Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 281 of 318
Found at i:88967179 original size:11 final size:11
Alignment explanation
Indices: 88967148--88967180 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
88967138 CACTTACCCC
*
88967148 TTTTT-TTTTC
1 TTTTTCTTTTT
88967158 TTTTTCTTTTT
1 TTTTTCTTTTT
88967169 TTTTTCTTTTT
1 TTTTTCTTTTT
88967180 T
1 T
88967181 CCGTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:88971004 original size:12 final size:12
Alignment explanation
Indices: 88970975--88971014 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
88970965 ATTTGCCTAC
88970975 TTATTT-TTTTA
1 TTATTTATTTTA
*
88970986 TCA-TTATTTTA
1 TTATTTATTTTA
88970997 TTATTTATTTTA
1 TTATTTATTTTA
88971009 TTATTT
1 TTATTT
88971015 TCGGCAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 9 0.36
12 14 0.56
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:88971152 original size:25 final size:25
Alignment explanation
Indices: 88971119--88971167 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
88971109 TAGTATGATT
*
88971119 ATTATTGTTATTATTATTACCATTG
1 ATTAATGTTATTATTATTACCATTG
*
88971144 ATTAATGTTATTATTATTATCATT
1 ATTAATGTTATTATTATTACCATT
88971168 ATAGTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (25 bp):
ATTAATGTTATTATTATTACCATTG
Found at i:88971513 original size:33 final size:33
Alignment explanation
Indices: 88971476--88971541 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
88971466 TAAAAACACA
88971476 TAGAATTCAGGTAATAATCAAATAGTGATTATT
1 TAGAATTCAGGTAATAATCAAATAGTGATTATT
88971509 TAGAATTCAGGTAATAATCAAATAGTGATTATT
1 TAGAATTCAGGTAATAATCAAATAGTGATTATT
88971542 CTTGTTTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (33 bp):
TAGAATTCAGGTAATAATCAAATAGTGATTATT
Found at i:88978622 original size:2 final size:2
Alignment explanation
Indices: 88978615--88978645 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
88978605 GCAACAATTA
88978615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88978646 ACCATCCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88985818 original size:2 final size:2
Alignment explanation
Indices: 88985811--88985835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88985801 TTCCACATTC
88985811 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
88985836 AATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88991961 original size:12 final size:12
Alignment explanation
Indices: 88991944--88991968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88991934 ATATTTCATT
88991944 TGTTTTTAGACA
1 TGTTTTTAGACA
88991956 TGTTTTTAGACA
1 TGTTTTTAGACA
88991968 T
1 T
88991969 AGTAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TGTTTTTAGACA
Found at i:88992681 original size:12 final size:11
Alignment explanation
Indices: 88992662--88992701 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
88992652 TGTATAAAAC
88992662 TTATTTTATTA
1 TTATTTTATTA
88992673 TTAATTTTATTA
1 TT-ATTTTATTA
88992685 TTATTTTA--A
1 TTATTTTATTA
88992694 TTATTTTA
1 TTATTTTA
88992702 GAGATATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
11 8 0.29
12 11 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:88992693 original size:17 final size:17
Alignment explanation
Indices: 88992662--88992695 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
88992652 TGTATAAAAC
88992662 TTATTTTATTATTAATT
1 TTATTTTATTATTAATT
88992679 TTATTATTATT-TTAATT
1 TTATT-TTATTATTAATT
88992696 ATTTTAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTATTATTAATT
Found at i:88992864 original size:12 final size:12
Alignment explanation
Indices: 88992834--88992866 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
88992824 TATATTTTTT
88992834 AAAATT-ATATA
1 AAAATTAATATA
88992845 AAAA-TAATATA
1 AAAATTAATATA
88992856 AAAATTAATAT
1 AAAATTAATAT
88992867 GGGCGAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:88993503 original size:46 final size:46
Alignment explanation
Indices: 88993450--88993546 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
88993440 AATTGATACG
88993450 ACTATTGTTGTCAATATAGGACATAAAAGAACATATATGATCAAAA
1 ACTATTGTTGTCAATATAGGACATAAAAGAACATATATGATCAAAA
*
88993496 ACTATTGTTGTCAATATAGGACATAAAAGAATATATATGATCAAAA
1 ACTATTGTTGTCAATATAGGACATAAAAGAACATATATGATCAAAA
*
88993542 CCTAT
1 ACTAT
88993547 ATTGATATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (46 bp):
ACTATTGTTGTCAATATAGGACATAAAAGAACATATATGATCAAAA
Found at i:88997803 original size:15 final size:15
Alignment explanation
Indices: 88997777--88997814 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
88997767 CCTCATGATT
88997777 TTAATG-AAATATGA
1 TTAATGTAAATATGA
88997791 TTAATGTAAATATGA
1 TTAATGTAAATATGA
88997806 TTAATGTAA
1 TTAATGTAA
88997815 CAATTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (15 bp):
TTAATGTAAATATGA
Found at i:88998375 original size:17 final size:17
Alignment explanation
Indices: 88998355--88998407 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
88998345 TAATTTATTT
88998355 TATTTTTTAAAATTTAA
1 TATTTTTTAAAATTTAA
** *
88998372 TATTTCATAAAATTATATG
1 TATTTTTTAAAATT-TA-A
*
88998391 TTTTTTTTAAAATTTAA
1 TATTTTTTAAAATTTAA
88998408 ACATTTACCC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
19 11 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTTTTTAAAATTTAA
Found at i:88998848 original size:25 final size:27
Alignment explanation
Indices: 88998793--88998844 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
88998783 TTATTATAGT
*
88998793 ATTTTTAATATAAATATAGATTTAATT
1 ATTTTTAATATAAATATAGATTTAATA
*
88998820 ATTTTTAA-AT-AAT-TAGATTTTATA
1 ATTTTTAATATAAATATAGATTTAATA
88998844 A
1 A
88998845 ATTTGGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 3 0.13
26 2 0.09
27 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
ATTTTTAATATAAATATAGATTTAATA
Found at i:89000574 original size:16 final size:17
Alignment explanation
Indices: 89000553--89000586 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
89000543 ATTCCATGTT
89000553 GAATTAAATTG-AATGA
1 GAATTAAATTGAAATGA
*
89000569 GAATTATATTGAAATGA
1 GAATTAAATTGAAATGA
89000586 G
1 G
89000587 TTAAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
GAATTAAATTGAAATGA
Found at i:89000960 original size:25 final size:25
Alignment explanation
Indices: 89000897--89000995 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 25
89000887 AGACACACCA
*
89000897 CAGCTCGTATGAGCTTACCGATT-T
1 CAGCTCGTGTGAGCTTACCGATTCT
* * * *
89000921 GCATCTCATGAGAGCTTACCAATTCT
1 -CAGCTCGTGTGAGCTTACCGATTCT
* *
89000947 CAGCTCGTGTGAGCTTATCGATTCA
1 CAGCTCGTGTGAGCTTACCGATTCT
** *
89000972 CAGCTCGTGAAAGCATACCGATTC
1 CAGCTCGTGTGAGCTTACCGATTC
89000996 ATAGCTCTTA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 57 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (25 bp):
CAGCTCGTGTGAGCTTACCGATTCT
Found at i:89000996 original size:25 final size:25
Alignment explanation
Indices: 89000937--89001002 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
89000927 CATGAGAGCT
* * ** *
89000937 TACCAATTCTCAGCTCGTGTGAGCT
1 TACCGATTCACAGCTCGTGAAAGCA
*
89000962 TATCGATTCACAGCTCGTGAAAGCA
1 TACCGATTCACAGCTCGTGAAAGCA
*
89000987 TACCGATTCATAGCTC
1 TACCGATTCACAGCTC
89001003 TTATGAGCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (25 bp):
TACCGATTCACAGCTCGTGAAAGCA
Found at i:89001002 original size:50 final size:50
Alignment explanation
Indices: 89000897--89001010 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 50
89000887 AGACACACCA
** * * *
89000897 CAGCTCGTATGAGCTTACCGATTTGCATCTCATGAGAGCTTACCAATTCT
1 CAGCTCGTATGAGCTTACCGATTCACAGCTCATGAAAGCATACCAATTCT
* * * *
89000947 CAGCTCGTGTGAGCTTATCGATTCACAGCTCGTGAAAGCATACCGATTCAT
1 CAGCTCGTATGAGCTTACCGATTCACAGCTCATGAAAGCATACCAATTC-T
*
89000998 -AGCTCTTATGAGC
1 CAGCTCGTATGAGC
89001011 ATACATATAC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 51 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACCGATTCACAGCTCATGAAAGCATACCAATTCT
Found at i:89007066 original size:168 final size:168
