Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold193
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: 886014
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 71246 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2485 original size:37 final size:37
Alignment explanation
Indices: 2444--2519 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
2434 AAATATATGA
*
2444 AAGACAAAAATAGCTTATTTATATAATTCAAAAGGTG
1 AAGACAAAAATAACTTATTTATATAATTCAAAAGGTG
*
2481 AAGACAAAAATAATTTATTTATATAATTCAAAAGGTG
1 AAGACAAAAATAACTTATTTATATAATTCAAAAGGTG
2518 AA
1 AA
2520 AATCATCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (37 bp):
AAGACAAAAATAACTTATTTATATAATTCAAAAGGTG
Found at i:8248 original size:37 final size:35
Alignment explanation
Indices: 8206--8313 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
8196 TAAGATAAGC
8206 ATTAAATTAAATTAAATT-TTAAGATAATTATTTTAA
1 ATTAAATTAAATTAAATTATTAAGATAATTA--TTAA
* *
8242 TATTAAATT-AATAAAATACTATTAAGATAAGTATTAA
1 -ATTAAATTAAATTAAAT--TATTAAGATAATTATTAA
*
8279 ATTAAATTTAATATTAAATTATTAAAATAA-TATTA
1 ATTAAA-TTAA-ATTAAATTATTAAGATAATTATTA
8314 TTTTTGGAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 18 0.30
37 24 0.39
38 2 0.03
39 17 0.28
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTAAATTAAATTAAATTATTAAGATAATTATTAA
Found at i:11453 original size:15 final size:14
Alignment explanation
Indices: 11392--11464 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
11382 CCCTAAGTGC
* *
11392 GTGAACCCACAAGT
1 GTGAACCTACATGT
* *
11406 GCGAACCTAGATGT
1 GTGAACCTACATGT
* * *
11420 GTGAACCCATATAT
1 GTGAACCTACATGT
11434 GTGAATCCTACATGT
1 GTGAA-CCTACATGT
11449 GTGAACCTTACATGT
1 GTGAACC-TACATGT
11464 G
1 G
11465 CAAACTCTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 27 0.59
15 19 0.41
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (14 bp):
GTGAACCTACATGT
Found at i:18976 original size:82 final size:82
Alignment explanation
Indices: 18873--19031 Score: 273
Period size: 82 Copynumber: 1.9 Consensus size: 82
18863 TTCATTGTCA
* * *
18873 ACTGATTTTGATGAAAAGATTATCAACTTCAAATAGGACAAGTTATTTGACTCACATAGTCCTAA
1 ACTGATTTTGATGAAAAGATTACCAACTTCAAATAAGACAAGTTATGTGACTCACATAGTCCTAA
18938 GAGCAGAGGATATTACG
66 GAGCAGAGGATATTACG
*
18955 ACTGATTTTGATGAAAAGATTACCAACTTCAAATAAGACAAGTTATGTGACTTACATAGTCCTAA
1 ACTGATTTTGATGAAAAGATTACCAACTTCAAATAAGACAAGTTATGTGACTCACATAGTCCTAA
*
19020 GAGTAGAGGATA
66 GAGCAGAGGATA
19032 GCTTAACTAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (82 bp):
ACTGATTTTGATGAAAAGATTACCAACTTCAAATAAGACAAGTTATGTGACTCACATAGTCCTAA
GAGCAGAGGATATTACG
Found at i:23903 original size:21 final size:22
Alignment explanation
Indices: 23853--23912 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 22
23843 TCAACAAAAA
*
23853 TTATAAAATAATTCAAAATAAG
1 TTATAAAAAAATTCAAAATAAG
* * *
23875 TT-TCAAAAAATTC-AAATTAT
1 TTATAAAAAAATTCAAAATAAG
*
23895 TTAT-AAAAATTTCAAAAT
1 TTATAAAAAAATTCAAAAT
23913 TTATATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 15 0.48
21 14 0.45
22 2 0.06
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.37
Consensus pattern (22 bp):
TTATAAAAAAATTCAAAATAAG
Found at i:23913 original size:21 final size:21
Alignment explanation
Indices: 23853--23913 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
23843 TCAACAAAAA
*
23853 TTATAAAATAATTCAAAATAAGT
1 TTAT-AAA-AATTCAAAATTAGT
23876 TTCA-AAAAATTC-AAATTA-T
1 TT-ATAAAAATTCAAAATTAGT
23895 TTATAAAAATTTCAAAATT
1 TTATAAAAA-TTCAAAATT
23914 TATATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
18 1 0.03
19 8 0.24
20 8 0.24
21 10 0.30
22 3 0.09
23 2 0.06
24 1 0.03
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (21 bp):
TTATAAAAATTCAAAATTAGT
Found at i:23914 original size:18 final size:19
Alignment explanation
Indices: 23879--23917 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
23869 AATAAGTTTC
23879 AAAAAATTCAAATTATTTAT
1 AAAAAATTCAAA-TATTTAT
*
23899 AAAAATTTCAAA-ATTTAT
1 AAAAAATTCAAATATTTAT
23917 A
1 A
23918 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTCAAATATTTAT
Found at i:30025 original size:12 final size:12
Alignment explanation
Indices: 30003--30031 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29993 GAACCATATG
30003 CTCTC-AGTTTT
1 CTCTCAAGTTTT
30014 CTCTCAAGTTTT
1 CTCTCAAGTTTT
30026 CTCTCA
1 CTCTCA
30032 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (12 bp):
CTCTCAAGTTTT
Found at i:37885 original size:21 final size:21
Alignment explanation
Indices: 37859--37963 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
37849 CACAGAAGCA
*
37859 CATAAGTGCTAAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
37880 CATAAGGGTTAAATGGAAGCT
1 CATAAGAGCTAAACGGAAACC
*
37901 CATAAGAGCTGAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
37922 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACC
* *
37943 CAAAAGAGCTAAACTGAAACC
1 CATAAGAGCTAAACGGAAACC
37964 TAGAAGAGTT
Statistics
Matches: 62, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACC
Found at i:37916 original size:42 final size:41
Alignment explanation
Indices: 37853--37988 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 41
37843 AGGCTGCACA
* *
37853 GAAGCACATAAGTGCTAAACGGAAACCCATAAGGGTTAAAT
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAAT
*
37894 GGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
1 -GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAA-T
* * * * *
37937 GAAGCTCAAAAGAGCTAAACTGAAACCTAGAAGAGTTAAATT
1 GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAA-T
*
37979 GAAACTCATA
1 GAAGCTCATA
37989 TAAGTTAACT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 80 0.99
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (41 bp):
GAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTAAAT
Found at i:42167 original size:46 final size:46
Alignment explanation
Indices: 42076--42219 Score: 247
Period size: 46 Copynumber: 3.2 Consensus size: 46
42066 CACTTGTCCC
*
42076 TGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
* *
42121 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATTTTGCCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
42167 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC-
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
42212 TGATCAGA
1 TGATCAGA
42220 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 27 0.29
46 66 0.71
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
Found at i:46348 original size:49 final size:47
Alignment explanation
Indices: 46276--46394 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 47
46266 TTCGTTTTGT
* * * *
46276 TGATGCCATAGTCCAACTATGGTCTTACACAT-AATCACATAATACATAC
1 TGATGCCATAGCCCAGCTATGGTCTTACAC-TGAAGCACAT-AT-CACAC
*
46325 TGATGCCATAGCCCAGCTATGGTCTTACACTGTAGCACATATCACAC
1 TGATGCCATAGCCCAGCTATGGTCTTACACTGAAGCACATATCACAC
* *
46372 TGATGCCATATCCCAGATATGGT
1 TGATGCCATAGCCCAGCTATGGT
46395 ATTATACGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 25 0.40
48 3 0.05
49 34 0.55
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (47 bp):
TGATGCCATAGCCCAGCTATGGTCTTACACTGAAGCACATATCACAC
Found at i:47427 original size:46 final size:44
Alignment explanation
Indices: 47317--47433 Score: 173
Period size: 46 Copynumber: 2.6 Consensus size: 44
47307 TACGTATGAT
* *
47317 CACTTATCAC-TTGTCCCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCCTTGATCAGATAAGTGTAGCTAAGCTAC
*
47360 CACTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTC-CTTGATCAGATAAGTGTAGCT-AAGCTAC
47406 CACTTATCACTTTGTCTCTTGATCAGAT
1 CACTTATCACTTTGTC-CTTGATCAGAT
47434 CATAAATGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 10 0.15
44 4 0.06
45 20 0.30
46 32 0.48
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (44 bp):
CACTTATCACTTTGTCCTTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:50765 original size:43 final size:43
Alignment explanation
Indices: 50635--50766 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
50625 TTATGTGAAA
* *
50635 AAACGCCGCTAAAGATCATGGTC-TTAGCGGTGCTTTTTTTAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTATTAC
* * *
50677 AAATGCCGCTAAAGATCATGGTCTTTAGAGGCGCTTTTCA-CAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTT-ATTAC
* * ** *
50720 AAACGCTGCTAAAAATCATGACCTTTAGCGGCGCTTCTATTAC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTATTAC
50763 AAAC
1 AAAC
50767 ACCATTATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
42 23 0.31
43 51 0.69
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTATTAC
Found at i:50827 original size:41 final size:43
Alignment explanation
Indices: 50717--50829 Score: 108
Period size: 41 Copynumber: 2.7 Consensus size: 43
50707 GCGCTTTTCA
* * *
50717 CACAAACGCTGCTAAAAATCATGACCTTTAGCGGCGCTTCTATT
1 CACAAACGCCGCTAAAAA-CATGACTTTTAGCGGCACTTCTATT
* ** * *
50761 -ACAAACACCATTATAAAA-ATAACTTTTAGTGGCACTT-T-TT
1 CACAAACGCCGCTA-AAAACATGACTTTTAGCGGCACTTCTATT
50801 CACAAACGCCGCTAAAAACATGACTTTTA
1 CACAAACGCCGCTAAAAACATGACTTTTA
50830 AAAAAATTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
40 6 0.11
41 20 0.37
42 15 0.28
43 9 0.17
44 4 0.07
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (43 bp):
CACAAACGCCGCTAAAAACATGACTTTTAGCGGCACTTCTATT
Found at i:56445 original size:21 final size:21
Alignment explanation
Indices: 56249--56485 Score: 83
Period size: 21 Copynumber: 10.7 Consensus size: 21
56239 ACCCATGAAT
56249 CCCTAAACCCTAAATCTCTAA
1 CCCTAAACCCTAAATCTCTAA
* * *
56270 CTCTTAACCCATAAA-GTCTAA
1 CCCTAAACCC-TAAATCTCTAA
* *
