Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004846.1 Hibiscus syriacus cultivar Beakdansim tig00010927_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: 1467214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:12726 original size:20 final size:20
Alignment explanation
Indices: 12701--12752 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
12691 ATAATGATGG
12701 TATCAATATTGTAAGAACAA
1 TATCAATATTGTAAGAACAA
12721 TATCAATATTGTAAGAACAA
1 TATCAATATTGTAAGAACAA
12741 TATCAATATTGT
1 TATCAATATTGT
12753 TCTTCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCAATATTGTAAGAACAA
Found at i:14776 original size:16 final size:16
Alignment explanation
Indices: 14729--14776 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
14719 AATGTATCAT
* * *
14729 AACTTAAGTTAACTTT
1 AACTTAAATCAACTTC
14745 AACTTAAATCAACTTC
1 AACTTAAATCAACTTC
14761 AACTTAAATCAACTTC
1 AACTTAAATCAACTTC
14777 CAGGCATGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (16 bp):
AACTTAAATCAACTTC
Found at i:20172 original size:24 final size:24
Alignment explanation
Indices: 20130--20184 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20120 CATATATTTC
*
20130 CAGGAGTACACAAATGTACTAACA
1 CAGGAGTACACAAAGGTACTAACA
* * *
20154 CAGGAGTACCCAGAGGTACTAATA
1 CAGGAGTACACAAAGGTACTAACA
*
20178 TAGGAGT
1 CAGGAGT
20185 GCATGGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (24 bp):
CAGGAGTACACAAAGGTACTAACA
Found at i:20198 original size:24 final size:24
Alignment explanation
Indices: 20171--20298 Score: 78
Period size: 24 Copynumber: 5.3 Consensus size: 24
20161 ACCCAGAGGT
**
20171 ACTAATATAGGAGTGCATGGATGC
1 ACTAATATAGGAGTGCATAAATGC
* * * *
20195 ACTATTATAAGAGTGTATAAATGT
1 ACTAATATAGGAGTGCATAAATGC
* * *
20219 ACTAATACAGGAGTGCATAAAAGA
1 ACTAATATAGGAGTGCATAAATGC
* ** *
20243 ACTAAT-TCAGAAGTGCACGAATTC
1 ACTAATAT-AGGAGTGCATAAATGC
* * * *
20267 ACTAATAAATGAGTGCAAAAAAGGC
1 ACTAATATAGGAGTGC-ATAAATGC
20292 ACTAATA
1 ACTAATA
20299 CTAGAGTTTA
Statistics
Matches: 75, Mismatches: 26, Indels: 5
0.71 0.25 0.05
Matches are distributed among these distances:
24 64 0.85
25 11 0.15
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (24 bp):
ACTAATATAGGAGTGCATAAATGC
Found at i:26112 original size:40 final size:42
Alignment explanation
Indices: 26057--26136 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 42
26047 GGCAATTGGT
*
26057 TAATTTTTCTTAGTTTAGCAATAGCATT-GTTT-TTTCTTAC
1 TAATTTTTCTTAGTTTAGCAATACCATTAGTTTATTTCTTAC
*
26097 TAATTTTTCTTAGTTTAGCTATACCATTAGTTTATTTCTT
1 TAATTTTTCTTAGTTTAGCAATACCATTAGTTTATTTCTT
26137 TTTCAAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 26 0.72
41 4 0.11
42 6 0.17
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (42 bp):
TAATTTTTCTTAGTTTAGCAATACCATTAGTTTATTTCTTAC
Found at i:31446 original size:41 final size:41
Alignment explanation
Indices: 31334--31683 Score: 253
Period size: 41 Copynumber: 8.5 Consensus size: 41
31324 CCTTGATTTA
* * * * * *
31334 AATTGATTTGGATTGTGAATTAATACATGTTACCATTATCT
1 AATTGAATTGAATTGTGAATTATTGCATGTTACCATGATCG
** * * * * *
31375 AATTGAATT-TTTCTATGAATAAATGAATGTTACCATAATCG
1 AATTGAATTGAAT-TGTGAATTATTGCATGTTACCATGATCG
* ** *
31416 AATTGAATTGAATTATGAATTATTGCATGTTGTCGTGATCG
1 AATTGAATTGAATTGTGAATTATTGCATGTTACCATGATCG
* * ** *
31457 AA-TCAAGTTGAATAGTGAATTCCTGCATGCTT-CCATGATTG
1 AATTGAA-TTGAATTGTGAATTATTGCATG-TTACCATGATCG
* * *
31498 AATTGAATCGAATTGTGAATTATTGCATGCTACGATGATCG
1 AATTGAATTGAATTGTGAATTATTGCATGTTACCATGATCG
* * *
31539 AA-TCAAGTTGAATGGTGAATTATTTCATGCTT-CCATGATCG
1 AATTGAA-TTGAATTGTGAATTATTGCATG-TTACCATGATCG
* * *
31580 AATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATTG
1 AATTGAATTGAATTGTGAATTATTGCATGTTACCATGATCG
* * * * * *
31621 AATTGAATCGAATGGTGAACTATTGTATGATT-TCATGATTG
1 AATTGAATTGAATTGTGAATTATTGCATG-TTACCATGATCG
* *
31662 AATTGAATTTAATTGTTAATTA
1 AATTGAATTGAATTGTGAATTA
31684 GCACATATTG
Statistics
Matches: 244, Mismatches: 54, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
40 10 0.04
41 222 0.91
42 12 0.05
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (41 bp):
AATTGAATTGAATTGTGAATTATTGCATGTTACCATGATCG
Found at i:31517 original size:123 final size:123
Alignment explanation
Indices: 31390--31639 Score: 281
Period size: 123 Copynumber: 2.0 Consensus size: 123
31380 AATTTTTCTA
* * * * *
31390 TGAATAAATGAATGTTACCATAATCGAATTGAA-TTGAATTATGAATTATTGCATG-TTGTCGTG
1 TGAATAAATGAATGCTACCATAATCGAA-TCAAGTTGAATGATGAATTATTGCATGCTT-CCATG
* * *
31453 ATCGAA-TCAAGTTGAATAGTGAATTCCTGCATGCTTCCATGATTGAATTGAATCGAATTG
64 ATCGAATTCAA-TCGAATAGTGAATTACTGCATGCTTCCATGATTGAATTGAATCGAATGG
* * * * * * *
31513 TGAATTATTGCATGCTACGATGATCGAATCAAGTTGAATGGTGAATTATTTCATGCTTCCATGAT
1 TGAATAAATGAATGCTACCATAATCGAATCAAGTTGAATGATGAATTATTGCATGCTTCCATGAT
* * * *
31578 CGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATTGAATTGAATCGAATGG
66 CGAATTCAATCGAATAGTGAATTACTGCATGCTTCCATGATTGAATTGAATCGAATGG
31636 TGAA
1 TGAA
31640 CTATTGTATG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
122 3 0.03
123 97 0.92
124 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (123 bp):
TGAATAAATGAATGCTACCATAATCGAATCAAGTTGAATGATGAATTATTGCATGCTTCCATGAT
CGAATTCAATCGAATAGTGAATTACTGCATGCTTCCATGATTGAATTGAATCGAATGG
Found at i:31618 original size:82 final size:82
Alignment explanation
Indices: 31407--31683 Score: 308
Period size: 82 Copynumber: 3.4 Consensus size: 82
31397 ATGAATGTTA
* * * * *
31407 CCATAATCGAATTGAATTGAATTATGAATTATTGCATGTTGT-CGTGATCGAATCAAGTTGAATA
1 CCATGATCGAATTGAATCGAATTGTGAATTATTGCATGTT-TCCATGATCGAATCAAGTTGAATG
** *
31471 GTGAATTCCTGCATGCTT
65 GTGAATTATTTCATGCTT
* * * *
31489 CCATGATTGAATTGAATCGAATTGTGAATTATTGCATGCTACGATGATCGAATCAAGTTGAATGG
1 CCATGATCGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATCGAATCAAGTTGAATGG
31554 TGAATTATTTCATGCTT
66 TGAATTATTTCATGCTT
* * *
31571 CCATGATCGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATTGAATTGAA-TCGAATG
1 CCATGATCGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATCGAA-TCAAGTTGAATG
* *
31635 GTGAACTATTGT-ATGATT
65 GTGAATTATT-TCATGCTT
* * ** *
31653 TCATGATTGAATTGAATTTAATTGTTAATTA
1 CCATGATCGAATTGAATCGAATTGTGAATTA
31684 GCACATATTG
Statistics
Matches: 166, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
82 162 0.98
83 4 0.02
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (82 bp):
CCATGATCGAATTGAATCGAATTGTGAATTATTGCATGTTTCCATGATCGAATCAAGTTGAATGG
TGAATTATTTCATGCTT
Found at i:37893 original size:29 final size:24
Alignment explanation
Indices: 37836--37896 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
37826 TTAATTGAGT
37836 GTTAAATTAATTGAATTACATAGG
1 GTTAAATTAATTGAATTACATAGG
37860 GTTAAATTAATTGAATTACATA-G
1 GTTAAATTAATTGAATTACATAGG
*
37883 GATAAATTTAATTG
1 GTTAAA-TTAATTG
37897 CCTAAGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 6 0.17
24 29 0.83
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.39
Consensus pattern (24 bp):
GTTAAATTAATTGAATTACATAGG
Found at i:39678 original size:82 final size:82
Alignment explanation
Indices: 39581--39885 Score: 315
Period size: 82 Copynumber: 3.7 Consensus size: 82
39571 GAATTGGTTT
* * * * ** *
39581 GTGAATAAATGCATGTTACCATGATCGAATTGAATTAAATTATGAATTATTGCATGTTGCCCTAA
1 GTGAATTATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
39646 TCGAATCAAGTTGAATG
66 TCGAATCAAGTTGAATG
* * * * * * * *
39663 TTTAATTCTTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTGTTGCATGCTACCGTGA
1 GTGAATTATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
39728 TCGAATCAAGTTGAATG
66 TCGAATCAAGTTGAATG
* * * * * *
39745 GTGAATTATTACACGCTGCCATGATTGAATTGAATCGAATTGTGAATTATTTCATGTTGCCATGA
1 GTGAATTATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
* * *
39810 TTGAATTGAA-TCGAATG
66 TCGAA-TCAAGTTGAATG
* * * * * * *
39827 GTAAACTATTGCAAGTTGTCATGATTGAATTGAATCGAATTGTAAATTAGTACATGTTG
1 GTGAATTATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTG
39886 TCAAGATCGA
Statistics
Matches: 184, Mismatches: 38, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
82 181 0.98
83 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (82 bp):
GTGAATTATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAATTATTGCATGTTGCCCTAA
TCGAATCAAGTTGAATG
Found at i:39821 original size:41 final size:41
Alignment explanation
Indices: 39504--39885 Score: 268
Period size: 41 Copynumber: 9.3 Consensus size: 41
39494 GGTGAATTAG
* * * * * *
39504 TATTGCTTGTTGCCTTGACTTAAATTTAATTGGATTGTGAAT
1 TATTGCATGTTGCCATGA-TTGAATTGAATCGAATTGTGAAT
* * * * * **
39546 TAATACATGTTACCATGGTCT-AATTGAATTGGTTTGTGAAT
1 TATTGCATGTTGCCATGAT-TGAATTGAATCGAATTGTGAAT
* * * * ** *
39587 AAATGCATGTTACCATGATCGAATTGAATTAAATTATGAAT
1 TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
* * * * * *
39628 TATTGCATGTTGCCCTAATCGAA-TCAAGTTGAA-TGTTTAAT
1 TATTGCATGTTGCCATGATTGAATTGAA-TCGAATTG-TGAAT
*
39669 TCTTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
1 TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
* * * * * * * *
39710 TGTTGCATGCTACCGTGATCGAA-TCAAGTTGAATGGTGAAT
1 TATTGCATGTTGCCATGATTGAATTGAA-TCGAATTGTGAAT
* * *
39751 TATTACACGCTGCCATGATTGAATTGAATCGAATTGTGAAT
1 TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
* * * *
39792 TATTTCATGTTGCCATGATTGAATTGAATCGAATGGTAAAC
1 TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
* * *
39833 TATTGCAAGTTGTCATGATTGAATTGAATCGAATTGTAAAT
1 TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
* *
39874 TAGTACATGTTG
1 TATTGCATGTTG
39886 TCAAGATCGA
Statistics
Matches: 269, Mismatches: 63, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
40 7 0.03
41 241 0.90
42 21 0.08
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (41 bp):
TATTGCATGTTGCCATGATTGAATTGAATCGAATTGTGAAT
Found at i:46568 original size:34 final size:34
Alignment explanation
Indices: 46530--46631 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
46520 CATTAAACTA
46530 AATTTAACTATTTTTCCAAAATAATGGGATACAC
1 AATTTAACTATTTTTCCAAAATAATGGGATACAC
46564 AATTTAACTATTTTTCCAAAATAATGGGATACAC
1 AATTTAACTATTTTTCCAAAATAATGGGATACAC
46598 AATTTAACTATTTTTCCAAAATAATGGGATACAC
1 AATTTAACTATTTTTCCAAAATAATGGGATACAC
46632 TTAGAGCTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (34 bp):
AATTTAACTATTTTTCCAAAATAATGGGATACAC
Found at i:48720 original size:13 final size:13
Alignment explanation
Indices: 48697--48731 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
48687 AATTAAGGTT
48697 AAATAAAAATAAAA