Alignment explanation
Indices: 89006782--89007099 Score: 537
Period size: 168 Copynumber: 1.9 Consensus size: 168
89006772 ACGTGCAAAA
* * *
89006782 AATAAATAAAATATATAGGATGTGACATTGGACACACGACTATGTACCTCCAACTTACACGACTC
1 AATAAATAAAATATATAGGAAGTGACACTGGACACACGACCATGTACCTCCAACTTACACGACTC
* * *
89006847 TAGTTTGTTATACAGTCTAGGACATGACCGTGTGACTTATGTTACGAATTTTACATTTAGGTCCA
66 CAGTTAGTTACACAGTCTAGGACATGACCGTGTGACTTATGTTACGAATTTTACATTTAGGTCCA
*
89006912 CACATCTACAGTCTATTACATAACCGTGTAATTCTTTT
131 CACAACTACAGTCTATTACATAACCGTGTAATTCTTTT
*
89006950 AATAAATAAAATATATGGGAAGTGACACTGGACACACGACCATGTACCTCCAACTTACACGACTC
1 AATAAATAAAATATATAGGAAGTGACACTGGACACACGACCATGTACCTCCAACTTACACGACTC
* *
89007015 CAGTTAGTTACACAGTTTAGGACATGACCGTGTGACTTATGTTAGGAATTTTACATTTAGGTCCA
66 CAGTTAGTTACACAGTCTAGGACATGACCGTGTGACTTATGTTACGAATTTTACATTTAGGTCCA
*
89007080 CACAACTACAGTCTGTTACA
131 CACAACTACAGTCTATTACA
89007100 CAGCTATGTA
Statistics
Matches: 139, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 139 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (168 bp):
AATAAATAAAATATATAGGAAGTGACACTGGACACACGACCATGTACCTCCAACTTACACGACTC
CAGTTAGTTACACAGTCTAGGACATGACCGTGTGACTTATGTTACGAATTTTACATTTAGGTCCA
CACAACTACAGTCTATTACATAACCGTGTAATTCTTTT
Found at i:89008524 original size:39 final size:40
Alignment explanation
Indices: 89008466--89008580 Score: 119
Period size: 39 Copynumber: 2.9 Consensus size: 40
89008456 TTTCTCATTT
* * *
89008466 AAGC-TACTTTCAATAGAATCATTAGGTATGGCTCGATA-
1 AAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGATAG
* *
89008504 AAGCATACTTTTAGTAGAATCAGTAGGTAAGGCTTGATAG
1 AAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGATAG
* * * *
89008544 CA-CATACATTTTAGTGGGATCGGTAGGTATGGCTCGA
1 AAGCATAC-TTTTAGTAGAATCAGTAGGTATGGCTCGA
89008581 AAGCACATAC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 4 0.06
39 34 0.54
40 25 0.40
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (40 bp):
AAGCATACTTTTAGTAGAATCAGTAGGTATGGCTCGATAG
Found at i:89008570 original size:40 final size:39
Alignment explanation
Indices: 89008470--89008590 Score: 111
Period size: 40 Copynumber: 3.1 Consensus size: 39
89008460 TCATTTAAGC
* * * *
89008470 TACTTTCAATAGAATCATTAGGTATGGCTCGATAA--AGCA
1 TACTTTTAGTAGAATCAGTAGGTAAGGCTCGA-AAGCA-CA
* *
89008509 TACTTTTAGTAGAATCAGTAGGTAAGGCTTGATAGCACA
1 TACTTTTAGTAGAATCAGTAGGTAAGGCTCGAAAGCACA
* * * *
89008548 TACATTTTAGTGGGATCGGTAGGTATGGCTCGAAAGCACA
1 TAC-TTTTAGTAGAATCAGTAGGTAAGGCTCGAAAGCACA
89008588 TAC
1 TAC
89008591 GTTTCGATAG
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 32 0.48
40 34 0.51
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (39 bp):
TACTTTTAGTAGAATCAGTAGGTAAGGCTCGAAAGCACA
Found at i:89012485 original size:30 final size:30
Alignment explanation
Indices: 89012419--89012498 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
89012409 AAATTAAGAT
*
89012419 ATATAAAATTATTTAAATAATTATGTTGTA
1 ATATAAAATTATATAAATAATTATGTTGTA
* *
89012449 ATATAAAATTATATAATTATGTTATGATT-TA
1 ATATAAAATTATATAAATA-ATTATG-TTGTA
89012480 A-ATAAAATTACTTATAAAT
1 ATATAAAATTA--TATAAAT
89012499 CCGTGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 26 0.62
31 8 0.19
32 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (30 bp):
ATATAAAATTATATAAATAATTATGTTGTA
Found at i:89026348 original size:20 final size:20
Alignment explanation
Indices: 89026325--89026368 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89026315 GATTTATTTA
89026325 ATATTT-TAATTATTTAAAAT
1 ATATTTATAATT-TTTAAAAT
*
89026345 ATATTTATAATTTTTAATAT
1 ATATTTATAATTTTTAAAAT
89026365 ATAT
1 ATAT
89026369 CATTCAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTATAATTTTTAAAAT
Found at i:89031719 original size:23 final size:23
Alignment explanation
Indices: 89031668--89031719 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
89031658 TTAGATTATT
89031668 AAAT-TTTAAAATAAAATAATAA
1 AAATATTTAAAATAAAATAATAA
* *
89031690 AATTATTTAAAAT-TAATAATAA
1 AAATATTTAAAATAAAATAATAA
89031712 ATAATATT
1 A-AATATT
89031720 GCAGATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATTTAAAATAAAATAATAA
Found at i:89039735 original size:45 final size:45
Alignment explanation
Indices: 89039683--89039769 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
89039673 AATTGCATCC
* * *
89039683 CTATTAAATGGTTGATTTTCAGTATCAGTAATGAATTGCAGTGTT
1 CTATTAAATGGTTGATCTTCAGTATCAGTAACGAAATGCAGTGTT
* *
89039728 CTATTAAATGGTTGGTCTTCAGTATGAGTAACGAAATGCAGT
1 CTATTAAATGGTTGATCTTCAGTATCAGTAACGAAATGCAGT
89039770 TGTCAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (45 bp):
CTATTAAATGGTTGATCTTCAGTATCAGTAACGAAATGCAGTGTT
Found at i:89044844 original size:20 final size:21
Alignment explanation
Indices: 89044796--89044843 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
89044786 AACCATTATC
*
89044796 TTTTTGTAGAAACCTTTCATA
1 TTTTTTTAGAAACCTTTCATA
89044817 TTTTTTTAGAAACCTTTCATA
1 TTTTTTTAGAAACCTTTCATA
89044838 TTTTTT
1 TTTTTT
89044844 ACAATGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTTTTAGAAACCTTTCATA
Found at i:89050637 original size:23 final size:23
Alignment explanation
Indices: 89050611--89050668 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
89050601 TTCATGTGCA
89050611 CAAGTGATAGTGGCACTTCAATG
1 CAAGTGATAGTGGCACTTCAATG
* **
89050634 CAAGTGATAGGGGCACTTCTTTG
1 CAAGTGATAGTGGCACTTCAATG
*
89050657 CAAGTGACAGTG
1 CAAGTGATAGTG
89050669 ACACCTTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (23 bp):
CAAGTGATAGTGGCACTTCAATG
Found at i:89050681 original size:23 final size:23
Alignment explanation
Indices: 89050655--89050705 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
89050645 GGCACTTCTT
*
89050655 TGCAAGTGACAGTGACACCTTGG
1 TGCAAGTGACAATGACACCTTGG
* *
89050678 TGCATGTGACAATGACACTTTGG
1 TGCAAGTGACAATGACACCTTGG
89050701 TGCAA
1 TGCAA
89050706 ATTATTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (23 bp):
TGCAAGTGACAATGACACCTTGG
Found at i:89058147 original size:2 final size:2
Alignment explanation
Indices: 89058142--89058166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89058132 ACATATATTC
89058142 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
89058167 CTCAACCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89058600 original size:24 final size:24
Alignment explanation
Indices: 89058569--89058618 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
89058559 CTATCATCTC
*
89058569 ACTATATCAATAACAATTTCATGA
1 ACTATATCAATAACAATTCCATGA
*
89058593 ACTATATCAATAACCATTCCATGA
1 ACTATATCAATAACAATTCCATGA
89058617 AC
1 AC
89058619 CCATTGGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (24 bp):
ACTATATCAATAACAATTCCATGA
Found at i:89059104 original size:5 final size:5
Alignment explanation
Indices: 89059067--89059102 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
89059057 ATATACTCAA
* *
89059067 AATTT AATTC AATTC AATTC AATTC AATTC ATTTC A
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC A
89059103 TTACCACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (5 bp):
AATTC
Found at i:89063613 original size:35 final size:35
Alignment explanation
Indices: 89063529--89063616 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
89063519 TACACAGTTA
* * * *
89063529 ACCATTCAGCACACCAGATGTTTATAAGAGCTAGT
1 ACCATCCAGCACACCAGATGCTCATAAGAGCCAGT
* * *
89063564 GCCACCCAACACACCAGATGCTCATAAGAGCCAGT
1 ACCATCCAGCACACCAGATGCTCATAAGAGCCAGT
*
89063599 ACCATCCAGTACACCAGA
1 ACCATCCAGCACACCAGA
89063617 AACACTGTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.17
Consensus pattern (35 bp):
ACCATCCAGCACACCAGATGCTCATAAGAGCCAGT
Found at i:89065901 original size:51 final size:50
Alignment explanation
Indices: 89065841--89065944 Score: 172
Period size: 51 Copynumber: 2.1 Consensus size: 50
89065831 TTCTGGCACT
*
89065841 CAAGCAACATGCTTCGGAATTAGGCCTTATTTCTGTTGAAACTAAAAAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACT-AAAAAGG
* *
