Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 35 of 226
Found at i:12213665 original size:18 final size:20
Alignment explanation
Indices: 12213630--12213680 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
12213620 ATAATTGTGT
12213630 TATTATATTATATGATTATAA
1 TATTATA-TATATGATTATAA
*
12213651 TATTATATA-AT-ATTATAT
1 TATTATATATATGATTATAA
12213669 TATTATATATAT
1 TATTATATATAT
12213681 AAAACAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 15 0.54
19 4 0.14
20 2 0.07
21 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTATATATATGATTATAA
Found at i:12214815 original size:22 final size:22
Alignment explanation
Indices: 12214790--12214903 Score: 111
Period size: 22 Copynumber: 5.0 Consensus size: 22
12214780 CTTTCTGATA
*
12214790 TTTAGCACGTCAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
*
12214812 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
* *
12214834 ATTATTAGCACGTCAATGCTCTCTG
1 --T-TTAGCACATCAGTGCTCTCTG
* * *
12214859 TTTAACACATCTGTGCTTTCTG
1 TTTAGCACATCAGTGCTCTCTG
* * *
12214881 TATAGCACTTTAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
12214903 T
1 T
12214904 CCATTAGTTC
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
22 53 0.73
23 1 0.01
24 1 0.01
25 18 0.25
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.40
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTG
Found at i:12214854 original size:47 final size:47
Alignment explanation
Indices: 12214783--12214880 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 47
12214773 TAGCGCGCTT
* *
12214783 TCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGTGCTC
1 TCTGATATTTAGCACGTCAATGCTCTCTGTTTAACACATCTGTGCTC
*
12214830 TCTGAT-TATTAGCACGTCAATGCTCTCTGTTTAACACATCTGTGCTT
1 TCTGATAT-TTAGCACGTCAATGCTCTCTGTTTAACACATCTGTGCTC
12214877 TCTG
1 TCTG
12214881 TATAGCACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 1 0.02
47 46 0.98
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.40
Consensus pattern (47 bp):
TCTGATATTTAGCACGTCAATGCTCTCTGTTTAACACATCTGTGCTC
Found at i:12220548 original size:24 final size:24
Alignment explanation
Indices: 12220501--12220548 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12220491 ATTATGAATT
*
12220501 AAATAAATCTAATTTTTTCTAAAA
1 AAATAAATCTAATTTTTTCGAAAA
12220525 AAATAAATCTAATTTTATT-GAAAA
1 AAATAAATCTAATTTT-TTCGAAAA
12220549 TTGATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATAAATCTAATTTTTTCGAAAA
Found at i:12220795 original size:13 final size:13
Alignment explanation
Indices: 12220777--12220806 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12220767 TTCAATTTTT
12220777 TTTATTACAATTA
1 TTTATTACAATTA
*
12220790 TTTATTATAATTA
1 TTTATTACAATTA
12220803 TTTA
1 TTTA
12220807 AGCGTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATTACAATTA
Found at i:12227136 original size:71 final size:71
Alignment explanation
Indices: 12227017--12227158 Score: 205
Period size: 71 Copynumber: 2.0 Consensus size: 71
12227007 TTTGGTAAGG
* * ** *
12227017 TTAAAAACAACGATGATGGTGAGATTAATTACTATAGCTGTAAGATAAAAATTTTTACCATACCA
1 TTAAAAACAACGATGACGGTGAGATTAATTACTATAGCTATAAGATAAAAAAATTCACCATACCA
12227082 TAACCA
66 TAACCA
* *
12227088 TTAAAACCAACGATGACGGTG-GTATTAATTACTATAGCTATAATATAAAAAAATTCACCATACC
1 TTAAAAACAACGATGACGGTGAG-ATTAATTACTATAGCTATAAGATAAAAAAATTCACCATACC
12227152 ATAACCA
65 ATAACCA
12227159 CCCACGAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 62 0.98
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (71 bp):
TTAAAAACAACGATGACGGTGAGATTAATTACTATAGCTATAAGATAAAAAAATTCACCATACCA
TAACCA
Found at i:12227520 original size:21 final size:23
Alignment explanation
Indices: 12227489--12227530 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
12227479 AAAATAATTA
12227489 TAAAAATTATAT-TATTTTAAAT
1 TAAAAATTATATATATTTTAAAT
12227511 TAAAAA-TATATATATTTTAA
1 TAAAAATTATATATATTTTAA
12227531 TTTTTGTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAATTATATATATTTTAAAT
Found at i:12229208 original size:18 final size:18
Alignment explanation
Indices: 12229187--12229221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12229177 ATTTTGAAAT
*
12229187 TAATTTGAATTTAATTTC
1 TAATTTAAATTTAATTTC
*
12229205 TAATTTAAATTTGATTT
1 TAATTTAAATTTAATTT
12229222 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (18 bp):
TAATTTAAATTTAATTTC
Found at i:12231880 original size:61 final size:59
Alignment explanation
Indices: 12231810--12231987 Score: 150
Period size: 61 Copynumber: 2.9 Consensus size: 59
12231800 TTGTTAAATT
*
12231810 ATATTTAATAATAATTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
1 ATATTTAATAATAA-TATTTTATA-TATTATATATTATGATTTTAATAAATTCATATAAGA
* * * * * *
12231871 ATATTTAATACTAAGAATTTTATTAAATTATATATT-T--TTGTTAAATTATATTTA-ATAATA
1 ATATTTAATAATAA-TATTTTA-TATATTATATATTATGATT-TT-AA-TAAATTCATATAAGA
* * *
12231931 ATTATTTTA-AATTATATTTTATAATATTATATATTATAATTTTAATAAATTCATATA
1 A-TATTTAATAATAATATTTTAT-ATATTATATATTATGATTTTAATAAATTCATATA
12231988 TTTTATCAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
58 3 0.03
59 25 0.27
60 17 0.18
61 43 0.47
62 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (59 bp):
ATATTTAATAATAATATTTTATATATTATATATTATGATTTTAATAAATTCATATAAGA
Found at i:12231940 original size:26 final size:25
Alignment explanation
Indices: 12231902--12231960 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
12231892 ATTAAATTAT
*
12231902 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
12231928 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
12231954 ATATTAT
1 ATATTAT
12231961 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:12231959 original size:15 final size:15
Alignment explanation
Indices: 12231915--12231970 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
12231905 TTTTTGTTAA
*
12231915 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
12231930 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
12231941 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
12231956 ATTATATATTATAAT
1 ATTATATTTTATAAT
12231971 TTTAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:12231986 original size:24 final size:22
Alignment explanation
Indices: 12231941--12232009 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
12231931 ATTATTTTAA
12231941 ATTATATTTTATAATATTATAT
1 ATTATATTTTATAATATTATAT
* *
12231963 ATTATAATTT-TAATA-AAT-T
1 ATTATATTTTATAATATTATAT
12231982 CA-TATATTTTATCAA-ATTATAT
1 -ATTATATTTTAT-AATATTATAT
12232004 ATTATA
1 ATTATA
12232010 AAAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 8 0.22
20 5 0.14
21 10 0.27
22 14 0.38
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATATTTTATAATATTATAT
Found at i:12232005 original size:17 final size:17
Alignment explanation
Indices: 12231887--12232026 Score: 61
Period size: 17 Copynumber: 8.6 Consensus size: 17
12231877 AATACTAAGA
*
12231887 ATTTTATTAAATTATAT
1 ATTTTAATAAATTATAT
**
12231904 ATTTTTGTTAAA-T-TAT
1 A-TTTTAATAAATTATAT
*
12231920 A-TTTAAT-AATAAT-T
1 ATTTTAATAAATTATAT
* *
12231934 ATTTTAAATTATATTTTAT
1 ATTTT-AA-TAAATTATAT
* *
12231953 AATATT-ATATATTATA-
1 -ATTTTAATAAATTATAT
12231969 ATTTTAATAAATTCATAT
1 ATTTTAATAAATT-ATAT
12231987 ATTTT-ATCAAATTATAT
1 ATTTTAAT-AAATTATAT
*
12232004 ATTATAA-AAA--ATAT
1 ATTTTAATAAATTATAT
12232018 A-TTTAATAA
1 ATTTTAATAA
12232027 TAATTATGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 33
0.67 0.09 0.23
Matches are distributed among these distances:
13 6 0.06
14 13 0.14
15 8 0.08
16 15 0.16
17 24 0.25
18 24 0.25
19 1 0.01
20 4 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTTAATAAATTATAT
Found at i:12232275 original size:16 final size:16
Alignment explanation
Indices: 12232254--12232321 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
12232244 GATTTGCTAT
*
12232254 TACACCTCTAATCCGA
1 TACACCTCTAATCCAA
** *
12232270 TACACCTCTCTTCCAT
1 TACACCTCTAATCCAA
*
12232286 TACAACTCTAATCCAA
1 TACACCTCTAATCCAA
12232302 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12232318 TACA
1 TACA
12232322 GCGAACCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.34, C:0.37, G:0.01, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12235634 original size:51 final size:51
Alignment explanation
Indices: 12235550--12235816 Score: 428
Period size: 51 Copynumber: 5.3 Consensus size: 51
12235540 ACTTCTGATC
* * *
12235550 AGTGACAAGTGATAAGTAGTAGCTTCAGTTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
12235601 AGTAGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
12235652 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
12235703 AGTGGCAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
12235754 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACA
1 AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
**
12235804 AGTGATAAGTGAT
1 AGTGGCAAGTGAT
12235817 CATACGTAAG
Statistics
Matches: 203, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
50 35 0.17
51 168 0.83
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGGCAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:12238837 original size:3 final size:3
Alignment explanation
Indices: 12238829--12238855 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12238819 TGCATTACTG
12238829 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
12238856 TTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:12240231 original size:3 final size:3
Alignment explanation
Indices: 12240223--12240253 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12240213 AAGAGATATG
12240223 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
