTGTAA
1 TTGTTTAATTGATGTGTAA
24127 CTAATTCTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
26 13 0.21
27 21 0.34
28 3 0.05
29 3 0.05
32 3 0.05
33 3 0.05
34 16 0.26
ACGTcount: A:0.28, C:0.01, G:0.20, T:0.51
Consensus pattern (27 bp):
TTGTTTAATTGATGTGTAAAAGTTGAT
Found at i:24106 original size:61 final size:63
Alignment explanation
Indices: 24011--24175 Score: 264
Period size: 64 Copynumber: 2.7 Consensus size: 63
24001 TGGGGTACAC
24011 TTTTTTTTGCTTGTTTAATTGA-TTGTAAAAGTTGATTTGTTTAATTGATGAGGAA-TAA-GA
1 TTTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAACTAATGA
* * **
24071 TTTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAACTAATTC
1 TTTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAACTAATGA
24134 TTATTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
1 TT-TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
24176 GTAACACCCC
Statistics
Matches: 97, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
60 22 0.23
61 31 0.32
62 3 0.03
63 2 0.02
64 39 0.40
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.55
Consensus pattern (63 bp):
TTTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAACTAATGA
Found at i:27116 original size:31 final size:32
Alignment explanation
Indices: 27078--27139 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
27068 ACCGGTCAAC
* *
27078 GGTCAACGGGTCGGGACGGGT-AAACGGGTTG
1 GGTCAACGGGTCGGGACCGGTCAAACCGGTTG
*
27109 GGTCAACGGGTCGTGACCGGTCAAACCGGTT
1 GGTCAACGGGTCGGGACCGGTCAAACCGGTT
27140 AAAACCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.18
Consensus pattern (32 bp):
GGTCAACGGGTCGGGACCGGTCAAACCGGTTG
Found at i:27132 original size:18 final size:18
Alignment explanation
Indices: 27077--27132 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
27067 CACCGGTCAA
*
27077 CGGTCAACGGGTCGGGAC
1 CGGTCAACGGGTCGTGAC
* *
27095 GGGTAAACGGGT--TG--
1 CGGTCAACGGGTCGTGAC
27109 -GGTCAACGGGTCGTGAC
1 CGGTCAACGGGTCGTGAC
27126 CGGTCAA
1 CGGTCAA
27133 ACCGGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 10 0.34
15 2 0.07
16 1 0.03
18 16 0.55
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.16
Consensus pattern (18 bp):
CGGTCAACGGGTCGTGAC
Found at i:34594 original size:13 final size:13
Alignment explanation
Indices: 34562--34608 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
34552 ACCGGTCACC
34562 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34575 GGT---CGGGTCG
1 GGTCAACGGGTCG
*
34585 GGTCAACGGGTCA
1 GGTCAACGGGTCG
*
34598 GGTAAACGGGT
1 GGTCAACGGGT
34609 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 10 0.34
13 19 0.66
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:36804 original size:24 final size:24
Alignment explanation
Indices: 36770--36823 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36760 CTGAAACATC
36770 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
36794 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
36818 ATCAAA
1 ATCAAA
36824 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:36837 original size:24 final size:24
Alignment explanation
Indices: 36770--36837 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
36760 CTGAAACATC
* * *
36770 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
36794 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
36818 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
36838 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:36966 original size:12 final size:12
Alignment explanation
Indices: 36949--36981 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
36939 GGTTGTGGGT
36949 TTTGATATTGTG
1 TTTGATATTGTG
36961 TTTGATATTGTG
1 TTTGATATTGTG
*
36973 TTTGGTATT
1 TTTGATATT
36982 AGAAATGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:37773 original size:20 final size:20
Alignment explanation
Indices: 37748--37838 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
37738 CAAAACATTT
37748 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
37768 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* * *
37788 GAGTTGTGAAATCAAAATTC
1 GTGTTGCGAAATTAAAATTC
* * *
37808 CTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
*
37828 TTGTTGCGAAA
1 GTGTTGCGAAA
37839 AGGAAACATG
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
19 11 0.20
20 35 0.65
21 8 0.15
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:37813 original size:40 final size:40
Alignment explanation
Indices: 37750--37838 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
37740 AAACATTTGT
* * *
37750 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATCAAAATTCCTGTTGCGAATTAGAAAATCGA
* * **
37790 GTTGTGAAATCAAAATTCCTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAATCAAAATTCCTGTTGCGAATTAGAAAATCGA
37830 GTTGCGAAA
1 GTTGCGAAA
37839 AGGAAACATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (40 bp):
GTTGCGAAATCAAAATTCCTGTTGCGAATTAGAAAATCGA
Found at i:37887 original size:20 final size:20
Alignment explanation
Indices: 37864--37999 Score: 163
Period size: 20 Copynumber: 6.8 Consensus size: 20
37854 TGAAAAATAA
* *
37864 ATTCGCGTTACGATTTACCT
1 ATTCGCGTTGCGATTTACAT
37884 ATTCGCGTTGCGAATTTGAC-T
1 ATTCGCGTTGCG-ATTT-ACAT
37905 -TTCGCGTTGCGATTTTGAC-T
1 ATTCGCGTTGCGA-TTT-ACAT
*
37925 -TTCGCGTTGCAATTTACAT
1 ATTCGCGTTGCGATTTACAT
**
37944 ATTATCGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
37964 ATTCGCGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
37984 ATTCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
38000 TGGAACCTGT
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 90 0.87
21 5 0.05
22 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACAT
Found at i:40722 original size:29 final size:29
Alignment explanation
Indices: 40690--40748 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40680 CCTAAATTAA
*
40690 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCATACATCAATTTAGT
40719 TTTGATGTCATTGCATACATCAATTTAGT
1 TTTGATGTCATTGCATACATCAATTTAGT
40748 T
1 T
40749 AGGTGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGTCATTGCATACATCAATTTAGT
Found at i:41464 original size:246 final size:246
Alignment explanation
Indices: 41030--41519 Score: 953
Period size: 246 Copynumber: 2.0 Consensus size: 246
41020 TGGCATCAGA
*
41030 GCCAAGTTATAAGGTCTCTTGAAATTTCGAGTATGCTCTGTGTCTGCAGTTTTTAACTGATCTTC
1 GCCAAGTTATAAGGTCTCTTGAAATTTCGAGTATGCTCTGTGGCTGCAGTTTTTAACTGATCTTC
*
41095 TACATCAGAAAATATTTCTTGAGATTATTTTTAGGGTTATTACAAACCTTGTAGAGCTTCTTTGT
66 CACATCAGAAAATATTTCTTGAGATTATTTTTAGGGTTATTACAAACCTTGTAGAGCTTCTTTGT
41160 GTTTAGAGTAATTTAGTACTCTACACGTTTGTTACTCAAGCTTGTTCGGTGTAGTCAAAGCCTTG
131 GTTTAGAGTAATTTAGTACTCTACACGTTTGTTACTCAAGCTTGTTCGGTGTAGTCAAAGCCTTG
41225 CCGTTACGATGGGTGACCTTCAAGTAGTTAGAGGAATCAAGAAGCTCAAAT
196 CCGTTACGATGGGTGACCTTCAAGTAGTTAGAGGAATCAAGAAGCTCAAAT
41276 GCCAAGTTATAAGGTCTCTTGAAATTTCGAGTATGCTCTGTGGCTGCAGTTTTTAACTGATCTTC
1 GCCAAGTTATAAGGTCTCTTGAAATTTCGAGTATGCTCTGTGGCTGCAGTTTTTAACTGATCTTC
41341 CACATCAGAAAATATTTCTTGAGATTATTTTTAGGGTTATTACAAACCTTGTAGAGCTTCTTTGT
66 CACATCAGAAAATATTTCTTGAGATTATTTTTAGGGTTATTACAAACCTTGTAGAGCTTCTTTGT
41406 GTTTAGAGTAATTTAGTACTCTACACGTTTGTTACTCAAGCTTGTTCGGTGTAGTCAAAGCCTTG
131 GTTTAGAGTAATTTAGTACTCTACACGTTTGTTACTCAAGCTTGTTCGGTGTAGTCAAAGCCTTG
*
41471 CCGTTACGATGGGTGACCTTCAAGTAGTTGGAGGAATCAAGAAGCTCAA
196 CCGTTACGATGGGTGACCTTCAAGTAGTTAGAGGAATCAAGAAGCTCAA
41520 CAACCAAAAC
Statistics
Matches: 241, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
246 241 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (246 bp):
GCCAAGTTATAAGGTCTCTTGAAATTTCGAGTATGCTCTGTGGCTGCAGTTTTTAACTGATCTTC
CACATCAGAAAATATTTCTTGAGATTATTTTTAGGGTTATTACAAACCTTGTAGAGCTTCTTTGT
GTTTAGAGTAATTTAGTACTCTACACGTTTGTTACTCAAGCTTGTTCGGTGTAGTCAAAGCCTTG
CCGTTACGATGGGTGACCTTCAAGTAGTTAGAGGAATCAAGAAGCTCAAAT
Found at i:45662 original size:29 final size:29
Alignment explanation
Indices: 45620--45707 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
45610 CCTATATTAA
45620 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
45649 TTTGATGTCATTGCTTACATCAATTTTGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
45678 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
45707 T
1 T
45708 AGGTGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:49916 original size:24 final size:24
Alignment explanation
Indices: 49884--49929 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
49874 TCTTCCAGAT
49884 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
49908 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
49930 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:57156 original size:24 final size:24
Alignment explanation
Indices: 57124--57169 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
57114 TCTTCCAGAT
57124 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
57148 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
57170 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:60251 original size:2 final size:2
Alignment explanation
Indices: 60244--60270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60234 TCATAAAATT
60244 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60271 TACAAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63363 original size:6 final size:6
Alignment explanation
Indices: 63352--63381 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