56291 CCCCTAAACCCTAACTTGACCCATGAA
1 -CCCTAAACCCTAA-AT--CTC-T-AA
* *
56318 TCCCTAAACCCTAGATCCCTAA
1 -CCCTAAACCCTAAATCTCTAA
* * *
56340 CTCTTAACCCATAAA-GTCTAA
1 CCCTAAACCC-TAAATCTCTAA
* *
56361 CCCCTAAACCCTAACTTGACCCATGAA
1 -CCCTAAACCCTAA-AT--CTC-T-AA
56388 TCCCTAAACCCTAAATCTCTAA
1 -CCCTAAACCCTAAATCTCTAA
* * *
56410 CTCTTAACCCATAAA-GTCTAA
1 CCCTAAACCC-TAAATCTCTAA
*
56431 CCCCTAAACCCTAAA-C-CGAA
1 -CCCTAAACCCTAAATCTCTAA
* *
56451 TCTCTAACCCCTAAA-CTCTAA
1 -CCCTAAACCCTAAATCTCTAA
56472 CCC-AAATCCCTAAA
1 CCCTAAA-CCCTAAA
56486 CCAATTAAAT
Statistics
Matches: 159, Mismatches: 37, Indels: 41
0.67 0.16 0.17
Matches are distributed among these distances:
19 2 0.01
20 25 0.16
21 51 0.32
22 39 0.25
23 2 0.01
24 5 0.03
25 2 0.01
26 4 0.03
27 29 0.18
ACGTcount: A:0.36, C:0.37, G:0.04, T:0.23
Consensus pattern (21 bp):
CCCTAAACCCTAAATCTCTAA
Found at i:56466 original size:70 final size:70
Alignment explanation
Indices: 56196--56444 Score: 480
Period size: 70 Copynumber: 3.6 Consensus size: 70
56186 NNNNNNATCC
56196 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
1 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
56261 AATCT
66 AATCT
56266 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
1 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
* *
56331 GATCC
66 AATCT
56336 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
1 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
56401 AATCT
66 AATCT
56406 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAA
1 CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAA
56445 ACCGAATCTC
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 175 1.00
ACGTcount: A:0.36, C:0.36, G:0.04, T:0.24
Consensus pattern (70 bp):
CTAACTCTTAACCCATAAAGTCTAACCCCTAAACCCTAACTTGACCCATGAATCCCTAAACCCTA
AATCT
Found at i:56479 original size:27 final size:27
Alignment explanation
Indices: 56408--56484 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
56398 CTAAATCTCT
**
56408 AACTCTTAACCCATAAAGTCTAACCCCTA
1 AACTC-TAACCCA-AATCTCTAACCCCTA
* * *
56437 AACCCTAAACCGAATCTCTAACCCCTA
1 AACTCTAACCCAAATCTCTAACCCCTA
*
56464 AACTCTAACCCAAATCCCTAA
1 AACTCTAACCCAAATCTCTAA
56485 ACCAATTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 30 0.77
28 5 0.13
29 4 0.10
ACGTcount: A:0.39, C:0.38, G:0.03, T:0.21
Consensus pattern (27 bp):
AACTCTAACCCAAATCTCTAACCCCTA
Found at i:56553 original size:81 final size:74
Alignment explanation
Indices: 56453--56627 Score: 179
Period size: 74 Copynumber: 2.3 Consensus size: 74
56443 AAACCGAATC
* * * * *
56453 TCTAACCCCTAAACTCTAACCCAAATCCCTAAACCAATTAAATAAGCTTATTTAATATATAAATT
1 TCTAAACCCTAAACCCTAACCCAAATACCT-AACC-ACT--A-AACCTTATTT-A-ATATAAATT
56518 AAAAAACACTAATTAA
59 AAAAAACACTAATTAA
* ** * * *
56534 TCTAAACCCTAACCCCTAACCTGAATACCTAACCCCTAAACCTTATTTAATATAAATTAAAACAT
1 TCTAAACCCTAAACCCTAACCCAAATACCTAACCACTAAACCTTATTTAATATAAATTAAAAAAC
*
56599 ACTAGTTAA
66 ACTAATTAA
56608 TCTAAACCCTAAACCCTAAC
1 TCTAAACCCTAAACCCTAAC
56628 TTGACATCGA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
74 41 0.51
75 1 0.01
76 9 0.11
77 1 0.01
79 1 0.01
80 4 0.05
81 24 0.30
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (74 bp):
TCTAAACCCTAAACCCTAACCCAAATACCTAACCACTAAACCTTATTTAATATAAATTAAAAAAC
ACTAATTAA
Found at i:56727 original size:14 final size:15
Alignment explanation
Indices: 56708--56740 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56698 CTTAAACCAG
56708 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
56722 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
56737 AATC
1 AATC
56741 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:56808 original size:14 final size:14
Alignment explanation
Indices: 56789--56825 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
56779 ATCTTAAATT
56789 AACCATATACCCTA
1 AACCATATACCCTA
56803 AACCATATACCCTA
1 AACCATATACCCTA
56817 AACCATATA
1 AACCATATA
56826 TATTAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:57169 original size:41 final size:41
Alignment explanation
Indices: 57112--57433 Score: 486
Period size: 41 Copynumber: 7.9 Consensus size: 41
57102 AAATATTTTT
* * *
57112 GAGCATTAGCGGCGCTTTTTCGAAAATGCCACTAAAGACCA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
*
57153 GAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACCA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
* * * *
57194 GAGCATTAGCGGCGCTTTTTTAAAAACGCCACTAAAGTCCC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
**
57235 GAGCATTAATGGCGCTTTTTC-AAAACGCCGCTAAAGACCA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
*
57275 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACTA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
* *
57316 GAGCATTAGTGGCGCTTTTTCAAAGACGCCGCTAAAGACCA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
* *
57357 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGC-AAAGTCCC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
*
57397 GAGCATTAGTGGCGCTTTTTCAAAAACGCCGCTAAAG
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
57434 CCCCGAAAGG
Statistics
Matches: 255, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
40 72 0.28
41 183 0.72
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCA
Found at i:57300 original size:81 final size:81
Alignment explanation
Indices: 57112--57433 Score: 493
Period size: 81 Copynumber: 4.0 Consensus size: 81
57102 AAATATTTTT
* * * *
57112 GAGCATTAGCGGCGCTTTTTCGAAAATGCCACTAAAGACCAGAGCATTAGCGGCGCTTTTTTAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCAGAGCATTAGTGGCGC-TTTTTCAA
57177 AACGCCGCTAAAGACCA
65 AACGCCGCTAAAGACCA
* * * *
57194 GAGCATTAGCGGCGCTTTTTTAAAAACGCCACTAAAGTCCCGAGCATTAATGGCGCTTTTTCAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCAGAGCATTAGTGGCGCTTTTTCAAA
57259 ACGCCGCTAAAGACCA
66 ACGCCGCTAAAGACCA
* *
57275 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTAGTGGCGCTTTTTCAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCAGAGCATTAGTGGCGCTTTTTCAAA
57340 GACGCCGCTAAAGACCA
66 -ACGCCGCTAAAGACCA
* * *
57357 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGC-AAAGTCCCGAGCATTAGTGGCGCTTTTTCAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCAGAGCATTAGTGGCGCTTTTTC-AA
57421 AACGCCGCTAAAG
65 AACGCCGCTAAAG
57434 CCCCGAAAGG
Statistics
Matches: 221, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
81 121 0.55
82 100 0.45
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (81 bp):
GAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCAGAGCATTAGTGGCGCTTTTTCAAA
ACGCCGCTAAAGACCA
Found at i:57330 original size:122 final size:123
Alignment explanation
Indices: 57112--57433 Score: 486
Period size: 122 Copynumber: 2.6 Consensus size: 123
57102 AAATATTTTT
* * * *
57112 GAGCATTAGCGGCGCTTTTTCGAAAATGCCACTAAAGACCAGAGCATTAGCGGCGCTTTTTTAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAA
* * *
57177 AACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTTAAAAACGCCACTAAAGTCCC
66 AACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCA
**
57235 GAGCATTAATGGCGCTTTTTC-AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAA
* * * *
57299 AACGCCGCTAAAGACTAGAGCATTAGTGGCGCTTTTTCAAAGACGCCGCTAAAGACCA
66 AACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCA
* * *
57357 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGC-AAAGTCCCGAGCATTAGTGGCGCTTTTTCAAA
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAA
57421 AACGCCGCTAAAG
66 AACGCCGCTAAAG
57434 CCCCGAAAGG
Statistics
Matches: 181, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
122 152 0.84
123 29 0.16
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (123 bp):
GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAA
AACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGACCA
Found at i:57521 original size:40 final size:40
Alignment explanation
Indices: 57471--57605 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
57461 TGGGCTTACG
* * *
57471 TTTTTTGCGGCGTTTTCTAGAAAAACGCCACTAATGCTC-A
1 TTTTTAGCGGCGTTTTCT-GTAAAGCGCCACTAATGCTCGA
* *
57511 TTTTTAGCGGCACTTTCCT-TAAAGCGCCACT-ATGCTCGA
1 TTTTTAGCGGC-GTTTTCTGTAAAGCGCCACTAATGCTCGA
* * * *
57550 TCTTTAGTGGCGTTTTATGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCTGTAAAGCGCCACTAATGCTCGA
57590 TTTTTAGCGGCGTTTT
1 TTTTTAGCGGCGTTTT
57606 TTTATCCAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
38 10 0.13
39 31 0.40
40 32 0.41
41 5 0.06
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCTGTAAAGCGCCACTAATGCTCGA
Found at i:59166 original size:13 final size:14
Alignment explanation
Indices: 59136--59174 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
59126 GTCACATGTC
*
59136 AATTAAATTTATTTA
1 AATTAAAATTA-TTA
59151 AA-TAAAATTATTA
1 AATTAAAATTATTA
59164 AATTAAAATTA
1 AATTAAAATTA
59175 AAATAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAAAATTATTA
Found at i:59184 original size:13 final size:13
Alignment explanation
Indices: 59168--59192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59158 TTATTAAATT
59168 AAAATTAAAATAG
1 AAAATTAAAATAG
59181 AAAATTAAAATA
1 AAAATTAAAATA
59193 TTAAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATTAAAATAG
Found at i:59264 original size:11 final size:11
Alignment explanation
Indices: 59248--59281 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
59238 TTAATCAATG
59248 TTGACCAACCA
1 TTGACCAACCA
*
59259 TTGACC-AGCA
1 TTGACCAACCA
59269 TTGACCAACCA
1 TTGACCAACCA
59280 TT
1 TT
59282 AATCGGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (11 bp):