12240254 TGCTTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:12241020 original size:3 final size:3
Alignment explanation
Indices: 12241012--12241040 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12241002 AACTCTTGAG
12241012 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12241041 GGTTTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12248665 original size:28 final size:28
Alignment explanation
Indices: 12248611--12248665 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
12248601 ATCAGACTCG
* * *
12248611 TCTTTCGGGGTTTTCTCTTGTTTTTCTT
1 TCTTTCGGAGTTTTCTCTTCTTCTTCTT
12248639 TCTTT-GGAGTTTTCTTCTTCTTCTTCT
1 TCTTTCGGAGTTTTC-TCTTCTTCTTCT
12248666 CAGGCATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.02, C:0.20, G:0.15, T:0.64
Consensus pattern (28 bp):
TCTTTCGGAGTTTTCTCTTCTTCTTCTT
Found at i:12254311 original size:5 final size:5
Alignment explanation
Indices: 12254303--12254327 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12254293 TTTTATTATG
12254303 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
12254328 AACCTCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:12258834 original size:3 final size:3
Alignment explanation
Indices: 12258828--12258853 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12258818 GGTGGGGGCA
12258828 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
12258854 ACCTTGTTTC
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:12265250 original size:13 final size:12
Alignment explanation
Indices: 12265214--12265250 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
12265204 CCTTTCCCCC
12265214 TCCCTTCTCTC-
1 TCCCTTCTCTCT
12265225 TCCCTTCTCTCT
1 TCCCTTCTCTCT
12265237 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
12265250 T
1 T
12265251 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 5 0.21
13 8 0.33
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:12265778 original size:23 final size:23
Alignment explanation
Indices: 12265734--12265779 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12265724 ATATTACCAT
*
12265734 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
12265757 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
12265780 CCTATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:12266043 original size:19 final size:19
Alignment explanation
Indices: 12266008--12266044 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12265998 ATATATTACC
**
12266008 TAAATATTTTAGTATTATG
1 TAAATATTTTAACATTATG
12266027 TAAATATTTTAACATTAT
1 TAAATATTTTAACATTAT
12266045 ATTATATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAATATTTTAACATTATG
Found at i:12300990 original size:98 final size:98
Alignment explanation
Indices: 12300814--12301010 Score: 342
Period size: 98 Copynumber: 2.0 Consensus size: 98
12300804 TTACAATAAA
*
12300814 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
12300879 CCTCTAGAATCCCAAACTCGGAATATTTCTTTT
66 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
*
12300912 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
12300977 CCTTTA-AAGTCCCAAACTCGGAATATTTCCTTT
66 CCTCTAGAA-TCCCAAACTCGGAATATTTCCTTT
12301010 A
1 A
12301011 TTATTTTTAA
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 2 0.02
98 92 0.98
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:12302332 original size:19 final size:19
Alignment explanation
Indices: 12302308--12302420 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
12302298 AATCATATAT
12302308 TCTAAGATTGTATATCATA
1 TCTAAGATTGTATATCATA
* *
12302327 TCTAAGATTATATATCATC
1 TCTAAGATTGTATATCATA
* *
12302346 TCTAAGATTGCATAGCATA
1 TCTAAGATTGTATATCATA
12302365 TCTAAGATTGCATATATCATA
1 TCTAAGATTG--TATATCATA
** *
12302386 TCTTGGATTGCATATCATA
1 TCTAAGATTGTATATCATA
12302405 TCTAAGATTGTATATC
1 TCTAAGATTGTATATC
12302421 CTCAAAAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 63 0.81
21 15 0.19
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGTATATCATA
Found at i:12302395 original size:40 final size:39
Alignment explanation
Indices: 12302308--12302420 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 39
12302298 AATCATATAT
* *
12302308 TCTAAGATTGTATATCATATCTAAGATT-ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGATATATCATA
*
12302346 TCTAAGATTGCATAGCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTG-ATATATCATA
**
12302386 TCTTGGATTGCATATCATATCTAAGATTG-TATATC
1 TCTAAGATTGCATATCATATCTAAGATTGATATATC
12302421 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 32 0.48
40 35 0.52
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (39 bp):
TCTAAGATTGCATATCATATCTAAGATTGATATATCATA
Found at i:12302739 original size:44 final size:44
Alignment explanation
Indices: 12302624--12303402 Score: 120
Period size: 44 Copynumber: 17.9 Consensus size: 44
12302614 GGAATTAGTG
* *
12302624 CTTCAATCTACTCCACTGCAACTTT-AGGGGGATAAGACTTGCCAT
1 CTTCAGTCTGCTCCACTGCAA-TTTCA-GGGGATAAGACTTGCCAT
* * *
12302669 CTTCAGTCTGC-CTCACTGTAACTTCAGGAGGATAAGACTTG-CTT
1 CTTCAGTCTGCTC-CACTGCAATTTCAGG-GGATAAGACTTGCCAT
* *
12302713 CCTT-AGTCTGCTCCATTGCAATTTCAGGGAGATAAGACTAG--A-
1 -CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * * *
12302755 -TGC-GATCTGCT-CTCTGTAACTTCAGAGAGATAAGATCTGTG--AT
1 CTTCAG-TCTGCTCCACTGCAATTTCAG-GGGATAAGA-CT-TGCCAT
* * * * * * * ** **
12302798 -TTTAATCCGCTCTACTGTAACTTCAGGGAGATAGGA-TTATCGG
1 CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * *
12302841 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT
1 CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * *
12302886 CTTCAGTCTGC-CTCATTGTAACTTCAGGAGGATAAGACTTG-CTT
1 CTTCAGTCTGCTC-CACTGCAATTTCAGG-GGATAAGACTTGCCAT
* * *
12302930 ACTT-AGTCTTG-TCCACCGCAACTTCAGGGAGATAAGACTAG--A-
1 -CTTCAGTC-TGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * * * * **
12302972 -TGC-GATATGCT-CTCTGTAACTTCAGAGAGATAAGA-TCTGTAAT
1 CTTCAG-TCTGCTCCACTGCAATTTCAG-GGGATAAGACT-TGCCAT
* * * * * *
12303015 -TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGTCGA-
1 CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACTTG-CCAT
* * * * *
12303058 CTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCAT
1 CTTCAGTCTGCTCCACTGCAATTTCAGG-GGATAAGACTTGCCAT
* * ** * *
12303103 CTTCAGTCTGC-CTCACTGTAACTTCAAAAGAATAAGACTTG-CTT
1 CTTCAGTCTGCTC-CACTGCAATTTC-AGGGGATAAGACTTGCCAT
* * *
12303147 ACTT-AGTCTTG-TCCACCGCAACTTCAGGGAGATAAGACTAG--A-
1 -CTTCAGTC-TGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * * * **
12303189 -TGC-GATCTGCT-CTCTGTAACTTCAGAGAGATAAGA-TCTGTAAT
1 CTTCAG-TCTGCTCCACTGCAATTTCAG-GGGATAAGACT-TGCCAT
* * * * * **
12303232 -TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTGTCGG
1 CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACTTGCCAT
* * * * *
12303275 CTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGA-TATGCCAT
1 CTTCAGTCTGCTCCACTGCAATTTCAGG-GGATAAGACT-TGCCAT
* * *
12303320 CTTCAGTCTGC-CTCACTGTAACTTT-AGAAGGATAAGACTTG-CTT
1 CTTCAGTCTGCTC-CACTGCAA-TTTCAG-GGGATAAGACTTGCCAT
*
12303364 ACTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 -CTTCAGTCTGCTCCACTGCAATTTCAGGG-GATAAGACT
12303403 AGATGCGATC
Statistics
Matches: 547, Mismatches: 118, Indels: 139
0.68 0.15 0.17
Matches are distributed among these distances:
39 2 0.00
40 65 0.12
41 17 0.03
42 5 0.01
43 33 0.06
44 275 0.50
45 145 0.27
46 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTCAGTCTGCTCCACTGCAATTTCAGGGGATAAGACTTGCCAT
Found at i:12303009 original size:217 final size:217
Alignment explanation
Indices: 12302623--12303503 Score: 1426
Period size: 217 Copynumber: 4.1 Consensus size: 217
12302613 AGGAATTAGT
* * * ** *
12302623 GCTTCAATCTACTCCACTGCAACTTTAGGGGGATAAGACTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* * ** *
12302688 AACTTCAGGAGGATAAGACTTGCTTCCTTAGTCTGCTCCATTGCAATTTCAGGGAGATAAGACTA
66 AACTTCAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACCGCAACTTCAGGGAGATAAGACTA
* * *
12302753 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGTAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
*
12302818 CTTCAGGGAGATAGGATTATCG
196 CTTCAGGGAGATAGGATTGTCG
* *
12302840 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCATTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
*
12302905 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTG-TCCACCGCAACTTCAGGGAGATAAGACT
66 AACTTCAGAAGGATAAGACTTGCTTACTTAGTC-TGCTCCACCGCAACTTCAGGGAGATAAGACT
*
12302969 AGATGCGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCA
130 AGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCA
12303034 ACTTCAGGGAGATAGGATTGTCG
195 ACTTCAGGGAGATAGGATTGTCG
*
12303057 ACTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* *
12303122 AACTTCAAAAGAATAAGACTTGCTTACTTAGTCTTG-TCCACCGCAACTTCAGGGAGATAAGACT
66 AACTTCAGAAGGATAAGACTTGCTTACTTAGTC-TGCTCCACCGCAACTTCAGGGAGATAAGACT
*
12303186 AGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCTGCTCCACTGCA
130 AGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCA
12303251 ACTTCAGGGAGATAGGATTGTCG
195 ACTTCAGGGAGATAGGATTGTCG
* *
12303274 GCTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGATATGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* *
12303339 AACTTTAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
66 AACTTCAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACCGCAACTTCAGGGAGATAAGACTA
* * * *
12303404 GATGCGATCTTCTCTCTGTAACTTCAGA-AGGATAAGATCTGTGATTTTAATTCGCTCCACTACA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGA-GATAAGATCTGTAATTTTAATCCGCTCCACTGCA
12303468 ACTTCAGGGAGATAGGATTGTCG