89065892 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGGAACTAAGAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
89065942 CAA
1 CAA
89065945 ATTAAGGACT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
50 9 0.18
51 41 0.82
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (50 bp):
CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
Found at i:89069724 original size:15 final size:16
Alignment explanation
Indices: 89069704--89069736 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
89069694 TATATATTTT
89069704 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
89069719 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
89069736 T
1 T
89069737 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:89069822 original size:22 final size:22
Alignment explanation
Indices: 89069783--89069841 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
89069773 GTTTTAAGAA
*
89069783 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
89069804 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
89069826 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
89069842 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:89069858 original size:26 final size:24
Alignment explanation
Indices: 89069812--89069859 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
89069802 ATTTGTTTTA
*
89069812 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
89069836 ATATTTGATTTATTATATTTTTAA
1 ATATTT-ATTT-TTATATTTTTAA
89069860 TTTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:89070679 original size:17 final size:19
Alignment explanation
Indices: 89070649--89070687 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
89070639 ACATTACTCA
89070649 CAACTTAAAAAATTC-ACC
1 CAACTTAAAAAATTCAACC
*
89070667 CAAC-TAAATAATTCAACC
1 CAACTTAAAAAATTCAACC
89070685 CAA
1 CAA
89070688 AATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (19 bp):
CAACTTAAAAAATTCAACC
Found at i:89073351 original size:20 final size:22
Alignment explanation
Indices: 89073326--89073366 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
89073316 AATATAAAAA
89073326 AATTA-TT-TAATTTTTATAAC
1 AATTATTTGTAATTTTTATAAC
89073346 AATTATTTGTAATTTTTATAA
1 AATTATTTGTAATTTTTATAA
89073367 TACATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTATTTGTAATTTTTATAAC
Found at i:89073393 original size:17 final size:18
Alignment explanation
Indices: 89073360--89073397 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
89073350 ATTTGTAATT
89073360 TTTATAATACATTTTATA
1 TTTATAATACATTTTATA
*
89073378 TTTATAATA-TTTTTATA
1 TTTATAATACATTTTATA
89073395 TTT
1 TTT
89073398 TAAAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATACATTTTATA
Found at i:89073399 original size:18 final size:19
Alignment explanation
Indices: 89073359--89073399 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
89073349 TATTTGTAAT
89073359 TTTTATAATACATTTTATA
1 TTTTATAATACATTTTATA
*
89073378 -TTTATAATA-TTTTTATA
1 TTTTATAATACATTTTATA
89073395 TTTTA
1 TTTTA
89073400 AAAAACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATACATTTTATA
Found at i:89075718 original size:7 final size:7
Alignment explanation
Indices: 89075706--89075736 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
89075696 TAAATAAAAT
89075706 AATTATA
1 AATTATA
*
89075713 AATTATT
1 AATTATA
89075720 AATTATA
1 AATTATA
89075727 AATTATA
1 AATTATA
89075734 AAT
1 AAT
89075737 CTAACGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AATTATA
Found at i:89077459 original size:26 final size:28
Alignment explanation
Indices: 89077417--89077474 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
89077407 TGACAAATCT
*
89077417 AATATTTTTTAATATG-TTTATAAAGGA
1 AATATTTTTTAATATGTTTTATAAAGAA
*
89077444 AATATTTTTTGA-ATGTTTTATAAAGAA
1 AATATTTTTTAATATGTTTTATAAAGAA
89077471 AATA
1 AATA
89077475 ATTACTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (28 bp):
AATATTTTTTAATATGTTTTATAAAGAA
Found at i:89078089 original size:35 final size:33
Alignment explanation
Indices: 89078039--89078115 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 33
89078029 AATGGTAAGA
* *
89078039 ATATTTCTTATTATATTTTAATGTTGTATAATTTT-T
1 ATATTT-TTATTATATTTAAAT-TT-AAT-ATTTTGT
*
89078075 ATATTTTTGTTATATTTAAATTTAATATTTTGT
1 ATATTTTTATTATATTTAAATTTAATATTTTGT
89078108 ATATTTTT
1 ATATTTTT
89078116 TCCTTGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.14
33 11 0.30
34 2 0.05
35 13 0.35
36 6 0.16
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (33 bp):
ATATTTTTATTATATTTAAATTTAATATTTTGT
Found at i:89080063 original size:23 final size:23
Alignment explanation
Indices: 89080033--89080078 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
89080023 ACCGTCGACC
* *
89080033 ACCCTAATGTGGGCACATTCTAA
1 ACCCTAATGTAGACACATTCTAA
89080056 ACCCTAATGTAGACACATTCTAA
1 ACCCTAATGTAGACACATTCTAA
89080079 CATATGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (23 bp):
ACCCTAATGTAGACACATTCTAA
Found at i:89089873 original size:3 final size:3
Alignment explanation
Indices: 89089867--89089896 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
89089857 ACGGGGGTTT
89089867 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
89089897 TAATGGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:89098661 original size:21 final size:19
Alignment explanation
Indices: 89098610--89098671 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
89098600 ATAATAACAT
89098610 AAATAAAATAATATTATATA
1 AAATAAAATAA-ATTATATA
*
89098630 AAA-AGATATAAATTAATGATA
1 AAATA-AAATAAATT-AT-ATA
89098651 AAATAAAATAAATGTATATA
1 AAATAAAATAAAT-TATATA
89098671 A
1 A
89098672 CGTTTTTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
21 15 0.43
22 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATAAAATAAATTATATA
Found at i:89100824 original size:2 final size:2
Alignment explanation
Indices: 89100817--89100851 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
89100807 TTTAAGAATG
*
89100817 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89100852 CTTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:89101744 original size:132 final size:131
Alignment explanation
Indices: 89101565--89102073 Score: 509
Period size: 132 Copynumber: 3.8 Consensus size: 131
89101555 AATGAAGGTG
** * * * * * *
89101565 ATATTCGATACTTGGTAATTCGAGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTCGC
1 ATATTCGATGTTTGGCAATTCG-GGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGT
* ** *
89101630 TCAAAGTAATCGAAGGTCCCTTCAAAATTTCACTCATGTCTTCTAAAAAACCCTTTAAAACAAAG
65 TCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTTCTAAAAAACCCTTTAAAACAAA-
89101695 GCA
129 GCA
* * * **
89101698 ATACTCGGTGTTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGTT
1 ATATTCGATGTTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTT
* * *** * *
89101763 CAAAATAATCGAATATTCCTTTATGTTTTCACTCATGTTTTTTTTAGAAAACCCTTTAAAACAAA
66 CAAAATAATCGAATATCCCTTCAAAATTTCACTCATG--TTTTCTAAAAAACCCTTTAAAAC-AA
*
89101828 AGCG
128 AGCA
* * * * ** * *
89101832 ATGTTCGATGTTCGGCAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTGTT
1 ATATTCGATGTTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTT
** * ** * *
89101897 CAAAACGATCGAAAATCCCTTCGGAATTTCACTCACGTTTTCT-AAAAACTCTTTAAAACGAAAG
66 CAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTTCTAAAAAACCCTTTAAAAC-AAAG
*
89101961 AA
130 CA
* *
89101963 ATATTCGATGTTTGGCAATTCGGAGAAT-AGTGTCCTATCGTGCTGGGTTGCAATTTCCCGTTTG
1 ATATTCGATGTTTGGCAATTCGG-GAATCA-TGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTG
* * * *
89102027 TTCAAAATAATCGAATATCTCTTCGAAATTTCACTCGTATTTTCTAA
64 TTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTTCTAA
89102074 GGTGAGGCAA
Statistics
Matches: 300, Mismatches: 70, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
131 38 0.13
132 139 0.46
133 17 0.06
134 103 0.34
135 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (131 bp):
ATATTCGATGTTTGGCAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTT
CAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTTCTAAAAAACCCTTTAAAACAAAGC
A
Found at i:89114715 original size:16 final size:16
Alignment explanation
Indices: 89114694--89114724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89114684 AACATTATGA
*
89114694 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
89114710 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
89114725 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:89119486 original size:16 final size:16
Alignment explanation
Indices: 89119465--89119495 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89119455 AACATTATGA
*
89119465 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
89119481 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
89119496 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:89122493 original size:2 final size:2
Alignment explanation
Indices: 89122486--89122518 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
89122476 GTACATGTAA
*
89122486 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89122519 ACTAACATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:89133158 original size:39 final size:39
Alignment explanation
Indices: 89133103--89133337 Score: 389
Period size: 39 Copynumber: 6.0 Consensus size: 39
89133093 CAAGACACTA
89133103 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * *
89133142 GAAATGTATCCAGGCTAAAGTCCCGCAGGCTTCATGTTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
*
89133181 AAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * *
89133220 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCATGTTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
*
89133259 GAAATGTATCCGAGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
*
89133298 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
89133337 G
1 G
89133338 TAATATAATT
Statistics
Matches: 179, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 179 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
Found at i:89135034 original size:35 final size:35
Alignment explanation
Indices: 89134990--89135156 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
89134980 TCCTCATTGA
** *
89134990 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
89135025 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
89135065 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
89135100 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
89135135 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
89135157 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:89135073 original size:75 final size:73
Alignment explanation
Indices: 89134985--89135156 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
89134975 GGTTTTCCTC
** * * **
89134985 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
89135049 TCAGTATGG
65 TCAGTATGG
*
89135058 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
89135123 CTCAGTATGG
64 CTCAGTATGG
89135133 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
89135157 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:89139517 original size:35 final size:35
Alignment explanation
Indices: 89139450--89139617 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
89139440 TCCTCATTGA
*** *
89139450 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
89139486 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
89139526 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
89139561 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
89139596 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
89139618 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:89139576 original size:75 final size:73
Alignment explanation
Indices: 89139445--89139617 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
89139435 GGTTTTCCTC
*** * * **
89139445 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
89139510 TCAGTATGG
65 TCAGTATGG
*
89139519 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
89139583 ACTCAGTATGG
63 ACTCAGTATGG
89139594 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
89139618 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:89146992 original size:35 final size:35
Alignment explanation
Indices: 89146948--89147114 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
89146938 TCCTCATTGA
** *
89146948 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
89146983 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
89147023 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
89147058 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
89147093 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
89147115 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:89147031 original size:75 final size:73
Alignment explanation
Indices: 89146943--89147114 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
89146933 GGTTTTCCTC
** * * **
89146943 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
89147007 TCAGTATGG
65 TCAGTATGG
*
89147016 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
89147081 CTCAGTATGG
64 CTCAGTATGG
89147091 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
89147115 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:89153973 original size:21 final size:21
Alignment explanation
Indices: 89153949--89154003 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
89153939 TAATTTAATA
89153949 ATAATTAAATTAAATTTTT-TT
1 ATAATT-AATTAAATTTTTATT
*
89153970 ATAATTAATTAGATTTTTATT
1 ATAATTAATTAAATTTTTATT
**
89153991 ATTTTTAATTAAA
1 ATAATTAATTAAA
89154004 AATTATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATAATTAATTAAATTTTTATT
Found at i:89155131 original size:33 final size:33
Alignment explanation
Indices: 89155094--89155165 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
89155084 TGAACCAATT
* *
89155094 AAAAAATCAATTGAATTGGCAGTTGAATCGACCA
1 AAAAAAT-AATTGAACTGGCAGTTGAACCGACCA
* * *
89155128 AAAAAATGATTGAACTGGCGGTTGAACCGACTA
1 AAAAAATAATTGAACTGGCAGTTGAACCGACCA
89155161 AAAAA
1 AAAAA
89155166 TGATTAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (33 bp):
AAAAAATAATTGAACTGGCAGTTGAACCGACCA
Found at i:89156634 original size:2 final size:2
Alignment explanation
Indices: 89156629--89156657 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
89156619 TTAGTTTATC
89156629 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
89156658 TAGTGTGAGG
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:89157566 original size:18 final size:18
Alignment explanation
Indices: 89157529--89157566 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
89157519 ATTCGAGTCA
**
89157529 AAAAATATAATTTACTTG
1 AAAAATATAATTTAAATG
89157547 AAAAATATAATTTAAATG
1 AAAAATATAATTTAAATG
89157565 AA
1 AA
89157567 TAACATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAAATATAATTTAAATG
Found at i:89160124 original size:12 final size:12
Alignment explanation
Indices: 89160102--89160155 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
89160092 CCATACAGAT
*
89160102 AATATAAAATTA
1 AATAAAAAATTA
* *
89160114 TATGAAAAATTA
1 AATAAAAAATTA
89160126 AATAAAAAATTA
1 AATAAAAAATTA
89160138 AATTAAATTAAATTA
1 AA-TAAA--AAATTA
89160153 AAT
1 AAT
89160156 TAAATTAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
12 21 0.62
13 4 0.12
14 1 0.03
15 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAAAAAATTA
Found at i:89160140 original size:5 final size:5
Alignment explanation
Indices: 89160120--89160163 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
89160110 ATTATATGAA
89160120 AAATT AAA-T AAA-- AAATT AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AA
89160164 CCATGTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 30 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AAATT
Found at i:89165886 original size:21 final size:20
Alignment explanation
Indices: 89165862--89165901 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89165852 TTTTTATTGG
89165862 ATGTTTGGTTGGTTATGAAAT
