Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 7 of 31
Found at i:3490386 original size:2 final size:2
Alignment explanation
Indices: 3490381--3490416 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3490371 GGGGGGGTTA
3490381 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
3490417 TTGGGAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3506929 original size:14 final size:14
Alignment explanation
Indices: 3506906--3506955 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
3506896 GGGTCTATTT
*
3506906 TTCTTTGTTTAATG
1 TTCTTAGTTTAATG
* *
3506920 TTCTTAGTTTATTT
1 TTCTTAGTTTAATG
*
3506934 TTCTTTGTTTAATG
1 TTCTTAGTTTAATG
3506948 TTCTTAGT
1 TTCTTAGT
3506956 GTTGAGGCTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (14 bp):
TTCTTAGTTTAATG
Found at i:3506933 original size:28 final size:28
Alignment explanation
Indices: 3506901--3506955 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3506891 TAGTGGGGTC
3506901 TATTTTTCTTTGTTTAATGTTCTTAGTT
1 TATTTTTCTTTGTTTAATGTTCTTAGTT
3506929 TATTTTTCTTTGTTTAATGTTCTTAGT
1 TATTTTTCTTTGTTTAATGTTCTTAGT
3506956 GTTGAGGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.15, C:0.07, G:0.11, T:0.67
Consensus pattern (28 bp):
TATTTTTCTTTGTTTAATGTTCTTAGTT
Found at i:3528996 original size:12 final size:12
Alignment explanation
Indices: 3528979--3529007 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3528969 GGCATCAAGC
3528979 TTAAAAAAAAAA
1 TTAAAAAAAAAA
3528991 TTAAAAAAAAAA
1 TTAAAAAAAAAA
3529003 -TAAAA
1 TTAAAA
3529008 CGTACCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
TTAAAAAAAAAA
Found at i:3530889 original size:24 final size:23
Alignment explanation
Indices: 3530862--3530917 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
3530852 TTGATTTATG
3530862 TCACATTTGTTTTTATATATCC-CT
1 TCACATTTG--TTTATATATCCTCT
* *
3530886 TCACATCTGTTTATATATCCTTT
1 TCACATTTGTTTATATATCCTCT
3530909 TCACATTTG
1 TCACATTTG
3530918 ATTAGATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.39
23 9 0.32
24 8 0.29
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.52
Consensus pattern (23 bp):
TCACATTTGTTTATATATCCTCT
Found at i:3540232 original size:17 final size:17
Alignment explanation
Indices: 3540206--3540239 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3540196 TTTGATATCA
* *
3540206 TTTAATATTTATAATTT
1 TTTAAAATTTAAAATTT
3540223 TTTAAAATTTAAAATTT
1 TTTAAAATTTAAAATTT
3540240 ATTTTTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAAATTTAAAATTT
Found at i:3540239 original size:24 final size:22
Alignment explanation
Indices: 3540205--3540248 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
3540195 TTTTGATATC
*
3540205 ATTTAATATTTATAATTTTTTAAA
1 ATTTAAAATTTAT--TTTTTTAAA
3540229 ATTTAAAATTTATTTTTTTA
1 ATTTAAAATTTATTTTTTTA
3540249 TGATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTAAAATTTATTTTTTTAAA
Found at i:3544110 original size:32 final size:32
Alignment explanation
Indices: 3544073--3544168 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
3544063 TTAAGCGTCC
3544073 CACTTCCATGTGCCACTCCAAGTTCTTGTTCT
1 CACTTCCATGTGCCACTCCAAGTTCTTGTTCT
* * *
3544105 CACTTCCATGATG-CTCT-TAAGTAT-TTGCTTCC
1 CACTTCCATG-TGCCACTCCAAGT-TCTTG-TTCT
*
3544137 CACTT-CAGTGTGCCACACCAAGTTCTTGTTCT
1 CACTTCCA-TGTGCCACTCCAAGTTCTTGTTCT
3544169 TGCTTCCTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
31 11 0.22
32 30 0.60
33 9 0.18
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.38
Consensus pattern (32 bp):
CACTTCCATGTGCCACTCCAAGTTCTTGTTCT
Found at i:3544112 original size:61 final size:64
Alignment explanation
Indices: 3544036--3544168 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
3544026 GCACACAGGG
* * *
3544036 CTTGTTCTTACTTCCACGCTGCTC-CAA-T-TAAGCGTCCCACTTCCA-TGTGCCACTCCAAGTT
1 CTTGTTCTCACTTCCACGATGCTCTCAAGTATAAGCGTCCCACTT-CAGTGTGCCACACCAAGTT
* * ** *
3544097 CTTGTTCTCACTTCCATGATGCTCTTAAGTATTTGCTTCCCACTTCAGTGTGCCACACCAAGTT
1 CTTGTTCTCACTTCCACGATGCTCTCAAGTATAAGCGTCCCACTTCAGTGTGCCACACCAAGTT
3544161 CTTGTTCT
1 CTTGTTCT
3544169 TGCTTCCTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
61 21 0.35
62 2 0.03
63 3 0.05
64 34 0.57
ACGTcount: A:0.17, C:0.32, G:0.14, T:0.37
Consensus pattern (64 bp):
CTTGTTCTCACTTCCACGATGCTCTCAAGTATAAGCGTCCCACTTCAGTGTGCCACACCAAGTT
Found at i:3552681 original size:36 final size:36
Alignment explanation
Indices: 3552625--3552729 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
3552615 GGCCCAGTAC
* *
3552625 GCCGGCCAGGCCCAACACCATTGCTAACACCAACAG
1 GCCGGCCAGCCCCAATACCATTGCTAACACCAACAG
* * *
3552661 GCCGGCCTGCCCCGATACCATTGCTGACACCAACAG
1 GCCGGCCAGCCCCAATACCATTGCTAACACCAACAG
* * **
3552697 GCCGTCCAGGCCCAATACCATTATTAACACCAA
1 GCCGGCCAGCCCCAATACCATTGCTAACACCAA
3552730 GCTGCTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.29, C:0.40, G:0.18, T:0.13
Consensus pattern (36 bp):
GCCGGCCAGCCCCAATACCATTGCTAACACCAACAG
Found at i:3567858 original size:18 final size:18
Alignment explanation
Indices: 3567835--3567871 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3567825 CATGGAGAGG
3567835 GAATGGCTGACCATCCAT
1 GAATGGCTGACCATCCAT
3567853 GAATGGCTGACCATCCAT
1 GAATGGCTGACCATCCAT
3567871 G
1 G
3567872 TCTCTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (18 bp):
GAATGGCTGACCATCCAT
Found at i:3568195 original size:91 final size:91
Alignment explanation
Indices: 3568040--3568409 Score: 677
Period size: 91 Copynumber: 4.1 Consensus size: 91
3568030 GTAAAATAGT
* * *
3568040 AGTATTGGTCATAAGGTTTGTGTCGTATATGTTACTCTCTGTCATTCGAAATATCATTTATTAAT
1 AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
*
3568105 TTTAAATTTATAATACTATAACAAAA
66 TTTAAATTTATAATGCTATAACAAAA
* *
3568131 AGTATTGATCATAAGGTTTGAATCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
1 AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
3568196 TTTAAATTTATAATGCTATAACAAAA
66 TTTAAATTTATAATGCTATAACAAAA
3568222 AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
1 AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
3568287 TTTAAATTTATAATGCTATAACAAAA
66 TTTAAATTTATAATGCTATAACAAAA
*
3568313 AGTATTGGTCATAAGGTTTGGGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
1 AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
3568378 TTTAAATTTATAATGCTATAACAAAA
66 TTTAAATTTATAATGCTATAACAAAA
3568404 AGTATT
1 AGTATT
3568410 TTCATTTGTA
Statistics
Matches: 270, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 270 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (91 bp):
AGTATTGGTCATAAGGTTTGAGTCGTATATGTTGCTCTCTGCCATTCGAAATATCATTTATTAAT
TTTAAATTTATAATGCTATAACAAAA
Found at i:3570117 original size:20 final size:21
Alignment explanation
Indices: 3570080--3570134 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
3570070 TTACACAGTG
3570080 TAATCTTTTATTTAATTA-T-TA
1 TAAT-TTTT-TTTAATTAGTCTA
3570101 TAATTTTTTTTATATTAGTTCTA
1 TAATTTTTTTTA-ATTAG-TCTA
3570124 TAATTTTTTTT
1 TAATTTTTTTT
3570135 TTCAAATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 8 0.27
21 4 0.13
22 1 0.03
23 13 0.43
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TAATTTTTTTTAATTAGTCTA
Found at i:3595295 original size:15 final size:15
Alignment explanation
Indices: 3595275--3595304 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3595265 GATAGTGATT
3595275 CTTAATGATAATTAC
1 CTTAATGATAATTAC
3595290 CTTAATGATAATTAC
1 CTTAATGATAATTAC
3595305 TTAGTGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
CTTAATGATAATTAC
Found at i:3603163 original size:2 final size:2
Alignment explanation
Indices: 3603156--3603180 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3603146 AAAGAAATAA
3603156 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3603181 AAATAAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3604794 original size:22 final size:23
Alignment explanation
Indices: 3604764--3604806 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3604754 AAATTTCCAA
*
3604764 AAATTAAATCTT-AATATTGAAC
1 AAATAAAATCTTAAATATTGAAC
*
3604786 AAATAAAATGTTAAATATTGA
1 AAATAAAATCTTAAATATTGA
