Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 1 of 18
Found at i:1302 original size:20 final size:20
Alignment explanation
Indices: 1279--1341 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1269 AACATTGTTC
*
1279 AACATATAAACTTATCATGA
1 AACATATAAACCTATCATGA
1299 AACATATAAACCTATCATGA
1 AACATATAAACCTATCATGA
1319 AACATATAAACC-A-CAT-A
1 AACATATAAACCTATCATGA
1336 AACATA
1 AACATA
1342 GCTAACATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 7 0.17
18 3 0.07
19 1 0.02
20 31 0.74
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (20 bp):
AACATATAAACCTATCATGA
Found at i:12205 original size:47 final size:46
Alignment explanation
Indices: 12109--12210 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
12099 GTTCTTTCTC
* * ** * *
12109 TTTTTCTTTTTCTTTTTCTTCCTCATTCTCTTTTGTGGTAGTTTTT
1 TTTTTCTTTTCCTTTTTCTTCCTCATGCTCTTCAGTGGTAGGTTGT
12155 TTTTTACTTTTCCTTTTTCTTCCTCATGCTCTTCAGTGGGT-GGTTG-
1 TTTTT-CTTTTCCTTTTTCTTCCTCATGCTCTTCAGT-GGTAGGTTGT
12201 TTTTTCTTTT
1 TTTTTCTTTT
12211 TCCTGTTCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
45 5 0.10
46 10 0.21
47 30 0.62
48 3 0.06
ACGTcount: A:0.05, C:0.19, G:0.12, T:0.65
Consensus pattern (46 bp):
TTTTTCTTTTCCTTTTTCTTCCTCATGCTCTTCAGTGGTAGGTTGT
Found at i:17425 original size:21 final size:21
Alignment explanation
Indices: 17401--17443 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17391 GTTTTTTGAA
17401 ATTTAGCTTATAAA-CAGTCAT
1 ATTTAGCTTATAAATCA-TCAT
* *
17422 ATTTATCTTGTAAATCATCAT
1 ATTTAGCTTATAAATCATCAT
17443 A
1 A
17444 AGAAATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (21 bp):
ATTTAGCTTATAAATCATCAT
Found at i:21019 original size:29 final size:28
Alignment explanation
Indices: 20986--21060 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
20976 ATGTTTTTCC
20986 TAATTTAGACAAGAAAACACATTTGGTCT
1 TAATTTAGACAAGAAAACACATTT-GTCT
* * **
21015 TAATTTAGATAAGAAAATATGTTTGTCT
1 TAATTTAGACAAGAAAACACATTTGTCT
*
21043 TAATTTAAAGCAAGAAAA
1 TAATTTAGA-CAAGAAAA
21061 ATATTTTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (28 bp):
TAATTTAGACAAGAAAACACATTTGTCT
Found at i:21074 original size:31 final size:28
Alignment explanation
Indices: 20976--21075 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
20966 TAGCTTTAAC
* * * *
20976 ATGTTTTTCCTAATTTAGACAAGAAAAC
1 ATGTTTGTCTTAATTTAAACAAGAAAAT
** * *
21004 ACATTTGGTCTTAATTTAGATAAGAAAAT
1 ATGTTT-GTCTTAATTTAAACAAGAAAAT
21033 ATGTTTGTCTTAATTTAAAGCAAGAAAAAT
1 ATGTTTGTCTTAATTTAAA-CAAG-AAAAT
*
21063 ATTTTTTGTCTTA
1 A-TGTTTGTCTTA
21076 TGTCTTAATC
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.28
29 25 0.44
30 6 0.11
31 10 0.18
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAAACAAGAAAAT
Found at i:33410 original size:15 final size:16
Alignment explanation
Indices: 33360--33417 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 16
33350 TAATTTTTAG
33360 TTATTTTTATAATTAGT
1 TTATTTTTATAATTA-T
*
33377 TTATTTTTGAGTGAGTTAT
1 TTATTTTT-A-T-AATTAT
33396 TTATTTTTAT-ATTAT
1 TTATTTTTATAATTAT
*
33411 TTCTTTT
1 TTATTTT
33418 CATTTGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 10 0.29
17 9 0.26
18 2 0.06
19 10 0.29
20 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (16 bp):
TTATTTTTATAATTAT
Found at i:41557 original size:32 final size:32
Alignment explanation
Indices: 41521--41581 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
41511 GATTTACTTG
41521 GGTTATGTGTTGATGCAACATAGGAAAGTTTA
1 GGTTATGTGTTGATGCAACATAGGAAAGTTTA
41553 GGTTATGTGTTGATGCAACATAGGAAAGT
1 GGTTATGTGTTGATGCAACATAGGAAAGT
41582 CATAACATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.30, T:0.33
Consensus pattern (32 bp):
GGTTATGTGTTGATGCAACATAGGAAAGTTTA
Found at i:53945 original size:12 final size:12
Alignment explanation
Indices: 53928--53953 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53918 ATGAATAAAG
53928 AAAAGGAAAGAA
1 AAAAGGAAAGAA
53940 AAAAGGAAAGAA
1 AAAAGGAAAGAA
53952 AA
1 AA
53954 TAATAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAGAA
Found at i:56541 original size:18 final size:19
Alignment explanation
Indices: 56515--56562 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
56505 ATAATGGTCG
*
56515 AAAAGAATATTTTA-GAAT
1 AAAATAATATTTTATGAAT
*
56533 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATGAAT
56552 AAAATAATATT
1 AAAATAATATT
56563 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:57352 original size:21 final size:22
Alignment explanation
Indices: 57315--57359 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
57305 AGAGAAAAAG
57315 AGAAAGGAGAGGAAAGGAAGAA
1 AGAAAGGAGAGGAAAGGAAGAA
*
57337 AGAAAGTAGA-GAAAGGAAGAA
1 AGAAAGGAGAGGAAAGGAAGAA
57358 AG
1 AG
57360 GAGGAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (22 bp):
AGAAAGGAGAGGAAAGGAAGAA
Found at i:61728 original size:19 final size:19
Alignment explanation
Indices: 61704--61741 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
61694 CTTCTTACCC
61704 CCTCTAAATACTTTCTTTT
1 CCTCTAAATACTTTCTTTT
61723 CCTCTAAATACTTTCTTTT
1 CCTCTAAATACTTTCTTTT
61742 ATATTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (19 bp):
CCTCTAAATACTTTCTTTT
Found at i:66801 original size:43 final size:43
Alignment explanation
Indices: 66750--66833 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
66740 GTATCGATAG
*
66750 ATAGCCTCTAAACCTCTATTATTTAAGCCAAATTGTGTATTAA
1 ATAGCCTCTAAACCTCTATTATTTAAGCAAAATTGTGTATTAA
* * **
66793 ATAGCCTCTAAACCTTTGTTATTTGGGCAAAATTGTGTATT
1 ATAGCCTCTAAACCTCTATTATTTAAGCAAAATTGTGTATT
66834 TTCCCATTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (43 bp):
ATAGCCTCTAAACCTCTATTATTTAAGCAAAATTGTGTATTAA
Found at i:68317 original size:21 final size:21
Alignment explanation
Indices: 68291--68332 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
68281 ATCATTTATT
*
68291 GATAGATTCGGTCTATCTATC
1 GATAGATTCGGGCTATCTATC
*
68312 GATAGATTGGGGCTATCTATC
1 GATAGATTCGGGCTATCTATC
68333 AATAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
GATAGATTCGGGCTATCTATC
Found at i:75776 original size:167 final size:167
Alignment explanation
Indices: 75500--75830 Score: 626
Period size: 167 Copynumber: 2.0 Consensus size: 167
75490 TTAAAATATT
75500 TTCTTCACCCACAAATAAATTTTTAGTTCATAAATATTTATAGAAAATCATATTCACCATGAAAC
1 TTCTTCACCCACAAATAAATTTTTAGTTCATAAATATTTATAGAAAATCATATTCACCATGAAAC
* *
75565 TTTTAATCATGCTTCAACTTTAGATATCAAAATAGTTTTGAAAGTGGTGTATCCATTCACCTTGC
66 TTTTAATCATGCTTCAACTTTAGATATCAAAATAGTTTTGAAAGTGGTGTATCCACTCACCTTAC
*
75630 AAGAAGCTTGATTATAACTCTGATTCCATTAATTTGG
131 AAAAAGCTTGATTATAACTCTGATTCCATTAATTTGG
75667 TTCTTCACCCACAAATAAATTTTTAGTTCATAAATATTTATAGAAAATCATATTCACCATGAAAC
1 TTCTTCACCCACAAATAAATTTTTAGTTCATAAATATTTATAGAAAATCATATTCACCATGAAAC
*
75732 TTTTAATCATGCTTCAACTTTAGATATCAAAATAGTTTTGAAAGTGGTGTATCTACTCACCTTAC
66 TTTTAATCATGCTTCAACTTTAGATATCAAAATAGTTTTGAAAGTGGTGTATCCACTCACCTTAC
75797 AAAAAGCTTGATTATAACTCTGATTCCATTAATT
131 AAAAAGCTTGATTATAACTCTGATTCCATTAATT
75831 CGGTGTGTTT
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 160 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (167 bp):
TTCTTCACCCACAAATAAATTTTTAGTTCATAAATATTTATAGAAAATCATATTCACCATGAAAC
TTTTAATCATGCTTCAACTTTAGATATCAAAATAGTTTTGAAAGTGGTGTATCCACTCACCTTAC
AAAAAGCTTGATTATAACTCTGATTCCATTAATTTGG
Found at i:79391 original size:34 final size:34
Alignment explanation
Indices: 79347--79417 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
79337 ATCAAGCAAT
* * *
79347 AACCCTTACAATGCCTTTTACTAAGAGTAAGCAC
1 AACCCATACAATGCCTTTTACCAAGAGCAAGCAC
*
79381 AACCCATACAATGCCTTTTGCCAAGAGCAAGCAC
1 AACCCATACAATGCCTTTTACCAAGAGCAAGCAC
79415 AAC
1 AAC
79418 TCATGTACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.21
Consensus pattern (34 bp):
AACCCATACAATGCCTTTTACCAAGAGCAAGCAC
Found at i:86814 original size:15 final size:15
Alignment explanation
Indices: 86794--86823 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
86784 TTAGTGACAA
86794 TTCTTATAAAAAAGC
1 TTCTTATAAAAAAGC
*
86809 TTCTTATCAAAAAGC
1 TTCTTATAAAAAAGC
86824 AAGAATCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (15 bp):
TTCTTATAAAAAAGC
Found at i:86900 original size:50 final size:50
Alignment explanation
Indices: 86817--86943 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
86807 GCTTCTTATC
* **
86817 AAAAAGCAAGAAT-CCTTCATGGATTGTGTGGGTTACCGCTCGATCCCAT-
1 AAAAAGCAAGAATCCCTTTATGGATTGTAAGGGTTACC-CTCGATCCCATG
* * * *
86866 ATAAAGCAAGAATCCCTTTATGGATTGTAAGGGTTATCCTTGATCTCATG
1 AAAAAGCAAGAATCCCTTTATGGATTGTAAGGGTTACCCTCGATCCCATG
* * *
86916 AAAAAGCAAGAATCACATTGTGGATTGT
1 AAAAAGCAAGAATCCCTTTATGGATTGT
86944 GTGAGGGTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 21 0.32
50 44 0.68
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (50 bp):
AAAAAGCAAGAATCCCTTTATGGATTGTAAGGGTTACCCTCGATCCCATG
Found at i:87267 original size:14 final size:14
Alignment explanation
Indices: 87250--87283 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
87240 TTGATTTTAA
*
87250 TAAATAGATTTTTT
1 TAAATAAATTTTTT
*
87264 TAAAGAAATTTTTT
1 TAAATAAATTTTTT
87278 TAAATA
1 TAAATA
87284 CTAATTCACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TAAATAAATTTTTT
Found at i:111189 original size:24 final size:24
Alignment explanation
Indices: 111162--111211 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
111152 TTATTTTATC
* **
111162 TATTAACCTATCTTGGCTATCATA
1 TATTAACCCATCTCAGCTATCATA
