Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:793556 original size:26 final size:25
Alignment explanation
Indices: 793522--793643 Score: 88
Period size: 26 Copynumber: 4.6 Consensus size: 25
793512 TATTTTAAAA
*
793522 TATGAATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTA-TTG
*
793548 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTA--TT--AT--TGTATT-G
* ***
793580 TATAGATTGATTTA-T-TT-TAAAA
1 TATGGATTGATTTATTATTGTATTG
793602 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTA-TTG
793628 TATGGATTGATTTATT
1 TATGGATTGATTTATT
793644 TTAAATAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
22 13 0.17
23 3 0.04
24 3 0.04
25 2 0.03
26 30 0.40
28 2 0.03
29 1 0.01
30 2 0.03
31 2 0.03
32 17 0.23
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (25 bp):
TATGGATTGATTTATTATTGTATTG
Found at i:793575 original size:40 final size:40
Alignment explanation
Indices: 793531--793658 Score: 128
Period size: 40 Copynumber: 3.2 Consensus size: 40
793521 ATATGAATTG
793531 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA
1 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA
793571 ATTTATTA--GTA----TA--GATTGATTTATTTTAAAATATGGA
1 ATTTATTATTGTAGTTGTATGGATTGATTTATTTT--AA-AT--A
793608 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA
1 ---ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA
793651 ATTTATTA
1 ATTTATTA
793659 GTATGAATTG
Statistics
Matches: 72, Mismatches: 0, Indels: 32
0.69 0.00 0.31
Matches are distributed among these distances:
32 14 0.19
34 4 0.06
35 2 0.03
37 1 0.01
38 3 0.04
40 24 0.33
42 3 0.04
43 1 0.01
45 2 0.03
46 4 0.06
48 14 0.19
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (40 bp):
ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA
Found at i:793685 original size:22 final size:22
Alignment explanation
Indices: 793660--793702 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
793650 AATTTATTAG
793660 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
793682 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
793703 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:793693 original size:54 final size:54
Alignment explanation
Indices: 793468--793712 Score: 181
Period size: 54 Copynumber: 4.6 Consensus size: 54
793458 AATTTATTAG
**
793468 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATAAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
* * *
793522 TATGAATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAAA
* * * * * * * ***
793569 TA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGAATTGATTTA-T-TT-TA-AAA
793628 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
793682 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
793713 TTGTAGTTGT
Statistics
Matches: 146, Mismatches: 24, Indels: 42
0.69 0.11 0.20
Matches are distributed among these distances:
43 3 0.02
44 4 0.03
45 1 0.01
47 5 0.03
48 20 0.14
49 2 0.01
50 5 0.03
51 2 0.01
52 2 0.01
54 58 0.40
55 3 0.02
56 4 0.03
57 2 0.01
58 14 0.10
59 2 0.01
60 2 0.01
62 11 0.08
63 6 0.04
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
Found at i:793762 original size:31 final size:31
Alignment explanation
Indices: 793727--793785 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
793717 AGTTGTATGG
*
793727 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGTAAAACTAAA
793758 ATTATTTAAATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
793786 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAAA
Found at i:798034 original size:3 final size:3
Alignment explanation
Indices: 798026--798050 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
798016 CTAATAAAAG
798026 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
798051 AAATCAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:800243 original size:2 final size:2
Alignment explanation
Indices: 800236--800273 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
800226 AAATTCGCTC
800236 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
800274 ATAGGATTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:801878 original size:2 final size:2
Alignment explanation
Indices: 801873--801922 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
801863 AAGCTATCAT
* *
801873 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
801915 TA TA TA TA
1 TA TA TA TA
801923 CAATCACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:802684 original size:29 final size:29
Alignment explanation
Indices: 802633--802690 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
802623 GTGTTGGCCG
* * *
802633 TAGGTTGCCATGCCTTTCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
802662 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
802691 AAGAGATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:802743 original size:10 final size:10
Alignment explanation
Indices: 802730--802787 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
802720 ACACGCTGGG
*
802730 CATCAGAGGC
1 CATCCGAGGC
802740 CATCCGAGAG-
1 CATCCGAG-GC
*
802750 CATCTGAGGC
1 CATCCGAGGC
802760 CATCCGAGAG-
1 CATCCGAG-GC
802770 CATCCGAGGC
1 CATCCGAGGC
802780 CATCCGAG
1 CATCCGAG
802788 AGCATATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.05
10 37 0.90
11 2 0.05
ACGTcount: A:0.26, C:0.33, G:0.29, T:0.12
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:802758 original size:20 final size:20
Alignment explanation
Indices: 802729--802806 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
802719 AACACGCTGG
*
802729 GCATCAGAGGCCATCCGAGA
1 GCATCTGAGGCCATCCGAGA
802749 GCATCTGAGGCCATCCGAGA
1 GCATCTGAGGCCATCCGAGA
*
802769 GCATCCGAGGCCATCCGAGA
1 GCATCTGAGGCCATCCGAGA
* *
802789 GCATATGAGACCATCCGA
1 GCATCTGAGGCCATCCGA
802807 ACGAGCTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (20 bp):
GCATCTGAGGCCATCCGAGA
Found at i:802784 original size:40 final size:42
Alignment explanation
Indices: 802729--802830 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 42
802719 AACACGCTGG
* * *
802729 GCATCAGAGGCCATCCGAGAGCATCTGAGGCCATCCG-A-GA
1 GCATCCGAGGCCATCCGAGAGCATATGAGACCATCCGAACGA
802769 GCATCCGAGGCCATCCGAGAGCATATGAGACCATCCGAACGA
1 GCATCCGAGGCCATCCGAGAGCATATGAGACCATCCGAACGA
* *
802811 GCTATGCGAGGGCATCCGAG
1 GC-ATCCGAGGCCATCCGAG
802831 GGTAACCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 34 0.63
41 1 0.02
42 4 0.07
43 15 0.28
ACGTcount: A:0.27, C:0.29, G:0.30, T:0.13
Consensus pattern (42 bp):
GCATCCGAGGCCATCCGAGAGCATATGAGACCATCCGAACGA
Found at i:802846 original size:33 final size:33
Alignment explanation
Indices: 802803--802877 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
802793 ATGAGACCAT
* * * *
802803 CCGAACGAGCTATGCGAGGGCATCCGAGGGTAA
1 CCGAGCGAGCTATGCAAGGGAATCCGAGGGCAA
*
802836 CCGAGCGAGCTATGCAAGGGAATCCGAGGGCAG
1 CCGAGCGAGCTATGCAAGGGAATCCGAGGGCAA
802869 CCGAGCGAG
1 CCGAGCGAG
802878 GGTAGGTCGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.39, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCAAGGGAATCCGAGGGCAA
Found at i:802914 original size:29 final size:29
Alignment explanation
Indices: 802881--802965 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
802871 GAGCGAGGGT
802881 AGGTCGCCCGGAGTACATGGCGACCTACA
1 AGGTCGCCCGGAGTACATGGCGACCTACA
* *
802910 AGGTCGCCCGGAGTGCATAGCGACCTACA
1 AGGTCGCCCGGAGTACATGGCGACCTACA
*
802939 AGGTCGCCCGGAGGACATGGCGACCTA
1 AGGTCGCCCGGAGTACATGGCGACCTA
802966 TGTGTTGGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.24, C:0.31, G:0.33, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGTACATGGCGACCTACA
Found at i:803076 original size:29 final size:29
Alignment explanation
Indices: 803024--803079 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
803014 GAGCAAGGGT
*
803024 AGGTCGCCCGGAGTGCATGGCGACCTATA
1 AGGTCGCCCGGAGTGCATGACGACCTATA
*
803053 AGGTCGCCCGGAAG-GTATGACGACCTA
1 AGGTCGCCCGG-AGTGCATGACGACCTA
803080 CTGCCAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.23, C:0.27, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGACGACCTATA
Found at i:811234 original size:129 final size:128
Alignment explanation
Indices: 810984--811239 Score: 322
Period size: 129 Copynumber: 2.0 Consensus size: 128
810974 TGAAATGATA
* *
810984 TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCTTTCTATCCTTTGCTTTGCCTTTTCCCCTTCTTT
1 TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCTTTCCATCCTTTGCTTTGCCTTTTCCCCCTCTTT
* * * ** * * *
811049 TTTCTTTCCTTTTGTGTGGTGTTGCTATTTAGGCTATTCACGTGGGAGACAGGGTAAAAGGGT
66 TATCTTTCCTTTCGTGTGGTATTAATATTTAGGCGATTCACATGGGAGACAAGGTAAAAGGGT
* *
811112 TTGTTTGCC-TGTTTTGGTAAGTGGTTTGTTTCTTTCCATCCTTTGTTTTGCCTTTTTTCCCCCT
1 TTGTTT-CCTTGTTTT-GTAAGTGGGTTGTTTCTTTCCATCCTTTGCTTTGCC--TTTTCCCCCT
*
811176 C-TTTATCTTT-CTTTCGTGTGGTATTAATATTTAGGGGATTCACATGGGATG-CAAGGTAAAAG
62 CTTTTATCTTTCCTTTCGTGTGGTATTAATATTTAGGCGATTCACATGGGA-GACAAGGTAAAAG
811238 GG
126 GG
811240 GAACCTGATT
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 12 0.11
129 79 0.72
130 9 0.08
131 10 0.09
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (128 bp):
TTGTTTCCTTGTTTTGTAAGTGGGTTGTTTCTTTCCATCCTTTGCTTTGCCTTTTCCCCCTCTTT
TATCTTTCCTTTCGTGTGGTATTAATATTTAGGCGATTCACATGGGAGACAAGGTAAAAGGGT
Found at i:834002 original size:31 final size:31
Alignment explanation
Indices: 833967--834035 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
833957 AATATATGTT
*
833967 ATATCAACACTTAAACCTGAGTAGAGATATC
1 ATATCAACACTTAAACCCGAGTAGAGATATC
833998 ATATCAACACTTAAACCCGAGTAGAGATATC
1 ATATCAACACTTAAACCCGAGTAGAGATATC
834029 ATATCAA
1 ATATCAA
834036 TAGTAATCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (31 bp):
ATATCAACACTTAAACCCGAGTAGAGATATC
Found at i:844343 original size:20 final size:20
Alignment explanation
Indices: 844306--844344 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
844296 GAAGTGCATA
* * *
844306 TATTCAGAAGAAAGAAAAAC
1 TATTCAAAAAAAAAAAAAAC
844326 TATTCAAAAAAAAAAAAAA
1 TATTCAAAAAAAAAAAAAA
844345 AAACAGAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (20 bp):
TATTCAAAAAAAAAAAAAAC
Found at i:851586 original size:43 final size:40
Alignment explanation
Indices: 851496--851591 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
851486 AGTTTGTTTA
*
851496 TGTTCGTTTATTT-ATTAAATGAACGAACATGAACAAGAT
1 TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
*
851535 T-TTGCGTTCGTTTAATTAAATGAACGAACATGAACAAAGAGCT
1 TGTT-CGTTCATTTAATTAAATGAACGAACATGAAC-AAGA--T
851578 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
851592 CGTTCGTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 2 0.04
39 8 0.17
40 21 0.44
41 4 0.08
43 11 0.23
44 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (40 bp):
TGTTCGTTCATTTAATTAAATGAACGAACATGAACAAGAT
Found at i:863147 original size:128 final size:128
Alignment explanation
Indices: 862750--863633 Score: 1655
Period size: 128 Copynumber: 6.9 Consensus size: 128
862740 TAATCGGAGT
862750 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
862815 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
862878 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
862943 CATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
863005 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
863069 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
863133 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
863198 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
863261 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
863326 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
863389 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
863454 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
863517 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
863582 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
863634 AATCAGGTAA
Statistics
Matches: 734, Mismatches: 19, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
126 1 0.00
127 118 0.16
128 614 0.84
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:864095 original size:33 final size:34
Alignment explanation
Indices: 864034--864102 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 34
864024 AAATTTAATG
*
864034 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
864068 TTAAATTT-GAATAATATTATTTTTATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
864101 TT
1 TT
864103 TGAATAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:864125 original size:33 final size:33
Alignment explanation
Indices: 864027--864126 Score: 104
Period size: 28 Copynumber: 3.2 Consensus size: 33
864017 TAAGTTGAAA
* *
864027 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTTGAATAATATAATTTATAT
864061 TTTAAATTTAAA-TTTGAAT-A-AT-A-TTAT-T
1 TTT-AATTTAAATTTTGAATAATATAATTTATAT
* *
864089 TTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTAAATTTTGAATAATATAATTTATAT
864122 TTTAA
1 TTTAA
864127 AAACATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
27 7 0.13
28 11 0.20
29 5 0.09
30 3 0.06
31 3 0.06
32 3 0.06
33 11 0.20
34 8 0.15
35 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTAATTTAAATTTTGAATAATATAATTTATAT
Found at i:864733 original size:21 final size:21
Alignment explanation
Indices: 864645--864735 Score: 123
Period size: 21 Copynumber: 4.3 Consensus size: 21
864635 TATGGTATAA
*
864645 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
864666 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
864687 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
864708 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
864729 AACCCTG
1 AACCCTG
864736 AGGAGATGGC
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
20 3 0.05
21 60 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:864768 original size:21 final size:21
Alignment explanation
Indices: 864742--864789 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
864732 CCTGAGGAGA
*
864742 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
864763 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
864784 GGGCAT
1 TGGCAT
864790 GTACCCCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:866552 original size:34 final size:31
Alignment explanation
Indices: 866509--866597 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
866499 TTAATAATTC
* *
866509 TAAATAAATAATAATTATATAAATGTTATTTTAA
1 TAAAAAAATAATAATTATATAAA---TATATTAA
* *
866543 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
866574 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
866598 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 9 0.20
32 17 0.37
34 20 0.43
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:869288 original size:3 final size:3
Alignment explanation
Indices: 869274--869327 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
869264 TCTACAAAAA
869274 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
869320 TAT TAT TA
1 TAT TAT TA
869328 CATATTTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:880595 original size:31 final size:31
Alignment explanation
Indices: 880572--880774 Score: 352
Period size: 31 Copynumber: 6.5 Consensus size: 31
880562 CATAGATTCT
* *
880572 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