3604807 TATAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (23 bp):
AAATAAAATCTTAAATATTGAAC
Found at i:3607651 original size:8 final size:8
Alignment explanation
Indices: 3607640--3607668 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3607630 TGGATATATA
3607640 TATATTAT
1 TATATTAT
3607648 TATATTAT
1 TATATTAT
3607656 TATATTAT
1 TATATTAT
3607664 TATAT
1 TATAT
3607669 ATATATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:3607675 original size:16 final size:16
Alignment explanation
Indices: 3607633--3607676 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
3607623 TGTACGATGG
3607633 ATATATATATATTATT
1 ATATATATATATTATT
3607649 ATAT-TATTATATTATT
1 ATATATA-TATATTATT
3607665 ATATATATATAT
1 ATATATATATAT
3607677 GTACGTACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATATATATTATT
Found at i:3617227 original size:2 final size:2
Alignment explanation
Indices: 3617220--3617245 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3617210 TTCCATCATA
3617220 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
3617246 TATTATGTGT
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):
AT
Found at i:3625737 original size:2 final size:2
Alignment explanation
Indices: 3625730--3625766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3625720 GAGAGCTCCA
*
3625730 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3625767 TAAAAAAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3638522 original size:2 final size:2
Alignment explanation
Indices: 3638515--3638545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3638505 TCAGAGAAAC
3638515 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3638546 AAATACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3647768 original size:60 final size:60
Alignment explanation
Indices: 3647700--3647860 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
3647690 ACAACCCCCT
3647700 CCACAGCCACTGCTGTTCACCATGCTTCCACACCCACCACCGCATCCAGCACCGCAACCA
1 CCACAGCCACTGCTGTTCACCATGCTTCCACACCCACCACCGCATCCAGCACCGCAACCA
3647760 CCACAGCCACTGCTGTTCACCATGCTTCCACACCCACCACCGCATCCAGCACCGCAACCA
1 CCACAGCCACTGCTGTTCACCATGCTTCCACACCCACCACCGCATCCAGCACCGCAACCA
** * * *
3647820 CCACAGCCACCACTCTTCACCATG-TTACCACATCCAGCACC
1 CCACAGCCACTGCTGTTCACCATGCTT-CCACACCCACCACC
3647861 ACAGCCACCA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 2 0.02
60 93 0.98
ACGTcount: A:0.25, C:0.50, G:0.11, T:0.14
Consensus pattern (60 bp):
CCACAGCCACTGCTGTTCACCATGCTTCCACACCCACCACCGCATCCAGCACCGCAACCA
Found at i:3676326 original size:28 final size:27
Alignment explanation
Indices: 3676270--3676336 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
3676260 GATAATGGAA
*
3676270 ATATAAAATTAAATAAAAAATTATAAT
1 ATATAAAATTAAATAAAAAATTACAAT
* *
3676297 ATATAAAATATAAATAATTAAA-TACGAT
1 ATATAAAAT-TAAATAA-AAAATTACAAT
*
3676325 ATATAATATTAA
1 ATATAAAATTAA
3676337 TAATTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 12 0.35
28 19 0.56
29 3 0.09
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
ATATAAAATTAAATAAAAAATTACAAT
Found at i:3676738 original size:5 final size:5
Alignment explanation
Indices: 3676720--3676763 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
3676710 ACATATAAAC
* *
3676720 AAATA GAATAA AAATA AAATA AAATA AAATA ATAATA ATATA AA
1 AAATA AAAT-A AAATA AAATA AAATA AAATA A-AATA AAATA AA
3676764 TTGAAAGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:3676745 original size:16 final size:16
Alignment explanation
Indices: 3676720--3676763 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3676710 ACATATAAAC
*
3676720 AAATAGAATAAAAATA
1 AAATAAAATAAAAATA
3676736 AAATAAAAT-AAAATA
1 AAATAAAATAAAAATA
*
3676751 ATAATAATATAAA
1 A-AATAAAATAAA
3676764 TTGAAAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 15 0.62
17 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:3676745 original size:21 final size:21
Alignment explanation
Indices: 3676720--3676763 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3676710 ACATATAAAC
*
3676720 AAATAGAATAAAAATAAAATA
1 AAATAAAATAAAAATAAAATA
* *
3676741 AAATAAAATAATAATAATATA
1 AAATAAAATAAAAATAAAATA
3676762 AA
1 AA
3676764 TTGAAAGAAC
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:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAATA
Found at i:3682097 original size:25 final size:25
Alignment explanation
Indices: 3682069--3682121 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
3682059 TCTCTTTTTT
3682069 CTTGTTTCTTTAATGGTCAAGTTTA
1 CTTGTTTCTTTAATGGTCAAGTTTA
3682094 CTTGTTTCTTTAATGGTCAAGTTTA
1 CTTGTTTCTTTAATGGTCAAGTTTA
3682119 CTT
1 CTT
3682122 ATACTAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.53
Consensus pattern (25 bp):
CTTGTTTCTTTAATGGTCAAGTTTA
Found at i:3702883 original size:66 final size:67
Alignment explanation
Indices: 3702764--3702894 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 67
3702754 GAAACAGGAA
*
3702764 TATTTACCCATGGGCCTTTAAGTCTTAAACTGGCCAGCCCAAAATGTCATGAAAAATAAAACGAA
1 TATTTACCCATGGGCCTTTAAG-CTTAAACTAGCCAGCCCAAAATGTCATGAAAAATAAAACGAA
3702829 GAT
65 GAT
* *
3702832 TATTTGCCCATGGGCCTTTAAG-TTAACCTAGCCAGCCCAAAATGTCATGAAAAATAAAACGAA
1 TATTTACCCATGGGCCTTTAAGCTTAAACTAGCCAGCCCAAAATGTCATGAAAAATAAAACGAA
3702895 AACGCTAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 39 0.65
68 21 0.35
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (67 bp):
TATTTACCCATGGGCCTTTAAGCTTAAACTAGCCAGCCCAAAATGTCATGAAAAATAAAACGAAG
AT
Found at i:3707612 original size:44 final size:44
Alignment explanation
Indices: 3707538--3707624 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
3707528 TAGCATTGTC
* * *
3707538 TTAAACAAAAATTCTAATGAGTGCCTCTTGACTTATTTCTTTCT
1 TTAAACAAAAAGTCTAATGAGTACCTCTTGACTCATTTCTTTCT
* *
3707582 TTAAAC-AAAAGTCTAATTAGTACCTACTTGAGTCATTTCTTTC
1 TTAAACAAAAAGTCTAATGAGTACCT-CTTGACTCATTTCTTTC
3707625 CTCCTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 16 0.43
44 21 0.57
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.41
Consensus pattern (44 bp):
TTAAACAAAAAGTCTAATGAGTACCTCTTGACTCATTTCTTTCT
Found at i:3714832 original size:2 final size:2
Alignment explanation
Indices: 3714825--3714859 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3714815 AAGTAGTTTG
* *
3714825 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3714860 TGAAGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3716260 original size:2 final size:2
Alignment explanation
Indices: 3716244--3716282 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3716234 TCATTTAAAC
*
3716244 TA TA -A TA TG TA TA 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 TA TA TA TA TA TA TA
3716283 AAATCTTAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3725700 original size:30 final size:32
Alignment explanation
Indices: 3725638--3725721 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
3725628 TACATTATAG
*
3725638 GGATTAAATTAAACAAAAATATATAGTATAAA
1 GGATTAAATTGAACAAAAATATATAGTATAAA
*
3725670 -GATTAAATTGAACAAAATTGATAT-GT-TAAA
1 GGATTAAATTGAACAAAAAT-ATATAGTATAAA
* *
3725700 GGACTAAATTGAAAAAAAATAT
1 GGATTAAATTGAACAAAAATAT
3725722 TTGAAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 6 0.13
31 35 0.78
32 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.29
Consensus pattern (32 bp):
GGATTAAATTGAACAAAAATATATAGTATAAA
Found at i:3727208 original size:24 final size:24
Alignment explanation
Indices: 3727146--3727214 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
3727136 CTTAATAAAA
3727146 TTACACGTCAT-TTACAAAAATATG
1 TTACACGTCATATTA-AAAAATATG
* *
3727170 TTACATGCCATTATTAAAAAAGT-TG
1 TTACACGTCA-TATTAAAAAA-TATG
3727195 TTACACGTCATATTAAAAAA
1 TTACACGTCATATTAAAAAA
3727215 ATATTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 18 0.47
25 16 0.42
26 4 0.11
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (24 bp):
TTACACGTCATATTAAAAAATATG
Found at i:3727215 original size:25 final size:25
Alignment explanation
Indices: 3727146--3727407 Score: 95
Period size: 26 Copynumber: 10.0 Consensus size: 25
3727136 CTTAATAAAA
*
3727146 TTACACGTCAT-TTACAAAAATATG