111186 TATTAACCCATCTCAGCTATCATA
1 TATTAACCCATCTCAGCTATCATA
111210 TA
1 TA
111212 ACTTAGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (24 bp):
TATTAACCCATCTCAGCTATCATA
Found at i:117424 original size:22 final size:22
Alignment explanation
Indices: 117399--117441 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
117389 ACTCTATCAT
117399 ATAGAGTTATTTTAACACATTG
1 ATAGAGTTATTTTAACACATTG
*
117421 ATAGAGTTATTTTGACACATT
1 ATAGAGTTATTTTAACACATT
117442 TTTGAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (22 bp):
ATAGAGTTATTTTAACACATTG
Found at i:120377 original size:34 final size:34
Alignment explanation
Indices: 120338--120404 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
120328 GAACCTTTAC
*
120338 AACAATGCCTTTTCACGAG-AGCAAGCATAACCCA
1 AACAATGCCTTTTCA-GAGAAGCAAACATAACCCA
*
120372 AACAATGCCTTTTCATAGAAGCAAACATAACCC
1 AACAATGCCTTTTCAGAGAAGCAAACATAACCC
120405 TTCACCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.19
Consensus pattern (34 bp):
AACAATGCCTTTTCAGAGAAGCAAACATAACCCA
Found at i:120464 original size:29 final size:29
Alignment explanation
Indices: 120377--120464 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
120367 ACCCAAACAA
* * *
120377 TGCCTTTTCATAGAAGCAAACATAACC-CT
1 TGCCTTTTCA-AGGATCAAGCATAACCTCT
* * * * * *
120406 TCACCTTTTTAAGGATTAGGCAGAATCTCT
1 T-GCCTTTTCAAGGATCAAGCATAACCTCT
120436 TGCCTTTTCAAGGATCAAGCATAACCTCT
1 TGCCTTTTCAAGGATCAAGCATAACCTCT
120465 ATACAACACT
Statistics
Matches: 42, Mismatches: 15, Indels: 4
0.69 0.25 0.07
Matches are distributed among these distances:
29 32 0.76
30 10 0.24
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (29 bp):
TGCCTTTTCAAGGATCAAGCATAACCTCT
Found at i:131400 original size:77 final size:77
Alignment explanation
Indices: 131193--131478 Score: 285
Period size: 77 Copynumber: 3.7 Consensus size: 77
131183 CAATTGTTAG
* * *
131193 ATGTCATTGACATCTTGTCGTGATACGCTAAGTCG-T--AGTATTTTAGGGTGACAAACCACACT
1 ATGTCATTGACATCTTGTCGTGACACGCTAAGTCGTTGCAGTATTATAGGGTGACACACCACACT
131255 CCAATTTCACCT
66 CCAATTTCACCT
* * * * *
131267 ATGTCGTTGACATTTTGTCATGACACGCTGAGTCATTGCAGTATTATAGGGTGACACACCACACT
1 ATGTCATTGACATCTTGTCGTGACACGCTAAGTCGTTGCAGTATTATAGGGTGACACACCACACT
131332 CCAATTTCACCT
66 CCAATTTCACCT
* * * * ** * *
131344 ATGTCATTGGCATCTTGTTGTGACATGCTAAGTCGTTGCAGTATTATAAGAAGACACGCCACATT
1 ATGTCATTGACATCTTGTCGTGACACGCTAAGTCGTTGCAGTATTATAGGGTGACACACCACACT
* * *
131409 TCAATTGTTA--G
66 CCAATT-TCACCT
* * * * *
131420 ATGTCGTTGACATCTTGTCGTGACACACCGCCATGTCGTTGTAGTATTATAAGGTGACA
1 ATGTCATTGACATCTTGTCGTG--ACA-CGCTAAGTCGTTGCAGTATTATAGGGTGACA
131479 TGCCACGCTT
Statistics
Matches: 172, Mismatches: 33, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
74 29 0.17
75 1 0.01
76 19 0.11
77 93 0.54
78 5 0.03
79 25 0.15
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (77 bp):
ATGTCATTGACATCTTGTCGTGACACGCTAAGTCGTTGCAGTATTATAGGGTGACACACCACACT
CCAATTTCACCT
Found at i:131517 original size:74 final size:74
Alignment explanation
Indices: 131417--131592 Score: 271
Period size: 74 Copynumber: 2.4 Consensus size: 74
131407 TTTCAATTGT
* *
131417 TAGATGTCGTTGACATCTTGTCGTGACACACCGCCATGTCGTTGTAGTATTATAAGGTGACATGC
1 TAGATGTCGTTGACATCTTGTCGTGACACACCGCCATGTCGTTATAGTATTATAAGGTGACACGC
131482 CACGCTTGA
66 CACGCTTGA
* * * * *
131491 TAGATGTTGTTGACATCTTGTTGTGACACTCTGCCATGTGGTTATAGTATTATAAGGTGACACGC
1 TAGATGTCGTTGACATCTTGTCGTGACACACCGCCATGTCGTTATAGTATTATAAGGTGACACGC
*
131556 CACGCTTGT
66 CACGCTTGA
*
131565 TAGATGTCATTGACATCTTGTCGTGACA
1 TAGATGTCGTTGACATCTTGTCGTGACA
131593 TGTTGAGTCA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 91 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (74 bp):
TAGATGTCGTTGACATCTTGTCGTGACACACCGCCATGTCGTTATAGTATTATAAGGTGACACGC
CACGCTTGA
Found at i:136037 original size:21 final size:21
Alignment explanation
Indices: 136008--136054 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
135998 TTGACTTTGA
* *
136008 ATGATGGCATCAGTCCTTGTC
1 ATGAAGGCATCAATCCTTGTC
*
136029 ATGAAGGCATCAATCTTTGTC
1 ATGAAGGCATCAATCCTTGTC
136050 ATGAA
1 ATGAA
136055 TTGCATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
ATGAAGGCATCAATCCTTGTC
Found at i:138895 original size:81 final size:81
Alignment explanation
Indices: 138755--138925 Score: 220
Period size: 81 Copynumber: 2.1 Consensus size: 81
138745 AGCTTGAACT
* * * *
138755 GATTCAAGGTTTCCATCCCTTCCCTCAGCTGCCTCGATAACTGCATCAGCTTGAAGAACATGGTC
1 GATTCAAGGTTCCCATCCCCTCCCTCAGCTGCCTCGACAACTGCATCAACTTGAAGAACATGGTC
**
138820 TCTTTCAACCTAAACC
66 TAATTCAACCTAAACC
*
138836 GATTCAAGGTTCCCATCCCCTCCCAT-AGCTGCCTCGACAACCT-CATCAACTTGAGGAACATGG
1 GATTCAAGGTTCCCATCCCCTCCC-TCAGCTGCCTCGACAA-CTGCATCAACTTGAAGAACATGG
** *
138899 TCTAATTCAGTCTCAACC
64 TCTAATTCAACCTAAACC
138917 GATTCAAGG
1 GATTCAAGG
138926 CCCTTATCCC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 75 0.96
82 3 0.04
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (81 bp):
GATTCAAGGTTCCCATCCCCTCCCTCAGCTGCCTCGACAACTGCATCAACTTGAAGAACATGGTC
TAATTCAACCTAAACC
Found at i:138947 original size:81 final size:80
Alignment explanation
Indices: 138755--138948 Score: 196
Period size: 81 Copynumber: 2.4 Consensus size: 80
138745 AGCTTGAACT
* * * *
138755 GATTCAAGGTTTCCAT-CCCTTCCCTCAGCTGCCTCGATAACTGCATCAGCTTGAAGAACATGGT
1 GATTCAAGG-TCCCATCCCCTT-CCACAGCTGCCTCGACAACTGCATCAACTTGAAGAACATGGT
**
138819 CTCTTTCAACCTAAACC
64 CTAATTCAACCTAAACC
* * *
138836 GATTCAAGGTTCCCATCCCCTCCCATAGCTGCCTCGACAACCT-CATCAACTTGAGGAACATGGT
1 GATTCAAGG-TCCCATCCCCTTCCACAGCTGCCTCGACAA-CTGCATCAACTTGAAGAACATGGT
** *
138900 CTAATTCAGTCTCAACC
64 CTAATTCAACCTAAACC
*
138917 GATTCAAGG-CCCTTATCCCCTTCCGCAGCTGC
1 GATTCAAGGTCCC--ATCCCCTTCCACAGCTGC
138949 ATCAATAATC
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
79 3 0.03
81 85 0.90
82 6 0.06
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (80 bp):
GATTCAAGGTCCCATCCCCTTCCACAGCTGCCTCGACAACTGCATCAACTTGAAGAACATGGTCT
AATTCAACCTAAACC
Found at i:139773 original size:151 final size:151
Alignment explanation
Indices: 139577--140013 Score: 385
Period size: 151 Copynumber: 2.9 Consensus size: 151
139567 AACCGGCGAA
* * * * * * * *
139577 TCGTTACCACTTTGCGTTTGAGTAGGTCTTGTCGATCGTTGAGGAGATGTCGTCGCATGGCTTC-
1 TCGTTACCACTATGCGTCTGAGCAGATCTTGTCGATCATTAAGGAGATGTCATCGCATGG-GTCA
** ** * * * * * *
139641 ACTGTAATAACAGATATTATTTTGTTATTTGATAATCATATATGGAATTGTTGAACTTAAACCGT
65 ACTACAATAACAGATATTATAGTGTTACTCGATAATCATATATAGAATTATTGAACATAAACCAT
*
139706 TAGAACTGTCCTTACCAACGGC
130 TAGAACTATCCTTACCAACGGC
* * **
139728 TCGTTACCACTATGTGTCTGAGCAGATCTTGTCGGTCATTAAGGAGATGTCATCTTATGGGTCAA
1 TCGTTACCACTATGCGTCTGAGCAGATCTTGTCGATCATTAAGGAGATGTCATCGCATGGGTCAA
*
139793 CTACAATAACAGATATTATAGTGTTACTCGATAATCATTTATAGAATTATTGAACATAAACCATT
66 CTACAATAACAGATATTATAGTGTTACTCGATAATCATATATAGAATTATTGAACATAAACCATT
**
139858 AGAACTATCCTTACCAGTGGC
131 AGAACTATCCTTACCAACGGC
* * * * * * * * ** **
139879 TCGTTACCACTGTGCGTCTAAGTA-AGTCCTATCAATCGTTAAAGAGATGTTGTCGCATGAATCA
1 TCGTTACCACTATGCGTCTGAGCAGA-TCTTGTCGATCATTAAGGAGATGTCATCGCATGGGTCA
* * * * * * * * * *
139943 ACTATAATAATAGGTATTAATA-TATTATTCAATAATCAAATATGGAATTATTAAATATAAACCA
65 ACTACAATAACAGATATT-ATAGTGTTACTCGATAATCATATATAGAATTATTGAACATAAACCA
*
140007 TAAGAAC
129 TTAGAAC
140014 CGCCCTTACT
Statistics
Matches: 229, Mismatches: 54, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
150 3 0.01
151 223 0.97
152 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (151 bp):
TCGTTACCACTATGCGTCTGAGCAGATCTTGTCGATCATTAAGGAGATGTCATCGCATGGGTCAA
CTACAATAACAGATATTATAGTGTTACTCGATAATCATATATAGAATTATTGAACATAAACCATT
AGAACTATCCTTACCAACGGC
Found at i:141580 original size:23 final size:23
Alignment explanation
Indices: 141528--141574 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
141518 AAATTTATGT
*
141528 CGTGTCACTTATTCAAGCCATGG
1 CGTGTCACATATTCAAGCCATGG
* *
141551 CGTGTCACATATTCCATCCATGG
1 CGTGTCACATATTCAAGCCATGG
141574 C
1 C
141575 AGGTCATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (23 bp):
CGTGTCACATATTCAAGCCATGG
Found at i:141704 original size:23 final size:23
Alignment explanation
Indices: 141674--141737 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
141664 CACAGCCATG
* *
141674 TCACATATTTTCACCATGCTGTC
1 TCACATATTCTCACCATGATGTC
*
141697 TCACATATTCTCACCATGATGTG
1 TCACATATTCTCACCATGATGTC
*
141720 TCACATATTCACACCATG
1 TCACATATTCTCACCATG
141738 GCATGCCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (23 bp):
TCACATATTCTCACCATGATGTC
Found at i:141747 original size:23 final size:23
Alignment explanation
Indices: 141698--141748 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
141688 CATGCTGTCT
* ** *
141698 CACATATTCTCACCATGATGTGT
1 CACATATTCACACCATGACATGC
*
141721 CACATATTCACACCATGGCATGC
1 CACATATTCACACCATGACATGC
141744 CACAT
1 CACAT
141749 TCTCACATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.27
Consensus pattern (23 bp):
CACATATTCACACCATGACATGC
Found at i:141912 original size:23 final size:23
Alignment explanation
Indices: 141882--141936 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
141872 ATGTCATAAT
*
141882 CATGTCACATACTCTCACCATGG
1 CATGTCACATACTCTCACCATGC
* *
141905 CATGTCACATATTCTCACCATTC
1 CATGTCACATACTCTCACCATGC
141928 CATGTCACA
1 CATGTCACA
141937 AATTTTCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.29
Consensus pattern (23 bp):
CATGTCACATACTCTCACCATGC
Found at i:162976 original size:2 final size:2
