Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007844.1 Hibiscus syriacus cultivar Beakdansim tig00110198_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2094103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:672874 original size:60 final size:60
Alignment explanation
Indices: 672742--672874 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
672732 TTTTTTTGGT
* * *
672742 AAAG-TACAGAAATGATTCTTCTACTATATGTTATTGTTTTGTTGAGTCCTCTAACTATTA
1 AAAGTTACA-AAATAATTCTTCTACTATATGTGATTGTTTTGTTGAATCCTCTAACTATTA
* * * * *
672802 AAAGTAATAAAATAATTCTT-TGACTATAT-TGAGTTGTTTTGTTGAATCTTTTGACTATTA
1 AAAGTTACAAAATAATTCTTCT-ACTATATGTGA-TTGTTTTGTTGAATCCTCTAACTATTA
672862 AAAGTTACAAAAT
1 AAAGTTACAAAAT
672875 GGTAATCTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.05
60 55 0.92
61 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (60 bp):
AAAGTTACAAAATAATTCTTCTACTATATGTGATTGTTTTGTTGAATCCTCTAACTATTA
Found at i:676272 original size:84 final size:84
Alignment explanation
Indices: 676123--676276 Score: 222
Period size: 84 Copynumber: 1.8 Consensus size: 84
676113 TTTTGCATAC
* * *
676123 ATATATTCATTGAATTTTGGTTGTTATTTGTATGCAATTTAGCTTGATGGTTTGTGTTGTATCTG
1 ATATATTCAATGAATTTGGGTTGTTATTTGTATGCAATTTAGCTTGATGGATTGTGTTGTATCTG
676188 TTTTTGCATATATTTATAT
66 TTTTTGCATATATTTATAT
** *
676207 ATATATTCAATGAATTCTGGGTTGTTATTTGTATGTGATATTAGCTTGATGGATT-T-TTGTGTC
1 ATATATTCAATGAATT-TGGGTTGTTATTTGTATGCAAT-TTAGCTTGATGGATTGTGTTGTATC
676270 TGTTTTT
64 TGTTTTT
676277 TGAATCTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
84 28 0.45
85 20 0.32
86 14 0.23
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.54
Consensus pattern (84 bp):
ATATATTCAATGAATTTGGGTTGTTATTTGTATGCAATTTAGCTTGATGGATTGTGTTGTATCTG
TTTTTGCATATATTTATAT
Found at i:679851 original size:15 final size:15
Alignment explanation
Indices: 679818--679850 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
679808 TCAAATTTTT
679818 AAAATGATTAAAATA
1 AAAATGATTAAAATA
*
679833 AAAATG-TTAAATTA
1 AAAATGATTAAAATA
679847 AAAA
1 AAAA
679851 AATAATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (15 bp):
AAAATGATTAAAATA
Found at i:679865 original size:18 final size:19
Alignment explanation
Indices: 679824--679872 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
679814 TTTTAAAATG
679824 ATTAAAATAAAAATGTTAA
1 ATTAAAATAAAAATGTTAA
*
679843 ATTAAAA-AAATAATG-TGA
1 ATTAAAATAAA-AATGTTAA
679861 ATTAAAATAAAA
1 ATTAAAATAAAA
679873 TTTGAAGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
ATTAAAATAAAAATGTTAA
Found at i:684802 original size:2 final size:2
Alignment explanation
Indices: 684795--684820 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
684785 TTCATATCTT
684795 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
684821 GAATTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:687425 original size:13 final size:13
Alignment explanation
Indices: 687407--687456 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
687397 TCATCCATAC
687407 TATAATTTTTTTA
1 TATAATTTTTTTA
*
687420 TATAATTTTTCTA
1 TATAATTTTTTTA
687433 TATAATTTTTCATTCA
1 TATAATTTTT--TT-A
687449 TATAATTT
1 TATAATTT
687457 CATTTTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 22 0.69
15 1 0.03
16 9 0.28
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (13 bp):
TATAATTTTTTTA
Found at i:688199 original size:29 final size:29
Alignment explanation
Indices: 688163--688275 Score: 183
Period size: 29 Copynumber: 3.9 Consensus size: 29
688153 CAACATAGGT
*
688163 CGCCATGCACGCCCGACGTCCT-TATAGGT
1 CGCCATGCACGCCCGACGTCCTATA-AGGA
*
688192 CGCCATGCACGCCCGGCGTCCTATAAGGA
1 CGCCATGCACGCCCGACGTCCTATAAGGA
688221 CGCCATGCACGCCCGACGTCCTATAAGGA
1 CGCCATGCACGCCCGACGTCCTATAAGGA
*
688250 CGCCATGCACGCCCGGCGTCCTATAA
1 CGCCATGCACGCCCGACGTCCTATAA
688276 TTATTTGCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 77 0.97
30 2 0.03
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.16
Consensus pattern (29 bp):
CGCCATGCACGCCCGACGTCCTATAAGGA
Found at i:688327 original size:40 final size:40
Alignment explanation
Indices: 688272--688351 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
688262 CCGGCGTCCT
688272 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
688312 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
688352 CTTTGGGGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.10, C:0.17, G:0.38, T:0.35
Consensus pattern (40 bp):
ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
Found at i:688346 original size:13 final size:13
Alignment explanation
Indices: 688328--688384 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 13
688318 ATTTGCTTGG
688328 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
688341 GGTGGCCGCTGCTTT
1 GGTGGCCGCTG--TT
688356 GGGGTGGCCGCTGTT
1 --GGTGGCCGCTGTT
*
688371 GGTGGCCGATGTT
1 GGTGGCCGCTGTT
688384 G
1 G
688385 CTCGTCCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 24 0.62
15 4 0.10
17 11 0.28
ACGTcount: A:0.02, C:0.21, G:0.47, T:0.30
Consensus pattern (13 bp):
GGTGGCCGCTGTT
Found at i:688667 original size:12 final size:12
Alignment explanation
Indices: 688650--688674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
688640 CCGACGACAT
688650 GGTAGGTGGTAG
1 GGTAGGTGGTAG
688662 GGTAGGTGGTAG
1 GGTAGGTGGTAG
688674 G
1 G
688675 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:688750 original size:35 final size:35
Alignment explanation
Indices: 688711--688778 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
688701 TCCTGCATCG
*
688711 CGACCCAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
688746 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
688779 GTTGCATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:689240 original size:21 final size:21
Alignment explanation
Indices: 689215--689258 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
689205 AATCTAGTTA
*
689215 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
689236 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
689257 AT
1 AT
689259 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:689290 original size:8 final size:8
Alignment explanation
Indices: 689277--689308 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
689267 TTATATAAAA
689277 AATTAGTT
1 AATTAGTT
689285 AATTAGTT
1 AATTAGTT
689293 AATTAGTT
1 AATTAGTT
689301 AATTAGTT
1 AATTAGTT
689309 TAAGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
AATTAGTT
Found at i:689788 original size:18 final size:20
Alignment explanation
Indices: 689764--689812 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
689754 GAGATAATTT
*
689764 TTGTTTAAAAAT-TATATTG
1 TTGTTTAAAAATATATAGTG
*
689783 -TGTTTAAAAATATTTAGTG
1 TTGTTTAAAAATATATAGTG
689802 TTGTTTAAAAA
1 TTGTTTAAAAA
689813 AAATATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (20 bp):
TTGTTTAAAAATATATAGTG
Found at i:689825 original size:18 final size:18
Alignment explanation
Indices: 689762--689825 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
689752 GCGAGATAAT
*
689762 TTTTGTTTAAAAATTATA
1 TTTTGTTTAAAAAATATA
* *
689780 TTGTGTTTAAAAATATTTA
1 TTTTGTTTAAAAA-ATATA
* *
689799 GTGTTGTTTAAAAAAAATA
1 -TTTTGTTTAAAAAATATA
689818 TTTTGTTT
1 TTTTGTTT
689826 TATTTATATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 19 0.53
19 6 0.17
20 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTTGTTTAAAAAATATA
Found at i:689831 original size:23 final size:23
Alignment explanation
Indices: 689788--689831 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
689778 TATTGTGTTT
*
689788 AAAAATATTTAGTGTTGTTTAAA
1 AAAAATATTTAGTGTTATTTAAA
* *
689811 AAAAATATTTTGTTTTATTTA
1 AAAAATATTTAGTGTTATTTA
689832 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTATTTAAA
Found at i:690065 original size:26 final size:25
Alignment explanation
Indices: 690036--690100 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
690026 AAATCATATT
*