195 ACTTCAGGGAGATAGGATTGTCG
*
12303491 ACTTTAATCTGCT
1 GCTTTAATCTGCT
12303504 TCCCACTATC
Statistics
Matches: 625, Mismatches: 36, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
216 3 0.00
217 620 0.99
218 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (217 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
AACTTCAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACCGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
CTTCAGGGAGATAGGATTGTCG
Found at i:12303662 original size:132 final size:132
Alignment explanation
Indices: 12303496--12303975 Score: 782
Period size: 132 Copynumber: 3.6 Consensus size: 132
12303486 TGTCGACTTT
*
12303496 AATCTGCTTCCCACTATCTTGGAAAGATATGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * ** * *
12303561 GAGAGATAATATCTACAATCTTCAACCTACTCTACTGCTGCTTAGGGAAACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
12303626 TA
131 TA
12303628 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
12303693 GGGAGATAAGATCTACAATTTTCCACCTTCTCCGCTGCTGCTCAGGGAGACAAGACTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
12303758 TA
131 TA
* *
12303760 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACTC-TCTTCGATTTGCTCCACTACTGCTT
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTT-GTCGTCTTCGATCTGCTCCACTACTGCTT
*
12303824 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGGC
65 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
12303889 TTA
130 TTA
* * * *
12303892 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCTACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
12303957 GGGAGATAAGATCTACAAT
66 GGGAGATAAGATCTACAAT
12303976 TGTCACTGAT
Statistics
Matches: 323, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 320 0.99
133 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (132 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
TA
Found at i:12303700 original size:44 final size:44
Alignment explanation
Indices: 12303457--12303968 Score: 146
Period size: 44 Copynumber: 11.6 Consensus size: 44
12303447 ATTTTAATTC
** * * *
12303457 GCTCCACTACAACTTCAGGGAGATAGGA-TTGTCGACTTTAATCT
1 GCTCCACTACTGCTT-AGGGAGATAAGATTTGTCGTCTTCAATCT
* * *
12303501 GCTTCCCACTA-T-CTT-GGAAAGATATGATTTGTCGTCTTCGATCT
1 GC-T-CCACTACTGCTTAGG-GAGATAAGATTTGTCGTCTTCAATCT
* * * * * *
12303545 GCTCCACTACTGCTTAGAGAGATAATATCT-ACAATCTTCAACCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTTGTC-GTCTTCAATCT
* * * * * * * * *
12303589 ACTCTACTGCTGCTTAGGGAAACAAGGCTTGGT-GGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAA-GATTTGTCGTCTTCAATCT
* *
12303633 GCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGTCGTCTTCGATCT
1 GC-T-CCACTACTGCTTAGG-GAGATAAGATTTGTCGTCTTCAATCT
* * * * * *
12303677 GCTCCACTACTGCTTAGGGAGATAAGATCT-ACAATTTTCCACCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTTGTC-GTCTTCAATCT
* * * * * * * *
12303721 TCTCCGCTGCTGCTCAGGGAGACAAGACTTGGT-GGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAAGA-TTTGTCGTCTTCAATCT
* * * *
12303765 GCTTCCCACTA-T-CTT-GGAAAGATAAGATTTACTC-TCTTCGATTT
1 GC-T-CCACTACTGCTTAGG-GAGATAAGATTT-GTCGTCTTCAATCT
* * * *
12303809 GCTCCACTACTGCTTAGGGAGATAAGATCT-ACAATCTTCAACCT
1 GCTCCACTACTGCTTAGGGAGATAAGATTTGTC-GTCTTCAATCT
* * * * * * * * *
12303853 TCTCCGCTGCTGCTCAGGGAGACAATGCTTGGT-GGCTTAAATCT
1 GCTCCACTACTGCTTAGGGAGATAA-GATTTGTCGTCTTCAATCT
* * * *
12303897 GCTTCCCACTA-T-CTT-GGAAAGATAAGATTCGCCGTCTTCGATCT
1 GC-T-CCACTACTGCTTAGG-GAGATAAGATTTGTCGTCTTCAATCT
* *
12303941 GCTCTACTACTGTTTAGGGAGATAAGAT
1 GCTCCACTACTGCTTAGGGAGATAAGAT
12303969 CTACAATTGT
Statistics
Matches: 321, Mismatches: 108, Indels: 78
0.63 0.21 0.15
Matches are distributed among these distances:
42 26 0.08
43 34 0.11
44 225 0.70
45 18 0.06
46 18 0.06
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (44 bp):
GCTCCACTACTGCTTAGGGAGATAAGATTTGTCGTCTTCAATCT
Found at i:12305217 original size:8 final size:7
Alignment explanation
Indices: 12305201--12305246 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
12305191 TTACTTTTAC
12305201 TTTTTCT
1 TTTTTCT
*
12305208 TTTTTCC
1 TTTTTCT
12305215 TTTTTC-
1 TTTTTCT
12305221 TTTTTCT
1 TTTTTCT
12305228 TTTTCCTCT
1 TTTT--TCT
12305237 TTTTT-T
1 TTTTTCT
12305243 TTTT
1 TTTT
12305247 GAAATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
6 11 0.31
7 17 0.49
9 7 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:12305217 original size:14 final size:14
Alignment explanation
Indices: 12305195--12305225 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12305185 CTCCTTTTAC
12305195 TTTTACTTTTTCTT
1 TTTTACTTTTTCTT
*
12305209 TTTTCCTTTTTCTT
1 TTTTACTTTTTCTT
12305223 TTT
1 TTT
12305226 CTTTTTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTACTTTTTCTT
Found at i:12305217 original size:20 final size:20
Alignment explanation
Indices: 12305189--12305231 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12305179 TGGCCTCTCC
12305189 TTTTACTTTTACTTTTTCTT
1 TTTTACTTTTACTTTTTCTT
* *
12305209 TTTTCCTTTTTCTTTTTCTT
1 TTTTACTTTTACTTTTTCTT
12305229 TTT
1 TTT
12305232 CCTCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTACTTTTACTTTTTCTT
Found at i:12305224 original size:5 final size:6
Alignment explanation
Indices: 12305188--12305232 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
12305178 TTGGCCTCTC
* *
12305188 CTTTTA CTTTTA CTTTTT CTTTTTT CCTTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT C-TTTTT -CTTTTT CTTTTT CTTTTT C
12305233 CTCTTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 25 0.69
7 10 0.28
8 1 0.03
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:12305239 original size:14 final size:14
Alignment explanation
Indices: 12305194--12305239 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
12305184 TCTCCTTTTA
12305194 CTTTTACTTTTTCT
1 CTTTTACTTTTTCT
* *
12305208 TTTTTCCTTTTTCT
1 CTTTTACTTTTTCT
12305222 -TTTT-CTTTTTCCT
1 CTTTTACTTTTT-CT
12305235 CTTTT
1 CTTTT
12305240 TTTTTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.21
13 6 0.21
14 16 0.57
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTACTTTTTCT
Found at i:12305239 original size:20 final size:21
Alignment explanation
Indices: 12305194--12305245 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
12305184 TCTCCTTTTA
12305194 CTTTTACTTTTTCTTTTTTCCT
1 CTTTT-CTTTTTCTTTTTTCCT
12305216 -TTTTCTTTTTC-TTTTTCCT
1 CTTTTCTTTTTCTTTTTTCCT
*
12305235 CTTTTTTTTTT
1 CTTTTCTTTTT
12305246 TGAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTCTTTTTCTTTTTTCCT
Found at i:12309507 original size:98 final size:98
Alignment explanation
Indices: 12309333--12309529 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
12309323 GTACAATAAA
*
12309333 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATT
*
12309398 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
* * *
12309431 ACTTTAAAAGAACATCCACTTATCTAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATT
*
12309496 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
12309529 A
1 A
12309530 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:12310932 original size:40 final size:40
Alignment explanation
Indices: 12310845--12310956 Score: 156
Period size: 40 Copynumber: 2.9 Consensus size: 40
12310835 AATCATATAT
* * *
12310845 TCTAAAATTGCATATCATGTCTAAGATT--ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
12310883 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
** *
12310923 TCTTGGATTGCATATCATATCTAAAATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
12310957 CCTTAAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 26 0.39
40 40 0.61
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:12310951 original size:19 final size:19
Alignment explanation
Indices: 12310845--12310957 Score: 136
Period size: 19 Copynumber: 5.8 Consensus size: 19
12310835 AATCATATAT
* *
12310845 TCTAAAATTGCATATCATG
1 TCTAAGATTGCATATCATA
** *
12310864 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
12310883 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
12310902 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
12310923 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12310942 TCTAAAATTGCATATC
1 TCTAAGATTGCATATC
12310958 CTTAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
19 63 0.79
21 17 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12311629 original size:18 final size:18
Alignment explanation
Indices: 12311606--12311647 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
12311596 AAAATAGGTT
12311606 TTTAAG-GGTTAAAAGAAA
1 TTTAAGTGGTTAAAA-AAA
12311624 TTTAAGTGGTTAAAAAAA
1 TTTAAGTGGTTAAAAAAA
12311642 TGTTAA
1 T-TTAA
12311648 ATAGTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
TTTAAGTGGTTAAAAAAA
Found at i:12312730 original size:10 final size:10
Alignment explanation
Indices: 12312715--12312767 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
12312705 AAGTCGTAAG
12312715 AAAATTATAA
1 AAAATTATAA
12312725 AAAATTATAA
1 AAAATTATAA
12312735 AAAATTAT--
1 AAAATTATAA
*
12312743 AAAATTCGTAAA
1 AAAATT-AT-AA
12312755 AAAATTATAA
1 AAAATTATAA
12312765 AAA
1 AAA
12312768 CTATCATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 6 0.16
9 1 0.03
10 23 0.62
11 1 0.03
12 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATTATAA
Found at i:12312967 original size:10 final size:9
Alignment explanation
Indices: 12312953--12313086 Score: 61
Period size: 9 Copynumber: 13.4 Consensus size: 9
12312943 TTTTGATGTA
12312953 TTTTATAAT
1 TTTTATAAT
*
12312962 TATTTATGAT
1 T-TTTATAAT
* *
12312972 TTTGATAAAA
1 TTTTAT-AAT