1 ATGTTTGGTT-GTTATGAAAT
* *
89165883 ATGTTTTGTTTTTATGAAA
1 ATGTTTGGTTGTTATGAAA
89165902 GAGAATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (20 bp):
ATGTTTGGTTGTTATGAAAT
Found at i:89167851 original size:12 final size:12
Alignment explanation
Indices: 89167834--89167866 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
89167824 CGTCCCGTCG
89167834 ATATTAATTTTT
1 ATATTAATTTTT
89167846 ATATT-ATTTTT
1 ATATTAATTTTT
89167857 ATA-TAATTTT
1 ATATTAATTTT
89167867 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:89169377 original size:32 final size:32
Alignment explanation
Indices: 89169341--89169404 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
89169331 GATCATGCAA
*
89169341 AATCTTATAAATATGTCAGTATGAGATCAAAT
1 AATCTTATAAATATGTCAATATGAGATCAAAT
89169373 AATCTTATAAATATGTCAATATGAGATCAAAT
1 AATCTTATAAATATGTCAATATGAGATCAAAT
89169405 TTAACTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (32 bp):
AATCTTATAAATATGTCAATATGAGATCAAAT
Found at i:89173327 original size:14 final size:15
Alignment explanation
Indices: 89173308--89173344 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
89173298 ATAATTTAAA
89173308 ATATAATAATAAT-G
1 ATATAATAATAATAG
89173322 ATATAAT-ATAATAG
1 ATATAATAATAATAG
*
89173336 TTATAATAA
1 ATATAATAA
89173345 AAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATAATAATAG
Found at i:89174290 original size:6 final size:6
Alignment explanation
Indices: 89174281--89174312 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
89174271 CTTGACTATG
89174281 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
89174313 CCTACGGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (6 bp):
ACTGTT
Found at i:89178926 original size:108 final size:111
Alignment explanation
Indices: 89178801--89179030 Score: 378
Period size: 108 Copynumber: 2.1 Consensus size: 111
89178791 TGAAGTCTTG
89178801 AAAATGTTTAATGAGATTTTCAATAAAATGTCTACAAAATAACTTAAAAGTAAACATATAAAATT
1 AAAATGTTTAATGAGATTTTCAATAAAATGTCTACAAAATAACTTAAAAGTAAACATATAAAATT
*
89178866 TATCTT-AA-ATA-TTATACTTTAATAAATTAAAACTAATAATATC
66 TATCTTAAATATAGTTACACTTTAATAAATTAAAACTAATAATATC
* * * *
89178909 AAAATGTTTAATGAGATTTTCAATAAAATTTCTGCAAAATGACTTAAAAGTAACCATATAAAATT
1 AAAATGTTTAATGAGATTTTCAATAAAATGTCTACAAAATAACTTAAAAGTAAACATATAAAATT
*
89178974 TATCTTAAATATAGTTACACTTTTATAAATTAAAACTAATAATATC
66 TATCTTAAATATAGTTACACTTTAATAAATTAAAACTAATAATATC
89179020 AAAAT-TTTAAT
1 AAAATGTTTAAT
89179031 AAATCTAATT
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
108 67 0.59
109 2 0.02
110 9 0.08
111 35 0.31
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (111 bp):
AAAATGTTTAATGAGATTTTCAATAAAATGTCTACAAAATAACTTAAAAGTAAACATATAAAATT
TATCTTAAATATAGTTACACTTTAATAAATTAAAACTAATAATATC
Found at i:89179721 original size:40 final size:40
Alignment explanation
Indices: 89179670--89179756 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 40
89179660 GCAAAAATTG
* *
89179670 TAAAACACAGAATAATAGCGGCT-TTTCA-CAAAAAACGCCGC
1 TAAAA-ACAGAACAATAGCGG-TGTTTCACCAAAAAA-GACGC
*
89179711 TAAAAACAGAACAATAGCGGTGTTTTACCAAAAAAGACGC
1 TAAAAACAGAACAATAGCGGTGTTTCACCAAAAAAGACGC
89179751 TAAAAA
1 TAAAAA
89179757 ATGGAGCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 1 0.02
40 28 0.68
41 12 0.29
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (40 bp):
TAAAAACAGAACAATAGCGGTGTTTCACCAAAAAAGACGC
Found at i:89179743 original size:41 final size:40
Alignment explanation
Indices: 89179670--89179798 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
89179660 GCAAAAATTG
* *
89179670 TAAAACACAGAATAATAGCGGCTTTT-CACAAAAAACGCCGC
1 TAAAA-ACAGAACAATAGCGGGTTTTAC-CAAAAAACGCCGC
*
89179711 TAAAAACAGAACAATAGCGGTGTTTTACCAAAAAA-GACGC
1 TAAAAACAGAACAATAGCGG-GTTTTACCAAAAAACGCCGC
* * *
89179751 TAAAAA-ATGGAGCAATAGCGGCGTTTTACC-GAAAGCGCCGC
1 TAAAAACA--GAACAATAGCGG-GTTTTACCAAAAAACGCCGC
89179792 TAAAAAC
1 TAAAAAC
89179799 TGAGCATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
39 1 0.01
40 27 0.36
41 45 0.61
42 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (40 bp):
TAAAAACAGAACAATAGCGGGTTTTACCAAAAAACGCCGC
Found at i:89179813 original size:40 final size:41
Alignment explanation
Indices: 89179683--89179877 Score: 161
Period size: 41 Copynumber: 4.8 Consensus size: 41
89179673 AACACAGAAT
** *
89179683 AATAGCGGC-TTTTCACAAAAAACGCCGCTAAAAAC-AGAAC
1 AATAGCGGCGTTTT-ACCGAAAACGCCGCTAAAAACTAGAGC
* * * * * *
89179723 AATAGCGGTGTTTTACCAAAAAAGACGCTAAAAAATGGAGC
1 AATAGCGGCGTTTTACCGAAAACGCCGCTAAAAACTAGAGC
*
89179764 AATAGCGGCGTTTTACCGAAAGCGCCGCTAAAAACT-GAGC
1 AATAGCGGCGTTTTACCGAAAACGCCGCTAAAAACTAGAGC
* * *
89179804 ATTAACGGCGCTTTT--GGTAAAACGCCGCTAAAAACTAGAGC
1 AATAGCGGCG-TTTTACCG-AAAACGCCGCTAAAAACTAGAGC
* *
89179845 ATTAGCGGCGCTTT--CGATAAAACGCCGCTAAAA
1 AATAGCGGCGTTTTACCG--AAAACGCCGCTAAAA
89179878 TTCATATAAC
Statistics
Matches: 129, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 58 0.45
41 70 0.54
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (41 bp):
AATAGCGGCGTTTTACCGAAAACGCCGCTAAAAACTAGAGC
Found at i:89179973 original size:16 final size:15
Alignment explanation
Indices: 89179954--89180011 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
89179944 ACTAAACCCC
89179954 TAAACCCTAAAAACCA
1 TAAACCCT-AAAACCA
* *
89179970 TAAACACT-AAACTA
1 TAAACCCTAAAACCA
* *
89179984 TAACCCCTAAAACCC
1 TAAACCCTAAAACCA
89179999 TAAACCCTCAAAA
1 TAAACCCT-AAAA
89180012 ACATCATATG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
14 11 0.33
15 11 0.33
16 11 0.33
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAACCCTAAAACCA
Found at i:89180128 original size:7 final size:7
Alignment explanation
Indices: 89180117--89180180 Score: 65
Period size: 7 Copynumber: 9.0 Consensus size: 7
89180107 TTTATTTTTG
*
89180117 GGTTTAG
1 GGTTTAA
89180124 GGTTTAA
1 GGTTTAA
**
89180131 TATTTAA
1 GGTTTAA
89180138 GGTTTAA
1 GGTTTAA
* *
89180145 GGTCTAT
1 GGTTTAA
89180152 GGTTTAA
1 GGTTTAA
*
89180159 GGTTTTAT
1 GG-TTTAA
89180167 GGTTTAA
1 GGTTTAA
89180174 GGTTTAA
1 GGTTTAA
89180181 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:89180169 original size:15 final size:15
Alignment explanation
Indices: 89180133--89180183 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
89180123 GGGTTTAATA
*
89180133 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
*
89180147 TCTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
89180162 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
89180177 TTAATGG
1 TTTATGG
89180184 CCATGGGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:89180179 original size:14 final size:14
Alignment explanation
Indices: 89180117--89180179 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
89180107 TTTATTTTTG
*
89180117 GGTTTAGGGTTTAA
1 GGTTTATGGTTTAA
** *
89180131 TATTTAAGGTTTAA
1 GGTTTATGGTTTAA
*
89180145 GGTCTATGGTTTAA
1 GGTTTATGGTTTAA
89180159 GGTTTTATGGTTTAA
1 GG-TTTATGGTTTAA
89180174 GGTTTA
1 GGTTTA
89180180 ATGGCCATGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 27 0.68
15 13 0.32
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.48
Consensus pattern (14 bp):
GGTTTATGGTTTAA
Found at i:89181242 original size:66 final size:66
Alignment explanation
Indices: 89181172--89181301 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
89181162 TAACCCCTTA
* * * *
89181172 AATCAACAACTTTTTAAACCCCAAACCTTAAATCTCTAATCATAAACCCCTAAAACTATAAACAC
1 AATCAACAACTCTTTAAACACCAAACCCTAAATCTCAAATCATAAACCCCTAAAACTATAAACAC
89181237 T
66 T
* * * * * *
89181238 AATCAATAACTCTTTAAACACTAGACCCTAAATTTCAAATCATAAACCCTTAAAACTCTAAACA
1 AATCAACAACTCTTTAAACACCAAACCCTAAATCTCAAATCATAAACCCCTAAAACTATAAACA
89181302 ATAAACCTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (66 bp):
AATCAACAACTCTTTAAACACCAAACCCTAAATCTCAAATCATAAACCCCTAAAACTATAAACAC
T
Found at i:89181356 original size:22 final size:22
Alignment explanation
Indices: 89181262--89181356 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
89181252 TAAACACTAG
*
89181262 ACCC-TAAATTTCAAATCATAA