880603 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
880634 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* *
880665 GAAGAACATAGGTAAACATTCTATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
880696 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* *
880727 GAAGAATATAGGTAAATAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
880758 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
880775 CCTTGACCCT
Statistics
Matches: 162, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 162 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:886408 original size:33 final size:31
Alignment explanation
Indices: 886355--886419 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
886345 TTTTAACATT
*
886355 TTGATTATTTTGGAATGTTTGAATTTGTGGA
1 TTGATTATTTTGGAATGTTTGAATTTATGGA
*
886386 TTGATTGATTTT-GAATTTGTTTGGATTTATGGA
1 TTGATT-ATTTTGGAA--TGTTTGAATTTATGGA
886419 T
1 T
886420 GGTGAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.54
Consensus pattern (31 bp):
TTGATTATTTTGGAATGTTTGAATTTATGGA
Found at i:889075 original size:12 final size:12
Alignment explanation
Indices: 889058--889083 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
889048 AAAAGTAAAA
889058 AAATATATTTTT
1 AAATATATTTTT
889070 AAATATATTTTT
1 AAATATATTTTT
889082 AA
1 AA
889084 TTTAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:889096 original size:16 final size:17
Alignment explanation
Indices: 889067--889104 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
889057 AAAATATATT
889067 TTTAAATATATTTTTAA
1 TTTAAATATATTTTTAA
889084 TTTAAAT-TATTTTTAA
1 TTTAAATATATTTTTAA
*
889100 ATTAA
1 TTTAA
889105 CATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATATATTTTTAA
Found at i:891479 original size:110 final size:110
Alignment explanation
Indices: 891286--891491 Score: 306
Period size: 110 Copynumber: 1.9 Consensus size: 110
891276 GGAAGGTGCG
* * ** *
891286 CTTCATGATCCACGTTTTCTGTATATGTTAAAGGTTTAGTTAAGGTGTGAATGACGATTCATGTC
1 CTTCATGATCCACCTTTTCTGTATATGTTAAAGGTTCAGTTAAGGCATGAATGACGATCCATGTC
891351 TTTCCTTACGTGGCGTTAGCTCGAACAAAACTCTGCGAATGGGCA
66 TTTCCTTACGTGGCGTTAGCTCGAACAAAACTCTGCGAATGGGCA
*
891396 CTTCATGATCCACACTTTT-TGTATATGTTAAAGGTTCATTTAAGGCATGAATGACGATCCATGT
1 CTTCATGATCCAC-CTTTTCTGTATATGTTAAAGGTTCAGTTAAGGCATGAATGACGATCCATGT
* * * *
891460 CTTTTCTTATGTGGCGTTAGTTCGAATAAAAC
65 CTTTCCTTACGTGGCGTTAGCTCGAACAAAAC
891492 CCCGCGAAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 81 0.95
111 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (110 bp):
CTTCATGATCCACCTTTTCTGTATATGTTAAAGGTTCAGTTAAGGCATGAATGACGATCCATGTC
TTTCCTTACGTGGCGTTAGCTCGAACAAAACTCTGCGAATGGGCA
Found at i:891992 original size:29 final size:28
Alignment explanation
Indices: 891959--892037 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
891949 CGGTGACGGG
* *
891959 TATATTTATCGATCTAATACCGATCAGAC
1 TATATTT-TCGATCTAACACCGATAAGAC
*
891988 TATATTTTCTGATCTAACACCGGTAAGAC
1 TATATTTTC-GATCTAACACCGATAAGAC
*
892017 TATATTTCCCGATCTAACACC
1 TATATTT-TCGATCTAACACC
892038 CTTAGCAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 2 0.05
29 41 0.93
30 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (28 bp):
TATATTTTCGATCTAACACCGATAAGAC
Found at i:895956 original size:35 final size:34
Alignment explanation
Indices: 895871--895957 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
895861 AAACTAATTT
* *
895871 TAAATACAACAAACTTACAATAATTATTAAATGG
1 TAAATACAACAAAATTACAATAATTATTAAATGA
* *
895905 TAAATGATAACCAAATTACAATAATTAATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA-T--TATTAAATGA
895943 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
895958 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 2 0.05
37 3 0.07
38 10 0.23
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAATTATTAAATGA
Found at i:898293 original size:25 final size:25
Alignment explanation
Indices: 898239--898290 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
898229 TTATATATGC
*
898239 AAAA-AAATTAAATAAGTAAAATATT
1 AAAATAAATTAAAT-AGCAAAATATT
898264 -AAATAAATTAAATA-CAAAATATT
1 AAAATAAATTAAATAGCAAAATATT
898287 AAAA
1 AAAA
898291 ATATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 8 0.33
24 7 0.29
25 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAAATTAAATAGCAAAATATT
Found at i:898336 original size:10 final size:10
Alignment explanation
Indices: 898323--898362 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
898313 AGAGATTATA
*
898323 AGAGTATTTG
1 AGAGAATTTG
*
898333 AGAGAAGTTG
1 AGAGAATTTG
898343 AGAGAATTTG
1 AGAGAATTTG
898353 AGAGAATTTG
1 AGAGAATTTG
898363 GTGTGATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.30
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:907004 original size:51 final size:50
Alignment explanation
Indices: 906944--907044 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 50
906934 TCGAATAATC
906944 TTAAAAATTTAATTTTAATCTTGAATAGTCTATCTATTTTTTTTATTTAAA
1 TTAAAAATTTAATTTTAATCTTGAATAGTCTATCTA-TTTTTTTATTTAAA
*
906995 TTAAAAATTTAATTTTAATCTTTAATAGTCTATCTATTTTTTTATTTAAA
1 TTAAAAATTTAATTTTAATCTTGAATAGTCTATCTATTTTTTTATTTAAA
907045 AGAAACTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 14 0.29
51 35 0.71
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (50 bp):
TTAAAAATTTAATTTTAATCTTGAATAGTCTATCTATTTTTTTATTTAAA
Found at i:914304 original size:130 final size:130
Alignment explanation
Indices: 914093--914333 Score: 403
Period size: 130 Copynumber: 1.9 Consensus size: 130
914083 TTCAAAGATC
* *
914093 ATGAATTAAATTAATAAATATCCCTTTTATTAACGTGTTATGATATCGAACTAATGAGAGTTAAT
1 ATGAATTAAATTAATAAATATCACTTTTATTAACGTGTCATGATATCGAACTAATGAGAGTTAAT
*
914158 AGTTCAATGATTAAAATATAAAAAATCAATAATATAAGTGATTAAAATGTTATTTTTTTAAATTA
66 AGTTCAATGATTAAAATATAAAAAATCAATAATATAAGTAATTAAAATGTTATTTTTTTAAATTA
* *
914223 ATGAATTAAATTAATAAATATCATTTTTATTAACGTGTCATG-TCCTCGAACTAATGAGAGTTAA
1 ATGAATTAAATTAATAAATATCACTTTTATTAACGTGTCATGAT-ATCGAACTAATGAGAGTTAA
* *
914287 TAGTTTAATGATTAAAATATAATAAATCAATAATATAAGTAATTAAA
65 TAGTTCAATGATTAAAATATAAAAAATCAATAATATAAGTAATTAAA
914334 TATTAGTTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
129 1 0.01
130 102 0.99
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (130 bp):
ATGAATTAAATTAATAAATATCACTTTTATTAACGTGTCATGATATCGAACTAATGAGAGTTAAT
AGTTCAATGATTAAAATATAAAAAATCAATAATATAAGTAATTAAAATGTTATTTTTTTAAATTA
Found at i:914649 original size:2 final size:2
Alignment explanation
Indices: 914642--914697 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
914632 ATCGTACTGA
*
914642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT -T GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
914684 AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT
914698 TGTAAAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
1 3 0.06
2 44 0.90
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:914707 original size:15 final size:17
Alignment explanation
Indices: 914645--914701 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
914635 GTACTGAATA
*
914645 TATATATATATATATATATA
1 TATATA-AT-TATATAT-TG
*
914665 TATATATATGATATATTG
1 TATATA-ATTATATATTG
914683 TATATAATTATATATTG
1 TATATAATTATATATTG
914700 TA
1 TA
914702 AAATTAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 12 0.35
18 7 0.21
19 6 0.18
20 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TATATAATTATATATTG
Found at i:915336 original size:20 final size:20
Alignment explanation
Indices: 915301--915338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
915291 TCACACCAAA
* *
