Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 189 of 198
Found at i:58631147 original size:18 final size:18
Alignment explanation
Indices: 58631117--58631169 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
58631107 TTCATCTTGA
58631117 TTTTT-CTTCTTTTTTTGT
1 TTTTTGCTT-TTTTTTTGT
58631135 TTTTTGCTTTTTTTTTGT
1 TTTTTGCTTTTTTTTTGT
58631153 TGTTGTTG-TTTTTTTTT
1 T-TT-TTGCTTTTTTTTT
58631170 TTAGGCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 15 0.47
19 14 0.44
20 3 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTGT
Found at i:58631547 original size:29 final size:29
Alignment explanation
Indices: 58631514--58631590 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
58631504 AGAAAATTTT
*
58631514 GGGGTCAAAATGTTATTTTAAAAAGTTGA
1 GGGGTCAAAATGTAATTTTAAAAAGTTGA
* * * * * *
58631543 GGGGTTAAAGTGAAATTTCAAAAATTTTA
1 GGGGTCAAAATGTAATTTTAAAAAGTTGA
58631572 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATGTAATTTT
58631591 TTATTTTGTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAAAAAGTTGA
Found at i:58631836 original size:27 final size:25
Alignment explanation
Indices: 58631796--58631881 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 25
58631786 CTAAATGCAC
58631796 ATTTTTATTATTTTATTATTTTTTATA
1 ATTTTTATT-TTTTA-TATTTTTTATA
*
58631823 ATTTTTAATTTTTTGA-ATTTTTT-TCC
1 ATTTTT-ATTTTTT-ATATTTTTTAT-A
*
58631849 ATATTTTATTTTTTATAATATTTTATA
1 AT-TTTTATTTTTTAT-ATTTTTTATA
58631876 ATTTTT
1 ATTTTT
58631882 TTAATAGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
25 2 0.04
26 20 0.41
27 22 0.45
28 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (25 bp):
ATTTTTATTTTTTATATTTTTTATA
Found at i:58631872 original size:10 final size:10
Alignment explanation
Indices: 58631859--58631913 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
58631849 ATATTTTATT
58631859 TTTTATAATA
1 TTTTATAATA
58631869 TTTTATAAT-
1 TTTTATAATA
*
58631878 TTTTTTAATA
1 TTTTATAATA
*
58631888 -GTTATAAATA
1 TTTTAT-AATA
*
58631898 TTTTTATAATT
1 -TTTTATAATA
58631909 TTTTA
1 TTTTA
58631914 AGTTTTTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 11 0.31
10 18 0.50
11 3 0.08
12 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAATA
Found at i:58631886 original size:19 final size:19
Alignment explanation
Indices: 58631798--58631921 Score: 70
Period size: 18 Copynumber: 6.7 Consensus size: 19
58631788 AAATGCACAT
* * *
58631798 TTTTATTATTTTATT-ATT
1 TTTTATAATTTTTTTAATA
58631816 TTTTATAA--TTTTTAAT-
1 TTTTATAATTTTTTTAATA
*
58631832 TTTT-TGAATTTTTTTCCATA
1 TTTTAT-AATTTTTTT-AATA
*
58631852 TTTTAT--TTTTTATAATA
1 TTTTATAATTTTTTTAATA
58631869 TTTTATAATTTTTTTAATA
1 TTTTATAATTTTTTTAATA
*
58631888 -GTTATAAATATTTTTATAAT-
1 TTTTAT-AAT-TTTTT-TAATA
58631908 TTTT-TAAGTTTTTT
1 TTTTATAA-TTTTTT
58631922 CTTTTAATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 27
0.71 0.07 0.23
Matches are distributed among these distances:
15 1 0.01
16 10 0.12
17 11 0.13
18 22 0.26
19 22 0.26
20 11 0.13
21 7 0.08
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTATAATTTTTTTAATA
Found at i:58631899 original size:46 final size:43
Alignment explanation
Indices: 58631811--58631901 Score: 101
Period size: 46 Copynumber: 2.0 Consensus size: 43
58631801 TATTATTTTA
** * **
58631811 TTATTTTTTATAATTTTTAATTTTTTGAATTTTTTTCCATATT
1 TTATTTTTTATAATTTTTAATTTTTTGAATAGTTATAAATATT
*
58631854 TTATTTTTTATAATATTTTATAATTTTTTTAATAGTTATAAATATT
1 TTATTTTTTAT-A-ATTTT-TAATTTTTTGAATAGTTATAAATATT
58631900 TT
1 TT
58631902 TATAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 11 0.28
44 1 0.03
45 5 0.13
46 22 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (43 bp):
TTATTTTTTATAATTTTTAATTTTTTGAATAGTTATAAATATT
Found at i:58631911 original size:9 final size:9
Alignment explanation
Indices: 58631796--58631920 Score: 57
Period size: 9 Copynumber: 13.7 Consensus size: 9
58631786 CTAAATGCAC
*
58631796 ATTTTTATT
1 ATTTTTATA
58631805 A-TTTTATTA
1 ATTTTTA-TA
*
58631814 TTTTTTATA
1 ATTTTTATA
58631823 A-TTTT-TA
1 ATTTTTATA
58631830 ATTTTT-TGA
1 ATTTTTAT-A
* *
58631839 ATTTTTTTCC
1 ATTTTTAT-A
58631849 ATATTTTAT-
1 AT-TTTTATA
58631858 -TTTTTATA
1 ATTTTTATA
58631866 ATATTTTATA
1 AT-TTTTATA
*
58631876 ATTTTTTTA
1 ATTTTTATA
* *
58631885 ATAGTTATAAA
1 AT--TTTTATA
58631896 TATTTTTATA
1 -ATTTTTATA
58631906 ATTTTT-TA
1 ATTTTTATA
58631914 AGTTTTT
1 A-TTTTT
58631921 TCTTTTAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
7 9 0.10
8 18 0.20
9 31 0.34
10 22 0.24
11 9 0.10
12 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTATA
Found at i:58633086 original size:46 final size:46
Alignment explanation
Indices: 58632979--58633182 Score: 351
Period size: 46 Copynumber: 4.5 Consensus size: 46
58632969 TACGTATGGT
*
58632979 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
58633022 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
58633068 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGATAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
58633114 CACTTATCATTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
58633160 CACTTATCACTTTCTCACTTGAT
1 CACTTATCACTTTCTCACTTGAT
58633183 TATCACTTTG
Statistics
Matches: 153, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
43 10 0.07
44 5 0.03
45 21 0.14
46 117 0.76
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:58633187 original size:19 final size:19
Alignment explanation
Indices: 58633163--58633201 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
58633153 AGGCTACCAC
58633163 TTATCACTTTCTCACTTGA
1 TTATCACTTTCTCACTTGA
*
58633182 TTATCACTTTGTCACTTGA
1 TTATCACTTTCTCACTTGA
58633201 T
1 T
58633202 CAGAAGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.49
Consensus pattern (19 bp):
TTATCACTTTCTCACTTGA
Found at i:58640700 original size:381 final size:378
Alignment explanation
Indices: 58639990--58640700 Score: 907
Period size: 381 Copynumber: 1.9 Consensus size: 378
58639980 ACTATAACAA
* * *
58639990 CCTAATTTTCAGTGGTGTCAGAAACAGTGGTTCGAGACCACTAAATCCGATGAGTGAGTTCAAAA
1 CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGATGAATGAGTTCAAAA
* * * * * * * * *
58640055 TTTTTATTATTTAGTATTTATGAGCCAAATGTGATTTTAGGAAGACTTTTGAATTAGTGAATTGT
66 TTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAATTGT
* * * ** *
58640120 GTTTTAGAAGAATTTATTAGGATAATTCGTTTCGAAAATAAGGTATCAAGACCTCAGTTTTATAA
131 GTTTAAAAAGAATTTAATAGGATAATTCGGGTCGAAAATAAGGTATCAAGACCTCAGTTTCATAA
* * * * **
58640185 ATCAAGCCGTGAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATTAAAGTTTTGTTA
196 ACCAAGCCATAAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATAAAAGTTTCATTA
* * * *
58640250 GAAAATTTTAACGTTTTGATAGTTAATTAATTAAAAAGGACTAGATTGAAAAAGGTGCAAAACTT
261 GAAAATTTTAACGTTTTGATAGTCAATTAATTAAAAAGAACTAAATTGAAAAAGGTACAAAACTT
58640315 GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
326 GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
* * * *
58640368 CCTAATTTTCAGTGGTGTCGGAAACAGTGATCCGAGATCACTAAATCTGACT-AATGAGTCTTAA
1 CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGA-TGAATGAGT-TCAA
* * *
58640432 AA-TTTAATAAATTAATAATTATGGGTCAAGTGTGAATTTAGAAAAAATTTTGAATTAGTGAATT
64 AATTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAA--
* *
58640496 TTGTGATTTAAAAAGAATTTAATAGG-TAAATT-GGGTCTAAAATGAGGTATCAAGACCTCGAG-
127 TTGTG-TTTAAAAAGAATTTAATAGGAT-AATTCGGGTCGAAAATAAGGTATCAAGACCTC-AGT
*
58640558 TTCATAAACCAAGCCATAAATATTTTTATAAATATTTATGGAGTGTCATT-GAGTTAGTATAAAA
189 TTCATAAACCAAGCCATAAATA-TTTTATAAATATTTATGGAGTCTCATTAGAG-TAGTATAAAA
58640622 GTTTCATTAGAAAATTTTAACG-TTTGAATAGTCAATTAATTAAAAAGAACTAAATTGAAAATA-
252 GTTTCATTAGAAAATTTTAACGTTTTG-ATAGTCAATTAATTAAAAAGAACTAAATTGAAAA-AG
* *
58640685 GTATAAAATTTGTTAA
315 GTACAAAACTTGTTAA
58640701 ATTGTGATTA
Statistics
Matches: 282, Mismatches: 40, Indels: 19
0.83 0.12 0.06
Matches are distributed among these distances:
378 99 0.35
379 6 0.02
380 54 0.19
381 122 0.43
382 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (378 bp):
CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGATGAATGAGTTCAAAA
TTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAATTGT
GTTTAAAAAGAATTTAATAGGATAATTCGGGTCGAAAATAAGGTATCAAGACCTCAGTTTCATAA
ACCAAGCCATAAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATAAAAGTTTCATTA
GAAAATTTTAACGTTTTGATAGTCAATTAATTAAAAAGAACTAAATTGAAAAAGGTACAAAACTT
GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
Found at i:58641808 original size:46 final size:46
Alignment explanation
Indices: 58641730--58641868 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
58641720 CATGGAAAAA
* * *
58641730 TGTGAAAAGCAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
58641776 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
58641822 TGTGAAAAGTAGGTATGGTATTTCCGTGAATAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
58641868 T
1 T
58641869 ATAGCATTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:58642188 original size:2 final size:2
Alignment explanation
Indices: 58642181--58642236 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
58642171 TTGTAGATTG
58642181 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
58642223 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
58642237 TCGGAGGATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58644442 original size:21 final size:21
Alignment explanation
Indices: 58644416--58644493 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
58644406 CAGTTTAATC
* *
58644416 CTTATGGGTTTTTGTTCAGCT
1 CTTATGGGTTTCTGTTCAGCA
* * * * *
58644437 CTTATGAGCTTCCGTTCAACC
1 CTTATGGGTTTCTGTTCAGCA
*
58644458 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGTTTCTGTTCAGCA
* *
58644479 CTTATGTGCTTCTGT
1 CTTATGGGTTTCTGT
58644494 GCAACCTTCG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (21 bp):
CTTATGGGTTTCTGTTCAGCA
Found at i:58644499 original size:42 final size:42
Alignment explanation
Indices: 58644355--58644499 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 42
58644345 AGTTAAGTCA
* * * *
58644355 TATGAGTTTTAGTTTAACCC-TATTGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTCAACCCTTA-TGGGTTTCTGTTTAGCTCT
* * * * *
58644397 TTTGAGCTTCAGTTTAATCCTTATGGGTTTTTGTTCAGCTCT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* *
58644439 TATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* * *
58644481 TATGTGCTTCTGTGCAACC
1 TATGAGCTTCAGTTCAACC
58644500 TTCGGGCTTT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