1 ACCCTTAAATCTCAAATCATAA
*
89181283 ACCCTTAAAACTCTAAA-CAATAA
1 ACCCTTAAATCTC-AAATC-ATAA
* * *
89181306 A-CCTT-AATCCCAACACCCTAA
1 ACCCTTAAATCTCAA-ATCATAA
* *
89181327 ACTC-TAAATCTCAAATCGTAA
1 ACCCTTAAATCTCAAATCATAA
89181348 ACCCTTAAA
1 ACCCTTAAA
89181357 ACTCTAACCC
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
20 2 0.04
21 22 0.39
22 24 0.43
23 8 0.14
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.24
Consensus pattern (22 bp):
ACCCTTAAATCTCAAATCATAA
Found at i:89181670 original size:7 final size:7
Alignment explanation
Indices: 89181660--89181751 Score: 80
Period size: 7 Copynumber: 12.7 Consensus size: 7
89181650 ACATTAAACC
89181660 AAAATAA
1 AAAATAA
89181667 AAAAT--
1 AAAATAA
*
89181672 AAACTCAA
1 AAAAT-AA
89181680 AAAATAA
1 AAAATAA
89181687 AAAATAA
1 AAAATAA
89181694 AAAATAA
1 AAAATAA
*
89181701 AAATTTAA
1 AAA-ATAA
*
89181709 AAATTAA
1 AAAATAA
89181716 AAAATTTAA
1 AAAA--TAA
* *
89181725 AAATTTA
1 AAAATAA
89181732 AAAATAA
1 AAAATAA
89181739 AAAACTAA
1 AAAA-TAA
89181747 AAAAT
1 AAAAT
89181752 TTAAAATTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.06
7 43 0.61
8 17 0.24
9 6 0.09
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATAA
Found at i:89181696 original size:8 final size:8
Alignment explanation
Indices: 89181678--89181762 Score: 81
Period size: 8 Copynumber: 11.2 Consensus size: 8
89181668 AAATAAACTC
89181678 AAAAAA-T
1 AAAAAATT
89181685 AAAAAA-T
1 AAAAAATT
89181692 AAAAAA-T
1 AAAAAATT
89181699 -AAAAATT
1 AAAAAATT
*
89181706 TAAAAATT
1 AAAAAATT
89181714 AAAAAATT
1 AAAAAATT
*
89181722 TAAAAATT
1 AAAAAATT
*
89181730 TAAAAA-T
1 AAAAAATT
*
89181737 AAAAAACT
1 AAAAAATT
89181745 AAAAAATT
1 AAAAAATT
* *
89181753 TAAAATTT
1 AAAAAATT
89181761 AA
1 AA
89181763 TATTTTAGTC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.07
7 21 0.31
8 42 0.62
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAAATT
Found at i:89183194 original size:16 final size:16
Alignment explanation
Indices: 89183145--89183194 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
89183135 ATAACCATGG
89183145 TTCATATAAGGATCCT
1 TTCATATAAGGATCCT
* **
89183161 TTCAT-TCA--ATTGT
1 TTCATATAAGGATCCT
89183174 TTCATATAAGGATCCT
1 TTCATATAAGGATCCT
89183190 TTCAT
1 TTCAT
89183195 TTCCATGTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 2 0.08
16 13 0.52
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (16 bp):
TTCATATAAGGATCCT
Found at i:89183203 original size:29 final size:28
Alignment explanation
Indices: 89183139--89183203 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
89183129 CTTCATATAA
*
89183139 CCATGGTTCATATAAGGATCCTTTCATT
1 CCATGTTTCATATAAGGATCCTTTCATT
*
89183167 CAATTGTTTCATATAAGGATCCTTTCATTT
1 CCA-TGTTTCATATAAGGATCCTTTCA-TT
89183197 CCATGTT
1 CCATGTT
89183204 GATAACCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 26 0.81
30 4 0.12
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (28 bp):
CCATGTTTCATATAAGGATCCTTTCATT
Found at i:89185677 original size:25 final size:24
Alignment explanation
Indices: 89185608--89185689 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 24
89185598 TGGTGGTTTA
*
89185608 TTATTTTGATTCTATATTTATA-T
1 TTATTTTGATTCTATATTTTTATT
* * * *
89185631 TTAATCTAATT-TTTATTATTTATT
1 TTATTTTGATTCTATATT-TTTATT
89185655 TTAGTTTTGATTCTATATTTTTATT
1 TTA-TTTTGATTCTATATTTTTATT
*
89185680 TTAATTTGAT
1 TTATTTTGAT
89185690 AATGAATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
22 5 0.11
23 11 0.24
24 10 0.22
25 14 0.31
26 5 0.11
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.66
Consensus pattern (24 bp):
TTATTTTGATTCTATATTTTTATT
Found at i:89185876 original size:43 final size:43
Alignment explanation
Indices: 89185815--89186051 Score: 350
Period size: 43 Copynumber: 5.5 Consensus size: 43
89185805 ATTTAAATTT
89185815 CATGACCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
*
89185858 CATGATCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
* * *
89185901 CATGATCTTTAACGGCGTTTGTGGGAGAGAAGTGCCGCTAAAGGC
1 CATGACCTTTAGCGGCGTTTGT-GGAGA-AAGCGCCGCTAAAGGC
* *
89185946 CATGACCTTTAGCGGCGTTTATGGAGAAAGCGCCGCTAAAGGT
1 CATGACCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
* * *
89185989 CATGACTTTTAGCGGCGTTTATGG-GAAAAGCGCCGCTAAAGGT
1 CATGACCTTTAGCGGCGTTTGTGGAG-AAAGCGCCGCTAAAGGC
*
89186032 CATGACCTTTAGCGGTGTTT
1 CATGACCTTTAGCGGCGTTT
89186052 TTTCAAATAA
Statistics
Matches: 180, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
42 1 0.01
43 135 0.75
44 10 0.06
45 34 0.19
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGC
Found at i:89185962 original size:88 final size:86
Alignment explanation
Indices: 89185815--89186051 Score: 352
Period size: 88 Copynumber: 2.7 Consensus size: 86
89185805 ATTTAAATTT
* *
89185815 CATGACCTTTAGCGGCGTTTGT-GGAGAAAGCGCCGCTAAAGGCCATGATCTTTAGCGGCGTTTG
1 CATGA-CTTTAGCGGCGTTTGTGGGAGAAAGCGCCGCTAAAGGCCATGACCTTTAGCGGCGTTTA
89185879 TGGAGAAAGCGCCGCTAAAGGC
65 TGGAGAAAGCGCCGCTAAAGGC
* *
89185901 CATGATCTTTAACGGCGTTTGTGGGAGAGAAGTGCCGCTAAAGGCCATGACCTTTAGCGGCGTTT
1 CATGA-CTTTAGCGGCGTTTGTGGGAGA-AAGCGCCGCTAAAGGCCATGACCTTTAGCGGCGTTT
*
89185966 ATGGAGAAAGCGCCGCTAAAGGT
64 ATGGAGAAAGCGCCGCTAAAGGC
* * *
89185989 CATGACTTTTAGCGGCGTTTATGGGA-AAAGCGCCGCTAAAGGTCATGACCTTTAGCGGTGTTT
1 CATGAC-TTTAGCGGCGTTTGTGGGAGAAAGCGCCGCTAAAGGCCATGACCTTTAGCGGCGTTT
89186052 TTTCAAATAA
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
86 53 0.39
87 7 0.05
88 77 0.56
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (86 bp):
CATGACTTTAGCGGCGTTTGTGGGAGAAAGCGCCGCTAAAGGCCATGACCTTTAGCGGCGTTTAT
GGAGAAAGCGCCGCTAAAGGC
Found at i:89190342 original size:59 final size:57
Alignment explanation
Indices: 89190225--89190360 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 57
89190215 TTAATTCATA
* * *
89190225 TAATAATTATTTTATTAAGAATGTTATTAAATTATATAATATTTTATTAAATTGTATT
1 TAATAATTATTTTATTAAAAATG-TATTAAATTATATAATATTTTATTAAAATATATT
* **
89190283 TAATAATTATTATATTAAAAATG-ATTAAATTATTTATTTTTATTTTATTAAAATATATT
1 TAATAATTATTTTATTAAAAATGTATTAAATTA--TA-TAATATTTTATTAAAATATATT
*
89190342 TAATAATAATTTTATTAAA
1 TAATAATTATTTTATTAAA
89190361 TTTTAATAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
56 9 0.13
58 23 0.34
59 35 0.52
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (57 bp):
TAATAATTATTTTATTAAAAATGTATTAAATTATATAATATTTTATTAAAATATATT
Found at i:89191249 original size:14 final size:15
Alignment explanation
Indices: 89191225--89191253 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
89191215 TAAATTATTT
89191225 ATTATTTTTTAATAA
1 ATTATTTTTTAATAA
89191240 ATTA-TTTTTAATAA
1 ATTATTTTTTAATAA
89191254 TAATCTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTTTTTAATAA
Found at i:89191456 original size:16 final size:16
Alignment explanation
Indices: 89191435--89191486 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
89191425 TGAATTACTT
*
89191435 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
89191451 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
89191467 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
89191483 ATTA
1 ATTA
89191487 TAGTGAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:89196487 original size:19 final size:20
Alignment explanation
Indices: 89196463--89196513 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
89196453 ATAAATTTTG
89196463 GAATTTTTATAAA-TAGTTT
1 GAATTTTTATAAATTAGTTT
* *
89196482 GAA-TTTTAAAAATTATTTT
1 GAATTTTTATAAATTAGTTT
89196501 GAATCTTTTATAA
1 GAAT-TTTTATAA
89196514 TTTTTTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
21 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (20 bp):
GAATTTTTATAAATTAGTTT
Found at i:89196519 original size:19 final size:18
Alignment explanation
Indices: 89196452--89196519 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
89196442 TTAAAAAATA
* *
89196452 TATAAATTTTGGAATTTT
1 TATAATTTTTTGAATTTT
**
89196470 TATAAATAGTTTGAATTTT
1 TAT-AATTTTTTGAATTTT
* *
89196489 AAAAATTATTTTGAATCTTT