690036 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
690062 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
690088 ATTATT-AATAATA
1 ATTATTAAATAATA
690101 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:691590 original size:26 final size:26
Alignment explanation
Indices: 691564--691915 Score: 265
Period size: 26 Copynumber: 14.2 Consensus size: 26
691554 GATGATTTAG
*
691564 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
691590 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
691616 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
691642 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
691665 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
691688 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
691714 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
691740 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
691766 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
691789 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
691812 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
691838 TAATGATTTTATAATAATTATTAT-G
1 TAATGATTTGATAATAATCATTATAA
* * *
691863 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
691887 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
691912 TAAT
1 TAAT
691916 TATTACTAAT
Statistics
Matches: 261, Mismatches: 44, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
21 8 0.03
22 6 0.02
23 28 0.11
24 27 0.10
25 35 0.13
26 155 0.59
27 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:691726 original size:124 final size:124
Alignment explanation
Indices: 691506--691899 Score: 695
Period size: 124 Copynumber: 3.2 Consensus size: 124
691496 ATGTATTTAT
691506 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
691571 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
691630 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
691695 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
691754 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
691819 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTAT-GTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
691877 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
691900 CTAATGATTT
Statistics
Matches: 262, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.07
123 15 0.06
124 229 0.87
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:691906 original size:14 final size:14
Alignment explanation
Indices: 691874--691915 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
691864 TATTATTTAG
*
691874 TAATTATTT-ATAA
1 TAATGATTTAATAA
*
691887 TAATGATTTAATAC
1 TAATGATTTAATAA
691901 TAATGATTTAATAA
1 TAATGATTTAATAA
691915 T
1 T
691916 TATTACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:691938 original size:38 final size:38
Alignment explanation
Indices: 691868--691941 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
691858 TTATGTTATT
* **
691868 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
691906 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
691942 CAAAGTAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:692036 original size:14 final size:14
Alignment explanation
Indices: 692017--692099 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 14
692007 TTTAAATATT
692017 TAATGATTTGATAC
1 TAATGATTTGATAC
692031 TAATGA-TT--TAC
1 TAATGATTTGATAC
*
692042 TAAT--TAT--TAC
1 TAATGATTTGATAC
*
692052 TAATGATTTAATAC
1 TAATGATTTGATAC
*
692066 TAATTATTTGATAC
1 TAATGATTTGATAC
692080 TAGTAATGATTTGATAC
1 ---TAATGATTTGATAC
692097 TAA
1 TAA
692100 ACATCATTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.14
11 7 0.12
12 2 0.04
13 2 0.04
14 24 0.43
17 13 0.23
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAC
Found at i:692053 original size:10 final size:11
Alignment explanation
Indices: 692028--692061 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
692018 AATGATTTGA
692028 TACTAATGATT
1 TACTAATGATT
*
692039 TACTAATTA-T
1 TACTAATGATT
692049 TACTAATGATT
1 TACTAATGATT
692060 TA
1 TA
692062 ATACTAATTA
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:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:692071 original size:21 final size:21
Alignment explanation
Indices: 692028--692071 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
692018 AATGATTTGA
* *
692028 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
692049 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
692070 TA
1 TA
692072 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:692091 original size:17 final size:17
Alignment explanation
Indices: 692066--692098 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
692056 GATTTAATAC
*
692066 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
692083 TAATGATTTGATACTA
1 TAATGATTTGATACTA
692099 AACATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:694266 original size:15 final size:14
Alignment explanation
Indices: 694243--694273 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
694233 TACAACACTA
694243 AACTTTAATATAAT
1 AACTTTAATATAAT
694257 AACTTATAATATAAT
1 AACTT-TAATATAAT
694272 AA
1 AA
694274 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:694281 original size:16 final size:16
Alignment explanation
Indices: 694248--694294 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
694238 CACTAAACTT
*
694248 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
694263 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
694279 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
694295 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:694411 original size:31 final size:33
Alignment explanation
Indices: 694335--694414 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
694325 CCAAACCCTT
* *
694335 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTCATATAACTA
694367 AAACTAACTAATAAACTATTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTCA-TATAACTA
*
694399 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
694415 TACTAACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.26
32 8 0.19
33 19 0.44
34 5 0.12
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTCATATAACTA
Found at i:694544 original size:46 final size:49
Alignment explanation
Indices: 694453--694544 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 49
694443 CAACAAACAA
694453 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
*
694502 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
694545 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 12 0.29
46 11 0.27
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
Found at i:694555 original size:47 final size:48
Alignment explanation
Indices: 694453--694557 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 48
694443 CAACAAACAA
*
694453 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTCT
*
694502 ATATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT--CT
694549 ATATAACTA
1 ATATAACTA
694558 TCAAACATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
45 12 0.24
46 11 0.22
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTCT
Found at i:694613 original size:41 final size:40
Alignment explanation
Indices: 694525--694613 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
694515 TTAACAAAAC
* *
694525 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
694566 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
694607 AAACTAA
1 AAACTAA
694614 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:694678 original size:16 final size:18
Alignment explanation
Indices: 694649--694687 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
694639 ACTAATTAAC
*
694649 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
694667 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
694683 ATTTA
1 ATTTA
694688 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:694981 original size:50 final size:50