12312982 TTTTATAATTT
1 TTTTATAA--T
*
12312993 TTTTACAAT
1 TTTTATAAT
12313002 TTTTATAATTTT
1 TTTTATAA---T
*
12313014 TTTTCTAAT
1 TTTTATAAT
12313023 TTTTCATAAAT
1 TTTT-AT-AAT
* *
12313034 TTTAAATACTT
1 TTT-TATA-AT
*
12313045 TTTTATTAAAA
1 TTTTA-T-AAT
12313056 TTTTATAAT
1 TTTTATAAT
**
12313065 TTTTATTTT
1 TTTTATAAT
12313074 TTTTATAAT
1 TTTTATAAT
12313083 TTTT
1 TTTT
12313087 TCCACATGTC
Statistics
Matches: 92, Mismatches: 20, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
9 40 0.43
10 18 0.20
11 25 0.27
12 9 0.10
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:12313087 original size:11 final size:10
Alignment explanation
Indices: 12312953--12313087 Score: 71
Period size: 10 Copynumber: 13.4 Consensus size: 10
12312943 TTTTGATGTA
12312953 TTTTATAATT
1 TTTTATAATT
* *
12312963 ATTTATGA-T
1 TTTTATAATT
* **
12312972 TTTGATAAAA
1 TTTTATAATT
12312982 TTTTATAATT
1 TTTTATAATT
*
12312992 TTTT-TACAAT
1 TTTTATA-ATT
12313002 TTTTATAATTTT
1 TTTTATAA--TT
*
12313014 TTTTCTAATT
1 TTTTATAATT
*
12313024 TTTCATAAATT
1 TTTTAT-AATT
** *
12313035 TTAAATACTT
1 TTTTATAATT
**
12313045 TTTTATTAAAA
1 TTTTA-TAATT
12313056 TTTTATAA-T
1 TTTTATAATT
*
12313065 TTTTAT-TTT
1 TTTTATAATT
12313074 TTTTATAATT
1 TTTTATAATT
12313084 TTTT
1 TTTT
12313088 CCACATGTCA
Statistics
Matches: 91, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
9 21 0.23
10 45 0.49
11 17 0.19
12 8 0.09
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12331764 original size:25 final size:25
Alignment explanation
Indices: 12331736--12331865 Score: 113
Period size: 25 Copynumber: 5.2 Consensus size: 25
12331726 GGACACACCA
12331736 TAGCTCTCATGAGCTTCCCGATATT
1 TAGCTCTCATGAGCTTCCCGATATT
*
12331761 TAGCTCGCATGAGCTTCCC-A-ATT
1 TAGCTCTCATGAGCTTCCCGATATT
* * * *
12331784 TCAGCTCTTATGAGCTTCTCAATATA
1 T-AGCTCTCATGAGCTTCCCGATATT
* * * * *
12331810 CAGCTCGCATGAGCTTTCTGTTATT
1 TAGCTCTCATGAGCTTCCCGATATT
* *
12331835 TAGCT-TACATGAGCTTCCCGTTATA
1 TAGCTCT-CATGAGCTTCCCGATATT
12331860 TAGCTC
1 TAGCTC
12331866 GGAAGAACTT
Statistics
Matches: 81, Mismatches: 19, Indels: 9
0.74 0.17 0.08
Matches are distributed among these distances:
23 4 0.05
24 16 0.20
25 59 0.73
26 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (25 bp):
TAGCTCTCATGAGCTTCCCGATATT
Found at i:12333042 original size:50 final size:50
Alignment explanation
Indices: 12332941--12333058 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
12332931 AGTAAGTCTT
* *
12332941 AACGCCAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTGC
1 AACGCCAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTACTCCACTGC
* * * *
12332991 AACGCCAGGGA-AGTAAGATTCGTCGTTGTGGCTTCAATCTATTCCATTGC
1 AACGCCAGGGAGA-TAAGATTCGCCGTCGTGGCTTCAATCTACTCCACTGC
* * *
12333041 AACGTCAAGGCGATAAGA
1 AACGCCAGGGAGATAAGA
12333059 CCGGTGTCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.02
50 55 0.96
51 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (50 bp):
AACGCCAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTACTCCACTGC
Found at i:12333168 original size:88 final size:88
Alignment explanation
Indices: 12333065--12333237 Score: 258
Period size: 88 Copynumber: 2.0 Consensus size: 88
12333055 AAGACCGGTG
* * * * *
12333065 TCTTCGATCTGCTTCGCTGCCAGTGCAGGAAGGCAAAATCTG-TCATTTTTAACCTACTCCACTG
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATCTGCT-ATTTTCAACCTACTCCACTG
*
12333129 CTGCTCAGGTAGACAAGGCTGGTA
65 CTGCTCAGGGAGACAAGGCTGGTA
*
12333153 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATCTGCTATTTTCAACCTACTCCACTGC
*
12333218 TGCTCAGGGAGATAAGGCTG
66 TGCTCAGGGAGACAAGGCTG
12333238 AAGTTTCACT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
88 75 0.99
89 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTGGTA
Found at i:12334499 original size:17 final size:16
Alignment explanation
Indices: 12334468--12334509 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
12334458 GAATTTAGAA
12334468 GAATTTTTGAATTAGT
1 GAATTTTTGAATTAGT
*
12334484 GAATTTTGTGATTTAGT
1 GAATTTT-TGAATTAGT
12334501 GAATTTTTG
1 GAATTTTTG
12334510 CGATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (16 bp):
GAATTTTTGAATTAGT
Found at i:12335810 original size:46 final size:46
Alignment explanation
Indices: 12335743--12335881 Score: 215
Period size: 46 Copynumber: 3.0 Consensus size: 46
12335733 TGGCAAAGTG
* *
12335743 TGAAAAGTAAGTATGGTGTTTCGGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
*
12335789 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
** * *
12335835 TGAAAAGTAGGTATGGTAATTCCGTGAAGAAAGCCATACTGAGTTA
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
12335881 T
1 T
12335882 AGCAATGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:12346924 original size:252 final size:252
Alignment explanation
Indices: 12346469--12346988 Score: 986
Period size: 252 Copynumber: 2.1 Consensus size: 252
12346459 TTTTTGTACA
* * * * *
12346469 ATTTTTGGTAATTTTCCGAATTTAGAATAGGGGATCTCGAAATCAATCCAGCCCTGTTTCAGTAA
1 ATTTTTGAT-ATTTTCCAAAGTTAGAACAGGGGATCTCGAAATCAATACAGCCCTGTTTCAGTAA
12346534 AATTCAGATATCTCCAAAAATACAACTCTTTTGCTTATTCTATTTCTTTCATATGAAAATAGACA
65 AATTCAGATATCTCCAAAAATACAACTCTTTTGCTTATTCTATTTCTTTCATATGAAAATAGACA
12346599 CATTCAGCTTCAATTTCATATATTATTCAGCTTCCCATTCATTTTCCACCATTTATGGTGATTTT
130 CATTCAGCTTCAATTTCATATATTATTCAGCTTCCCATTCATTTTCCACCATTTATGGTGATTTT
12346664 TCAAATTTACCCAACTGCTGTTGTTCAACACAGTTTATAATTAAATCGTTCCTTTTTC
195 TCAAATTTACCCAACTGCTGTTGTTCAACACAGTTTATAATTAAATCGTTCCTTTTTC
12346722 ATTTTTGATATTTTCCAAAGTTAGAACAGGGGATCTCGAAATCAATACAGCCCTGTTTCAGTAAA
1 ATTTTTGATATTTTCCAAAGTTAGAACAGGGGATCTCGAAATCAATACAGCCCTGTTTCAGTAAA
12346787 ATTCAGATATCTCCAAAAATACAACTCTTTTGCTTATTCTATTTCTTTCATATGAAAATAGACAC
66 ATTCAGATATCTCCAAAAATACAACTCTTTTGCTTATTCTATTTCTTTCATATGAAAATAGACAC
12346852 ATTCAGCTTCAATTTCATATATTATTCAGCTTCCCATTCATTTTCCACCATTTATGGTGATTTTT
131 ATTCAGCTTCAATTTCATATATTATTCAGCTTCCCATTCATTTTCCACCATTTATGGTGATTTTT
12346917 CAAATTTACCCAACTGCTGTTGTTCAACACAGTTTATAATTAAATCGTTCCTTTTTC
196 CAAATTTACCCAACTGCTGTTGTTCAACACAGTTTATAATTAAATCGTTCCTTTTTC
12346974 ATTTTTGATATTTTC
1 ATTTTTGATATTTTC
12346989 TCCCATCTCA
Statistics
Matches: 262, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
252 254 0.97
253 8 0.03
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (252 bp):
ATTTTTGATATTTTCCAAAGTTAGAACAGGGGATCTCGAAATCAATACAGCCCTGTTTCAGTAAA
ATTCAGATATCTCCAAAAATACAACTCTTTTGCTTATTCTATTTCTTTCATATGAAAATAGACAC
ATTCAGCTTCAATTTCATATATTATTCAGCTTCCCATTCATTTTCCACCATTTATGGTGATTTTT
CAAATTTACCCAACTGCTGTTGTTCAACACAGTTTATAATTAAATCGTTCCTTTTTC
Found at i:12347540 original size:21 final size:21
Alignment explanation
Indices: 12347514--12347566 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12347504 CGCTATTTCT
*
12347514 AATCTCACTGCTACAATACCC
1 AATCTCACTGCTACAATAACC
* * * *
12347535 AATCTCACCGCTATAGTAACT
1 AATCTCACTGCTACAATAACC
12347556 AATCTCACTGC
1 AATCTCACTGC
12347567 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACC
Found at i:12347857 original size:19 final size:19
Alignment explanation
Indices: 12347833--12347872 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12347823 TACGGTGGAT
12347833 ATCGCACTTAGCACCACCA
1 ATCGCACTTAGCACCACCA
12347852 ATCGCACTTAGCACCACCA
1 ATCGCACTTAGCACCACCA
12347871 AT
1 AT
12347873 GAACCGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (19 bp):
ATCGCACTTAGCACCACCA
Found at i:12347909 original size:27 final size:27
Alignment explanation
Indices: 12347878--12347930 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
12347868 CCAATGAACC
*
12347878 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACATAGCAACCCCTTG
12347905 GGGGAATCAGCACATAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
12347931 TTCACATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTTG
Found at i:12355663 original size:21 final size:21
Alignment explanation
Indices: 12355637--12355689 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12355627 CGCTATTTCT
*
12355637 AATCTCACTGCTACAATACCC
1 AATCTCACTGCTACAATAACC
* * * *
12355658 AATCTCACCGCTATAGTAACT
1 AATCTCACTGCTACAATAACC
12355679 AATCTCACTGC
1 AATCTCACTGC
12355690 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACC
Found at i:12356095 original size:104 final size:104
Alignment explanation
Indices: 12355846--12356214 Score: 607
Period size: 104 Copynumber: 3.6 Consensus size: 104
12355836 AACCGTTATT
* * * *
12355846 GGTGGATCTCGCGCTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
*
12355911 ATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
12355949 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
12356014 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
12356053 GGTGGATATCGCACTGAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* *
12356118 ATCAGCACATAGCAACCCCTTTTCACATTTCAAAGATAT
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* * **
12356157 GGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCT
12356215 TTATATACAA
Statistics
Matches: 251, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
103 84 0.33
104 166 0.66
105 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:12356117 original size:27 final size:27
Alignment explanation
Indices: 12356086--12356137 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12356076 CCAATGAACC
*
12356086 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
12356113 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
12356138 TTTCACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:12359880 original size:19 final size:18
Alignment explanation