1 AAAT-AAAATAAAA
48711 AAATAAAATAAAA
1 AAATAAAATAAAA
*
48724 TAATAAAA
1 AAATAAAA
48732 AGTACTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:48766 original size:26 final size:25
Alignment explanation
Indices: 48720--48783 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
48710 AAAATAAAAT
* *
48720 AAAATAAT-AAAAAGTACTAAAATAA
1 AAAATATTGAAAAAGGACT-AAATAA
* **
48745 AAAATATTGAAAAAGGATTAAATTG
1 AAAATATTGAAAAAGGACTAAATAA
48770 AAAATAATTGAAAA
1 AAAAT-ATTGAAAA
48784 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (25 bp):
AAAATATTGAAAAAGGACTAAATAA
Found at i:48780 original size:10 final size:10
Alignment explanation
Indices: 48765--48794 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
48755 AAAAGGATTA
48765 AATTGAAAAT
1 AATTGAAAAT
48775 AATTGAAAAT
1 AATTGAAAAT
*
48785 AATTAAAAAT
1 AATTGAAAAT
48795 TAAGGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (10 bp):
AATTGAAAAT
Found at i:49944 original size:20 final size:19
Alignment explanation
Indices: 49910--49949 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
49900 ATATAATATA
*
49910 ATATAATACTATAAATAAT
1 ATATAATAATATAAATAAT
49929 ATATAATATATATAAATAAT
1 ATATAATA-ATATAAATAAT
49949 A
1 A
49950 CGTATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATAATATAAATAAT
Found at i:51275 original size:31 final size:30
Alignment explanation
Indices: 51237--51296 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
51227 TTATATAAGC
51237 TATGTGATAAAGTGATGGAACATGATATGTT
1 TATGTGATAAAGTGATGGAA-ATGATATGTT
*
51268 TATGTGATAAAGTGATGGAAATTATATGT
1 TATGTGATAAAGTGATGGAAATGATATGT
51297 CTATACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGTGATGGAAATGATATGTT
Found at i:51545 original size:23 final size:23
Alignment explanation
Indices: 51519--51572 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
51509 AATCTTATAT
51519 GGCACTAT-AGTACAATTCTACGC
1 GGCACT-TCAGTACAATTCTACGC
* * *
51542 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCAGTACAATTCTACGC
51565 GGCACTTC
1 GGCACTTC
51573 GGTGCATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (23 bp):
GGCACTTCAGTACAATTCTACGC
Found at i:51573 original size:23 final size:23
Alignment explanation
Indices: 51531--51578 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
51521 CACTATAGTA
51531 CAATTCTACGCGGCACTTCGGTG
1 CAATTCTACGCGGCACTTCGGTG
*
51554 CAATTCTACGTGGCACTTCGGTG
1 CAATTCTACGCGGCACTTCGGTG
51577 CA
1 CA
51579 TTTATATGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTCGGTG
Found at i:52300 original size:22 final size:22
Alignment explanation
Indices: 52233--52304 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
52223 TTTTAAAAAC
* *
52233 TATTTTCAATAGCCATATACTATA
1 TATTTTCAAAAACCATATA-T-TA
* *
52257 TGTTTTC-AAAACTATATA-TA
1 TATTTTCAAAAACCATATATTA
52277 TATTTTCAAAAACCATATATTA
1 TATTTTCAAAAACCATATATTA
52299 TATTTT
1 TATTTT
52305 TTTTGAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 8 0.20
21 10 0.25
22 8 0.20
23 8 0.20
24 6 0.15
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (22 bp):
TATTTTCAAAAACCATATATTA
Found at i:59146 original size:15 final size:15
Alignment explanation
Indices: 59126--59159 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
59116 GTTAGGTTAG
*
59126 ATTTTTGGGAGTATC
1 ATTTTTGGGACTATC
59141 ATTTTTGGGACTATC
1 ATTTTTGGGACTATC
59156 ATTT
1 ATTT
59160 CCCCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (15 bp):
ATTTTTGGGACTATC
Found at i:61943 original size:22 final size:22
Alignment explanation
Indices: 61915--61963 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
61905 AGAATTTTCA
61915 GCTTCTAGCTTTCTCAGTCTTT
1 GCTTCTAGCTTTCTCAGTCTTT
61937 GCTTCTAGCTTTCTCAGTCTTT
1 GCTTCTAGCTTTCTCAGTCTTT
61959 GCTTC
1 GCTTC
61964 AATTCCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.29, G:0.14, T:0.49
Consensus pattern (22 bp):
GCTTCTAGCTTTCTCAGTCTTT
Found at i:63499 original size:40 final size:39
Alignment explanation
Indices: 63433--63509 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
63423 AAAAATAAAA
* *
63433 TCCTACCCCGCATGATATTTACCCCACATGTTTTTTTAT
1 TCCTACCCCGCATGATATCTACCCCACATGTTATTTTAT
* * *
63472 TCCTACCCGGACATGATCTCTATCCCACATGTTATTTT
1 TCCTACCCCG-CATGATATCTACCCCACATGTTATTTT
63510 CCTAACCGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 9 0.28
40 23 0.72
ACGTcount: A:0.21, C:0.31, G:0.09, T:0.39
Consensus pattern (39 bp):
TCCTACCCCGCATGATATCTACCCCACATGTTATTTTAT
Found at i:66546 original size:81 final size:80
Alignment explanation
Indices: 66276--66677 Score: 522
Period size: 81 Copynumber: 5.0 Consensus size: 80
66266 ATTTTTTTTA
* * **
66276 AGTAAAATATTAATGGCCTAGCTGTGCATTTGACATAAATATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAAT-GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
66341 AGGTTAGATACCTTTG
65 AGGTTAAATACCTTTG
* * *
66357 AGTAAAAGATTAATGGCATAGATGTGCATTTGACAGAAAGATGTCAATTATG-CAGTTAGATGAA
1 AGTAAAAGATTAAT-GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
66421 AGGTTAGATACCTTTG
65 AGGTTAAATACCTTTG
* * *
66437 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGA-AAAAATGTGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAAT-GCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
66501 AAGGTTAAATACCTTTC
64 AAGGTTAAATACCTTTG
* * *
66518 AGTAAAAGATTAAATGTCTAGCTATGCATTTGACAGAAAGGTGTCAACTATGCCAGTTAGATGAA
1 AGTAAAAGATT-AATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
66583 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * ** *
66599 AGTAAAAGATTAAATGTCTAGTTGTGCATTTGGTAGAAAGGTG-CCATTCATGCCAGTTAGATGA
1 AGTAAAAGATT-AATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGA
*
66663 AAGGTTAAATGCCTT
64 AAGGTTAAATACCTT
66678 CACGTGAATG
Statistics
Matches: 290, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
80 77 0.27
81 210 0.72
82 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (80 bp):
AGTAAAAGATTAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTG
Found at i:66548 original size:161 final size:162
Alignment explanation
Indices: 66276--66677 Score: 571
Period size: 161 Copynumber: 2.5 Consensus size: 162
66266 ATTTTTTTTA
* * * *
66276 AGTAAAATATTAATGGCCTAGCTGTGCATTT-GACATAAATATGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGA-AAAAATGTGTCAATTATGCCAGTTAGATGA
* * * *
66340 AAGGTTAGATACCTTTGAGTAAAAGATTAATGGCATAGATGTGCATTTGACAGAAAGATGTCAAT
65 AAGGTTAAATACCTTTCAGTAAAAGATTAATGGCATAGATATGCATTTGACAGAAAGATGTCAAC
*
66405 TATG-CAGTTAGATGAAAGGTTAGATACCTTTG
130 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
66437 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
* * *
66502 AGGTTAAATACCTTTCAGTAAAAGATTAAATGTC-TAGCTATGCATTTGACAGAAAGGTGTCAAC
66 AGGTTAAATACCTTTCAGTAAAAGATT-AATGGCATAGATATGCATTTGACAGAAAGATGTCAAC
66566 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
130 TATGCCAGTTAGATGAAAGGTTAAATACCTTTG
* * * * *
66599 AGTAAAAGATTAAAT-GTCTAGTTGTGCATTTGGTAGAAAGGTG-CCATTCATGCCAGTTAGATG
1 AGTAAAAGATT-AATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATT-ATGCCAGTTAGATG
*
66662 AAAGGTTAAATGCCTT
64 AAAGGTTAAATACCTT
66678 CACGTGAATG
Statistics
Matches: 218, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
161 117 0.54
162 98 0.45
163 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (162 bp):
AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTCAGTAAAAGATTAATGGCATAGATATGCATTTGACAGAAAGATGTCAACT
ATGCCAGTTAGATGAAAGGTTAAATACCTTTG
Found at i:66740 original size:45 final size:45
Alignment explanation
Indices: 66702--66960 Score: 376
Period size: 45 Copynumber: 5.8 Consensus size: 45
66692 AATGCTTAGA
* * * *
66702 GGTGCATTAAAGACATGAAAGGATTCTATATATGAAATGCATAGA-
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATA-AC
* *
66747 GGTGCATTAAAGGCATGAAAGGACGCCATAAATTAAATGCATAAC
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
*
66792 GGTGCATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAAC
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
* * * *
66837 GGTGTATTAAAAGCACGAATGGATGCCATAAATGAAATGCATAAC
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
*
66882 GGTTCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
* *
66927 AGTGCATTAAAGGCATGAAATGATGCCATAAATG
1 GGTGCATTAAAGGCATGAAAGGATGCCATAAATG
66961 GAAACAATGA
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 1 0.01
45 192 0.99
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (45 bp):
GGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAC
Found at i:66783 original size:26 final size:26
Alignment explanation
Indices: 66752--66833 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
66742 ATAGAGGTGC
*
66752 ATTAAAGGCATGAAAGGACGCCATAA
1 ATTAAAGGCATGAAAGGATGCCATAA
* *
66778 ATTAAATGCAT-AACGG-TG-C----
1 ATTAAAGGCATGAAAGGATGCCATAA
66797 ATTAAAGGCATGAAAGGATGCCATAA
1 ATTAAAGGCATGAAAGGATGCCATAA
*
66823 ATTAAATGCAT
1 ATTAAAGGCAT
66834 AACGGTGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
19 10 0.23
20 4 0.09
21 2 0.05
22 1 0.02
23 1 0.02
24 1 0.02
25 4 0.09
26 20 0.47
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (26 bp):
ATTAAAGGCATGAAAGGATGCCATAA
Found at i:76411 original size:81 final size:80
Alignment explanation
Indices: 76222--76411 Score: 274
Period size: 81 Copynumber: 2.4 Consensus size: 80
76212 AATTGTTATA
* * *
76222 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTTGCCATTTAGATGAAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGAGTCAATTTGCCAGTTAGATAAAA
* *
76287 GGTTAGATCCCTTTG
66 GGTTAAATACCTTTG
* * *
76302 AGTAAAAGATTAATGGCTTAGTTGTGCATTTGACAGAAAGGAGTCAATTATGCTAGTTAGATAAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGAGTCAATT-TGCCAGTTAGATAAA
76367 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
*
76383 AGTAAAAGATTAAAT-GCCTAGCTATGCAT
1 AGTAAAAGATT-AATGGCCTAGCTGTGCAT
76412 ATAAAGAACA
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
80 46 0.47
81 48 0.49
82 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (80 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGAGTCAATTTGCCAGTTAGATAAAA
GGTTAAATACCTTTG
Found at i:77334 original size:81 final size:81
Alignment explanation
Indices: 76864--77327 Score: 694
Period size: 81 Copynumber: 5.7 Consensus size: 81
76854 CTGTTTTAAA
* * * *
76864 TAAAAGATTAATGGCCTAGTTTTTCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
76929 GTTAAATGCCTTTGAC
66 GTTAAATGCCTTTGAG
* * * * *
76945 TAAAAGATTACTGGCCTAGTTGTGCATTTAAAAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