Alignment explanation
Indices: 694902--695010 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 50
694892 TAGGATCACA
*
694902 TGGCATGC-TGTAGGCATGCAGCGGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGGAGCAGGAGCACGTGAAGTTAT-T
694952 TGGCATGCATGCAGGCATGCAGC-GGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGGGAGCAGGAGCACGTGAAGTTATT
695001 TGGC-TGCATG
1 TGGCATGCATG
695011 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
48 6 0.11
49 5 0.09
50 33 0.58
51 13 0.23
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.20
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGGAGCAGGAGCACGTGAAGTTATT
Found at i:695077 original size:29 final size:29
Alignment explanation
Indices: 695045--695101 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
695035 GGGACGCCGG
695045 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
695074 GGCGACCTACAAGGTCGCCGGGACTACA
1 GGCGACCTACAAGGTCGCCGGGACTACA
695102 AGGTCGCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.32, T:0.12
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:695102 original size:17 final size:17
Alignment explanation
Indices: 695051--695109 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
695041 CCGGGGCGAC
695051 CTACAAGGTCGCCGGGA
1 CTACAAGGTCGCCGGGA
* *
695068 CTACATGG-CGAC----
1 CTACAAGGTCGCCGGGA
695080 CTACAAGGTCGCCGGGA
1 CTACAAGGTCGCCGGGA
695097 CTACAAGGTCGCC
1 CTACAAGGTCGCC
695110 CAGACTGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
16 3 0.09
17 20 0.61
ACGTcount: A:0.24, C:0.32, G:0.31, T:0.14
Consensus pattern (17 bp):
CTACAAGGTCGCCGGGA
Found at i:695115 original size:17 final size:17
Alignment explanation
Indices: 695080--695115 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
695070 ACATGGCGAC
**
695080 CTACAAGGTCGCCGGGA
1 CTACAAGGTCGCCCAGA
695097 CTACAAGGTCGCCCAGA
1 CTACAAGGTCGCCCAGA
695114 CT
1 CT
695116 GCATGGCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.14
Consensus pattern (17 bp):
CTACAAGGTCGCCCAGA
Found at i:695156 original size:32 final size:32
Alignment explanation
Indices: 695114--695185 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
695104 GTCGCCCAGA
*
695114 CTGCATGGCGACCTCTCTATTGGCTGGCTCCT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
* * *
695146 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
695178 CTGCATGG
1 CTGCATGG
695186 TGAGTATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.08, C:0.32, G:0.29, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
Found at i:695225 original size:39 final size:33
Alignment explanation
Indices: 695170--695282 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
695160 CTCCGTTGGC
695170 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
695203 TGGCTCGTCTGCATGGTGATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGC------ATGGTGAGTATATGGCTTGTA
695242 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
695275 TGGCTCGT
1 TGGCTCGT
695283 ATGTCACTCG
Statistics
Matches: 74, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
33 41 0.55
39 33 0.45
ACGTcount: A:0.14, C:0.15, G:0.35, T:0.36
Consensus pattern (33 bp):
TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
Found at i:706644 original size:19 final size:19
Alignment explanation
Indices: 706605--706651 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
706595 TTTGTCGCAA
**
706605 GGAACACTTGACGACTTAT
1 GGAACACTTGACGACCAAT
*
706624 GGAACACTTGGCGACCAAT
1 GGAACACTTGACGACCAAT
706643 GGAATCACT
1 GGAA-CACT
706652 GTAACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (19 bp):
GGAACACTTGACGACCAAT
Found at i:708691 original size:196 final size:197
Alignment explanation
Indices: 708357--708749 Score: 779
Period size: 196 Copynumber: 2.0 Consensus size: 197
708347 CAATGAGCTT
708357 TGCTACTTATTATAGCAAGCTAGGTTTAGAGGTTTTGGTTTCTTTCAAGTAGTTATGGAGAAGAG
1 TGCTACTTATTATAGCAAGCTAGGTTTAGAGGTTTTGGTTTCTTTCAAGTAGTTATGGAGAAGAG
708422 CAAGTCCTTCCCTCAATATTCTTCGTCTTTCTCTGGCGAGTTTGACTTCGAGAACCGACAGAATT
66 CAAGTCCTTCCCTCAATATTCTTCGTCTTTCTCTGGCGAGTTTGACTTCGAGAACCGACAGAATT
708487 CGTACAATTTCAACGGGCCATGCAGCAAGAGTAACGGG-TTGCGGCGTCGAACAATCCGGAGCTC
131 CGTACAATTTCAACGGGCCATGCAGCAAGAGTAACGGGTTTGCGGCGTCGAACAATCCGGAGCTC
708551 AA
196 AA
708553 TGCTACTTATTATAGCAAGCTAGGTTTAGAGGTTTTGGTTTCTTTCAAGTAGTTATGGAGAAGAG
1 TGCTACTTATTATAGCAAGCTAGGTTTAGAGGTTTTGGTTTCTTTCAAGTAGTTATGGAGAAGAG
708618 CAAGTCCTTCCCTCAATATTCTTCGTCTTTCTCTGGCGAGTTTGACTTCGAGAACCGACAGAATT
66 CAAGTCCTTCCCTCAATATTCTTCGTCTTTCTCTGGCGAGTTTGACTTCGAGAACCGACAGAATT
708683 CGTACAATTTCAACGGGCCATGCAGCAAGAGTAACGGGTTTGCGGCGTCGAACAATCCGGAGCTC
131 CGTACAATTTCAACGGGCCATGCAGCAAGAGTAACGGGTTTGCGGCGTCGAACAATCCGGAGCTC
708748 AA
196 AA
708750 GAGGAAGAAG
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 168 0.86
197 28 0.14
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (197 bp):
TGCTACTTATTATAGCAAGCTAGGTTTAGAGGTTTTGGTTTCTTTCAAGTAGTTATGGAGAAGAG
CAAGTCCTTCCCTCAATATTCTTCGTCTTTCTCTGGCGAGTTTGACTTCGAGAACCGACAGAATT
CGTACAATTTCAACGGGCCATGCAGCAAGAGTAACGGGTTTGCGGCGTCGAACAATCCGGAGCTC
AA
Found at i:710990 original size:31 final size:31
Alignment explanation
Indices: 710955--711017 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
710945 TCACCTCCTG
710955 ATTGAAG-GATTAATTTATTAAATTAAATTAA
1 ATTGAAGAG-TTAATTTATTAAATTAAATTAA
710986 ATTGAAGAGTTAATTTATTAAATTAAATTAA
1 ATTGAAGAGTTAATTTATTAAATTAAATTAA
711017 A
1 A
711018 ATTGTAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (31 bp):
ATTGAAGAGTTAATTTATTAAATTAAATTAA
Found at i:729383 original size:3 final size:3
Alignment explanation
Indices: 729375--729415 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
729365 AAAGACTACG
729375 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
729416 TTCAATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:730204 original size:24 final size:25
Alignment explanation
Indices: 730154--730209 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
730144 AAAAAATATT
*
730154 TTATTT-TTATTTATTAAATTAATA
1 TTATTTATTATTTATTAAATTAAAA
*
730178 TTATTTATTTTTTATTAAA-TAAAA
1 TTATTTATTATTTATTAAATTAAAA
730202 TTAATTTA
1 TT-ATTTA
730210 ATAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTTATTATTTATTAAATTAAAA
Found at i:731249 original size:28 final size:28
Alignment explanation
Indices: 731216--731272 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
731206 TCGTCGTTGC
731216 TTTCAAGCATTGGCTCTG-TGACATAATA
1 TTTCAAGCATTGGCTC-GATGACATAATA
731244 TTTCAAGCATTGGCTCGATGACATAATA
1 TTTCAAGCATTGGCTCGATGACATAATA
731272 T
1 T
731273 AAACAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (28 bp):
TTTCAAGCATTGGCTCGATGACATAATA
Found at i:740379 original size:20 final size:20
Alignment explanation
Indices: 740311--740534 Score: 215
Period size: 21 Copynumber: 11.0 Consensus size: 20
740301 CAATACATAT
* *
740311 TCGCATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
* *
740331 TTCGCATTGCGATTTTCCTAA
1 -TCGCATTGCGATTTACGTAA
*
740352 TTCGCATTGCGATTTATGTAA
1 -TCGCATTGCGATTTACGTAA
* * * *
740373 ACGCATTACAATTTTTC-TAA
1 TCGCATTGCGA-TTTACGTAA
*
740393 TTCGCATTGCGATTTTTC-TAA
1 -TCGCATTGCGA-TTTACGTAA
740414 TTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
* *
740435 CCGCATTGTGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
*
740455 CCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
740475 TCGCATTGCGATTTTAC-TAA
1 TCGCATTGCGA-TTTACGTAA
740495 TTCGCACTT-CGATTTACGTAA
1 -TCGCA-TTGCGATTTACGTAA
740516 TCGCATTGCGATTTA-GTAA
1 TCGCATTGCGATTTACGTAA
740535 ATCGTAACGA
Statistics
Matches: 179, Mismatches: 16, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.03
20 82 0.46
21 89 0.50
22 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:740414 original size:62 final size:62
Alignment explanation
Indices: 740312--740488 Score: 214
Period size: 62 Copynumber: 2.9 Consensus size: 62
740302 AATACATATT
* * *