Indices: 12359847--12359886 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
12359837 ATGTATATGC
12359847 ATATATTAAAATATGTAT
1 ATATATTAAAATATGTAT
*
12359865 ATATATGTATAATATGTAT
1 ATATAT-TAAAATATGTAT
12359884 ATA
1 ATA
12359887 AAAAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
ATATATTAAAATATGTAT
Found at i:12364129 original size:62 final size:62
Alignment explanation
Indices: 12364032--12364178 Score: 267
Period size: 62 Copynumber: 2.4 Consensus size: 62
12364022 GAAGGTTGAG
* * *
12364032 CAGAAGCTCATGAGAGCTAAACGGAAACGTATAAGGGTTGAATGGAAACTCATATGAGTTAA
1 CAGAAGCTCGTGAGAGCTAAACGGAAACCTATAAGGGTTGAACGGAAACTCATATGAGTTAA
12364094 CAGAAGCTCGTGAGAGCTAAACGGAAACCTATAAGGGTTGAACGGAAACTCATATGAGTTAA
1 CAGAAGCTCGTGAGAGCTAAACGGAAACCTATAAGGGTTGAACGGAAACTCATATGAGTTAA
12364156 CAGAAGCTCGTGAGAGCTAAACG
1 CAGAAGCTCGTGAGAGCTAAACG
12364179 AAAAGTAAAC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (62 bp):
CAGAAGCTCGTGAGAGCTAAACGGAAACCTATAAGGGTTGAACGGAAACTCATATGAGTTAA
Found at i:12387867 original size:18 final size:18
Alignment explanation
Indices: 12387840--12387932 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
12387830 TACGACCGTT
*
12387840 TACGGTACTATTCACGTA
1 TACGATACTATTCACGTA
*
12387858 TACGACACTATTCACGTA
1 TACGATACTATTCACGTA
* *
12387876 TATGGTACTATTCACGTA
1 TACGATACTATTCACGTA
*
12387894 TACGATACTATTTACGTA
1 TACGATACTATTCACGTA
* *
12387912 TACGGTACTGTTCACGTA
1 TACGATACTATTCACGTA
12387930 TAC
1 TAC
12387933 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (18 bp):
TACGATACTATTCACGTA
Found at i:12387890 original size:36 final size:36
Alignment explanation
Indices: 12387840--12387932 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
12387830 TACGACCGTT
12387840 TACGGTACTATTCACGTATACGACACTATTCACGTA
1 TACGGTACTATTCACGTATACGACACTATTCACGTA
* * *
12387876 TATGGTACTATTCACGTATACGATACTATTTACGTA
1 TACGGTACTATTCACGTATACGACACTATTCACGTA
*
12387912 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
12387933 AGTAGTTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGACACTATTCACGTA
Found at i:12406845 original size:50 final size:49
Alignment explanation
Indices: 12406732--12406914 Score: 237
Period size: 50 Copynumber: 3.7 Consensus size: 49
12406722 TCACATATCG
* * *
12406732 GTGCCGATGCCATATCCCAGACATGGTCTTACACTGGCACTCATC-T-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCGTCC
** * * *
12406779 AAGCCGATGCCATGTCCCAAACATGGTCTCACACTGACTCTCCTCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTC-GTCC
*
12406829 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCACTCCTCGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCCTC-GTCC
12406879 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTG
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTG
12406915 GCACACTCAC
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
47 37 0.32
49 2 0.02
50 77 0.66
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (49 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCTCGTCC
Found at i:12406942 original size:100 final size:97
Alignment explanation
Indices: 12406733--12406931 Score: 231
Period size: 97 Copynumber: 2.0 Consensus size: 97
12406723 CACATATCGG
* * *
12406733 TGCCGATGCCATATCCCAGACATGGTCTTACACTGGCACTCATCTCAAGCCGATGCCATGTCCCA
1 TGCCGATACCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATGCCATGTCCCA
* * *
12406798 AACATGGTCTCACACTGACTCTCCTCTGTCCG
66 AACATGGTCTCACACTGACACTCCACTGTCCA
* * **
12406830 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCGGTCTGTGCCGATGCCATGTC
1 TGCCGATACCATGTCCCAGACATGGTCTTACACTAGCACTCATC--TC-AAGCCGATGCCATGTC
* *
12406895 CCAGACATGGTCTTACACTGGCACACT-CACTG-CCA
63 CCAAACATGGTCTCACACT-G-ACACTCCACTGTCCA
12406930 TG
1 TG
12406932 GTCCAACCAT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
97 41 0.47
99 2 0.02
100 35 0.40
101 5 0.06
102 4 0.05
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.25
Consensus pattern (97 bp):
TGCCGATACCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATGCCATGTCCCA
AACATGGTCTCACACTGACACTCCACTGTCCA
Found at i:12412200 original size:146 final size:147
Alignment explanation
Indices: 12411877--12412312 Score: 698
Period size: 146 Copynumber: 3.0 Consensus size: 147
12411867 ACTTTAATGG
* * * * *
12411877 AAGTCACATTCCAAATGTTTTAAAACTGACATTTTAAGTCTCACCACTCCTTTTTGGAAGTATAG
1 AAGTTACATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACCAGTCTTTTTTGAAAGTATAG
*
12411942 TTATAAATTAATGTGTTTACTATAAGAAATTATTTTATGGACTCTTTTCACCACATCATCCATAG
66 TTATAAATTAATGTGTTTAC-ATGAGAAATTATTTTATGGACTCTTTTCACCACATCATCCATAG
12412007 TCCTGCCCAATTTCATGA
130 TCCTGCCCAATTTCATGA
*
12412025 AAGTTAGATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACCAGTCTTTTTTGAAAGTATAG
1 AAGTTACATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACCAGTCTTTTTTGAAAGTATAG
* * * *
12412090 TTATAAATTAATGTGTTTATCATGAGAAA-T-TTTTAGGGACTCTTTTCGCCACATCAACCATGG
66 TTATAAATTAATGTGTTTA-CATGAGAAATTATTTTATGGACTCTTTTCACCACATCATCCATAG
12412153 TCCTGCCCAATTTCATGA
130 TCCTGCCCAATTTCATGA
*
12412171 AAGTTACATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACTAGTCTTTTTTGAAAGTATAG
1 AAGTTACATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACCAGTCTTTTTTGAAAGTATAG
*
12412236 TTATAAATTAATGTGTTTACCATGAGAAATTATTTTATTGACTC-TTTCTACCACATCATCCATA
66 TTATAAATTAATGTGTTTA-CATGAGAAATTATTTTATGGACTCTTTTC-ACCACATCATCCATA
12412300 GTCCTGCCCAATT
129 GTCCTGCCCAATT
12412313 AAAAGAAGAC
Statistics
Matches: 265, Mismatches: 19, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
146 138 0.52
147 6 0.02
148 120 0.45
149 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (147 bp):
AAGTTACATTCCAAATGTTTTAAAACTGCCATTTTAAGTCTCACCAGTCTTTTTTGAAAGTATAG
TTATAAATTAATGTGTTTACATGAGAAATTATTTTATGGACTCTTTTCACCACATCATCCATAGT
CCTGCCCAATTTCATGA
Found at i:12418062 original size:29 final size:30
Alignment explanation
Indices: 12417997--12418064 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
12417987 TTGTTTATTA
*
12417997 TTTCTTA-TAATTATTATTTTATTTTTCTAG
1 TTTCTTATTAATTATTA-TTTATTTTTCAAG
*
12418027 -TTATTATTAATTAATTA-TTATTTTT-AAG
1 TTTCTTATTAATT-ATTATTTATTTTTCAAG
12418055 TTTCTTATTA
1 TTTCTTATTA
12418065 TTCTTAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.06
29 21 0.66
30 5 0.16
31 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTCTTATTAATTATTATTTATTTTTCAAG
Found at i:12418064 original size:18 final size:18
Alignment explanation
Indices: 12418040--12418080 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12418030 TTATTAATTA
*
12418040 ATTATTATTTTTAAGTTTC
1 ATTATTATTCTT-AGTTTC
12418059 -TTATTATTCTTAGTTTC
1 ATTATTATTCTTAGTTTC
12418076 ATTAT
1 ATTAT
12418081 CATCAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
ATTATTATTCTTAGTTTC
Found at i:12418342 original size:12 final size:12
Alignment explanation
Indices: 12418310--12418348 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
12418300 TTGCTTATCA
12418310 TTATTATTAATTGT
1 TTATTATT-ATT-T
*
12418324 ATATTATTATTT
1 TTATTATTATTT
12418336 TTATTATTATTT
1 TTATTATTATTT
12418348 T
1 T
12418349 AGTTTTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 3 0.13
14 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:12418394 original size:16 final size:15
Alignment explanation
Indices: 12418363--12418396 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12418353 TTCCATTTCG
*
12418363 TTTCTTATTTTTATT
1 TTTCTTATTATTATT
12418378 TTTCTTCATTATTATT
1 TTTCTT-ATTATTATT
12418394 TTT
1 TTT
12418397 TGTACTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTATTATTATT
Found at i:12426168 original size:26 final size:24
Alignment explanation
Indices: 12426108--12426171 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
12426098 AAATAAAAAT
*
12426108 ATTATCGTATTAATATTAAAATGA
1 ATTATCGTATTAAAATTAAAATGA
* * *
12426132 TTATATTGTATTGAAAATTAAATCTGA
1 AT-TATCGTATT-AAAATTAAA-ATGA
12426159 ATTATCGTATTAA
1 ATTATCGTATTAA
12426172 TTATGATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 16 0.52
27 4 0.13
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (24 bp):
ATTATCGTATTAAAATTAAAATGA
Found at i:12438843 original size:6 final size:6
Alignment explanation
Indices: 12438832--12438865 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12438822 GGTTGCAAAA
* *
12438832 ATGACG ATGACG ATGATG ATGACG ATGAGG ATGA
1 ATGACG ATGACG ATGACG ATGACG ATGACG ATGA
12438866 TGTTTCTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (6 bp):
ATGACG
Found at i:12438855 original size:18 final size:18
Alignment explanation
Indices: 12438832--12438867 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12438822 GGTTGCAAAA
12438832 ATGACGATGACGATGATG
1 ATGACGATGACGATGATG
*
12438850 ATGACGATGAGGATGATG
1 ATGACGATGACGATGATG
12438868 TTTCTTCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.22
Consensus pattern (18 bp):
ATGACGATGACGATGATG
Found at i:12439509 original size:37 final size:37
Alignment explanation
Indices: 12439459--12439530 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
12439449 TAAACTCATA
*
12439459 ATTAATTAAATAGTAAGTGAATTCTAATTTAATGGTG
1 ATTAATTAAATAGTAAGTGAATTCTAATCTAATGGTG
*
12439496 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGG
1 ATTAATTAAATAGTAAGTGAATTCTAATCTAATGG
12439531 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTAATTAAATAGTAAGTGAATTCTAATCTAATGGTG
Found at i:12445049 original size:49 final size:49
Alignment explanation
Indices: 12444992--12445095 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
12444982 TCATGTGTTA
* * * *
12444992 TAATTTTATACAA-TGTTGAGCTTCTGATTCATGATATTTAACTTAATTT