77010 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * *
77026 TAAAAGATTAGTGGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATACCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
77091 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * *
77107 TAAAATATTAATGTCCTAGCTGTGCATTTGACAGAAAGGTGTAAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
77172 GTTAAGTGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * *
77188 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTAAATTATTCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
77253 GTTAAGTGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * *
77269 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
77328 CAAAAGGCCA
Statistics
Matches: 352, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 352 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATGCCTTTGAG
Found at i:77738 original size:20 final size:20
Alignment explanation
Indices: 77713--77768 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
77703 ATTTACAAAG
*
77713 TGATGTACCGATGTACTACA
1 TGATGTACCGATGCACTACA
77733 TGATGTACCGATGCACTACA
1 TGATGTACCGATGCACTACA
*
77753 TGATGTATCGATGCAC
1 TGATGTACCGATGCAC
77769 ACCCATTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
TGATGTACCGATGCACTACA
Found at i:83774 original size:23 final size:22
Alignment explanation
Indices: 83702--83793 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 22
83692 TAGACAGTGA
83702 ATCGATGCATCCCTTGAATGTGC
1 ATCGATGCAT-CCTTGAATGTGC
* *
83725 ATCGATACA-CCATGAA-GTGC
1 ATCGATGCATCCTTGAATGTGC
*
83745 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCA-TCCTTGAATGTGC
*
83768 ATTGATGCA--CTCTG-ATGTGC
1 ATCGATGCATCCT-TGAATGTGC
83788 ATCGAT
1 ATCGAT
83794 ACACCTCGGG
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 24 0.42
21 8 0.14
22 6 0.11
23 19 0.33
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (22 bp):
ATCGATGCATCCTTGAATGTGC
Found at i:83788 original size:43 final size:43
Alignment explanation
Indices: 83679--83769 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
83669 TTGTGCGTAA
* * *
83679 TGCATCGATACACTA-GACAGTGAATCGATGCATCCCTTGAATG
1 TGCATCGATACACCATGA-AGTGCACCGATGCATCCCTTGAATG
*
83722 TGCATCGATACACCATGAAGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCATGAAGTGCACCGATGCATCCCTTGAATG
83765 TGCAT
1 TGCAT
83770 TGATGCACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 41 0.95
44 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (43 bp):
TGCATCGATACACCATGAAGTGCACCGATGCATCCCTTGAATG
Found at i:86552 original size:64 final size:65
Alignment explanation
Indices: 86422--86577 Score: 219
Period size: 64 Copynumber: 2.4 Consensus size: 65
86412 GCACACCCTT
* *
86422 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTCATGAATATTTTGAAACA
*
86487 TCGAATGCATTTTGTGTACCGATGCAC-AGACATGCATCGATGCACTCCATG-CTCA-TTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACT-CATGAAT-ATTTTGAAA
86549 CA
64 CA
* * *
86551 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
86578 GCCTAGTGTA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
64 52 0.63
65 31 0.37
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTCATGAATATTTTGAAACA
Found at i:93817 original size:81 final size:81
Alignment explanation
Indices: 93685--94174 Score: 542
Period size: 81 Copynumber: 6.1 Consensus size: 81
93675 TGTTTAAATC
* * ** *
93685 AAAGATTAAAGGCCTAGTTGTGCATTCAACA-AAAGATGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* *
93749 TAAACGTCTTTGAGTA
66 TAAATGCCTTTGAGTA
* * *
93765 AAAGGTTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
93830 TAAA--CCTTTGAGTA
66 TAAATGCCTTTGAGTA
* * * * * * *
93844 AAAGATTAGTGGTCTAGCTATGCATTTGACAGAAAGATGCCAATTATGCCAGTTAGGTGAAAAGT
1 AAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
93909 TAAATGCCTTTGAGTA
66 TAAATGCCTTTGAGTA
* **
93925 AAATATTAAAAGCCTA-CATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAGATTAATGGCCTAGC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
*
93989 TTAAATGCCTTTGAGTG
65 TTAAATGCCTTTGAGTA
* * * * * * * * *
94006 AAAGATGAATTGCCTAGTTGTGCATTTGGCAAAAAGGTGTCAATCATGTCAGTTAAATGAAAGGC
1 AAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
94071 TAAATGCCTTTGAGTTA
66 TAAATGCCTTTGAG-TA
* * ** * * *
94088 AAGATATTAAAT-GCATATATGTGCATTTGGA-AGAAAGATGTCAATCATGCAAGTTAGATGAAA
1 AA-AGATT-AATGGCCTAGCTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
94151 GATTAAATGCCTTTGGGTA
63 GGTTAAATGCCTTTGAGTA
94170 AAAGA
1 AAAGA
94175 CTAAATGCTT
Statistics
Matches: 346, Mismatches: 55, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
79 70 0.20
80 26 0.08
81 182 0.53
82 7 0.02
83 57 0.16
84 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATGCCTTTGAGTA
Found at i:93922 original size:160 final size:159
Alignment explanation
Indices: 93715--94174 Score: 528
Period size: 160 Copynumber: 2.8 Consensus size: 159
93705 TGCATTCAAC
* * **
93715 AAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAACGTCTTTGAGTAAAAGGTTAATGGCCT
1 AAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAATATTAAT-GCCT
* *
93780 AGCTATGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGTTAAA-CCTTTGAGTA
65 A-CTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGCCTTTGAGTA
* * *
93844 AAAGATTAGTGGTCTAGCTATGCATTTGACA
129 AAAGATGAATGGCCTAGCTATGCATTTGACA
* * * * *
93875 GAAAGATGCCAATTATGCCAGTTAGGTGAAAAGTTAAATGCCTTTGAGTAAAATATTAAAAGCCT
1 AAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAATATT-AATGCCT
93940 ACATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGT
65 AC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA-GCCTTTGAGT
* * * * *
94005 GAAAGATGAATTGCCTAGTTGTGCATTTGGCA
128 AAAAGATGAATGGCCTAGCTATGCATTTGACA
* * * * *
94037 AAAAGGTGTCAATCATGTCAGTTAAATGAAAGGCTAAATGCCTTTGAGTTAAAGATATTAAATGC
1 AAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAG-TAAA-ATATT-AATGC
* * * * * *
94102 ATATATGTGCATTTGGA-AGAAAGATGTCAATCATGCAAGTTAGATGAAAGATTAAATGCCTTTG
63 CTA-CTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA-GCCTTTG
*
94166 GGTAAAAGA
125 AGTAAAAGA
94175 CTAAATGCTT
Statistics
Matches: 255, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
159 1 0.00
160 103 0.40
161 2 0.01
162 72 0.28
163 4 0.02
164 71 0.28
165 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (159 bp):
AAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAATATTAATGCCTA
CTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGCCTTTGAGTAAA
AGATGAATGGCCTAGCTATGCATTTGACA
Found at i:96221 original size:147 final size:146
Alignment explanation
Indices: 96049--96343 Score: 344
Period size: 146 Copynumber: 2.0 Consensus size: 146
96039 TAATAAATAA
* * * *
96049 ATATTTATATTATGACATAAGTCTTAAAGAATAA-AATTAATATAATTAAATATTAATCTAAATT
1 ATATTTATATTAAGACATAAATCTTAAAGAATAAGAATTAATAT-ATTAAATATTAATCCAAAAT
* *
96113 CTAATT-TACAACCAG-TTAACTGTTGAAGTACAATTTTACTTGTTATTAGATGACTAAATTTAT
65 CT-ATTCTACAACCAGTTTAA--GTTGAAGTACAATTTTAATGGTTATTAGATGACTAAATTTAT
* *
96176 GTAATAAATATTCATTTTAT
127 CTAATAAATATTCATATTAT
* * * * *
96196 ATATTTATATTAAGTCATAAATCTTAGAGATTAAGAATTAATGTGTTAAATATTAATCCAAAATC
1 ATATTTATATTAAGACATAAATCTTAAAGAATAAGAATTAATATATTAAATATTAATCCAAAATC
* ** * ** * *
96261 TATTCTATATTCAGTTTGAGTTGAAGTGTAATTTTAATGGTTATTTGATGACTAAATTTATCTGA
66 TATTCTACAACCAGTTTAAGTTGAAGTACAATTTTAATGGTTATTAGATGACTAAATTTATCTAA
96326 TAAATATTCATATTAT
131 TAAATATTCATATTAT
96342 AT
1 AT
96344 TAAAAATCTT
Statistics
Matches: 124, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
146 59 0.48
147 54 0.44
148 11 0.09
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (146 bp):
ATATTTATATTAAGACATAAATCTTAAAGAATAAGAATTAATATATTAAATATTAATCCAAAATC
TATTCTACAACCAGTTTAAGTTGAAGTACAATTTTAATGGTTATTAGATGACTAAATTTATCTAA
TAAATATTCATATTAT
Found at i:99004 original size:136 final size:136
Alignment explanation
Indices: 98760--99004 Score: 463
Period size: 136 Copynumber: 1.8 Consensus size: 136
98750 TAGGGTCAAG
* *
98760 CATAGGTGAAGGAATCCATTAAAGCAAATCATAAGTAGGGTTTTATATCGTAGTTGGGATCTTCC
1 CATAGGTGAAGGAATCCATTAAAGCAAATCATAAGTAGGGTTTTATATCGCAGTTGAGATCTTCC
98825 CTCAATGTTTCTGTTTCTTTAATCATCATATGACCAGTTATATCATGTTATATATAAAGTAAATG
66 CTCAATGTTTCTGTTTCTTTAATCATCATATGACCAGTTATATCATGTTATATATAAAGTAAATG
98890 AAATGT
131 AAATGT
*
98896 CATAGGTGAAGGAATCCATTAAAGCAAATCATAAGTAGGGTTTTATATCGCAGTTTAGATCTTCC
1 CATAGGTGAAGGAATCCATTAAAGCAAATCATAAGTAGGGTTTTATATCGCAGTTGAGATCTTCC
98961 CTCAATGTTTCTGTTTCTTTAATCATCATATGACCAGTTATATC
66 CTCAATGTTTCTGTTTCTTTAATCATCATATGACCAGTTATATC
99005 GTAGTTTGAA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 106 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (136 bp):
CATAGGTGAAGGAATCCATTAAAGCAAATCATAAGTAGGGTTTTATATCGCAGTTGAGATCTTCC
CTCAATGTTTCTGTTTCTTTAATCATCATATGACCAGTTATATCATGTTATATATAAAGTAAATG
AAATGT
Found at i:99055 original size:35 final size:35
Alignment explanation
Indices: 99009--99122 Score: 158
Period size: 35 Copynumber: 3.2 Consensus size: 35
98999 TATATCGTAG
*
99009 TTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAATGGTTTTCAAAATTTGGTAAATGTTTT
* *
99044 TTTGAAAATGGTTTTCAAAATGTGGTAAATGTTTC
1 TTTGAAAATGGTTTTCAAAATTTGGTAAATGTTTT
*
99079 TTTGAAAAATGGTTTTTCAAAATTTGGTATATG-TTT
1 TTTG-AAAATGG-TTTTCAAAATTTGGTAAATGTTTT
*
99115 GTTGAAAA
1 TTTGAAAA
99123 ATTGTAATGG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 40 0.57
36 12 0.17
37 18 0.26
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.46
Consensus pattern (35 bp):
TTTGAAAATGGTTTTCAAAATTTGGTAAATGTTTT
Found at i:103499 original size:36 final size:37
Alignment explanation
Indices: 103384--103500 Score: 154
Period size: 35 Copynumber: 3.3 Consensus size: 37
103374 TGACAACCAG
*
103384 CTTTG-AAAATGG-TTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
* *
103419 CTTTG-AAAATGGTTTTT-AAAATTTGATAAATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
103454 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
103491 -GTTGAAAAAT
1 CTTTGAAAAAT
103501 TGTAATGGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 32 0.44
36 25 0.35
37 15 0.21
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:106919 original size:15 final size:15
Alignment explanation
Indices: 106891--106941 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
106881 CCCAACTGAA
106891 TCAACTCA--CTAAG
1 TCAACTCATGCTAAG
106904 TCAACTCATGCTAAG
1 TCAACTCATGCTAAG
* *
106919 TTAATTCATGCTAAG
1 TCAACTCATGCTAAG
106934 TCAACTCA
1 TCAACTCA