1 TTACACGTCATATTAAAAAAATATG
* * *
3727170 TTACATGCCATTATTAAAAAAGT-TG
1 TTACACGTCA-TATTAAAAAAATATG
*
3727195 TTACACGTCATATTAAAAAAATATTATTA
1 TTACACGTCATATT-AAAAAA-A-TA-TG
* * *
3727224 TTACACCTCATA-TATAAAAATATA
1 TTACACGTCATATTAAAAAAATATG
* * **
3727248 TTATACGTTACGGTTAAAAAAAGT-TG
1 TTACACGTCA-TATTAAAAAAA-TATG
* *
3727274 TTACATGTCATGTTGAAAAAAAATATTATTG
1 TTACACGTCATATT---AAAAAA-A-TA-TG
* * * *
3727305 TTACCCGTCAT-GTACAAAAACATG
1 TTACACGTCATATTAAAAAAATATG
* * * *
3727329 TTATATGTCATGGTTAAAAAAAGT-TA
1 TTACACGTCAT-ATTAAAAAAA-TATG
* *
3727355 TTATACGTCATATTAAAAAAAATTAATA
1 TTACACGTCATATT-AAAAAAA-T-ATG
3727383 TTACACGTCATATTGAAAAAAATAT
1 TTACACGTCATATT-AAAAAAATAT
3727408 TATTGTTACA
Statistics
Matches: 177, Mismatches: 39, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
24 31 0.18
25 25 0.14
26 53 0.30
27 13 0.07
28 29 0.16
29 14 0.08
30 1 0.01
31 11 0.06
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (25 bp):
TTACACGTCATATTAAAAAAATATG
Found at i:3727234 original size:29 final size:30
Alignment explanation
Indices: 3727195--3727251 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3727185 AAAAAAGTTG
*
3727195 TTACACGTCATAT-TAAAAAAATATTATTA
1 TTACACCTCATATATAAAAAAATATTATTA
*
3727224 TTACACCTCATATATAAAAATATATTAT
1 TTACACCTCATATATAAAAAAATATTAT
3727252 ACGTTACGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (30 bp):
TTACACCTCATATATAAAAAAATATTATTA
Found at i:3727344 original size:81 final size:80
Alignment explanation
Indices: 3727145--3727395 Score: 269
Period size: 81 Copynumber: 3.2 Consensus size: 80
3727135 CCTTAATAAA
* * * * **
3727145 ATTACACGTCATTTACAAAAATATGTTACATGCCATTATT-AAAAAAGTTGTTACACGTCATATT
1 ATTACCCGTCATATACAAAAATATGTTATATGTCATGGTTAAAAAAAGTTGTTACACGTCATATT
3727209 -AAAAAAATATTATT
66 AAAAAAAATATTATT
* * * * * * *
3727223 ATTACACC-TCATATATAAAAATATATTATACGTTACGGTTAAAAAAAGTTGTTACATGTCATGT
1 ATTAC-CCGTCATATACAAAAATATGTTATATGTCATGGTTAAAAAAAGTTGTTACACGTCATAT
3727287 TGAAAAAAAATATTATT
65 T-AAAAAAAATATTATT
* * * * *
3727304 GTTACCCGTCATGTACAAAAACATGTTATATGTCATGGTTAAAAAAAGTTATTATACGTCATATT
1 ATTACCCGTCATATACAAAAATATGTTATATGTCATGGTTAAAAAAAGTTGTTACACGTCATATT
*
3727369 -AAAAAAA-ATTAAT
66 AAAAAAAATATTATT
*
3727382 ATTACACGTCATAT
1 ATTACCCGTCATAT
3727396 TGAAAAAAAT
Statistics
Matches: 139, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
78 43 0.31
79 30 0.22
80 2 0.01
81 64 0.46
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (80 bp):
ATTACCCGTCATATACAAAAATATGTTATATGTCATGGTTAAAAAAAGTTGTTACACGTCATATT
AAAAAAAATATTATT
Found at i:3727376 original size:26 final size:27
Alignment explanation
Indices: 3727344--3727404 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
3727334 TGTCATGGTT
*
3727344 AAAAAAAGT-TATTATACGTCATATTA
1 AAAAAAAGTATATTACACGTCATATTA
* *
3727370 AAAAAAATTAATATTACACGTCATATTG
1 AAAAAAAGT-ATATTACACGTCATATTA
3727398 AAAAAAA
1 AAAAAAA
3727405 TATTATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 8 0.27
28 22 0.73
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAAAAAGTATATTACACGTCATATTA
Found at i:3727417 original size:30 final size:28
Alignment explanation
Indices: 3727353--3727432 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 28
3727343 TAAAAAAAGT
*
3727353 TATTATACGTCATATTAAAAAAAATTAA
1 TATTACACGTCATATTAAAAAAAATTAA
*
3727381 TATTACACGTCATATTGAAAAAAATATTAT
1 TATTACACGTCATATT-AAAAAAA-ATTAA
* * * *
3727411 TGTTACAGGTCATGTTCAAAAA
1 TATTACACGTCATATTAAAAAA
3727433 CAGTTTGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.34
29 12 0.27
30 17 0.39
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (28 bp):
TATTACACGTCATATTAAAAAAAATTAA
Found at i:3752064 original size:15 final size:14
Alignment explanation
Indices: 3752040--3752073 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3752030 GGGTGTCATT
*
3752040 ATTAATATATATTG
1 ATTAATATATATTA
3752054 ATTATATATATATTA
1 ATTA-ATATATATTA
3752069 ATTAA
1 ATTAA
3752074 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTAATATATATTA
Found at i:3776746 original size:13 final size:13
Alignment explanation
Indices: 3776728--3776759 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3776718 AAAAAAGCCG
3776728 GGACTTGAACCTA
1 GGACTTGAACCTA
3776741 GGACTTGAACCTA
1 GGACTTGAACCTA
3776754 GGACTT
1 GGACTT
3776760 CCTAGTTCCT
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:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (13 bp):
GGACTTGAACCTA
Found at i:3779355 original size:25 final size:26
Alignment explanation
Indices: 3779327--3779381 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
3779317 ATTTTATTTT
* *
3779327 ATTTTTT-AAATATTTATAATTTATA
1 ATTTTTTAAAATATTAATAATTAATA
3779352 ATTTTTTAAAATATTAATAATTAATA
1 ATTTTTTAAAATATTAATAATTAATA
3779378 ATTT
1 ATTT
3779382 AAATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTTTAAAATATTAATAATTAATA
Found at i:3779364 original size:26 final size:25
Alignment explanation
Indices: 3779327--3779392 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
3779317 ATTTTATTTT
* *
3779327 ATTTTTTAAATATTTATAATTTATA
1 ATTTTTTAAATATTAATAATTAATA
3779352 ATTTTTTAAAATATTAATAATTAATA
1 ATTTTTT-AAATATTAATAATTAATA
3779378 A---TTTAAATATTAATA
1 ATTTTTTAAATATTAATA
3779393 TTTTAGTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 11 0.29
23 3 0.08
25 7 0.18
26 17 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTTTTAAATATTAATAATTAATA
Found at i:3779396 original size:40 final size:39
Alignment explanation
Indices: 3779352--3779480 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 39
3779342 ATAATTTATA
* *
3779352 ATTTTTTAAAATATTAATAATTAATAATTTAAATATTAAT
1 ATTTTTTATAAT-TTAATAATTAATATTTTAAATATTAAT
* * *
3779392 ATTTTAGTATACTTTAATTATTAATATTTTAAATATTAAAT
1 ATTTT-TTATAATTTAATAATTAATATTTTAAATATT-AAT
3779433 ATTTTATTTATAATTTAATAA-TAATATTATTAAGATATTAAT
1 A-TTT-TTTATAATTTAATAATTAATATT-TTAA-ATATTAAT
*
3779475 AATTTT
1 ATTTTT
3779481 AATTAATATC
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
40 29 0.39
41 17 0.23
42 22 0.30
43 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (39 bp):
ATTTTTTATAATTTAATAATTAATATTTTAAATATTAAT
Found at i:3779435 original size:16 final size:15
Alignment explanation
Indices: 3779371--3779482 Score: 64
Period size: 15 Copynumber: 7.9 Consensus size: 15
3779361 AATATTAATA
*
3779371 ATTAATAATTTAAAT
1 ATTAATATTTTAAAT
3779386 ATTAATA-TTT---T
1 ATTAATATTTTAAAT
* * *
3779397 AGT-ATACTTTAATT
1 ATTAATATTTTAAAT
3779411 ATTAATATTTTAAAT
1 ATTAATATTTTAAAT
3779426 ATTAAATATTTT--AT
1 ATT-AATATTTTAAAT
*
3779440 -TT-ATAATTT-AAT
1 ATTAATATTTTAAAT
*
3779452 AATAATATTATTAAGAT
1 ATTAATATT-TTAA-AT
3779469 ATTAATAATTTTAA
1 ATTAAT-ATTTTAA
3779483 TTAATATCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
10 3 0.04
11 12 0.16
12 2 0.03
13 3 0.04
14 12 0.16
15 21 0.28
16 9 0.12
17 11 0.14
18 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTAATATTTTAAAT
Found at i:3784084 original size:45 final size:45
Alignment explanation
Indices: 3784035--3784126 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
3784025 ATTCAAACAT
*
3784035 TATTAATA-TTAATTTGATTAAAGTATTAAAATGTT-AATATTTAAA
1 TATTAATATTTAATTT-ATTAAAGTATTAAAATATTAAAT-TTTAAA
* * * *
3784080 TATTACTATTTTATTTATTAAATTATTAATATATTAAATTTTAAA
1 TATTAATATTTAATTTATTAAAGTATTAAAATATTAAATTTTAAA
3784125 TA
1 TA
3784127 AGTATAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 31 0.77
46 9 0.22
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (45 bp):
TATTAATATTTAATTTATTAAAGTATTAAAATATTAAATTTTAAA
Found at i:3784429 original size:22 final size:23
Alignment explanation
Indices: 3784381--3784429 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3784371 ATTAATTAAA
* * *
3784381 ATTATTAATATTTTAATTATAAT
1 ATTATTAATATTATAAATAAAAT
3784404 ATTATTAA-ATTATAAATAAAAT
1 ATTATTAATATTATAAATAAAAT
3784426 ATTA
1 ATTA
3784430 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTATTAATATTATAAATAAAAT
Found at i:3784502 original size:39 final size:40
Alignment explanation
Indices: 3784369--3784492 Score: 137
Period size: 40 Copynumber: 3.1 Consensus size: 40