915301 TTCTCTCAATTTCTCTTAAC
1 TTCTCTCAAATACTCTTAAC
915321 TTCTCTCAAATACTCTTA
1 TTCTCTCAAATACTCTTA
915339 TAATATCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (20 bp):
TTCTCTCAAATACTCTTAAC
Found at i:915395 original size:9 final size:9
Alignment explanation
Indices: 915383--915408 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
915373 TAATATTTTG
915383 TATTTAATT
1 TATTTAATT
915392 TATTTAATT
1 TATTTAATT
915401 TATTTAAT
1 TATTTAAT
915409 ATTTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:915411 original size:25 final size:25
Alignment explanation
Indices: 915383--915431 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
915373 TAATATTTTG
* *
915383 TATTTAATTTATTTAATTTATTTAA
1 TATTTAACTTAATTAATTTATTTAA
* *
915408 TATTTTACTTAATTAATTTTTTTA
1 TATTTAACTTAATTAATTTATTTA
915432 CAGATATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTAACTTAATTAATTTATTTAA
Found at i:917693 original size:13 final size:12
Alignment explanation
Indices: 917648--917689 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
917638 TATTTAGTAC
917648 TTTTTATTGTAGT
1 TTTTTATTGTA-T
* *
917661 TGTTTATTGGAT
1 TTTTTATTGTAT
917673 TTTTTATTGTAT
1 TTTTTATTGTAT
917685 TTTTT
1 TTTTT
917690 TATTTATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (12 bp):
TTTTTATTGTAT
Found at i:917783 original size:34 final size:34
Alignment explanation
Indices: 917728--917798 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
917718 CGTTAATATG
917728 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGATTAAATTT
*
917761 GTTGGACTTT-TTGTTAATTTATTTTGATTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGATTAAATTT
917796 GTT
1 GTT
917799 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.21, C:0.01, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGATTAAATTT
Found at i:921161 original size:16 final size:16
Alignment explanation
Indices: 921136--921166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
921126 TATTTTTTCA
*
921136 AATAATTATAATAAAC
1 AATAAGTATAATAAAC
921152 AATAAGTATAATAAA
1 AATAAGTATAATAAA
921167 AAAATGTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAGTATAATAAAC
Found at i:921877 original size:18 final size:19
Alignment explanation
Indices: 921842--921878 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
921832 CACGGAATGT
921842 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
921862 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
921879 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:925692 original size:2 final size:2
Alignment explanation
Indices: 925685--925713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
925675 TTTACATTCT
925685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
925714 TAATGACCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:941484 original size:17 final size:19
Alignment explanation
Indices: 941454--941493 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
941444 TTTGAAAAAC
*
941454 TTATAATATTTATTT-AAT
1 TTATAATATCTATTTCAAT
941472 TTAT-ATATCTATTTCAAT
1 TTATAATATCTATTTCAAT
941490 TTAT
1 TTAT
941494 CAAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATAATATCTATTTCAAT
Found at i:944159 original size:66 final size:66
Alignment explanation
Indices: 944015--944138 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
944005 TTTAGATTGC
* *
944015 TTCTCATAAATTATGAAAGGATTGATAGGAGCATTCACGCCTTTAGATTTCTTAGCTTTGTCACG
1 TTCTCATAAATTATGAATGGATTGATAGGAGCATTCACGCCTTTAGAGTTCTTAGCTTTGTCACG
944080 A
66 A
* * * *
944081 TTCTCATAAATTATGAATGGATTGATAGGGGCATTCACTCC-TTCGAGTTCTTTGCTTT
1 TTCTCATAAATTATGAATGGATTGATAGGAGCATTCACGCCTTTAGAGTTCTTAGCTTT
944139 TGTCGATGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
65 14 0.27
66 38 0.73
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (66 bp):
TTCTCATAAATTATGAATGGATTGATAGGAGCATTCACGCCTTTAGAGTTCTTAGCTTTGTCACG
A
Found at i:944457 original size:66 final size:66
Alignment explanation
Indices: 944367--944505 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 66
944357 GGGGTTAATG
* * * *
944367 GGAGCATTCACGCCTTTGGGTTCTTTATTTT-TATCGGTGCTT-TCATAAATTATAAATGGATTG
1 GGAGCATTCACCCCTTTGGATTCTTCATTTTCT-TCGGCG-TTCTCATAAATTATAAATGGATTG
944430 ACA
64 ACA
*
944433 GGAGCATTCACCCCTCTT-GATTCTTCATTTTCTTCGGCGTTCTCATAGATTATAAATGGATTGA
1 GGAGCATTCACCCCT-TTGGATTCTTCATTTTCTTCGGCGTTCTCATAAATTATAAATGGATTGA
*
944497 TA
65 CA
*
944499 GGCGCAT
1 GGAGCAT
944506 CATTATCTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.03
66 58 0.92
67 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (66 bp):
GGAGCATTCACCCCTTTGGATTCTTCATTTTCTTCGGCGTTCTCATAAATTATAAATGGATTGAC
A
Found at i:945923 original size:14 final size:14
Alignment explanation
Indices: 945904--945932 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
945894 TTTTATTAGC
945904 GAAACCAACGTACG
1 GAAACCAACGTACG
945918 GAAACCAACGTACG
1 GAAACCAACGTACG
945932 G
1 G
945933 CTACCTGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.28, G:0.24, T:0.07
Consensus pattern (14 bp):
GAAACCAACGTACG
Found at i:949581 original size:7 final size:7
Alignment explanation
Indices: 949569--949595 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
949559 ACTTTACTTT
949569 AATTTTA
1 AATTTTA
949576 AATTTTA
1 AATTTTA
949583 AATTTTA
1 AATTTTA
949590 AATTTT
1 AATTTT
949596 TTATTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:954987 original size:13 final size:13
Alignment explanation
Indices: 954969--955000 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
954959 GTTCCATTCT
954969 AAGCATTGAATAA
1 AAGCATTGAATAA
954982 AAGCATTGAATAA
1 AAGCATTGAATAA
954995 AAGCAT
1 AAGCAT
955001 AAAGTTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (13 bp):
AAGCATTGAATAA
Found at i:963619 original size:37 final size:37
Alignment explanation
Indices: 963546--963620 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
963536 AGTTGAAAAT
*
963546 ATTTATATATTTTCTTTAAAGAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAGAAATTAAAATCATAAA
* *
963583 ATTTATATAATTTTTTTTACA-AAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAGAAATT-AAAATCATAAA
963620 A
1 A
963621 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAGAAATTAAAATCATAAA
Found at i:964106 original size:12 final size:12
Alignment explanation
Indices: 964066--964111 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
964056 TTTTCTTTTC
964066 TTTTATTTTTAAG
1 TTTTA-TTTTAAG
*
964079 TTTTCATTTTTA-
1 TTTT-ATTTTAAG
964091 TTTTATTTTAAG
1 TTTTATTTTAAG
964103 TTTTATTTT
1 TTTTATTTT
964112 TAAACATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 13 0.45
13 9 0.31
14 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:964112 original size:24 final size:25
Alignment explanation
Indices: 964061--964113 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
964051 CTCTTTTTTC
*
964061 TTTTCTTTTATTTTTAAGTTTTCAT
1 TTTTATTTTATTTTTAAGTTTTCAT
964086 TTTTATTTTA-TTTTAAGTTTT-AT
1 TTTTATTTTATTTTTAAGTTTTCAT
964109 TTTTA
1 TTTTA
964114 AACATGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.26
24 11 0.41
25 9 0.33
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTATTTTATTTTTAAGTTTTCAT
Found at i:980654 original size:6 final size:6
Alignment explanation
Indices: 980643--980673 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
980633 TTAATAATTC
980643 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A
980674 CCCTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:981225 original size:32 final size:33
Alignment explanation
Indices: 981181--981251 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