740312 CGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTATGTAAA
1 CGCATTACAATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAAA
* * *
740374 CGCATTACAATTTTTCTAATTCGCATTGCGATTTTTCTAATTCGCATTGCGATTTACGTAAC
1 CGCATTACAATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAAA
*** * * * * *
740436 CGCATTGTGATTTACGTAA-CCGCATTGCGATTTACGTAA-TCGCATTGCGATTT
1 CGCATTACAATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTT
740489 TACTAATTCG
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
60 14 0.14
61 16 0.16
62 69 0.70
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (62 bp):
CGCATTACAATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAAA
Found at i:740467 original size:40 final size:41
Alignment explanation
Indices: 740311--740534 Score: 210
Period size: 41 Copynumber: 5.5 Consensus size: 41
740301 CAATACATAT
* * * * *
740311 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAATCCGCATTGCGATTTACGTAA
* * * * *
740352 TTCGCATTGCGATTTATGTAA-ACGCATTACAATTTTTC-TAA
1 -TCGCATTGCGATTTACGTAATCCGCATTGCGA-TTTACGTAA
* *
740393 TTCGCATTGCGATTTTTC-TAATTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGA-TTTACGTAATCCGCATTGCGATTTACGTAA
* *
740435 CCGCATTGTGATTTACGTAA-CCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAATCCGCATTGCGATTTACGTAA
*
740475 TCGCATTGCGATTTTAC-TAATTCGCACTT-CGATTTACGTAA
1 TCGCATTGCGA-TTTACGTAATCCGCA-TTGCGATTTACGTAA
740516 TCGCATTGCGATTTA-GTAA
1 TCGCATTGCGATTTACGTAA
740535 ATCGTAACGA
Statistics
Matches: 154, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
40 42 0.27
41 74 0.48
42 38 0.25
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCCGCATTGCGATTTACGTAA
Found at i:740537 original size:20 final size:20
Alignment explanation
Indices: 740311--740538 Score: 144
Period size: 20 Copynumber: 11.2 Consensus size: 20
740301 CAATACATAT
** *
740311 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTAGTAAA
** *
740332 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTAGTAAA
740353 TCGCATTGCGATTTATGTAAA
1 TCGCATTGCGATTTA-GTAAA
* * ** *
740374 -CGCATTACAATTTTTCTAAT
1 TCGCATTGCGA-TTTAGTAAA
** *
740394 TCGCATTGCGATTTTTCTAAT
1 TCGCATTGCGA-TTTAGTAAA
740415 TCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTA-GTAAA
* *
740435 CCGCATTGTGATTTACGT-AA
1 TCGCATTGCGATTTA-GTAAA
*
740455 CCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTA-GTAAA
* *
740475 TCGCATTGCGATTTTACTAAT
1 TCGCATTGCGA-TTTAGTAAA
740496 TCGCACTT-CGATTTACGT-AA
1 TCGCA-TTGCGATTTA-GTAAA
740516 TCGCATTGCGATTTAGTAAA
1 TCGCATTGCGATTTAGTAAA
740536 TCG
1 TCG
740539 TAACGAGATT
Statistics
Matches: 176, Mismatches: 21, Indels: 21
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.02
20 88 0.50
21 82 0.47
22 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTAGTAAA
Found at i:740538 original size:61 final size:60
Alignment explanation
Indices: 740312--740538 Score: 201
Period size: 62 Copynumber: 3.7 Consensus size: 60
740302 AATACATATT
* * ** * * *
740312 CGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTATGTAAA
1 CGCATTGCGATTTACGTAA-TCGCATTGCGA-TTTAGTAAATCGCATTGCGATTTACGTAAC
* * * ** *
740374 CGCATTACAATTTTTC-TAATTCGCATTGCGATTTTTCTAATTCGCATTGCGATTTACGTAAC
1 CGCATTGCGA-TTTACGTAA-TCGCATTGCGA-TTTAGTAAATCGCATTGCGATTTACGTAAC
* * *
740436 CGCATTGTGATTTACGTAACCGCATTGCGATTTACGT-AATCGCATTGCGATTTTAC-TAATT
1 CGCATTGCGATTTACGTAATCGCATTGCGATTTA-GTAAATCGCATTGCGA-TTTACGTAA-C
740497 CGCACTT-CGATTTACGTAATCGCATTGCGATTTAGTAAATCG
1 CGCA-TTGCGATTTACGTAATCGCATTGCGATTTAGTAAATCG
740539 TAACGAGATT
Statistics
Matches: 142, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
60 20 0.14
61 54 0.38
62 63 0.44
63 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (60 bp):
CGCATTGCGATTTACGTAATCGCATTGCGATTTAGTAAATCGCATTGCGATTTACGTAAC
Found at i:744849 original size:9 final size:9
Alignment explanation
Indices: 744835--744866 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
744825 CTCACAATAC
744835 TTTTAATTT
1 TTTTAATTT
744844 TTTTAATTT
1 TTTTAATTT
744853 TTTTAATTT
1 TTTTAATTT
*
744862 ATTTA
1 TTTTA
744867 CTCAACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTAATTT
Found at i:754686 original size:16 final size:16
Alignment explanation
Indices: 754665--754695 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
754655 CGACCGCGCA
754665 GGGCCCCAAAAAAATG
1 GGGCCCCAAAAAAATG
754681 GGGCCCCAAAAAAAT
1 GGGCCCCAAAAAAAT
754696 ATATAGTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.23, T:0.06
Consensus pattern (16 bp):
GGGCCCCAAAAAAATG
Found at i:761631 original size:50 final size:50
Alignment explanation
Indices: 761556--761656 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
761546 TTTAAATAGA
761556 CCATATGGAGAAAGAACCTGCAATGCCCTTAGAGGTCAGACCATTGAACT
1 CCATATGGAGAAAGAACCTGCAATGCCCTTAGAGGTCAGACCATTGAACT
761606 CCATATGGAGAAAGAACCTGCAATGCCCTTAGAGGTCAGACCATTGAACT
1 CCATATGGAGAAAGAACCTGCAATGCCCTTAGAGGTCAGACCATTGAACT
761656 C
1 C
761657 AAATAGTTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (50 bp):
CCATATGGAGAAAGAACCTGCAATGCCCTTAGAGGTCAGACCATTGAACT
Found at i:767074 original size:12 final size:12
Alignment explanation
Indices: 767057--767081 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
767047 ATGCTATTAA
767057 TATTTTATATTT
1 TATTTTATATTT
767069 TATTTTATATTT
1 TATTTTATATTT
767081 T
1 T
767082 TCTTGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATATTT
Found at i:772761 original size:21 final size:21
Alignment explanation
Indices: 772735--772779 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
772725 GATTTCTGGG
* *
772735 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
772756 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
772777 CAA
1 CAA
772780 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:773382 original size:18 final size:18
Alignment explanation
Indices: 773359--773393 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
773349 CTAGGAGATT
773359 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
773377 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
773394 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:773637 original size:2 final size:2
Alignment explanation
Indices: 773630--773667 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
773620 AATCTTGAGG
773630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
773668 GAAATGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:774463 original size:13 final size:13
Alignment explanation
Indices: 774445--774507 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
774435 TTATATGGCA
774445 CTACGGTGCAATT
1 CTACGGTGCAATT
774458 CTACGG-GC-A--
1 CTACGGTGCAATT
*
774467 CTTCGGTGCAATT
1 CTACGGTGCAATT
774480 CTACGG-GC-A--
1 CTACGGTGCAATT
*
774489 CTTCGGTGCAATT
1 CTACGGTGCAATT
774502 CTACGG
1 CTACGG
774508 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:774473 original size:22 final size:22
Alignment explanation
Indices: 774441--774521 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
774431 ATCATTATAT
*
774441 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
774463 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
774485 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
774508 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
774522 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:776745 original size:16 final size:16
Alignment explanation
Indices: 776724--776770 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
776714 GATAATTAAA
776724 GATTGATAAAGAATTT
1 GATTGATAAAGAATTT
* *
776740 GATTGATTAAGGATTTT
1 GATTGA-TAAAGAATTT
*
776757 GAGTGAT-AAGAATT
1 GATTGATAAAGAATT
776771 GATGCTATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (16 bp):
GATTGATAAAGAATTT
Found at i:777678 original size:21 final size:21
Alignment explanation
Indices: 777652--777696 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
777642 GATTTCTGGG
* *
777652 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