1 TAATTTTATA-AAGTGTTCACCTTCTAATTCATGATATTAAACTTAATTT
*
12445041 TAATTTTATAAAGTGTTCACCTTTTAATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTCTAATTCATGATATTAAACTTAATTT
12445090 TAATTT
1 TAATTT
12445096 GTTTTTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
48 2 0.04
49 47 0.96
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTCTAATTCATGATATTAAACTTAATTT
Found at i:12446306 original size:9 final size:9
Alignment explanation
Indices: 12446292--12446319 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12446282 TTATGACATA
12446292 GAATTTCAT
1 GAATTTCAT
12446301 GAATTTCAT
1 GAATTTCAT
12446310 GAATTTCAT
1 GAATTTCAT
12446319 G
1 G
12446320 TAACCTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (9 bp):
GAATTTCAT
Found at i:12446627 original size:120 final size:120
Alignment explanation
Indices: 12446492--12447327 Score: 1456
Period size: 120 Copynumber: 7.0 Consensus size: 120
12446482 TAGATTATAC
* *
12446492 ATTAT-TTTTATAGCATTACATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
12446556 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
*
12446611 ATTATATTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
12446676 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
12446731 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
12446796 AAATTTATTAAATTAT-T-TTTTTATTAAATTATATTTAAAAATAATTAAT-TTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATT-ATGTTAA
12446849 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
12446911 AATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATGTTAA
* *
12446968 ATTATATTTTATAGTATTATATATTATGGTTTTAGTAAATTCATTTAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
12447033 AATTTTATTAAATTATATATTTTTATTAAA-TATAATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTAT-ATTTAATAATAATTATGTTAA
*
12447088 ATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
12447153 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
*
12447208 ATTATA-TTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
12447272 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
12447327 A
1 A
12447328 ATATGATTAA
Statistics
Matches: 690, Mismatches: 15, Indels: 24
0.95 0.02 0.03
Matches are distributed among these distances:
115 35 0.05
116 1 0.00
117 15 0.02
118 76 0.11
119 176 0.26
120 331 0.48
121 6 0.01
122 50 0.07
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:12446934 original size:18 final size:17
Alignment explanation
Indices: 12446913--12446950 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
12446903 ATATTAAGAA
*
12446913 TTTTATTAAATTATATAT
1 TTTTACTAAATTATAT-T
12446931 TTTTACTAAATTATATT
1 TTTTACTAAATTATATT
12446948 TTT
1 TTT
12446951 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTACTAAATTATATT
Found at i:12447074 original size:47 final size:44
Alignment explanation
Indices: 12447018--12447194 Score: 125
Period size: 38 Copynumber: 4.2 Consensus size: 44
12447008 TCATTTAAGA
12447018 ATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAAT
1 ATATTTAATATTAAGAATTTTATTAAATTATATA-TTTTA-TAAAT
* *
12447064 ATAATTT-A-A-TAATAATTATT-TTAAA-T-TATATTTTAT-AGT
1 AT-ATTTAATATTAAGAATT-TTATTAAATTATATATTTTATAAAT
* * * *
12447103 AT-TAT-ATATTATG-ATTTTATTAAATT-CATA---TA-AGA-
1 ATATTTAATATTAAGAATTTTATTAAATTATATATTTTATAAAT
12447138 ATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTTAATATTAAGAATTTTATTAAATTATATA-TTTTA-TAAA-T
12447185 ATATTTAATA
1 ATATTTAATA
12447195 ATAATTATTT
Statistics
Matches: 100, Mismatches: 12, Indels: 37
0.67 0.08 0.25
Matches are distributed among these distances:
35 2 0.02
36 4 0.04
37 12 0.12
38 22 0.22
39 13 0.13
40 1 0.01
41 5 0.05
42 4 0.04
43 3 0.03
44 12 0.12
45 5 0.05
46 3 0.03
47 14 0.14
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (44 bp):
ATATTTAATATTAAGAATTTTATTAAATTATATATTTTATAAAT
Found at i:12447531 original size:44 final size:45
Alignment explanation
Indices: 12447478--12447565 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
12447468 ATTACATTCA
*
12447478 TCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCTATTACAT
1 TCAACCAAACA-ATAGAATTACTATTACGCCTCTATTCAATTACAT
* *
12447522 TCAACCAAACAATTGAATTACTATTACGCTTCTATTCAATTACA
1 TCAACCAAACAATAGAATTACTATTACGCCTCTATTCAATTACA
12447566 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 14 0.36
45 24 0.62
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (45 bp):
TCAACCAAACAATAGAATTACTATTACGCCTCTATTCAATTACAT
Found at i:12453369 original size:8 final size:10
Alignment explanation
Indices: 12453342--12453371 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12453332 CTTGCGTCTA
12453342 ATACATATAT
1 ATACATATAT
12453352 ATACATATAT
1 ATACATATAT
*
12453362 ATAAATATAT
1 ATACATATAT
12453372 TAAAACATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATATAT
Found at i:12463367 original size:22 final size:22
Alignment explanation
Indices: 12463342--12463384 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12463332 CTCCGATTAT
12463342 TAGCACATTAGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
* *
12463364 TAGCACTTTAGTGCTTTCTGT
1 TAGCACATTAGTGCTCTCTGT
12463385 TTAATAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:12466422 original size:125 final size:125
Alignment explanation
Indices: 12466193--12466513 Score: 581
Period size: 125 Copynumber: 2.6 Consensus size: 125
12466183 ATAGAGTGCA
* * *
12466193 TCAGTTGTAAAACTTATATGGTAAATTTTGCAATAATTCATTTTGATATAAAGGATTTCATTCAA
1 TCAGTTATAAAACTTATATGGTGAATTTTGCAATAATTCATTTTGATATAAAGAATTTCATTCAA
12466258 ATTCAACACTTATGTAGCAAACAATTCACAATCAAAACCGTTGCTAATAAGTTGATTGAG
66 ATTCAACACTTATGTAGCAAACAATTCACAATCAAAACCGTTGCTAATAAGTTGATTGAG
*
12466318 TTAGTTATAAAACTTATATGGTGAATTTTGCAATAATTCATTTTGATATAAAGAATTTCATTCAA
1 TCAGTTATAAAACTTATATGGTGAATTTTGCAATAATTCATTTTGATATAAAGAATTTCATTCAA
12466383 ATTCAACACTTATGTAGCAAACAATTCACAATCAAAACCGTTGCTAATAAGTTGATTGAG
66 ATTCAACACTTATGTAGCAAACAATTCACAATCAAAACCGTTGCTAATAAGTTGATTGAG
*
12466443 TCAGTTATAAAACTTAGATGGTGAATTTTGCAATAATTCATTTTGATATAAA-ATATTTCATTCA
1 TCAGTTATAAAACTTATATGGTGAATTTTGCAATAATTCATTTTGATATAAAGA-ATTTCATTCA
12466507 AATTCAA
65 AATTCAA
12466514 TACTAGATTA
Statistics
Matches: 189, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
124 1 0.01
125 188 0.99
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (125 bp):
TCAGTTATAAAACTTATATGGTGAATTTTGCAATAATTCATTTTGATATAAAGAATTTCATTCAA
ATTCAACACTTATGTAGCAAACAATTCACAATCAAAACCGTTGCTAATAAGTTGATTGAG
Found at i:12468604 original size:15 final size:14
Alignment explanation
Indices: 12468583--12468623 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12468573 GCTTGGGGAA
*
12468583 GAAAAAATAAAAGG
1 GAAAAAAAAAAAGG
*
12468597 GAAAAAAAGAAAGG
1 GAAAAAAAAAAAGG
*
12468611 GAGAAAAAAAAAG
1 GAAAAAAAAAAAG
12468624 AAAAGGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (14 bp):
GAAAAAAAAAAAGG
Found at i:12471333 original size:25 final size:25
Alignment explanation
Indices: 12471297--12471369 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
12471287 GCTCTCCTTC
12471297 GAGCCATATAACAAGAAGCTCATGT
1 GAGCCATATAACAAGAAGCTCATGT
* *
12471322 GAGCCATGTAACAAGAAGCTCATTT
1 GAGCCATATAACAAGAAGCTCATGT
** **
12471347 GAGCTGTATAACGGGAAGCTCAT
1 GAGCCATATAACAAGAAGCTCAT
12471370 AAAAGCCGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCCATATAACAAGAAGCTCATGT
Found at i:12475795 original size:28 final size:28
Alignment explanation
Indices: 12475753--12475806 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12475743 ATATTGATTA
*
12475753 TAATTAGATTATTTGGTAAGAATAAAAT
1 TAATTACATTATTTGGTAAGAATAAAAT
* *
12475781 TAATTACATTGTTTGGTAGGAATAAA
1 TAATTACATTATTTGGTAAGAATAAA
12475807 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.39
Consensus pattern (28 bp):
TAATTACATTATTTGGTAAGAATAAAAT
Found at i:12476642 original size:20 final size:20
Alignment explanation
Indices: 12476619--12476664 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12476609 AATAAACACC
12476619 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
* *
12476639 AAAAAATTATTTTAAAATTA
1 AAAAATTTATTTTAAAAATA
12476659 AAAAAT
1 AAAAAT
12476665 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATA
Found at i:12486384 original size:3 final size:3
Alignment explanation
Indices: 12486376--12486445 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
12486366 ATATGAAAGT
* * * *
12486376 ATA ATA ATA ATA ATA ATAA ATT GTA ATA TTA AT- ATGC ATA ATA A-A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* *
12486421 ATA ATA ATC ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12486446 CAAAAATAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12486702 original size:4 final size:4
Alignment explanation
Indices: 12486693--12486798 Score: 65
Period size: 4 Copynumber: 26.8 Consensus size: 4
12486683 AAAGGAATTA
* * * * *
12486693 AAAT AAAT AAGT AAAT GAAT GAAT -AAT ATAT AAAT AAAT AAGT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * **
12486740 AAGT AAGT AAAT GAAT AAAAT CAAAG GAAT -AAT AAAT AAAT ATGT AAAT
1 AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12486789 AAA- AAAT AAA
1 AAAT AAAT AAA
12486799 AGGAAACCGT
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
3 9 0.11
4 64 0.81
5 6 0.08
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:12487785 original size:27 final size:25
Alignment explanation
Indices: 12487755--12487815 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
12487745 AAAAACTACC
12487755 TTCTTTTAACTCTTTACTTTTTTTGTA
1 TTCTTTT--CTCTTTACTTTTTTTGTA
* **
12487782 TTCTATTTTTCTTTGTTTTTTTTGTA