TTGACCAACCA
Found at i:59294 original size:22 final size:21
Alignment explanation
Indices: 59248--59301 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
59238 TTAATCAATG
*
59248 TTGACCAACCATTGACCAGCA
1 TTGACCAACCATTAACCAGCA
**
59269 TTGACCAACCATTAATCGGGCA
1 TTGACCAACCATTAA-CCAGCA
*
59291 TTGACCTACCA
1 TTGACCAACCA
59302 CTTGACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.22
Consensus pattern (21 bp):
TTGACCAACCATTAACCAGCA
Found at i:59698 original size:32 final size:33
Alignment explanation
Indices: 59642--59709 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
59632 TCTTTAAGCT
* * *
59642 TTTTTTTAAATATTTGTTTTATAATTTTATAAA
1 TTTTTTTAAATATTTGTGTAATAATATTATAAA
* *
59675 TTTTTTTACATATTT-TGTAATAATATTATTAA
1 TTTTTTTAAATATTTGTGTAATAATATTATAAA
59707 TTT
1 TTT
59710 CAACTAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (33 bp):
TTTTTTTAAATATTTGTGTAATAATATTATAAA
Found at i:59756 original size:17 final size:18
Alignment explanation
Indices: 59736--59769 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59726 ATTATTGTAT
*
59736 TTTTTTTGTA-AATTTTA
1 TTTTTATGTATAATTTTA
59753 TTTTTATGTATAATTTT
1 TTTTTATGTATAATTTT
59770 CTGAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTATGTATAATTTTA
Found at i:63354 original size:21 final size:21
Alignment explanation
Indices: 63313--63355 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
63303 ATTATAAAAC
* * *
63313 ATAAAAATGTAAAATTTTATA
1 ATAAAAAGGTAAAAATATATA
63334 ATAAAAAGGTAAAAATATATA
1 ATAAAAAGGTAAAAATATATA
63355 A
1 A
63356 AATATATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAAAAAGGTAAAAATATATA
Found at i:63443 original size:20 final size:19
Alignment explanation
Indices: 63402--63457 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
63392 ATAAAGTCAT
63402 AAGAAAATTATAAAAAATGTA
1 AAGAAAA-TAT-AAAAATGTA
*
63423 AAGAAAATATAAAATTCGTA
1 AAGAAAATATAAAAAT-GTA
*
63443 AA-AAAGTATAAAAAT
1 AAGAAAATATAAAAAT
63458 TATCGTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 16 0.52
20 8 0.26
21 7 0.23
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AAGAAAATATAAAAATGTA
Found at i:63458 original size:20 final size:19
Alignment explanation
Indices: 63405--63458 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
63395 AAGTCATAAG
* *
63405 AAAATTATAAAAAATGTAA
1 AAAAATATAAAAATTGTAA
63424 AGAAAATAT-AAAATTCGTAA
1 A-AAAATATAAAAATT-GTAA
*
63444 AAAAGTATAAAAATT
1 AAAAATATAAAAATT
63459 ATCGTACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAAATTGTAA
Found at i:64413 original size:67 final size:67
Alignment explanation
Indices: 64305--64439 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
64295 TAATTGATGG
64305 TTCAATTGATTATAAAATTATTTTACAGGGACTTTTTGATATATTAAACCTAAAAGAATTAAATT
1 TTCAATTGATTATAAAATTATTTTACAGGGACTTTTTGATATATTAAACCTAAAAGAATTAAATT
64370 TC
66 TC
64372 TTCAATTGATTATAAAATTATTTTACAGGGACTTTTTGATATATTAAACCTAAAAGAATTAAATT
1 TTCAATTGATTATAAAATTATTTTACAGGGACTTTTTGATATATTAAACCTAAAAGAATTAAATT
64437 TC
66 TC
64439 T
1 T
64440 AACTCTACTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (67 bp):
TTCAATTGATTATAAAATTATTTTACAGGGACTTTTTGATATATTAAACCTAAAAGAATTAAATT
TC
Found at i:70514 original size:9 final size:9
Alignment explanation
Indices: 70500--70576 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
70490 TTTGGTTAAA
70500 AATTACCCG
1 AATTACCCG
70509 AATTACCCG
1 AATTACCCG
*
70518 AATTACCCA
1 AATTACCCG
70527 AATTACCCG
1 AATTACCCG
*
70536 AATTAACCG
1 AATTACCCG
70545 AATTA-CCG
1 AATTACCCG
*
70553 AAAAATACCCG
1 --AATTACCCG
70564 AATTACCCG
1 AATTACCCG
70573 AATT
1 AATT
70577 TTTTTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.05
9 50 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:70537 original size:27 final size:28
Alignment explanation
Indices: 70498--70576 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 28
70488 TTTTTGGTTA
70498 AAAATTACCCGAATTACCCGAATTACC-
1 AAAATTACCCGAATTACCCGAATTACCG
* *
70525 CAAATTACCCGAATTAACCGAATTACCG
1 AAAATTACCCGAATTACCCGAATTACCG
*
70553 AAAAATACCCGAATTACCCGAATT
1 AAAATTACCCGAATTACCCGAATT
70577 TTTTTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.54
28 21 0.46
ACGTcount: A:0.42, C:0.28, G:0.09, T:0.22
Consensus pattern (28 bp):
AAAATTACCCGAATTACCCGAATTACCG
Found at i:72433 original size:37 final size:37
Alignment explanation
Indices: 72383--72547 Score: 267
Period size: 37 Copynumber: 4.5 Consensus size: 37
72373 NNNNNNNNNN
72383 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
1 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
72420 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
1 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
*
72457 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAG
1 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
* * **
72494 ATAAAGTGATAAGTGGCTACACTTATCTGATCAAGTG
1 ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
**
72531 GTAAAGTGATAAGTGGT
1 ACAAAGTGATAAGTGGT
72548 AGCCTAGCTA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 122 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (37 bp):
ACAAAGTGATAAGTGGTTACACTTATCTGATCAAGAA
Found at i:77841 original size:116 final size:117
Alignment explanation
Indices: 77703--77939 Score: 449
Period size: 116 Copynumber: 2.0 Consensus size: 117
77693 GTTTGGACTT
77703 AATTTTTTTAATATTTATATTGTAGTAAATATATTTTTATATGATATAAATTGATGCGGAAATCC
1 AATTTTTTTAATATTTATATTGTAGTAAATATATTTTTATATGATATAAATTGATGCGGAAATCC
77768 CGGATCTAGACACAAGAGAAACAAAAATTAGAAATAAAACGAGAATAAATAA
66 CGGATCTAGACACAAGAGAAACAAAAATTAGAAATAAAACGAGAATAAATAA
77820 AATTTTTTTAATA-TTATATTGTAGTAAATATATTTTTATATGATATAAATTGATGCGGAAATCC
1 AATTTTTTTAATATTTATATTGTAGTAAATATATTTTTATATGATATAAATTGATGCGGAAATCC
* *
77884 CGGATCTAGACACAAGAGAAACAAAAATTTGGAATAAAACGAGAATAAATAA
66 CGGATCTAGACACAAGAGAAACAAAAATTAGAAATAAAACGAGAATAAATAA
77936 AATT
1 AATT
77940 AGTTAAATAA
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
116 105 0.89
117 13 0.11
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (117 bp):
AATTTTTTTAATATTTATATTGTAGTAAATATATTTTTATATGATATAAATTGATGCGGAAATCC
CGGATCTAGACACAAGAGAAACAAAAATTAGAAATAAAACGAGAATAAATAA
Found at i:77953 original size:3 final size:3
Alignment explanation
Indices: 77945--77979 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
77935 AAATTAGTTA
77945 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
77980 AAGGATATAT
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:82694 original size:3 final size:3
Alignment explanation
Indices: 82686--82711 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
82676 ATATATCCTT
82686 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
82712 TAACTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:82926 original size:28 final size:28
Alignment explanation
Indices: 82881--82935 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
82871 TTTGCTAAAA
* *
82881 CTTATTTTTCTAATCTAACATTTTTATT
1 CTTATTTTTCTAACCTAACATTATTATT
*
82909 CTTA-TTTTCTAAACCTAATATTATTAT
1 CTTATTTTTCT-AACCTAACATTATTAT
82936 GATTTGAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (28 bp):
CTTATTTTTCTAACCTAACATTATTATT
Found at i:87845 original size:2 final size:2
Alignment explanation
Indices: 87838--87867 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
87828 ACATTTACAC
87838 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
87868 CAATTCAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88643 original size:3 final size:3
Alignment explanation
Indices: 88637--88676 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
88627 ATACTTTAAT
88637 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
88677 ACANNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93662 original size:13 final size:13
Alignment explanation
Indices: 93644--93668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93634 TAATTTATAA
93644 GTGTGAAAATTTC
1 GTGTGAAAATTTC
93657 GTGTGAAAATTT
1 GTGTGAAAATTT
93669 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:94858 original size:42 final size:42
Alignment explanation
Indices: 94770--94919 Score: 131
Period size: 43 Copynumber: 3.5 Consensus size: 42
94760 TAAGAGCACA
* * * * *
94770 TCTGGGACGTTGGCATCGATTTGTGATTTACGTGTAAGACCATG
1 TCTGGGACATTGGCATTG-TATATGA-TTACGTGTAAGACCCTG
*
94814 TCTGGGACATTGGCATTGTATATGGTTACGTGTAAGACCCTG
1 TCTGGGACATTGGCATTGTATATGATTACGTGTAAGACCCTG
* * * * *
94856 TCTGGGACAATGACATCGTTATTTGATTACATGTAAGACCAC-G
1 TCTGGGACATTGGCATTG-TATATGATTACGTGTAAGACC-CTG
** *
94899 TAAGGGACGTTGGCATTGTAT
1 TCTGGGACATTGGCATTGTAT
94920 GAGCTTTTTG
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
42 34 0.40
43 35 0.41
44 17 0.20
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
TCTGGGACATTGGCATTGTATATGATTACGTGTAAGACCCTG
Found at i:102498 original size:13 final size:13
Alignment explanation
Indices: 102480--102504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
102470 NNNNNNNNNN
102480 GTGTGAAAATTTC
1 GTGTGAAAATTTC
102493 GTGTGAAAATTT
1 GTGTGAAAATTT
102505 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:103693 original size:42 final size:42
Alignment explanation
Indices: 103605--103754 Score: 131
Period size: 43 Copynumber: 3.5 Consensus size: 42
103595 TAAGAGCACA
* * * * *
103605 TCTGGGACGTTGGCATCGATTTGTGATTTACGTGTAAGACCATG
1 TCTGGGACATTGGCATTG-TATATGA-TTACGTGTAAGACCCTG
*
103649 TCTGGGACATTGGCATTGTATATGGTTACGTGTAAGACCCTG
1 TCTGGGACATTGGCATTGTATATGATTACGTGTAAGACCCTG
* * * * *