3784359 TTAAATTTAG
* * *
3784369 AAATTA-ATTAAAATTATTAATATTTTAATTATAATATTATT
1 AAATTATA-TAAAAATATTAATATTTAAATTATTA-ATTATT
* * *
3784410 AAATTATAAATAAAATATTAATTTTTAAA-AATTAA-TAGTT
1 AAATTATATA-AAAATATTAATATTTAAATTATTAATTA-TT
3784450 AAATTATATAAAAATATTAATATTTAAATTATTAATTATT
1 AAATTATATAAAAATATTAATATTTAAATTATTAATTATT
3784490 AAA
1 AAA
3784493 ATTTTAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
39 19 0.28
40 22 0.32
41 12 0.17
42 16 0.23
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (40 bp):
AAATTATATAAAAATATTAATATTTAAATTATTAATTATT
Found at i:3784503 original size:40 final size:39
Alignment explanation
Indices: 3784378--3784507 Score: 122
Period size: 39 Copynumber: 3.3 Consensus size: 39
3784368 GAAATTAATT
* * * *
3784378 AAAATTATTAATATTTTAATTATAATATTATTAAATTATAA
1 AAAAATATTAATATTTAAATTATTA-ATTATTAAATT-TTA
* * *
3784419 ATAAAATATTAATTTTTAAA-AATTAA-TAGTTAAATTATA
1 A-AAAATATTAATATTTAAATTATTAATTA-TTAAATTTTA
3784458 TAAAAATATTAATATTTAAATTATTAATTATTAAAATTTTA
1 -AAAAATATTAATATTTAAATTATTAATTATT-AAATTTTA
3784499 AAAAA-ATTA
1 AAAAATATTA
3784508 TAAATTATTA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
39 24 0.33
40 21 0.29
41 13 0.18
42 15 0.21
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAAATATTAATATTTAAATTATTAATTATTAAATTTTA
Found at i:3785688 original size:17 final size:17
Alignment explanation
Indices: 3785668--3785701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3785658 TTTATTCTAT
*
3785668 TTATAATTTAAATATTA
1 TTATAATTAAAATATTA
*
3785685 TTATGATTAAAATATTA
1 TTATAATTAAAATATTA
3785702 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATAATTAAAATATTA
Found at i:3786169 original size:15 final size:17
Alignment explanation
Indices: 3786144--3786183 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3786134 AAAATAATAT
3786144 TTATA-ATTTTAAAA-A
1 TTATATATTTTAAAACA
3786159 -TATATATTTTAAAACA
1 TTATATATTTTAAAACA
3786175 TTATATATT
1 TTATATATT
3786184 GATGGTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 1 0.05
17 8 0.36
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATATATTTTAAAACA
Found at i:3786584 original size:29 final size:29
Alignment explanation
Indices: 3786522--3786598 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
3786512 ATATGTTGAA
* * * *
3786522 AAAAAAATATTATTGTTATAGGTCATGTT
1 AAAAAAATATTATTGTTACACGACATATT
3786551 AAAAAAATATTATTGTTACACGACATATT
1 AAAAAAATATTATTGTTACACGACATATT
* *
3786580 -TAAAAATATT-TTATTACAC
1 AAAAAAATATTATTGTTACAC
3786599 TTTAATACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 8 0.19
28 9 0.21
29 25 0.60
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (29 bp):
AAAAAAATATTATTGTTACACGACATATT
Found at i:3788894 original size:3 final size:3
Alignment explanation
Indices: 3788886--3788913 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3788876 CATCACAAAT
3788886 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3788914 GTAAAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3805911 original size:2 final size:2
Alignment explanation
Indices: 3805904--3805928 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3805894 TCACACGTGG
3805904 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3805929 GGATTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3807216 original size:2 final size:2
Alignment explanation
Indices: 3807204--3807234 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3807194 TCTTTCCTTG
3807204 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3807235 GTTTCCCCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3814844 original size:12 final size:12
Alignment explanation
Indices: 3814809--3814844 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3814799 TTAAATTTTG
*
3814809 TTAAATTTAAAT
1 TTAAATTTTAAT
3814821 TTAAATTATTAAT
1 TTAAATT-TTAAT
3814834 TTAAATTTTAA
1 TTAAATTTTAA
3814845 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTTAAT
Found at i:3815953 original size:20 final size:20
Alignment explanation
Indices: 3815908--3815947 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3815898 CAATGCCATG
* *
3815908 TCATCATCTCAAATGTCACG
1 TCATCATCTCAAATGCCACA
3815928 TCATCATCTCAAATGCCACA
1 TCATCATCTCAAATGCCACA
3815948 ATATCAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.28
Consensus pattern (20 bp):
TCATCATCTCAAATGCCACA
Found at i:3816505 original size:21 final size:20
Alignment explanation
Indices: 3816413--3816507 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 20
3816403 TCGATTACTA
*
3816413 AAACTCTAAAACCAATTCATC
1 AAAC-CTAAAACTAATTCATC
* *
3816434 AAACCTTAAAACTAATTTAATT
1 AAACC-TAAAACTAA-TTCATC
* * *
3816456 AAACTTAAAAATCAATTCATT
1 AAACCTAAAACT-AATTCATC
3816477 AAACCCTAAAACTAATTCATC
1 AAA-CCTAAAACTAATTCATC
3816498 AAATCCTAAA
1 AAA-CCTAAA
3816508 TCAATGCACC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 42 0.70
22 17 0.28
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (20 bp):
AAACCTAAAACTAATTCATC
Found at i:3816586 original size:21 final size:20
Alignment explanation
Indices: 3816549--3816587 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3816539 GATTCACTGA
*
3816549 AAACCCTAAATCAATTCACC
1 AAACCCTAAAACAATTCACC
3816569 AAACCCTAAAAACAATTCA
1 AAACCCT-AAAACAATTCA
3816588 TAAAATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACCCTAAAACAATTCACC
Found at i:3818561 original size:19 final size:19
Alignment explanation
Indices: 3818529--3818566 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3818519 CAAACACTAA
*
3818529 ACTTATTAAATAGACCTAC
1 ACTTAATAAATAGACCTAC
*
3818548 ACTTAATAACTAGACCTAC
1 ACTTAATAAATAGACCTAC
3818567 CAATGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
ACTTAATAAATAGACCTAC
Found at i:3826779 original size:30 final size:30
Alignment explanation
Indices: 3826745--3826806 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3826735 GACGCAGTTG
*
3826745 AAGAAAATAAGGGAAAGGGGATGACTATAT
1 AAGAAAATAAGGAAAAGGGGATGACTATAT
3826775 AAGAAAATAAGGAAAAGGGGATGACTATAT
1 AAGAAAATAAGGAAAAGGGGATGACTATAT
3826805 AA
1 AA
3826807 CCTTGGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.16
Consensus pattern (30 bp):
AAGAAAATAAGGAAAAGGGGATGACTATAT
Found at i:3848594 original size:15 final size:15
Alignment explanation
Indices: 3848574--3848612 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3848564 TTCTATATTC
3848574 TTTTTATTCTTTCTA
1 TTTTTATTCTTTCTA
*
3848589 TTTTTA-TCTTTTTA
1 TTTTTATTCTTTCTA
3848603 TTATTTATTC
1 TT-TTTATTC
3848613 ACTTTTAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 10 0.48
16 2 0.10
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTCTTTCTA
Found at i:3848638 original size:28 final size:27
Alignment explanation
Indices: 3848604--3848684 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
3848594 ATCTTTTTAT
*
3848604 TATTTATTCACTTTTAGTGGGTTGA-ACG
1 TATTTATTCACTTTT-GTGGGTT-ATAAG
* *
3848632 TATTTATTCACTTTTGGTAGATTATAAG
1 TATTTATTCACTTTT-GTGGGTTATAAG
3848660 TATTTATTCACTTTTGATGGGTTAT
1 TATTTATTCACTTTTG-TGGGTTAT
3848685 CTACTTCTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.04
28 43 0.96
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (27 bp):
TATTTATTCACTTTTGTGGGTTATAAG
Found at i:3849453 original size:13 final size:13
Alignment explanation
Indices: 3849435--3849459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3849425 AAATAAAGAT
3849435 AATAGATTAAATG
1 AATAGATTAAATG
3849448 AATAGATTAAAT
1 AATAGATTAAAT
3849460 TTTAATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
AATAGATTAAATG
Found at i:3854120 original size:38 final size:38
Alignment explanation
Indices: 3854071--3854148 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
3854061 TCAGCTAAGC
*
3854071 AAAACGAGAATAAGTCATATCTTCTGTGA-CTCGGAATG
1 AAAACGAGAATAAGTCATATCTTCTCTGACCT-GGAATG
*
3854109 AAAACGTGAATAAGTCATATCTTCTCTGACCTGGAATG
1 AAAACGAGAATAAGTCATATCTTCTCTGACCTGGAATG
3854147 AA
1 AA
3854149 TGCCAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.95
39 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (38 bp):
AAAACGAGAATAAGTCATATCTTCTCTGACCTGGAATG