981171 TTGGTATTCA
981181 GGTCGG-ATTTTTTAAAAAAAAAATCGGGATCG
1 GGTCGGAATTTTTTAAAAAAAAAATCGGGATCG
*** *
981213 GGTCGGAATTTTTTTTTAAAAAAATCGGGTTCG
1 GGTCGGAATTTTTTAAAAAAAAAATCGGGATCG
981246 GGTCGG
1 GGTCGG
981252 GTCGGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTCGGAATTTTTTAAAAAAAAAATCGGGATCG
Found at i:981896 original size:18 final size:17
Alignment explanation
Indices: 981860--981905 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
981850 TCAGATTCAG
* *
981860 ATTCTAATTCCTGACAT
1 ATTCCAATTCCTCACAT
981877 ATTCCAATTCCTTCACAT
1 ATTCCAATTCC-TCACAT
981895 ATTCCAATTCC
1 ATTCCAATTCC
981906 ATCAGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTCCAATTCCTCACAT
Found at i:984240 original size:23 final size:23
Alignment explanation
Indices: 984210--984343 Score: 142
Period size: 23 Copynumber: 5.8 Consensus size: 23
984200 TGCCATATAA
* *
984210 AATTGTCTCGAAGGACCTCGTAG
1 AATTGTCCCGAAGGACCACGTAG
* ** *
984233 AATTGTCTCGAAGGACCTTGTAA
1 AATTGTCCCGAAGGACCACGTAG
* *
984256 AATTTTCCTGAAGGACCACGTAG
1 AATTGTCCCGAAGGACCACGTAG
* * *
984279 AAATATCCCGAAGGACCACGTAT
1 AATTGTCCCGAAGGACCACGTAG
* *
984302 AAATGTCCCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACGTAG
*
984325 AATTGTCCCTAAGGACCAC
1 AATTGTCCCGAAGGACCAC
984344 ATATACATTC
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 94 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACGTAG
Found at i:984381 original size:42 final size:42
Alignment explanation
Indices: 984328--984432 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
984318 CACATAGAAT
*
984328 TGTCCCTAAGGACCACATATACATTCCAAAGAACCAAATATA
1 TGTCCCGAAGGACCACATATACATTCCAAAGAACCAAATATA
* * * * *
984370 TGTCCCGAAGGACCGCATATATATTCCAAAGGATCACATATA
1 TGTCCCGAAGGACCACATATACATTCCAAAGAACCAAATATA
*
984412 TGTCCCGAAGGACCACGTATA
1 TGTCCCGAAGGACCACATATA
984433 ACCCTCGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (42 bp):
TGTCCCGAAGGACCACATATACATTCCAAAGAACCAAATATA
Found at i:984389 original size:21 final size:21
Alignment explanation
Indices: 984284--984432 Score: 127
Period size: 21 Copynumber: 6.9 Consensus size: 21
984274 CGTAGAAATA
*
984284 TCCCGAAGGACCACGTATAAATG
1 TCCCGAAGGACCAC--ATATATG
*
984307 TCCCGAAGGACCACATAGAATTG
1 TCCCGAAGGACCACATA-TA-TG
* **
984330 TCCCTAAGGACCACATATACA
1 TCCCGAAGGACCACATATATG
* * * *
984351 TTCCAAAGAACCAAATATATG
1 TCCCGAAGGACCACATATATG
* *
984372 TCCCGAAGGACCGCATATATA
1 TCCCGAAGGACCACATATATG
* * *
984393 TTCCAAAGGATCACATATATG
1 TCCCGAAGGACCACATATATG
*
984414 TCCCGAAGGACCACGTATA
1 TCCCGAAGGACCACATATA
984433 ACCCTCGATT
Statistics
Matches: 99, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
21 64 0.65
22 3 0.03
23 32 0.32
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:984391 original size:23 final size:23
Alignment explanation
Indices: 984265--984432 Score: 129
Period size: 23 Copynumber: 7.7 Consensus size: 23
984255 AAATTTTCCT
* * * *
984265 GAAGGACCACGTAGAAATATCCC
1 GAAGGACCACATATATATGTCCC
* *
984288 GAAGGACCACGTATAAATGTCCC
1 GAAGGACCACATATATATGTCCC
*
984311 GAAGGACCACATAGA-ATTGTCCC
1 GAAGGACCACATATATA-TGTCCC
* *
984334 TAAGGACCACATATACAT-T-CC
1 GAAGGACCACATATATATGTCCC
* *
984355 AAAGAACCA-A-ATATATGTCCC
1 GAAGGACCACATATATATGTCCC
*
984376 GAAGGACCGCATATATAT-T-CC
1 GAAGGACCACATATATATGTCCC
* *
984397 AAAGGATCAC--ATATATGTCCC
1 GAAGGACCACATATATATGTCCC
*
984418 GAAGGACCACGTATA
1 GAAGGACCACATATA
984433 ACCCTCGATT
Statistics
Matches: 118, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
19 11 0.09
20 3 0.03
21 36 0.31
22 4 0.03
23 63 0.53
24 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (23 bp):
GAAGGACCACATATATATGTCCC
Found at i:985317 original size:35 final size:35
Alignment explanation
Indices: 985270--985339 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
985260 CATTGTAAAA
* *
985270 ATGGTACCGATACTTCCACATT-GGTATCGATACCC
1 ATGGTACCGATACTACCAC-TTCGGTATAGATACCC
*
985305 ATGGTACTGATACTACCACTTCGGTATAGATACCC
1 ATGGTACCGATACTACCACTTCGGTATAGATACCC
985340 CATGAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (35 bp):
ATGGTACCGATACTACCACTTCGGTATAGATACCC
Found at i:985569 original size:20 final size:20
Alignment explanation
Indices: 985544--985590 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
985534 TTTTATTCCA
*
985544 TTAAACTCAACTATACTCAC
1 TTAAACCCAACTATACTCAC
985564 TTAAACCCAACTATACTCAC
1 TTAAACCCAACTATACTCAC
985584 TTAAACC
1 TTAAACC
985591 ATCTTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAACCCAACTATACTCAC
Found at i:986642 original size:14 final size:14
Alignment explanation
Indices: 986623--986657 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
986613 GACATGTCTG
*
986623 CCCGACCCGTATGA
1 CCCGACCCATATGA
986637 CCCGACCCATATGA
1 CCCGACCCATATGA
*
986651 CCTGACC
1 CCCGACC
986658 AGAACAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.46, G:0.17, T:0.14
Consensus pattern (14 bp):
CCCGACCCATATGA
Found at i:988378 original size:20 final size:22
Alignment explanation
Indices: 988333--988394 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
988323 TGCATGATAG
988333 TGCATCGATGCACCTGTTAAAGAA
1 TGCATCGATGCA-CTGTT-AAGAA
988357 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
988377 TGCACCGATGCACT-TTAA
1 TGCATCGATGCACTGTTAA
988395 TGGGAAATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 18 0.51
21 1 0.03
22 1 0.03
23 3 0.09
24 12 0.34
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:991098 original size:2 final size:2
Alignment explanation
Indices: 991091--991136 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
991081 AGTAAGAAAG
991091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
991133 AT AT
1 AT AT
991137 TGAGTATAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:992163 original size:20 final size:22
Alignment explanation
Indices: 992118--992175 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
992108 TGCATGGTAG
992118 TGCATCGATGCACCTATTAAAGAA
1 TGCATCGATGCA-CTATT-AAGAA
992142 TGCATCGATGCACTA-T-AGAA
1 TGCATCGATGCACTATTAAGAA
* *
992162 TGCACCAATGCACT
1 TGCATCGATGCACT
992176 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTATTAAGAA
Found at i:994809 original size:18 final size:17
Alignment explanation
Indices: 994786--994819 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
994776 CAGTCTGTTT
994786 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
994804 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
994820 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:995697 original size:17 final size:18
Alignment explanation
Indices: 995675--995709 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
995665 GAGGGTCTAC
995675 GTGGT-CTTCGGGACATA
1 GTGGTCCTTCGGGACATA
995692 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
995710 TATGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:997506 original size:19 final size:19
Alignment explanation
Indices: 997457--997511 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
997447 GAAATACAGG
*
997457 TTGACCTCTGATTTCTGTT
1 TTGAACTCTGATTTCTGTT
* * *
997476 CTGAACTTTGATATCTGTT
1 TTGAACTCTGATTTCTGTT
*
997495 TTGATCTCTGATTTCTG
1 TTGAACTCTGATTTCTG
997512 ATATGATTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGAACTCTGATTTCTGTT
Found at i:997518 original size:19 final size:19
Alignment explanation
Indices: 997462--997518 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
997452 ACAGGTTGAC
* *
997462 CTCTGATTTCTGTTCTGAA
1 CTCTGATTTCTGTTATGAT
* * *
997481 CTTTGATATCTGTTTTGAT
1 CTCTGATTTCTGTTATGAT
*
997500 CTCTGATTTCTGATATGAT