103691 TCTGGGACAATGACATCGTTATTTGATTACATGTAAGACCAC-G
1 TCTGGGACATTGGCATTG-TATATGATTACGTGTAAGACC-CTG
** *
103734 TAAGGGACGTTGGCATTGTAT
1 TCTGGGACATTGGCATTGTAT
103755 GAGCTTTTTG
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
42 34 0.40
43 35 0.41
44 17 0.20
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
TCTGGGACATTGGCATTGTATATGATTACGTGTAAGACCCTG
Found at i:105251 original size:21 final size:22
Alignment explanation
Indices: 105221--105262 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
105211 CACTTCACAA
*
105221 TCATAAGTCATACATCATCATC
1 TCATAAGTCAAACATCATCATC
105243 TCAT-AGTCAAACATCATCAT
1 TCATAAGTCAAACATCATCAT
105263 AAAGTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (22 bp):
TCATAAGTCAAACATCATCATC
Found at i:109238 original size:28 final size:28
Alignment explanation
Indices: 109193--109250 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
109183 TTGAATATAT
109193 TATGTTATAAAAATATTATAT-TAATTTA
1 TATGTTATAAAAATATTATATAT-ATTTA
*
109221 TATGTTA-AATAATAATTATATATATTTA
1 TATGTTATAAAAAT-ATTATATATATTTA
109249 TA
1 TA
109251 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 5 0.19
28 21 0.78
29 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATGTTATAAAAATATTATATATATTTA
Found at i:109255 original size:27 final size:27
Alignment explanation
Indices: 109200--109257 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
109190 TATTATGTTA
*
109200 TAAA-AATATTATATTAATTTATATGT
1 TAAATAATATTATATTAATTTATATAT
109226 TAAATAATAATTATA-TATATTTATA-AT
1 TAAATAAT-ATTATATTA-ATTTATATAT
109253 TAAAT
1 TAAAT
109258 TAAATCACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.14
27 11 0.39
28 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAATAATATTATATTAATTTATATAT
Found at i:109950 original size:49 final size:49
Alignment explanation
Indices: 109896--109995 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
109886 ACTTTACTAC
* * *
109896 TTGTCAATTCGTTTTGTCTTATTTTTTATATGAATTATTTCATGTTTAA
1 TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTACTTCATGTTTAA
* *
109945 TTGTCATTTCGTTTCGTTTTATTTTATATATGAATTACTTCATGTTTAA
1 TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTACTTCATGTTTAA
109994 TT
1 TT
109996 CTCTTCTACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (49 bp):
TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTACTTCATGTTTAA
Found at i:122319 original size:28 final size:28
Alignment explanation
Indices: 122286--122340 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
122276 GTAACAGTAT
*
122286 AGTGTGGGCCTTATCCCAATACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAGTAAC
*
122314 AGTGTGGGCCTTAGCCTAATACAGTAA
1 AGTGTGGGCCTTAGCCCAATACAGTAA
122341 TAGTACAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGTAAC
Found at i:122633 original size:27 final size:27
Alignment explanation
Indices: 122585--122636 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
122575 AAGGCCATAT
* *
122585 CAGTCATTTTATCTCCTAGGGGTATAA
1 CAGTCATTTTACCTCATAGGGGTATAA
* *
122612 CAGTCATTTTACCTGATGGGGGTAT
1 CAGTCATTTTACCTCATAGGGGTAT
122637 TTCGGTCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (27 bp):
CAGTCATTTTACCTCATAGGGGTATAA
Found at i:130665 original size:21 final size:23
Alignment explanation
Indices: 130641--130685 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
130631 AATTAAAAAA
130641 AAAACT-AA-AAGAAAAACAAAG
1 AAAACTGAAGAAGAAAAACAAAG
*
130662 AAAATTGGAAGAAGAAAAACAAAG
1 AAAACT-GAAGAAGAAAAACAAAG
130686 GCAAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
23 2 0.10
24 13 0.65
ACGTcount: A:0.71, C:0.07, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAACTGAAGAAGAAAAACAAAG
Found at i:131281 original size:3 final size:3
Alignment explanation
Indices: 131266--131327 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
131256 TCTAATTTTT
* *
131266 AAC AAC AAA AAC AAC AAC AAC AAA AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
131314 AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AA
131328 TCTAAAAGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:137772 original size:41 final size:38
Alignment explanation
Indices: 137698--137774 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
137688 TTTGAGATAA
* *
137698 ATTTCAGTTGGTTTCATAAAAAAAATCTTTTAAAAAAG
1 ATTTCAGTTGATTTCATAAAAAAAACCTTTTAAAAAAG
*
137736 ATTTCAGTTGATTTCTTCAAAAAAAAACCCTTTTAAAAA
1 ATTTCAGTTGATTTCAT--AAAAAAAA-CCTTTTAAAAA
137775 GCTTGGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 15 0.45
40 8 0.24
41 10 0.30
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (38 bp):
ATTTCAGTTGATTTCATAAAAAAAACCTTTTAAAAAAG
Found at i:143378 original size:23 final size:23
Alignment explanation
Indices: 143335--143383 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
143325 ACCCTTCTCA
* * *
143335 TCTCTTCACTTCTCTTTCATTTT
1 TCTCTTCACTTCCCTTCCATTGT
143358 TCTCTCTCA-TTCCCTTCCATTGT
1 TCTCT-TCACTTCCCTTCCATTGT
143381 TCT
1 TCT
143384 TCACTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.08, C:0.35, G:0.02, T:0.55
Consensus pattern (23 bp):
TCTCTTCACTTCCCTTCCATTGT
Found at i:150553 original size:22 final size:19
Alignment explanation
Indices: 150528--150569 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
150518 TGACAATCAT
150528 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
150550 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
150569 T
1 T
150570 CAACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:160595 original size:31 final size:31
Alignment explanation
Indices: 160557--160620 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
160547 AGCAAAAATA
160557 GTAAGGTTTTTTTATTGAAAATTCGGGTTGG
1 GTAAGGTTTTTTTATTGAAAATTCGGGTTGG
160588 GTAAGGTTTTTTTATTGAAAATTCGGGTTGG
1 GTAAGGTTTTTTTATTGAAAATTCGGGTTGG
160619 GT
1 GT
160621 CGAGCCCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.45
Consensus pattern (31 bp):
GTAAGGTTTTTTTATTGAAAATTCGGGTTGG
Found at i:161789 original size:14 final size:14
Alignment explanation
Indices: 161770--161799 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
161760 ATACATAGAC
161770 AACCTAAATTTCAA
1 AACCTAAATTTCAA
161784 AACCTAAATTTCAA
1 AACCTAAATTTCAA
161798 AA
1 AA
161800 TGACATCCTT
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:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCTAAATTTCAA
Found at i:162233 original size:31 final size:31
Alignment explanation
Indices: 162176--162234 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
162166 AACAATGACC
* * *
162176 TACCACCCTGGATTGCCTAGCGACGATGTTT
1 TACCACCCTGGATTGCCCAACAACGATGTTT
162207 TACCATCCC-GGATTGCCCAACAACGATG
1 TACCA-CCCTGGATTGCCCAACAACGATG
162235 GTCTCTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (31 bp):
TACCACCCTGGATTGCCCAACAACGATGTTT
Found at i:164179 original size:18 final size:19
Alignment explanation
Indices: 164150--164193 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
164140 TAAAAAAATT
*
164150 ATATTTTCATAATTTTATA
1 ATATTTTAATAATTTTATA
164169 AT-TTTTAATAATTTTATA
1 ATATTTTAATAATTTTATA
164187 ATATTTT
1 ATATTTT
164194 GAATCAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTAATAATTTTATA
Found at i:165920 original size:2 final size:2
Alignment explanation
Indices: 165913--165937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
165903 TTATTCATAA
165913 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
165938 ACAGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184928 original size:28 final size:27
Alignment explanation
Indices: 184895--184988 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
184885 ATTACAAATA
184895 ACGATAAGCACCGAAGTGCAAAATAATT
1 ACGATAAGCACCGAAGTGCAAAATAA-T
* * *
184923 ACGATAAGCACCAAAGTTCAAATTTTACA-
1 ACGATAAGCACCGAAGTGCAAA--ATA-AT
* *
184952 ACAATAAGCACCGAAGTGCGAAATAAT
1 ACGATAAGCACCGAAGTGCAAAATAAT
184979 ACGATAAGCA
1 ACGATAAGCA
184989 TGCTAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
26 1 0.02
27 11 0.21
28 20 0.38
29 18 0.34
30 2 0.04
31 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (27 bp):
ACGATAAGCACCGAAGTGCAAAATAAT
Found at i:185078 original size:12 final size:13
Alignment explanation
Indices: 185055--185083 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
185045 ACATGGGCTT
185055 TTCTTATTATTCA
1 TTCTTATTATTCA
185068 TTCTT-TTATTCA
1 TTCTTATTATTCA
185080 TTCT
1 TTCT
185084 CTTGACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTATTATTCA
Found at i:186941 original size:6 final size:7
Alignment explanation
Indices: 186920--186944 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
186910 TTTCATAAAA
186920 TTTATTT
1 TTTATTT
186927 TTTATTT
1 TTTATTT
186934 TTTATTT
1 TTTATTT
186941 TTTA
1 TTTA
186945 AAATGGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:186986 original size:46 final size:47
Alignment explanation
Indices: 186928--187018 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 47
186918 AATTTATTTT
*
186928 TTATTTTTTA-TTTTTTAAAATGGTGTATTTAATAAAATTGTTAAAA
1 TTATTTTTTATTTTTTTAAAATGATGTATTTAATAAAATTGTTAAAA
186974 TTATTTTTTATTTTTTTTAAAATGATGTATTTAATAAAATTGTTA
1 TTATTTTTTA-TTTTTTTAAAATGATGTATTTAATAAAATTGTTA
187019 GGATATCGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 10 0.24
48 32 0.76
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (47 bp):
TTATTTTTTATTTTTTTAAAATGATGTATTTAATAAAATTGTTAAAA
Found at i:187123 original size:5 final size:5
Alignment explanation
Indices: 187113--187138 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
187103 CATATTCAAG