Found at i:3857629 original size:38 final size:38
Alignment explanation
Indices: 3857587--3857711 Score: 90
Period size: 38 Copynumber: 3.2 Consensus size: 38
3857577 CTAAATAAAC
3857587 CAAAATAATTTGGAGATAATATTTATATTTTGACCAAT
1 CAAAATAATTTGGAGATAATATTTATATTTTGACCAAT
* * * * * * ** ** *
3857625 CAAAA-AATTAGTTATTGGTCATTCAATTTATCTCTAAATAAAC
1 CAAAATAATTTG-GA--GAT-AAT--ATTTATATTTTGACCAAT
3857668 CAAAATAATTTGGAGATAATATTTATATTTTGACCAAT
1 CAAAATAATTTGGAGATAATATTTATATTTTGACCAAT
3857706 CAAAAT
1 CAAAAT
3857712 TTAATTATTG
Statistics
Matches: 58, Mismatches: 22, Indels: 14
0.62 0.23 0.15
Matches are distributed among these distances:
37 5 0.09
38 23 0.40
40 4 0.07
41 4 0.07
43 17 0.29
44 5 0.09
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (38 bp):
CAAAATAATTTGGAGATAATATTTATATTTTGACCAAT
Found at i:3857639 original size:81 final size:81
Alignment explanation
Indices: 3857520--3857710 Score: 323
Period size: 81 Copynumber: 2.4 Consensus size: 81
3857510 TTTATCTCTT
* * *
3857520 GAGATAATATTTA-AATTGGGCCAATC-AAAAATTAGTTATGGGTCATCCAATTTATCTCTAAAT
1 GAGATAATATTTATATTTTGACCAATCAAAAAATTAGTTATGGGTCATCCAATTTATCTCTAAAT
3857583 AAACCAAAATAATTTG
66 AAACCAAAATAATTTG
* *
3857599 GAGATAATATTTATATTTTGACCAATCAAAAAATTAGTTATTGGTCATTCAATTTATCTCTAAAT
1 GAGATAATATTTATATTTTGACCAATCAAAAAATTAGTTATGGGTCATCCAATTTATCTCTAAAT
3857664 AAACCAAAATAATTTG
66 AAACCAAAATAATTTG
3857680 GAGATAATATTTATATTTTGACCAATCAAAA
1 GAGATAATATTTATATTTTGACCAATCAAAA
3857711 TTTAATTATT
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
79 13 0.12
80 10 0.10
81 82 0.78
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (81 bp):
GAGATAATATTTATATTTTGACCAATCAAAAAATTAGTTATGGGTCATCCAATTTATCTCTAAAT
AAACCAAAATAATTTG
Found at i:3857784 original size:55 final size:56
Alignment explanation
Indices: 3857717--3857821 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 56
3857707 AAAATTTAAT
*
3857717 TATTGATCATTTAAATTATCTCT-AAT-AATTATA-TTAATTTAGAGATAAAAATCA
1 TATTGATCATTTAAATTATCTCTAAATAAATTA-AGATAATTTAGAGATAAAAATCA
* *
3857771 TATTGGATTATTTAATTTATCTCTAAATAAATTAAGATAATTTAGAGATAA
1 TATT-GATCATTTAAATTATCTCTAAATAAATTAAGATAATTTAGAGATAA
3857822 CACTTAACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
54 4 0.09
55 17 0.39
56 4 0.09
57 19 0.43
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (56 bp):
TATTGATCATTTAAATTATCTCTAAATAAATTAAGATAATTTAGAGATAAAAATCA
Found at i:3873798 original size:25 final size:26
Alignment explanation
Indices: 3873760--3873808 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3873750 CTTTAGGATC
3873760 TTGTTTTTCTTCTTTTCGATTTAAGG
1 TTGTTTTTCTTCTTTTCGATTTAAGG
*
3873786 TTGTTTTT-TTCTTTTTGATTTAA
1 TTGTTTTTCTTCTTTTCGATTTAA
3873809 AGTGCAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.12, C:0.08, G:0.12, T:0.67
Consensus pattern (26 bp):
TTGTTTTTCTTCTTTTCGATTTAAGG
Found at i:3876498 original size:32 final size:32
Alignment explanation
Indices: 3876444--3876521 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 32
3876434 TAAAAAATTT
*
3876444 AATATTTTTT-TGTAGTTTGAATAAACTATGA-AA
1 AATATTTTTTAT-TAGTTAGAATAAA-T-TGAGAA
3876477 AATATTTTTTATT-GTTAGAATAAATTGAGGAA
1 AATATTTTTTATTAGTTAGAATAAATTGA-GAA
*
3876509 AATATTTTCTATT
1 AATATTTTTTATT
3876522 CACTTATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 3 0.08
31 1 0.03
32 24 0.60
33 11 0.28
34 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (32 bp):
AATATTTTTTATTAGTTAGAATAAATTGAGAA
Found at i:3878091 original size:2 final size:2
Alignment explanation
Indices: 3878084--3878122 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3878074 TCTCTTAAGG
* *
3878084 TA TA TA TA CA TA CA 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 TA TA TA TA TA T
3878123 CTAAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3889703 original size:113 final size:113
Alignment explanation
Indices: 3889501--3889707 Score: 333
Period size: 113 Copynumber: 1.8 Consensus size: 113
3889491 GTAAAGTACT
* * *
3889501 TAGTCAAATAGAGGTTCAAGCAAAATCAAGAGAGTTAGATAAGCATGGTAGAGTTTGAGTTTGAT
1 TAGTCAAATAGAGGTTCAAGCAAAATCAAGAGAGTTAGACAAGCATGGTAGAGCTTGAGTCTGAT
*
3889566 TCAATCAAAAGCTGAAAAAAGTTAAAAAAATTAAAGCCAAGGTACAAA
66 TCAATCAAAAACTGAAAAAAGTTAAAAAAATTAAAGCCAAGGTACAAA
* * * *
3889614 TAGTCAGATAGATGTTGAAGCAAAATCAAGAGAGTTAGGCAAGCATGGTAGAGCTTGAGTCTGAT
1 TAGTCAAATAGAGGTTCAAGCAAAATCAAGAGAGTTAGACAAGCATGGTAGAGCTTGAGTCTGAT
*
3889679 TCAATCAAAAACTGAAAAAGGTTAAAAAA
66 TCAATCAAAAACTGAAAAAAGTTAAAAAA
3889708 TTCAAGTTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 85 1.00
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (113 bp):
TAGTCAAATAGAGGTTCAAGCAAAATCAAGAGAGTTAGACAAGCATGGTAGAGCTTGAGTCTGAT
TCAATCAAAAACTGAAAAAAGTTAAAAAAATTAAAGCCAAGGTACAAA
Found at i:3899234 original size:13 final size:13
Alignment explanation
Indices: 3899216--3899240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3899206 ATTTTTAAAT
3899216 TTATATAAAATAC
1 TTATATAAAATAC
3899229 TTATATAAAATA
1 TTATATAAAATA
3899241 TAATATACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TTATATAAAATAC
Found at i:3899296 original size:22 final size:22
Alignment explanation
Indices: 3899257--3899318 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
3899247 ACATATAATA
*
3899257 TTTTCACTTCTTCA-TTTTCATT
1 TTTTCAATTCTT-ATTTTTCATT
*
3899279 TTTTCAATTCTTATTTTTTTATT
1 TTTTCAATTCTTA-TTTTTCATT
*
3899302 TCTTTTAATTCTT-TTTT
1 T-TTTCAATTCTTATTTT
3899319 GTTTATGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 15 0.44
23 8 0.24
24 10 0.29
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTCAATTCTTATTTTTCATT
Found at i:3899311 original size:24 final size:22
Alignment explanation
Indices: 3899257--3899324 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
3899247 ACATATAATA
* ** *
3899257 TTTTCACTTCTTCATTTTCATT
1 TTTTCAATTCTTTTTTTTTATT
3899279 TTTTCAATTCTTATTTTTTTATT
1 TTTTCAATTCTT-TTTTTTTATT
*
3899302 TCTTTTAATTCTTTTTTGTTTAT
1 T-TTTCAATTCTTTTTT-TTTAT
3899325 GCATTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 11 0.29
23 12 0.32
24 15 0.39
ACGTcount: A:0.15, C:0.13, G:0.01, T:0.71
Consensus pattern (22 bp):
TTTTCAATTCTTTTTTTTTATT
Found at i:3899331 original size:24 final size:24
Alignment explanation
Indices: 3899279--3899333 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
3899269 CATTTTCATT
*
3899279 TTTTCAATTCTTATTTTTTTATTTC
1 TTTT-AATTCTTATTTTTTTATTGC
3899304 TTTTAATTCTT-TTTTGTTTA-TGC
1 TTTTAATTCTTATTTT-TTTATTGC
3899327 ATTTTAA
1 -TTTTAA
3899334 AAAAAGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.22
24 17 0.63
25 4 0.15
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTAATTCTTATTTTTTTATTGC
Found at i:3901314 original size:31 final size:31
Alignment explanation
Indices: 3901253--3901318 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3901243 ATAAAAAGAT
* *
3901253 TTATTTTTTTTTAATATAACTCTTCAAATAA
1 TTATTTTTTTATAATATAACTATTCAAATAA
* *
3901284 TTATTTTTTTCATAATATAATTATT-TAATAA
1 TTATTTTTTT-ATAATATAACTATTCAAATAA
3901315 TTAT
1 TTAT
3901319 ATCTAATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (31 bp):
TTATTTTTTTATAATATAACTATTCAAATAA
Found at i:3907841 original size:32 final size:32
Alignment explanation
Indices: 3907777--3907841 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3907767 GATACGATTA
*
3907777 TGGGTCTGAGTGAGATGGGCTTGACAATTTTT
1 TGGGTCTGAGTGAGATGGGCTTGACAACTTTT
**
3907809 TGGGTCTGAGTGAGATTGGG-TTGAGGACTTTT
1 TGGGTCTGAGTGAGA-TGGGCTTGACAACTTTT
3907841 T
1 T
3907842 TGACGGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.17, C:0.08, G:0.37, T:0.38
Consensus pattern (32 bp):
TGGGTCTGAGTGAGATGGGCTTGACAACTTTT
Found at i:3930087 original size:11 final size:11
Alignment explanation
Indices: 3930071--3930101 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3930061 AAGACAGTCG
3930071 AGCTGTAACTA
1 AGCTGTAACTA
3930082 AGCTGTAACTA
1 AGCTGTAACTA
3930093 AGCTGTAAC
1 AGCTGTAAC
3930102 GATGGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (11 bp):
AGCTGTAACTA
Found at i:3930834 original size:40 final size:40