1 TTCT-TTTCTCTTTACTTTTTTTGTA
12487808 TATCTTTT
1 T-TCTTTT
12487816 TGTCTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 19 0.66
27 7 0.24
28 3 0.10
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.72
Consensus pattern (25 bp):
TTCTTTTCTCTTTACTTTTTTTGTA
Found at i:12487801 original size:26 final size:27
Alignment explanation
Indices: 12487772--12487822 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
12487762 AACTCTTTAC
12487772 TTTTTTTGTAT-TCTATTTT-TCTTTGT
1 TTTTTTTGTATATCT-TTTTGTCTTTGT
12487798 TTTTTTTGTATATCTTTTTGTCTTT
1 TTTTTTTGTATATCTTTTTGTCTTT
12487823 TTTACGTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (27 bp):
TTTTTTTGTATATCTTTTTGTCTTTGT
Found at i:12489050 original size:27 final size:27
Alignment explanation
Indices: 12489020--12489071 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12489010 AATGCCATAA
* *
12489020 AGGATTTTAAAATAGAAATTGAAACAC
1 AGGATTTGAAAATAAAAATTGAAACAC
*
12489047 AGGATTTGCAAATAAAAATTGAAAC
1 AGGATTTGAAAATAAAAATTGAAAC
12489072 GCAACAGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (27 bp):
AGGATTTGAAAATAAAAATTGAAACAC
Found at i:12500637 original size:22 final size:23
Alignment explanation
Indices: 12500609--12500656 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
12500599 TCACAAGAAA
*
12500609 CAAAGAAACTC-ATAAT-AATCTT
1 CAAAGAAAC-CAAAAATGAATCTT
12500631 CAAAGAAACCAAAAATGAATCTT
1 CAAAGAAACCAAAAATGAATCTT
12500654 CAA
1 CAA
12500657 TCTTGATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 9 0.39
ACGTcount: A:0.54, C:0.19, G:0.06, T:0.21
Consensus pattern (23 bp):
CAAAGAAACCAAAAATGAATCTT
Found at i:12508683 original size:46 final size:46
Alignment explanation
Indices: 12508630--12508722 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
12508620 ATGAATCAAG
* *
12508630 TTAGTTCAAGTAAGTCAAATGAGCCTATTTAATTAGTTGGCCTCCA
1 TTAGTTCAAGTAAGTCAAATAAGCCTATTTAATTAGTTGACCTCCA
12508676 TTAGTTCAAGTAAGTCAAATAAGCCTATTTAATTAGTTGACCTCCA
1 TTAGTTCAAGTAAGTCAAATAAGCCTATTTAATTAGTTGACCTCCA
12508722 T
1 T
12508723 AAAACGATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (46 bp):
TTAGTTCAAGTAAGTCAAATAAGCCTATTTAATTAGTTGACCTCCA
Found at i:12509982 original size:32 final size:30
Alignment explanation
Indices: 12509930--12509995 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
12509920 CGTTTTGGTA
12509930 ACTAAATTATTAAAACTTTTTAATTTAAGTC
1 ACTAAATTATTAAAACTTTTT-ATTTAAGTC
* * *
12509961 ACTAAATTATTTAAAAGTTTTTGTTTGAGTC
1 ACTAAATTA-TTAAAACTTTTTATTTAAGTC
12509992 ACTA
1 ACTA
12509996 GGTTAGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (30 bp):
ACTAAATTATTAAAACTTTTTATTTAAGTC
Found at i:12511789 original size:22 final size:22
Alignment explanation
Indices: 12511764--12511805 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12511754 GGAATAATAT
*
12511764 TTTATAAAATAGTAACAAAATG
1 TTTATAAAATAGTAAAAAAATG
* *
12511786 TTTATAGAATTGTAAAAAAA
1 TTTATAAAATAGTAAAAAAA
12511806 AAAGATATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (22 bp):
TTTATAAAATAGTAAAAAAATG
Found at i:12514235 original size:7 final size:7
Alignment explanation
Indices: 12514225--12514268 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
12514215 AGGATTTCAA
*
12514225 AAAAAAA
1 AAAAAAC
12514232 AAAAAAC
1 AAAAAAC
12514239 AAAAAAC
1 AAAAAAC
12514246 AAAAAAC
1 AAAAAAC
12514253 AAAAAAC
1 AAAAAAC
12514260 -AAAAAC
1 AAAAAAC
12514266 AAA
1 AAA
12514269 GAGGAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:12514550 original size:30 final size:31
Alignment explanation
Indices: 12514485--12514542 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
12514475 CTATTTTAAT
*
12514485 AAAATCCATATAATGAATCACAATTATAAAA
1 AAAATCCATATAATGAATCACAATTACAAAA
*
12514516 AAAAT-CATATAATG-ATCATAATTACAA
1 AAAATCCATATAATGAATCACAATTACAA
12514543 TACAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 9 0.36
31 5 0.20
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAATCCATATAATGAATCACAATTACAAAA
Found at i:12516748 original size:21 final size:21
Alignment explanation
Indices: 12516722--12516771 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
12516712 ATCGCTATCA
12516722 GAAGCTCAATAGAGCTGAACG
1 GAAGCTCAATAGAGCTGAACG
12516743 GAAGCTCAATAGAGCTGAACG
1 GAAGCTCAATAGAGCTGAACG
*
12516764 GAAACTCA
1 GAAGCTCA
12516772 TATGGGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCTCAATAGAGCTGAACG
Found at i:12517594 original size:40 final size:39
Alignment explanation
Indices: 12517550--12517657 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 39
12517540 TATTGCTTGG
* *
12517550 ATGCATATGTGTGTCCCTGTTTGTACTTCAGTACCCCTGA
1 ATGCATATGCGTG-CCCTGTTTGTACTTCAGTACCCCTAA
* * * *
12517590 ATGCATATACATGCCCTTATTTGTACTTCGGTACCCCTAA
1 ATGCATATGCGTGCCC-TGTTTGTACTTCAGTACCCCTAA
* * *
12517630 ATACACATGCGTGCCCCTGTTTATACTT
1 ATGCATATGCGTG-CCCTGTTTGTACTT
12517658 TGGCAACCCT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.06
40 48 0.89
41 3 0.06
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (39 bp):
ATGCATATGCGTGCCCTGTTTGTACTTCAGTACCCCTAA
Found at i:12519256 original size:5 final size:5
Alignment explanation
Indices: 12519242--12519282 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
12519232 TCCTTAGTTT
12519242 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG ATATG AT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG AT
12519283 GTGAAAAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:12520450 original size:25 final size:25
Alignment explanation
Indices: 12520422--12520497 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 25
12520412 GAAAGTGAAA
12520422 GTGATGGTCACGTGTGTAGTACTAT
1 GTGATGGTCACGTGTGTAGTACTAT
* * * *
12520447 GTGAAGGCTACTACGTGTATCGGA-TA-
1 GTGATGG-T-C-ACGTGTGTAGTACTAT
*
12520473 GTGATGGTCACATGTGTAGTACTAT
1 GTGATGGTCACGTGTGTAGTACTAT
12520498 ATGCAGGCTA
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
23 8 0.22
24 3 0.08
25 7 0.19
26 7 0.19
27 3 0.08
28 9 0.24
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (25 bp):
GTGATGGTCACGTGTGTAGTACTAT
Found at i:12520476 original size:51 final size:51
Alignment explanation
Indices: 12520421--12520520 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
12520411 TGAAAGTGAA
* * *
12520421 AGTGATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGAT
1 AGTGATGGTCACATGTGTAGTACTATATGAAGGCTACTACGTGAATCGGAT
* *
12520472 AGTGATGGTCACATGTGTAGTACTATATGCAGGCTACTATGTGAATCGG
1 AGTGATGGTCACATGTGTAGTACTATATGAAGGCTACTACGTGAATCGG
12520521 TATCATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (51 bp):
AGTGATGGTCACATGTGTAGTACTATATGAAGGCTACTACGTGAATCGGAT
Found at i:12520759 original size:16 final size:16
Alignment explanation
Indices: 12520738--12520769 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12520728 TGATTGAAAG
*
12520738 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
12520754 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
12520770 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:12523621 original size:19 final size:21
Alignment explanation
Indices: 12523597--12523638 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12523587 TTTTTCCTTT
*
12523597 AATTC-AAAGCCAC-AAAGCC
1 AATTCAAAACCCACAAAAGCC
12523616 AATTCAAAACCCACAAAAGCC
1 AATTCAAAACCCACAAAAGCC
12523637 AA
1 AA
12523639 AGCCTAGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.52, C:0.31, G:0.07, T:0.10
Consensus pattern (21 bp):
AATTCAAAACCCACAAAAGCC
Found at i:12533854 original size:7 final size:7
Alignment explanation
Indices: 12533842--12533871 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
12533832 CCGATTTAAT
12533842 GGCTTGA
1 GGCTTGA
12533849 GGCTTGA
1 GGCTTGA
12533856 GGCTTGA
1 GGCTTGA
12533863 GGCTTGA
1 GGCTTGA
12533870 GG
1 GG
12533872 TTATGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (7 bp):
GGCTTGA
Found at i:12536045 original size:114 final size:114
Alignment explanation
Indices: 12535741--12536049 Score: 311
Period size: 114 Copynumber: 2.7 Consensus size: 114
12535731 TGGTCATAAA
* * * *
12535741 CGCCGCAAAAACTGTTAAGAAAAACGCTGTCGTTTTCAGTTTAGGTTTTGGGGACTTTAGTGGCG
1 CGCCGC-AAAACTGTTAAG-AAAACGATGTCGTTTTCAATTTAGGTTTTAGAGACTTTAGTGGCG
*
12535806 CTTAAT-GAAAAACGCCGCTATAGTCAAGAATTAGCGACGCTTTATCATAAG
64 CTT-ATCGAAAAACGCCGCTATAGTCAAGAATTAGCGACGCTTTATCAGAAG
* * * * ** * * *
12535857 CGCCGCAAGACTGTTAAGAAAAAGTTGCCGTTTTTC-ATTTATCTTTTCGAGACATTAGTGGCGA
1 CGCCGCAAAACTGTTAAGAAAACGATGTCG-TTTTCAATTTAGGTTTTAGAGACTTTAGTGGCGC
* * ** * *
12535921 TTTTCGAAAAATGCCG-TAGTAG-CGAAGCTTTAGTGGCGCTTTATCAGAAG
65 TTATCGAAAAACGCCGCTA-TAGTC-AAGAATTAGCGACGCTTTATCAGAAG
* * *
12535971 TGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTCAATTTAGGTTTTAAAGACTTTAGTAGCGCT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTCAATTTAGGTTTTAGAGACTTTAGTGGCGCT
* *
12536036 TGTCTAAAAACGCC
66 TATCGAAAAACGCC
12536050 ACCAAATATA
Statistics
Matches: 155, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
113 9 0.06
114 124 0.80
115 16 0.10
116 6 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (114 bp):
CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTCAATTTAGGTTTTAGAGACTTTAGTGGCGCT
TATCGAAAAACGCCGCTATAGTCAAGAATTAGCGACGCTTTATCAGAAG
Found at i:12536738 original size:14 final size:14
Alignment explanation
Indices: 12536721--12536788 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
12536711 TTAAGGATTG
* *
12536721 GGGTTAAGGGTTTA
1 GGGTTTAGGGTTAA
*
12536735 GGGTTTAGGGGTCAA
1 GGGTTTA-GGGTTAA
*
12536750 GGGTTAAGGGTTAA
1 GGGTTTAGGGTTAA
* *
12536764 GGG-CTAGGGTTAG
1 GGGTTTAGGGTTAA
*