187113 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
187139 TAAATGACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:190284 original size:26 final size:27
Alignment explanation
Indices: 190248--190300 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
190238 TCATTGTCTC
190248 TCATTTTCAACATTCTAACTT-AAAAG
1 TCATTTTCAACATTCTAACTTGAAAAG
* *
190274 TCATTTTCAACCTTCTGACTTGAAAAG
1 TCATTTTCAACATTCTAACTTGAAAAG
190301 ATTGATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (27 bp):
TCATTTTCAACATTCTAACTTGAAAAG
Found at i:196740 original size:19 final size:18
Alignment explanation
Indices: 196718--196763 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
196708 AAAATTCTTG
196718 AAAAACACAAAAAACAAAA
1 AAAAACAC-AAAAACAAAA
*
196737 AAAAAAACAAAAACAAAA
1 AAAAACACAAAAACAAAA
196755 ACAAAACAC
1 A-AAAACAC
196764 TTACCCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAACACAAAAACAAAA
Found at i:196742 original size:6 final size:6
Alignment explanation
Indices: 196727--196760 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
196717 GAAAAACACA
*
196727 AAAAAC AAAAAA AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
196761 CACTTACCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:197908 original size:13 final size:13
Alignment explanation
Indices: 197892--197916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197882 TTTATTTGTT
197892 ATATTTTAATTTG
1 ATATTTTAATTTG
197905 ATATTTTAATTT
1 ATATTTTAATTT
197917 TTTATACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTTAATTTG
Found at i:197943 original size:24 final size:25
Alignment explanation
Indices: 197901--197949 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
197891 TATATTTTAA
** *
197901 TTTGATATTTTAATTTTTTATACTT
1 TTTGATATTTTAAAATTTTAGACTT
197926 TTTGA-ATTTTAAAATTTTAGACTT
1 TTTGATATTTTAAAATTTTAGACTT
197950 GACCAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (25 bp):
TTTGATATTTTAAAATTTTAGACTT
Found at i:198690 original size:55 final size:55
Alignment explanation
Indices: 198617--198790 Score: 339
Period size: 55 Copynumber: 3.2 Consensus size: 55
198607 TTTTTATTTT
198617 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
1 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
198672 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
1 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
*
198727 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAATTTTTTAAA
1 ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
198782 ATTTTATTT
1 ATTTTATTT
198791 ATCAAATAGT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 118 1.00
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (55 bp):
ATTTTATTTTATTTCTTTAAACATTATCCAAATACTTTGTTTTTAAATTTTTAAA
Found at i:199346 original size:22 final size:22
Alignment explanation
Indices: 199276--199346 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
199266 TCCTTAACTA
*
199276 AGTATATATAATTAAATAATAAAT
1 AGTATA-ATAATT-AATAAAAAAT
* * *
199300 ACTAT-ATAATTTAATTAAAATT
1 AGTATAATAA-TTAATAAAAAAT
199322 AGTATAATAATTAATAAAAAAT
1 AGTATAATAATTAATAAAAAAT
199344 AGT
1 AGT
199347 TCCATGTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 28 0.74
23 6 0.16
24 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (22 bp):
AGTATAATAATTAATAAAAAAT
Found at i:210642 original size:15 final size:14
Alignment explanation
Indices: 210622--210674 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
210612 TTTAAACTCA
210622 TTTATATATTATTAC
1 TTTATATATTATT-C
210637 TTTATATATTACTTC
1 TTTATATATTA-TTC
210652 TTT-T-TATT-TT-
1 TTTATATATTATTC
210662 TTTATATATTATT
1 TTTATATATTATT
210675 TATTCCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 4 0.12
13 6 0.18
14 1 0.03
15 15 0.44
16 2 0.06
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATATTATTC
Found at i:212598 original size:19 final size:19
Alignment explanation
Indices: 212574--212618 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
212564 TCTTTCTTTT
* *
212574 TGCATT-CATTCCATGCATC
1 TGCATTACATTACAT-CATA
212593 TGCATTACATTACATCATA
1 TGCATTACATTACATCATA
212612 TGCATTA
1 TGCATTA
212619 GATTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (19 bp):
TGCATTACATTACATCATA
Found at i:217291 original size:44 final size:42
Alignment explanation
Indices: 217133--217296 Score: 114
Period size: 44 Copynumber: 3.8 Consensus size: 42
217123 AGAAGATGAC
* * * * * ***
217133 AAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAACCA
1 AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACT-GAAGTG
* * * * *
217176 ATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTGAAGTG
1 A-AATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGTG
* * *
217219 AAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
1 AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAG-T-G
* *
217263 AAAATCTTATTTCCCT-AAATTGCAGTGGAACAGA
1 -AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGA
217297 TTAAAGCTAT
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
42 35 0.35
43 5 0.05
44 47 0.47
45 12 0.12
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (42 bp):
AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGTG
Found at i:217450 original size:44 final size:43
Alignment explanation
Indices: 217356--217533 Score: 153
Period size: 44 Copynumber: 4.0 Consensus size: 43
217346 AATCATGACG
* * * * * * *
217356 AATCTAATCTCCCTAAAGATGCAGTGGAGGAGATTAAAGCCA-AT
1 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAG--ATAC
* * *
217400 AATCTTATCTCTC-TGAAGTTGTAGTGGAGTAGATTGAAGTTAC
1 AATCTTATCTC-CATGAAGTTGCAGTGGAGCAGATTGAAGATAC
* * *
217443 AAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGATAGC
1 AA-TCTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGATA-C
* *
217488 GAATCTTATCTCCATGAAGTTGCAGTAGAGCAGATTGAAGCTAC
1 -AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGATAC
217532 AA
1 AA
217534 ATCCTTGCCT
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
43 6 0.05
44 65 0.59
45 37 0.34
46 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGATAC
Found at i:217508 original size:45 final size:42
Alignment explanation
Indices: 217400--217533 Score: 133
Period size: 45 Copynumber: 3.0 Consensus size: 42
217390 TAAAGCCAAT
* * * * *
217400 AATCTTATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAGTTAC
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAAACTGAAGATAC
217443 AAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGATAGC
1 AA-TCTTATCTCC-TGAAGTTGCAGTGGAGCAAACTGAAGATA-C
* * * *
217488 GAATCTTATCTCCATGAAGTTGCAGTAGAGCAGATTGAAGCTAC
1 -AATCTTATCTCC-TGAAGTTGCAGTGGAGCAAACTGAAGATAC
217532 AA
1 AA
217534 ATCCTTGCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
43 5 0.06
44 34 0.44
45 36 0.47
46 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
AATCTTATCTCCTGAAGTTGCAGTGGAGCAAACTGAAGATAC
Found at i:217661 original size:89 final size:89
Alignment explanation
Indices: 217536--217913 Score: 481
Period size: 89 Copynumber: 4.2 Consensus size: 89
217526 AGCTACAAAT
* * *
217536 CCTTGCCTCCCTGAGTTTGCAGCGGAACTGACTGAAGATAACAGATCTTGTCTTCCTATATTGGC
1 CCTTGCCTCCCTGAGTTTGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGC
217601 AGCGAAGCAGATCAAAGACACCAG
66 AGCGAAGCAGATCAAAGACACCAG
* * * * * *
217625 CCTTTCCTCCCTGAGTTTGCAGCAGAGCAGATTGAAGATAGCAGATCTTGTCTTTCTGTATTGAC
1 CCTTGCCTCCCTGAGTTTGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGC
*
217690 AGCGAAGCAGATCGAAGACACCAG
66 AGCGAAGCAGATCAAAGACACCAG
* * * * *
217714 CCTTACCTCTCTGAGTTTGCAGC-GAAACAGACTAAAGATAGCATATCTTGTCTTCCTGTATTGG
1 CCTTGCCTCCCTGAGTTTGCAGCAG-AACAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGG
* *
217778 CAGCGAAGCAGATCGAAGACACTAG
65 CAGCGAAGCAGATCAAAGACACCAG
* * * * * *
217803 CCTTGCCTCCTTGAGTTTGCAGCAGAACAAACTGAAAACAACAGATCTTGTCTTCCTGTACTGGT
1 CCTTGCCTCCCTGAGTTTGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGC
* *
217868 AGTGAAGCAGATCGAAA-ACACTAG
66 AGCGAAGCAGATC-AAAGACACCAG
* *
217892 TCTTGCCTCTCTGAGTTTGCAG
1 CCTTGCCTCCCTGAGTTTGCAG
217914 TGGAGTAGGT
Statistics
Matches: 251, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
88 1 0.00
89 247 0.98
90 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (89 bp):
CCTTGCCTCCCTGAGTTTGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGC
AGCGAAGCAGATCAAAGACACCAG
Found at i:218207 original size:131 final size:132
Alignment explanation
Indices: 217910--218327 Score: 601
Period size: 131 Copynumber: 3.2 Consensus size: 132
217900 CTCTGAGTTT
* * * * *
217910 GCAGTGGAGTAGGTTGAAGATTGTAGATTTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAATAT
1 GCAGTGGAATAGGTTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
** *
217975 GGTGAATCTTATCTTTTCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
66 GGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
218040 CA
131 CA
* * *
218042 GCAGTGGAGTAGGTTGAAGATTCTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAA-A
1 GCAGTGGAATAGGTTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC-AAAGA
*
218106 TGGTGAATCTTATCTTCCCGAGATAGTA-GGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGA
65 TGGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGA
218170 GCA
130 GCA
* * * *
218173 GTAGTGGAATAGGTTGAAGATTATATATCTTGTCTCCCAAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAATAGGTTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
*
218238 GGTGAGTCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAG-CCTTATCTCCCTGA