Alignment explanation
Indices: 3930779--3930860 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
3930769 TTCAAACGAG
3930779 TTCGTTGGGCTTGCGTGAGAGTTCCCAAAGATAGGAACTA
1 TTCGTTGGGCTTGCGTGAGAGTTCCCAAAGATAGGAACTA
3930819 TTCGTTGGGCTTGCGTGAGAGTTCCCAAAGATAGGAACTA
1 TTCGTTGGGCTTGCGTGAGAGTTCCCAAAGATAGGAACTA
3930859 TT
1 TT
3930861 GCAAAAAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (40 bp):
TTCGTTGGGCTTGCGTGAGAGTTCCCAAAGATAGGAACTA
Found at i:3940004 original size:16 final size:16
Alignment explanation
Indices: 3939983--3940014 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3939973 CAAAACACTA
3939983 TCACTGACAACAAGGG
1 TCACTGACAACAAGGG
3939999 TCACTGACAACAAGGG
1 TCACTGACAACAAGGG
3940015 GTAATACAAC
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:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (16 bp):
TCACTGACAACAAGGG
Found at i:3942446 original size:2 final size:2
Alignment explanation
Indices: 3942441--3942468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3942431 AAAATAAAGA
3942441 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
3942469 TAGGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3943890 original size:28 final size:32
Alignment explanation
Indices: 3943820--3943890 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 32
3943810 ATAAATTATT
3943820 TAAATAATTTTAAATAATTTTTTATTTTTAAAA
1 TAAATAATTTT-AATAATTTTTTATTTTTAAAA
*
3943853 TCAAGT--TTTT-AT-A-TTTTTA-TTTTAAAA
1 T-AAATAATTTTAATAATTTTTTATTTTTAAAA
3943880 TAAATAATTTT
1 TAAATAATTTT
3943891 TTATAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
26 3 0.09
27 9 0.27
28 10 0.30
29 1 0.03
30 2 0.06
32 4 0.12
33 1 0.03
34 3 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
TAAATAATTTTAATAATTTTTTATTTTTAAAA
Found at i:3943922 original size:25 final size:25
Alignment explanation
Indices: 3943894--3943941 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3943884 TAATTTTTTA
3943894 TAATTAAAA-ATTGATTAATTATTAT
1 TAATTAAAATATT-ATTAATTATTAT
*
3943919 TAATTAAAATATTATTTATTATT
1 TAATTAAAATATTATTAATTATT
3943942 TTATTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATTAAAATATTATTAATTATTAT
Found at i:3953183 original size:14 final size:14
Alignment explanation
Indices: 3953164--3953192 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3953154 TCAGCAGACA
3953164 AGAAGACAAGGTGT
1 AGAAGACAAGGTGT
3953178 AGAAGACAAGGTGT
1 AGAAGACAAGGTGT
3953192 A
1 A
3953193 AACCGGATAT
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:0.45, C:0.07, G:0.34, T:0.14
Consensus pattern (14 bp):
AGAAGACAAGGTGT
Found at i:3965308 original size:24 final size:22
Alignment explanation
Indices: 3965258--3965309 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
3965248 TGTGATTATT
**
3965258 AAAAATTTAAATTTAAATTTTT
1 AAAAATTTAAATTTAAATTTAA
*
3965280 CAAAATTATATAATTTAAATTTAA
1 AAAAATT-TA-AATTTAAATTTAA
3965304 AAAAAT
1 AAAAAT
3965310 GATTGAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 2 0.08
24 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATTTAAATTTAAATTTAA
Found at i:3973398 original size:231 final size:228
Alignment explanation
Indices: 3973038--3973637 Score: 543
Period size: 231 Copynumber: 2.6 Consensus size: 228
3973028 TAAGTATCAG
* * * * * * *
3973038 CTGATGCAGAAAGAGCTCG-GTAGATGTAAAGAAATGCTGGAGGAATCATCCAGGTGTCAACTTC
1 CTGATGCAGAAAGAGCTTGAG-AGGTATAAAGAAATGCTCGAGGAAACATCTAGGTGTCAA-ATC
* * * * * * *
3973102 GGTTGAAAGAGCAAGCTTTGCAGGTGGACAATGATTCAAAAG-GAAAAATT-AGAGAAGTCTGTG
64 AGTTGGAAGAGCAAGCTTTGCAGATGGA-AATGAATCAAGAGAG-AAACTTCA-AGAAGTTTGTG
* ** * ** * * * *
3973165 ATGCTTTAGATGTGGCAAATTCTGAACTGGCTGAAGAACAGGAGAAGGTAGCATCTTTGTT-ATG
126 ATGCTTTAGAAGCAGCAAAATCTGAACTAACAGAAGAAC--GAGAAAG-AGCAGCTTCGTTGAT-
*
3973229 GAA-A-GTTGAGTCCTTGGAT-ATTATTGAAG-GACAGCGGCTC
187 GAAGAGGTTGAGTCCTTGGATCA-AATTGAAGAG-CAGCGGCTC
* * *
3973269 CTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAAAGCTTGAGGAAGCATCTAGGTGTCAAATACA
1 CTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAATGCTCGAGGAAACATCTAGGTGTCAAAT-CA
* *
3973334 CTTGGAAGAGCAAGCTTTGCAGATGGAAAGTGAATCCAGAGAGAAACTTCAAGAAGTTTGTGATG
65 GTTGGAAGAGCAAGCTTTGCAGATGGAAA-TGAATCAAGAGAGAAACTTCAAGAAGTTTGTGATG
* *
3973399 CTTTACAAGCAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAGCAGCTTCGTTGATGAAGAGG
129 CTTTAGAAGCAGCAAAATCTGAACTAACAGAAGAACGAGAAAGAGCAGCTTCGTTGATGAAGA-G
* *
3973464 GTTGAGTCTTTGGATCAAATTGAAGAGCAGTGGCTC
193 GTTGAGTCCTTGGATCAAATTGAAGAGCAGCGGCTC
* ** * ** * *
3973500 CAGACACAGAAAGAGCTTGAGAGGTATAAGGATTTGCTCGAGGAAACATCTAGGAGTCAACGTCA
1 CTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAATGCTCGAGGAAACATCTAGGTGTCAA-ATCA
** * * ** *
3973565 GTTGGAAGAGCAAGCAGTGCATATGCAAAATGAAT-TTGAAGAGAAACTTCGAGAAGTTTGTGAT
65 GTTGGAAGAGCAAGCTTTGCAGATG-GAAATGAATCAAG-AGAGAAACTTCAAGAAGTTTGTGAT
3973629 GCTTTAGAA
128 GCTTTAGAA
3973638 ACTGCAAACT
Statistics
Matches: 303, Mismatches: 52, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
228 13 0.04
229 9 0.03
230 4 0.01
231 268 0.88
232 9 0.03
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.23
Consensus pattern (228 bp):
CTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAATGCTCGAGGAAACATCTAGGTGTCAAATCAG
TTGGAAGAGCAAGCTTTGCAGATGGAAATGAATCAAGAGAGAAACTTCAAGAAGTTTGTGATGCT
TTAGAAGCAGCAAAATCTGAACTAACAGAAGAACGAGAAAGAGCAGCTTCGTTGATGAAGAGGTT
GAGTCCTTGGATCAAATTGAAGAGCAGCGGCTC
Found at i:3973783 original size:231 final size:231
Alignment explanation
Indices: 3973251--3973808 Score: 563
Period size: 231 Copynumber: 2.4 Consensus size: 231
3973241 CTTGGATATT
* * * *
3973251 ATTGAAG-GACAGCGGCTCCTGATGCAGAAAGAGCTTGAGAGGTATAAAGAAAAGCTTGAGGAAG
1 ATTGAAGAG-CAGTGGCTCCTGACGCAGAAAGAGCTTGAGAGGTATAAGGAAATGCTTGAGGAAG
* ** * *
3973315 CATCTAGGTGTCAA-ATACACTTGGAAGAGCAAGCTTTGCAGATGGAAAGTGAATCCAGAGAGAA
65 CATCTAGGTGTCAACAT-CAATTGGAAGAGCAAGCAGTGCAGATGCAAAATGAATCCAGAGAGAA
*
3973379 ACTTCAAGAAGTTTGTGATGCTTTACAAGCAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAG
129 ACTTCAAGAAGTTTGTGATGCTTTACAAACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAG
* * * * * **
3973444 CAGCTTCGTTGATGAAGAGGGTTGAGTCTTTGGATCAA
194 CAGCTTAGTTAAAGAAGAGGATTGAATCTTCAGATCAA
* * ** * *
3973482 ATTGAAGAGCAGTGGCTCCAGACACAGAAAGAGCTTGAGAGGTATAAGGATTTGCTCGAGGAAAC
1 ATTGAAGAGCAGTGGCTCCTGACGCAGAAAGAGCTTGAGAGGTATAAGGAAATGCTTGAGGAAGC
* * * * **
3973547 ATCTAGGAGTCAACGTCAGTTGGAAGAGCAAGCAGTGCATATGCAAAATGAAT-TTGAAGAGAAA
66 ATCTAGGTGTCAACATCAATTGGAAGAGCAAGCAGTGCAGATGCAAAATGAATCCAG-AGAGAAA
* * * * * ** * * *
3973611 CTTCGAGAAGTTTGTGATGCTTTAGAAACTGCAAACTTTGAATTGGCTGAAGAACGTGAGAG-GA
130 CTTCAAGAAGTTTGTGATGCTTTACAAACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAG-
*
3973675 CAGCTTATTTAAAGAAGAGGATTGAATCTTCAGATC-A
194 CAGCTTAGTTAAAGAAGAGGATTGAATCTTCAGATCAA
* * * * * *
3973712 CTTGGAAGAGCAGTGGGC-CCTGAGGCAGAAAGAACTTGAGTGGTACAAGGAAATGTTTGA-GAA
1 ATT-GAAGAGCAGT-GGCTCCTGACGCAGAAAGAGCTTGAGAGGTATAAGGAAATGCTTGAGGAA
* * *
3973775 GTCATCTAGGTGCCAACTTCAATTAGAAGAGCAA
64 G-CATCTAGGTGTCAACATCAATTGGAAGAGCAA
3973809 ATGTCTCAGA
Statistics
Matches: 264, Mismatches: 56, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
230 8 0.03
231 251 0.95
232 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (231 bp):
ATTGAAGAGCAGTGGCTCCTGACGCAGAAAGAGCTTGAGAGGTATAAGGAAATGCTTGAGGAAGC
ATCTAGGTGTCAACATCAATTGGAAGAGCAAGCAGTGCAGATGCAAAATGAATCCAGAGAGAAAC
TTCAAGAAGTTTGTGATGCTTTACAAACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAGCA
GCTTAGTTAAAGAAGAGGATTGAATCTTCAGATCAA
Found at i:3977759 original size:3 final size:3
Alignment explanation
Indices: 3977753--3977792 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3977743 ATTAAAGTTA
*
3977753 TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3977793 TTTGGTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:3992699 original size:17 final size:18
Alignment explanation
Indices: 3992677--3992714 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3992667 TATGTATATC
3992677 TAAATT-TAAATATAAAT
1 TAAATTATAAATATAAAT
* *
3992694 TAAATTATAATTATAATT
1 TAAATTATAAATATAAAT
3992712 TAA
1 TAA