Alignment explanation
Indices: 162969--162993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
162959 TGATAAAATT
162969 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
162994 CTTTTAACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:169168 original size:103 final size:106
Alignment explanation
Indices: 168981--169189 Score: 307
Period size: 103 Copynumber: 2.0 Consensus size: 106
168971 AATGAGAACA
* * *
168981 AACACAAAAAAACTATGTCGCGTGGAGAGTAGTAAAAATAACTTTGAACAATTGACAAGGTTCAT
1 AACACAAAAAAACTACGTCGCGTGGAGAGTAATAAAAATAACTCTGAACAATTGACAAGGTTCAT
169046 GAGTTTGGCTTATTGGCTTAAACATAGAGGTAGTTAAGAGG
66 GAGTTTGGCTTATTGGCTTAAACATAGAGGTAGTTAAGAGG
* ** *
169087 AACAC-AAAAAACTACGTCTCGT-G-GAGTAATAAAAATAACTCTGAACAATTGGTAAGGTTTAT
1 AACACAAAAAAACTACGTCGCGTGGAGAGTAATAAAAATAACTCTGAACAATTGACAAGGTTCAT
* * *
169149 GAGTTTGGCTTGTTGGCTTAAATATGGAGGTAGTTAAGAGG
66 GAGTTTGGCTTATTGGCTTAAACATAGAGGTAGTTAAGAGG
169190 CCTTTCTCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
103 72 0.77
104 1 0.01
105 15 0.16
106 5 0.05
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (106 bp):
AACACAAAAAAACTACGTCGCGTGGAGAGTAATAAAAATAACTCTGAACAATTGACAAGGTTCAT
GAGTTTGGCTTATTGGCTTAAACATAGAGGTAGTTAAGAGG
Found at i:179367 original size:20 final size:20
Alignment explanation
Indices: 179315--179356 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
179305 AAAATCATTG
** *
179315 AAAAAAAAATCCATATAACA
1 AAAAAAAAATAAACATAACA
179335 AAAAAAAAATAAACATAACA
1 AAAAAAAAATAAACATAACA
179355 AA
1 AA
179357 TAGAAGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAAAAATAAACATAACA
Found at i:184533 original size:25 final size:25
Alignment explanation
Indices: 184496--184554 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
184486 TGATTCACAC
*
184496 ATTATAGGTTATCCATTTTTGGTGG
1 ATTATAGGCTATCCATTTTTGGTGG
184521 ATTATAGGCTATCCATTTTTGGTGG
1 ATTATAGGCTATCCATTTTTGGTGG
184546 ATTATAGGC
1 ATTATAGGC
184555 ATCTATCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (25 bp):
ATTATAGGCTATCCATTTTTGGTGG
Found at i:184594 original size:26 final size:26
Alignment explanation
Indices: 184555--184608 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
184545 GATTATAGGC
* * *
184555 ATCTATCTATTTTTTATAGTAAAATT
1 ATCTATCCACTTTTAATAGTAAAATT
*
184581 ATCTATCCACTTTTAATGGTAAAATT
1 ATCTATCCACTTTTAATAGTAAAATT
184607 AT
1 AT
184609 TCTTAAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (26 bp):
ATCTATCCACTTTTAATAGTAAAATT
Found at i:184872 original size:53 final size:53
Alignment explanation
Indices: 184798--184918 Score: 161
Period size: 53 Copynumber: 2.3 Consensus size: 53
184788 TTTATAATTT
* * *
184798 TTTTTATTAGTATCTCGTTTGTCATATTCACTTCAAGGAATGAACATTCATAA
1 TTTTTATTAGTAGCTCATTTGTCACATTCACTTCAAGGAATGAACATTCATAA
* * * *
184851 TTTTTATTAGTAGCTCATTTGTCACATTTACTTTAGGGAATGGACATTCATAA
1 TTTTTATTAGTAGCTCATTTGTCACATTCACTTCAAGGAATGAACATTCATAA
* *
184904 TTTTCATTAATAGCT
1 TTTTTATTAGTAGCT
184919 ATATATTAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTTATTAGTAGCTCATTTGTCACATTCACTTCAAGGAATGAACATTCATAA
Found at i:185496 original size:20 final size:21
Alignment explanation
Indices: 185458--185498 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
185448 AACAATATTA
*
185458 ATATTTTAATAATTTTTAAAT
1 ATATTTTAATAATTATTAAAT
185479 ATATTTTAA-AATTATTAAAT
1 ATATTTTAATAATTATTAAAT
185499 TAAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTTTAATAATTATTAAAT
Found at i:186859 original size:16 final size:17
Alignment explanation
Indices: 186813--186882 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
186803 CAAAAGAGAA
186813 AAAAGGGAAAAGAAAAAA-
1 AAAA-GGAAAA-AAAAAAG
*** *
186831 AAAAGGGGGAAAAAGAG
1 AAAAGGAAAAAAAAAAG
186848 AGAAAGGAAAAAAAAAAG
1 A-AAAGGAAAAAAAAAAG
186866 AAAAGGAAACAAAAAAA
1 AAAAGGAAA-AAAAAAA
186883 ATTAGTGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
16 5 0.12
17 12 0.29
18 24 0.59
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGGAAAAAAAAAAG
Found at i:186959 original size:16 final size:15
Alignment explanation
Indices: 186933--187041 Score: 74
Period size: 15 Copynumber: 6.7 Consensus size: 15
186923 AAGGAGAAAA
*
186933 AAAAGAAAAAAAGTG
1 AAAAGAAAAAAAGGG
*
186948 AAAGGAAAAAAAGGG
1 AAAAGAAAAAAAGGG
*
186963 AAAAGAAAAAAGAGAGA
1 AAAAGAAAAAA-AG-GG
* *
186980 AAGAAGGAAAAAAGGAT
1 AA-AAGAAAAAAAGG-G
* *
186997 AAGAACAAAAAAAAGGA
1 AA-AA-GAAAAAAAGGG
*
187014 AAAAAAAAGAAAAGGGG
1 AAAAGAAA-AAAA-GGG
187031 AAAAGAAAAAA
1 AAAAGAAAAAA
187042 TATTGTGAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
15 27 0.36
16 12 0.16
17 21 0.28
18 16 0.21
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAAAGGG
Found at i:186967 original size:159 final size:161
Alignment explanation
Indices: 186804--187146 Score: 381
Period size: 159 Copynumber: 2.2 Consensus size: 161
186794 AACCTATGCC
* **
186804 AAAAGAGAAAAAAGGGA-AAAGAAAAAAAAAAGG-GGGAA-AAAGAGAGAAAGGAAAAAAAAAAG
1 AAAAGAGAAAAAAGAGAGAAAGAAAAAAAAAAGGAAAGAACAAA-A-A-AAAGG-AAAAAAAAAG
* * * * *
186866 AAAA-GGAAACA-AAAAAA-ATTAGTGAAATTGAGCTTGAGGAGAATCGAACTTAGGTCAAAGGA
62 AAAAGGGAAA-AGAAAAAATATT-GTGAAATTGAGCCTGAGAAGAATCAAACATAGATCAAAGGA
* *
186928 GAAAAAAAAGAAAAAAAGTG-AAAG-GAAAAAAAGGG
125 GAAAAAAAAGAAAAAAAGCGAAAAGAAAAAAAAAGGG
**
186963 -AAA-AGAAAAAAGAGAGAAAGAAGGAAAAAAGGATAAGAACAAAAAAAAGGAAAAAAAAAGAAA
1 AAAAGAGAAAAAAGAGAGAAAGAAAAAAAAAAGGA-AAGAACAAAAAAAAGGAAAAAAAAAGAAA
*
187026 AGGGGAAAAGAAAAAATATTGTGAAATTGGGCCTGAGAAGAATCAAACATAGATCAAAGGAGAAA
65 A-GGGAAAAGAAAAAATATTGTGAAATTGAGCCTGAGAAGAATCAAACATAGATCAAAGGAGAAA
* *
187091 CAAAAGAAAAGAAGCGAAAAGAAAAAAAAAGGG
129 AAAAAGAAAAAAAGCGAAAAGAAAAAAAAAGGG
187124 AAAAG-G-AAAAA-A-AGAAAGAAAAA
1 AAAAGAGAAAAAAGAGAGAAAGAAAAA
187147 GAGAAAAGAA
Statistics
Matches: 155, Mismatches: 17, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
157 25 0.16
158 23 0.15
159 73 0.47
160 12 0.08
161 18 0.12
162 4 0.03
ACGTcount: A:0.65, C:0.04, G:0.24, T:0.07
Consensus pattern (161 bp):
AAAAGAGAAAAAAGAGAGAAAGAAAAAAAAAAGGAAAGAACAAAAAAAAGGAAAAAAAAAGAAAA
GGGAAAAGAAAAAATATTGTGAAATTGAGCCTGAGAAGAATCAAACATAGATCAAAGGAGAAAAA
AAAGAAAAAAAGCGAAAAGAAAAAAAAAGGG
Found at i:187026 original size:18 final size:18
Alignment explanation
Indices: 186963--187040 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
186953 AAAAAAAGGG
*
186963 AAAAGAAAAAAGAGAGAAA
1 AAAAGAAAAAAG-GAAAAA
* * *
186982 GAAGGAAAAAAGGATAAGA
1 AAAAGAAAAAAGGA-AAAA
*
187001 ACAA-AAAAAAGGAAAAA
1 AAAAGAAAAAAGGAAAAA
**
187018 AAAAGAAAAGGGGAAAAGA
1 AAAAGAAAAAAGGAAAA-A
187037 AAAA
1 AAAA
187041 ATATTGTGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
17 6 0.13
18 21 0.47
19 18 0.40
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.01
Consensus pattern (18 bp):
AAAAGAAAAAAGGAAAAA
Found at i:187117 original size:17 final size:18
Alignment explanation
Indices: 187097--187136 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
187087 GAAACAAAAG
*
187097 AAAAGAAGCGAAAA-GAA
1 AAAAAAAGCGAAAAGGAA
*
187114 AAAAAAAGGGAAAAGGAA
1 AAAAAAAGCGAAAAGGAA
187132 AAAAA
1 AAAAA
187137 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAAAGCGAAAAGGAA
Found at i:187145 original size:26 final size:26
Alignment explanation
Indices: 187095--187162 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
187085 GAGAAACAAA
*
187095 AGAAAAGAAGCGAAAAGAAAAAAAAAG
1 AGAAAAGAAAC-AAAAGAAAAAAAAAG
* *
187122 GGAAAAGGAAA-AAAAGAAAGAAAAAG
1 AGAAAA-GAAACAAAAGAAAAAAAAAG
187148 AGAAAAGAAACAAAA
1 AGAAAAGAAACAAAA
187163 TTGTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 23 0.66
27 5 0.14
28 3 0.09
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (26 bp):
AGAAAAGAAACAAAAGAAAAAAAAAG
Found at i:198225 original size:12 final size:12
Alignment explanation
Indices: 198208--198233 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
198198 TGCTAGAAAA
198208 TGATAAGTGATT
1 TGATAAGTGATT
198220 TGATAAGTGATT
1 TGATAAGTGATT
198232 TG
1 TG
198234 TGATTTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (12 bp):
TGATAAGTGATT
Found at i:200953 original size:11 final size:10
Alignment explanation
Indices: 200931--200978 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
200921 CAACAATATT
*
200931 AAAAATAGAA
1 AAAAAAAGAA
200941 AAAGAAAAGAAA
1 AAA-AAAAG-AA
*
200953 AAAAAAAGAG
1 AAAAAAAGAA
200963 AAAAAAAGAA
1 AAAAAAAGAA
200973 AAAAAA
1 AAAAAA
200979 CTAAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 19 0.58
11 9 0.27
12 5 0.15
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:200956 original size:21 final size:21
Alignment explanation
Indices: 200931--200978 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
200921 CAACAATATT
*
200931 AAAAATAGAAAAAGAAAAGAAA
1 AAAAAAAGAAAAA-AAAAGAAA
*
200953 AAAAAAAGAGAAAAAAAGAAA
1 AAAAAAAGAAAAAAAAAGAAA
200974 AAAAA
1 AAAAA
200979 CTAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAGAAA
Found at i:205444 original size:16 final size:16
Alignment explanation
Indices: 205419--205449 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
205409 AGAGCTTCAG
*
205419 CAAAAGGAGTATTAAA
1 CAAAAAGAGTATTAAA
205435 CAAAAAGAGTATTAA
1 CAAAAAGAGTATTAA
205450 TATGTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
CAAAAAGAGTATTAAA
Found at i:205917 original size:21 final size:21
Alignment explanation
Indices: 205893--205950 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
205883 NNNNNNNNNN
* *
205893 TTGTTATGAATGCATCAGTCT