777673 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
777694 CAA
1 CAA
777697 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:778304 original size:18 final size:18
Alignment explanation
Indices: 778281--778315 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
778271 CTAGGAGATT
778281 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
778299 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
778316 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:779354 original size:13 final size:13
Alignment explanation
Indices: 779336--779398 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
779326 TTATATGGCA
779336 CTACGGTGCAATT
1 CTACGGTGCAATT
779349 CTACGG-GC-A--
1 CTACGGTGCAATT
*
779358 CTTCGGTGCAATT
1 CTACGGTGCAATT
779371 CTACGG-GC-A--
1 CTACGGTGCAATT
*
779380 CTTCGGTGCAATT
1 CTACGGTGCAATT
779393 CTACGG
1 CTACGG
779399 GCACTTCGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:779419 original size:22 final size:22
Alignment explanation
Indices: 779332--779411 Score: 151
Period size: 22 Copynumber: 3.6 Consensus size: 22
779322 ATCATTATAT
*
779332 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
779354 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
779376 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
779398 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
779412 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:781630 original size:16 final size:16
Alignment explanation
Indices: 781609--781655 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
781599 GATAATTAAA
781609 GATTGATAAAGAATTT
1 GATTGATAAAGAATTT
* *
781625 GATTGATTAAGGATTTT
1 GATTGA-TAAAGAATTT
*
781642 GAGTGAT-AAGAATT
1 GATTGATAAAGAATT
781656 GATGCTATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (16 bp):
GATTGATAAAGAATTT
Found at i:782563 original size:21 final size:21
Alignment explanation
Indices: 782537--782581 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
782527 GATTTCTGGG
* *
782537 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
782558 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
782579 CAA
1 CAA
782582 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:783187 original size:18 final size:18
Alignment explanation
Indices: 783164--783198 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
783154 CTAGGAGATT
783164 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
783182 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
783199 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:784304 original size:23 final size:22
Alignment explanation
Indices: 784231--784319 Score: 133
Period size: 22 Copynumber: 4.0 Consensus size: 22
784221 ATCATTATAT
* *
784231 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTATACG
*
784253 GGCACTTCGGTGCAATTTTACG
1 GGCACTTCGGTGCAATTATACG
784275 GGCACTTCGGTGCAATTATACGG
1 GGCACTTCGGTGCAATTATAC-G
*
784298 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
784320 AGCTGTAGTG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 41 0.66
23 21 0.34
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTATACG
Found at i:785857 original size:24 final size:24
Alignment explanation
Indices: 785762--785859 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
785752 TTCTATTATA
* **
785762 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATATG
785786 ATACTTGACCTGGATTCTGAT-TG
1 ATACTTGACCTGGATTCTGATATG
* *
785809 AATACTTGACATGGATTTTGATATG
1 -ATACTTGACCTGGATTCTGATATG
* *
785834 ATACTTGACCTGGATTATGTTATG
1 ATACTTGACCTGGATTCTGATATG
785858 AT
1 AT
785860 TTTTGATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.95
25 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATATG
Found at i:796890 original size:17 final size:18
Alignment explanation
Indices: 796868--796902 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
796858 CACCTTCATA
796868 TTAAATTAGTTC-AGCTC
1 TTAAATTAGTTCGAGCTC
*
796885 TTAAATTTGTTCGAGCTC
1 TTAAATTAGTTCGAGCTC
796903 GATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (18 bp):
TTAAATTAGTTCGAGCTC
Found at i:797111 original size:16 final size:17
Alignment explanation
Indices: 797090--797121 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
797080 ATACATTCTA
797090 TTAATTTAATC-TTATT
1 TTAATTTAATCATTATT
797106 TTAATTTAATCATTAT
1 TTAATTTAATCATTAT
797122 AAATATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATTTAATCATTATT
Found at i:797583 original size:20 final size:21
Alignment explanation
Indices: 797560--797601 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
797550 ATTAAAATTA
797560 AATTAATAA-AAATATATAAT
1 AATTAATAATAAATATATAAT
797580 AATTAATAATTAAATATATAAT
1 AATTAATAA-TAAATATATAAT
797602 TATATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAATAATAAATATATAAT
Found at i:805735 original size:2 final size:2
Alignment explanation
Indices: 805730--805779 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
805720 TACACACACA
*
805730 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
805772 AT AT AT AT
1 AT AT AT AT
805780 TCAGTTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:823228 original size:16 final size:16
Alignment explanation
Indices: 823207--823238 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
823197 TGGATACTTC
823207 ACATCGATTACTCCTA
1 ACATCGATTACTCCTA
823223 ACATCGATTACTCCTA
1 ACATCGATTACTCCTA
823239 CCCTGTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (16 bp):
ACATCGATTACTCCTA
Found at i:833077 original size:2 final size:2
Alignment explanation
Indices: 833037--833065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
833027 AAGCTAATTA
833037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
833066 CTTAACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:840703 original size:186 final size:186
Alignment explanation
Indices: 840372--840763 Score: 671
Period size: 186 Copynumber: 2.1 Consensus size: 186
840362 TTTTATAATT
* * * *
840372 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAACTAATTTAAATAATATATA
840436 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
840501 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGTTAAGCCCATATGTTA
*
840557 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAACTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAACTAATTTAAATAATATATA
840622 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
840687 TT-AGATCTTTAATTATTAATTGGATTTTAAATGGTTTGGGTTAAGTCCATATGTTA
131 TTGA-ATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGTTAAGCCCATATGTTA
*
840743 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
840764 AAAATTTTAT
Statistics
Matches: 195, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
185 8 0.04
186 187 0.96
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAACTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGTTAAGCCCATATGTTA
Found at i:843188 original size:26 final size:26
Alignment explanation
Indices: 843157--843213 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
843147 CTTTTGCAAC
*
843157 TAATATTTTTTACTCTATGTAGGCAT
1 TAATATTTTTTACACTATGTAGGCAT
843183 TAATATTTTTTACACTATGTAGGCAT
1 TAATATTTTTTACACTATGTAGGCAT
843209 TAATA
1 TAATA
843214 GCTTTGAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (26 bp):
TAATATTTTTTACACTATGTAGGCAT
Found at i:859903 original size:13 final size:13
Alignment explanation
Indices: 859885--859910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
859875 ATATTTTAGC
859885 AAAAAAGAAGATT
1 AAAAAAGAAGATT
859898 AAAAAAGAAGATT
1 AAAAAAGAAGATT
859911 TGTCTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAAGAAGATT
Found at i:859993 original size:25 final size:24
Alignment explanation
Indices: 859939--859993 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
859929 TCTAATTTTT
859939 TTTTATATATTTAATAAATTATTA
1 TTTTATATATTTAATAAATTATTA
* *
859963 TCTTATATATTTAATGAAATTATTG