1 CTCTGATTTCTGTTATGAT
997519 TATGATCTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.51
Consensus pattern (19 bp):
CTCTGATTTCTGTTATGAT
Found at i:1002149 original size:20 final size:21
Alignment explanation
Indices: 1002124--1002175 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1002114 TTTTCCCAAT
*
1002124 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1002144 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1002165 TCGCAATGCGA
1 TCGCAATGCGA
1002176 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1002189 original size:20 final size:20
Alignment explanation
Indices: 1002164--1002257 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
1002154 AATTGGGAAA
*
1002164 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
1002184 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
* *
1002205 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTTACT
* * *
1002225 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTTACT
*
1002245 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1002258 TTACATAATC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1002258 original size:20 final size:20
Alignment explanation
Indices: 1002206--1002258 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1002196 TAATACAAAA
* *
1002206 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1002226 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1002246 TCGCAACGCGATT
1 TCGCAACGCGATT
1002259 TACATAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1002474 original size:22 final size:22
Alignment explanation
Indices: 1002446--1002489 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1002436 CACTCTCTCA
1002446 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1002468 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1002490 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1002807 original size:20 final size:20
Alignment explanation
Indices: 1002753--1002811 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1002743 GCGATTCTCT
**
1002753 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1002773 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1002793 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1002812 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1003002 original size:25 final size:24
Alignment explanation
Indices: 1002948--1003002 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1002938 TGTTTATTAT
* *
1002948 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1002972 TAGTTTTTGGTATAT-TTAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1002998 TGTTT
1 TGTTT
1003003 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1004149 original size:18 final size:18
Alignment explanation
Indices: 1004128--1004172 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1004118 TCCAATTCGG
*
1004128 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1004146 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1004164 GAGCCATCA
1 GAGCCATCA
1004173 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1004679 original size:20 final size:20
Alignment explanation
Indices: 1004654--1004726 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1004644 TAGTTTACTT
* *
1004654 TCGCAACACGAAAATGACTA
1 TCGCAATACGAAAATGGCTA
* *
1004674 TCGCAATGCGGAAATGGCTA
1 TCGCAATACGAAAATGGCTA
* *
1004694 TCGCAATGCGGAAATGGCTA
1 TCGCAATACGAAAATGGCTA
1004714 TCGCAATACGAAA
1 TCGCAATACGAAA
1004727 TGAAAATCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAATACGAAAATGGCTA
Found at i:1004748 original size:14 final size:14
Alignment explanation
Indices: 1004729--1004786 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1004719 ATACGAAATG
*
1004729 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
1004743 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1004759 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1004775 AAAATCGCAACG
1 AAAATCGCAACG
1004787 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1004772 original size:32 final size:33
Alignment explanation
Indices: 1004713--1004791 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1004703 GGAAATGGCT
*
1004713 ATCGCAATACGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
1004746 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
1004778 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1004792 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:1004841 original size:14 final size:14
Alignment explanation
Indices: 1004822--1004877 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
1004812 TCATTTCGCA
1004822 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
1004836 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
1004852 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
1004868 TTGCGATTTT
1 TTGCGATTTT
1004878 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:1004884 original size:33 final size:33
Alignment explanation
Indices: 1004803--1004888 Score: 165
Period size: 32 Copynumber: 2.6 Consensus size: 33
1004793 ACAAATCGCA
1004803 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1004836 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1004868 TTGCGATTTTCATTTCGCATT
1 TTGCGATTTTCATTTCGCATT
1004889 TTGATAGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 32 0.62
33 20 0.38
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1004920 original size:20 final size:20
Alignment explanation
Indices: 1004891--1004933 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1004881 TTCGCATTTT
1004891 GATAGCCA-TTTCTGCGTTGC
1 GATAGCCATTTTC-GCGTTGC
*
1004911 GATAGTCATTTTCGCGTTGC
1 GATAGCCATTTTCGCGTTGC
1004931 GAT
1 GAT
1004934 TTTAAGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
GATAGCCATTTTCGCGTTGC
Found at i:1006970 original size:19 final size:19
Alignment explanation
Indices: 1006948--1007031 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
1006938 GCAACGAGAG
1006948 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1006967 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1006986 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1007005 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
1007019 AATCGCAATGCGA
1 AATCGCAATGCGA
1007032 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
19 46 0.74
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1006990 original size:38 final size:33
Alignment explanation
Indices: 1006938--1007031 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 33
1006928 ACTGACTAAT
*
1006938 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAACGAGAAAATCGCAATGCGAAATGAAAATC
1006971 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATC
1 GCAA--CG--A-GAAAATCGCAATGCGAAATGAAAATC
1007009 GCAACGAGAAAATCGCAATGCGA
1 GCAACGAGAAAATCGCAATGCGA
1007032 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
33 20 0.36
34 1 0.02
35 2 0.04
36 2 0.04
37 1 0.02
38 29 0.53
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
GCAACGAGAAAATCGCAATGCGAAATGAAAATC
Found at i:1007081 original size:19 final size:20
Alignment explanation
Indices: 1007057--1007106 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1007047 GCGATTTTGT
1007057 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
1007076 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1007096 CGTTGCGATAG
1 CGTTGCGATAG
1007107 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1007341 original size:20 final size:20
Alignment explanation
Indices: 1007316--1007366 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1007306 AAATGATTGC
