Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 59 of 345
Found at i:18046796 original size:30 final size:30
Alignment explanation
Indices: 18046760--18046822 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
18046750 ACTTAACAAG
*
18046760 CAAATGTCTCTAAAATAATAATAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
18046790 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
18046820 CAA
1 CAA
18046823 TAAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:18048719 original size:11 final size:11
Alignment explanation
Indices: 18048703--18048729 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18048693 AAGGTGAGGT
18048703 CCTATAGATAC
1 CCTATAGATAC
18048714 CCTATAGATAC
1 CCTATAGATAC
18048725 CCTAT
1 CCTAT
18048730 TGTCTAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (11 bp):
CCTATAGATAC
Found at i:18050122 original size:43 final size:43
Alignment explanation
Indices: 18050075--18050186 Score: 129
Period size: 42 Copynumber: 2.6 Consensus size: 43
18050065 CTTGATTTGA
*
18050075 GATTTACGTGTAAGACCATGTCTGGGACATAGGCATC-ATATCT
1 GATTTACGTGTAAGACCATGTCTGGGACAGAGGCATCGATA-CT
* *
18050118 GATTT-CGTGTAAGACCCTGTTTGGGACAGAGGCATCGATACT
1 GATTTACGTGTAAGACCATGTCTGGGACAGAGGCATCGATACT
* * * * *
18050160 AAATTACATGTAAGACCACGTCCGGGA
1 GATTTACGTGTAAGACCATGTCTGGGA
18050187 TGCCGACATT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 33 0.58
43 24 0.42
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
GATTTACGTGTAAGACCATGTCTGGGACAGAGGCATCGATACT
Found at i:18057464 original size:42 final size:42
Alignment explanation
Indices: 18057400--18057502 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
18057390 CTCGATTTGA
*
18057400 GATTTACGTGTAAGACCATGTCTAGGACATAGGCATCG-TATCT
1 GATTT-CGTGTAAGACCATGTCTAGGACAGAGGCATCGATA-CT
* *
18057443 GATTTCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATACT
1 GATTTCGTGTAAGACCATGTCTAGGACAGAGGCATCGATACT
* *
18057485 GAATTACATGTAAGACCA
1 G-ATTTCGTGTAAGACCA
18057503 CGTCCGGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 32 0.62
43 20 0.38
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTAGGACAGAGGCATCGATACT
Found at i:18066354 original size:65 final size:65
Alignment explanation
Indices: 18066250--18066383 Score: 250
Period size: 65 Copynumber: 2.1 Consensus size: 65
18066240 CAAGGTGGAG
*
18066250 ATTTGTTGAGTGTGCTACGTATTTCAGTCAAATTTGAAAGATAATCTCCCAGTTAAACTATGTTT
1 ATTTGTTGAGTGTGATACGTATTTCAGTCAAATTTGAAAGATAATCTCCCAGTTAAACTATGTTT
*
18066315 ATTTGTTGAGTGTGATACGTATTTCAGTCAAATTTGAAAGATAATCTCTCAGTTAAACTATGTTT
1 ATTTGTTGAGTGTGATACGTATTTCAGTCAAATTTGAAAGATAATCTCCCAGTTAAACTATGTTT
18066380 ATTT
1 ATTT
18066384 CTTTCAGTCG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (65 bp):
ATTTGTTGAGTGTGATACGTATTTCAGTCAAATTTGAAAGATAATCTCCCAGTTAAACTATGTTT
Found at i:18067137 original size:19 final size:18
Alignment explanation
Indices: 18067115--18067155 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
18067105 TATATTTTTT
18067115 AATTAATAAAAGAAATTAA
1 AATT-ATAAAAGAAATTAA
*
18067134 AATTATTAAAGAAATTAA
1 AATTATAAAAGAAATTAA
18067152 AATT
1 AATT
18067156 TTTTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTATAAAAGAAATTAA
Found at i:18067522 original size:16 final size:16
Alignment explanation
Indices: 18067501--18067534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18067491 TGGAGCCGAC
18067501 AAGTTAGAGGAACCAA
1 AAGTTAGAGGAACCAA
**
18067517 AAGTTAGATTAACCAA
1 AAGTTAGAGGAACCAA
18067533 AA
1 AA
18067535 AAAGAATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AAGTTAGAGGAACCAA
Found at i:18071946 original size:21 final size:22