106942 GACCCTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 8 0.25
15 24 0.75
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (15 bp):
TCAACTCATGCTAAG
Found at i:109931 original size:21 final size:22
Alignment explanation
Indices: 109895--109936 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
109885 TGCACAGAAG
109895 TCGGATTTCAATCCGATCCGGA
1 TCGGATTTCAATCCGATCCGGA
*
109917 TCGGTTTTC-ATCCGATCCGG
1 TCGGATTTCAATCCGATCCGG
109937 TTTTTTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGGATTTCAATCCGATCCGGA
Found at i:110053 original size:15 final size:15
Alignment explanation
Indices: 110033--110084 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
110023 ACCGGTTTCA
110033 GTTTTTAAAAAACCG
1 GTTTTTAAAAAACCG
110048 GTTTTTTTAAAAAACCG
1 G--TTTTTAAAAAACCG
* *
110065 GTTATAAAAAAACCG
1 GTTTTTAAAAAACCG
*
110080 ATTTT
1 GTTTT
110085 AATATTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 16 0.52
17 15 0.48
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (15 bp):
GTTTTTAAAAAACCG
Found at i:110056 original size:17 final size:17
Alignment explanation
Indices: 110034--110067 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
110024 CCGGTTTCAG
110034 TTTTTAAAAAACCGGTT
1 TTTTTAAAAAACCGGTT
110051 TTTTTAAAAAACCGGTT
1 TTTTTAAAAAACCGGTT
110068 ATAAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTTAAAAAACCGGTT
Found at i:110176 original size:33 final size:33
Alignment explanation
Indices: 110138--110230 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
110128 CGATAATTGG
* *
110138 AATACTTAAATACTTCCAAGTTTGATAAATTCA
1 AATACTTAAAAACTTCCAAGTTCGATAAATTCA
*
110171 AATACTTAAAAACGTCCAAGTTCGATAAATTCA
1 AATACTTAAAAACTTCCAAGTTCGATAAATTCA
110204 AATACTTAAAAACTT-CAAGTTCGATAA
1 AATACTTAAAAACTTCCAAGTTCGATAA
110231 TTGAAACAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 12 0.21
33 44 0.79
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (33 bp):
AATACTTAAAAACTTCCAAGTTCGATAAATTCA
Found at i:110249 original size:21 final size:21
Alignment explanation
Indices: 110225--110266 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
110215 ACTTCAAGTT
110225 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
* *
110246 CGATAATTGAAATAATGTTTA
1 CGATAATTGAAACAAAGTTTA
110267 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:112723 original size:27 final size:28
Alignment explanation
Indices: 112686--112743 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
112676 AAAAAACCGG
112686 TTTTTCCC-AAATCCGAT-TTCGGATATT
1 TTTTTCCCAAAATCCGATATTCGGAT-TT
* *
112713 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAATCCGATATTCGGATTT
112741 TTT
1 TTT
112744 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTTTCCCAAAATCCGATATTCGGATTT
Found at i:115402 original size:17 final size:17
Alignment explanation
Indices: 115382--115432 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
115372 TCTTTTATTA
115382 TACTGATTCCTTTACTG
1 TACTGATTCCTTTACTG
*
115399 TACT-ATTTCATTTACTG
1 TACTGA-TTCCTTTACTG
*
115416 TATTG-TATCCTTTACTG
1 TACTGAT-TCCTTTACTG
115433 CACAGTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (17 bp):
TACTGATTCCTTTACTG
Found at i:115697 original size:91 final size:91
Alignment explanation
Indices: 115600--115787 Score: 209
Period size: 92 Copynumber: 2.1 Consensus size: 91
115590 TAACTGTATG
** * *
115600 GCACATT-AGTGCCCTGTATGCAACATAGCTACTAGTAATTGTATGACACA-TTAGTGACCAATA
1 GCACATTCAGTGCCCAATATGCAACATA-CTACCAGTAATAGTATGACACATTTAGTGACCAATA
*
115663 TGTAATATAAACTGCCAGTAACAATATA
65 TGCAATATAAACTGCCAGTAACAA-ATA
* * * * *
115691 GCACATTCAGTGTCCAATATGCAATATACTGCCAGTAATAGTATGACATATTTAGTGCCCAATAT
1 GCACATTCAGTGCCCAATATGCAACATACTACCAGTAATAGTATGACACATTTAGTGACCAATAT
* ** * *
115756 GCACTATGTACTGCTAGTAACAAATC
66 GCAATATAAACTGCCAGTAACAAATA
115782 GCACAT
1 GCACAT
115788 AAAGTGCCAG
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
91 33 0.41
92 47 0.59
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (91 bp):
GCACATTCAGTGCCCAATATGCAACATACTACCAGTAATAGTATGACACATTTAGTGACCAATAT
GCAATATAAACTGCCAGTAACAAATA
Found at i:115717 original size:47 final size:43
Alignment explanation
Indices: 115641--115787 Score: 125
Period size: 45 Copynumber: 3.2 Consensus size: 43
115631 CTAGTAATTG
*
115641 TATGACACATTAGTGACCAATATGTAATATAAACTGCCAGTAACAA
1 TATG-CACATTAGTGACCAATATGCAATAT--ACTGCCAGTAACAA
* * *
115687 TATAGCACATTCAGTGTCCAATATGCAATATACTGCCAGTAATAG
1 TAT-GCACATT-AGTGACCAATATGCAATATACTGCCAGTAACAA
* * * *
115732 TATGACATATTTAGTGCCCAATATGCACTATGTACTGCTAGTAACAA
1 TATG-CACA-TTAGTGACCAATATGCA--ATATACTGCCAGTAACAA
115779 -ATCGCACAT
1 TAT-GCACAT
115788 AAAGTGCCAG
Statistics
Matches: 83, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
44 1 0.01
45 33 0.40
46 16 0.19
47 33 0.40
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (43 bp):
TATGCACATTAGTGACCAATATGCAATATACTGCCAGTAACAA
Found at i:115753 original size:45 final size:45
Alignment explanation
Indices: 115595--115758 Score: 145
Period size: 45 Copynumber: 3.6 Consensus size: 45
115585 TCCTGTAACT
* ** * * * *
115595 GTATGGCACA-TTAGTGCCCTGTATGCAACATAGCTACTAGTAATT
1 GTATGACACATTTAGTGCCCAATATGCAATATA-CTGCCAGTAATA
* * *
115640 GTATGACACA-TTAGTGACCAATATGTAATATAAACTGCCAGTAACA
1 GTATGACACATTTAGTGCCCAATATGCAATAT--ACTGCCAGTAATA
* * *
115686 ATAT-AGCACATTCAGTGTCCAATATGCAATATACTGCCAGTAATA
1 GTATGA-CACATTTAGTGCCCAATATGCAATATACTGCCAGTAATA
*
115731 GTATGACATATTTAGTGCCCAATATGCA
1 GTATGACACATTTAGTGCCCAATATGCA
115759 CTATGTACTG
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 60 0.63
46 16 0.17
47 19 0.20
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (45 bp):
GTATGACACATTTAGTGCCCAATATGCAATATACTGCCAGTAATA
Found at i:117787 original size:26 final size:26
Alignment explanation
Indices: 117734--117788 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
117724 ACATTTCCAT
*
117734 TAAATTCTCATAATTTCATCATATGA
1 TAAATTCTCATAATTTCATCATAAGA
117760 TAAATT-TCATAATTATCATGC-TAAGA
1 TAAATTCTCATAATT-TCAT-CATAAGA
117786 TAA
1 TAA
117789 TAGAGTTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.31
26 17 0.65
27 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (26 bp):
TAAATTCTCATAATTTCATCATAAGA
Found at i:119011 original size:39 final size:39
Alignment explanation
Indices: 118963--119040 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
118953 AGTTGCATCG
* * *
118963 AAGTGCTTACGCATAAGGTTTCATCCACCATTTGCACTA
1 AAGTGCTTACACATAAGGTTGCATCCACCATATGCACTA
* *
119002 AAGTTCTTACACATAAGGTTGCGTCCACCATATGCACTA
1 AAGTGCTTACACATAAGGTTGCATCCACCATATGCACTA
119041 GGTATCCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (39 bp):
AAGTGCTTACACATAAGGTTGCATCCACCATATGCACTA
Found at i:123801 original size:39 final size:39
Alignment explanation
Indices: 123753--123860 Score: 126
Period size: 39 Copynumber: 2.8 Consensus size: 39
123743 CGAGTCGCAC
* * * * *
123753 CGAAGTGCTTATGTATGAGGTTGCGTCCGCCATTTGCAT
1 CGAAGTGCTTACGTATAAGGTTGCATCCACAATTTGCAT
*
123792 CGAGGTGCTTACGTATAAGGTTGCATCCACAATTTGCAT
1 CGAAGTGCTTACGTATAAGGTTGCATCCACAATTTGCAT
* ** *
123831 CGAAGTGCTTGCACATAAGGTTGCGTCCAC
1 CGAAGTGCTTACGTATAAGGTTGCATCCAC
123861 CATATCCGCT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (39 bp):
CGAAGTGCTTACGTATAAGGTTGCATCCACAATTTGCAT
Found at i:126807 original size:20 final size:18
Alignment explanation
Indices: 126782--126820 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
126772 ATTCTTAAGG
126782 ATAAAATATTCATTTATGGA
1 ATAAAAT-TTC-TTTATGGA
*
126802 ATAAAATTTCTTTTTGGA
1 ATAAAATTTCTTTATGGA
126820 A
1 A
126821 AAATTACCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (18 bp):
ATAAAATTTCTTTATGGA
Found at i:132050 original size:36 final size:36
Alignment explanation
Indices: 132007--132086 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
131997 CTTGTGTAAC
132007 ATTTTTAAGCGTTGGATTTTAAGGGTAAAGTGGTCA
1 ATTTTTAAGCGTTGGATTTTAAGGGTAAAGTGGTCA
132043 ATTTTTAAGCGTTGGATTTTAAGGGTAAAGTGGTCA
1 ATTTTTAAGCGTTGGATTTTAAGGGTAAAGTGGTCA
132079 ATTTTTAA
1 ATTTTTAA
132087 TAAATGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (36 bp):
ATTTTTAAGCGTTGGATTTTAAGGGTAAAGTGGTCA
Found at i:135982 original size:15 final size:15
Alignment explanation
Indices: 135951--135986 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
135941 GTTGAGGTCC
**
135951 ATATTGTCCAGGTGG
1 ATATTGTCCAGAAGG
135966 ATATTGTCCAGAAGG
1 ATATTGTCCAGAAGG
135981 ATATTG
1 ATATTG
135987 GCCGTACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (15 bp):
ATATTGTCCAGAAGG
Found at i:137554 original size:20 final size:18
Alignment explanation
Indices: 137529--137567 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
137519 ATTCTTAAGG
137529 ATAAAATATTCATTTATGGA
1 ATAAAAT-TTC-TTTATGGA
*
137549 ATAAAATTTCTTTTTGGA
1 ATAAAATTTCTTTATGGA
137567 A
1 A
137568 AAATTACCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (18 bp):
ATAAAATTTCTTTATGGA
Found at i:141279 original size:16 final size:15
Alignment explanation
Indices: 141232--141279 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
141222 TTTTCTTCGA
141232 TATTAAAAAATAAA-
1 TATTAAAAAATAAAT
*
141246 TATT--AAAATAATT
1 TATTAAAAAATAAAT
141259 TATTAAAAAACTAAAT
1 TATTAAAAAA-TAAAT
141275 TATTA
1 TATTA
141280 TTTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 4 0.14
15 4 0.14
16 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TATTAAAAAATAAAT
Found at i:142713 original size:24 final size:22
Alignment explanation
Indices: 142680--142729 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
142670 TGGGCTTGTA
142680 TATATATTTTTTTATTATTATT
1 TATATATTTTTTTATTATTATT
142702 TATATA-TTTTTTATTATTATT
1 TATATATTTTTTTATTATTATT
142723 TATATAT
1 TATATAT
142730 GCATTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATATATTTTTTTATTATTATT
Found at i:142719 original size:10 final size:10
Alignment explanation
Indices: 142690--142725 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
142680 TATATATTTT
142690 TTTATTATTA
1 TTTATTATTA
*
142700 TTTATATATTT
1 TTTAT-TATTA
142711 TTTATTATTA
1 TTTATTATTA
142721 TTTAT
1 TTTAT
142726 ATATGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTATTA
Found at i:142752 original size:3 final size:3
Alignment explanation
Indices: 142744--142799 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
142734 TTAATATATT
*
142744 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
142791 TAA TAA TAA
1 TAA TAA TAA