1 TTTTATATATTTAAT-AAATTATTA
859988 TTTTAT
1 TTTTAT
859994 CTTTTTCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTATATATTTAATAAATTATTA
Found at i:866783 original size:21 final size:21
Alignment explanation
Indices: 866759--866832 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
866749 GAACGGTGCT
866759 CAAGCTGAACTGGTTATCTCA
1 CAAGCTGAACTGGTTATCTCA
866780 CAAGCTGAACTGGTTATCTCA
1 CAAGCTGAACTGGTTATCTCA
866801 CAAGCTGAACTGGTTATCTCA
1 CAAGCTGAACTGGTTATCTCA
* *
866822 GAACCTGAACT
1 CAAGCTGAACT
866833 AGTCAAAGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (21 bp):
CAAGCTGAACTGGTTATCTCA
Found at i:870912 original size:188 final size:188
Alignment explanation
Indices: 870595--870971 Score: 754
Period size: 188 Copynumber: 2.0 Consensus size: 188
870585 AGTCACTACA
870595 ATCTAAATGCTACCATCAACAATTGGTGTAGTAAGTAGGGAAGACTTCATGATGGAAAAGAATCA
1 ATCTAAATGCTACCATCAACAATTGGTGTAGTAAGTAGGGAAGACTTCATGATGGAAAAGAATCA
870660 ACCGAGATGCACCCTCAAGAAAACAATAACCAACATCACCCATATTCTCTTCCAAAAATCTCCCT
66 ACCGAGATGCACCCTCAAGAAAACAATAACCAACATCACCCATATTCTCTTCCAAAAATCTCCCT
870725 AAATGCGCACAATTTACCAGGTTACGCAACTGCAGATCAAGCTGTATAACTTGCATGC
131 AAATGCGCACAATTTACCAGGTTACGCAACTGCAGATCAAGCTGTATAACTTGCATGC
870783 ATCTAAATGCTACCATCAACAATTGGTGTAGTAAGTAGGGAAGACTTCATGATGGAAAAGAATCA
1 ATCTAAATGCTACCATCAACAATTGGTGTAGTAAGTAGGGAAGACTTCATGATGGAAAAGAATCA
870848 ACCGAGATGCACCCTCAAGAAAACAATAACCAACATCACCCATATTCTCTTCCAAAAATCTCCCT
66 ACCGAGATGCACCCTCAAGAAAACAATAACCAACATCACCCATATTCTCTTCCAAAAATCTCCCT
870913 AAATGCGCACAATTTACCAGGTTACGCAACTGCAGATCAAGCTGTATAACTTGCATGC
131 AAATGCGCACAATTTACCAGGTTACGCAACTGCAGATCAAGCTGTATAACTTGCATGC
870971 A
1 A
870972 CAATCTTAGG
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 189 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (188 bp):
ATCTAAATGCTACCATCAACAATTGGTGTAGTAAGTAGGGAAGACTTCATGATGGAAAAGAATCA
ACCGAGATGCACCCTCAAGAAAACAATAACCAACATCACCCATATTCTCTTCCAAAAATCTCCCT
AAATGCGCACAATTTACCAGGTTACGCAACTGCAGATCAAGCTGTATAACTTGCATGC
Found at i:878857 original size:13 final size:13
Alignment explanation
Indices: 878841--878871 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
878831 AATCAATTTC
878841 TCAAATCAGCTAA
1 TCAAATCAGCTAA
*
878854 TCAAATCAGTTAA
1 TCAAATCAGCTAA
878867 TCAAA
1 TCAAA
878872 CTAGCTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (13 bp):
TCAAATCAGCTAA
Found at i:889193 original size:27 final size:27
Alignment explanation
Indices: 889119--889194 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
889109 GACGTAGCAA
* *
889119 TTTCTAGAAGGTTCAGTCAGCAGCAGT
1 TTTCTAGAAGGTTCAGTCAGTAACAGT
* *
889146 TTTTTAGAAGGTCCAGTCAGTAACAGT
1 TTTCTAGAAGGTTCAGTCAGTAACAGT
* *
889173 TTTCTAGAAGATTTAGTCAGTA
1 TTTCTAGAAGGTTCAGTCAGTA
889195 CCTTCTTGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (27 bp):
TTTCTAGAAGGTTCAGTCAGTAACAGT
Found at i:901094 original size:21 final size:23
Alignment explanation
Indices: 901069--901121 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
901059 TCATAATGAA
901069 ATTTATTGAGCT-GA-AAAAATT
1 ATTTATTGAGCTGGACAAAAATT
*
901090 ATTTATTAAGCTGGACAAAAATT
1 ATTTATTGAGCTGGACAAAAATT
*
901113 ATTTTTTGA
1 ATTTATTGA
901122 ATGAAGGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 2 0.07
23 14 0.52
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (23 bp):
ATTTATTGAGCTGGACAAAAATT
Found at i:901113 original size:23 final size:21
Alignment explanation
Indices: 901069--901116 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
901059 TCATAATGAA
*
901069 ATTTATTGAGCTGAAAAAATT
1 ATTTATTAAGCTGAAAAAATT
901090 ATTTATTAAGCTGGACAAAAATT
1 ATTTATTAAGCT-GA-AAAAATT
901113 ATTT
1 ATTT
901117 TTTGAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTTATTAAGCTGAAAAAATT
Found at i:901702 original size:35 final size:34
Alignment explanation
Indices: 901658--901770 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
901648 AAAACAATTC
*
901658 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
901693 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
901728 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
901763 TCAATTTC
1 TCAATTTC
901771 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 62 0.90
36 6 0.09
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:902841 original size:33 final size:33
Alignment explanation
Indices: 902763--902871 Score: 121
Period size: 33 Copynumber: 3.2 Consensus size: 33
902753 TATTTCCCTT
* *
902763 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAA-TT-GGGTTTAGAATG
*
902798 TAATTGAATTATTTTGGAATTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATT-GGGTTTAGAATG
* * *
902832 -AATTGAATTACTTTGAAATTGGGATTTATAATG
1 AAATTGAATTATTTTGGAATTGGG-TTTAGAATG
902865 AAATTGA
1 AAATTGA
902872 GGAATGTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.05
33 26 0.40
34 20 0.31
35 16 0.25
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (33 bp):
AAATTGAATTATTTTGGAATTGGGTTTAGAATG
Found at i:905298 original size:52 final size:54
Alignment explanation
Indices: 905242--905399 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 54
905232 TTAATATTAT
* * *
905242 TTATTAATATAGTTAATAATAATTAATATTTGATGCTTAAAATATT-TATA-AA
1 TTATTAATATAATTGATAATAATTAATATTTGATGCTTAAAATATTAAATACAA
* * * *
905294 TTATTAATATAATTGATAGTAATTAATATTGGATGTTTAAAATATTAAATACTA
1 TTATTAATATAATTGATAATAATTAATATTTGATGCTTAAAATATTAAATACAA
**
905348 TTCATTAATATAATTGAT-AGCATTAAATATTTGATGCTTAAAATATTAAATA
1 TT-ATTAATATAATTGATAATAATT-AATATTTGATGCTTAAAATATTAAATA
905400 GTATCTATCA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
52 41 0.46
53 3 0.03
54 6 0.07
55 40 0.44
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (54 bp):
TTATTAATATAATTGATAATAATTAATATTTGATGCTTAAAATATTAAATACAA
Found at i:915276 original size:31 final size:29
Alignment explanation
Indices: 915213--915288 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
915203 TATTAAAAGC
*
915213 TTTTATAATTTATTTTTGTAGAATTTTTA
1 TTTTATAATTTATTTTTGTAGAATTTTAA
* * *
915242 TTTTATATATTTGATTTTTTTATAGTTTTAA
1 TTTTATA-ATTT-ATTTTTGTAGAATTTTAA
915273 TTTTATAATTT-TTTTT
1 TTTTATAATTTATTTTT
915289 ATCATCTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.12
29 7 0.17
30 8 0.20
31 21 0.51
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTATAATTTATTTTTGTAGAATTTTAA
Found at i:926142 original size:16 final size:16
Alignment explanation
Indices: 926106--926144 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
926096 AATATTCAAA
*
926106 ATATTATAAATATAAAT
1 ATATT-TAAATATAAAC
*
926123 ATATTTAAATATATAC
1 ATATTTAAATATAAAC
926139 ATATTT
1 ATATTT
926145 TATTTGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTAAATATAAAC
Found at i:926587 original size:36 final size:32
Alignment explanation
Indices: 926519--926587 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 32
926509 GATATTTAAT
926519 TTAATTAAAAAATTGTTTTTATTAATTTCAAG
1 TTAATTAAAAAATTGTTTTTATTAATTTCAAG
* *
926551 TTAATTAAATTAAATTGATTTTTTTTTATTTACAAG
1 TTAATTAAA--AAATTG-TTTTTATTAATTT-CAAG
926587 T
1 T
926588 ATAAGTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.29
34 6 0.19
35 11 0.35
36 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (32 bp):
TTAATTAAAAAATTGTTTTTATTAATTTCAAG
Found at i:928642 original size:21 final size:21
Alignment explanation
Indices: 928617--928665 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
928607 TTTACGTTAT
*
928617 ATTTTT-ATTGAATTTTATTC
1 ATTTTTAATTCAATTTTATTC
* *
928637 ATTTTTAATTCATTTTTATTT
1 ATTTTTAATTCAATTTTATTC
928658 ATTTTTAA
1 ATTTTTAA
928666 AAAAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTAATTCAATTTTATTC
Found at i:928647 original size:11 final size:10
Alignment explanation
Indices: 928617--928664 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
928607 TTTACGTTAT
*
928617 ATTTTTATTG
1 ATTTTTATTC
*
928627 AATTTTATTC
1 ATTTTTATTC
928637 ATTTTTAATTC
1 ATTTTT-ATTC
*
928648 ATTTTTATTT
1 ATTTTTATTC