Alignment explanation
Indices: 18071894--18071946 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
18071884 ATTTTTCTAA
*
18071894 TTTTTT-TAAATTTGAATACTT
1 TTTTTTATAAATTTGAATACAT
*
18071915 TTTTTTCATAAATTTTAATA-AT
1 TTTTTT-ATAAATTTGAATACAT
18071937 TTTTTTATAA
1 TTTTTTATAA
18071947 TCCTCTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 7 0.25
23 11 0.39
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTTATAAATTTGAATACAT
Found at i:18088887 original size:56 final size:56
Alignment explanation
Indices: 18088801--18088918 Score: 236
Period size: 56 Copynumber: 2.1 Consensus size: 56
18088791 CTAATCATAA
18088801 TTAAAACAAAAATTTTATTCTGAGTGGAAATAATTCAAATTTTCGGTCCCCCCAAC
1 TTAAAACAAAAATTTTATTCTGAGTGGAAATAATTCAAATTTTCGGTCCCCCCAAC
18088857 TTAAAACAAAAATTTTATTCTGAGTGGAAATAATTCAAATTTTCGGTCCCCCCAAC
1 TTAAAACAAAAATTTTATTCTGAGTGGAAATAATTCAAATTTTCGGTCCCCCCAAC
18088913 TTAAAA
1 TTAAAA
18088919 TGAACAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (56 bp):
TTAAAACAAAAATTTTATTCTGAGTGGAAATAATTCAAATTTTCGGTCCCCCCAAC
Found at i:18090541 original size:25 final size:24
Alignment explanation
Indices: 18090499--18090555 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
18090489 TTTAATTTAT
*
18090499 AAAATTAATAATTCAATAAACTGA
1 AAAATTAATAATTCAATAAAATGA
* *
18090523 AAAATTAACTAATTGAATAAAATTA
1 AAAATTAA-TAATTCAATAAAATGA
18090548 AAAATTAA
1 AAAATTAA
18090556 GAGAAACTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAATTAATAATTCAATAAAATGA
Found at i:18091224 original size:22 final size:23
Alignment explanation
Indices: 18091199--18091250 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
18091189 AATTCTATGC
18091199 TAAATTAATAA-AGAT-TAATATA
1 TAAATTAATAATAGATATAAT-TA
18091221 TAAATT-ATAATAGATATAATTA
1 TAAATTAATAATAGATATAATTA
*
18091243 TATATTAA
1 TAAATTAA
18091251 AGATTATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATTAATAATAGATATAATTA
Found at i:18109942 original size:67 final size:64
Alignment explanation
Indices: 18109829--18109982 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 64
18109819 AACACTCAAT
* * * * * * * *
18109829 ACCACCTATGTGACCTAGCCA-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACCTA
1 ACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCTACATGGTG---TACACATA
18109893 GA
63 GA
* *
18109895 ACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCTACATGGTGTACACATAGT
1 ACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCTACATGGTGTACACATAGA
*
18109959 ATCACCCATGCGACCTAGCTACAT
1 ACCACCCATGCGACCTAGCTACAT
18109983 CATAATGTCT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
64 29 0.39
66 17 0.23
67 29 0.39
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (64 bp):
ACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCTACATGGTGTACACATAGA
Found at i:18111584 original size:61 final size:61
Alignment explanation
Indices: 18111490--18111612 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
18111480 ATGCAATCAT
*
18111490 ATCATAGACCTCAAAATAATCATAAAATAATTATTTCTATCTTGGATTTTGTGGTCCCAAA
1 ATCATAGACCTCAAAATAATCATAAAATAATTATTTCTATCTCGGATTTTGTGGTCCCAAA
18111551 ATCATAGACCTCAAAATAATCATAAAATAATTATTTCTATCTCGGATTTTGTGGTCCCAAA
1 ATCATAGACCTCAAAATAATCATAAAATAATTATTTCTATCTCGGATTTTGTGGTCCCAAA
18111612 A
1 A
18111613 CCTCTGTTCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (61 bp):
ATCATAGACCTCAAAATAATCATAAAATAATTATTTCTATCTCGGATTTTGTGGTCCCAAA
Found at i:18112308 original size:22 final size:23
Alignment explanation
Indices: 18112266--18112308 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
18112256 AATGATACTT