1007316 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1007336 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
*
1007356 CTTTCGTAACG
1 CTTTCGCAACG
1007367 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:1007557 original size:20 final size:20
Alignment explanation
Indices: 1007520--1007557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1007510 CTCTCTCTGG
*
1007520 CGACATCCGTTCCTATCCAA
1 CGACATCCGTTCCCATCCAA
1007540 CGACATCC-TTCCCCATCC
1 CGACATCCGTT-CCCATCC
1007558 GGCAACAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.21, C:0.47, G:0.08, T:0.24
Consensus pattern (20 bp):
CGACATCCGTTCCCATCCAA
Found at i:1010809 original size:33 final size:33
Alignment explanation
Indices: 1010767--1010889 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 33
1010757 AATTACTATC
1010767 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
** *
1010800 GCAATGCG-AATGAAAATCGCAACGCTA-ATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
* * *
1010831 CGTAATGCGAAATGAAAATCGCAACGAGGGAATC
1 -GCAATGCGAAATGAAAATCGCAACGAGAGAATT
1010865 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
1010890 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.04
32 24 0.31
33 48 0.62
34 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATT
Found at i:1010873 original size:65 final size:66
Alignment explanation
Indices: 1010769--1010896 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 66
1010759 TTACTATCGC
* *
1010769 AATGCGAAATGAAAATCGCAACGAGAGAATTGCAATGCG-AATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
1010833 T
66 T
*
1010834 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1010897 AATTTCGCGT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 37 0.63
66 22 0.37
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:1010911 original size:19 final size:19
Alignment explanation
Indices: 1010889--1010963 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
1010879 AAATCGCAAC
*
1010889 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1010908 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
1010922 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1010941 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
1010960 GCGA
1 GCGA
1010964 TTCTCTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 9 0.19
16 3 0.06
17 2 0.04
18 1 0.02
19 32 0.68
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:1010960 original size:52 final size:53
Alignment explanation
Indices: 1010889--1010998 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 53
1010879 AAATCGCAAC
* * *
1010889 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTTGCGA-TTTTCATTTCGCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCATTGCGATTTTTCATTTCGCATT
*
1010941 GCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATTTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCATTGCGATTTTTCATTTCGCATT
1010994 GCGAT
1 GCGAT
1010999 AGTACTATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 34 0.64
53 19 0.36
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (53 bp):
GCGATTTTAATTTCGCGTTGCGATTCTCTCATTGCGATTTTTCATTTCGCATT
Found at i:1010964 original size:19 final size:19
Alignment explanation
Indices: 1010918--1010965 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1010908 GCGATTCTCT
1010918 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1010937 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1010956 CGTTGCGATT
1 CGTTGCGATT
1010966 CTCTCATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1012231 original size:13 final size:13
Alignment explanation
Indices: 1012213--1012241 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1012203 CCGGCACGTC
1012213 AGAGGGTTTCTCA
1 AGAGGGTTTCTCA
1012226 AGAGGGTTTCTCA
1 AGAGGGTTTCTCA
1012239 AGA
1 AGA
1012242 ATCTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (13 bp):
AGAGGGTTTCTCA
Found at i:1012329 original size:42 final size:41
Alignment explanation
Indices: 1012270--1012473 Score: 146
Period size: 42 Copynumber: 4.9 Consensus size: 41
1012260 GTGAATCGGG
* *
1012270 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1012312 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
1012354 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* *
1012396 CTCTTGAACGGT-GGAGGGGACTC-TCGAGGAATGATAG-GGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
1012436 CTCTTCAACGATAGGAGTGGACTTTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1012474 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 28, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
40 17 0.14
41 34 0.27
42 67 0.54
43 7 0.06
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1012336 original size:21 final size:21
Alignment explanation
Indices: 1012270--1012336 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1012260 GTGAATCGGG
*
1012270 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1012290 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1012312 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1012333 CTCT
1 CTCT
1012337 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1012464 original size:82 final size:84
Alignment explanation
Indices: 1012300--1012473 Score: 316
Period size: 82 Copynumber: 2.1 Consensus size: 84
1012290 CCTCTTCAAC
*
1012300 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1012365 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1012384 GATGACAGTGGCCTCTTGAACGGT-GGAGGGGACTCTCGAGGAATGATA-GGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
*
1012447 TAGGAGTGGACTTTTGAGG
66 TAGGAGTGGACTCTTGAGG
1012466 GATGACAG
1 GATGACAG
1012474 GCGAGTCGGG
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
82 40 0.45
83 24 0.27
84 24 0.27
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1013027 original size:63 final size:63
Alignment explanation
Indices: 1012950--1013080 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
1012940 TAAAGTAGAC
1012950 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
1013013 ACCTCCACATGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1013076 ACCTC
1 ACCTC
1013081 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:1014558 original size:39 final size:38
Alignment explanation
Indices: 1014515--1014626 Score: 135
Period size: 33 Copynumber: 3.1 Consensus size: 38
1014505 TCTTTTGGTT
*
1014515 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGC
*
1014554 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
* * *
1014590 G--A-GAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
1014625 GA
1 GA
1014627 TTTTTGGTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
33 29 0.43
34 1 0.01
35 2 0.03
36 2 0.03
38 13 0.19
39 20 0.30
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:1014565 original size:19 final size:19
Alignment explanation
Indices: 1014515--1014626 Score: 144
Period size: 19 Copynumber: 6.1 Consensus size: 19
1014505 TCTTTTGGTT
*
1014515 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1014534 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1014554 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1014573 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1014590 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1014606 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1014625 GA
1 GA
1014627 TTTTTGGTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 48 0.59
20 17 0.21
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1014645 original size:20 final size:20
Alignment explanation