66 GGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCC-TATCTCCCTG-
**
218302 AGTT
129 AGCA
*
218306 GCAGTGGAACAGGTTGAA-ATTA
1 GCAGTGGAATAGGTTGAAGATTA
218328 CCAATTCCTA
Statistics
Matches: 260, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
130 3 0.01
131 120 0.46
132 116 0.45
133 21 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (132 bp):
GCAGTGGAATAGGTTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
GGTGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
CA
Found at i:219966 original size:22 final size:21
Alignment explanation
Indices: 219924--219998 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
219914 AAACTAATAC
**
219924 TCTCTCAATTATTTTCTCAATT
1 TCTCTCAATT-TCCTCTCAATT
*
219946 TCCTCTCAATTTGCTCTCAATT
1 T-CTCTCAATTTCCTCTCAATT
*
219968 TGCTCTCAATTTCCTTTCAAATT
1 T-CTCTCAATTTCCTCTC-AATT
219991 TCTCTCAA
1 TCTCTCAA
219999 ATCCATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 32 0.70
23 14 0.30
ACGTcount: A:0.21, C:0.28, G:0.03, T:0.48
Consensus pattern (21 bp):
TCTCTCAATTTCCTCTCAATT
Found at i:220000 original size:11 final size:11
Alignment explanation
Indices: 219938--219998 Score: 79
Period size: 11 Copynumber: 5.5 Consensus size: 11
219928 TCAATTATTT
219938 TCTCAATTTCC
1 TCTCAATTTCC
*
219949 TCTCAATTTGC
1 TCTCAATTTCC
*
219960 TCTCAATTTGC
1 TCTCAATTTCC
219971 TCTCAATTTCC
1 TCTCAATTTCC
*
219982 TTTCAAATTT-C
1 TCTC-AATTTCC
219993 TCTCAA
1 TCTCAA
219999 ATCCATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
10 2 0.04
11 38 0.84
12 5 0.11
ACGTcount: A:0.21, C:0.30, G:0.03, T:0.46
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:221904 original size:18 final size:18
Alignment explanation
Indices: 221868--221910 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
221858 TGCCAGGTGC
* * *
221868 GTATCCTAGCCTTTTTAT
1 GTATCCTAACCCTTATAT
221886 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
221904 GTTTCCT
1 GTATCCT
221911 TTTTCGAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:222533 original size:7 final size:7
Alignment explanation
Indices: 222523--222554 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
222513 AAAATTTAAA
222523 AATTTAT
1 AATTTAT
222530 AATTTAT
1 AATTTAT
222537 AA-TTA-
1 AATTTAT
222542 AATTTAT
1 AATTTAT
222549 AATTTA
1 AATTTA
222555 ATTGACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.09
6 6 0.26
7 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:222601 original size:110 final size:107
Alignment explanation
Indices: 222376--222617 Score: 349
Period size: 110 Copynumber: 2.2 Consensus size: 107
222366 TTGAGGTACT
* *
222376 ACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAGTTTATAACTAAATTTATAA
1 ACTTAAAAACCCTAAACTAATTTATTAAAAATTTAAAAATTTATAATTTATAACTAAATTTATAA
222441 ATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTAACCC
66 ATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTAACCC
*
222483 TTAACTTAAAAACCCTAAACTAATTTATTAAAAATTTAAAAATTTATAATTTATAATTAAATTTA
1 ---ACTTAAAAACCCTAAACTAATTTATTAAAAATTTAAAAATTTATAATTTATAACTAAATTTA
*
222548 TAATTTAATTGACAAACCCTAACAAAAATCCTAACCCTAAACCCTAACCC
63 T-A---AATTGACAAACCCTAACAAAAACCCTAACCCT-AACCCTAACCC
222598 TTAACTTAAAAACCCTAAAC
1 ---ACTTAAAAACCCTAAAC
222618 CCTTAATTTA
Statistics
Matches: 123, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
110 60 0.49
111 1 0.01
114 31 0.25
115 31 0.25
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (107 bp):
ACTTAAAAACCCTAAACTAATTTATTAAAAATTTAAAAATTTATAATTTATAACTAAATTTATAA
ATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTAACCC
Found at i:222621 original size:22 final size:22
Alignment explanation
Indices: 222586--222761 Score: 244
Period size: 22 Copynumber: 8.4 Consensus size: 22
222576 TCCTAACCCT
222586 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
222607 AAACCCTAAACCCTTAATTTAA
1 AAACCCTAAACCCTTAACTTAA
222629 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
222650 AAACCTTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
222672 AAACCCTAAA-CC----CTTAA
1 AAACCCTAAACCCTTAACTTAA
*
222689 AAACCAT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
222710 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
222731 AAATCCTAAACTCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
222753 AAACCCTAA
1 AAACCCTAA
222762 CCATAACCGT
Statistics
Matches: 138, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.01
17 13 0.09
21 59 0.43
22 64 0.46
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:222637 original size:43 final size:43
Alignment explanation
Indices: 222586--222763 Score: 267
Period size: 43 Copynumber: 4.3 Consensus size: 43
222576 TCCTAACCCT
*
222586 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
222629 AAACCCTAACCCTTAACTTAAAAACCTTAAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
222672 AAACCCTAAACC----CTTAAAAACCAT-AACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
222710 AAACCCTAACCCTTAACTTAAAAATCCTAAACTCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
222753 AAACCCTAACC
1 AAACCCTAACC
222764 ATAACCGTTA
Statistics
Matches: 122, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
38 25 0.20
39 11 0.09
42 10 0.08
43 76 0.62
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (43 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:222677 original size:15 final size:16
Alignment explanation
Indices: 222657--222704 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
222647 TAAAAACCTT
*
222657 AAACCCTTAA-CTTAA
1 AAACCCTAAACCTTAA
222672 AAACCCTAAACCCTTAA
1 AAACCCTAAA-CCTTAA
* *
222689 AAACCATAACCCTTAA
1 AAACCCTAAACCTTAA
222705 CTTAAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.32
16 6 0.21
17 13 0.46
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACCCTAAACCTTAA
Found at i:222699 original size:16 final size:17
Alignment explanation
Indices: 222667--222704 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
222657 AAACCCTTAA
*
222667 CTTAAAAACCCTAAACC
1 CTTAAAAACCATAAACC
222684 CTTAAAAACCAT-AACC
1 CTTAAAAACCATAAACC
222700 CTTAA
1 CTTAA
222705 CTTAAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (17 bp):
CTTAAAAACCATAAACC
Found at i:222715 original size:81 final size:82
Alignment explanation
Indices: 222602--222761 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 82
222592 TAACCCTTAA
* *
222602 CTTAAAAACCCTAAACCCTTAATTTAAAAACCCTAACCCTTAACTTAAAAA-CCTTAAACCCTTA
1 CTTAAAAACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAATCC-TAAACCCTTA
222666 ACTTAAAAACCCTAAACC
65 ACTTAAAAACCCTAAACC
*
222684 CTTAAAAACCAT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAATCCTAAACTCTTAA
1 CTTAAAAACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAATCCTAAACCCTTAA
222748 CTTAAAAACCCTAA
66 CTTAAAAACCCTAA
222762 CCATAACCGT
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
81 61 0.82
82 13 0.18
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (82 bp):
CTTAAAAACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAATCCTAAACCCTTAA
CTTAAAAACCCTAAACC
Found at i:222784 original size:21 final size:21
Alignment explanation
Indices: 222586--222763 Score: 247
Period size: 21 Copynumber: 8.5 Consensus size: 21
222576 TCCTAACCCT
222586 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
*
222607 AAACCCTAAACCCTTAATTTAA
1 AAACCCT-AACCCTTAACTTAA
222629 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
*
222650 AAACCTTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
*
222672 AAACCCTAAACC----CTTAA
1 AAACCCTAACCCTTAACTTAA
*
222689 AAACCATAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
222710 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* *
222731 AAATCCTAAACTCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
222753 AAACCCTAACC
1 AAACCCTAACC
222764 ATAACCGTTA
Statistics
Matches: 138, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
17 15 0.11
21 64 0.46
22 59 0.43
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:222834 original size:6 final size:6
Alignment explanation
Indices: 222823--222854 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
222813 TCTTAACAAA
222823 AACCCT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AA
222855 TATGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:222837 original size:18 final size:18
Alignment explanation
Indices: 222803--222854 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
222793 TCCAAGCCTC
* *
222803 AAAACCCTAATCTTAACA
1 AAAACCCTAACCCTAACA
*
222821 AAAACCCTAACCCTAACC
1 AAAACCCTAACCCTAACA
**
222839 CTAACCCTAACCCTAA
1 AAAACCCTAACCCTAA
222855 TATGATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAACCCTAACCCTAACA
Found at i:222993 original size:21 final size:21
Alignment explanation
Indices: 222969--223133 Score: 242
Period size: 21 Copynumber: 7.9 Consensus size: 21
222959 AATATAATAT
* *
222969 TTAACTTAAATACCCTAACCT
1 TTAACTTAAAAACCCTAACCC
*
222990 TTAACTTAAAAACTCTAACCC
1 TTAACTTAAAAACCCTAACCC
223011 TTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AACCC
*
223033 TTAACTTAAAAACCCTAACCA
1 TTAACTTAAAAACCCTAACCC
*
223054 TTAACTTAAAAATCCTAACCC
1 TTAACTTAAAAACCCTAACCC
*
223075 TTAACTTAAAAACCATAACCC
1 TTAACTTAAAAACCCTAACCC
* *
223096 TTAACTTAAAAACCCCAACTC
1 TTAACTTAAAAACCCTAACCC
223117 TTAACTT-AAAACCCTAA
1 TTAACTTAAAAACCCTAA
223134 AACCCTACTC
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
20 9 0.07
21 100 0.77
22 21 0.16
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAACCC
Found at i:223135 original size:28 final size:28
Alignment explanation