18112266 ATTTACATAAATGATTGGTTGAA
1 ATTTACATAAATGATTGGTTGAA
* *
18112289 ATTTACA-AAATTATTTGTTG
1 ATTTACATAAATGATTGGTTG
18112309 TTGCTCCGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (23 bp):
ATTTACATAAATGATTGGTTGAA
Found at i:18113734 original size:17 final size:16
Alignment explanation
Indices: 18113703--18113742 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
18113693 TTTAAAATAA
18113703 TTTTAATAATTTTAAT
1 TTTTAATAATTTTAAT
*
18113719 TTTTATATATTTTTAAT
1 TTTTA-ATAATTTTAAT
18113736 TTATTAA
1 TT-TTAA
18113743 ATTAACTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATAATTTTAAT
Found at i:18125936 original size:20 final size:22
Alignment explanation
Indices: 18125891--18125938 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
18125881 TTTTAAGTTT
*
18125891 TTTTATTTGTCCTTATTTATTTA
1 TTTTATTTGT-CTTATTTATTGA
18125914 TTTTATTTGT-TTA-TTATTGA
1 TTTTATTTGTCTTATTTATTGA
18125934 TTTTA
1 TTTTA
18125939 AAAAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 3 0.12
23 10 0.42
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTATTTGTCTTATTTATTGA
Found at i:18126012 original size:19 final size:21
Alignment explanation
Indices: 18125940--18126047 Score: 130
Period size: 21 Copynumber: 5.1 Consensus size: 21
18125930 TTGATTTTAA
* * * *
18125940 AAAATTTGAAATGTATATTTA
1 AAAATTTTAAATATATTTTTT
18125961 AAATATTTTATAATATTATTTTTT
1 AAA-ATTTTA-AATA-TATTTTTT
18125985 AAAATTTTAAATATATTTTTT
1 AAAATTTTAAATATATTTTTT
*
18126006 -TAA-TTTAAATATATTTTTT
1 AAAATTTTAAATATATTTTTT
18126025 AAAATTTTAAATATATTTTTT
1 AAAATTTTAAATATATTTTTT
18126046 AA
1 AA
18126048 TAATATAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
19 16 0.21
20 4 0.05
21 29 0.38
22 9 0.12
23 9 0.12
24 9 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAAATTTTAAATATATTTTTT
Found at i:18126028 original size:40 final size:41
Alignment explanation
Indices: 18125967--18126062 Score: 142
Period size: 40 Copynumber: 2.3 Consensus size: 41
18125957 TTTAAAATAT
18125967 TTTATAATATTATTTTTTAAAATTTTAAATATATTTTTT-TAA
1 TTTA-AATA-TATTTTTTAAAATTTTAAATATATTTTTTATAA
18126009 TTTAAATATATTTTTTAAAATTTTAAATATATTTTTTAATAA
1 TTTAAATATATTTTTTAAAATTTTAAATATATTTTTT-ATAA
*
18126051 TATAAA-ATATTT
1 TTTAAATATATTT
18126063 AAATATTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
40 29 0.57
41 10 0.20
42 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (41 bp):
TTTAAATATATTTTTTAAAATTTTAAATATATTTTTTATAA
Found at i:18126071 original size:39 final size:38
Alignment explanation
Indices: 18125981--18126079 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 38
18125971 TAATATTATT
*
18125981 TTTTAAAATTTTAAATATATTTTTTTAATTTAAATATA
1 TTTTAAAATTTTAAATATATTTTTTTAATATAAATATA
18126019 TTTTTTAAAATTTTAAATATATTTTTTAATAATATAAA-ATA
1 --TTTTAAAATTTTAAATATATTTTTT--TAATATAAATATA
*
18126060 -TTTAAATATTTTAAAGATAT
1 TTTTAAA-ATTTTAAATATAT
18126080 GAACTTTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
38 6 0.11
39 12 0.22
40 25 0.46
41 3 0.06
42 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (38 bp):
TTTTAAAATTTTAAATATATTTTTTTAATATAAATATA
Found at i:18126136 original size:9 final size:9
Alignment explanation
Indices: 18126119--18126180 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
18126109 ATATTTTAAA
*
18126119 TTTTAAATT
1 TTTTTAATT
18126128 TTTTTAATT
1 TTTTTAATT
*
18126137 TGTTTTATAAT
1 T-TTTTA-ATT
*
18126148 TTTTTAA-A
1 TTTTTAATT
18126156 TTTTTAATT
1 TTTTTAATT
18126165 TTTTTAATT
1 TTTTTAATT
18126174 TTTTTAA
1 TTTTTAA
18126181 AATATATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 7 0.15
9 26 0.57
10 10 0.22