3992715 TCTATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTATAAATATAAAT
Found at i:3997067 original size:18 final size:18
Alignment explanation
Indices: 3997020--3997063 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3997010 CTTATTTTTC
*
3997020 TTTAAAATTAAATATTAT
1 TTTAAAATTAAATATAAT
3997038 TTTGAAAA-TAAATA-AAT
1 TTT-AAAATTAAATATAAT
3997055 TTTAAAATT
1 TTTAAAATT
3997064 TAAAATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 9 0.39
19 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAAATTAAATATAAT
Found at i:4013851 original size:19 final size:18
Alignment explanation
Indices: 4013813--4013853 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4013803 TATTAAGTCC
*
4013813 TTTAAAATTTTGAATTTA
1 TTTAAAATTTTGAATATA
*
4013831 TTTAAAATTTTTAATAATA
1 TTTAAAATTTTGAAT-ATA
4013850 TTTA
1 TTTA
4013854 TTTTTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAAATTTTGAATATA
Found at i:4019258 original size:20 final size:22
Alignment explanation
Indices: 4019233--4019272 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4019223 TATTTAAGCT
4019233 TATAATAC-T-AAATATAAAAC
1 TATAATACATAAAATATAAAAC
4019253 TATAATACATAAAATATAAA
1 TATAATACATAAAATATAAA
4019273 TAATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
TATAATACATAAAATATAAAAC
Found at i:4019752 original size:17 final size:18
Alignment explanation
Indices: 4019710--4019752 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
4019700 TTTATTTATT
4019710 TATATTAATTATTAAATAA
1 TATATT-ATTATTAAATAA
* *
4019729 AAAATTATT-TTAAATAA
1 TATATTATTATTAAATAA
4019746 TATATTA
1 TATATTA
4019753 AAAATTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.65
18 3 0.15
19 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATTATTATTAAATAA
Found at i:4022062 original size:21 final size:20
Alignment explanation
Indices: 4022038--4022087 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4022028 TTTCACTTTT
4022038 TATTAATTTTTATAATTATTA
1 TATTAATTTTTAT-ATTATTA
* * *
4022059 TATTATAATTTTATTTTTTTA
1 TATTA-ATTTTTATATTATTA
4022080 TATTAATT
1 TATTAATT
4022088 AAGAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTAATTTTTATATTATTA
Found at i:4041423 original size:18 final size:20
Alignment explanation
Indices: 4041378--4041425 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
4041368 ATAGAAAAAA
4041378 ATTTTATAATAATATTTTCAT
1 ATTTTA-AATAATATTTTCAT
*
4041399 TTTTTAAAT-ATATTTT-AT
1 ATTTTAAATAATATTTTCAT
4041417 ATTTTAAAT
1 ATTTTAAAT
4041426 TAAACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 3 0.12
21 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTAAATAATATTTTCAT
Found at i:4064827 original size:22 final size:21
Alignment explanation
Indices: 4064796--4064868 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 21
4064786 TTGAATATAG
* *
4064796 AATAATAAATTATATTTTAATA
1 AATAAAAAATTA-ATTTAAATA
4064818 AATAAAAAATTAATTTAAAATAA
1 AATAAAAAATTAATTT-AAAT-A
4064841 AATATAAAAATTAA-TTAAATA
1 AATA-AAAAATTAATTTAAATA
4064862 AATAAAA
1 AATAAAA
4064869 TATATTTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.07
21 9 0.20
22 18 0.39
23 7 0.15
24 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAAAAATTAATTTAAATA
Found at i:4064854 original size:24 final size:26
Alignment explanation
Indices: 4064817--4064872 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
4064807 ATATTTTAAT
*
4064817 AAATA-AAAAATTAATT-TA-AAATA
1 AAATATAAAAATTAATTAAATAAATA
4064840 AAATATAAAAATTAATTAAATAAATA
1 AAATATAAAAATTAATTAAATAAATA
4064866 AAATATA
1 AAATATA
4064873 TTTTTCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
25 1 0.03
26 12 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATATAAAAATTAATTAAATAAATA
Found at i:4072876 original size:40 final size:40
Alignment explanation
Indices: 4072804--4072879 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
4072794 TATCTAGATT
* *
4072804 AAATTCAAATGTAGATAAGATTTTTTCACTTATCATGATC
1 AAATTCAAATGTAGATAAGAATTTATCACTTATCATGATC
4072844 AAATTCAAATGTTA-ATAA-AATTTATCATCTTATCAT
1 AAATTCAAATG-TAGATAAGAATTTATCA-CTTATCAT
4072880 TAACGTATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 7 0.22
40 23 0.72
41 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (40 bp):
AAATTCAAATGTAGATAAGAATTTATCACTTATCATGATC
Found at i:4073077 original size:50 final size:50
Alignment explanation
Indices: 4073002--4073097 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
4072992 GTCTTGTTAT
4073002 ATTTATTTACATAACAGTTTTCAATTTTCTTTTAAAATTTATATTTACTA
1 ATTTATTTACATAACAGTTTTCAATTTTCTTTTAAAATTTATATTTACTA
* * *
4073052 ATTTATTTACTTAATAGTTTTCAATTTTCTTTTAAAGTTTATATTT
1 ATTTATTTACATAACAGTTTTCAATTTTCTTTTAAAATTTATATTT
4073098 GCTTGTGTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.57
Consensus pattern (50 bp):
ATTTATTTACATAACAGTTTTCAATTTTCTTTTAAAATTTATATTTACTA
Found at i:4073890 original size:46 final size:46
Alignment explanation
Indices: 4073834--4073924 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
4073824 AAACCCGCCC
* * *
4073834 ACGAATAACTCTAAGGTGGCGTTT-AGTATC-AGGAAAGTGAGAGCAT
1 ACGAACAACTCTAAGATAGCGTTTGA-TATCAAGG-AAGTGAGAGCAT
4073880 ACGAACAACTCTAAGATAGCGTTTGATATCAAGGAAGTGAGAGCA
1 ACGAACAACTCTAAGATAGCGTTTGATATCAAGGAAGTGAGAGCA
4073925 CATCTCCTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 36 0.90
47 4 0.10
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (46 bp):
ACGAACAACTCTAAGATAGCGTTTGATATCAAGGAAGTGAGAGCAT
Found at i:4074176 original size:15 final size:15
Alignment explanation
Indices: 4074156--4074187 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4074146 TATTGTTATA
4074156 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
4074171 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
4074186 AT
1 AT
4074188 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:4074285 original size:15 final size:15
Alignment explanation
Indices: 4074267--4074411 Score: 50
Period size: 15 Copynumber: 10.0 Consensus size: 15
4074257 AAATTAAAAT
4074267 AAAATATATAATATA
1 AAAATATATAATATA
4074282 AAAATATAT--TA-A
1 AAAATATATAATATA
4074294 AGAAATA-A-AA-AT-
1 A-AAATATATAATATA
4074306 AAAATATATAAGATTATA
1 AAAATATAT-A-A-TATA
* *
4074324 ATAATAAATGAA-ATA
1 AAAATATAT-AATATA
4074339 AAAATATATGACAT-TA
1 AAAATATAT-A-ATATA
*
4074355 CAAATATAT--T-TA
1 AAAATATATAATATA
* *
4074367 AGAGATGATATTATATA
1 A-AAAT-ATATAATATA
4074384 AAAAT-TAATAATA-A
1 AAAATAT-ATAATATA
4074398 AAAATATA-AATATA
1 AAAATATATAATATA
4074412 TTAAAAATAA
Statistics
Matches: 99, Mismatches: 10, Indels: 43
0.65 0.07 0.28
Matches are distributed among these distances:
11 5 0.05
12 9 0.09
13 14 0.14
14 14 0.14
15 28 0.28
16 15 0.15
17 6 0.06
18 8 0.08
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (15 bp):
AAAATATATAATATA
Found at i:4074311 original size:39 final size:38
Alignment explanation
Indices: 4074257--4074344 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
4074247 TAGGTAAAAC
* *
4074257 AAATTAAAATAAAATATATAATATAAAAATATATTAAA-G
1 AAATAAAAATAAAATATATAAGATAAAAATA-A-TAAATG
* *
4074296 AAATAAAAATAAAATATATAAGATTATAATAATAAATG
1 AAATAAAAATAAAATATATAAGATAAAAATAATAAATG
4074334 AAATAAAAATA
1 AAATAAAAATA
4074345 TATGACATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 4 0.09
38 13 0.30
39 27 0.61
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (38 bp):
AAATAAAAATAAAATATATAAGATAAAAATAATAAATG
Found at i:4074405 original size:24 final size:24
Alignment explanation
Indices: 4074378--4074445 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
4074368 GAGATGATAT
4074378 TATATAAAAATTAATAATAAAAAA
1 TATATAAAAATTAATAATAAAAAA
* *
4074402 TATA-AATATATTAA-AA-ATAAAA
1 TATATAA-AAATTAATAATAAAAAA
* *
4074424 TATATAAGATTATAATAATAAA
1 TATATAAAAAT-TAATAATAAA
4074446 TGAAAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAATAATAAAAAA
Found at i:4074417 original size:16 final size:16
Alignment explanation
Indices: 4074397--4074428 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
4074387 ATTAATAATA
4074397 AAAAATATAAATATATT
1 AAAAATA-AAATATATT
4074414 AAAAATAAAATATAT
1 AAAAATAAAATATAT