63342 AACAAAACCT
63352 GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA
1 GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA
63382 TGATGATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
GCCTCA
Found at i:65174 original size:188 final size:194
Alignment explanation
Indices: 64103--67475 Score: 5853
Period size: 191 Copynumber: 17.8 Consensus size: 194
64093 AACCAATTTA
* * * *
64103 ATATATATTA-AGTTAATGTTTGA-AAAAAATTTAAAA-TTATTAAAACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
* * *
64165 TCACGTAATGTAATGGAATGACTCTAGAACAAGTAACACGCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
* *
64230 CTTTAGAATGAGTAATAATCACCATAATCACTTTAAATTATTAAAAAGATATTTCTTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
* * *
64294 GTATATATAAAAGTTAATGTTTGACAGAAAAAATTAAAATTTATTAATACTGTACATCAAGTATA
1 ATATATATAATAGTTAATGTCTGACA-AAAAAATTAAAATTTATTAATACTGTACATCAAGTATA
64359 CT-CCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACG
65 CTCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACG
64423 ACTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
130 ACTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
64488 ATATATAT-ATAGTTAATGTCTAACAAAAAAATTAAAA-TTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
64551 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGT-ACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
64615 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
64679 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
*
64744 T-CCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATAGGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
64808 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATT-AAAAGATATTTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATA-TTTATTTTGAAAC
*
64872 ATATATAT-A-AGGTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
64935 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
*
65000 CTTTAGAA-G-G-AGTAATCACCATAATCTCTTTAAATTATTAAAAAGATA-TTATTTTG-AAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
65059 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATAC-GTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
65123 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
65188 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
65252 --ATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATATTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
*
65315 TCCCATAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
65380 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
65444 ATATATATAATAGTTAATG--T-AC-AAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
65505 T-CCGTAAAGTAATGGAATGACTCTAGAACAAGTAACA-CCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
65568 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATT-AAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
65631 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
65696 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGT-ACACCCCGATA-GTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
65759 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATT-AAAAGATATTTA-TTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
65821 --ATATATAATAGTT--TGTCTGAC-AAAAAATT-AAATTTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
65880 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
65945 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATT-AAAAGATATTTATTTTG-AAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
66007 ATATATATATTAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTA-AC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
66071 T-CCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66135 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
66199 ATATATAT-ATAGTTAATGTCTGACAAAAAAATTAAAATGTATTAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
66263 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
*
66328 CTTTAGAATGAGTAAT-ATCACCATAATCTCCTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
66391 --ATATAT-ATAGTTAATGTCTGACAAAAAAATTAAAA-TTATTAATACTGTACATC-AGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
66451 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGAT----
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
66512 -TTTAGAATGAGTTAATAATCACCATAATCTCTTTAAATTATT-AAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAG-TAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
66575 ATATATATATTAGTTAATGT-TGACAAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATA
1 ATATATATAATAGTTAATGTCTGAC-AAAAAAATTAAAATTTATTAATACTGTACATCAAGTATA