1 TATAATT-TTTTGAAT-TTT
89196509 TATAATTTTTT
1 TATAATTTTTT
89196520 TAGAGAGATC
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
18 6 0.16
19 23 0.62
20 8 0.22
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (18 bp):
TATAATTTTTTGAATTTT
Found at i:89201012 original size:12 final size:12
Alignment explanation
Indices: 89200995--89201020 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
89200985 AGGTGAAATT
89200995 ATCTTTTACTAC
1 ATCTTTTACTAC
89201007 ATCTTTTACTAC
1 ATCTTTTACTAC
89201019 AT
1 AT
89201021 GTTTCTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (12 bp):
ATCTTTTACTAC
Found at i:89209097 original size:63 final size:63
Alignment explanation
Indices: 89209017--89209163 Score: 179
Period size: 63 Copynumber: 2.3 Consensus size: 63
89209007 TTACATTTGG
* * * * * * **
89209017 ACCACAACACGCGCAATCATTCAT-TGCACCAACATAGTCATCACTATTTTATTTTACTTAAGC
1 ACCACAACATGCACAATCATTC-TCTACACCAACACAGTCATCACCAATTTATTTTACACAAGC
*
89209080 ACCACGACATGCACAATCATTCTCTACACCAACACAGTCATCACCAATTTATTTTACACAAGC
1 ACCACAACATGCACAATCATTCTCTACACCAACACAGTCATCACCAATTTATTTTACACAAGC
* *
89209143 ACCACAACATGCGCAGTCATT
1 ACCACAACATGCACAATCATT
89209164 TCCTGCATCG
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 1 0.01
63 70 0.99
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.26
Consensus pattern (63 bp):
ACCACAACATGCACAATCATTCTCTACACCAACACAGTCATCACCAATTTATTTTACACAAGC
Found at i:89210139 original size:20 final size:20
Alignment explanation
Indices: 89210100--89210139 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
89210090 TTATTATAGC
*
89210100 TTTTTTTATAATTTTAGTTA
1 TTTTTTTATAATTTAAGTTA
89210120 TTTTTTTAT-ATTTAATGTTA
1 TTTTTTTATAATTTAA-GTTA
89210140 AAAAAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTTTATAATTTAAGTTA
Found at i:89210442 original size:29 final size:30
Alignment explanation
Indices: 89210391--89210463 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
89210381 ATGAAATTAG
* * * *
89210391 AATAATTTAGTGATTAAATTGTAACTTT-T
1 AATAATTGAGTGATCAAAATGTAAATTTAT
*
89210420 TATAATTGAGTGATCAAAATGTAAATTTACT
1 AATAATTGAGTGATCAAAATGTAAATTTA-T
89210451 AATAATTGAGTGA
1 AATAATTGAGTGA
89210464 CTATAAGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 23 0.64
31 13 0.36
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (30 bp):
AATAATTGAGTGATCAAAATGTAAATTTAT
Found at i:89211648 original size:16 final size:16
Alignment explanation
Indices: 89211627--89211657 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89211617 AACATTATGA
*
89211627 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
89211643 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
89211658 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:89214474 original size:21 final size:21
Alignment explanation
Indices: 89214448--89214488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
89214438 AGACGAGCGA
* *
89214448 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
89214469 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
89214489 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:89216424 original size:16 final size:16
Alignment explanation
Indices: 89216403--89216433 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89216393 AACATTATGA
*
89216403 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
89216419 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
89216434 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:89219252 original size:21 final size:21
Alignment explanation
Indices: 89219226--89219266 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
89219216 AGACGAGCGA
* *
89219226 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
89219247 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
89219267 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:89221202 original size:16 final size:16
Alignment explanation
Indices: 89221181--89221211 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89221171 AACATTATGA
*
89221181 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
89221197 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
89221212 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:89223862 original size:28 final size:28
Alignment explanation
Indices: 89223822--89223877 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
89223812 GCACAACTCA
89223822 AAGATTTGCTTCAATAAATTAC-CAATCT
1 AAGATTTGCTTCAATAAATT-CTCAATCT
*
89223850 AAGATTTGTTTCAATAAATTCTCAATCT
1 AAGATTTGCTTCAATAAATTCTCAATCT
89223878 TTCAAATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (28 bp):
AAGATTTGCTTCAATAAATTCTCAATCT
Found at i:89224115 original size:30 final size:31
Alignment explanation
Indices: 89224061--89224121 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
89224051 TTTGTTACTG
**
89224061 AACTATTTGAAAGTTTTCATTTAAGTCACTA
1 AACTATTCCAAAGTTTTCATTTAAGTCACTA
89224092 AACTATTCCAAAGTTTT-ATTTAAGTCACTA
1 AACTATTCCAAAGTTTTCATTTAAGTCACTA
89224122 GATTGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTATTCCAAAGTTTTCATTTAAGTCACTA
Found at i:89227706 original size:9 final size:9
Alignment explanation
Indices: 89227692--89227716 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
89227682 TAATAGGTAA
89227692 AGAAGGGAG
1 AGAAGGGAG
89227701 AGAAGGGAG
1 AGAAGGGAG
89227710 AGAAGGG
1 AGAAGGG
89227717 TGGACTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (9 bp):
AGAAGGGAG
Found at i:89236195 original size:44 final size:44
Alignment explanation
Indices: 89236147--89236234 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
89236137 TTTCTATTAA
89236147 ACTATTAAGTTGTGTTATGTATTATTTTTAATTAATTAAAATTT
1 ACTATTAAGTTGTGTTATGTATTATTTTTAATTAATTAAAATTT
89236191 ACTATTAAGTTGTGTTATGTATTATTTTTAATTAATTAAAATTT
1 ACTATTAAGTTGTGTTATGTATTATTTTTAATTAATTAAAATTT
89236235 TCGAAACTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (44 bp):
ACTATTAAGTTGTGTTATGTATTATTTTTAATTAATTAAAATTT
Found at i:89236260 original size:44 final size:43
Alignment explanation
Indices: 89236156--89236243 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
89236146 AACTATTAAG
* *
89236156 TTGTGTTATGTATTATTTTTAATTAATTAAAATTTACTATTAAG
1 TTGTGTTATGTATTATTTTTAATTAATTAAAATTTACGA-TAAC
*
89236200 TTGTGTTATGTATTATTTTTAATTAATTAAAATTTTCGA-AAC
1 TTGTGTTATGTATTATTTTTAATTAATTAAAATTTACGATAAC
89236242 TT
1 TT
89236244 TTGATTTCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 4 0.10
44 37 0.90
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (43 bp):
TTGTGTTATGTATTATTTTTAATTAATTAAAATTTACGATAAC
Found at i:89238610 original size:13 final size:13
Alignment explanation
Indices: 89238592--89238616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89238582 TAGAAGTAAT
89238592 AAGAAATATATAA
1 AAGAAATATATAA
89238605 AAGAAATATATA
1 AAGAAATATATA
89238617 CATACATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAGAAATATATAA
Found at i:89239034 original size:24 final size:24
Alignment explanation
Indices: 89238992--89239037 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
89238982 AATAATACTA
*
89238992 TACACATGCAGAAATGTATATACG
1 TACACATGCAGAAAAGTATATACG
89239016 TACACATGCA-ATAAAGTATATA
1 TACACATGCAGA-AAAGTATATA
89239038 TTAATAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (24 bp):
TACACATGCAGAAAAGTATATACG
Found at i:89239175 original size:20 final size:19
Alignment explanation
Indices: 89239132--89239200 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
89239122 AGGTATGTAT
*
89239132 ATATATAATAATAATAATG
1 ATATATAATAATAATAATA
*
89239151 GTATAGTAATAATAATAATA
1 ATATA-TAATAATAATAATA
*
89239171 ATATATTAATGAAT-ATGATA
1 ATATA-TAAT-AATAATAATA
89239191 ATA-ATAATAA
1 ATATATAATAA
89239201 AAACAGTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.05
18 4 0.09
19 5 0.12
20 29 0.67
21 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATATAATAATAATAATA
Found at i:89239220 original size:3 final size:3
Alignment explanation
Indices: 89239136--89239200 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