Found at i:58646217 original size:17 final size:17
Alignment explanation
Indices: 58646162--58646223 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
58646152 GAAACAACAT
* *
58646162 AATTAAAAACAAGAACCA
1 AATTAAAAAGAA-AACGA
* *
58646180 AAATAATAAACAAAACGA
1 AATTAA-AAAGAAAACGA
58646198 AATTGAAAAAGAAAAC-A
1 AATT-AAAAAGAAAACGA
58646215 AATTAAAAA
1 AATTAAAAA
58646224 CCAGCCTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 5 0.13
17 5 0.13
18 20 0.53
19 8 0.21
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (17 bp):
AATTAAAAAGAAAACGA
Found at i:58647161 original size:7 final size:7
Alignment explanation
Indices: 58647151--58647179 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
58647141 AAATTTTTTT
58647151 ATATAAA
1 ATATAAA
58647158 ATATAAA
1 ATATAAA
58647165 ATATAAA
1 ATATAAA
58647172 ATATAAA
1 ATATAAA
58647179 A
1 A
58647180 AACATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATATAAA
Found at i:58649491 original size:2 final size:2
Alignment explanation
Indices: 58649484--58649512 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58649474 TTGGTAGCGT
58649484 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58649513 AATAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58649738 original size:26 final size:26
Alignment explanation
Indices: 58649694--58649745 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
58649684 AATTATAAAG
*
58649694 AATATAATTTAAACTTAAATTTCATA
1 AATAAAATTTAAACTTAAATTTCATA
58649720 AATAAAATTATAAAC-TAAATTTCATA
1 AATAAAATT-TAAACTTAAATTTCATA
58649746 CATATATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATTTAAACTTAAATTTCATA
Found at i:58649764 original size:2 final size:2
Alignment explanation
Indices: 58649747--58649780 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
58649737 AATTTCATAC
*
58649747 AT AT AT AG AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58649781 ATAAAACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58660533 original size:17 final size:17
Alignment explanation
Indices: 58660511--58660545 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
58660501 AAGAAAGTGG
*
58660511 AGTGTAAAATCTAAAGC
1 AGTGTAAAATATAAAGC
58660528 AGTGTAAAATATAAAGC
1 AGTGTAAAATATAAAGC
58660545 A
1 A
58660546 CATAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (17 bp):
AGTGTAAAATATAAAGC
Found at i:58668989 original size:19 final size:20
Alignment explanation
Indices: 58668965--58669002 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
58668955 AATTTCCGAC
58668965 TTTTTTGATTAATT-TATTA
1 TTTTTTGATTAATTCTATTA
58668984 TTTTTTGATTAATTCTATT
1 TTTTTTGATTAATTCTATT
58669003 TGAATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTGATTAATTCTATTA
Found at i:58686858 original size:19 final size:20
Alignment explanation
Indices: 58686826--58686869 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
58686816 AATAATTTAT
58686826 TAAAAATTCAT-AAAATAGA
1 TAAAAATTCATAAAAATAGA
58686845 TAAAAATT-ATTAAAAATAGA
1 TAAAAATTCA-TAAAAATAGA
*
58686865 GAAAA
1 TAAAA
58686870 GCGGCTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 12 0.55
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
TAAAAATTCATAAAAATAGA
Found at i:58695919 original size:21 final size:21
Alignment explanation
Indices: 58695893--58695941 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
58695883 AATAGAAGTT
58695893 GTGAATGAC-GGGAAATTGACA
1 GTGAATGACAGGG-AATTGACA
58695914 GTGAATGACAGGGAATTGACA
1 GTGAATGACAGGGAATTGACA
58695935 -TGAATGA
1 GTGAATGA
58695942 TTTTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.26
21 17 0.63
22 3 0.11
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (21 bp):
GTGAATGACAGGGAATTGACA
Found at i:58701793 original size:41 final size:40
Alignment explanation
Indices: 58701736--58701902 Score: 199
Period size: 41 Copynumber: 4.1 Consensus size: 40
58701726 CAGTACAAAT
58701736 CAGATTTATTGCCAGTGAAATAATTCAAACTTTATGTCTAG
1 CAGATTTA-TGCCAGTGAAATAATTCAAACTTTATGTCTAG
58701777 CAGATTTATTGCCAGTGAAATAATTCAAACTTTATGTCTAG
1 CAGATTTA-TGCCAGTGAAATAATTCAAACTTTATGTCTAG
* * * *
58701818 CAGGTTTGATGCCGGTGAAATATTTCAGACTTTATGTCTAG
1 CAGATTT-ATGCCAGTGAAATAATTCAAACTTTATGTCTAG
* * ** ** *
58701859 CAAGCTTGATGCCAGTGAAATGTTTCGGACTTTACGTCTAG
1 C-AGATTTATGCCAGTGAAATAATTCAAACTTTATGTCTAG
58701900 CAG
1 CAG
58701903 GCTAAGTGCC
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.02
41 107 0.94
42 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (40 bp):
CAGATTTATGCCAGTGAAATAATTCAAACTTTATGTCTAG
Found at i:58703684 original size:42 final size:42
Alignment explanation
Indices: 58703631--58703823 Score: 201
Period size: 42 Copynumber: 4.6 Consensus size: 42
58703621 AAGGCTGAAT
* * * ** *
58703631 AGAAGCACATAAGTGCTAAACAGAAATTCATAAGGGTTGAAC
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * *
58703673 GGAAGCTCATAAGAGCTGAACAAAAACCCATAAGGGTTAAAT
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* *
58703715 AGAAGCTCAAAAGAGCTGAACAGAAACCCATCAGGGTTAAAC
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
58703757 AGAAGCTCA-ATAGAGCTGAACGGGAACTCATATGAGTTAAAC
1 AGAAGCTCATA-AGAGCTGAACAGAAACCCATAAGGGTTAAAC
* *
58703799 AGAAGCTCGTAAGAGCTAAAC-GAAA
1 AGAAGCTCATAAGAGCTGAACAGAAA
58703824 AGTAAACACG
Statistics
Matches: 126, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 4 0.03
42 121 0.96
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (42 bp):
AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
Found at i:58703692 original size:21 final size:21
Alignment explanation
Indices: 58703631--58703819 Score: 103
Period size: 21 Copynumber: 9.0 Consensus size: 21
58703621 AAGGCTGAAT
* *
58703631 AGAAGCACATAAGTGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
** * * *
58703652 AGAAATTCATAAGGGTTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* *
58703673 GGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* * * * * *
58703694 AAAAACCCATAAGGGTTAAAT
1 AGAAGCTCATAAGAGCTAAAC
* *
58703715 AGAAGCTCAAAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* * * * *
58703736 AGAAACCCATCAGGGTTAAAC
1 AGAAGCTCATAAGAGCTAAAC
*
58703757 AGAAGCTCA-ATAGAGCTGAAC
1 AGAAGCTCATA-AGAGCTAAAC
* * *
58703778 GGGAA-CTCATATGAGTTAAAC
1 -AGAAGCTCATAAGAGCTAAAC
*
58703799 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
58703820 GAAAAGTAAA
Statistics
Matches: 116, Mismatches: 48, Indels: 8
0.67 0.28 0.05
Matches are distributed among these distances:
20 3 0.03
21 109 0.94
22 4 0.03
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTAAAC
Found at i:58705356 original size:9 final size:10
Alignment explanation
Indices: 58705328--58705365 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
58705318 TTAATTTAAT
58705328 AATATTATAAA
1 AATA-TATAAA
58705339 AATATATAAA
1 AATATATAAA
*
58705349 ACTA-ATAAA
1 AATATATAAA
58705358 AATATATA
1 AATATATA
58705366 TATGAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
AATATATAAA
Found at i:58713052 original size:15 final size:15
Alignment explanation
Indices: 58713017--58713045 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58713007 AACAATCGCC
58713017 ATGTTT-TTTTTTAA
1 ATGTTTATTTTTTAA
58713031 ATGTTTATTTTTTAA
1 ATGTTTATTTTTTAA
58713046 TATTTTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
ATGTTTATTTTTTAA
Found at i:58714013 original size:10 final size:8
Alignment explanation
Indices: 58713975--58714027 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
58713965 ATAAATTATT
58713975 TAAAAATTA
1 TAAAAA-TA
*
58713984 TAAAAATGG
1 TAAAAAT-A
58713993 TAAAAA-A
1 TAAAAATA
58714000 TAAAAATCA
1 TAAAAAT-A
58714009 TTAAAAATA
1 -TAAAAATA
58714018 TAAAAATA
1 TAAAAATA
58714026 TA
1 TA
58714028 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.16
8 11 0.29
9 14 0.37
10 7 0.18
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:58714021 original size:25 final size:25
Alignment explanation
Indices: 58713975--58714023 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
58713965 ATAAATTATT
* *
58713975 TAAAAATTATAAAAATGGTAAAAAA
1 TAAAAATCATAAAAATGATAAAAAA
58714000 TAAAAATCATTAAAAAT-ATAAAAA
1 TAAAAATCA-TAAAAATGATAAAAA
58714024 TATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (25 bp):
TAAAAATCATAAAAATGATAAAAAA
Found at i:58714213 original size:27 final size:24
Alignment explanation
Indices: 58714174--58714243 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
58714164 TAACTATTTT
58714174 TAAAAAAAATAAA-GACTAAATTTAA
1 TAAAAAAAATAAATGA-TAAA-TTAA
58714199 CTAAAATAAAATAAATGATAAATTAA
1 -TAAAA-AAAATAAATGATAAATTAA
* *
58714225 T-AAAAATATAAATGTTAAA
1 TAAAAAAAATAAATGATAAA
58714244 AATTAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 13 0.32
24 3 0.08
25 1 0.03
26 9 0.22
27 12 0.30
28 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (24 bp):
TAAAAAAAATAAATGATAAATTAA
Found at i:58714224 original size:26 final size:25
Alignment explanation
Indices: 58714174--58714230 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
58714164 TAACTATTTT
58714174 TAAAAAAAATAAAGACTAAATTTAA
1 TAAAAAAAATAAAGACTAAATTTAA
58714199 CTAAAATAAAATAAATGA-TAAA-TTAA
1 -TAAAA-AAAATAAA-GACTAAATTTAA
58714225 TAAAAA
1 TAAAAA
58714231 TATAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 9 0.31
27 12 0.41
28 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
TAAAAAAAATAAAGACTAAATTTAA
Found at i:58715018 original size:3 final size:3
Alignment explanation
Indices: 58715010--58715044 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
58715000 GTAACTTCAA
58715010 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58715045 AAGATTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58719533 original size:12 final size:12
Alignment explanation
Indices: 58719516--58719569 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
58719506 AACTAATCCT
58719516 CTCTCAAATTTC
1 CTCTCAAATTTC
*
58719528 CTCTC-AATTTG
1 CTCTCAAATTTC
58719539 CTCTCAAA-TTC
1 CTCTCAAATTTC
58719550 CT-TCAAAATTT-
1 CTCTC-AAATTTC
58719561 CTCTCAAAT
1 CTCTCAAAT
58719570 CCATATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.06
11 23 0.64
12 11 0.31
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:58719542 original size:23 final size:22
Alignment explanation
Indices: 58719515--58719569 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
58719505 AAACTAATCC
58719515 TCTCTCAAATTTCCTCTC-AATT
1 TCTCTCAAATTTCCT-TCAAATT
58719537 TGCTCTCAAA-TTCCTTCAAAATT
1 T-CTCTCAAATTTCCTTC-AAATT
58719560 TCTCTCAAAT