1 TTGTCATGAATGCATCAGCCT
* *
205914 TTGTCAAGAATGCGTCAGCCT
1 TTGTCATGAATGCATCAGCCT
205935 TTGTCATGAATTGCAT
1 TTGTCATGAA-TGCAT
205951 GAACATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (21 bp):
TTGTCATGAATGCATCAGCCT
Found at i:221561 original size:21 final size:21
Alignment explanation
Indices: 221537--221593 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
221527 AAGTTCTAGA
*
221537 CTTGAGGATTGATTGCCACAC
1 CTTGAGGATCGATTGCCACAC
*
221558 CTTGAGGATCGATTGCCATAC
1 CTTGAGGATCGATTGCCACAC
*
221579 TTTGAGGATCGATTG
1 CTTGAGGATCGATTG
221594 GGGACTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (21 bp):
CTTGAGGATCGATTGCCACAC
Found at i:221858 original size:21 final size:21
Alignment explanation
Indices: 221820--221859 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
221810 CATTTTGCCC
*
221820 TAGGATCGATTGATGCTTTTT
1 TAGGATCGATGGATGCTTTTT
221841 TAGGATCGACTGGA-GCTTT
1 TAGGATCGA-TGGATGCTTT
221860 GTTTTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (21 bp):
TAGGATCGATGGATGCTTTTT
Found at i:224187 original size:20 final size:20
Alignment explanation
Indices: 224158--224211 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
224148 ACATTCACAT
*
224158 TGTATCGATACATTTGAGAA
1 TGTATTGATACATTTGAGAA
224178 TGTATTGATACATTTGAGAA
1 TGTATTGATACATTTGAGAA
224198 TGTATTGATACATT
1 TGTATTGATACATT
224212 AATTGCATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (20 bp):
TGTATTGATACATTTGAGAA
Found at i:226602 original size:35 final size:35
Alignment explanation
Indices: 226494--226606 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 35
226484 TATGCAATAT
* * *
226494 TATGCCACACCCCATTACTACAGCAAACGACGGAGTC
1 TATGTCACACCCCATTGC--CAGCAAACGATGGAGTC
* * *
226531 -ATGTCACTCCCCATTGCCATGGAAAATGATGGAGTC
1 TATGTCACACCCCATTGCCA--GCAAACGATGGAGTC
*
226567 TA-GTTACACCCCATTGCCGAGCAAACGATGGAGTC
1 TATGTCACACCCCATTGCC-AGCAAACGATGGAGTC
226602 T-TGTC
1 TATGTC
226607 GTGCCCTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
34 2 0.03
35 16 0.27
36 40 0.67
37 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (35 bp):
TATGTCACACCCCATTGCCAGCAAACGATGGAGTC
Found at i:226805 original size:91 final size:91
Alignment explanation
Indices: 226634--226819 Score: 239
Period size: 91 Copynumber: 2.0 Consensus size: 91
226624 CAAATGATGA
* *
226634 AGTCAATAATCATCATACAATACCATGTCATGCCCAATTGCCATGGCAAACAACGGAGTTTAGTC
1 AGTCAATAATCATCATACAATACCATGTCACGCCCAATTGCCATGGCAAACAACGGAGTCTAGTC
* * *
226699 ACATCCCATTTTTGAGCAAACGACGG
66 ACAGCCCATTGTTGAGCAAACAACGG
* ** * **
226725 AGTCAATAATGATCATACAATACCATGTCACGCCTTATTGCCATGGCTAATGACGGAGTCTAGTC
1 AGTCAATAATCATCATACAATACCATGTCACGCCCAATTGCCATGGCAAACAACGGAGTCTAGTC
* *
226790 AC-GCCTTATTGTTGAGTAAACAACGG
66 ACAGCC-CATTGTTGAGCAAACAACGG
226816 AGTC
1 AGTC
226820 TACGGTCATC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 2 0.02
91 79 0.98
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (91 bp):
AGTCAATAATCATCATACAATACCATGTCACGCCCAATTGCCATGGCAAACAACGGAGTCTAGTC
ACAGCCCATTGTTGAGCAAACAACGG
Found at i:233768 original size:39 final size:39
Alignment explanation
Indices: 233714--233790 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
233704 GAACATTAAG
*
233714 ACCTAAAACTGAGTCTAAGGGATGTTCTACCACAATAAA
1 ACCTAAAACTGAGTCTAAGGAATGTTCTACCACAATAAA
* * * *
233753 ACCTAAAATTGAGTCTGAGGAATGTTTTACCGCAATAA
1 ACCTAAAACTGAGTCTAAGGAATGTTCTACCACAATAA
233791 TCCTTTTTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (39 bp):
ACCTAAAACTGAGTCTAAGGAATGTTCTACCACAATAAA
Found at i:238431 original size:74 final size:74
Alignment explanation
Indices: 238284--238431 Score: 165
Period size: 74 Copynumber: 2.0 Consensus size: 74
238274 CAAGCAGAGT
* * * *
238284 GCTCTTAGTTGACTAGCCATACTTCTTAGTTGATTAAGCCTTCTCTGTCTCGTAATTGAATTCAT
1 GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGCCTTCTCTGTCTCATAATTGAAGTCAT
* *
238349 TGGTAGTGA
66 TAGCAGTGA
** * * *
238358 GCTCTTAGTTGACTAACCATGTTTTTTAGTCGATTAAG-TTCTCTCTGTCTTATAATTGAAGTC-
1 GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGCCT-TCTCTGTCTCATAATTGAAGTCA
238421 TCTAGCAGTGA
65 T-TAGCAGTGA
238432 ACTATGAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
73 2 0.03
74 59 0.97
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGCCTTCTCTGTCTCATAATTGAAGTCAT
TAGCAGTGA
Found at i:247560 original size:74 final size:74
Alignment explanation
Indices: 247458--247618 Score: 189
Period size: 74 Copynumber: 2.2 Consensus size: 74
247448 AGTGCTTTTA
* ** * * *
247458 TTGACTAACCATACTTCTTAGTTGATTAAGT-CTTCTCTATCTTGTAATTGAATTCTTTGACAAT
1 TTGACTAACCATGCTTCTTAGTCAATTAAGTGC-TCTCTATATTGTAATTGAAGTCTCTGACAAT
*
247522 GATCTCTTAG
65 GAGCTCTTAG
* * * * * *
247532 TTGACTAGCCATGCTTTTTAGTCAATTAAGTGCTCTCTATATTGTATTTTAAGTCTCTGATAGTG
1 TTGACTAACCATGCTTCTTAGTCAATTAAGTGCTCTCTATATTGTAATTGAAGTCTCTGACAATG
247597 AGCTCTTAG
66 AGCTCTTAG
247606 TTGACTAACCATG
1 TTGACTAACCATG
247619 TTGATTAGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 71 0.99
75 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (74 bp):
TTGACTAACCATGCTTCTTAGTCAATTAAGTGCTCTCTATATTGTAATTGAAGTCTCTGACAATG
AGCTCTTAG
Found at i:247643 original size:74 final size:73
Alignment explanation
Indices: 247458--247643 Score: 185
Period size: 74 Copynumber: 2.5 Consensus size: 73
247448 AGTGCTTTTA
* * * * *
247458 TTGACTAACCATACTTCTTAGTTGATTAAGTCTTCTCTATCTTGTAATTGAATTCTTTGACAATG
1 TTGACTAACCAT-GTTATTAGTTGATTAAGTCTTCTCTATATTGTAATTGAAGTCTCTGACAATG
*
247523 ATCTCTTAG
65 AGCTCTTAG
* * ** * * * *
247532 TTGACTAGCCATGCTTTTTAGTCAATTAAGTGC-TCTCTATATTGTATTTTAAGTCTCTGATAGT
1 TTGACTAACCATG-TTATTAGTTGATTAAGT-CTTCTCTATATTGTAATTGAAGTCTCTGACAAT
247596 GAGCTCTTAG
64 GAGCTCTTAG
* *
247606 TTGACTAACCATGTTGATTAGTTGACTAAATCTTCTCT
1 TTGACTAACCATGTT-ATTAGTTGATTAAGTCTTCTCT
247644 GTTTTACAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
73 3 0.03
74 85 0.96
75 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (73 bp):
TTGACTAACCATGTTATTAGTTGATTAAGTCTTCTCTATATTGTAATTGAAGTCTCTGACAATGA
GCTCTTAG
Found at i:257508 original size:50 final size:50
Alignment explanation
Indices: 257433--257532 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
257423 ATTCATTCTT
257433 AGTGCTAGAAAATTATTATCAAAGATTTATGGAGGGATATTTAATAAGGA
1 AGTGCTAGAAAATTATTATCAAAGATTTATGGAGGGATATTTAATAAGGA
257483 AGTGCTAGAAAATTATTATCAAAGATTTATGGAGGGATATTTAATAAGGA
1 AGTGCTAGAAAATTATTATCAAAGATTTATGGAGGGATATTTAATAAGGA
257533 CACACTAACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (50 bp):
AGTGCTAGAAAATTATTATCAAAGATTTATGGAGGGATATTTAATAAGGA
Found at i:262469 original size:22 final size:23
Alignment explanation
Indices: 262444--262490 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
262434 CTACATGGCA
*
262444 TTAG-AGATTCTAATGCATGTGG
1 TTAGAAGATTCTAATGCACGTGG
262466 TTAGTAAAGATTCTAATGCACGTGG
1 TTAG--AAGATTCTAATGCACGTGG
262491 CCTCCAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
25 17 0.81
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (23 bp):
TTAGAAGATTCTAATGCACGTGG
Found at i:264904 original size:21 final size:19
Alignment explanation
Indices: 264868--264908 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
264858 ACATGTTGAG
264868 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
264887 TAGTTATATTTTATGTTATTT
1 TAGTTA-A-TTTAAGTTATTT
264908 T
1 T
264909 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:270322 original size:44 final size:43
Alignment explanation
Indices: 270198--270336 Score: 167
Period size: 43 Copynumber: 3.2 Consensus size: 43
270188 ATCACAACAA
* * *
270198 AATCCACT-TCACAAAACAATCATGGAACTGTGAAGACCTTC-C
1 AATCCA-TATCACAACACAATCATGGAACTATGGAGACCTTCTC
*
270240 TAATCCATTTCACAACACAATCATGGAACTATGGAGACCTTCTC
1 -AATCCATATCACAACACAATCATGGAACTATGGAGACCTTCTC
* *
270284 AATCCATATCACAATACTTATCATAGGAA-TATGGAGACCTTCTC
1 AATCCATATCACAACAC-AATCAT-GGAACTATGGAGACCTTCTC
270328 AATCCATAT
1 AATCCATAT
270337 TTAAAGCACT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
42 1 0.01
43 51 0.59
44 30 0.35
45 4 0.05
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.27
Consensus pattern (43 bp):
AATCCATATCACAACACAATCATGGAACTATGGAGACCTTCTC
Found at i:289866 original size:77 final size:77
Alignment explanation
Indices: 289781--289942 Score: 222
Period size: 77 Copynumber: 2.1 Consensus size: 77
289771 TGAATTTCTC
* *
289781 AAATTAAAATGCTATCCTTAATTTGAAGAATTTC-TTTTAAAGTAGGAAA-ATATTTCCTACTT-
1 AAATTAAAATGCTAACCTTAATTTGAAGAA-TTCACTTTAAAGTAGGAAACA-ATTTCCTA-TTC
289843 TTTATGAATCACCCA
63 TTTATGAATCACCCA
** * *
289858 AAATTAAAATTTTAACCTTAATTTTAGGAATTCACTTTAAAGTAGGAAACAATTTCCTATTCTTT
1 AAATTAAAATGCTAACCTTAATTTGAAGAATTCACTTTAAAGTAGGAAACAATTTCCTATTCTTT
289923 ATGAATCACCCA
66 ATGAATCACCCA
289935 AAATTAAA
1 AAATTAAA
289943 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
76 5 0.07
77 70 0.92
78 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (77 bp):
AAATTAAAATGCTAACCTTAATTTGAAGAATTCACTTTAAAGTAGGAAACAATTTCCTATTCTTT
ATGAATCACCCA
Found at i:292775 original size:36 final size:36
Alignment explanation
Indices: 292669--292879 Score: 204
Period size: 36 Copynumber: 6.0 Consensus size: 36
292659 NNNNNNNNNN
*
292669 ATTAGGCCTAATAACTTAATTAAAC-AATTTAATTC-
1 ATTAAGCCTAATAACTTAATTAAACAAATTTAA-TCA
* * *
292704 ATTAAG-TTCAATAACTTAATT-AATAAATTTGATCA
1 ATTAAGCCT-AATAACTTAATTAAACAAATTTAATCA
*
292739 ATTAAGCCTAATAACTTGATTAAACAAATTTAATCA