89239126 ATGTATATAT
* * * *
89239136 ATA ATA ATA ATA ATG GT- ATA GTA ATA ATA ATA ATA AT- ATA TTA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
89239183 AT- ATG ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
89239201 AAACAGTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:89240702 original size:42 final size:43
Alignment explanation
Indices: 89240595--89240707 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 43
89240585 ATATTTAATT
* *
89240595 TTCAACCTGTTACCCTACTGCTTAGGGGATTAAGGCATGTCATC
1 TTCAACCTGTTACCCTACTGCTTA-GGGATTAAGGCATGTAAAC
* * * * * *
89240639 TTCGATCTGTTTCCCTACTGCTTAGGGTTTCAGATC-TGTAAAC
1 TTCAACCTGTTACCCTACTGCTTAGGGATTAAG-GCATGTAAAC
89240682 -TCAACCTGTTACCCTACTGCTTAGGG
1 TTCAACCTGTTACCCTACTGCTTAGGG
89240708 GTTTAAGGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 23 0.40
43 12 0.21
44 22 0.39
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (43 bp):
TTCAACCTGTTACCCTACTGCTTAGGGATTAAGGCATGTAAAC
Found at i:89240705 original size:86 final size:85
Alignment explanation
Indices: 89240596--89240879 Score: 358
Period size: 86 Copynumber: 3.3 Consensus size: 85
89240586 TATTTAATTT
* * *
89240596 TCAACCTGTTACCCTACTGCTTAGGGGATTAAGG-CATGTCATCTTCGATCTGTTTCC-CTACTG
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTC-T-TCGTCTTCGATCTG-CTCCACTACTG
** *
89240659 CTTAGGG-TTTCAGATCTGTAAAC
63 CTTAGGGAGATAAGATCTG-AAAC
89240682 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCT
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG-TCTTCGTCTTCGATCTGCTCCACTACTGCT
* *
89240747 TAGGGAGATAAGATCTGCAAT
65 TAGGGAGATAAGATCTGAAAC
*
89240768 TTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCT
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG-TCTTCGTCTTCGATCTGCTCCACTACTGCT
* *
89240833 TAGGGAGATAAGATCTGGAAT
65 TAGGGAGATAAGATCTGAAAC
*** *
89240854 TTGGCCTGTTTCCCTACTGCTTAGGG
1 TCAACCTGTTACCCTACTGCTTAGGG
89240880 CGATAATATC
Statistics
Matches: 181, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
85 3 0.02
86 168 0.93
87 9 0.05
88 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (85 bp):
TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTTCGTCTTCGATCTGCTCCACTACTGCTT
AGGGAGATAAGATCTGAAAC
Found at i:89240749 original size:44 final size:44
Alignment explanation
Indices: 89240695--89240837 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 44
89240685 ACCTGTTACC
89240695 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
* * * * * * *
89240739 CTACTGCTTAGGGAG-ATAA-GATCTGCAAT-TT-AACCTGTTACC-
1 CTACTGCTTAGGG-GTTTAAGGTTCTTC-GTCTTCGATCTGCT-CCA
89240781 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
89240825 CTACTGCTTAGGG
1 CTACTGCTTAGGG
89240838 AGATAAGATC
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
41 1 0.01
42 22 0.29
43 18 0.23
44 35 0.45
45 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (44 bp):
CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
Found at i:89240793 original size:42 final size:43
Alignment explanation
Indices: 89240594--89240923 Score: 153
Period size: 44 Copynumber: 7.7 Consensus size: 43
89240584 GATATTTAAT
*
89240594 TTTCAACCTGTTACCCTACTGCTTAGGG-GATTAAG-GCATGTC-A
1 TTTCAACCTGTTACCCTACTGCTTAGGGAGA-TAAGATC-TG-CAA
* * * ** * *
89240637 TCTTCGATCTGTTTCCCTACTGCTTAGGG-TTTCAGATCTGTAA
1 T-TTCAACCTGTTACCCTACTGCTTAGGGAGATAAGATCTGCAA
** * * * *
89240680 ACTCAACCTGTTACCCTACTGCTTAGGG-GTTTAAGGTTCTTC-G
1 TTTCAACCTGTTACCCTACTGCTTAGGGAG-ATAA-GATCTGCAA
* * *
89240723 TCTTCGATCTGCT-CCACTACTGCTTAGGGAGATAAGATCTGCAA
1 T-TTCAACCTGTTACC-CTACTGCTTAGGGAGATAAGATCTGCAA
* * * *
89240767 TTT-AACCTGTTACCCTACTGCTTAGGG-GTTTAAGGTTCTTC-G
1 TTTCAACCTGTTACCCTACTGCTTAGGGAG-ATAA-GATCTGCAA
* * * *
89240809 TCTTCGATCTGCT-CCACTACTGCTTAGGGAGATAAGATCTGGAA
1 T-TTCAACCTGTTACC-CTACTGCTTAGGGAGATAAGATCTGCAA
** * * * **
89240853 TTT-GGCCTGTTTCCCTACTGCTTAGGGCGATAATATCTATAAA
1 TTTCAACCTGTTACCCTACTGCTTAGGGAGATAAGATCT-GCAA
* *
89240896 TTTCAGCTTGTTACCCTACTGCTTAGGG
1 TTTCAACCTGTTACCCTACTGCTTAGGG
89240924 GGTTAAAGCT
Statistics
Matches: 214, Mismatches: 53, Indels: 39
0.70 0.17 0.13
Matches are distributed among these distances:
41 1 0.00
42 72 0.34
43 43 0.20
44 96 0.45
45 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (43 bp):
TTTCAACCTGTTACCCTACTGCTTAGGGAGATAAGATCTGCAA
Found at i:89240921 original size:44 final size:42
Alignment explanation
Indices: 89240739--89240923 Score: 133
Period size: 42 Copynumber: 4.3 Consensus size: 42
89240729 ATCTGCTCCA
* *
89240739 CTACTGCTTAGGGAGATAAGATCTGCAATTTAACCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGAAATTTAGCCTGTTACC
* * *** * * *
89240781 CTACTGCTTAGGG-GTTTAAGGTTCT-TCGTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGAG-ATAA-GATCTGAAAT-TTAG-CCTGTTACC
* * *
89240824 ACTACTGCTTAGGGAGATAAGATCTGGAATTTGGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGAAATTTAGCCTGTTACC
* * * *
89240867 CTACTGCTTAGGGCGATAATATCTATAAATTTCAGCTTGTTACC
1 CTACTGCTTAGGGAGATAAGATCT-GAAATTT-AGCCTGTTACC
89240911 CTACTGCTTAGGG
1 CTACTGCTTAGGG
89240924 GGTTAAAGCT
Statistics
Matches: 109, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 43 0.39
43 22 0.20
44 42 0.39
45 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (42 bp):
CTACTGCTTAGGGAGATAAGATCTGAAATTTAGCCTGTTACC
Found at i:89252154 original size:16 final size:16
Alignment explanation
Indices: 89252133--89252166 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
89252123 TTTCGATAAA
89252133 AAGACAAGAGTTAATC
1 AAGACAAGAGTTAATC
89252149 AAGACAAGAGTTAATC
1 AAGACAAGAGTTAATC
89252165 AA
1 AA
89252167 CTTGTGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AAGACAAGAGTTAATC
Found at i:89253307 original size:13 final size:13
Alignment explanation
Indices: 89253289--89253313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89253279 TAGAAGTAAT
89253289 AAGAAATATATAA
1 AAGAAATATATAA
89253302 AAGAAATATATA
1 AAGAAATATATA
89253314 CATACATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAGAAATATATAA
Found at i:89253872 original size:20 final size:19
Alignment explanation
Indices: 89253829--89253897 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
89253819 AGGTATGTAT
*
89253829 ATATATAATAATAATAATG
1 ATATATAATAATAATAATA
*
89253848 GTATAGTAATAATAATAATA
1 ATATA-TAATAATAATAATA
*
89253868 ATATATTAATGAAT-ATGATA
1 ATATA-TAAT-AATAATAATA
89253888 ATA-ATAATAA
1 ATATATAATAA
89253898 AAACAGTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.05
18 4 0.09
19 5 0.12
20 29 0.67
21 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATATAATAATAATAATA
Found at i:89253917 original size:3 final size:3
Alignment explanation
Indices: 89253833--89253897 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
89253823 ATGTATATAT
* * * *
89253833 ATA ATA ATA ATA ATG GT- ATA GTA ATA ATA ATA ATA AT- ATA TTA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
89253880 AT- ATG ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
89253898 AAACAGTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:89255390 original size:28 final size:28
Alignment explanation
Indices: 89255357--89255411 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
89255347 TAATATTTTA
89255357 AACTTATTCAACTAATACATATTTACAC
1 AACTTATTCAACTAATACATATTTACAC
*
89255385 AACTTATTTAACTAATACATATTTACA
1 AACTTATTCAACTAATACATATTTACA
89255412 TACAAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (28 bp):
AACTTATTCAACTAATACATATTTACAC
Found at i:89255409 original size:15 final size:15
Alignment explanation
Indices: 89255361--89255409 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
89255351 ATTTTAAACT
*
89255361 TATTCAACTAATACA
1 TATTTAACTAATACA
*
89255376 TATTT-AC-ACA-ACT
1 TATTTAACTA-ATACA
89255389 TATTTAACTAATACA
1 TATTTAACTAATACA
89255404 TATTTA
1 TATTTA
89255410 CATACAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 8 0.30
14 6 0.22
15 13 0.48
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTTAACTAATACA
Done.