Indices: 223104--223161 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
223094 CCTTAACTTA
* *
223104 AAAACCCCAACTCTTAA-CTTAAAACCCT
1 AAAA-CCCAACTCTAAACCCTAAAACCCT
*
223132 AAAACCCTACTCTAAACCCTAAAACCCT
1 AAAACCCAACTCTAAACCCTAAAACCCT
223160 AA
1 AA
223162 CCCTAAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (28 bp):
AAAACCCAACTCTAAACCCTAAAACCCT
Found at i:223139 original size:64 final size:64
Alignment explanation
Indices: 222969--223133 Score: 246
Period size: 64 Copynumber: 2.6 Consensus size: 64
222959 AATATAATAT
* * * *
222969 TTAACTTAAATACCCTAACCTTTAACTTAAAAACTCTAACCCTTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAACCATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCC
*
223033 TTAACTTAAAAACCCTAACCATTAACTTAAAAATCCTAACCCTTAACTTAAAAACCAT-AACCC
1 TTAACTTAAAAACCCTAACCATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCC
*
223096 TTAACTTAAAAACCCCAACTC-TTAACTT-AAAACCCTAA
1 TTAACTTAAAAACCCTAAC-CATTAACTTAAAAACCCTAA
223134 AACCCTACTC
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
62 9 0.10
63 30 0.32
64 54 0.58
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (64 bp):
TTAACTTAAAAACCCTAACCATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCC
Found at i:223148 original size:20 final size:21
Alignment explanation
Indices: 223125--223170 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
223115 TCTTAACTTA
*
223125 AAACCCTAAAACCCT-ACTCT
1 AAACCCTAAAACCCTAACCCT
223145 AAACCCTAAAACCCTAACCCT
1 AAACCCTAAAACCCTAACCCT
223166 AAACC
1 AAACC
223171 TAACCCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACCCTAAAACCCTAACCCT
Found at i:223158 original size:63 final size:64
Alignment explanation
Indices: 222969--223159 Score: 216
Period size: 64 Copynumber: 3.0 Consensus size: 64
222959 AATATAATAT
* * * *
222969 TTAACTTAAATACCCTAACCTTTAACTTAAAAACTCTAACCCTTAACTTAAAAACCCT-AAACCC
1 TTAACTTAAAAACCCCAACCATTAACTTAAAAACCCTAACCCTTAACTT-AAAACCCTAAAACCC
* * * *
223033 TTAACTTAAAAACCCTAACCATTAACTTAAAAATCCTAACCCTTAACTTAAAAACC-ATAACCC
1 TTAACTTAAAAACCCCAACCATTAACTTAAAAACCCTAACCCTTAACTTAAAACCCTAAAACCC
223096 TTAACTTAAAAACCCCAACTC-TTAACTT-AAAACCCTAAAACCC-T-ACTCT-AAACCCTAAAA
1 TTAACTTAAAAACCCCAAC-CATTAACTTAAAAACCCT--AACCCTTAACT-TAAAACCCTAAAA
223156 CCC
62 CCC
223159 T
1 T
223160 AACCCTAAAC
Statistics
Matches: 111, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
62 15 0.14
63 45 0.41
64 51 0.46
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (64 bp):
TTAACTTAAAAACCCCAACCATTAACTTAAAAACCCTAACCCTTAACTTAAAACCCTAAAACCC
Found at i:223174 original size:12 final size:13
Alignment explanation
Indices: 223146--223179 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
223136 CCCTACTCTA
223146 AACCCTAAAACCCT
1 AACCCT-AAACCCT
223160 AACCCTAAA-CCT
1 AACCCTAAACCCT
223172 AACCCTAA
1 AACCCTAA
223180 TATGATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 3 0.15
14 6 0.30
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:223285 original size:325 final size:325
Alignment explanation
Indices: 222641--223291 Score: 876
Period size: 325 Copynumber: 2.0 Consensus size: 325
222631 ACCCTAACCC
*
222641 TTAACTTAAAAACCTTAAACCCTTAACTTAAAAACCCTAAACCCTTAAAAACCATAACCCTTAAC
1 TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAAAAACCATAACCCTTAAC
* * *
222706 TTAAAAACCCTAACCCTTAACTTAAAAATCCTAAACTCTTAACTTAAAAACCCTAACCATAACCG
66 TTAAAAACCCTAACCATTAACTTAAAAATCCTAAACCCTTAACTTAAAAACCATAACCATAACCG
* ** *
222771 TTACCTTAAAAACCCTTAACTATCCAAGCCTCAAAACCCTAATCTTAACAAAAACCCTAACCCTA
131 TTA-C-AAAAAACCCTTAACTATAAAACCCTCAAAACCCTAATCTT-ACAAAAACCCTAACCCTA
* *
222836 ACCCTAACCCTAACCCTAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAGCAA
193 ACCCTAAACCTAACCCTAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAA
**
222901 TTAATAATTTGACTAGCAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAAAAAATATAA
258 TTAATAATTTGACTAAAAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAAAAAATATAA
222966 TAT
323 TAT
* * * * *
222969 TTAACTTAAATACCCT-AACCTTTAACTTAAAAACTCTAACCCTTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACC----CTTAAAAACCAT-AACCC
*
223033 TTAACTTAAAAACCCTAACCATTAACTTAAAAATCCT-AACCCTTAACTTAAAAACCATAACCCT
61 TTAACTTAAAAACCCTAACCATTAACTTAAAAATCCTAAACCCTTAACTTAAAAACCATAA-CCA
* *
223097 TAA-C-TTA-AAAACCCCAACTCTTAACT-TAAAACCCT-AAAACCCT-A-C-T-C-TAAACCCT
125 TAACCGTTACAAAA----AACCCTTAACTATAAAACCCTCAAAACCCTAATCTTACAAAAACCCT
223152 AAAACCCTAACCCTAAACCTAACCCTAATATGATATAATTTGATAAATTTACTAACAATTAATAC
186 --AACCCTAACCCTAAACCTAACCCTAATATGATATAATTTGATAAATTTACTAACAATTAATAC
* * *
223217 AATTAATAATTAATAATTTTACTAAAAAAATGTTAGATTTTACAAAATGTTTTGATTGGTAGAAA
249 AATTAACAATTAATAATTTGACTAAAAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAA
223282 AAAATATAAT
314 AAAATATAAT
223292 TTTTTTACAA
Statistics
Matches: 288, Mismatches: 23, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
323 7 0.02
324 1 0.00
325 131 0.45
326 1 0.00
327 27 0.09
328 15 0.05
329 8 0.03
330 9 0.03
331 43 0.15
332 46 0.16
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (325 bp):
TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAAAAACCATAACCCTTAAC
TTAAAAACCCTAACCATTAACTTAAAAATCCTAAACCCTTAACTTAAAAACCATAACCATAACCG
TTACAAAAAACCCTTAACTATAAAACCCTCAAAACCCTAATCTTACAAAAACCCTAACCCTAACC
CTAAACCTAACCCTAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTA
ATAATTTGACTAAAAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAAAAAATATAATAT
Found at i:226525 original size:125 final size:125
Alignment explanation
Indices: 226250--226685 Score: 640
Period size: 125 Copynumber: 3.5 Consensus size: 125
226240 CAAACATGCT
* * *
226250 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTGATGAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
* *
226315 GAAGTATTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCT
66 GAAGCA-TTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* * *
226376 ACTGTAGCAAGAGTGCGTCTACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
*
226441 GAAGCATTTTTTATACTATTCGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGACCA
66 GAAGCATTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* * *
226501 ACTCTTA-CAAAAGCGAGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGCT
1 ACT-GTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCT
* * ** * * * *
226565 TGATGCGTTTTTTATACTATTTTCTCAAAAACATCATCTCAAAATTATTTTTTCAGGACCA
65 TGAAGCATTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* * *
226626 ACTGTAGCACAAGCGCGTCCACGTGGGCGCGAGTTCAGAAATTCTTCTAATAAAGCATCC
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCC
226686 AAAACCCTAA
Statistics
Matches: 278, Mismatches: 30, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
124 2 0.01
125 210 0.76
126 66 0.24
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
GAAGCATTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
Found at i:229800 original size:22 final size:22
Alignment explanation
Indices: 229775--229823 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
229765 ATATAATAAC
*
229775 GAAATGGTAGTAACACAACAGT
1 GAAATGGTAGTAAAACAACAGT
229797 GAAATGGTAGTAAAACAACAGT
1 GAAATGGTAGTAAAACAACAGT
*
229819 AAAAT
1 GAAAT
229824 AACAGCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.18
Consensus pattern (22 bp):
GAAATGGTAGTAAAACAACAGT
Found at i:231936 original size:18 final size:19
Alignment explanation
Indices: 231898--231938 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
231888 TCTCAATTCA
*
231898 TCATTTCATATATCATTTC
1 TCATCTCATATATCATTTC
*
231917 TCATCTCATA-ATCCTTTC
1 TCATCTCATATATCATTTC
231935 TCAT
1 TCAT
231939 ATTTTCCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (19 bp):
TCATCTCATATATCATTTC
Found at i:231978 original size:43 final size:43
Alignment explanation
Indices: 231898--231998 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
231888 TCTCAATTCA
*
231898 TCATTTCATATATCATTTCTCATCTCATAATCCTTTCTCATATTT-
1 TCATTTCA-ATAT--TTTCTCATCTCATAATCATTTCTCATATTTG
* * * * *
231943 TCCATTTTAATATTTTCTCATCTTATATTTATTTCTCTTATTTG
1 T-CATTTCAATATTTTCTCATCTCATAATCATTTCTCATATTTG
231987 TCATTTCAATAT
1 TCATTTCAATAT
231999 CAATCACATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
43 35 0.74
44 1 0.02
45 5 0.11
46 6 0.13
ACGTcount: A:0.24, C:0.20, G:0.01, T:0.55
Consensus pattern (43 bp):
TCATTTCAATATTTTCTCATCTCATAATCATTTCTCATATTTG
Found at i:233140 original size:4 final size:4
Alignment explanation
Indices: 233131--233162 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
233121 TTCTTCTCCT
233131 TTTC TTTC TTTC TTTC TTTC TTTC TTTAC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTT
233163 GTTTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:233206 original size:17 final size:18
Alignment explanation
Indices: 233184--233220 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
233174 ATGTCTCCAC
233184 TTTCTTTTC-TTTT-ATTA
1 TTTC-TTTCATTTTAATTA
233201 TTTCTTTCATTTTAATTA
1 TTTCTTTCATTTTAATTA
233219 TT
1 TT
233221 ATAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTTCATTTTAATTA
Found at i:239213 original size:20 final size:20
Alignment explanation
Indices: 239188--239227 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
239178 ATAACGCCAC
239188 TAAAGTTATTTGCGGCGCTT
1 TAAAGTTATTTGCGGCGCTT
239208 TAAAGTTATTTGCGGCGCTT
1 TAAAGTTATTTGCGGCGCTT
239228 CCTAAAGCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (20 bp):
TAAAGTTATTTGCGGCGCTT
Found at i:239391 original size:42 final size:42
Alignment explanation