1 ATTAAGCCTAATAACTTAATTAAACAAATTTAATCA
* * * *
292775 ATTAGGCCTAATAAGTTGATTAAACAAATTTATTCA
1 ATTAAGCCTAATAACTTAATTAAACAAATTTAATCA
* * *
292811 ATTACGCCCAATAACTTAATTAAAC-AATTTAATGA
1 ATTAAGCCTAATAACTTAATTAAACAAATTTAATCA
* * * *
292846 ATT-AG--GAACAACTTAATCAAACAATTTTAATCA
1 ATTAAGCCTAATAACTTAATTAAACAAATTTAATCA
292879 A
1 A
292880 GTGCTTGAGA
Statistics
Matches: 147, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
32 14 0.10
33 9 0.06
34 6 0.04
35 51 0.35
36 67 0.46
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (36 bp):
ATTAAGCCTAATAACTTAATTAAACAAATTTAATCA
Found at i:312488 original size:71 final size:71
Alignment explanation
Indices: 312388--312564 Score: 225
Period size: 71 Copynumber: 2.5 Consensus size: 71
312378 AACCTATGAT
* * * *
312388 AATCTATCGATACA-TTTGACAATGTATCGATGCATTTAGCTTAGTTTAAAATT-CAAGACATTC
1 AATCTATCGATACATTTTGACAATGTATCGATACATTTAGCTCAATTTAAAATTAAAAG-CATTC
*
312451 TATT-TA
65 TATTCCA
* * *
312457 AATTCTATCGACACATTTTGACAATGAATCGATACATTTAGCTCAATTTAGAATTAAAAGCATTC
1 AA-TCTATCGATACATTTTGACAATGTATCGATACATTTAGCTCAATTTAAAATTAAAAGCATTC
*
312522 TGTTCCA
65 TATTCCA
*
312529 AATCTATCGATATATTTTGACAATGTATCGATACAT
1 AATCTATCGATACATTTTGACAATGTATCGATACAT
312565 GAAGTTTGAC
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
69 2 0.02
70 11 0.12
71 73 0.79
72 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (71 bp):
AATCTATCGATACATTTTGACAATGTATCGATACATTTAGCTCAATTTAAAATTAAAAGCATTCT
ATTCCA
Found at i:324045 original size:15 final size:16
Alignment explanation
Indices: 324022--324054 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
324012 GACCGCATTG
*
324022 CACTTAAAGGC-TTAT
1 CACTGAAAGGCTTTAT
324037 CACTGAAAGGCTTTAT
1 CACTGAAAGGCTTTAT
324053 CA
1 CA
324055 AATTCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (16 bp):
CACTGAAAGGCTTTAT
Found at i:333195 original size:11 final size:11
Alignment explanation
Indices: 333179--333203 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
333169 ATTTTATATG
333179 TAATAAAATAA
1 TAATAAAATAA
333190 TAATAAAATAA
1 TAATAAAATAA
333201 TAA
1 TAA
333204 CATCTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:333909 original size:4 final size:4
Alignment explanation
Indices: 333895--333954 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
333885 AAAAATGAAA
333895 GAAG GAA- GAAG GAAG G-A- GAAG GAA- GAAG GAAG G-A- GAAG GAA-
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
333936 G-AG GAAG AGAAG GAAG GAA
1 GAAG GAAG -GAAG GAAG GAA
333955 AAACAAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
2 3 0.06
3 12 0.26
4 28 0.60
5 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:333916 original size:10 final size:10
Alignment explanation
Indices: 333895--333949 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
333885 AAAAATGAAA
333895 GAAGGAAGAAG
1 GAAGG-AGAAG
333906 GAAGGAGAAG
1 GAAGGAGAAG
333916 G-A--AGAAG
1 GAAGGAGAAG
333923 GAAGGAGAAG
1 GAAGGAGAAG
333933 GAA-GAGGAAG
1 GAAGGA-GAAG
333943 AGAAGGA
1 -GAAGGA
333950 AGGAAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 3 0.08
10 18 0.47
11 8 0.21
12 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (10 bp):
GAAGGAGAAG
Found at i:333916 original size:17 final size:17
Alignment explanation
Indices: 333894--333951 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
333884 GAAAAATGAA
333894 AGAAGGAAGAAGGAAGG
1 AGAAGGAAGAAGGAAGG
333911 AGAAGGAAGAAGGAAGG
1 AGAAGGAAGAAGGAAGG
333928 AGAAGGAAG-AGGAA-G
1 AGAAGGAAGAAGGAAGG
333943 AGAAGGAAG
1 AGAAGGAAG
333952 GAAAAACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.24
16 5 0.12
17 26 0.63
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
AGAAGGAAGAAGGAAGG
Found at i:339242 original size:54 final size:55
Alignment explanation
Indices: 339146--339249 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 55
339136 TCATTCCTCA
*
339146 TAAAGTTTGGAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTTAAACTATAC
1 TAAAGTTTGGAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAACTATAC
339201 TAAAGTTTGGAATGTGAGCA-TTGGGTCATCATTAGGTAGACCCTCAAAC
1 TAAAGTTTGGAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAAC
339250 CATTCCAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 28 0.58
55 20 0.42
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (55 bp):
TAAAGTTTGGAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAACTATAC
Found at i:339268 original size:54 final size:55
Alignment explanation
Indices: 339155--339268 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 55
339145 ATAAAGTTTG
* * * * *
339155 GAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTTAAACTATACTAAAGTTTG
1 GAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAACCATACCAAAGTCTC
*
339210 GAATGTGAGCA-TTGGGTCATCATTAGGTAGACCCTCAAACCATTCCAAA-TGCTC
1 GAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAACCATACCAAAGT-CTC
339264 GAATG
1 GAATG
339269 CAATCCTTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.02
54 40 0.77
55 11 0.21
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (55 bp):
GAATGTGAGCATTTGGGTCATCATTAGGTAGACCCTCAAACCATACCAAAGTCTC
Found at i:340893 original size:25 final size:25
Alignment explanation
Indices: 340842--340894 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
340832 GTTGCAACCG
*** *
340842 CGTATATCAACTTGTGGCCTAGCCA
1 CGTATATCAACCCATGGCCTAGACA
*
340867 CGTATATCAACCCATGGCCTTGACA
1 CGTATATCAACCCATGGCCTAGACA
340892 CGT
1 CGT
340895 GTATAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (25 bp):
CGTATATCAACCCATGGCCTAGACA
Found at i:342370 original size:11 final size:11
Alignment explanation
Indices: 342349--342381 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
342339 ATTTCCTCTA
342349 TTTTC-TTCTC
1 TTTTCTTTCTC
342359 TTTTCTTTCTC
1 TTTTCTTTCTC
*
342370 TTTTCTTCCTC
1 TTTTCTTTCTC
342381 T
1 T
342382 CGAGTGGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:346735 original size:36 final size:36
Alignment explanation
Indices: 346648--346831 Score: 207
Period size: 36 Copynumber: 5.2 Consensus size: 36
346638 TCTCAAGCAC
**
346648 TTGATTAAAATTGTTTAATTAAG---TTGTACCTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* * *
346681 TTAATT-ACATTGTTTAATTAAGTCATTGGGCCTAG
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
*
346716 TTGATTAAAATTGTTTAATTAAGTCATTAGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* ** *
346752 TTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* ** *
346788 TTAATT-AAATTACTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
346823 TTGATTAAA
1 TTGATTAAA
346832 TTAAACAATT
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
32 15 0.12
33 5 0.04
35 41 0.33
36 64 0.51
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (36 bp):
TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
Found at i:346820 original size:71 final size:72
Alignment explanation
Indices: 346676--346831 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 72
346666 TTAAGTTGTA
* * * * * **
346676 CCTAATTAATT-ACATTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAGT
1 CCTAATTGATTAAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAAATTACTTAATTAAGT
346740 CATTAGG
66 CATTAGG
** *
346747 CCTAATTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT-AAATTACTTAATTAAGT
1 CCTAATTGATTAAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAAATTACTTAATTAAGT
* *
346811 TATTGGG
66 CATTAGG
346818 CCTAATTGATTAAA
1 CCTAATTGATTAAA
346832 TTAAACAATT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
71 44 0.61
72 28 0.39
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (72 bp):
CCTAATTGATTAAAATTGTTTAATTAAATCATTGGGCCTAATTAATTAAAATTACTTAATTAAGT
CATTAGG
Found at i:350805 original size:20 final size:20
Alignment explanation
Indices: 350754--350805 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
350744 CTTTGCTTCG
*
350754 CTTTGTTTTTTTGTTTGGTTT
1 CTTTG-TTTTTTGTTTGGGTT
****
350775 CTTCAACTTTTGTTTGGGTT
1 CTTTGTTTTTTGTTTGGGTT
350795 CTTTGTTTTTT
1 CTTTGTTTTTT
350806 TTTTTTTGGA
Statistics
Matches: 22, Mismatches: 9, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.04, C:0.10, G:0.17, T:0.69
Consensus pattern (20 bp):
CTTTGTTTTTTGTTTGGGTT
Found at i:354726 original size:20 final size:20
Alignment explanation
Indices: 354699--354767 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
354689 AAAAAATTGT
*
354699 AAATTATTTAAAAAATAA-A
1 AAATTATTTAAAAAAGAATA
354718 AAATATATTTTAAAAAAGAATA
1 AAAT-TA-TTTAAAAAAGAATA
*
354740 AAATGTATTATAAATAAAAATATA
1 AAAT-TATT-TAAA-AAAGA-ATA
354764 AAAT
1 AAAT
354768 AGTATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 13 0.32
22 11 0.27
23 4 0.10
24 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATTATTTAAAAAAGAATA
Found at i:354742 original size:22 final size:22
Alignment explanation
Indices: 354705--354768 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
354695 TTGTAAATTA
*
354705 TTTAAAAAATAA-AAAATATAT
1 TTTAAAAAAAAATAAAATATAT
* *
354726 TTTAAAAAAGAATAAAATGTAT
1 TTTAAAAAAAAATAAAATATAT
*
354748 TATAAATAAAAATATAAAATA
1 TTTAAA-AAAAA-ATAAAATA
354769 GTATAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 11 0.31
22 13 0.37
23 4 0.11
24 7 0.20
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (22 bp):
TTTAAAAAAAAATAAAATATAT
Found at i:356246 original size:38 final size:39
Alignment explanation
Indices: 356191--356265 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