1 TCTCTCAAAT
58719570 CCATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 13 0.45
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTCTCAAATTTCCTTCAAATT
Found at i:58719591 original size:51 final size:51
Alignment explanation
Indices: 58719531--58719628 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
58719521 AAATTTCCTC
*
58719531 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCCCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * * *
58719582 TCAATTTGCTCCCAAGTTCCTCTTAAATTTCTTTTAAATCCCTATTT
1 TCAATTTGCTCCCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
58719629 TTAAATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCCCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:58721439 original size:124 final size:124
Alignment explanation
Indices: 58721218--58721779 Score: 791
Period size: 124 Copynumber: 4.5 Consensus size: 124
58721208 CCTAAACATG
* *
58721218 CTACTGTAGTAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
58721283 TAGAAGCGATTTTATACTGTTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * *
58721342 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
58721407 TTGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * * * *
58721466 CTATTGTAGCAAAAGCGCGTTCACGTGGGCGCAACTTCACAAATTCTTCTTATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
58721531 TTGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 TTGAAGCG--TTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGAC
* * *
58721593 CAACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
58721658 TTGAAGCGTTTTTAAACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * * * * *
58721717 CTACTGTAGCAAAAGCGCGTACATGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
58721780 ACTTTGATTT
Statistics
Matches: 390, Mismatches: 45, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
124 237 0.61
125 38 0.10
126 41 0.11
127 74 0.19
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
Found at i:58721668 original size:251 final size:248
Alignment explanation
Indices: 58721218--58721783 Score: 844
Period size: 251 Copynumber: 2.3 Consensus size: 248
58721208 CCTAAACATG
* * * * *
58721218 CTACTGTAGTAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTAC
* * * * * *
58721283 TAGAAGCGATTTTATACTGTTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTG
66 TTGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
* *
58721348 TAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCTTGCTTGAAG
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* *
58721413 CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
196 CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
* * * *
58721466 CTATTGTAGCAAAAGCGCGTTCACGTGGGCGCAACTTCACAAATTCTTCTTATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTAC
*
58721531 TTGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTCTTCCAGGACCAA
66 TTGAAGCG--ATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGACCAA
*
58721596 CTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
128 CTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
* * *
58721661 AAGCGTTTTTAAACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
193 AAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
* * * * *
58721717 CTACTGTAGCAAAAGCGCGTACATGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTAC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTAC
58721782 TT
66 TT
58721784 TGATTTTATC
Statistics
Matches: 284, Mismatches: 31, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
248 64 0.23
250 37 0.13
251 183 0.64
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (248 bp):
CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTAC
TTGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
Found at i:58730543 original size:112 final size:112
Alignment explanation
Indices: 58730363--58731066 Score: 1173
Period size: 112 Copynumber: 6.3 Consensus size: 112
58730353 AACACCTAGA
* * * *
58730363 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGACACAAAACGGCACCGTCTTG
1 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* *
58730428 GTGTATTAGTTGCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTTCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
*
58730475 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACAGCACCGTCTGG
1 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
58730540 GTGTATTA-TTTCTGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTTC-GGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
58730587 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
58730652 GTGTATTA-TTTCTGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTTC-GGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
58730699 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * *
58730764 GTGTATTATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCT
66 GTGTATTATTTTCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
58730811 TTAGC-AGCGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTG
1 TTAGCGA-CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTG
*
58730875 GGTGTATTATTTCCGGCG-TTTTTATAAACGCTGCTAATGTTCACTCT
65 GGTGTATTATTTTCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
*
58730922 TTAGCGGCGCTTTACAATAAACGCCACTAATTCCCCCCCCCAAAGGCCACAAAACGGCACCGTCT
1 TTAGCGACGCTTTACAATAAACGCCACTAATT--CCCCCCCAAAGGCCACAAAACGGCACCGTCT
* *
58730987 GGGTGTATTATTTCCGGCGTTTTTTATAAACGCTGCTAATGCTCACTCT
64 GGGTGTATTATTTTCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
* * **
58731036 TTAGCGGCGCTTTTCCTTAAACGCCACTAAT
1 TTAGCGACGCTTTACAATAAACGCCACTAAT
58731067 GCTCACTCTT
Statistics
Matches: 566, Mismatches: 19, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
111 61 0.11
112 396 0.70
113 53 0.09
114 56 0.10
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (112 bp):
TTAGCGACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTTCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
Found at i:58731057 original size:40 final size:40
Alignment explanation
Indices: 58731013--58731146 Score: 214
Period size: 40 Copynumber: 3.3 Consensus size: 40
58731003 GCGTTTTTTA
*
58731013 TAAACGCTGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
58731053 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
* * *
58731093 TAAACGCCGCTAATGCTCACTCTTTAGCAGCGTTTTTGCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
58731133 CTAAACGCCGCTAA
1 -TAAACGCCGCTAA
58731147 AAGTGCCGCT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 74 0.85
41 13 0.15
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (40 bp):
TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
Found at i:58732425 original size:11 final size:11
Alignment explanation
Indices: 58732405--58732441 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
58732395 GGCCCGGCCC
58732405 ATATTAAATAT
1 ATATTAAATAT
*
58732416 ATATTTAATAT
1 ATATTAAATAT
*
58732427 ATATAAAATAT
1 ATATTAAATAT
58732438 ATAT
1 ATAT
58732442 ATTTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:58732444 original size:24 final size:23
Alignment explanation
Indices: 58732410--58732477 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
58732400 GGCCCATATT
58732410 AAATATATATTTAATATATATAA
1 AAATATATATTTAATATATATAA
* * *
58732433 AATATATATATTTGATTAAAAATAA
1 AA-ATATATATTT-AATATATATAA
58732458 AAATATATATTTAATATATA
1 AAATATATATTTAATATATA
58732478 ATTCAGGCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 7 0.19
24 20 0.54
25 10 0.27
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
AAATATATATTTAATATATATAA
Found at i:58734353 original size:22 final size:24
Alignment explanation
Indices: 58734314--58734364 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
58734304 TAGTAGAACT
* *
58734314 GAAATTAAATTATAATTTT-TTGA
1 GAAATAAAAATATAATTTTATTGA
58734337 GAAATAAAAATAT-ATTTTATTGA
1 GAAATAAAAATATAATTTTATTGA
*
58734360 TAAAT
1 GAAAT
58734365 TCATAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
GAAATAAAAATATAATTTTATTGA
Found at i:58735713 original size:24 final size:25
Alignment explanation
Indices: 58735681--58735734 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
58735671 ATTTAATACA
*
58735681 TTAAAAAAA-TATAGTAAATATATT
1 TTAAAAAAACTATAGTAAATAAATT
58735705 TTAAAAAAACTATAGTAAATAAATT
1 TTAAAAAAACTATAGTAAATAAATT
58735730 TTAAA
1 TTAAA
58735735 TATATTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAAAAAAACTATAGTAAATAAATT
Found at i:58737147 original size:17 final size:19
Alignment explanation
Indices: 58737110--58737151 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
58737100 ATTTTTTTAA
58737110 TAAAAATTAAAAATTTATTT
1 TAAAAATTAAAAA-TTATTT
58737130 TAAAAA-TAAAAA-TATTT
1 TAAAAATTAAAAATTATTT
58737147 TAAAA
1 TAAAA
58737152 GTATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTAAAAATTATTT
Found at i:58740248 original size:10 final size:10
Alignment explanation
Indices: 58740233--58740261 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
58740223 TATTATATTC
58740233 GGGCCGGGCA
1 GGGCCGGGCA
58740243 GGGCCGGGCA
1 GGGCCGGGCA
58740253 GGGCCGGGC
1 GGGCCGGGC
58740262 CCGGGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.31, G:0.62, T:0.00
Consensus pattern (10 bp):
GGGCCGGGCA
Found at i:58744304 original size:26 final size:26
Alignment explanation
Indices: 58744226--58744311 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 26
58744216 ATTGAACCTA
* *
58744226 AAAAAAAGCTTAGGTACCAAATTAGGAA
1 AAAAAAAGTTTAGGTACCAAATT--GAG
**
58744254 AAAAAGTCAAGTTTAGGTATTAAATTGAG
1 AAAAA---AAGTTTAGGTACCAAATTGAG
*
58744283 AAAAAAAGTTTAGGTACCAAATTCAG
1 AAAAAAAGTTTAGGTACCAAATTGAG
58744309 AAA
1 AAA
58744312 CTAAATGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 21 0.44
28 5 0.10
29 7 0.15
31 15 0.31
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.23
Consensus pattern (26 bp):
AAAAAAAGTTTAGGTACCAAATTGAG
Found at i:58749644 original size:5 final size:5
Alignment explanation
Indices: 58749636--58749682 Score: 76
Period size: 5 Copynumber: 9.2 Consensus size: 5
58749626 TATTTTATTA
*
58749636 AATCT AATCT AATCT AATCT AATGT AATCT AATCT AATCTT AATCT A
1 AATCT AATCT AATCT AATCT AATCT AATCT AATCT AATC-T AATCT A
58749683 TTCCATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:58753157 original size:19 final size:19
Alignment explanation
Indices: 58753128--58753180 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
58753118 ACAAGTTAAC