142800 ATCAATATGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:144159 original size:562 final size:557
Alignment explanation
Indices: 143059--144697 Score: 1992
Period size: 562 Copynumber: 2.9 Consensus size: 557
143049 TCTTGATGAG
* * **
143059 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTTCGATGAGTTCTTCTCATTATGAACT-TTCTC
1 TTCTTCTCATTATGAATTTCTTCATTCTTCAGAT-GA-GAGTTCTTCTCATTATGAACTCTTC-C
* * * * *
143122 TAGAAAAGTTGATCCATCA-AGTGATGGATTTGAGCAAAAATCTGAACAAATTCTTCTCATTATG
63 TAGCAATGTT-ATCCATCATA-TGATGAATTTAAACAAAAAT-TGAACAAATTCTTCTCATTATG
* * ** *
143186 AACTTCTTCATCCTTCTTCAGATGAGTTCTCCTTATTATGAAC-TCGAACTGGAAAAGCTAATCT
125 AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-CTCTGGAAAAGCTAATCC
*
143250 ATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC
189 ATCAAGTGAT-GATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
* * * *
143315 TTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTG
253 TTCAGATGAGTTCTTCTCATTATGAACTC-TACTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* *
143380 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTGTTCATCCTTCTTCAGATGAGTTCTTCT
317 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * *
143445 CATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGAT-AGATTTGAGCAAAAGGTTGAACA
382 CATTATGAACTTTATCTGGAAAAGATGATCCATCAA-TGATGA-ATTAG-GCAAAAGGTTGAACA
* *
143509 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTT
444 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTC
* * * * *
143574 TGGAAAAGCGGATCTATCAAGTGATGGATTTA-AAAAAAGTTGAACAAA
509 TGAAAAAGCGGATCCATCAAGTGATGAATTCAGAAAAAAGTTAAACAAA
* *
143622 TTCTTCTCATTATGAATTTCTTC-TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAATTTCTTCATTCTTCAGATGA-GAGTTCTTCTCATTATGAACTCTTCCTA
*
143686 GCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 GCAATGTT-ATCCATCATATGATGAATTTAAACAAAA-ATTGAACAAATTCTTCTCATTATGAAC
*
143751 TTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTGATCCATCA
128 TTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTAATCCATCA
*
143816 AATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
193 AGTGAT-GATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
143881 AATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
257 GATGAGTTCTTCTCATTATGAAC-TCTACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
* * *
143946 TAAGGTTTAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATT
321 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
144011 ATGAACTTTTTCTGGAAAGGATGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAGTTC
386 ATGAACTTTATCTGGAAAAGATGATCCATCAA-TGATGAATT-AGGCAAAAGGTTGAACAAATTC
*
144076 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAA
449 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGAAA
* * *
144141 AAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAA
514 AAGCGGATCCATCAAGTGATGAATTCA-GAAAAAAGTTAAACAAA
*
144186 TTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGAT-A-AGTTCTTCTCATTATGAACTTCTTCT
1 TTCTTCTCATTATGAATTTCTTCAT--TCTTCAGATGAGAGTTCTTCTCATTATGAA---C-TCT
** * * * *** ***** * * *
144249 TCCTCTTCAGATAAGTTCTTC-TCAT-T-ATGAACTTCTTCTTCCTCTTTAGATAAGTTCTTCTC
60 TCCT-AGCA-AT--GTTATCCATCATATGATGAATTTAAAC-AAAAATTGA-ACAAATTCTTCTC
* * * **
144311 ATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAAT
119 ATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCT
* * * * *
144375 AATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
184 AATCCATCAAGTGATGATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
* ** * ** * *
144440 CC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGGGTGTTGA
248 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-ACTGGAAAAGCTGATCCATCAAGTGATGG
* * * *
144504 ATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTT
312 ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * * *
144569 CTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTG
377 CTTCTCATTATGAACTTTATCTGGAAAAGATGATCCATC-AATGATGAATTAG-GCAAAAGGTTG
*
144634 AACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
440 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
144698 CGACCTGGAA
Statistics
Matches: 940, Mismatches: 109, Indels: 50
0.86 0.10 0.05
Matches are distributed among these distances:
562 453 0.48
563 33 0.04
564 54 0.06
565 1 0.00
566 5 0.01
567 237 0.25
568 114 0.12
569 32 0.03
570 6 0.01
571 2 0.00
572 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (557 bp):
TTCTTCTCATTATGAATTTCTTCATTCTTCAGATGAGAGTTCTTCTCATTATGAACTCTTCCTAG
CAATGTTATCCATCATATGATGAATTTAAACAAAAATTGAACAAATTCTTCTCATTATGAACTTC
TTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGCTAATCCATCAAGT
GATGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
AGTTCTTCTCATTATGAACTCTACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGG
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTATCTGGAAAAGATGATCCATCAATGATGAATTAGGCAAAAGGTTGAACAAATTCTTCTCAT
TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGAAAAAGCGGA
TCCATCAAGTGATGAATTCAGAAAAAAGTTAAACAAA
Found at i:144230 original size:19 final size:19
Alignment explanation
Indices: 144206--144269 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
144196 TATGAATTTC
144206 TTCTTCCTCTTCAGATAAG
1 TTCTTCCTCTTCAGATAAG
**
144225 TTCTT-CTCATT-ATGA-ACTTC
1 TTCTTCCTC-TTCA-GATA--AG
144245 TTCTTCCTCTTCAGATAAG
1 TTCTTCCTCTTCAGATAAG
144264 TTCTTC
1 TTCTTC
144270 TCATTATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 5 0.15
19 15 0.44
20 9 0.26
21 5 0.15
ACGTcount: A:0.19, C:0.27, G:0.08, T:0.47
Consensus pattern (19 bp):
TTCTTCCTCTTCAGATAAG
Found at i:144231 original size:39 final size:39
Alignment explanation
Indices: 144186--144360 Score: 332
Period size: 39 Copynumber: 4.5 Consensus size: 39
144176 GTTAAACAAA
*
144186 TTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
144225 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
*
144264 TTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGATAAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
144303 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
144342 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
144361 TCTCTGGAAA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
Found at i:144286 original size:17 final size:17
Alignment explanation
Indices: 144264--144326 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
144254 TTCAGATAAG
144264 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* * *
144281 TTCTTCTTCCTCTTTAGATAAG
1 TTCTTC-TCAT-TAT-G--AAC
144303 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
144320 TTCTTCT
1 TTCTTCT
144327 TCCTCTTCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 15 0.43
18 3 0.09
19 3 0.09
20 3 0.09
21 3 0.09
22 8 0.23
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.51
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:144603 original size:113 final size:113
Alignment explanation
Indices: 143059--144697 Score: 1906
Period size: 113 Copynumber: 14.5 Consensus size: 113
143049 TCTTGATGAG
*
143059 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
143123 AGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGT-TGAACAAA
* * * ****
143172 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTCCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
143237 GAAAAGCTAATCTATCAAGTGAT-AGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGA-ATTTGAGCAAAAGGTTGAACAAA
* ****
143285 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
143350 GAAAAGATAATCCATCAAGTGAT-AGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGA-ATTTGAGCAAAAGGTTGAACAAA
* * ****
143398 TTCTTCTCATTATGAACTTGTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
143463 GAAAAGATAATCCATCAAGTGAT-AGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGA-ATTTGAGCAAAAGGTTGAACAAA
* * *
143511 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
143576 GAAAAGCGGATCTATCAAGTGATGGATTT-A-AAAAAAGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
*
143622 TTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTC
* * * * * *
143683 -CTGGCAATGTTAATCCATCATA-TGATGAATTTAAACAAAAGGTTGAACAAA
62 TCTGGAAAAGCTGATCCATCA-AGTGATGAATTTGAGCAAAAGGTTGAACAAA
* *
143734 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
143799 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
*
143847 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAAC-TTCTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCT
* * *
143911 GGAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTTAACAAA
65 GGAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
* *
143960 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
144025 GAAAGGATGATCCATCAATTGATGAA-TTCAGGTAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGAATTTGA-GCAAAAGGTTGAACAAA
144073 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
144138 AAAAAGCTGATCCATCAAGTGATGAA-TTCAGGCAAAAGGTTAAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTTGA-GCAAAAGGTTGAACAAA
* *
144186 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTCTTCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA---C-T-TT
* * ** * * * *** ****** * * *
144250 CCTCTTCAGATAAG-TTCTTC-TC-A-TTATGAACTTCTTCTTCCTCTTTAGATAAG
61 -CTC-T-GGAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGA-ACAAA
*
144303 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * * * *
144367 GAAAAAATAATTCATCAAGTGATGAA-TTCAGGGAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTTGA-GCAAAAGGTTGAACAAA
* * **
144415 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* ** * ** * * * *
144479 GCACTGCTGATCCACCGGGTGTTGAATTTAAGCAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
*
144527 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
144592 GAAATGCTGATCCATCGAA-TGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AAGTGATGAATTTGAGCAAAAGGTTGAACAAA
*
144640 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
144698 CGACCTGGAA
Statistics
Matches: 1334, Mismatches: 154, Indels: 76
0.85 0.10 0.05
Matches are distributed among these distances:
107 11 0.01
108 4 0.00
109 5 0.00
110 48 0.04
111 39 0.03
112 192 0.14
113 927 0.69
114 5 0.00
115 5 0.00
116 22 0.02
117 63 0.05
118 5 0.00
119 4 0.00
120 4 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
Found at i:144706 original size:113 final size:113
Alignment explanation
Indices: 144303--144734 Score: 493
Period size: 112 Copynumber: 3.8 Consensus size: 113
144293 TTTAGATAAG