Indices: 239299--239455 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
239289 CAAAAACGCT
* * * * *
239299 GCTAAAGAACATAT-TCCTTAGCGGCGCTTTGAGAAAAACGCC
1 GCTAAAGAACAT-TGTCTTTAGCGGCGCTTTTATATAAGCGCC
* * *
239341 ACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCC
1 GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
* * * * *
239383 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACC
1 GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
*
239425 GCTGAAGAACA-TGTTCTTTAGCGGCGCTTTT
1 GCTAAAGAACATTG-TCTTTAGCGGCGCTTTT
239456 GTACAAAAAC
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 94 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
Found at i:239805 original size:42 final size:42
Alignment explanation
Indices: 239713--239869 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
239703 CAAAAACGCT
* * * * *
239713 GCTAAAGAACATAT-TCCTTAGCGGCGCTTTGAGAAAAACGCC
1 GCTAAAGAACAT-TGTCTTTAGCGGCGCTTTTATATAAGCGCC
* * *
239755 ACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCC
1 GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
* * * * *
239797 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACC
1 GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
*
239839 GCTGAAGAACA-TGTTCTTTAGCGGCGCTTTT
1 GCTAAAGAACATTG-TCTTTAGCGGCGCTTTT
239870 GTACAAAAAC
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 94 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
GCTAAAGAACATTGTCTTTAGCGGCGCTTTTATATAAGCGCC
Found at i:239972 original size:414 final size:415
Alignment explanation
Indices: 239190--240019 Score: 1608
Period size: 414 Copynumber: 2.0 Consensus size: 415
239180 AACGCCACTA
239190 AAGTTATTTGCGGCGCTTTAAAGTTATTTGCGGCGCTTCCTAAAGCGCCGCAAAAAAGGCCGCTA
1 AAGTTATTTGCGGCGCTTTAAAGTTATTTGCGGCGCTTCCTAAAGCGCCGCAAAAAAGGCCGCTA
239255 ACGAAACGTCGCAAATGTTTGCAGCGTTTACAACCAAAAACGCTGCTAAAGAACATATTCCTTAG
66 ACGAAACGTCGCAAATGTTTGCAGCGTTTACAACCAAAAACGCTGCTAAAGAACATATTCCTTAG
239320 CGGCGCTTTGAGAAAAACGCCACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCCGC
131 CGGCGCTTTGAGAAAAACGCCACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCCGC
239385 TAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTGAAGAACATGTTCTTTAGCGGC
196 TAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTGAAGAACATGTTCTTTAGCGGC
239450 GCTTTTGTACAAAAACGCCACTATTTTTGGGATTTTTTATATTAAACTTTTCATTTTTTCAGCCC
261 GCTTTTGTACAAAAACGCCACTATTTTTGGGATTTTTTATATTAAACTTTTCATTTTTTCAGCCC
* * *
239515 TCCTGTAGCAACAAATCAAAAGCTATCAGATCTAAACCAGCCAAAAGCAATAAATTTATATAATA
326 TCCTGTAGCAACAAAACAAAAGCAACCAGATCTAAACCAGCCAAAAGCAATAAATTTATATAATA
239580 TTTCAAATTAAACGAATAAAATAAT
391 TTTCAAATTAAACGAATAAAATAAT
239605 AAGTTATTTGC-GCGCTTTAAAGTTATTTGCGGCGCTTCCTAAAGCGCCGCAAAAAAGGCCGCTA
1 AAGTTATTTGCGGCGCTTTAAAGTTATTTGCGGCGCTTCCTAAAGCGCCGCAAAAAAGGCCGCTA
239669 ACGAAACGTCGCAAATGTTTGCAGCGTTTACAACCAAAAACGCTGCTAAAGAACATATTCCTTAG
66 ACGAAACGTCGCAAATGTTTGCAGCGTTTACAACCAAAAACGCTGCTAAAGAACATATTCCTTAG
239734 CGGCGCTTTGAGAAAAACGCCACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCCGC
131 CGGCGCTTTGAGAAAAACGCCACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCCGC
239799 TAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTGAAGAACATGTTCTTTAGCGGC
196 TAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTGAAGAACATGTTCTTTAGCGGC
*
239864 GCTTTTGTACAAAAACGCCACTATTTTTGGGATTTTTTATATTAAATTTTTCATTTTTTCAGCCC
261 GCTTTTGTACAAAAACGCCACTATTTTTGGGATTTTTTATATTAAACTTTTCATTTTTTCAGCCC
*
239929 TCCTGTAGCAACAAAACAAAAGCAACCAGATCTAAACCAGCCAAAATCAATAAATTTATATAATA
326 TCCTGTAGCAACAAAACAAAAGCAACCAGATCTAAACCAGCCAAAAGCAATAAATTTATATAATA
239994 TTTCAAATTAAACGAATAAAATAAT
391 TTTCAAATTAAACGAATAAAATAAT
240019 A
1 A
240020 TTAATATCAA
Statistics
Matches: 410, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
414 399 0.97
415 11 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (415 bp):
AAGTTATTTGCGGCGCTTTAAAGTTATTTGCGGCGCTTCCTAAAGCGCCGCAAAAAAGGCCGCTA
ACGAAACGTCGCAAATGTTTGCAGCGTTTACAACCAAAAACGCTGCTAAAGAACATATTCCTTAG
CGGCGCTTTGAGAAAAACGCCACTGAAGAACATTGTCTTTAGCGGCGTTTTTATATAAGCGCCGC
TAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTGAAGAACATGTTCTTTAGCGGC
GCTTTTGTACAAAAACGCCACTATTTTTGGGATTTTTTATATTAAACTTTTCATTTTTTCAGCCC
TCCTGTAGCAACAAAACAAAAGCAACCAGATCTAAACCAGCCAAAAGCAATAAATTTATATAATA
TTTCAAATTAAACGAATAAAATAAT
Found at i:240321 original size:21 final size:21
Alignment explanation
Indices: 240254--240309 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
240244 TTTGAACCTT
240254 TGCTTCTCTCGCTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
240275 TGCTTCTCTCGTTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
240296 TGCTTCCCTCGCTG
1 TGCTTCTCTCGCTG
240310 TCGCGTCTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.04, C:0.41, G:0.20, T:0.36
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:245334 original size:9 final size:9
Alignment explanation
Indices: 245293--245627 Score: 102
Period size: 9 Copynumber: 35.7 Consensus size: 9
245283 TATGTATTAA
*
245293 GTAAATTAT
1 GTAAGTTAT
*
245302 GTAAGTTAG
1 GTAAGTTAT
*
245311 GTACGTGTA-
1 GTAAGT-TAT
245320 -TAAGTTAT
1 GTAAGTTAT
245328 GTAAGTTAT
1 GTAAGTTAT
*
245337 GT-A-TTAA
1 GTAAGTTAT
*
245344 GTAAGCTAT
1 GTAAGTTAT
*
245353 GTAAGTTGT
1 GTAAGTTAT
245362 GT-A-TTAT
1 GTAAGTTAT
* *
245369 ATAAGTTGT
1 GTAAGTTAT
* *
245378 GTCAGATAT
1 GTAAGTTAT
*
245387 TTAAGTTAT
1 GTAAGTTAT
*
245396 GTAAGTTTTTT
1 GTAAG--TTAT
*
245407 GT-A-CTAT
1 GTAAGTTAT
245414 GTAAGTTAT
1 GTAAGTTAT
*
245423 GCTATGTTATT
1 G-TAAGTTA-T
245434 ACGTAAGTTAT
1 --GTAAGTTAT
*
245445 GCAAGTTAT
1 GTAAGTTAT
* * *
245454 GCTTA-TAAC
1 G-TAAGTTAT
245463 G--AGTTAT
1 GTAAGTTAT
*
245470 GTAAGCTAT
1 GTAAGTTAT
245479 GTAAGTTAT
1 GTAAGTTAT
245488 GTAAGTTAT
1 GTAAGTTAT
*
245497 TTAAGTGGTGTAT
1 GTAA---GT-TAT
245510 -TAAGTTAT
1 GTAAGTTAT
*
245518 GGAAGTTGTTAT
1 GTAA---GTTAT
245530 -TAAGTTAT
1 GTAAGTTAT
*
245538 GCAAGATTATAAT
1 GTAAG--T-T-AT
*
245551 ATAAGTTAT
1 GTAAGTTAT
245560 GTATTATGTTAT
1 GTA--A-GTTAT
*
245572 GCAAGTTAT
1 GTAAGTTAT
245581 GTATAACGAGTTAT
1 G--T-A--AGTTAT
*
245595 GTAAGCTAT
1 GTAAGTTAT
245604 GTAAGTTAT
1 GTAAGTTAT
245613 GTAAGTTAT
1 GTAAGTTAT
*
245622 TTAAGT
1 GTAAGT
245628 GGTGTATTAA
Statistics
Matches: 239, Mismatches: 47, Indels: 80
0.65 0.13 0.22
Matches are distributed among these distances:
6 1 0.00
7 18 0.08
8 17 0.07
9 136 0.57
10 12 0.05
11 13 0.05
12 26 0.11
13 9 0.04
14 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:245373 original size:25 final size:25
Alignment explanation
Indices: 245282--245373 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
245272 TGATATATAT
**
245282 TTATGTATTA-AGTAAATTATGTAAG
1 TTATGTATTATA-TAAGCTATGTAAG
* * * *
245307 TTAGGTACGTGTATAAGTTATGTAAG
1 TTATGTA-TTATATAAGCTATGTAAG
245333 TTATGTATTA-AGTAAGCTATGTAAG
1 TTATGTATTATA-TAAGCTATGTAAG
*
245358 TTGTGTATTATATAAG
1 TTATGTATTATATAAG
245374 TTGTGTCAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.02
25 32 0.59
26 20 0.37
27 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (25 bp):
TTATGTATTATATAAGCTATGTAAG
Found at i:245515 original size:21 final size:20
Alignment explanation
Indices: 245483--245538 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
245473 AGCTATGTAA
**
245483 GTTATGTAAGTTATTTAAGTG
1 GTTAT-TAAGTTATGGAAGTG
*
245504 GTGTATTAAGTTATGGAAGTT
1 GT-TATTAAGTTATGGAAGTG
245525 GTTATTAAGTTATG
1 GTTATTAAGTTATG
245539 CAAGATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
21 16 0.52
22 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (20 bp):
GTTATTAAGTTATGGAAGTG
Found at i:245601 original size:125 final size:126
Alignment explanation
Indices: 245440--245696 Score: 480
Period size: 125 Copynumber: 2.0 Consensus size: 126
245430 TATTACGTAA
245440 GTTATGCAAGTTATGCTTATAACGAGTTATGTAAGCTATGTAAGTTATGTAAGTTATTTAAGTGG
1 GTTATGCAAGTTATGC-TATAACGAGTTATGTAAGCTATGTAAGTTATGTAAGTTATTTAAGTGG
*
245505 TGTATTAAGTTATGGAAGTTGTTATTAAGTTATGCAAGATTATAATATAAGTTATGTATTAT
65 TGTATTAAGTTATGGAAGTTGTTATTAAGTTATACAAGATTATAATATAAGTTATGTATTAT
245567 GTTATGCAAGTTATG-TATAACGAGTTATGTAAGCTATGTAAGTTATGTAAGTTATTTAAGTGGT
1 GTTATGCAAGTTATGCTATAACGAGTTATGTAAGCTATGTAAGTTATGTAAGTTATTTAAGTGGT
*
245631 GTATTAAGTTATGGAAGTTGTTATTAAGTTATATAAGATTATAATATAAGTTATGTATTAT
66 GTATTAAGTTATGGAAGTTGTTATTAAGTTATACAAGATTATAATATAAGTTATGTATTAT
245692 GTTAT
1 GTTAT
245697 TATGTATTAT
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
125 113 0.88
127 15 0.12
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (126 bp):
GTTATGCAAGTTATGCTATAACGAGTTATGTAAGCTATGTAAGTTATGTAAGTTATTTAAGTGGT
GTATTAAGTTATGGAAGTTGTTATTAAGTTATACAAGATTATAATATAAGTTATGTATTAT
Found at i:245699 original size:8 final size:7
Alignment explanation
Indices: 245681--245718 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
245671 ATAATATAAG
245681 TTATGTA
1 TTATGTA
245688 TTATGTTA
1 TTATG-TA
245696 TTATGTA
1 TTATGTA
245703 TTATGTA
1 TTATGTA
245710 --ATGTA
1 TTATGTA
245715 TTAT
1 TTAT
245719 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:245699 original size:27 final size:26
Alignment explanation
Indices: 245666--245738 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
245656 AAGTTATATA
*
245666 AGATTATAATATAAGTTATGTATTATG
1 AGATTAT-ATATAAGTTATGTATTATC
** * * *
245693 TTATTATGTATTATGTAATGTATTATC
1 AGATTATATA-TAAGTTATGTATTATC
245720 AGATTATATATAAGTTATG
1 AGATTATATATAAGTTATG
245739 GAAGTTATTA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (26 bp):
AGATTATATATAAGTTATGTATTATC
Done.