58753128 AAATAATTTAAAAAATTATA
1 AAAT-ATTTAAAAAATTATA
*
58753148 AAATATTTAAAAAATTTTA
1 AAATATTTAAAAAATTATA
* *
58753167 AATTTTTTAAAAAA
1 AAATATTTAAAAAA
58753181 GTCTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTTAAAAAATTATA
Found at i:58756335 original size:2 final size:2
Alignment explanation
Indices: 58756328--58756358 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58756318 AATATACACA
58756328 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
58756359 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:58759840 original size:45 final size:45
Alignment explanation
Indices: 58759776--58759865 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
58759766 TCTTTGTAAA
58759776 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
58759821 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
58759866 TGTCTGGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (45 bp):
AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
Found at i:58761388 original size:13 final size:13
Alignment explanation
Indices: 58761366--58761417 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
58761356 ATTGTAAAAG
58761366 TTAT-TAAAAATT
1 TTATATAAAAATT
58761378 TTATATAAAAATT
1 TTATATAAAAATT
* *
58761391 GTATTTTAAAATATT
1 TTA-TATAAAA-ATT
58761406 TTA-ATAAAAATT
1 TTATATAAAAATT
58761418 GAATAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 7 0.21
13 15 0.45
14 6 0.18
15 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTATATAAAAATT
Found at i:58762665 original size:21 final size:20
Alignment explanation
Indices: 58762626--58762666 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
58762616 CATTTTTTTC
58762626 TTCTTTTTTACTGTCTTGTT
1 TTCTTTTTTACTGTCTTGTT
* *
58762646 TTCTTTATTTTCTTTCTTGTT
1 TTCTTT-TTTACTGTCTTGTT
58762667 CTTTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (20 bp):
TTCTTTTTTACTGTCTTGTT
Found at i:58763602 original size:2 final size:2
Alignment explanation
Indices: 58763595--58763626 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58763585 GATTTTAGTA
58763595 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
58763627 GCATTAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58774356 original size:2 final size:2
Alignment explanation
Indices: 58774349--58774379 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58774339 ATTCCTAGAC
58774349 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
58774380 AGCTTCAAAA
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:58779033 original size:30 final size:30
Alignment explanation
Indices: 58778993--58779058 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
58778983 TTTAAATTCG
* *
58778993 CCTTAATTTTCGTTTGAGAATATTCAACTT
1 CCTTATTTTTCGTTTCAGAATATTCAACTT
* *
58779023 CTTTATTTTTCGTTTCAGAATATTCAATTT
1 CCTTATTTTTCGTTTCAGAATATTCAACTT
58779053 CCTTAT
1 CCTTAT
58779059 CAAAAACAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.52
Consensus pattern (30 bp):
CCTTATTTTTCGTTTCAGAATATTCAACTT
Found at i:58781643 original size:84 final size:83
Alignment explanation
Indices: 58781476--58781969 Score: 487
Period size: 84 Copynumber: 5.9 Consensus size: 83
58781466 ATGCAGTACT
* * * ** * * * *
58781476 TGCAGACCAAACGAAACGTTCCCTGTATGATATGAAAA-CTGCATCAAA--GACTCCTCACCCAT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATA-CAAAACCTGCACCAAAGCGACTCCTCGCCCGT
* **
58781538 CGAATACCGCCAGTACCAA
65 CGAATACCACCAGCGCCAA
* * * *
58781557 TGCAGGCCTATCGAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGCAGACTCCTCGCCCGT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGC-GACTCCTCGCCCGT
**
58781622 TTAATACCACCAGCGCCAA
65 CGAATACCACCAGCGCCAA
* * *
58781641 TGCTGACCGAACAAAAAGTTCTCAGTATGATACAAAACCTGCACCAAAGCCGACTCCTCGCCCGT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAG-CGACTCCTCGCCCGT
58781706 CGAATACCACCAGCGCCAA
65 CGAATACCACCAGCGCCAA
* *
58781725 TGCAGACCAAACAAAAAGTTCTCAATATGGTACAAAACCTGCAGCAAAGTCGACTCCTC-CCCTG
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAG-CGACTCCTCGCCC-G
*
58781789 TCGAATACCGCCAGCGCCAA
64 TCGAATACCACCAGCGCCAA
* * * * * * *
58781809 TGCAGACCAAACAAAAAGTTCTCAATCTGAAACGGAAA-CTGCACTAAAGTCGACTTCTCACCCA
1 TGCAGACCAAACAAAAAGTTCTCAATATGATAC-AAAACCTGCACCAAAG-CGACTCCTCGCCCG
* ** * **
58781873 TCGAACACCACTTGTGCCTG
64 TCGAATACCACCAGCGCCAA
* * *
58781893 TGCAGACCAAACAAAAAGTTCTCAATATGATACTAAAA-CTGCACCAAACCCGACTCCTCACCCA
1 TGCAGACCAAACAAAAAGTTCTCAATATGATAC-AAAACCTGCACCAAA-GCGACTCCTCGCCCG
* *
58781957 TTGAATAGCACCA
64 TCGAATACCACCA
58781970 ATACCATTGT
Statistics
Matches: 346, Mismatches: 58, Indels: 15
0.83 0.14 0.04
Matches are distributed among these distances:
80 4 0.01
81 34 0.10
83 3 0.01
84 298 0.86
85 7 0.02
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (83 bp):
TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGCGACTCCTCGCCCGTC
GAATACCACCAGCGCCAA
Found at i:58783800 original size:28 final size:30
Alignment explanation
Indices: 58783766--58783830 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
58783756 TGGTTTAATG
*
58783766 TGCAATTGTATACATG-AATTTTGATTT-A
1 TGCAATTGTATACATGAAATTTTAATTTGA
*
58783794 TGCAATTTTATACATGAAATTTTAATTTGA
1 TGCAATTGTATACATGAAATTTTAATTTGA
*
58783824 TCCAATT
1 TGCAATT
58783831 CTTGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 15 0.47
29 10 0.31
30 7 0.22
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (30 bp):
TGCAATTGTATACATGAAATTTTAATTTGA
Found at i:58790620 original size:11 final size:11
Alignment explanation
Indices: 58790598--58790633 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
58790588 AACTAATCCT
58790598 CTCTCAAATTTC
1 CTCTC-AATTTC
58790610 CTCTCAATTTC
1 CTCTCAATTTC
58790621 CTCTCAATTTC
1 CTCTCAATTTC
58790632 CT
1 CT
58790634 TCCAAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:58793589 original size:124 final size:124
Alignment explanation
Indices: 58793272--58793646 Score: 653
Period size: 124 Copynumber: 3.0 Consensus size: 124
58793262 CCCAAACATG
*
58793272 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
58793337 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
58793395 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
58793460 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
*
58793519 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * ** *
58793584 TAGAAGTGATTTTATACTATTTGATCACAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
58793644 CTA
1 CTA
58793647 AAAACCCTAA
Statistics
Matches: 240, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
123 99 0.41
124 120 0.50
125 21 0.09
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:58794232 original size:17 final size:18
Alignment explanation
Indices: 58794212--58794248 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
58794202 AACTTAATCA
*
58794212 TTTTTA-AAATTTAAATT
1 TTTTTATAAATATAAATT
58794229 TTTTTATAAATATAAATT
1 TTTTTATAAATATAAATT
58794247 TT
1 TT
58794249 ACCTAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTATAAATATAAATT
Found at i:58796331 original size:41 final size:41
Alignment explanation
Indices: 58796222--58796342 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 41
58796212 NNNNNAAATT
***
58796222 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGATTT
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
* *
58796263 GGA-ATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGAC
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
* * *
58796303 CGAGATAGCTTTGGCTATGTAAGGCACTTAGTGTGCGAGA
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGA
58796343 TTATGATAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
40 35 0.51
41 34 0.49
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
Found at i:58796351 original size:41 final size:41
Alignment explanation
Indices: 58796225--58796355 Score: 153
Period size: 41 Copynumber: 3.2 Consensus size: 41
58796215 NNAAATTCGA
58796225 GATAGCTTCGGCTATTTATGGCACTTAGTGTGC--GATT-T
1 GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
* **
58796263 GGAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACCGA-
1 -G-ATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGA-TTAT
* * *
58796306 GATAGCTTTGGCTATGTAAGGCACTTAGTGTGCGAGATTAT
1 GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
58796347 GATAGCTTC
1 GATAGCTTC
58796356 AGCCATACGA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
39 1 0.01
40 32 0.42
41 40 0.53
42 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (41 bp):
GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
Found at i:58796687 original size:47 final size:48
Alignment explanation
Indices: 58796632--58796850 Score: 302
Period size: 47 Copynumber: 4.5 Consensus size: 48
58796622 AGTGAGTGTG
58796632 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
58796680 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
*
58796727 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATTAGTTTTGAGT
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGA-T-G---AGAGT
* *
58796779 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGTGA-T
1 -CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGATGAGAGT
*
58796828 CCCA-TGTAAGACCATATCTGGGA
1 -CCAGTGTAAGACCATGTCTGGGA
58796851 TATGACATTG
Statistics
Matches: 159, Mismatches: 4, Indels: 16
0.89 0.02 0.09
Matches are distributed among these distances:
47 87 0.55
48 19 0.12
49 5 0.03
50 3 0.02
52 4 0.03
53 1 0.01
54 35 0.22
55 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (48 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
Found at i:58799611 original size:9 final size:9
Alignment explanation
Indices: 58799593--58799658 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
58799583 TTTGGTTAAA
58799593 AATTAACCG
1 AATTAACCG
*
58799602 AATTACCCG
1 AATTAACCG
58799611 AATTAACCG
1 AATTAACCG
* *
58799620 GATTACCCG
1 AATTAACCG
58799629 AATTAACCG
1 AATTAACCG
*
58799638 AATT-CCCG
1 AATTAACCG
58799646 AATTAACCG
1 AATTAACCG
58799655 AATT
1 AATT
58799659 GAATCACTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
8 7 0.15
9 41 0.85
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:58799616 original size:18 final size:18
Alignment explanation
Indices: 58799593--58799658 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
58799583 TTTGGTTAAA
58799593 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
58799611 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
58799629 AATTAACCGAATT-CCCG
1 AATTAACCGAATTACCCG