*
144303 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-CT
** * * * * *
144366 GGAAAAAATAATTCATCAAGTGAT-GAATTCAGGGAAAAGGTTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGATGGATTTGA-GCAAAAGGTTGAACAAA
* **
144415 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTG
* ** * ** * * * * *
144479 GCACTGCTGATCCACCGGGTGTTGAATTTAAGCAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
*
144527 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-CT
*
144591 GGAAATGCTGATCCATCGAA-TGATGGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGCTGATCCATC-AAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* **
144640 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTG
* * *
144705 G-AATGTTGATCCATTGAA-TGATGGATTTGA
66 GAAAAGCTGATCCA-TCAAGTGATGGATTTGA
144735 ACTTTGCTAA
Statistics
Matches: 272, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
112 136 0.50
113 135 0.50
114 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:153935 original size:18 final size:18
Alignment explanation
Indices: 153900--153952 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
153890 GAATATAATA
*
153900 AATAAATAAAATAAAAAAT
1 AATAAATAATA-AAAAAAT
153919 AA-AAATATATAAAAAAAT
1 AATAAATA-ATAAAAAAAT
*
153937 AATAAGTAATAAAAAA
1 AATAAATAATAAAAAA
153953 TTTGAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AATAAATAATAAAAAAAT
Found at i:153947 original size:22 final size:22
Alignment explanation
Indices: 153894--153941 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
153884 ATTCTTGAAT
153894 ATAATAAATAAATAAAATAAAAA
1 ATAA-AAATAAATAAAATAAAAA
* *
153917 ATAAAAATATATAAAA-AAATA
1 ATAAAAATAAATAAAATAAAAA
153938 ATAA
1 ATAA
153942 GTAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 11 0.48
23 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAAAATAAATAAAATAAAAA
Found at i:156100 original size:3 final size:3
Alignment explanation
Indices: 156092--156171 Score: 144
Period size: 3 Copynumber: 27.0 Consensus size: 3
156082 TTAATATATT
*
156092 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
156140 TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
156172 ATCAATATGG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:157707 original size:25 final size:26
Alignment explanation
Indices: 157675--157723 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
157665 CTAAAAAATA
* *
157675 TTTTTAAATAATT-ATAAATTTAACT
1 TTTTTAAAAAATTAAAAAATTTAACT
157700 TTTTTAAAAAATTAAAAAATTTAA
1 TTTTTAAAAAATTAAAAAATTTAA
157724 AAAGATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTTTAAAAAATTAAAAAATTTAACT
Found at i:162190 original size:15 final size:15
Alignment explanation
Indices: 162159--162194 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
162149 GTTGAGGTCC
**
162159 ATATTGTCCAGGTGG
1 ATATTGTCCAGAAGG
162174 ATATTGTCCAGAAGG
1 ATATTGTCCAGAAGG
162189 ATATTG
1 ATATTG
162195 GCCGTACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (15 bp):
ATATTGTCCAGAAGG
Found at i:163253 original size:3 final size:3
Alignment explanation
Indices: 163238--163273 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
163228 AGATATATCC
*
163238 AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
163274 TTTAGCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:167614 original size:21 final size:22
Alignment explanation
Indices: 167590--167645 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
167580 AACCATTCAA
167590 GGGGAATCGGTA-CCCCTTGGGGGG
1 GGGGAATCGGTACCCCCTT---GGG
167614 GGGGAATCGGTACCCCCTT-GG
1 GGGGAATCGGTACCCCCTTGGG
*
167635 GGAGAATCGGT
1 GGGGAATCGGT
167646 TCCCTCTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 12 0.40
24 12 0.40
25 6 0.20
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (22 bp):
GGGGAATCGGTACCCCCTTGGG
Found at i:167619 original size:24 final size:25
Alignment explanation
Indices: 167590--167636 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
167580 AACCATTCAA
167590 GGGGAATCGGTA-CCCCTTGGGGGG
1 GGGGAATCGGTACCCCCTTGGGGGG
167614 GGGGAATCGGTACCCCCTTGGGG
1 GGGGAATCGGTACCCCCTTGGGG
167637 AGAATCGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (25 bp):
GGGGAATCGGTACCCCCTTGGGGGG
Found at i:177307 original size:271 final size:273
Alignment explanation
Indices: 176824--178047 Score: 1897
Period size: 271 Copynumber: 4.5 Consensus size: 273
176814 TATTTCCTAA
* * * * * *
176824 ATTTGTAACTCATTTGGGCCATCAGTAAGTCTTTCGATCATGATGCTTAAATCCTTCGGGTCATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* * *
176889 TATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCGAGCATGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTT
* *
176954 TTCAAATGAGATTTTAGAAATTAAGCCTAATTTTAAGGGGTTTCTT-A-ATTATCTCAAAATAGT
131 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTGAGATTATCTCAAAAGAGT
177017 TGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTT
196 TGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTT
177082 CAAGGGTTTCTTG
261 CAAGGGTTTCTTG
* * * * *
177095 ATTTGTAAGTCCTTCAGGCCATTAGTAAGTCTTTCGAGCATCATGCTTAAATCCTTCGGGTCATT
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* * * *
177160 TGTAAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCATAAGATCTTCGGGCATGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTT
177225 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTT-A-ATTATCTCAAAAGAGT
131 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTGAGATTATCTCAAAAGAGT
* *
177288 TGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTACCTTGACAACTAAGAAACTAAGATTGATTTT
196 TGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTT
*
177353 TAAGGGTTTCTTG
261 CAAGGGTTTCTTG
* *
177366 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATC
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* * * * *
177431 TGTAAGTCTTTCGAGTAAGATGATAAGTCCTCCGAGCCATCCATAAGACCTTCGGGCAGGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTT
* *
177496 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTTAAAAGAG
131 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTGA-GATTATCTCAAAAGAG
177561 TTGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAA-CTTGATTT
195 TTGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTT
177625 TCAAGGGTTTCTTG
260 TCAAGGGTTTCTTG
* * *
177639 ATTTATAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGTTCATT
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* *
177704 TGTAAGCCTTTCGATCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACATGATGTT
66 TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTT
* * *
177769 TTCAAATGAGATTTTAGAAACTAATCCTGATTTTTAGGGGTTTCTTGATGATTATCTCAAAAGAG
131 TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTGA-GATTATCTCAAAAGAG
* * *
177834 TTGTTAAAGGAAGCTAAGCGTAATTTTAAGGGGTTCCTTGAAAACTAAAAAACTAAG-TCTGATT
195 TTGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCT-TGATT
177898 TTCAAGGGTTTCTTG
259 TTCAAGGGTTTCTTG
* * *
177913 ATTTGTAAATCCTTCGAGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGAC-TT
1 ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* * * *
177977 CTGTAAGCCTTTCGAGCAAGATGATAAGTTCTTTGGGCCATCTATAAGTCCTTCGGGCA-GAATG
66 -TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATG-ATG
178041 TTTTCAA
129 TTTTCAA
178048 CATTTTCATT
Statistics
Matches: 876, Mismatches: 70, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
271 412 0.47
272 1 0.00
273 256 0.29
274 207 0.24
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (273 bp):
ATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
TGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTT
TTCAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTGAGATTATCTCAAAAGAGT
TGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGATTTT
CAAGGGTTTCTTG
Found at i:184160 original size:2 final size:2
Alignment explanation
Indices: 184153--184181 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
184143 CATTATACTT
184153 TA 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 TA T
184182 GATACATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:189844 original size:13 final size:13
Alignment explanation
Indices: 189820--189865 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
189810 TGAATGAATG
189820 TAAATATTTATTTA
1 TAAAT-TTTATTTA
189834 TAAATTTTA-TT-
1 TAAATTTTATTTA
189845 T--ATTTTATTTA
1 TAAATTTTATTTA
189856 TAAATTTTAT
1 TAAATTTTAT
189866 AAATGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 2 0.07
12 2 0.07
13 11 0.39
14 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAAATTTTATTTA
Found at i:193329 original size:2 final size:2
Alignment explanation
Indices: 193322--193360 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
193312 AATTATTATC
*
193322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
193361 GTTATTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:194624 original size:22 final size:21
Alignment explanation
Indices: 194593--194633 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
194583 CATCTCCATT
194593 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
194614 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
194634 TTCCGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:198651 original size:29 final size:29
Alignment explanation
Indices: 198609--198751 Score: 94
Period size: 29 Copynumber: 4.9 Consensus size: 29
198599 CCCGACCCAG
198609 TGACATTTTGGGAATTATTTTGAAAAAGT
1 TGACATTTTGGGAATTATTTTGAAAAAGT
* * * *
198638 TGACATTTTGGGAA-AATGTTCAAAAACAT
1 TGACATTTTGGGAATTATTTTGAAAAA-GT
* * * * *
198667 TTACATTCTGGTAATTATTTT-TAAAACT
1 TGACATTTTGGGAATTATTTTGAAAAAGT
* * *
198695 ATGACATTTTGAGAATTA-TTTGTAAAACGG
1 -TGACATTTTGGGAATTATTTTG-AAAAAGT
* ** *
198725 TGATATTTTGATAATTATTTTTAAAAA
1 TGACATTTTGGGAATTATTTTGAAAAA
198752 ATGTGTTATT
Statistics
Matches: 85, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
28 13 0.15
29 62 0.73
30 10 0.12
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTGAAAAAGT
Found at i:207487 original size:24 final size:24
Alignment explanation
Indices: 207460--207509 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
207450 TCCCATAATT
207460 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
207484 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
207508 CG
1 CG
207510 AGTCTTCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (24 bp):
CGTTATCCATATTATTACCAAATC
Found at i:208192 original size:30 final size:29
Alignment explanation