4074429 AAGATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAAAATATATT
Found at i:4074417 original size:114 final size:114
Alignment explanation
Indices: 4074265--4074530 Score: 412
Period size: 114 Copynumber: 2.3 Consensus size: 114
4074255 ACAAATTAAA
* *
4074265 ATAAAATATATAAT-ATAAAAATATATTAAAGA-AATAAAAATAAAATATATAAGATTATAATAA
1 ATAAAA-AT-TAATAATAAAAA-ATA-TAAATATATTAAAAATAAAATATATAAGATTATAATAA
* *
4074328 TAAATG-AAATAAAAATATATGACATTACAAATATATTTAAGAGATGATATTAT
62 TAAATGAAAAT-AAAATATATGACATTAAAAATATATTTAAAAGATGATATTAT
4074381 ATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
1 ATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
* *
4074446 TGAAAATAAGATATATGACATTAAAAATATATTTAAAAGATGGTATTAT
66 TGAAAATAAAATATATGACATTAAAAATATATTTAAAAGATGATATTAT
4074495 ATAAAAATTAATAATAAAAAATATAAATATATTAAA
1 ATAAAAATTAATAATAAAAAATATAAATATATTAAA
4074531 CTAATATTTT
Statistics
Matches: 141, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
113 5 0.04
114 117 0.83
115 13 0.09
116 6 0.04
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (114 bp):
ATAAAAATTAATAATAAAAAATATAAATATATTAAAAATAAAATATATAAGATTATAATAATAAA
TGAAAATAAAATATATGACATTAAAAATATATTTAAAAGATGATATTAT
Found at i:4079711 original size:2 final size:2
Alignment explanation
Indices: 4079704--4079734 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4079694 CCTAGTGTGC
*
4079704 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4079735 AATGAGGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4080176 original size:2 final size:2
Alignment explanation
Indices: 4080169--4080193 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4080159 CAAGTTTTAT
4080169 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4080194 GAGGTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4096505 original size:12 final size:12
Alignment explanation
Indices: 4096490--4096522 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
4096480 ACACTATCCC
4096490 AAACAAAACAAA
1 AAACAAAACAAA
4096502 AAACAAAAACAAA
1 AAAC-AAAACAAA
4096515 AAA-AAAAC
1 AAACAAAAC
4096523 CCTTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACAAAACAAA
Found at i:4099040 original size:2 final size:2
Alignment explanation
Indices: 4098992--4099020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4098982 TTTTAATTTC
4098992 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
4099021 NNNNNNNNNN
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:4099041 original size:2 final size:2
Alignment explanation
Indices: 4099031--4099056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4099021 NNNNNNNNNN
4099031 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
4099057 GCACTTGTTA
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):
AT
Found at i:4108415 original size:279 final size:277
Alignment explanation
Indices: 4107900--4108460 Score: 772
Period size: 279 Copynumber: 2.0 Consensus size: 277
4107890 TTCAACTAGG
* * *
4107900 GCAAACTTGAACAACCCTATATACCAATTTGTGCCAAGGACGTGACATGCTAGAAGACTTGAGCA
1 GCAAACTTGAACAACCCTATATA-CAATATGTGCCAAGGACGTGACATCCTAGAAGACTTAAGCA
* * * * *
4107965 AAGAACTAGTTAACTGCACGCTTGCAATTGGTTGGCAACAGTGACCTTTAACGTGAAAGTGACTG
65 AAGAACTAGTTAACTGCAAGCTTGCAATTGGTTCGCAACAGTAAACTCTAACGTGAAAGTGACTG
* * * *
4108030 TTTAAAATCAGACAGTGGTGAAAACAAAATTTAAGGGTTTAATATTTCCAGATTGTTTGGTTTCT
130 TTTAAAATCAAACAGTGGTGAAAACAAAACTTAAGGGTTTAATATTTCCAGACTGTTTGGTTTCA
* ** *
4108095 AGTACTTGAGACTGCTTGACAGAATTTGTTTTATTGAAAGTGTTGGTTTCTAGTAGCTCAGCTCA
195 AGTACTTGAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGG-TTCTAGTAGCTCAGCTCA
*
4108160 TTTAGCAG-CTGCCTCTAA
259 TTTAGCAGTCTGCATCTAA
* * *
4108178 GCAAACTTGAACAACCCTATAT-GAATATGTGCCTAGGATGTGACATCCTAGAAGACTTAAGCAA
1 GCAAACTTGAACAACCCTATATACAATATGTGCCAAGGACGTGACATCCTAGAAGACTTAAGCAA
* * *
4108242 AGACCTAGTTAACTGCAAAGCTTGCATTTGGTTCGCAACAGTAAACTCT-ACTGTGAAGGTGACT
66 AGAACTAGTTAACTGC-AAGCTTGCAATTGGTTCGCAACAGTAAACTCTAAC-GTGAAAGTGACT
* *
4108306 GTTTAAAATCAAACAAAGTGGTGAAAATAAAACTTAAGGGTTTAATTTTTCCAGACTGTTTGCG-
129 GTTTAAAATCAAAC--AGTGGTGAAAACAAAACTTAAGGGTTTAATATTTCCAGACTGTTTG-GT
*
4108370 TTCAAGTA-TCTGAGACTGCCTGACGGAATTTACTTTATCGAAAGTGTTGGTTCTAGTAGCTCAG
191 TTCAAGTACT-TGAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTCTAGTAGCTCAG
*
4108434 CTCATTTAGCAGTTTGCATCTAA
255 CTCATTTAGCAGTCTGCATCTAA
4108457 GCAA
1 GCAA
4108461 TACCAGTCAT
Statistics
Matches: 249, Mismatches: 27, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
276 53 0.21
277 50 0.20
278 49 0.20
279 96 0.39
280 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (277 bp):
GCAAACTTGAACAACCCTATATACAATATGTGCCAAGGACGTGACATCCTAGAAGACTTAAGCAA
AGAACTAGTTAACTGCAAGCTTGCAATTGGTTCGCAACAGTAAACTCTAACGTGAAAGTGACTGT
TTAAAATCAAACAGTGGTGAAAACAAAACTTAAGGGTTTAATATTTCCAGACTGTTTGGTTTCAA
GTACTTGAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTCTAGTAGCTCAGCTCATT
TAGCAGTCTGCATCTAA
Found at i:4112717 original size:46 final size:46
Alignment explanation
Indices: 4112625--4112717 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
4112615 TAAAATTACA
* *
4112625 ACTGCCAAATGAACTTCAATGTTGCAAACATTAAACATAAAGAAAG
1 ACTGCCAAATGAACTTCAATGTTGCAAACAATAAACATAAACAAAG
* *
4112671 ACTGCCCAATGAACTTCGATGTTGCAAACAATAAACA-AAGACAAAG
1 ACTGCCAAATGAACTTCAATGTTGCAAACAATAAACATAA-ACAAAG
4112717 A
1 A
4112718 AAAGGAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.19
Consensus pattern (46 bp):
ACTGCCAAATGAACTTCAATGTTGCAAACAATAAACATAAACAAAG
Found at i:4116492 original size:3 final size:3
Alignment explanation
Indices: 4116484--4116519 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4116474 AATTAGTTTA
*
4116484 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4116520 GTTGTTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:4127022 original size:9 final size:10
Alignment explanation
Indices: 4127000--4127024 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4126990 AATGTGGTAG
4127000 TTTTTCACAT
1 TTTTTCACAT
4127010 TTTTTCACAT
1 TTTTTCACAT
4127020 TTTTT
1 TTTTT
4127025 TAACTGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTCACAT
Found at i:4129549 original size:6 final size:6
Alignment explanation
Indices: 4129540--4129571 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4129530 GTGGTTGTCC
*
4129540 AAAGGG AAAGGG AAAGGG AAAGGG GAAGGG AA
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AA
4129572 CGGCAGCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:4131330 original size:17 final size:17
Alignment explanation
Indices: 4131293--4131330 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4131283 TGGCAGCCTT
*
4131293 TCTTTTCCTTTCCTCTT
1 TCTTTTCCTTTCCTCTC
*
4131310 TCTTTTCCTTTCTTCTC
1 TCTTTTCCTTTCCTCTC
4131327 TCTT
1 TCTT
4131331 CCAAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TCTTTTCCTTTCCTCTC
Found at i:4131494 original size:23 final size:22
Alignment explanation
Indices: 4131468--4131516 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
4131458 TATATGCGTA
*
4131468 TCTCTCTCATATCATAGTATGT-T
1 TCTCTCCCATA-CATA-TATGTCT
4131491 TCTC-CCCATACATATATGTCT
1 TCTCTCCCATACATATATGTCT
4131512 TCTCT
1 TCTCT
4131517 TTTCAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 5 0.22
23 4 0.17
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (22 bp):
TCTCTCCCATACATATATGTCT
Found at i:4131504 original size:21 final size:22
Alignment explanation
Indices: 4131475--4131515 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
4131465 GTATCTCTCT
4131475 CATATCATAGTATGT-TTCTCCC
1 CATATCATA-TATGTCTTCTCCC
4131497 CATA-CATATATGTCTTCTC
1 CATATCATATATGTCTTCTC
4131516 TTTTCAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.41
Consensus pattern (22 bp):
CATATCATATATGTCTTCTCCC
Found at i:4149154 original size:19 final size:19
Alignment explanation
Indices: 4149130--4149167 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4149120 AAATTTAAAC
*
4149130 TTTTTTTATTTTAAATTCA
1 TTTTTTAATTTTAAATTCA
4149149 TTTTTTAATTTTAAATTCA
1 TTTTTTAATTTTAAATTCA
4149168 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTAATTTTAAATTCA
Done.