58799646 AATTAACCGAATT
1 AATTAACCGAATT
58799659 GAATCACTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
17 17 0.37
18 29 0.63
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:58802574 original size:31 final size:31
Alignment explanation
Indices: 58802508--58802574 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
58802498 CGTAAAAATT
* *
58802508 TAAAAATTTTAATTAAACCTCTCAAACTTTT
1 TAAAAATTTTAATTAAACCTCTAAAACTTTG
*
58802539 TAAAAATTTTAATTAGA-CT-TAAAACTTAATG
1 TAAAAATTTTAATTAAACCTCTAAAACTT--TG
58802570 TAAAA
1 TAAAA
58802575 TTCTGCCACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 2 0.06
31 22 0.71
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAAAATTTTAATTAAACCTCTAAAACTTTG
Found at i:58804536 original size:30 final size:31
Alignment explanation
Indices: 58804496--58804558 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
58804486 ACTAAATTTT
*
58804496 AAAATGTTTCAAA-ATAATCACTGAATTATTA
1 AAAATGTTTCAAATA-AATCACTGAACTATTA
**
58804527 AAAAT-TTTCATTTAAATCACTGAACTATTA
1 AAAATGTTTCAAATAAATCACTGAACTATTA
58804557 AA
1 AA
58804559 GTCACGCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (31 bp):
AAAATGTTTCAAATAAATCACTGAACTATTA
Found at i:58804907 original size:31 final size:31
Alignment explanation
Indices: 58804839--58804907 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
58804829 AACTAAACAA
** * *
58804839 TCAATAACTTAAATAAAAACTTTTGAATAGT
1 TCAATAACTTAAATAAAAACTTGAGAACACT
* *
58804870 TTAATAACTTAAATGAAAACTTGAGAACACT
1 TCAATAACTTAAATAAAAACTTGAGAACACT
58804901 TCAATAA
1 TCAATAA
58804908 TTATTTTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (31 bp):
TCAATAACTTAAATAAAAACTTGAGAACACT
Found at i:58816785 original size:20 final size:21
Alignment explanation
Indices: 58816762--58816803 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
58816752 AAAATAAAAA
58816762 ATATATTTT-T-ATTAATATTT
1 ATATATTTTATAATTAAT-TTT
58816782 ATATATTTTATAATTAATTTT
1 ATATATTTTATAATTAATTTT
58816803 A
1 A
58816804 AATAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTTTATAATTAATTTT
Found at i:58817340 original size:20 final size:20
Alignment explanation
Indices: 58817315--58817355 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
58817305 CAAACCCTCT
58817315 CCCTCGCTCCCAAGTAAATG
1 CCCTCGCTCCCAAGTAAATG
58817335 CCCTCGCTCCCAAGTAAATG
1 CCCTCGCTCCCAAGTAAATG
58817355 C
1 C
58817356 AGAGCCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (20 bp):
CCCTCGCTCCCAAGTAAATG
Found at i:58822014 original size:30 final size:30
Alignment explanation
Indices: 58821979--58822087 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
58821969 AGAAGAAAAA
58821979 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
1 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
* **
58822009 AGATAATGAGGATGAACAAAAGAAGGACAAGAAGAAGAG
1 GGATAA--A-GA-G-A-AAAAGAAGG--AA-AAGAAGTC
* * *
58822048 GGATAAGGAGAAAAAGAAAGAAGAGAAGTC
1 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
58822078 GGATAAAGAG
1 GGATAAAGAG
58822088 GATGATGTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
30 19 0.32
31 2 0.03
32 1 0.02
33 10 0.17
34 2 0.03
35 2 0.03
36 11 0.18
38 2 0.03
39 11 0.18
ACGTcount: A:0.57, C:0.04, G:0.32, T:0.07
Consensus pattern (30 bp):
GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
Found at i:58822124 original size:3 final size:3
Alignment explanation
Indices: 58822110--58822140 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
58822100 GATGCCAAAG
*
58822110 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
58822141 AGATAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:58822233 original size:81 final size:81
Alignment explanation
Indices: 58822125--58822275 Score: 268
Period size: 81 Copynumber: 1.9 Consensus size: 81
58822115 GAGAAGAAGA
* *
58822125 AGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGT-GTGATAAAGA
1 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCG-GATAAAGA
58822189 GGATGAGGAAGAGGAGG
65 GGATGAGGAAGAGGAGG
58822206 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
1 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
58822271 GATGA
66 GATGA
58822276 TGTAGAAGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
81 66 0.99
82 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.33, T:0.08
Consensus pattern (81 bp):
AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
GATGAGGAAGAGGAGG
Found at i:58822245 original size:183 final size:187
Alignment explanation
Indices: 58822043--58822555 Score: 667
Period size: 183 Copynumber: 2.7 Consensus size: 187
58822033 GGACAAGAAG
* *
58822043 AAGAGGGATAAGGAGAAAAAGAAAGAAGAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
*
58822108 AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACA
66 AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGACA
*
58822173 AGAAGTGTGATAAAGAGGATGA-G-GAAGA-G-GAGGAGAAGAAGAAGAAGAAAGAT
131 AGAAGTGCGATAAAGAGGATGATGAGAAGACGAGAGGAGAAGAAGAAGAAGAAAGAT
58822226 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCC-A
58822291 AGAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGA
65 A-A-GAGAAGGAG-A--AG-A--AG-A--AGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGA
* *
58822356 AAAAGAAAGATAAGAAGTGCGATAAAGAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAG
119 AAAAGAAAGACAAGAAGTGCGATAAAGAGGATGATG-AGAAGA---CG-AGAGGAGAAGAAGAAG
58822421 AAGAAAGAT
179 AAGAAAGAT
* *
58822430 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGGA-GTAGAAGATGAC-
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGAT-GATGTAGAAGATGCCA
* * *
58822493 AA-AG-AGGAG-A-AA-AAGAAG-A-AA-AAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGAG
65 AAGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAC
58822550 AAGAAG
130 AAGAAG
58822556 CACGAGGATG
Statistics
Matches: 297, Mismatches: 11, Indels: 44
0.84 0.03 0.12
Matches are distributed among these distances:
183 100 0.34
184 4 0.01
185 2 0.01
186 14 0.05
187 1 0.00
188 1 0.00
189 2 0.01
190 2 0.01
192 3 0.01
193 1 0.00
194 1 0.00
195 67 0.23
196 1 0.00
198 10 0.03
199 2 0.01
201 1 0.00
202 2 0.01
204 81 0.27
205 2 0.01
ACGTcount: A:0.56, C:0.03, G:0.34, T:0.08
Consensus pattern (187 bp):
AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGACA
AGAAGTGCGATAAAGAGGATGATGAGAAGACGAGAGGAGAAGAAGAAGAAGAAAGAT
Found at i:58822300 original size:81 final size:81
Alignment explanation
Indices: 58822117--58822284 Score: 252
Period size: 81 Copynumber: 2.1 Consensus size: 81
58822107 AAGAGAAGGA
* *
58822117 GAAGAAGA--AGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGTG
1 GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG
58822180 TGATAAAGAGGATGAG
66 TGATAAAGAGGATGAG
* *
58822196 GAAGAGGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTC
1 GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-
*
58822261 G-GATAAAGAGGATGAT
65 GTGATAAAGAGGATGAG
*
58822277 GTAGAAGA
1 GAAGAAGA
58822285 TGCCAAAGAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 7 0.09
81 72 0.90
82 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.33, T:0.08
Consensus pattern (81 bp):
GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG
TGATAAAGAGGATGAG
Found at i:58822304 original size:6 final size:6
Alignment explanation
Indices: 58822293--58822335 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
58822283 GATGCCAAAG
* *
58822293 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGAAGA AGAAGA A
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA A
58822336 AGATAACAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AGGAGA
Found at i:58822347 original size:114 final size:114
Alignment explanation
Indices: 58822203--58822425 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 114
58822193 GAGGAAGAGG
*
58822203 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-CGGATAA
1 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGC-GATAA
* *
58822267 AGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGGAGAAGGAGAAGGAGA
65 AGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAAGGAGA
*
58822317 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGATAAA
1 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGCGATAAA
* *
58822382 GAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAGAAGAA
66 GAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAA
58822426 AGATAAGAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 101 0.99
115 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.35, T:0.08
Consensus pattern (114 bp):
AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGCGATAAA
GAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAAGGAGA
Found at i:58822411 original size:90 final size:90
Alignment explanation
Indices: 58822317--58822555 Score: 338
Period size: 90 Copynumber: 2.6 Consensus size: 90
58822307 GAGAAGGAGA
* *
58822317 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGT-GCGATAA
1 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCG-GATAA
* * *
58822381 AGAGGAT-GATGTAGAAGATGCCGAAG
65 AGAGCATGGA-GTAGAAGATGACAAAG
*
58822407 AGGAGGAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
1 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
58822472 GAGCATGGAGTAGAAGATGACAAAG
66 GAGCATGGAGTAGAAGATGACAAAG
* * *
58822497 AGGAGAAAAAGAAGAAAAAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGAGAAGAAG
1 AGGAG---AAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAG
58822556 CACGAGGATG
Statistics
Matches: 134, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
90 84 0.63
91 3 0.02
93 47 0.35
ACGTcount: A:0.57, C:0.03, G:0.33, T:0.07
Consensus pattern (90 bp):
AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
GAGCATGGAGTAGAAGATGACAAAG
Found at i:58822563 original size:27 final size:27
Alignment explanation
Indices: 58822509--58822563 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
58822499 GAGAAAAAGA
* *
58822509 AGAAAAAGAAAGAGAAGAAGGATAAGG
1 AGAAAAAGAAAGAGAAGAAGCACAAGG
*
58822536 AGAAAAAGAAAGAGAAGAAGCACGAGG
1 AGAAAAAGAAAGAGAAGAAGCACAAGG
58822563 A
1 A
58822564 TGAAGAGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.33, T:0.02
Consensus pattern (27 bp):
AGAAAAAGAAAGAGAAGAAGCACAAGG
Found at i:58822602 original size:204 final size:202
Alignment explanation
Indices: 58822119--58822563 Score: 505
Period size: 204 Copynumber: 2.2 Consensus size: 202
58822109 GAGAAGGAGA
* * * * * * *