356181 CTATGCATGC
*
356191 GTGGATGAATGAATACCCAC-CTTTATGA-TAATGTGAGT
1 GTGGATAAATGAATACCCACTCTTTATGACT-ATGTGAGT
* *
356229 GTGGATAAATGAGTACCCACTTTTTATGACTATGTGA
1 GTGGATAAATGAATACCCACTCTTTATGACTATGTGA
356266 TTAATATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 18 0.56
39 13 0.41
40 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (39 bp):
GTGGATAAATGAATACCCACTCTTTATGACTATGTGAGT
Found at i:359652 original size:26 final size:27
Alignment explanation
Indices: 359613--359666 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
359603 AAACAAATTG
*
359613 TGAAAAATGCTTTTA-ACTTGTCTTCAT
1 TGAAAAATGCTTTTACA-TTGCCTTCAT
*
359640 TGAAAAA-GTTTTTACATTGCCTTCAT
1 TGAAAAATGCTTTTACATTGCCTTCAT
359666 T
1 T
359667 AGGAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (27 bp):
TGAAAAATGCTTTTACATTGCCTTCAT
Found at i:360497 original size:2 final size:2
Alignment explanation
Indices: 360492--360532 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
360482 TGTGCGTGTG
* *
360492 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
360533 ACACCCCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:360805 original size:19 final size:21
Alignment explanation
Indices: 360776--360820 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
360766 AATCTAAAGG
360776 TTTGATGCTTAGATTGGAGT-
1 TTTGATGCTTAGATTGGAGTA
* *
360796 TTTGAT-CTTAGGTTTGAGTA
1 TTTGATGCTTAGATTGGAGTA
360816 TTTGA
1 TTTGA
360821 GTCATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.20, C:0.04, G:0.27, T:0.49
Consensus pattern (21 bp):
TTTGATGCTTAGATTGGAGTA
Found at i:368366 original size:55 final size:54
Alignment explanation
Indices: 368264--368378 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 54
368254 CTCACTAACC
* *
368264 TTACAAGAACACTTGCTTACAACCTTCTAGTTTTAGTTGAAGTAAAACACAAAT
1 TTACAAGAACACTTGCTTACAACCTTCTAGTTTCAGTTAAAGTAAAACACAAAT
* * * *
368318 TTACAAGAACACTTGCTTGCACCCATTCTAGTTTCGGTTAAAGTAAAACAGAAAT
1 TTACAAGAACACTTGCTTACAACC-TTCTAGTTTCAGTTAAAGTAAAACACAAAT
*
368373 ATACAA
1 TTACAA
368379 AGTGTTTCCC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 22 0.42
55 31 0.58
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (54 bp):
TTACAAGAACACTTGCTTACAACCTTCTAGTTTCAGTTAAAGTAAAACACAAAT
Found at i:376017 original size:77 final size:75
Alignment explanation
Indices: 375885--376125 Score: 297
Period size: 77 Copynumber: 3.1 Consensus size: 75
375875 ACCACCAGCG
* * * *
375885 GAAACAATTTCCTATTCTTTGTGAATCACCTAAAATTAAAATTCTATCTTTAATTTTAGGAGTTA
1 GAAAAAATTTCCTATTCTTTATGAATCACCCAAAATTAAAATTCTATC-TTAATTTTAGGAATTA
375950 CTTTTAAAGTA
65 CTTTTAAAGTA
* * *
375961 GAAAATAATTTCTTATTCTTTACGAATCACCCAAAACTAAAATTCTATTCTTAATTTTAGGAATT
1 GAAAA-AATTTCCTATTCTTTATGAATCACCCAAAATTAAAATTCTA-TCTTAATTTTAGGAATT
376026 GA-TTTTAAAGTA
64 -ACTTTTAAAGTA
* * *
376038 -AGAACAATTTCCTATTCTTGATGAATCACCCAAAAATTAAATTTCTATCTATAATTTTAGGAAT
1 GA-AAAAATTTCCTATTCTTTATGAATCACCC-AAAATTAAAATTCTATCT-TAATTTTAGGAAT
*
376102 TGCTTTTAAAGTAA
63 TACTTTTAAAGT-A
376116 GAAAAAATTT
1 GAAAAAATTT
376126 TCTGTTTTTT
Statistics
Matches: 141, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
76 31 0.22
77 98 0.70
78 11 0.08
79 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (75 bp):
GAAAAAATTTCCTATTCTTTATGAATCACCCAAAATTAAAATTCTATCTTAATTTTAGGAATTAC
TTTTAAAGTA
Found at i:386532 original size:21 final size:22
Alignment explanation
Indices: 386507--386550 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
386497 AAGTGATTAA
386507 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
386528 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
386550 T
1 T
386551 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:411288 original size:35 final size:34
Alignment explanation
Indices: 411249--411421 Score: 152
Period size: 36 Copynumber: 5.0 Consensus size: 34
411239 NNNNNNNNNC
411249 AATTAGGCTCAATAACTTAATTAAAAAATTTAATT
1 AATTAGGC-CAATAACTTAATTAAAAAATTTAATT
** * *
411284 AATTAGGTCCAATAGTTTAATTAAACAATTTTAATC
1 AATTAGG-CCAATAACTTAATTAAA-AAATTTAATT
* ** *
411320 AATTAGGCCCACTGCCTTAATTAAACAATTTTAATT
1 AATTAGG-CCAATAACTTAATTAAA-AAATTTAATT
** * *
411356 AACGAGGCCTAATGACTTAATTAAATAATTTAATT
1 AATTAGGCC-AATAACTTAATTAAAAAATTTAATT
* *
411391 AATTAGG-C-ATAACTTAATTAAACACTTTAAT
1 AATTAGGCCAATAACTTAATTAAAAAATTTAAT
411422 CAAGTGCTTG
Statistics
Matches: 114, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
32 20 0.18
34 1 0.01
35 36 0.32
36 57 0.50
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (34 bp):
AATTAGGCCAATAACTTAATTAAAAAATTTAATT
Found at i:424187 original size:19 final size:19
Alignment explanation
Indices: 424163--424206 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
424153 TTGTCATAAT
424163 CAAAACTATAATTTTATCA
1 CAAAACTATAATTTTATCA
* *
424182 CAAAACTATCATTTTGTCA
1 CAAAACTATAATTTTATCA
424201 CAAAAC
1 CAAAAC
424207 CTTGTAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (19 bp):
CAAAACTATAATTTTATCA
Found at i:433023 original size:18 final size:18
Alignment explanation
Indices: 433000--433041 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
432990 TTAATATTTT
*
433000 AATATTATTTT-TTTATAA
1 AATATTATTTTATTCA-AA
433018 AATATTATTTTATTCAAA
1 AATATTATTTTATTCAAA
433036 AATATT
1 AATATT
433042 CTTTCTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTATTTTATTCAAA
Found at i:454389 original size:18 final size:18
Alignment explanation
Indices: 454366--454425 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
454356 TAATATAATC
454366 AATTAAGCCTAATAACTT
1 AATTAAGCCTAATAACTT
* *
454384 AATTAA-ACAAATTTAA-TT
1 AATTAAGCCTAA--TAACTT
*
454402 AATTAGGCCTAATAACTT
1 AATTAAGCCTAATAACTT
454420 AATTAA
1 AATTAA
454426 ACAAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 6 0.19
18 20 0.62
19 6 0.19
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (18 bp):
AATTAAGCCTAATAACTT
Found at i:454406 original size:36 final size:35
Alignment explanation
Indices: 454374--454541 Score: 193
Period size: 36 Copynumber: 4.9 Consensus size: 35
454364 TCAATTAAGC
454374 CTAATAACTTAATTAAACAAATTTAATTAATTAGG
1 CTAATAACTTAATTAAACAAATTTAATTAATTAGG
*
454409 CCTAATAACTTAATTAAACAAATTTAATCAATTAGG
1 -CTAATAACTTAATTAAACAAATTTAATTAATTAGG
* ***
454445 TTCAATAACTTAATT-ATTTAATTTAATTAATTAGG
1 CT-AATAACTTAATTAAACAAATTTAATTAATTAGG
* *
454480 CTAAATGACTTAATTAAAC-AATTTAATGAATT-GG
1 CT-AATAACTTAATTAAACAAATTTAATTAATTAGG
* *
454514 C--ACAACTTAATTAAACAATTTTAATTAA
1 CTAATAACTTAATTAAACAAATTTAATTAA
454542 GTGCTTGAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
31 13 0.12
32 9 0.08
34 3 0.03
35 41 0.36
36 47 0.42
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (35 bp):
CTAATAACTTAATTAAACAAATTTAATTAATTAGG
Found at i:454477 original size:107 final size:102
Alignment explanation
Indices: 454345--454538 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 102
454335 AGCCCAATTG
* *
454345 ACTTAATTGTTTAATATAATCAATTAAGCCT-AATAACTTAATTAAACAAATTTAATTAATTAGG
1 ACTTAATTATTTAATATAATCAATT-AGCCTAAATAACTTAATTAAAC-AATTTAATGAATT-GG
*
454409 CCTAATAACTTAATTAAACAAATTTAATCAATTAGGTTCAATA
63 -C--ACAACTTAATTAAACAAATTTAATCAATTAGGTTCAATA
* * * *
454452 ACTTAATTATTTAATTTAATTAATTAGGCTAAATGACTTAATTAAACAATTTAATGAATTGGCAC
1 ACTTAATTATTTAATATAATCAATTAGCCTAAATAACTTAATTAAACAATTTAATGAATTGGCAC
*
454517 AACTTAATTAAACAATTTTAAT
66 AACTTAATTAAACAAATTTAAT
454539 TAAGTGCTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
102 22 0.28
104 1 0.01
105 2 0.03
106 16 0.21
107 37 0.47
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (102 bp):
ACTTAATTATTTAATATAATCAATTAGCCTAAATAACTTAATTAAACAATTTAATGAATTGGCAC
AACTTAATTAAACAAATTTAATCAATTAGGTTCAATA
Found at i:456234 original size:20 final size:19
Alignment explanation
Indices: 456201--456240 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
456191 CTATAGGGGA
456201 AAATGTATCAATACATCTCT
1 AAATGTATCAATACAT-TCT
**
456221 AAATGTATTGATACATTCT
1 AAATGTATCAATACATTCT
456240 A
1 A
456241 GGCAGGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (19 bp):
AAATGTATCAATACATTCT
Found at i:460683 original size:50 final size:50
Alignment explanation
Indices: 460608--460756 Score: 264
Period size: 50 Copynumber: 3.0 Consensus size: 50
460598 AAATTAAAAC
460608 AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
1 AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
460658 AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
1 AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
* * *
460708 AAACATGTTTTCTTATCTAGATTAAGAC-AATATGTTTTCTTGTCTAAAT
1 AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
460757 TAAGACAAAG
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 20 0.21
50 76 0.79
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (50 bp):
AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAAT
Found at i:460753 original size:27 final size:28
Alignment explanation
Indices: 460513--460765 Score: 255
Period size: 28 Copynumber: 9.4 Consensus size: 28
460503 TCTTATCTTT
* *
460513 AATTAAGACAAAACATCTTATCTTGTCTA
1 AATTAAGAC-AAACATGTTTTCTTGTCTA
* * * *
460542 AATTGATACAAACATGTTTTCTTATCGA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* * * *
460570 GATCAAGACTATATAT-TTTTCTTGTCTTA
1 AATTAAGAC-AAACATGTTTTCTTGTC-TA
*
460599 AATTAAAACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
460627 AATTAAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