66639 CTCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACG
65 CTCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACG
66704 ACTTTAGAATGAG---TAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
130 ACTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
66766 --ATATATAATAGTTAATGTCTGACAAAAAAATTAAAATGTA-TAATACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
66828 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGG
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATAC-G
*
66893 ACTTTAGAATGAGTAATAATCACCATAATCTCCTTAAATTATT-AAAA-ATATTTA-TTTGAAAC
130 ACTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
66955 --ATATAT-ATAGTTAATGTCTGAC--AAAAATTAAAATTTA-T--TACTGTACATCAAGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
*
67012 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATGTGTATCAGTAATGATAC-A
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
67076 C-TTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
67139 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATC-AGTATAC
1 ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
67203 TCCCGTAAAGTAATGGAATGACTCTAGAAC-AGTAAC-CCCCGATATGTATCAGTAATGATACGA
66 TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
*
67266 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTAATTTGAAAC
131 CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
*
67330 ATATATATAATAGTTAATGTCTGACAAAAAAAATTAAAATTTATTAATATTGTACATCAAGTATA
1 ATATATATAATAGTTAATGTCTGAC-AAAAAAATTAAAATTTATTAATACTGTACATCAAGTATA
* * *
67395 CTCCCGTAATGTAATGGAATGACTCTAGAACAAGTAACACACCGATATGGTATAAGTAATGAT--
65 CTCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATAT-GTATCAGTAATGATAC
67458 -AC-TTAGAATGAGTAATAA
129 GACTTTAGAATGAGTAATAA
67476 ACTCCTGTAT
Statistics
Matches: 3062, Mismatches: 43, Indels: 153
0.94 0.01 0.05
Matches are distributed among these distances:
181 39 0.01
182 6 0.00
183 18 0.01
184 178 0.06
185 43 0.01
186 114 0.04
187 94 0.03
188 377 0.12
189 287 0.09
190 254 0.08
191 619 0.20
192 558 0.18
193 254 0.08
194 174 0.06
195 34 0.01
196 13 0.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (194 bp):
ATATATATAATAGTTAATGTCTGACAAAAAAATTAAAATTTATTAATACTGTACATCAAGTATAC
TCCCGTAAAGTAATGGAATGACTCTAGAACAAGTAACACCCCGATATGTATCAGTAATGATACGA
CTTTAGAATGAGTAATAATCACCATAATCTCTTTAAATTATTAAAAAGATATTTATTTTGAAAC
Found at i:69027 original size:21 final size:24
Alignment explanation
Indices: 69003--69134 Score: 78
Period size: 26 Copynumber: 5.2 Consensus size: 24
68993 TATTAAAATA
69003 TTTAA-AATA-ATAAT-TATTTAC
1 TTTAATAATATATAATATATTTAC
69024 TTTAATTTAATATATAATAGTATTTAC
1 TTTAA--TAATATATAATA-TATTTAC
*
69051 TTTAATTAATATATAATAGT-TGTT-T
1 TTTAA-TAATATATAATA-TAT-TTAC
*
69076 TTTAATTTAATATATAATAGTTTTTAC
1 TTTAA--TAATATATAATA-TATTTAC
* *
69103 -TTAATTTAATATATAATAGTGTTTAT
1 TTTAA--TAATATATAATA-TATTTAC
69129 TTTAAT
1 TTTAAT
69135 TTAGGGATTT
Statistics
Matches: 96, Mismatches: 4, Indels: 18
0.81 0.03 0.15
Matches are distributed among these distances:
21 5 0.05
24 4 0.04
25 12 0.12
26 58 0.60
27 17 0.18
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (24 bp):
TTTAATAATATATAATATATTTAC
Found at i:69066 original size:26 final size:27
Alignment explanation
Indices: 69017--69137 Score: 169
Period size: 26 Copynumber: 4.6 Consensus size: 27
69007 AAATAATAAT
69017 TATTTACTTTAATTTAATATATAATAG
1 TATTTACTTTAATTTAATATATAATAG
69044 TATTTACTTTAA-TTAATATATAATAG
1 TATTTACTTTAATTTAATATATAATAG
*
69070 T-TGTT-TTTTAATTTAATATATAATAG
1 TAT-TTACTTTAATTTAATATATAATAG
*
69096 TTTTTAC-TTAATTTAATATATAATAG
1 TATTTACTTTAATTTAATATATAATAG
* *
69122 TGTTTATTTTAATTTA
1 TATTTACTTTAATTTA
69138 GGGATTTTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
25 6 0.07
26 58 0.68
27 21 0.25
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (27 bp):
TATTTACTTTAATTTAATATATAATAG
Found at i:69243 original size:25 final size:27
Alignment explanation
Indices: 69214--69270 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
69204 TATTCTAAAA
* * *
69214 AATAATTATTTATT-TTAATTTAATAT
1 AATAATTATTAATTAATAATTAAATAT
69240 -ATAA-TATTAATTAATAATTAAATAT
1 AATAATTATTAATTAATAATTAAATAT
69265 AATAAT
1 AATAAT
69271 AGTAAATCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATAATTATTAATTAATAATTAAATAT
Found at i:69249 original size:13 final size:13
Alignment explanation
Indices: 69229--69270 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
69219 TTATTTATTT
69229 TAATTTAATAT-A
1 TAATTTAATATAA
69241 TAATATTAAT-TAA
1 TAAT-TTAATATAA
*
69254 TAATTAAATATAA
1 TAATTTAATATAA
69267 TAAT
1 TAAT
69271 AGTAAATCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATTTAATATAA
Done.