58822119 AGAAGAAGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGTGTGAT
1 AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAA--GTGAT
*
58822184 AAAGAGGATGA-G--GAAGA----G--GAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
64 AAAGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
* * *
58822240 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGGAGA
129 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGATGTAGAAGATGACAAAGAGGAGAAGAAGA
**
58822305 AGGAGAAGG
194 AAAAGAAGG
* * * * *
58822314 AGAAGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGAT
1 AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAAGT--GAT
* *
58822379 AAAGAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
64 AAAGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
58822444 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGGA-GTAGAAGATGACAAAGAGGAGAAAAAG
129 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCAT-GATGTAGAAGATGACAAAGAGGAG---AAG
58822508 AAGAAAAAGAAAGAG
190 AAGAAAAAG-AAG-G
* * * *
58822523 AAGAAGGATAAGGAGAAAAAGAAAGAGAAGAAGCACGAGGA
1 -AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGA
58822564 TGAAGAGGAC
Statistics
Matches: 215, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
193 2 0.01
195 69 0.32
196 1 0.00
198 5 0.02
202 1 0.00
204 90 0.42
205 2 0.01
207 9 0.04
208 3 0.01
209 1 0.00
210 32 0.15
ACGTcount: A:0.56, C:0.03, G:0.34, T:0.07
Consensus pattern (202 bp):
AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAAGTGATAA
AGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGA
AAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGATGTAGAAGATGACAAAGAGGAGAAGAAGAAA
AAGAAGG
Found at i:58823048 original size:2 final size:2
Alignment explanation
Indices: 58823041--58823065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58823031 GATGAATAAT
58823041 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
58823066 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:58824314 original size:2 final size:2
Alignment explanation
Indices: 58824307--58824347 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
58824297 TTAGTGTAGC
* *
58824307 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58824348 CACGCAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58826044 original size:37 final size:38
Alignment explanation
Indices: 58825994--58826068 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
58825984 TAGTATTTTA
58825994 TAATAACTATCAATTT-TAAAAAAA-AATATGTCCAAAT
1 TAATAACTATCAATTTATAAAAAAATAA-ATGTCCAAAT
*
58826031 TAATAATTATCAATTTACTAAAAAAATAAATGTCCAAA
1 TAATAACTATCAATTTA-TAAAAAAATAAATGTCCAAA
58826069 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
37 15 0.44
39 17 0.50
40 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (38 bp):
TAATAACTATCAATTTATAAAAAAATAAATGTCCAAAT
Found at i:58826897 original size:2 final size:2
Alignment explanation
Indices: 58826892--58826917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58826882 TCACACACCC
58826892 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
58826918 CCCCTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58831511 original size:11 final size:11
Alignment explanation
Indices: 58831495--58831524 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
58831485 AAGTACTCAA
58831495 TTTTTTTAAAT
1 TTTTTTTAAAT
58831506 TTTTTTTAAAT
1 TTTTTTTAAAT
58831517 TTCTTTTT
1 TT-TTTTT
58831525 TTTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:58832296 original size:45 final size:45
Alignment explanation
Indices: 58832240--58832327 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
58832230 ACGGTAGCAG
* * ** *
58832240 TAACGGTAACAGTGACAGTATTCAACATGCAAAGTGCTGAATCTA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
*
58832285 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATC
58832328 GGTAATTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
Found at i:58842907 original size:3 final size:3
Alignment explanation
Indices: 58842899--58842931 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
58842889 GAATGTTTTC
58842899 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
58842932 TTTTGACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:58847016 original size:4 final size:4
Alignment explanation
Indices: 58847007--58847035 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
58846997 TAATTGACAT
58847007 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
58847036 CATCAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:58847060 original size:9 final size:9
Alignment explanation
Indices: 58847052--58847087 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
58847042 GCAAAACAAT
*
58847052 AATAACAATA
1 AATAA-AATG
58847062 AATAAAATG
1 AATAAAATG
58847071 AATAAAATG
1 AATAAAATG
58847080 AATAAAAT
1 AATAAAAT
58847088 TATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (9 bp):
AATAAAATG
Found at i:58847174 original size:3 final size:3
Alignment explanation
Indices: 58847166--58847212 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
58847156 ATGAGTCAAT
58847166 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
58847213 TAATAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:58853247 original size:21 final size:21
Alignment explanation
Indices: 58853223--58853264 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58853213 AAACCCCCTG
*
58853223 CAATTAAAACC-ATATCATTTC
1 CAATCAAAACCAAT-TCATTTC
*
58853244 CAATCACAACCAATTCATTTC
1 CAATCAAAACCAATTCATTTC
58853265 ACATCCTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (21 bp):
CAATCAAAACCAATTCATTTC
Found at i:58853749 original size:43 final size:43
Alignment explanation
Indices: 58853635--58854064 Score: 351
Period size: 43 Copynumber: 10.1 Consensus size: 43
58853625 TCTTTTACCG
*
58853635 CGCCACTATAGAATAC-GG-TCTTTAGCGGCGCTTACAC-AAAAA
1 CGCCACTATAG-AT-CGGGTTCTTTAGCGGCGCTTATACAAAAAA
* * **
58853677 CGCCACTATAGGT-GGGAGTCTTTCTCGGCGCTTATACAAAAAA
1 CGCCACTATAGATCGGG-TTCTTTAGCGGCGCTTATACAAAAAA
*
58853720 CGCCACTATAGATCGGGTTCTCTAGCGGCGCTTATACAAAAAA
1 CGCCACTATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
* * * ** * * *
58853763 TGCCACTATAGATTGGGATCTTTCTCGGCGTTTGTACAGAAAA
1 CGCCACTATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
* ** *
58853806 CGCCACTATAGATAGCGG--CTTTCCCGACGCTTATACAAAAAA
1 CGCCACTATAGATCG-GGTTCTTTAGCGGCGCTTATACAAAAAA
* * * *
58853848 CGCCACGATAGCTCGGG-TCTATAGCGGCGCTTATA-AAGAAA
1 CGCCACTATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
*** * * * *
58853889 CGCCA-TGATAGAGATGGCTCTTTCGTGGCGCTTATTCAAAAAA
1 CGCCACT-ATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
* * *
58853932 CGCCACTATAGATTGGAGTT-TTTTGCGGCGCTTATACAGAAAA
1 CGCCACTATAGATCGG-GTTCTTTAGCGGCGCTTATACAAAAAA
* * ** *
58853975 CGCCACTATAGATTGGGGTCTTTAGCGGCGCTTGGACAGAAAA
1 CGCCACTATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
* * * *
58854018 TGCCACTATAG-GCGGGGTTCTTTAGCGGCGCTTATCCAAGAAA
1 CGCCACTATAGATC-GGGTTCTTTAGCGGCGCTTATACAAAAAA
58854061 CGCC
1 CGCC
58854065 GCTAATTTTG
Statistics
Matches: 309, Mismatches: 65, Indels: 27
0.77 0.16 0.07
Matches are distributed among these distances:
40 2 0.01
41 19 0.06
42 87 0.28
43 193 0.62
44 8 0.03
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (43 bp):
CGCCACTATAGATCGGGTTCTTTAGCGGCGCTTATACAAAAAA
Found at i:58853912 original size:84 final size:86
Alignment explanation
Indices: 58853824--58853979 Score: 199
Period size: 84 Copynumber: 1.8 Consensus size: 86
58853814 TAGATAGCGG
*
58853824 CTTTCCCGACGCTTATACAAAAAACGCCACGATAGCTCGG-GTCTATAGCGGCGCTTATAAAG-A
1 CTTTCCCGACGCTTATACAAAAAACGCCACGATAGATCGGAGTCTATAGCGGCGCTTATAAAGAA
58853887 AACGCCATGATAGAGATGGCT
66 AACGCCATGATAGAGATGGCT
** * * * * * * * *
58853908 CTTTCGTGGCGCTTATTCAAAAAACGCCACTATAGATTGGAGTTTTTTGCGGCGCTTATACAGAA
1 CTTTCCCGACGCTTATACAAAAAACGCCACGATAGATCGGAGTCTATAGCGGCGCTTATAAAGAA
58853973 AACGCCA
66 AACGCCA
58853980 CTATAGATTG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 33 0.56
85 18 0.31
86 8 0.14
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (86 bp):
CTTTCCCGACGCTTATACAAAAAACGCCACGATAGATCGGAGTCTATAGCGGCGCTTATAAAGAA
AACGCCATGATAGAGATGGCT
Found at i:58854481 original size:21 final size:21
Alignment explanation
Indices: 58854439--58854484 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58854429 TTGAACCTCA
* *
58854439 GCTTCTCTCGCTGCTGCCTCT
1 GCTTCTCTCGCTGCCGCATCT
*
58854460 GCTTCTCTCGTTGCCGCATCT
1 GCTTCTCTCGCTGCCGCATCT
58854481 GCTT
1 GCTT
58854485 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.39, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCGCATCT
Found at i:58854520 original size:87 final size:87
Alignment explanation
Indices: 58854370--58854550 Score: 267
Period size: 87 Copynumber: 2.1 Consensus size: 87
58854360 TGTAAGCTGT
*
58854370 TCTGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAAC
1 TCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAAC
*
58854435 CTCAGCTTCTCTCGCTGCTGCC
66 CTCAGCTTCTCTCGATGCTGCC
* * *
58854457 TCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGTTG-TAGCTGGAGTTCTTCATATCTTT-TTTGA
1 TCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGA
*
58854520 ACCTCAGCTTCTCTCGATGTTGCC
64 ACCTCAGCTTCTCTCGATGCTGCC
*
58854544 TCCGCTT
1 TCTGCTT
58854551 TTAGTTGTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 1 0.01
87 80 0.94
88 4 0.05
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (87 bp):
TCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAAC
CTCAGCTTCTCTCGATGCTGCC
Found at i:58862532 original size:11 final size:11
Alignment explanation
Indices: 58862516--58862545 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
58862506 AAGTACTCAA
58862516 TTTTTTTAAAT
1 TTTTTTTAAAT
58862527 TTTTTTTAAAT
1 TTTTTTTAAAT
58862538 TTCTTTTT
1 TT-TTTTT
58862546 TTTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:58864543 original size:9 final size:9
Alignment explanation
Indices: 58864517--58864664 Score: 61
Period size: 9 Copynumber: 17.3 Consensus size: 9
58864507 TTGTTCAGTG
58864517 GTAAGTTAT
1 GTAAGTTAT
58864526 GT-A-TTAT
1 GTAAGTTAT
*
58864533 GTAACTTAT
1 GTAAGTTAT
58864542 GTAAGTTA-
1 GTAAGTTAT
*
58864550 -TAATATTAAT
1 GTAA-GTT-AT
*
58864560 GTATGTTAT
1 GTAAGTTAT
58864569 GTAAG-T-T
1 GTAAGTTAT
58864576 GTAAGTTAT
1 GTAAGTTAT
*
58864585 GT--TTTAT
1 GTAAGTTAT
* *
58864592 GTAACTTCT
1 GTAAGTTAT
* *
58864601 ATAACTTAT
1 GTAAGTTAT
* * *
58864610 -CAAATAAT
1 GTAAGTTAT