12536777 GGGTTTATGGTT
1 GGGTTTAGGGTT
12536789 TTATAGTTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
13 10 0.24
14 21 0.50
15 11 0.26
ACGTcount: A:0.19, C:0.03, G:0.46, T:0.32
Consensus pattern (14 bp):
GGGTTTAGGGTTAA
Found at i:12536751 original size:22 final size:22
Alignment explanation
Indices: 12536720--12536766 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
12536710 TTTAAGGATT
* * *
12536720 GGGGTTAAGGGTTTAGGGTTTA
1 GGGGTCAAGGGTTAAGGGTTAA
12536742 GGGGTCAAGGGTTAAGGGTTAA
1 GGGGTCAAGGGTTAAGGGTTAA
12536764 GGG
1 GGG
12536767 CTAGGGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.49, T:0.28
Consensus pattern (22 bp):
GGGGTCAAGGGTTAAGGGTTAA
Found at i:12536985 original size:29 final size:30
Alignment explanation
Indices: 12536931--12537016 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 30
12536921 TAAGGGATAT
* *
12536931 GGGTTAGAGGCTT-ATGGATTAT-GGTTTAA
1 GGGTTAG-GGCTTAAAGGTTTATGGGTTTAA
*
12536960 GGGTT-GGGGTTAAAGGTTTATGGGTTT-A
1 GGGTTAGGGCTTAAAGGTTTATGGGTTTAA
** *
12536988 GGGTTAGGGCTTATGGGTTTAGGGGTTTA
1 GGGTTAGGGCTTAAAGGTTTATGGGTTTA
12537017 TAGTTAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
27 4 0.09
28 14 0.30
29 28 0.61
ACGTcount: A:0.19, C:0.02, G:0.41, T:0.38
Consensus pattern (30 bp):
GGGTTAGGGCTTAAAGGTTTATGGGTTTAA
Found at i:12540503 original size:17 final size:17
Alignment explanation
Indices: 12540483--12540532 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
12540473 TTAATATCTA
12540483 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
12540500 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
12540514 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
12540530 TAT
1 TAT
12540533 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:12540519 original size:13 final size:13
Alignment explanation
Indices: 12540501--12540528 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12540491 TTCTAAATTT
12540501 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
12540514 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
12540527 AT
1 AT
12540529 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:12540559 original size:15 final size:15
Alignment explanation
Indices: 12540524--12540562 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
12540514 ATAAGTTTTC
*
12540524 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
12540539 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
12540555 TAAATTTA
1 TAAATTTA
12540563 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:12540605 original size:62 final size:61
Alignment explanation
Indices: 12540494--12540642 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 61
12540484 ATAAGTTTTC
* *** * *
12540494 TAAATTTATAAGTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGT-GTAT
** *
12540555 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATTTATGTGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
* *
12540617 TAATTTTATAAGTTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
12540643 TACATAATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 23 0.32
62 49 0.67
63 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.48
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
Found at i:12540806 original size:74 final size:72
Alignment explanation
Indices: 12540719--12540898 Score: 233
Period size: 74 Copynumber: 2.5 Consensus size: 72
12540709 TAACTTACAT
* * *
12540719 AATAATTTACATAACTTATATATAATAACATAATAAATTACATAATACTTTATGTTAT-A-ATAC
1 AATAACTTACATAACTTATATATAATAACATAATAAATTACATAATACTTTATATAATAACATA-
12540782 ATAACTTGTA
65 ATAAC-T-TA
* * *
12540792 TATAAGCTTGCATAACTTACATATAATAACATAATAAATTACATAATACTTTATATAATAACATA
1 AATAA-CTTACATAACTTATATATAATAACATAATAAATTACATAATACTTTATATAATAACATA
12540857 ATAACTTA
65 ATAACTTA
*
12540865 AATAACTTAAATAAC-T-TATATAATAACATAATAA
1 AATAACTTACATAACTTATATATAATAACATAATAA
12540899 CATAATAACT
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
70 17 0.18
71 1 0.01
72 8 0.09
73 10 0.11
74 49 0.52
75 6 0.06
76 3 0.03
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (72 bp):
AATAACTTACATAACTTATATATAATAACATAATAAATTACATAATACTTTATATAATAACATAA
TAACTTA
Found at i:12540839 original size:20 final size:19
Alignment explanation
Indices: 12540814--12540914 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 19
12540804 TAACTTACAT
*
12540814 ATAATAACATAATAAATTAC
1 ATAATAAC-TAATAAATAAC
*
12540834 ATAAT-ACTTTATATAATAAC
1 ATAATAAC-TAATA-AATAAC
12540854 ATAATAACT--TAAATAAC
1 ATAATAACTAATAAATAAC
* *
12540871 TTAAATAACTTATATAATAAC
1 AT-AATAACTAATA-AATAAC
*
12540892 ATAATAACATAATAACTAAC
1 ATAATAAC-TAATAAATAAC
12540912 ATA
1 ATA
12540915 CAATATATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.10
18 9 0.13
19 6 0.09
20 32 0.48
21 13 0.19
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAACTAATAAATAAC
Found at i:12540859 original size:8 final size:8
Alignment explanation
Indices: 12540846--12540907 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 8
12540836 AATACTTTAT
12540846 ATAATAAC
1 ATAATAAC
12540854 ATAATAAC
1 ATAATAAC
*
12540862 TTAAATAAC
1 AT-AATAAC
*
12540871 TTAAATAAC
1 AT-AATAAC
12540880 TTATATAATAAC
1 ----ATAATAAC
12540892 ATAATAAC
1 ATAATAAC
12540900 ATAATAAC
1 ATAATAAC
12540908 TAACATACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 25 0.53
9 15 0.32
12 6 0.13
13 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATAAC
Found at i:12540964 original size:9 final size:9
Alignment explanation
Indices: 12540936--12541160 Score: 243
Period size: 9 Copynumber: 24.8 Consensus size: 9
12540926 CATATATAGA
12540936 AACTTACAT
1 AACTTACAT
* *
12540945 AAATTAAAT
1 AACTTACAT
12540954 AACTTACAT
1 AACTTACAT
12540963 AACTTACAT
1 AACTTACAT
* *
12540972 AAATTAAAT
1 AACTTACAT
12540981 AACTTACAT
1 AACTTACAT
12540990 AACTTACAT
1 AACTTACAT
*
12540999 AAACTTGCAT
1 -AACTTACAT
* *
12541009 AAATTAAAT
1 AACTTACAT
12541018 AACTTACAT
1 AACTTACAT
12541027 AACTTACAT
1 AACTTACAT
*
12541036 AACCTACAT
1 AACTTACAT
* *
12541045 AAATTAAAT
1 AACTTACAT
12541054 AACTTACAT
1 AACTTACAT
12541063 AACTTACAT
1 AACTTACAT
* *
12541072 AAATTAAAT
1 AACTTACAT
12541081 AACTTACAT
1 AACTTACAT
12541090 AACTTACAT
1 AACTTACAT
* * *
12541099 AAATTCCGT
1 AACTTACAT
* *
12541108 GGACCTACAT
1 -AACTTACAT
* *
12541118 AAATTAAAT
1 AACTTACAT
12541127 AACTTACAT
1 AACTTACAT
12541136 AACTTACAT
1 AACTTACAT
* *
12541145 AAATTAAAT
1 AACTTACAT
12541154 AACTTAC
1 AACTTAC
12541161 CCGTGAAAAT
Statistics
Matches: 172, Mismatches: 42, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
9 160 0.93
10 12 0.07
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:12541156 original size:73 final size:72
Alignment explanation
Indices: 12540936--12541160 Score: 324
Period size: 73 Copynumber: 3.1 Consensus size: 72
12540926 CATATATAGA
* * * *
12540936 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
**
12541001 ACTTGCAT
66 A-TTAAAT
* * *
12541009 AAATTAAATAACTTACATAACTTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
12541074 ATTAAAT
66 ATTAAAT
* * *
12541081 AACTTACATAACTTACATAAATTCCGTGGACCTACATAAATTAAATAACTTACATAACTTACATA
1 AACTTACATAACTTACATAAATTACAT-AACCTACATAAATTAAATAACTTACATAACTTACATA
12541146 AATTAAAT
65 AATTAAAT
12541154 AACTTAC
1 AACTTAC
12541161 CCGTGAAAAT
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
72 26 0.19
73 112 0.81
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (72 bp):
AACTTACATAACTTACATAAATTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
ATTAAAT
Found at i:12546622 original size:21 final size:21
Alignment explanation
Indices: 12546596--12546646 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
12546586 CTACAACTTA
* *
12546596 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
12546617 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
12546638 AAGCAGAGG
1 AAGCAGAGG
12546647 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.47, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:12547147 original size:20 final size:20
Alignment explanation
Indices: 12547122--12547159 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12547112 CGCTCATATA
12547122 AAAAACACCGCTAAAGAATG
1 AAAAACACCGCTAAAGAATG
*
12547142 AAAAACGCCGCTAAAGAA
1 AAAAACACCGCTAAAGAA
12547160 CATGTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.21, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAAACACCGCTAAAGAATG
Found at i:12557262 original size:26 final size:26
Alignment explanation
Indices: 12557233--12557308 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
12557223 TACATATCTT
12557233 TTTTAGACCATTTAATAATGGTCAAA
1 TTTTAGACCATTTAATAATGGTCAAA
**
12557259 TTTTAG----TTT--TAAT--TCTTA
1 TTTTAGACCATTTAATAATGGTCAAA
*
12557277 TATTAGACCATTTAATAATGGTCAAA
1 TTTTAGACCATTTAATAATGGTCAAA
12557303 TTTTAG
1 TTTTAG
12557309 TTTTAATTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
18 8 0.22
20 4 0.11
22 6 0.17
24 4 0.11
26 14 0.39
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (26 bp):
TTTTAGACCATTTAATAATGGTCAAA
Found at i:12557298 original size:44 final size:44
Alignment explanation
Indices: 12557235--12557325 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
12557225 CATATCTTTT
12557235 TTAGACCATTTAATAATGGTCAAATTTTAGTTTTAATTCTTATA
1 TTAGACCATTTAATAATGGTCAAATTTTAGTTTTAATTCTTATA
12557279 TTAGACCATTTAATAATGGTCAAATTTTAGTTTTAATTCTTATA
1 TTAGACCATTTAATAATGGTCAAATTTTAGTTTTAATTCTTATA
12557323 TTA
1 TTA
12557326 TGTTGAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (44 bp):
TTAGACCATTTAATAATGGTCAAATTTTAGTTTTAATTCTTATA
Done.