460655 AA-T-----AAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
460677 AATTAAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
*
460705 AA-T-----AAACATGTTTTCTTATCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* *
460727 GATTAAGAC-AATATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
460754 AATTAAGACAAA
1 AATTAAGACAAA
460766 GCATCTTAAA
Statistics
Matches: 183, Mismatches: 25, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
22 40 0.22
23 2 0.01
27 26 0.14
28 87 0.48
29 28 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:470777 original size:73 final size:74
Alignment explanation
Indices: 470643--470829 Score: 211
Period size: 73 Copynumber: 2.6 Consensus size: 74
470633 GACAGAATGT
* * * * *
470643 TCTTAGTTGACTAA-CATGCTTTTTAGTCGACTAAGTCGTTTCTATCTTCTAATCTCAGTTTCTG
1 TCTTAGTCGACTAACCATGCTTCTTAGTCGACTAAGTAGTTTCTATCTTCTAATCCCAGTTTCTA
470707 GCAGTAAGC
66 GCAGTAAGC
* * * *
470716 TCTTAGTCGACTAACCATGCTTCTTAGTCGATTAGGTATTTTTTATCTT-TGAA-CCCAGTTTCT
1 TCTTAGTCGACTAACCATGCTTCTTAGTCGACTAAGTAGTTTCTATCTTCT-AATCCCAGTTTCT
470779 AGCAGTAAGC
65 AGCAGTAAGC
* * * * *
470789 TTTTAGTCGACTAACAATACCTCTTGGTCGACTAAGT-GTTT
1 TCTTAGTCGACTAACCATGCTTCTTAGTCGACTAAGTAGTTT
470830 TCAGTTTCAC
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
72 3 0.03
73 62 0.65
74 30 0.32
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (74 bp):
TCTTAGTCGACTAACCATGCTTCTTAGTCGACTAAGTAGTTTCTATCTTCTAATCCCAGTTTCTA
GCAGTAAGC
Found at i:500996 original size:15 final size:15
Alignment explanation
Indices: 500973--501006 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
500963 AACACACTAC
500973 AAAAGAAAATGAGAAAG
1 AAAA-AAAA-GAGAAAG
500990 AAAAAAAAGAGAAAG
1 AAAAAAAAGAGAAAG
501005 AA
1 AA
501007 CCCCAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGAGAAAG
Found at i:512441 original size:277 final size:277
Alignment explanation
Indices: 511942--512487 Score: 858
Period size: 277 Copynumber: 2.0 Consensus size: 277
511932 AGAAAAAATT
**********
511942 AATCATATCCAAACACTCAAAAATAATTGATTAACTAAAACTAATTAANNNNNNNNNNAACTAAT
1 AATCATATCCAAACACTCAAAAATAATTGATTAACTAAAACTAATTAACTAAAATTTAAACTAAT
* * *
512007 AGGAAAAATCAAAATAATGATAAATTGAGTAAATATCAAATCAAACAAGCCTAGGATTACAATAT
66 AAGAAAAATCAAAATAATAATAAATTGAGTAAATATCAAATCAAACAAGCCTAAGATTACAATAT
512072 CCCTCACACTTCATCTAAATCTTACCTCTCTTCCTTAACTTATTTCAATAGTTTGAATTACTAAC
131 CCCTCACACTTCATCTAAATCTTACCTCTCTTCCTTAACTTATTTCAATAGTTTGAATTACTAAC
* * *
512137 CTAGAGTCCTAAATTATTTATAAGGGTCTACCGACTCATCTTATAAAAATATCTGTTTTAACTAA
196 CTAAAGTCCTAAATTATTTATAAGGGTCTACCAACTCATCTTATAAAAATATCTATTTTAACTAA
*
512202 AATACTATAAACTAATC
261 AACACTATAAACTAATC
* *
512219 AATCTTATCCAAACACTCAAAATTAATTGATTAACTAAAACTAATTAACTAAAATTTAAACTAAT
1 AATCATATCCAAACACTCAAAAATAATTGATTAACTAAAACTAATTAACTAAAATTTAAACTAAT
* *
512284 AAGAAAAATCAAAATAATAATAACTTGAGTAAATATCAAATCAAACAAGCCTAAGATTATAATAT
66 AAGAAAAATCAAAATAATAATAAATTGAGTAAATATCAAATCAAACAAGCCTAAGATTACAATAT
* **
512349 CCCTCACACTTCATTTAAATCTTACCTCTCTTCCTTAACTTATTTCAATAGTTTGAATTGTTAAC
131 CCCTCACACTTCATCTAAATCTTACCTCTCTTCCTTAACTTATTTCAATAGTTTGAATTACTAAC
* *
512414 CTAAAGTTCTAAATTATTTATAAGGGTCTCCCAACTCATCTTATAAAAATATCTATTTTAACTAA
196 CTAAAGTCCTAAATTATTTATAAGGGTCTACCAACTCATCTTATAAAAATATCTATTTTAACTAA
512479 AACACTATA
261 AACACTATA
512488 TCCCTATCTG
Statistics
Matches: 243, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
277 243 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.32
Consensus pattern (277 bp):
AATCATATCCAAACACTCAAAAATAATTGATTAACTAAAACTAATTAACTAAAATTTAAACTAAT
AAGAAAAATCAAAATAATAATAAATTGAGTAAATATCAAATCAAACAAGCCTAAGATTACAATAT
CCCTCACACTTCATCTAAATCTTACCTCTCTTCCTTAACTTATTTCAATAGTTTGAATTACTAAC
CTAAAGTCCTAAATTATTTATAAGGGTCTACCAACTCATCTTATAAAAATATCTATTTTAACTAA
AACACTATAAACTAATC
Found at i:513796 original size:397 final size:397
Alignment explanation
Indices: 513063--513856 Score: 1313
Period size: 397 Copynumber: 2.0 Consensus size: 397
513053 NNNNNNNNGT
*
513063 CAACTTTTCTTATTTTTGGAAAGTCACCTAGCGTTGCAGCGCTGAGCTCTCTGGAAGTTTGTATG
1 CAACTTTTCTTATTTTTGGAAAGTCACCTAGCGCTGCAGCGCTGAGCTCTCTGGAAGTTTGTATG
**********
513128 TGTGCTTCCTTTCATCAAAGCTGCAACCTTGTTCTCCCAGTGTTGTGGCAGTCNNNNNNNNNNAA
66 TGTGCTTCCTTTCATCAAAGCTGCAACCTTGTTCTCCCAGTGTTGTGGCAGTCTTTCAATATCAA
513193 ACATAAGTTTCACCCTGATATGTTTCGTAATGGGCAAAGTCTCAAACATAAAAGTTTTATTCTTG
131 ACATAAGTTTCACCCTGATATGTTTCGTAATGGGCAAAGTCTCAAACATAAAAGTTTTATTCTTG
*
513258 TCTCTTAACTTTCAAATGGATAAAGAATCACATCAATTAGAGTTATGGATTGAAATATATGCTCC
196 TCTCTTAACATTCAAATGGATAAAGAATCACATCAATTAGAGTTATGGATTGAAATATATGCTCC
* * * *
513323 AAATACCGCATCATGTTCAATCTTTGCGTACTGCTGTAGTGCTTTGATTTTGACAAATATTTTGA
261 AAATACCACATCATGTTCAATCTTTGCATACTGCTGCAGTGCTCTGATTTTGACAAATATTTTGA
* *
513388 CCATGATACAATCAGAACTGGGCAAATTGGTCAAAATAAAAGTTATAGATATTCTTCTTATAATT
326 CCATGATACAATCAGAACTAGGCAAATCGGTCAAAATAAAAGTTATAGATATTCTTCTTATAATT
*
513453 CTATTGG
391 ATATTGG
* *
513460 CAACTTTTCTTATTTTTGGAAAGTCACCTAGCGCTGCGGCGTTGAGCTCTCTGGAAGTTTGTATG
1 CAACTTTTCTTATTTTTGGAAAGTCACCTAGCGCTGCAGCGCTGAGCTCTCTGGAAGTTTGTATG
**
513525 TGTGCTTCCTTTCATCAAAGCTGCAGTCTTGTTCTCCCAGTGTTGTGGCAGTCTTTCAATATCAA
66 TGTGCTTCCTTTCATCAAAGCTGCAACCTTGTTCTCCCAGTGTTGTGGCAGTCTTTCAATATCAA
513590 ACATAAGTTTCACCCTGATATG-TTCAGTAATGGGCAAAGTCTCAAACATAAAAGTTTTATT-TG
131 ACATAAGTTTCACCCTGATATGTTTC-GTAATGGGCAAAGTCTCAAACATAAAAGTTTTATTCT-
* *
513653 TGTCTCTTAACATTCAAATGGATCACGAATCACATCAATTAGAGTTATGGATTGAAATATATGCT
194 TGTCTCTTAACATTCAAATGGATAAAGAATCACATCAATTAGAGTTATGGATTGAAATATATGCT
*
513718 CCAAATACCACATCATGTTCAGTCTTTGCATACTGCTGCAGTGCTCTGATTTTGACAAATATTTT
259 CCAAATACCACATCATGTTCAATCTTTGCATACTGCTGCAGTGCTCTGATTTTGACAAATATTTT
*
513783 GACCATGATACAATCAGAACTAGGCAAATCGGTCAAAATAAAAGTTGTAGATATTCTTCTTATAA
324 GACCATGATACAATCAGAACTAGGCAAATCGGTCAAAATAAAAGTTATAGATATTCTTCTTATAA
513848 TTATATTGG
389 TTATATTGG
513857 TTTAAGAATC
Statistics
Matches: 368, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
396 4 0.01
397 364 0.99
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (397 bp):
CAACTTTTCTTATTTTTGGAAAGTCACCTAGCGCTGCAGCGCTGAGCTCTCTGGAAGTTTGTATG
TGTGCTTCCTTTCATCAAAGCTGCAACCTTGTTCTCCCAGTGTTGTGGCAGTCTTTCAATATCAA
ACATAAGTTTCACCCTGATATGTTTCGTAATGGGCAAAGTCTCAAACATAAAAGTTTTATTCTTG
TCTCTTAACATTCAAATGGATAAAGAATCACATCAATTAGAGTTATGGATTGAAATATATGCTCC
AAATACCACATCATGTTCAATCTTTGCATACTGCTGCAGTGCTCTGATTTTGACAAATATTTTGA
CCATGATACAATCAGAACTAGGCAAATCGGTCAAAATAAAAGTTATAGATATTCTTCTTATAATT
ATATTGG
Found at i:526399 original size:36 final size:36
Alignment explanation
Indices: 526324--526428 Score: 99
Period size: 36 Copynumber: 2.9 Consensus size: 36
526314 CATTCAATAT
*
526324 ATCCTAGATCATGGGAATCGTACCATTATCCTCAGTA
1 ATCCTAGAT-AAGGGAATCGTACCATTATCCTCAGTA
* *
526361 ATCCTAGATAAGGGGATCGTACC-TCTATCTTC-GATA
1 ATCCTAGATAAGGGAATCGTACCAT-TATCCTCAG-TA
* *
526397 ATCCTAGAT-AGTGGAGATTGTACCATTGTCCT
1 ATCCTAGATAAG-GGA-ATCGTACCATTATCCT
526429 TGTTAGGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
35 4 0.07
36 31 0.55
37 20 0.36
38 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (36 bp):
ATCCTAGATAAGGGAATCGTACCATTATCCTCAGTA
Found at i:528494 original size:28 final size:27
Alignment explanation
Indices: 528446--528713 Score: 186
Period size: 27 Copynumber: 9.9 Consensus size: 27
528436 AATGGTGTGA
*
528446 AATAACTAAATCTTCAACATGGCATGT
1 AATAACTAAATTTTCAACATGGCATGT
* * * * *
528473 GACAACTATAATTTTTAACATGGCTTGC
1 AATAACTA-AATTTTCAACATGGCATGT
*
528501 AATAACTAAATTTTCAGCATGGCATGT
1 AATAACTAAATTTTCAACATGGCATGT
*
528528 AATAACTAAATTTTCAACAT-GAAGTGT
1 AATAACTAAATTTTCAACATGGCA-TGT
** * ** *
528555 AATAGTTACATTTTCCAACATAACGTGT
1 AATAACTAAATTTT-CAACATGGCATGT
* * * *
528583 AACAATTAAATTTTCAATATAGCATG-
1 AATAACTAAATTTTCAACATGGCATGT
* * *
528609 AACAACTATATTTTCAACACGGCATGT
1 AATAACTAAATTTTCAACATGGCATGT
* * ***
528636 AATAA-T-TATTTCCAACATGATGTGT
1 AATAACTAAATTTTCAACATGGCATGT
* *
528661 AACAACTAAATTTTAGAACATGGCATGT
1 AATAACTAAATTTT-CAACATGGCATGT
* *
528689 AA-CACTACATTTTTCAACATGGCAT
1 AATAACTA-AATTTTCAACATGGCAT
528714 TAACAACATT
Statistics
Matches: 185, Mismatches: 47, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
25 18 0.10
26 25 0.14
27 85 0.46
28 57 0.31
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (27 bp):
AATAACTAAATTTTCAACATGGCATGT
Found at i:528535 original size:55 final size:54
Alignment explanation
Indices: 528446--528711 Score: 155
Period size: 55 Copynumber: 4.9 Consensus size: 54
528436 AATGGTGTGA
* *
528446 AATAACTAAATCTTCAACATGGCATGTGACAACTATAATTTTTAACATGGCTTGC
1 AATAACTAAATCTTCAACATGGCATGTAACAACTA-AATTTTCAACATGGCTTGC
* * * *** *
528501 AATAACTAAATTTTCAGCATGGCATGTAATAACTAAATTTTCAACATGAAGTGT
1 AATAACTAAATCTTCAACATGGCATGTAACAACTAAATTTTCAACATGGCTTGC
** * * ** * * * * *
528555 AATAGTTACATTTTCCAACATAACGTGTAACAATTAAATTTTCAATATAGCATG-
1 AATAACTAAATCTT-CAACATGGCATGTAACAACTAAATTTTCAACATGGCTTGC
* * * * * * * * *
528609 AACAACTATATTTTCAACACGGCATGTAATAA-T-TATTTCCAACAT-GATGTGT
1 AATAACTAAATCTTCAACATGGCATGTAACAACTAAATTTTCAACATGGCT-TGC
* * * *
528661 AACAACTAAATTTTAGAACATGGCATGTAAC-ACTACATTTTTCAACATGGC
1 AATAACTAAATCTT-CAACATGGCATGTAACAACTA-AATTTTCAACATGGC
528712 ATTAACAACA
Statistics
Matches: 158, Mismatches: 45, Indels: 15
0.72 0.21 0.07
Matches are distributed among these distances:
50 1 0.01
51 11 0.07
52 15 0.09
53 27 0.17
54 35 0.22
55 68 0.43
56 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (54 bp):