58864618 GTAAGTTAT
1 GTAAGTTAT
58864627 GTAAG-T-T
1 GTAAGTTAT
58864634 GTAAGTTGTTAT
1 GTAA---GTTAT
58864646 GT-A-TTAT
1 GTAAGTTAT
58864653 GTAAGTTAT
1 GTAAGTTAT
58864662 GTA
1 GTA
58864665 TGCTATATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
7 32 0.30
8 13 0.12
9 50 0.48
10 3 0.03
11 4 0.04
12 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:58864568 original size:27 final size:25
Alignment explanation
Indices: 58864517--58864575 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
58864507 TTGTTCAGTG
*
58864517 GTAAGTTATGTATTATGTAACTTAT
1 GTAAGTTATATATTATGTAACTTAT
**
58864542 GTAAGTTATAATATTAATGTATGTTAT
1 GTAAGTTAT-ATATT-ATGTAACTTAT
58864569 GTAAGTT
1 GTAAGTT
58864576 GTAAGTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.31
26 4 0.14
27 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (25 bp):
GTAAGTTATATATTATGTAACTTAT
Found at i:58864583 original size:16 final size:16
Alignment explanation
Indices: 58864517--58864586 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
58864507 TTGTTCAGTG
*
58864517 GTAAGTTATGT-ATTAT
1 GTAAGTTATGTAAGT-T
*
58864533 GTAACTTATGTAAGTT
1 GTAAGTTATGTAAGTT
*
58864549 ATAA--TAT-TAA--T
1 GTAAGTTATGTAAGTT
*
58864560 GTATGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
58864576 GTAAGTTATGT
1 GTAAGTTATGT
58864587 TTTATGTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
11 3 0.07
13 6 0.14
14 6 0.14
16 25 0.60
17 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (16 bp):
GTAAGTTATGTAAGTT
Found at i:58864757 original size:13 final size:15
Alignment explanation
Indices: 58864738--58864778 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
58864728 CATATAAGTT
58864738 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
58864752 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
58864766 TTATGTAAGTTAT
1 -TATGTAAGTTAT
58864779 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:58864773 original size:16 final size:16
Alignment explanation
Indices: 58864737--58864815 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
58864727 ACATATAAGT
58864737 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
58864752 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
58864766 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
58864784 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
58864800 TTAAGTAAGTCATGTA
1 TTATGTAAGTTATGTA
58864816 GGCTATGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:58866610 original size:11 final size:12
Alignment explanation
Indices: 58866596--58866629 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58866586 GGAAAAATCG
58866596 GGGGA-AATTTT
1 GGGGAGAATTTT
*
58866607 GGGGAGAAATTT
1 GGGGAGAATTTT
58866619 GGGGAGAATTT
1 GGGGAGAATTT
58866630 CGGCTAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (12 bp):
GGGGAGAATTTT
Found at i:58868825 original size:341 final size:340
Alignment explanation
Indices: 58868398--58869106 Score: 1202
Period size: 341 Copynumber: 2.1 Consensus size: 340
58868388 GCAGCCTATA
* * **
58868398 GCGGTGTTTTACTGAAGCGCCACTATTGGATCTATGCCTCATTTTTAAACGCTGCGTTTTGATTC
1 GCGGCGTTTTACAGAAGCGCCACTATTGGATCTATGCCTCATTTCCAAACGCTGCGTTTTGATTC
* * **
58868463 ACATATTTTGTGGCGCTTGTACTTTAGCGCCGCTAATGCTGTGATTCAGCGGCGTTTCTTTGGAA
66 ACATATTTTGTGGCGCTTGTACTTTAGCGCCACTAATGCTATGATTCAGCGGCGTTTCTAGGGAA
*
58868528 GCGCCACTAATTGTACTATAGCTCAATATTGTACGCTGCGTATAGTTTAACATTTTTTGTGGCGC
131 GCGCCACTAATTGTACTATAGCTCAATATTGTACGCTGCGTATAGTTTAACATTTTTTGTAGCGC
* *
58868593 TTACAAACAAACGCCGCTAATTCTGCTCTATAGTGGCGTTTTTAGAATGCGCCGCTACTGCCAGT
196 TTACAAAAAAACGCCGCTAATTCTGCTCTATAGTGGCGTTTTTAGAATGCGCCGCTACTGCCACT
* *
58868658 ATTCTTGAATATTAAACGATGCGTTTTGTCAGATTTATTACGGCTTTTTTGTTTAAAATCGCCAC
261 ATTCCTGAATATTAAACGATGCGTTTTGTCAGATTTATTACGGCGTTTTTGTTTAAAATCGCCAC
*
58868723 TAATGATGCTCTTTT
326 TAAAGATGCTCTTTT
* *
58868738 GCGGCGTTTTACAAAAGCGCCACTATTGGATCTATGCCTCATTTCCAAACGCTGCGTTTTTTATT
1 GCGGCGTTTTACAGAAGCGCCACTATTGGATCTATGCCTCATTTCCAAACGCTGCG-TTTTGATT
* *
58868803 CACATATTTTGTGGCGCTTGTACTTTAGCGCCACTAATGTTATGCTTCAGCGGCGTTTCTAGGGA
65 CACATATTTTGTGGCGCTTGTACTTTAGCGCCACTAATGCTATGATTCAGCGGCGTTTCTAGGGA
*
58868868 AGCGCCACTAATTGTACTATAGCTCAATATTGTACGCTGCGTATTGTTTAACATTTTTTGTAGCG
130 AGCGCCACTAATTGTACTATAGCTCAATATTGTACGCTGCGTATAGTTTAACATTTTTTGTAGCG
58868933 CTTACAAAAAAACGCCGCTAATTCTGCTCTATAGTGGCGTTTTTAGAATGCGCCGCTACTGCCAC
195 CTTACAAAAAAACGCCGCTAATTCTGCTCTATAGTGGCGTTTTTAGAATGCGCCGCTACTGCCAC
58868998 TATTCCTGAATATTAAACGATGCGTTTTGTCAGATTTATTACGGCGTTTTTGTTTAAAATCGCCA
260 TATTCCTGAATATTAAACGATGCGTTTTGTCAGATTTATTACGGCGTTTTTGTTTAAAATCGCCA
58869063 CTAAAGATGCTCTTTT
325 CTAAAGATGCTCTTTT
* * *
58869079 GCGGCATTTTCCTAGAAGCGCCGCTATT
1 GCGGCGTTTTAC-AGAAGCGCCACTATT
58869107 ACGGGATCTT
Statistics
Matches: 344, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
340 51 0.15
341 280 0.81
342 13 0.04
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (340 bp):
GCGGCGTTTTACAGAAGCGCCACTATTGGATCTATGCCTCATTTCCAAACGCTGCGTTTTGATTC
ACATATTTTGTGGCGCTTGTACTTTAGCGCCACTAATGCTATGATTCAGCGGCGTTTCTAGGGAA
GCGCCACTAATTGTACTATAGCTCAATATTGTACGCTGCGTATAGTTTAACATTTTTTGTAGCGC
TTACAAAAAAACGCCGCTAATTCTGCTCTATAGTGGCGTTTTTAGAATGCGCCGCTACTGCCACT
ATTCCTGAATATTAAACGATGCGTTTTGTCAGATTTATTACGGCGTTTTTGTTTAAAATCGCCAC
TAAAGATGCTCTTTT
Found at i:58869749 original size:45 final size:46
Alignment explanation
Indices: 58869649--58869750 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 46
58869639 ATCAGTAACG
* * *
58869649 GTAACGGTAACAGTGACAGTATTCAACACACAAAGTGCTAAATCTA
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCTA
* * *
58869695 -TAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATC-A
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCTA
*
58869739 GTAACTGTAACA
1 GTAACAGTAACA
58869751 CCCATTACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCTA
Found at i:58869857 original size:18 final size:18
Alignment explanation
Indices: 58869834--58869878 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
58869824 ACCGAGTTAT
58869834 AAAATTTCATCTAAATTA
1 AAAATTTCATCTAAATTA
58869852 AAAATTTCATCTAAATTA
1 AAAATTTCATCTAAATTA
*
58869870 AAACTTTCA
1 AAAATTTCA
58869879 AAATAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTCATCTAAATTA
Found at i:58870433 original size:45 final size:46
Alignment explanation
Indices: 58870360--58870476 Score: 195
Period size: 46 Copynumber: 2.6 Consensus size: 46
58870350 TACGTATGAT
* *
58870360 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
58870403 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
58870449 CACTTATCACTTTGTCACTTGATCAGAT
1 CACTTATCACTTTGTCACTTGATCAGAT
58870477 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
43 10 0.14
44 5 0.07
45 20 0.29
46 34 0.49
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:58870830 original size:45 final size:45
Alignment explanation
Indices: 58870774--58870861 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
58870764 ACGGTAGCAG
* * ** *
58870774 TAACGGTAACAGTGACAGTATTCAACATGCAAAGTGCTGAATCTA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
*
58870819 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATC
58870862 GGTAATTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
Found at i:58871569 original size:46 final size:46
Alignment explanation
Indices: 58871467--58871765 Score: 525
Period size: 46 Copynumber: 6.6 Consensus size: 46
58871457 TACGTATGAT
* *
58871467 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
58871510 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
58871556 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
58871601 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
58871647 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
58871693 CACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
58871739 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
58871766 AGTACTCAAA
Statistics
Matches: 246, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
43 10 0.04
44 5 0.02
45 64 0.26
46 167 0.68
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:58871586 original size:91 final size:91
Alignment explanation
Indices: 58871467--58871765 Score: 539
Period size: 91 Copynumber: 3.3 Consensus size: 91
58871457 TACGTATGAT
*
58871467 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
*
58871530 GATCAGATAAGTGTAGCTGAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
58871556 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
58871621 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
* *
58871647 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
58871712 TGATCAGATAAGTGTAGCTAAAGCTAC
65 TGATCAGATAAGTGTAGCTAAAGCTAC
58871739 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
58871766 AGTACTCAAA
Statistics
Matches: 203, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
89 10 0.05
90 5 0.02
91 110 0.54
92 78 0.38
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:58871729 original size:137 final size:137
Alignment explanation
Indices: 58871467--58871765 Score: 523
Period size: 137 Copynumber: 2.2 Consensus size: 137
58871457 TACGTATGAT
* *
58871467 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
* *
58871530 GATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-
66 GATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
*
58871594 AGGCTAC
131 AAGCTAC
58871601 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
58871666 TGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCT
65 TGATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCT
58871731 AAAGCTAC
130 AAAGCTAC
58871739 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
58871766 AGTACTCAAA
Statistics
Matches: 156, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
134 10 0.06
135 5 0.03
136 20 0.13
137 88 0.56
138 33 0.21
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (137 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTA
AAGCTAC
Found at i:58872184 original size:17 final size:17
Alignment explanation
Indices: 58872162--58872201 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
58872152 TCTAGCCCGG
*
58872162 CGCCGCCACCATTCTGT
1 CGCCGCCACCATTCTGA
*
58872179 CGCCGCCACCGTTCTGA
1 CGCCGCCACCATTCTGA
58872196 CGCCGC
1 CGCCGC
58872202 GCCGCACGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.10, C:0.50, G:0.23, T:0.17
Consensus pattern (17 bp):
CGCCGCCACCATTCTGA
Found at i:58872704 original size:44 final size:44