Indices: 208059--208179 Score: 138
Period size: 29 Copynumber: 4.1 Consensus size: 29
208049 ACCCGACCCA
* *
208059 GTGATATTTTAGG-AATTATTTTGAAAAAG
1 GTGACATTTT-GGTAATTATTTTTAAAAAG
*
208088 GTGACATTTTGGTAATTATTTTTAAAACG
1 GTGACATTTTGGTAATTATTTTTAAAAAG
* * *
208117 ATGACATTTTGGGAATTATTTGTAAAACA-
1 GTGACATTTTGGTAATTATTTTTAAAA-AG
*
208146 GTGATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGTAATTATTTTTAA-AAAG
208176 GTGA
1 GTGA
208180 TTTTTTTGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.03
29 69 0.90
30 6 0.08
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (29 bp):
GTGACATTTTGGTAATTATTTTTAAAAAG
Found at i:209176 original size:8 final size:8
Alignment explanation
Indices: 209163--209204 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
209153 GGGTAAGCCC
209163 TACGGACT
1 TACGGACT
209171 TACGGACT
1 TACGGACT
* *
209179 TACAGAAT
1 TACGGACT
209187 TACGGACT
1 TACGGACT
*
209195 TACGAACT
1 TACGGACT
209203 TA
1 TA
209205 AGGATACAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (8 bp):
TACGGACT
Found at i:210023 original size:45 final size:42
Alignment explanation
Indices: 209962--210059 Score: 96
Period size: 43 Copynumber: 2.3 Consensus size: 42
209952 TGCTTATTTC
* *
209962 ATAT-GTTATAATATAATTA-TTATCACATATATATATAT-AGATT
1 ATATAGTTATTATATAATAACTTATC-CAT-TA-ATATATGAGA-T
*
210005 ATATAGTTATTATGATAATAACTTATCCATTAATATGTGAGAT
1 ATATAGTTATTAT-ATAATAACTTATCCATTAATATATGAGAT
210048 ATA-AGTTATTAT
1 ATATAGTTATTAT
210060 TATATACTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
42 9 0.19
43 13 0.27
44 12 0.25
45 9 0.19
46 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (42 bp):
ATATAGTTATTATATAATAACTTATCCATTAATATATGAGAT
Found at i:217742 original size:10 final size:10
Alignment explanation
Indices: 217729--217761 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
217719 TATCTCACCT
217729 TATGAGACAA
1 TATGAGACAA
*
217739 TATGAGACAG
1 TATGAGACAA
217749 TATGAGACAA
1 TATGAGACAA
217759 TAT
1 TAT
217762 TACTGATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (10 bp):
TATGAGACAA
Found at i:227146 original size:45 final size:45
Alignment explanation
Indices: 227037--227309 Score: 361
Period size: 45 Copynumber: 6.0 Consensus size: 45
227027 ATTCTTTATC
* * * *
227037 TTCATTTATGACATCCTTTAATGT-ATATAATGCACGATTATGCATT
1 TTCATTTATGGCATCCTTTCATGTCGT-TAATGCACCATTATGCA-T
*
227083 TTCATTTATGGCATCCTTTCATG-CCTATAATGCACCATTATGCAT
1 TTCATTTATGGCATCCTTTCATGTCGT-TAATGCACCATTATGCAT
* * *
227128 TTCATTTATGGCATCCTTTCATGCCGTTAATGCACCGTTATACAT
1 TTCATTTATGGCATCCTTTCATGTCGTTAATGCACCATTATGCAT
** *
227173 TTCATTTATGAAATCCTTTCATGTCGTTAATGCACCGTTATGCAT
1 TTCATTTATGGCATCCTTTCATGTCGTTAATGCACCATTATGCAT
* * * *
227218 TTCATTTATGGCATCGTTTCATGTCGTTAATGCATCGTTATGTAT
1 TTCATTTATGGCATCCTTTCATGTCGTTAATGCACCATTATGCAT
*
227263 TTCATTTATGTCATCCTTTCATGTCGTTAATGCACCATTATGCAT
1 TTCATTTATGGCATCCTTTCATGTCGTTAATGCACCATTATGCAT
227308 TT
1 TT
227310 AGTCTTTTAG
Statistics
Matches: 204, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
45 163 0.80
46 41 0.20
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (45 bp):
TTCATTTATGGCATCCTTTCATGTCGTTAATGCACCATTATGCAT
Found at i:227901 original size:18 final size:18
Alignment explanation
Indices: 227880--227930 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
227870 TCAATTTCTA
227880 TTACAATTTCA-ACCTATC
1 TTACAATTTCAGA-CTATC
227898 TTACAATTTCAGACTATC
1 TTACAATTTCAGACTATC
227916 TTACAATTTCAGACT
1 TTACAATTTCAGACT
227931 CAATAGTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 31 0.97
19 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (18 bp):
TTACAATTTCAGACTATC
Found at i:228067 original size:20 final size:19
Alignment explanation
Indices: 228031--228100 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 19
228021 GTAATATATG
*
228031 GTATCGATAC-CTTTATCTTA
1 GTATCGATACTCTATATC--A
228051 GTATCGATACTC-ATATCA
1 GTATCGATACTCTATATCA
* *
228069 GTATCGATACTGATTTAATCA
1 GTATCGATACT-CTAT-ATCA
228090 GTATCGATACT
1 GTATCGATACT
228101 TATTCAACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.28
20 15 0.35
21 16 0.37
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (19 bp):
GTATCGATACTCTATATCA
Found at i:228073 original size:18 final size:20
Alignment explanation
Indices: 228050--228100 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
228040 CCTTTATCTT
228050 AGTATCGATACTCA-T-ATC
1 AGTATCGATACTCATTAATC
*
228068 AGTATCGATACTGATTTAATC
1 AGTATCGATACTCA-TTAATC
228089 AGTATCGATACT
1 AGTATCGATACT
228101 TATTCAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.45
20 1 0.03
21 15 0.52
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTCATTAATC
Found at i:229336 original size:22 final size:23
Alignment explanation
Indices: 229315--229358 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
229305 TCATTATTTC
*
229315 CTTT-CTTTTCTTTCA-ACCTTT
1 CTTTCCTTTGCTTTCATACCTTT
*
229336 CTTTCCTTTGCTTTTATACCTTT
1 CTTTCCTTTGCTTTCATACCTTT
229359 TGCCACAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.09, C:0.27, G:0.02, T:0.61
Consensus pattern (23 bp):
CTTTCCTTTGCTTTCATACCTTT
Found at i:234803 original size:23 final size:23
Alignment explanation
Indices: 234777--234825 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
234767 TTTGAATTAA
*
234777 TATAATTTATTTAATAA-TATTTT
1 TATAATTTAATT-ATAACTATTTT
234800 TATAATTTAATTATAACTTATTTT
1 TATAATTTAATTATAAC-TATTTT
234824 TA
1 TA
234826 AAGAATAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 11 0.48
24 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATAATTTAATTATAACTATTTT
Found at i:235318 original size:13 final size:13
Alignment explanation
Indices: 235302--235346 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
235292 TTTTATCCAT
235302 TTTAATTATAATA
1 TTTAATTATAATA
*
235315 TTTAATTATAGTA
1 TTTAATTATAATA
*
235328 -GTAATTATACATA
1 TTTAATTATA-ATA
235341 TTTAAT
1 TTTAAT
235347 GTAATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 8 0.31
13 14 0.54
14 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (13 bp):
TTTAATTATAATA
Found at i:237028 original size:60 final size:59
Alignment explanation
Indices: 236957--237230 Score: 307
Period size: 60 Copynumber: 4.6 Consensus size: 59
236947 CACCTTGGGT
* * * * * *
236957 TCATAAGGACTTACCTAATGCACAAAGCAAAGGAGTCGCCTGAGGGGAGTACCCCTAGG
1 TCATAAGGACTTACCCAATGCACAAAGCAAAAGAGCCACCTGAGGGGAGTGCCCCCAGG
* *
237016 TACATAAGGACTTACCCAATTCACAAA-CAAAAAGAGCCACCTGAGGAGAGTGCCCCCAGG
1 T-CATAAGGACTTACCCAATGCACAAAGC-AAAAGAGCCACCTGAGGGGAGTGCCCCCAGG
* * * * *
237076 TTCATAAGGACTTACCCAATGCATAAAGGAAAAGAGCCACCCGAGGGGAGTGCCCTCAGA
1 -TCATAAGGACTTACCCAATGCACAAAGCAAAAGAGCCACCTGAGGGGAGTGCCCCCAGG
* * * * * *
237136 TCCATAATGACTTACCCAATGCAAAAAGTAAAGGAGCCACCTGAAGGGAGTGCCCCCGGG
1 T-CATAAGGACTTACCCAATGCACAAAGCAAAAGAGCCACCTGAGGGGAGTGCCCCCAGG
* *
237196 TCAATAAGGACTTACCTAATACACAAAGCAAAAGA
1 TC-ATAAGGACTTACCCAATGCACAAAGCAAAAGA
237231 TCCATCCTAA
Statistics
Matches: 179, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
59 4 0.02
60 174 0.97
61 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (59 bp):
TCATAAGGACTTACCCAATGCACAAAGCAAAAGAGCCACCTGAGGGGAGTGCCCCCAGG
Found at i:237173 original size:120 final size:119
Alignment explanation
Indices: 236954--237230 Score: 342
Period size: 120 Copynumber: 2.3 Consensus size: 119
236944 GAGCACCTTG
* * * * *
236954 GGTTCATAAGGACTTACCTAATGCACAAAGCAAAGGAGTCGCCTGAGGGGAGTACCCCTAGGTAC
1 GGTTCATAAGGACTTACCTAATGCACAAAGCAAAAGAGCCACCCGAGGGGAGTACCCCTAGATAC
* *
237019 ATAAGGACTTACCCAATTCACAAACAAAAAGAGCCACCTG-AGGAGAGTGCCCCC
66 ATAAGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTGAAGG-GAGTGCCCCC
* * * *
237073 AGGTTCATAAGGACTTACCCAATGCATAAAGGAAAAGAGCCACCCGAGGGGAGT-GCCCTCAGAT
1 -GGTTCATAAGGACTTACCTAATGCACAAAGCAAAAGAGCCACCCGAGGGGAGTACCCCT-AGAT
* * ** *
237137 CCATAATGACTTACCCAATGCAAAAAGTAAAGGAGCCACCTGAAGGGAGTGCCCCC
64 ACATAAGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTGAAGGGAGTGCCCCC
* *
237193 GGGTCAATAAGGACTTACCTAATACACAAAGCAAAAGA
1 GGTTC-ATAAGGACTTACCTAATGCACAAAGCAAAAGA
237231 TCCATCCTAA
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
119 8 0.06
120 122 0.92
121 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (119 bp):
GGTTCATAAGGACTTACCTAATGCACAAAGCAAAAGAGCCACCCGAGGGGAGTACCCCTAGATAC
ATAAGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTGAAGGGAGTGCCCCC
Found at i:237261 original size:120 final size:120
Alignment explanation
Indices: 236957--237271 Score: 289
Period size: 120 Copynumber: 2.6 Consensus size: 120
236947 CACCTTGGGT
* * * * * * * * * *
236957 TCATAAGGACTTACCTAATGCACAAAGCAAAGGAGTCGCCTGAGGGGAGTACCC-CTAGGTA-CA
1 TCATAAGGACTTACCCAATACACAAAGCAAAAGAGCCACCCGAAGGGAATGCCCTC-A-GAACCA
* * *
237020 TAAGGACTTACCCAATTCACAAACAAAAAGAGCCACCTGAGGAGAGTGCCCCCAGGT
64 TAAGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTGAGGAGAGTGCCCCCAGGG
* * * * * *
237077 TCATAAGGACTTACCCAATGCATAAAGGAAAAGAGCCACCCGAGGGGAGTGCCCTCAGATCCATA
1 TCATAAGGACTTACCCAATACACAAAGCAAAAGAGCCACCCGAAGGGAATGCCCTCAGAACCATA
* ** *
237142 ATGACTTACCCAATGCAAAAAGTAAAGGAGCCACCTGAAGG-GAGTGCCCCC-GGG
66 AGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTG-AGGAGAGTGCCCCCAGGG
* * * * *
237196 TCAATAAGGACTTACCTAATACACAAAGCAAAAGATCCATCCTAAGGGAATG-CCTTAGGAACCA
1 TC-ATAAGGACTTACCCAATACACAAAGCAAAAGAGCCACCCGAAGGGAATGCCCTCA-GAACCA
*
237260 TAAGGTCTTACC
64 TAAGGACTTACC
237272 ACTGGGCCAA
Statistics
Matches: 160, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
119 9 0.06
120 147 0.92
121 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (120 bp):
TCATAAGGACTTACCCAATACACAAAGCAAAAGAGCCACCCGAAGGGAATGCCCTCAGAACCATA
AGGACTTACCCAATGCAAAAACAAAAAGAGCCACCTGAGGAGAGTGCCCCCAGGG
Found at i:239448 original size:15 final size:15
Alignment explanation
Indices: 239428--239482 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
239418 TTTACTGGTC
*
239428 TGAGTTGACTCGATA
1 TGAGTTGACTCGATG
239443 TGAGTTGACTCGATG
1 TGAGTTGACTCGATG
*
239458 TTAGTTGACTC-AGTG
1 TGAGTTGACTCGA-TG
239473 TGAGTTGACT
1 TGAGTTGACT
239483 TAATAGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (15 bp):
TGAGTTGACTCGATG
Found at i:249255 original size:18 final size:18
Alignment explanation
Indices: 249229--249281 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
249219 TGACCGGTCA
* *
249229 CGACCCGACCCGTTGACT
1 CGACACGACCCGTTGACC
249247 CGACACGACCCGTTGACC
1 CGACACGACCCGTTGACC
* *
249265 CGACCCGA-TCGTTGACC