AATAACTAAATCTTCAACATGGCATGTAACAACTAAATTTTCAACATGGCTTGC
Found at i:528671 original size:78 final size:81
Alignment explanation
Indices: 528504--528707 Score: 211
Period size: 78 Copynumber: 2.5 Consensus size: 81
528494 GGCTTGCAAT
* * * * *
528504 AACTAAATTTTCAGCATGGCATGTAATAACTAAATTTTCAACATGAAGTGTAATAGTTACATTTT
1 AACTAAATTTTCAACATAGCATGTAACAACTAAATTTTCAACAGGAAGTGTAATAATTA-ATTTT
528569 CCAACATAACGTGTAAC
65 CCAACATAACGTGTAAC
* * * *
528586 AATTAAATTTTCAATATAGCATG-AACAACTATATTTTCAACACGGCA-TGTAATAATT-A-TTT
1 AACTAAATTTTCAACATAGCATGTAACAACTAAATTTTCAACA-GGAAGTGTAATAATTAATTTT
* *
528647 CCAACATGATGTGTAAC
65 CCAACATAACGTGTAAC
* * *
528664 AACTAAATTTTAGAACATGGCATGTAAC-ACTACATTTTTCAACA
1 AACTAAATTTT-CAACATAGCATGTAACAACTA-AATTTTCAACA
528708 TGGCATTAAC
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
78 28 0.28
79 14 0.14
80 12 0.12
81 26 0.26
82 21 0.21
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (81 bp):
AACTAAATTTTCAACATAGCATGTAACAACTAAATTTTCAACAGGAAGTGTAATAATTAATTTTC
CAACATAACGTGTAAC
Found at i:528730 original size:26 final size:26
Alignment explanation
Indices: 528677--528726 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
528667 TAAATTTTAG
528677 AACATGGCATGTAACACTACATTTTTC
1 AACATGGCATGTAACAC-ACATTTTTC
528704 AACATGGCAT-TAACA-ACATTTTT
1 AACATGGCATGTAACACACATTTTT
528727 TTCATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
26 5 0.22
27 10 0.43
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (26 bp):
AACATGGCATGTAACACACATTTTTC
Found at i:536157 original size:17 final size:17
Alignment explanation
Indices: 536127--536176 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
536117 ATTATATTAT
*
536127 ATATATACTAATACTTTTA
1 ATATATA-T-ATACTTTAA
536146 ATATATATATACTTTAA
1 ATATATATATACTTTAA
*
536163 ATATAAATATACTT
1 ATATATATATACTT
536177 ACTTTCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 21 0.72
18 1 0.03
19 7 0.24
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATACTTTAA
Found at i:536611 original size:20 final size:20
Alignment explanation
Indices: 536582--536626 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
536572 AATTATTAAT
536582 TATA-ACACACACATATATA-
1 TATATACACACAC-TATATAG
*
536601 TATATACACACACTTTATAG
1 TATATACACACACTATATAG
536621 TATATA
1 TATATA
536627 ACTTGTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (20 bp):
TATATACACACACTATATAG
Found at i:540455 original size:2 final size:2
Alignment explanation
Indices: 540442--540478 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
540432 ATTATAATCA
*
540442 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540479 ACTATAGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:549987 original size:16 final size:16
Alignment explanation
Indices: 549966--550005 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
549956 TGTTAATATT
549966 TTTATTATTATTAAAA
1 TTTATTATTATTAAAA
* * *
549982 TTTATTAATATTGAAG
1 TTTATTATTATTAAAA
549998 TTTATTAT
1 TTTATTAT
550006 ATTTGATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTATTATTATTAAAA
Found at i:562447 original size:21 final size:19
Alignment explanation
Indices: 562423--562461 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
562413 TTGTAATAAG
562423 AATTGAACAATAATCTTTATA
1 AATTG-ACAA-AATCTTTATA
*
562444 AATTGACTAAATCTTTAT
1 AATTGACAAAATCTTTAT
562462 TCCACATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTGACAAAATCTTTATA
Found at i:564245 original size:2 final size:2
Alignment explanation
Indices: 564238--564273 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
564228 AACATTAACC
564238 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
564274 GGCAGCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570248 original size:18 final size:19
Alignment explanation
Indices: 570212--570249 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
570202 TTCAGAGAAG
* *
570212 CTTTAGTCTTCCTCCTTAT
1 CTTTAGTCTGCCTCATTAT
570231 CTTTA-TCTGCCTCATTAT
1 CTTTAGTCTGCCTCATTAT
570249 C
1 C
570250 ACCCAAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.13, C:0.32, G:0.05, T:0.50
Consensus pattern (19 bp):
CTTTAGTCTGCCTCATTAT
Found at i:574539 original size:39 final size:40
Alignment explanation
Indices: 574480--574583 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 40
574470 AGCTTGACTA
* * *
574480 GGTAATTGACATGGTCTTACCCTTTTATTTTGA-TTCG-TT
1 GGTAGTTGACATGGTCTTACCCTTTGA-TATGACTTCGTTT
*
574519 GGTAGTTGACATGGTCTTACCCCTTTGATATGACTTTGTTT
1 GGTAGTTGACATGGTCTTA-CCCTTTGATATGACTTCGTTT
*
574560 GGTAGTTGACTTGGTCTTACCCTT
1 GGTAGTTGACATGGTCTTACCCTT
574584 GATTTGGGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
39 22 0.39
40 15 0.26
41 20 0.35
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.45
Consensus pattern (40 bp):
GGTAGTTGACATGGTCTTACCCTTTGATATGACTTCGTTT
Found at i:582101 original size:39 final size:39
Alignment explanation
Indices: 582056--582259 Score: 166
Period size: 41 Copynumber: 5.2 Consensus size: 39
582046 ATTGACTTGA
* * *
582056 TAGTTGACATAGTCCTACCCCTTGATTTTGGTTCGTTGG
1 TAGTTGACATGGTCTTACCCCTTGATTTTGGTTTGTTGG
* *
582095 TAGTTGACATGGTCTTACCCCCTTGA-TATGACTTTGTTTGG
1 TAGTTGACATGGTCTTA-CCCCTTGATTTTG-GTTTG-TTGG
* *
582136 TATTTGACATGGTCTTACCCTTTGATTTTGGTTTGTTGG
1 TAGTTGACATGGTCTTACCCCTTGATTTTGGTTTGTTGG
** * ***
582175 TAGTCAACATGGTCATT-CCCCTTTGATATAACTTTGTTTGG
1 TAGTTGACATGGTC-TTACCCC-TTGATTTTGGTTTG-TTGG
* * *
582216 TAGTTGACATGGTCCTA--CCTTTAATTTGGTTT-TGTGG
1 TAGTTGACATGGTCTTACCCCTTGATTTTGGTTTGT-TGG
582253 TAGTTGA
1 TAGTTGA
582260 TATAGTCATA
Statistics
Matches: 130, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 10 0.08
38 7 0.05
39 38 0.29
40 35 0.27
41 39 0.30
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (39 bp):
TAGTTGACATGGTCTTACCCCTTGATTTTGGTTTGTTGG
Found at i:582143 original size:41 final size:41
Alignment explanation
Indices: 582091--582234 Score: 170
Period size: 41 Copynumber: 3.6 Consensus size: 41
582081 TTTTGGTTCG
*
582091 TTGGTAGTTGACATGGTCTTACCCCCTTGATATGACTTTGT
1 TTGGTAGTTGACATGGTCTTACCCCTTTGATATGACTTTGT
* * *
582132 TTGGTATTTGACATGGTCTTA-CCCTTTGATTTTG-GTTTG-
1 TTGGTAGTTGACATGGTCTTACCCCTTTGA-TATGACTTTGT
** *
582171 TTGGTAGTCAACATGGTCATT-CCCCTTTGATATAACTTTGT
1 TTGGTAGTTGACATGGTC-TTACCCCTTTGATATGACTTTGT
*
582212 TTGGTAGTTGACATGGTCCTACC
1 TTGGTAGTTGACATGGTCTTACC
582235 TTTAATTTGG
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
39 17 0.20
40 26 0.31
41 41 0.49
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (41 bp):
TTGGTAGTTGACATGGTCTTACCCCTTTGATATGACTTTGT
Found at i:582201 original size:80 final size:80
Alignment explanation
Indices: 582056--582256 Score: 266
Period size: 80 Copynumber: 2.5 Consensus size: 80
582046 ATTGACTTGA
* * * **
582056 TAGTTGACATAGTCCTACCCCTTGATTTTGGTTCGTTGGTAGTTGACATGGTCTTACCCCCTTGA
1 TAGTTGACATGGTCCTACCCTTTGATTTTGGTTTGTTGGTAGTCAACATGGTCTTACCCCCTTGA
*
582121 TATGACTTTGTTTGG
66 TATAACTTTGTTTGG
* * *
582136 TATTTGACATGGTCTTACCCTTTGATTTTGGTTTGTTGGTAGTCAACATGGTCATT-CCCCTTTG
1 TAGTTGACATGGTCCTACCCTTTGATTTTGGTTTGTTGGTAGTCAACATGGTC-TTACCCCCTTG
582200 ATATAACTTTGTTTGG
65 ATATAACTTTGTTTGG
*
582216 TAGTTGACATGGTCCTA-CCTTT-AATTTGGTTT-TGTGGTAGT
1 TAGTTGACATGGTCCTACCCTTTGATTTTGGTTTGT-TGGTAGT
582257 TGATATAGTC
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
77 1 0.01
78 16 0.15
79 5 0.05
80 83 0.78
81 2 0.02
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (80 bp):
TAGTTGACATGGTCCTACCCTTTGATTTTGGTTTGTTGGTAGTCAACATGGTCTTACCCCCTTGA
TATAACTTTGTTTGG
Found at i:582985 original size:14 final size:14
Alignment explanation
Indices: 582966--582995 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
582956 GTTTGGTAAA
582966 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
582980 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
582994 TT
1 TT
582996 ATAATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTATAAG
Found at i:584349 original size:17 final size:17
Alignment explanation
Indices: 584327--584367 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
584317 TCCACTACCA
584327 AGAAGAAAAG-AGAAAGG
1 AGAAGAAAAGAAGAAA-G
584344 AGAAG-AAAGAAGAAAG
1 AGAAGAAAAGAAGAAAG
584360 AGAA-AAAA
1 AGAAGAAAA
584368 ATAAAGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAGAAAAGAAGAAAG
Found at i:586837 original size:19 final size:18
Alignment explanation
Indices: 586815--586873 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
586805 TTCTCTTTTC
586815 TTCTTTCTCCTCTCTCCCT
1 TTCTTTCTCCTCTCT-CCT
* *
586834 TTCTTTGTTCCTTTCTCCT
1 TTCTTT-CTCCTCTCTCCT
*
586853 TTCTTTCT-TTCT-TCCT
1 TTCTTTCTCCTCTCTCCT
586869 TTCTT
1 TTCTT
586874 CCTTTGCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.26
17 2 0.06
18 1 0.03
19 15 0.44
20 7 0.21
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTTTCTCCTCTCTCCT
Found at i:586847 original size:27 final size:23
Alignment explanation
Indices: 586798--586878 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
586788 TAGGCCGAAC
*
586798 CTTCACTTTCTCTTTTC-TTCTTT
1 CTTC-CTTTCTCCTTTCTTTCTTT
*
586821 C-TCCTCTCTCC---CTTTCTTT
1 CTTCCTTTCTCCTTTCTTTCTTT
*
586840 GTTCCTTTCTCCTTTCTTTCTTT
1 CTTCCTTTCTCCTTTCTTTCTTT
586863 CTTCCTTTCTTCCTTT
1 CTTCCTTTC-TCCTTT
586879 GCTTCCTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 9 0.19
21 6 0.13
22 2 0.04
23 17 0.36
24 6 0.13
ACGTcount: A:0.01, C:0.36, G:0.01, T:0.62
Consensus pattern (23 bp):
CTTCCTTTCTCCTTTCTTTCTTT
Done.