Alignment explanation
Indices: 58872656--58872882 Score: 182
Period size: 44 Copynumber: 5.2 Consensus size: 44
58872646 AGACACAAAC
58872656 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * *
58872700 CTTGCCT-TCCTGCA-TTGACA-GCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCT-CT-CAGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
* *
58872744 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGAT
1 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * *
58872788 CTTGCCT-TCCTGCA-TTGACA-GCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCT-CT-CAGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
* *
58872832 CTTGCATCTCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGAT
1 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
58872876 CTTGCCT
1 CTTGCCT
58872883 TCCTGCATTG
Statistics
Matches: 136, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
43 35 0.26
44 65 0.48
45 36 0.26
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:58872735 original size:88 final size:88
Alignment explanation
Indices: 58872586--58873110 Score: 713
Period size: 88 Copynumber: 6.0 Consensus size: 88
58872576 TTATATTTGC
* *
58872586 GATGGATCTGGTTGAAGATAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
*
58872651 CAAACCTTGCCTCTCTCAGTTGT
66 CAAACCTTGCCTCTCTCGGTTGT
* *
58872674 GATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
58872739 CAAACCTTGCCTCTCTCGGTTGT
66 CAAACCTTGCCTCTCTCGGTTGT
*
58872762 GATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
* *
58872827 CAAACCTTGCATCTCTCAGTTGT
66 CAAACCTTGCCTCTCTCGGTTGT
*
58872850 GATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
*
58872915 CAAACCTTGCCTCTCTCGGTTAT
66 CAAACCTTGCCTCTCTCGGTTGT
* * * * * * * * *
58872938 GGTGGAGCTGATTGAAAATAGCAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATTGAA-A-A
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
* *
58873001 CAAAGCCTTGTCTC-CATCGGTTATT
66 CAAA-CCTTGCCTCTC-TCGGTT-GT
* * * * * *
58873026 G-TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGGAGCAGATCGAA-A-A
1 GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
58873088 CAAAGCCTTGCCTC-CATCGGTTG
66 CAAA-CCTTGCCTCTC-TCGGTTG
58873111 CAGTGAAGCT
Statistics
Matches: 404, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
86 6 0.01
87 93 0.23
88 305 0.75
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (88 bp):
GATGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
CAAACCTTGCCTCTCTCGGTTGT
Found at i:58873284 original size:44 final size:44
Alignment explanation
Indices: 58873177--58873907 Score: 321
Period size: 44 Copynumber: 16.8 Consensus size: 44
58873167 TCGCGTCAGG
* * *** *
58873177 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATA-GT-A-A
*
58873223 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
* * * * * *
58873267 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAACCAATGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGA-TAGTAA
* * * * * * * ** *
58873311 TCTTATCTCTCT-AAAGTTATAGTAGAGTAGATCGCA-CCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGATAGTAA
* * ** *
58873352 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATA-GT-A-A
* *
58873398 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
* * * * * *
58873442 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAACCAATGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGA-TAGTAA
* * * * ** *
58873486 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCACCA-GGT-A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTG-AAGATAGTAA
* * ** *
58873529 --TTATTTCCCTGAGATTACAGTGGAACAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATA-GT-A-A
* *
58873573 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
* * ** * *
58873617 TCCTATCTCCCTTAGATTACAGTGGAGTGGATT-AAAATAAAG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGAT--AGTAA
* * * * * *
58873661 TCTTATCTCTCT-AAAGTTACAGTGGAGAAGATCG--TATCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-AGTAA
* * *
58873702 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
* * * * *
58873746 TCCTATCTCCCTGAGATTACTGTGGAGCGGATT-AAAATAAAG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGAT--AGTAA
* * * * * *
58873790 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCG--TATCAG--G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGAT-AGTAA
* * * *
58873831 TCTTATCACCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
* * *
58873875 TCCTATCTCCCTGAGATTACAGTAGAGCGGATT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATT
58873908 AAAAAAAAGG
Statistics
Matches: 503, Mismatches: 140, Indels: 86
0.69 0.19 0.12
Matches are distributed among these distances:
40 2 0.00
41 100 0.20
42 14 0.03
43 27 0.05
44 250 0.50
45 8 0.02
46 99 0.20
47 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATAGTAA
Found at i:58873341 original size:175 final size:175
Alignment explanation
Indices: 58873111--58873723 Score: 1001
Period size: 175 Copynumber: 3.5 Consensus size: 175
58873101 CCATCGGTTG
* * * * * **
58873111 CAGTGAAGCTGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAG
1 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
*
58873176 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
58873241 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
* * *
58873286 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTATAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
58873351 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
*
58873416 ACAGCGGAGTAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
* * *
58873461 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
*
58873526 GTATTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
* *
58873591 ACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTTAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
* * * * * *
58873636 CAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTGGAGAAGATCGTATCAG
1 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
*
58873701 GTCTTATCTCCCTGAGATTACAG
66 GTCTTATTTCCCTGAGATTACAG
58873724 CGAAGCAGAT
Statistics
Matches: 409, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 409 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (175 bp):
CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
Found at i:58873377 original size:85 final size:84
Alignment explanation
Indices: 58873111--58873723 Score: 302
Period size: 87 Copynumber: 7.0 Consensus size: 84
58873101 CCATCGGTTG
* * ** * * **
58873111 CAGTGAAGCTGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCT-AAGTTACAGTAGAGTAGATCGCACCAG
58873176 GTCTTATTTCCCTGAGATTA
65 GTCTTATTTCCCTGAGATTA
* * ** * * * ** * * *
58873196 CAGTGGAACAGACCAAAGA--ATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAA
1 CAGTGGAGCGGATTAAA-ACCA-AT--GATCTTATCTCTCTAAG-TTACAGTAGAGTAGATCGCA
** * * *
58873259 GATAGTAATCCTATCTCCCTGAGATTA
61 -CCAG--GTCTTATTTCCCTGAGATTA
*
58873286 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTATAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCT-AAGTTACAGTAGAGTAGATCGCACCAG
58873351 GTCTTATTTCCCTGAGATTA
65 GTCTTATTTCCCTGAGATTA
* * ** * * * ** * *
58873371 CAGTGGAACAGACCGAAGAATTTC-A-GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAA
1 CAGTGGAGCGGA-TTAA-AA--CCAATGATCTTATCTCTCTAAG-TTACAGTAGAGTAGATCGCA
** * * *
58873434 GATAGTAATCCTATCTCCCTGAGATTA
61 -CCAG--GTCTTATTTCCCTGAGATTA
58873461 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCT-AAGTTACAGTAGAGTAGATCGCACCAG
*
58873526 GTATTATTTCCCTGAGATTA
65 GTCTTATTTCCCTGAGATTA
* * ** * * * ** * * *
58873546 CAGTGGAACAGACCGAAGAATTTC-A-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAA
1 CAGTGGAGCGGA-TTAA-AA--CCAATGATCTTATCTCTCTAAG-TTACAGTAGAGTAGATCGCA
** * * * *
58873609 GTTAGTAATCCTATCTCCCTTAGATTA
61 -CCAG--GTCTTATTTCCCTGAGATTA
* ** * * * * *
58873636 CAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTGGAGAAGATCGTATCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCT-AAGTTACAGTAGAGTAGATCGCACCAG
*
58873701 GTCTTATCTCCCTGAGATTA
65 GTCTTATTTCCCTGAGATTA
58873721 CAG
1 CAG
58873724 CGAAGCAGAT
Statistics
Matches: 389, Mismatches: 106, Indels: 66
0.69 0.19 0.12
Matches are distributed among these distances:
84 1 0.00
85 85 0.22
86 13 0.03
87 97 0.25
88 97 0.25
89 13 0.03
90 82 0.21
91 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (84 bp):
CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAGTTACAGTAGAGTAGATCGCACCAGG
TCTTATTTCCCTGAGATTA
Found at i:58873725 original size:129 final size:129
Alignment explanation
Indices: 58873568--58874014 Score: 687
Period size: 129 Copynumber: 3.5 Consensus size: 129
58873558 CCGAAGAATT
* * *
58873568 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTTAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
58873633 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTGGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
*
58873697 TCAGGTCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
58873762 TTACTGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* *
58873826 TCAGGTCTTATCACCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * * *
58873891 TTACAGTAGAGCGGATTAAAAAAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * * * * * * * *
58873955 TCAGGTTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
58874015 CGACGTTGCG
Statistics
Matches: 291, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 291 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
Found at i:58874573 original size:17 final size:17
Alignment explanation
Indices: 58874551--58874588 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
58874541 TCTAGCCCGG
*
58874551 CGCCGCCACCATTCTGT
1 CGCCGCCACCATTCTGA
*
58874568 CGCCGCCACCGTTCTGA
1 CGCCGCCACCATTCTGA
58874585 CGCC
1 CGCC
58874589 ACGCCGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.50, G:0.21, T:0.18
Consensus pattern (17 bp):
CGCCGCCACCATTCTGA
Found at i:58875885 original size:3 final size:3
Alignment explanation
Indices: 58875879--58875937 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
58875869 TAATGTTACC
* * *
58875879 ATT ATT ATT ATT ATT ATC ATCT -TT ATT ATT ATT ATT AAT ATCG A-T
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT
58875924 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
58875938 ATTTCCATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 43 0.93
4 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Done.