Indices: 1014622--1014667 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1014612 AAAATCGCAA
*
1014622 TGCGATTTTTGGTTTCGCGT
1 TGCGATTTTTGATTTCGCGT
*
1014642 TGCG-TTTTTTATTTCGCGT
1 TGCGATTTTTGATTTCGCGT
1014661 TGCGATT
1 TGCGATT
1014668 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (20 bp):
TGCGATTTTTGATTTCGCGT
Found at i:1015246 original size:20 final size:20
Alignment explanation
Indices: 1015221--1015273 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1015211 GCGCTATGTA
1015221 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
1015241 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
* *
1015261 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1015274 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1015307 original size:20 final size:20
Alignment explanation
Indices: 1015282--1015335 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1015272 GATTTTGTAT
1015282 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1015302 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1015322 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1015336 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1015324 original size:61 final size:61
Alignment explanation
Indices: 1015222--1015338 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1015212 CGCTATGTAA
* * * * * *
1015222 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1015283 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1015339 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1015354 original size:61 final size:61
Alignment explanation
Indices: 1015222--1015356 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
1015212 CGCTATGTAA
* * * * * * ** *
1015222 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1015283 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1015345 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1015357 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1015446 original size:21 final size:21
Alignment explanation
Indices: 1015406--1015446 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1015396 ACTGTAGATC
**
1015406 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1015427 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1015447 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1017903 original size:24 final size:24
Alignment explanation
Indices: 1017869--1017942 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
1017859 AAACAGAGAT
* *
1017869 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1017893 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1017917 GTCAGAAATCAGAATAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
1017941 AT
1 AT
1017943 GTATCAGAAC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1026311 original size:19 final size:20
Alignment explanation
Indices: 1026271--1026317 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1026261 ATTGAAGTTC
*
1026271 TACTTTTCTTTCCATCTTTT
1 TACTTTTCTTTCCATCTATT
1026291 TACTTTTCTTT-CATCTATT
1 TACTTTTCTTTCCATCTATT
1026310 TACTTTTC
1 TACTTTTC
1026318 ACAATGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (20 bp):
TACTTTTCTTTCCATCTATT
Found at i:1026946 original size:21 final size:21
Alignment explanation
Indices: 1026900--1026942 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1026890 TCTCTTTCAA
1026900 TTATTTATTTTTATTTCTTTG
1 TTATTTATTTTTATTTCTTTG
1026921 TTATTT-TTATTTATTT-TTTG
1 TTATTTATT-TTTATTTCTTTG
1026941 TT
1 TT
1026943 TATTCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (21 bp):
TTATTTATTTTTATTTCTTTG
Found at i:1032581 original size:2 final size:2
Alignment explanation
Indices: 1032574--1032615 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1032564 AATCATATGA
1032574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1032616 CTAATTCATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1033599 original size:20 final size:20
Alignment explanation
Indices: 1033576--1033613 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1033566 GAGGGATTAT
*
1033576 CAGTGGTCGTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
1033596 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
1033614 TAGTGGTTCT
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:0.21, C:0.24, G:0.34, T:0.21
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:1033620 original size:18 final size:18
Alignment explanation
Indices: 1033577--1033649 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
1033567 AGGGATTATC
* *
1033577 AGTGGTCGTTCGGGACAAAC
1 AGTGGTCCTTCGGGAC--AT
1033597 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1033615 AGTGGTTCTTCGGAACAT
1 AGTGGTCCTTCGGGACAT
* *
1033633 AGTAGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
1033650 AATATTCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
18 30 0.67
20 15 0.33
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1033923 original size:4 final size:4
Alignment explanation
Indices: 1033914--1033945 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1033904 ATGATAATGA
1033914 TATG TATG TATG TATG TATG TATG TAGTG TAT
1 TATG TATG TATG TATG TATG TATG TA-TG TAT
1033946 TTGTTACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1034805 original size:23 final size:23
Alignment explanation
Indices: 1034779--1034880 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
1034769 ATAAATGAAT
*
1034779 CGAAGTGCCACGTAGAATTTCAC
1 CGAAGTGCCACGTAGAATTGCAC
* *
1034802 CGAAGTGTCACGTAGAATTACAC
1 CGAAGTGCCACGTAGAATTGCAC
***
1034825 CGAAGTGCCGTATAGAATTGCAC
1 CGAAGTGCCACGTAGAATTGCAC
* **
1034848 CGAAGTGTCGTGTAGAATTGCAC
1 CGAAGTGCCACGTAGAATTGCAC
1034871 C-ATAGTGCCA
1 CGA-AGTGCCA
1034881 TATAAAATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
22 1 0.01
23 66 0.99
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
CGAAGTGCCACGTAGAATTGCAC
Found at i:1034832 original size:46 final size:46
Alignment explanation
Indices: 1034779--1034889 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
1034769 ATAAATGAAT
* *
1034779 CGAAGTGCCACGTAGAATTTCACCGAAGTGTCACGTAGAATTACAC
1 CGAAGTGCCACATAGAATTGCACCGAAGTGTCACGTAGAATTACAC
** ** *
1034825 CGAAGTGCCGTATAGAATTGCACCGAAGTGTCGTGTAGAATTGCAC
1 CGAAGTGCCACATAGAATTGCACCGAAGTGTCACGTAGAATTACAC
* *
1034871 C-ATAGTGCCATATAAAATT
1 CGA-AGTGCCACATAGAATT
1034890 TGTCCATAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 1 0.02
46 54 0.98
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (46 bp):
CGAAGTGCCACATAGAATTGCACCGAAGTGTCACGTAGAATTACAC
Found at i:1039134 original size:16 final size:19
Alignment explanation
Indices: 1039120--1039157 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1039110 TGATTATTTG
1039120 ATTA-TTATTTTATTTAGGA
1 ATTAGTTATTTTATTTA-GA
1039139 ATTAGTTATTTTA-TTAGA
1 ATTAGTTATTTTATTTAGA
1039157 A
1 A
1039158 CTCTTGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 7 0.39
20 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTTAGA
Found at i:1040034 original size:36 final size:36
Alignment explanation
Indices: 1039994--1040077 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
1039984 ACACTATTCT
*
1039994 ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
1 ATTTATTTTATTTAATTTATTTAATTTGAGATTTAA
1040030 ATTTATTTTATTTAATTTATTTAATTTGAGATTTAA
1 ATTTATTTTATTTAATTTATTTAATTTGAGATTTAA
*
1040066 GTTTA-TTTATTT
1 ATTTATTTTATTT
1040078 GACAATTATG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 7 0.15
36 39 0.85
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (36 bp):
ATTTATTTTATTTAATTTATTTAATTTGAGATTTAA
Done.