1 CGACACGACCCGTTGACC
249282 GTTGACCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.15
Consensus pattern (18 bp):
CGACACGACCCGTTGACC
Found at i:249331 original size:29 final size:30
Alignment explanation
Indices: 249289--249370 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 30
249279 ACCGTTGACC
*
249289 GGTGATATTCTGGTAAATAATTCA-GTTTT
1 GGTGCTATTCTGGTAAATAATTCATGTTTT
249318 GGTGCTATTCTGGTAAATAATT-ATGTTTT
1 GGTGCTATTCTGGTAAATAATTCATGTTTT
* *
249347 GATGCTATTCTGGTAATTAATTCA
1 GGTGCTATTCTGGTAAATAATTCA
249371 AAATAGGTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (30 bp):
GGTGCTATTCTGGTAAATAATTCATGTTTT
Found at i:249414 original size:29 final size:29
Alignment explanation
Indices: 249349--249414 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
249339 TATGTTTTGA
*
249349 TGCTATTCTGGTAATTAATTCAAAATAGG
1 TGCTATTTTGGTAATTAATTCAAAATAGG
* *
249378 TGCTATTTTGGTAATTATTTTAAAA-AGGG
1 TGCTATTTTGGTAATTAATTCAAAATA-GG
249407 TGCTATTT
1 TGCTATTT
249415 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
TGCTATTTTGGTAATTAATTCAAAATAGG
Found at i:251413 original size:17 final size:18
Alignment explanation
Indices: 251392--251439 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
251382 TATTTAAGCT
251392 TGTAGTTCATTTAGGGAA
1 TGTAGTTCATTTAGGGAA
*
251410 -GTAGTTCATTTA-TGAA
1 TGTAGTTCATTTAGGGAA
*
251426 TTTAGTTCATTTAG
1 TGTAGTTCATTTAG
251440 AAAGCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (18 bp):
TGTAGTTCATTTAGGGAA
Found at i:251452 original size:34 final size:35
Alignment explanation
Indices: 251394--251471 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
251384 TTTAAGCTTG
* * * *
251394 TAGTTCATTTAGGGAAGTAGTTCATTTATGAA-TT
1 TAGTTCATTTAGGAAAGTAATTCATTCATGAACCT
251428 TAGTTCATTTA-GAAAGCTAATTCATTCATGAACCT
1 TAGTTCATTTAGGAAAG-TAATTCATTCATGAACCT
251463 TAGTTCATT
1 TAGTTCATT
251472 CAATAAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 4 0.11
34 24 0.63
35 10 0.26
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (35 bp):
TAGTTCATTTAGGAAAGTAATTCATTCATGAACCT
Found at i:251504 original size:16 final size:17
Alignment explanation
Indices: 251483--251532 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
251473 AATAAAGTTT
251483 GTTCATTAAT-TAACTA
1 GTTCATTAATATAACTA
*
251499 GTTCATTCATATAACTA
1 GTTCATTAATATAACTA
* *
251516 GTTCATCAATCTAACTA
1 GTTCATTAATATAACTA
251533 ACCCTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (17 bp):
GTTCATTAATATAACTA
Found at i:252559 original size:18 final size:18
Alignment explanation
Indices: 252538--252580 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
252528 TACTTACCAT
* *
252538 GACAACACTACTTGCCTC
1 GACAACACCACTTGCCAC
*
252556 GACAGCACCACTTGCCAC
1 GACAACACCACTTGCCAC
252574 GACAACA
1 GACAACA
252581 TCATTCATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.14, T:0.14
Consensus pattern (18 bp):
GACAACACCACTTGCCAC
Found at i:253939 original size:45 final size:45
Alignment explanation
Indices: 253874--253983 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 45
253864 TTCTAAAGCA
* * * * *
253874 AATGCCCTAGCAATTTGCAAAGCCATTGCCGAAACCAGCAAAGGG
1 AATGCCCCAGCAATTCGCAAAGCCATTACCAAAACCAGCAAAGGC
* *
253919 AATGCCCCGGCAATTCGCAAAGCCATTACCAAAACCAGTAAAGGC
1 AATGCCCCAGCAATTCGCAAAGCCATTACCAAAACCAGCAAAGGC
*
253964 AATGCCCCAACAATTC-CAAA
1 AATGCCCCAGCAATTCGCAAA
253984 TCATTCCCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
44 4 0.07
45 52 0.93
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (45 bp):
AATGCCCCAGCAATTCGCAAAGCCATTACCAAAACCAGCAAAGGC
Found at i:256357 original size:17 final size:16
Alignment explanation
Indices: 256307--256359 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
256297 TCAATAAAGT
256307 TAGTTCATTAATTAAAC
1 TAGTTCATTAATT-AAC
*
256324 TAGTTCATTCATATAAC
1 TAGTTCATTAAT-TAAC
256341 TAGTTCATTAATCTAAC
1 TAGTTCATTAAT-TAAC
256358 TA
1 TA
256360 ACCCTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 31 0.97
18 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
TAGTTCATTAATTAAC
Found at i:257424 original size:18 final size:18
Alignment explanation
Indices: 257386--257426 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
257376 CTTACCACTG
***
257386 CAACACCACTTGCCTTGA
1 CAACACCACTTGCCACAA
257404 CAACACCACTTGCCACAA
1 CAACACCACTTGCCACAA
257422 CAACA
1 CAACA
257427 TCATTCATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (18 bp):
CAACACCACTTGCCACAA
Found at i:262117 original size:2 final size:2
Alignment explanation
Indices: 262050--262101 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
262040 AGAAAATCTT
262050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262092 TA TA TA TA TA
1 TA TA TA TA TA
262102 AGATTTTCTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:262707 original size:22 final size:22
Alignment explanation
Indices: 262679--262729 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
262669 CTGTATTAAG
262679 GGTGACCCATTCGATGGGTGCA
1 GGTGACCCATTCGATGGGTGCA
262701 GGTGACCCATTCGATGGGTGCA
1 GGTGACCCATTCGATGGGTGCA
262723 GGTGACC
1 GGTGACC
262730 ATTTGATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.22
Consensus pattern (22 bp):
GGTGACCCATTCGATGGGTGCA
Found at i:265404 original size:19 final size:20
Alignment explanation
Indices: 265365--265409 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
265355 GAAACCCCTT
265365 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
265386 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
265405 TGAAA
1 TGAAA
265410 GAACATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.46
21 13 0.54
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:267266 original size:19 final size:20
Alignment explanation
Indices: 267227--267271 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
267217 GAAACCCCTT
267227 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
267248 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
267267 TGAAA
1 TGAAA
267272 GAACATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.46
21 13 0.54
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:271387 original size:61 final size:61
Alignment explanation
Indices: 271292--271420 Score: 249
Period size: 61 Copynumber: 2.1 Consensus size: 61
271282 CTTTCACAGC
*
271292 AAAGTTAAATTATATTAATATGAGCAATATTGAGTTATTGACCAAAAGTAAAAAATTGCCA
1 AAAGTTAAATTATATTAATAAGAGCAATATTGAGTTATTGACCAAAAGTAAAAAATTGCCA
271353 AAAGTTAAATTATATTAATAAGAGCAATATTGAGTTATTGACCAAAAGTAAAAAATTGCCA
1 AAAGTTAAATTATATTAATAAGAGCAATATTGAGTTATTGACCAAAAGTAAAAAATTGCCA
271414 AAAGTTA
1 AAAGTTA
271421 CTTCAAAGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (61 bp):
AAAGTTAAATTATATTAATAAGAGCAATATTGAGTTATTGACCAAAAGTAAAAAATTGCCA
Found at i:273006 original size:16 final size:17
Alignment explanation
Indices: 272968--273007 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
272958 AATAACTATA
272968 TTAATTATATTTATTTC
1 TTAATTATATTTATTTC
272985 TT-ATTATA-TTATTT-
1 TTAATTATATTTATTTC
272999 TTAAATTAT
1 TT-AATTAT
273008 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 6 0.29
16 11 0.52
17 2 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTATATTTATTTC
Found at i:278599 original size:21 final size:20
Alignment explanation
Indices: 278558--278599 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
278548 TACTTTCACA
278558 TTTCAGATTCATAACTCTTTT
1 TTTCAGATTCA-AACTCTTTT
278579 TTTCAGATTC-AACTCATTTT
1 TTTCAGATTCAAACTC-TTTT
278599 T
1 T
278600 AGATTTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTCAGATTCAAACTCTTTT
Found at i:278603 original size:17 final size:18
Alignment explanation
Indices: 278562--278626 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
278552 TTCACATTTC
*
278562 AGATTCATAACTCTTTTTTT
1 AGATTCAT-ACTC-ATTTTT
278582 CAGATTCA-ACTCATTTTT
1 -AGATTCATACTCATTTTT
*
278600 AGATTTATACTCATTTTT
1 AGATTCATACTCATTTTT
278618 AGATTCATA
1 AGATTCATA
278627 GACCAATGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
17 6 0.15
18 23 0.57
19 4 0.10
21 7 0.17
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.49
Consensus pattern (18 bp):
AGATTCATACTCATTTTT
Found at i:278744 original size:34 final size:34
Alignment explanation
Indices: 278681--278773 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
278671 TAGTGTGCGC
* * *
278681 AATAAGCACTCCAGATGC-TATCATCAAAAACAGA
1 AATATGCACTCCAGGTGCAT-TCATAAAAAACAGA
*
278715 AGTATGCACTCCAGGTGCATTCATAAAAAACAGA
1 AATATGCACTCCAGGTGCATTCATAAAAAACAGA
* * * *
278749 AATATGGATTCTAGGTGCAATCATA
1 AATATGCACTCCAGGTGCATTCATA
278774 TAATGTACAC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 48 0.98
35 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (34 bp):
AATATGCACTCCAGGTGCATTCATAAAAAACAGA
Found at i:279307 original size:2 final size:2
Alignment explanation
Indices: 279300--279385 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
279290 TTTGCTAACG
279300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
279342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279384 AT
1 AT
279386 CGTAAAATAT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281501 original size:22 final size:21
Alignment explanation
Indices: 281476--281532 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
281466 AAAAGAATTG
281476 AAAAGATTTTATCTTTTATTTA
1 AAAAGATTTTAT-TTTTATTTA
* *
281498 AAAATTAATTTGATTTTTATTTA
1 AAAA--GATTTTATTTTTATTTA
*
281521 AAACTGATTTTA
1 AAA-AGATTTTA
281533 ATCCTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
22 9 0.33
23 12 0.44
24 6 0.22
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (21 bp):
AAAAGATTTTATTTTTATTTA
Found at i:283242 original size:29 final size:28
Alignment explanation
Indices: 283210--283276 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
283200 AAAAAAATAA
* *
283210 ATTATAAAATTAGGACCTTAATAATAAAT
1 ATTATAAAATAAGG-CCATAATAATAAAT
* *
283239 ATTAAAAAATAAGGCCATGATAATAAAT
1 ATTATAAAATAAGGCCATAATAATAAAT
283267 ATTAATAAAA
1 ATT-ATAAAA
283277 AATTGAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (28 bp):
ATTATAAAATAAGGCCATAATAATAAAT
Found at i:295354 original size:17 final size:18
Alignment explanation
Indices: 295334--295367 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
295324 AAATTAAATT
295334 TGATTTTTAT-TTAAAAC
1 TGATTTTTATCTTAAAAC
295351 TGATTTTTATCTTAAAA
1 TGATTTTTATCTTAAAA
295368 TATTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
TGATTTTTATCTTAAAAC
Done.