928658 ATTTTTA
1 ATTTTTA
928665 AAAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 23 0.70
11 10 0.30
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:929743 original size:19 final size:19
Alignment explanation
Indices: 929719--929784 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
929709 TTAAAAAATA
929719 TAATATAATAATTTTATTT
1 TAATATAATAATTTTATTT
* *
929738 TAATAT-AT-ATTTAATAT
1 TAATATAATAATTTTATTT
* * *
929755 AATATATAATATTTTTATTC
1 TA-ATATAATAATTTTATTT
*
929775 TAATAGAATA
1 TAATATAATA
929785 TACTAGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 15 0.43
20 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATAATAATTTTATTT
Found at i:929757 original size:16 final size:16
Alignment explanation
Indices: 929719--929762 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
929709 TTAAAAAATA
929719 TAATATAATA-AT-TT
1 TAATATAATATATATT
* *
929733 TATTTTAATATATATT
1 TAATATAATATATATT
929749 TAATATAATATATA
1 TAATATAATATATA
929763 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATAATATATATT
Found at i:933512 original size:35 final size:35
Alignment explanation
Indices: 933466--933536 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
933456 TCAGGCACAG
933466 TAAGCTGCCAAGTTGGGGATAAACTGTTGAGTTCT
1 TAAGCTGCCAAGTTGGGGATAAACTGTTGAGTTCT
933501 TAAGCTGCCAAGTTGGGGATAAACTGTTGAGTTCT
1 TAAGCTGCCAAGTTGGGGATAAACTGTTGAGTTCT
933536 T
1 T
933537 TGTGCTATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.32
Consensus pattern (35 bp):
TAAGCTGCCAAGTTGGGGATAAACTGTTGAGTTCT
Found at i:954725 original size:21 final size:21
Alignment explanation
Indices: 954695--954735 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
954685 AATCGTTAAA
*
954695 AAATATTAATATTTTAGGTAG
1 AAATAATAATATTTTAGGTAG
*
954716 AAATAATAATGTTTTAGGTA
1 AAATAATAATATTTTAGGTA
954736 ATTTTTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAG
Found at i:956650 original size:11 final size:11
Alignment explanation
Indices: 956634--956660 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
956624 AGATTCTCGT
956634 CATTTTTTCAC
1 CATTTTTTCAC
956645 CATTTTTTCAC
1 CATTTTTTCAC
956656 CATTT
1 CATTT
956661 GATAGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.56
Consensus pattern (11 bp):
CATTTTTTCAC
Found at i:958444 original size:2 final size:2
Alignment explanation
Indices: 958433--958462 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
958423 TGTATATGGA
958433 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
958463 AGTGTTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:958552 original size:23 final size:25
Alignment explanation
Indices: 958503--958552 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
958493 AAAACCTTTT
* *
958503 ATTTTCAATAAATTATTAATTTGAC
1 ATTTTCAAAAAATAATTAATTTGAC
*
958528 ATTTT-AAAAAATAATT-ATTTTAC
1 ATTTTCAAAAAATAATTAATTTGAC
958551 AT
1 AT
958553 AAAATTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 9 0.41
25 5 0.23
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTTCAAAAAATAATTAATTTGAC
Found at i:958651 original size:23 final size:23
Alignment explanation
Indices: 958602--958666 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
958592 GTTTACGAAA
* *
958602 ATGTTCAATTAATGTTCGTGAAG
1 ATGTTCATTTAATGTTCGTGAAC
*
958625 ATGTTCATTTAATGTTTGCT-AAC
1 ATGTTCATTTAATGTTCG-TGAAC
*
958648 ATGTTC-TTTATACGTTCGT
1 ATGTTCATTTA-ATGTTCGT
958667 TTCAACAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.14
23 29 0.83
24 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (23 bp):
ATGTTCATTTAATGTTCGTGAAC
Found at i:959191 original size:222 final size:228
Alignment explanation
Indices: 958792--959249 Score: 847
Period size: 222 Copynumber: 2.0 Consensus size: 228
958782 TCTTATATTT
*
958792 AATTTAATTTTTATCTTCACCAATATTTCAAATAAAAAAAAGAAAAGAAAATTTGAGTAAATGAG
1 AATTCAATTTTTATCTTCACCAATATTTCAAATAAAAAAAAGAAAAGAAAATTTGAGTAAATGAG
958857 TCGATAAAAAAAACTTATAAAAAAACCAATAAACGAACTTGTTCATTAATATAAACGAACTAAAC
66 TCGATAAAAAAAACTTATAAAAAAACCAATAAACGAAC-T-TTCATTAATATAAACGAACTAAAC
958922 ACACATATATTTATGTTCATTTATTAAACAAATATAAAAAAATTATTAATACTTATTTATTTAAT
129 ACACATATATTTATGTTCATTTATTAAACAAATATAAAAAAATTATTAATACTTATTTATTTAAT
958987 TTAATAGATAAATTATATATAAACATTATTCAAAC
194 TTAATAGATAAATTATATATAAACATTATTCAAAC
959022 AATTCAATTTTTATCTTCACCAATA-TTCAAAT-AAAAAAAGAAAAGAAAA-TTGAGTAAATGAG
1 AATTCAATTTTTATCTTCACCAATATTTCAAATAAAAAAAAGAAAAGAAAATTTGAGTAAATGAG
959084 TCGAT-AAAAAAACTTATAAAAAAACCAATAAACGAAC-TTCATT-ATATAAACGAACTAAACAC
66 TCGATAAAAAAAACTTATAAAAAAACCAATAAACGAACTTTCATTAATATAAACGAACTAAACAC
959146 ACATATATTTATGTTCATTTATTAAACAAATATAAAAAAATTATTAATACTTATTTATTTAATTT
131 ACATATATTTATGTTCATTTATTAAACAAATATAAAAAAATTATTAATACTTATTTATTTAATTT
959211 AATAGATAAATTATATATAAACATTATTCAAAC
196 AATAGATAAATTATATATAAACATTATTCAAAC
959244 AATTCA
1 AATTCA
959250 CAAATAATTT
Statistics
Matches: 227, Mismatches: 1, Indels: 8
0.96 0.00 0.03
Matches are distributed among these distances:
222 123 0.54
223 6 0.03
226 32 0.14
227 18 0.08
228 17 0.07
229 7 0.03
230 24 0.11
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (228 bp):
AATTCAATTTTTATCTTCACCAATATTTCAAATAAAAAAAAGAAAAGAAAATTTGAGTAAATGAG
TCGATAAAAAAAACTTATAAAAAAACCAATAAACGAACTTTCATTAATATAAACGAACTAAACAC
ACATATATTTATGTTCATTTATTAAACAAATATAAAAAAATTATTAATACTTATTTATTTAATTT
AATAGATAAATTATATATAAACATTATTCAAAC
Found at i:960397 original size:4 final size:4
Alignment explanation
Indices: 960388--960429 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
960378 CATTATATAC
* * *
960388 ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGC ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
960430 AGGTTCGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:960408 original size:16 final size:16
Alignment explanation
Indices: 960387--960429 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
960377 ACATTATATA
960387 CATGTATGTATGTATG
1 CATGTATGTATGTATG
960403 CATGTATGTATGTATG
1 CATGTATGTATGTATG
*
960419 CATGCATGTAT
1 CATGTATGTAT
960430 AGGTTCGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (16 bp):
CATGTATGTATGTATG
Found at i:976551 original size:6 final size:7
Alignment explanation
Indices: 976525--976550 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
976515 ATTATGAACT
976525 CCCCCCA
1 CCCCCCA
976532 CCCCCCA
1 CCCCCCA
976539 CCCCCCA
1 CCCCCCA
976546 CCCCC
1 CCCCC
976551 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (7 bp):
CCCCCCA
Found at i:994712 original size:3 final size:3
Alignment explanation
Indices: 994704--994752 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
994694 ATATAAGACA
994704 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
994751 TA
1 TA
994753 CCTAAGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:997542 original size:15 final size:15
Alignment explanation
Indices: 997503--997544 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
997493 TAGAAAACCA
997503 TAATCTAAATTAT-TCC
1 TAAT-TAAA-TATCTCC
997519 TAA-TAAATATCTCC
1 TAATTAAATATCTCC
997533 TAATTAAATATC
1 TAATTAAATATC
997545 AAATTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 8 0.33
16 3 0.12
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAAATATCTCC
Found at i:1004838 original size:35 final size:34
Alignment explanation
Indices: 1004792--1004858 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1004782 AGTTGCAGCA
* *
1004792 GCAGCTTCAGGTGGCAGTAGCACATCCGCACACG
1 GCAGCTTCAGGTGACAGTAGCACACCCGCACACG
* *
1004826 GCAGCTTTCAGGTGATAGTGGCACACCCGCACA
1 GCAGC-TTCAGGTGACAGTAGCACACCCGCACA
1004859 TGGCGGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.24, C:0.31, G:0.28, T:0.16
Consensus pattern (34 bp):
GCAGCTTCAGGTGACAGTAGCACACCCGCACACG
Found at i:1005250 original size:18 final size:18
Alignment explanation
Indices: 1005223--1005271 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1005213 ATTGCATGTG
*
1005223 ATAA-TACATATTAAATG
1 ATAACTACATATTAAATA
*
1005240 ATAGCTACATATTAAATA
1 ATAACTACATATTAAATA
*
1005258 ATAATTACATATTA
1 ATAACTACATATTA
1005272 TAAATAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAACTACATATTAAATA
Found at i:1005626 original size:112 final size:113
Alignment explanation
Indices: 1005505--1005725 Score: 417
Period size: 112 Copynumber: 2.0 Consensus size: 113
1005495 GTAGCCGGTT
1005505 TTTTTGTCGGAAATGGGGTAAATTGTTTTGCTTTAATTTTTAAACGAGACAACATATTAATTGTG
1 TTTTTGTCGGAAATGGGGTAAATTGTTTTGCTTTAATTTTTAAACGAGACAACATATTAATTGTG
*
1005570 GGGTTGCTTTTTAGGTTTTTGATGATGATA-TTTTTTTATCCTTCCGG
66 GGGTTGCTTTTTAGGTTTTTGATGATAATATTTTTTTTATCCTTCCGG
1005617 TTTTTGTCGGAAATGGGGTAAATTGTTTTGCTTTAATTTTTAAACGAGACAACATATTAATTGTG
1 TTTTTGTCGGAAATGGGGTAAATTGTTTTGCTTTAATTTTTAAACGAGACAACATATTAATTGTG
*
1005682 GTGTTGCTTTTTAGGTTTTTGATGATAATATTTTTTTTATCCTT
66 GGGTTGCTTTTTAGGTTTTTGATGATAATATTTTTTTTATCCTT
1005726 GTGAAGCCAT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
112 93 0.88
113 13 0.12
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.49
Consensus pattern (113 bp):
TTTTTGTCGGAAATGGGGTAAATTGTTTTGCTTTAATTTTTAAACGAGACAACATATTAATTGTG
GGGTTGCTTTTTAGGTTTTTGATGATAATATTTTTTTTATCCTTCCGG
Found at i:1006576 original size:20 final size:21
Alignment explanation
Indices: 1006540--1006587 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
1006530 GATTTTAGGT
*
1006540 GTTTTGATATAAAAAAAACTA
1 GTTTTAATATAAAAAAAACTA
1006561 GTTTTAATAT-AAAAAAACTA
1 GTTTTAATATAAAAAAAACTA
1006581 GTTTTAA
1 GTTTTAA
1006588 AATGGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (21 bp):
GTTTTAATATAAAAAAAACTA
Found at i:1007172 original size:19 final size:19
Alignment explanation
Indices: 1007148--1007194 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1007138 AGATTTTTTA
1007148 AATATTTTAATTTAACAC-T
1 AATATTTTAATTTAAC-CTT
**
1007167 AATATTAAAATTTAACCTT
1 AATATTTTAATTTAACCTT
1007186 AA-ATTTTAA
1 AATATTTTAA
1007195 GTTCTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATTTTAATTTAACCTT
Found at i:1008162 original size:28 final size:28
Alignment explanation
Indices: 1008130--1008209 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 28
1008120 ACTACAACAT
**
1008130 TCAGGCGGCAGAGCCGACCATATACCAA
1 TCAGGCGGCATTGCCGACCATATACCAA
* *
1008158 TCAGGCGGCATTGCCTATCATATACCAA
1 TCAGGCGGCATTGCCGACCATATACCAA
* *
1008186 TTAGACGGCATTGCCGACCATATA
1 TCAGGCGGCATTGCCGACCATATA
1008210 ATAAAACTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (28 bp):
TCAGGCGGCATTGCCGACCATATACCAA
Found at i:1012229 original size:16 final size:17
Alignment explanation
Indices: 1012208--1012240 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1012198 ACACACTAAA
1012208 TCGGTT-TCGATTTTTT
1 TCGGTTATCGATTTTTT
1012224 TCGGTTATCGATTTTTT
1 TCGGTTATCGATTTTTT
1012241 AGATCGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.09, C:0.12, G:0.18, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGATTTTTT
Found at i:1025237 original size:4 final size:4
Alignment explanation
Indices: 1025228--1025254 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1025218 TAAATCGAGA
1025228 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
1025255 CATTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1027743 original size:257 final size:259
Alignment explanation
Indices: 1027287--1027803 Score: 1020
Period size: 257 Copynumber: 2.0 Consensus size: 259
1027277 GATGACATAC
1027287 AAAGGATCACAATAACAATCAATACATTCATCATAACTGCCAACAGACTATCAGTTTATACAGAT
1 AAAGGATCACAATAACAATCAATACATTCATCATAACTGCCAACAGACTATCAGTTTATACAGAT
1027352 ACAACAGTCAACCATTAGATTTGGTTATCAACGTCAGATTAAAAGGAAGTGAAGGGGAGCTTCGA
66 ACAACAGTCAACCATTAGATTTGGTTATCAACGTCAGATTAAAAGGAAGTGAAGGGGAGCTTCGA
1027417 GTGACCATTTGGAGACGGTAATTCCTGCGGTAACTTGTCATTAATGAAGGGTCTTCCAGGGTTCC
131 GTGACCATTTGGAGACGGTAATTCCTGCGGTAACTTGTCATTAATGAAGGGTCTTCCAGGGTTCC
1027482 GTTAATTATTGCTCTAGGTGACATTATCTTAAGGGTATAACCCGGA-GTAGAAT-ATAAGAAAT
196 GTTAATTATTGCTCTAGGTGACATTATCTTAAGGGTATAACCCGGAGGTAGAATAATAAGAAAT
1027544 AAAGGATCACAATAACAATCAATACATTCATCATAACTGCCAACAGACTATCAGTTTATACAGAT
1 AAAGGATCACAATAACAATCAATACATTCATCATAACTGCCAACAGACTATCAGTTTATACAGAT
1027609 ACAACAGTCAACCATTAGATTTGGTTATCAACGTCAGATTAAAAGGAAGTGAAGGGGAGCTTCGA
66 ACAACAGTCAACCATTAGATTTGGTTATCAACGTCAGATTAAAAGGAAGTGAAGGGGAGCTTCGA
1027674 GTGACCATTTGGAGACGGTAATTCCTGCGGTAACTTGTCATTAATGAAGGGTCTTCCAGGGTTCC
131 GTGACCATTTGGAGACGGTAATTCCTGCGGTAACTTGTCATTAATGAAGGGTCTTCCAGGGTTCC
1027739 GTTAATTATTGCTCTAGGTGACATTATCTTAAGGGTATAACCCGGAGGTAGAATAATAAGAAAT
196 GTTAATTATTGCTCTAGGTGACATTATCTTAAGGGTATAACCCGGAGGTAGAATAATAAGAAAT
1027803 A
1 A
1027804 TATATGTGCA
Statistics
Matches: 258, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
257 241 0.93
258 7 0.03
259 10 0.04
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (259 bp):
AAAGGATCACAATAACAATCAATACATTCATCATAACTGCCAACAGACTATCAGTTTATACAGAT
ACAACAGTCAACCATTAGATTTGGTTATCAACGTCAGATTAAAAGGAAGTGAAGGGGAGCTTCGA
GTGACCATTTGGAGACGGTAATTCCTGCGGTAACTTGTCATTAATGAAGGGTCTTCCAGGGTTCC
GTTAATTATTGCTCTAGGTGACATTATCTTAAGGGTATAACCCGGAGGTAGAATAATAAGAAAT
Found at i:1032828 original size:21 final size:20
Alignment explanation
Indices: 1032804--1032867 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1032794 AACTTTGAAA
1032804 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1032825 AAATG-TTTC--A--TT-GA
1 AAATGTTTTCAAAGTTTGGT
1032839 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1032860 AAATGTTT
1 AAATGTTT
1032868 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 4 0.12
17 1 0.03
18 1 0.03
19 4 0.12
20 6 0.18
21 10 0.29
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1032842 original size:35 final size:36
Alignment explanation
Indices: 1032802--1032917 Score: 157
Period size: 35 Copynumber: 3.2 Consensus size: 36
1032792 CCAACTTTGA
1032802 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCATTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCATTG
* *
1032838 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCATTG
* *
1032873 AAAAAT-ATTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAATGA--TTTTCAAAGTTTGGTAAATGTTTCATTG
1032909 AAAAATGAT
1 AAAAATGAT
1032918 AATGGGATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
35 34 0.48
36 14 0.20
37 23 0.32
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.43
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCATTG
Found at i:1033345 original size:16 final size:16
Alignment explanation
Indices: 1033324--1033356 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1033314 TACTATTCAT
*
1033324 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
1033340 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
1033356 G
1 G
1033357 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:1037520 original size:37 final size:36
Alignment explanation
Indices: 1037421--1037540 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 36
1037411 TGGTAACCAA
* *
1037421 CTTTGAAAAAGTTGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TAGTTTTCAAAGTTTGGTAAGTGTTT
*
1037458 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAGTGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAGTGTTT
1037493 CTTTGAAAAATAGTTTTTCAAAGTTTGGT-AGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAG-TGTTT
*
1037530 -GTTGAAAAATA
1 CTTTGAAAAATA
1037541 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.38
36 22 0.29
37 25 0.33
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAGTGTTT
Found at i:1042466 original size:22 final size:22
Alignment explanation
Indices: 1042425--1042466 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1042415 TTCATCCCTA
* **
1042425 AAATTTTATAAATTCCTCTCTT
1 AAATTTTAAAAATTAATCTCTT
1042447 AAATTTTAAAAATTAATCTC
1 AAATTTTAAAAATTAATCTC
1042467 CCTAACTTAA
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:0.40, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTTTAAAAATTAATCTCTT
Done.