11 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTAATT
Found at i:18126147 original size:37 final size:37
Alignment explanation
Indices: 18126084--18126185 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
18126074 AGATATGAAC
* *
18126084 TTTTAAA-TTTATT-ATTAGTTTTATAATATTTTAAA
1 TTTTAAATTTTTTTAATTTGTTTTATAATATTTTAAA
*
18126119 TTTTAAATTTTTTTAATTTGTTTTATAATTTTTTAAA
1 TTTTAAATTTTTTTAATTTGTTTTATAATATTTTAAA
* *
18126156 TTTTTAATTTTTTTAATTT-TTTTAAAATAT
1 TTTTAAATTTTTTTAATTTGTTTTATAATAT
18126186 ATTATTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 7 0.12
36 14 0.24
37 38 0.64
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (37 bp):
TTTTAAATTTTTTTAATTTGTTTTATAATATTTTAAA
Found at i:18126176 original size:16 final size:16
Alignment explanation
Indices: 18126102--18126176 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 16
18126092 TTATTATTAG
*
18126102 TTTTATAATATTTTAAA
1 TTTT-TAATTTTTTAAA
* *
18126119 TTTTAAATTTTTTTAATTTG
1 TTTTTAA-TTTTTTAA---A
18126139 TTTTATAATTTTTTAAA
1 TTTT-TAATTTTTTAAA
*
18126156 TTTTTAATTTTTTTAA
1 TTTTTAATTTTTTAAA
18126172 TTTTT
1 TTTTT
18126177 TTAAAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
16 18 0.38
17 15 0.32
20 12 0.26
21 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTTAATTTTTTAAA
Found at i:18126177 original size:8 final size:8
Alignment explanation
Indices: 18126102--18126177 Score: 53
Period size: 8 Copynumber: 8.8 Consensus size: 8
18126092 TTATTATTAG
*
18126102 TTTTATAA
1 TTTTTTAA
*
18126110 TATTTTAA
1 TTTTTTAA
* *
18126118 ATTTTAAA
1 TTTTTTAA
18126126 TTTTTTTAA
1 -TTTTTTAA
18126135 TTTGTTTTATAA
1 --T-TTTT-TAA
18126147 TTTTTTAA
1 TTTTTTAA
*
18126155 ATTTTTAA
1 TTTTTTAA
18126163 TTTTTTTAA
1 -TTTTTTAA
18126172 TTTTTT
1 TTTTTT
18126178 TAAAATATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 27 0.50
9 17 0.31
10 3 0.06
11 4 0.07
12 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTTTTAA
Found at i:18128848 original size:22 final size:22
Alignment explanation
Indices: 18128820--18128863 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18128810 TTTGAGTAAA
*
18128820 AAAGTACATCGGTCGTCGGCCG
1 AAAGTACATCGGTCATCGGCCG
18128842 AAAGTACATCGGTCATCGGCCG
1 AAAGTACATCGGTCATCGGCCG
18128864 GGGATCCCGC
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:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (22 bp):
AAAGTACATCGGTCATCGGCCG
Found at i:18132529 original size:21 final size:21
Alignment explanation
Indices: 18132497--18132551 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
18132487 TGACTAGTTA
* *
18132497 TAATATATATTTTTATTTTTT
1 TAATATAAATTTTTACTTTTT
*
18132518 TAATTTAAATTTTTACTTTTT
1 TAATATAAATTTTTACTTTTT
*
18132539 TAATATATATTTT
1 TAATATAAATTTT
18132552 AAATAAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TAATATAAATTTTTACTTTTT
Found at i:18132877 original size:23 final size:21
Alignment explanation
Indices: 18132827--18132887 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
18132817 TTTTATATTA
**
18132827 TTAAAAATATATTTAAAATTT
1 TTAAAAATATATTTAAAACAT
18132848 TTAAAAATAATATTATAAAACAT
1 TTAAAAAT-ATATT-TAAAACAT
*
18132871 TTCAAAAT-T-TTTAAAAC
1 TTAAAAATATATTTAAAAC
18132888 CAATAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 9 0.26
22 5 0.14
23 13 0.37
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAATATATTTAAAACAT
Found at i:18132877 original size:24 final size:21
Alignment explanation
Indices: 18132829--18132877 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
18132819 TTATATTATT
* *
18132829 AAAAATATATTTAAAATTTTT
1 AAAAATATATTTAAAAATTTC
18132850 AAAAATAATATTATAAAACATTTC
1 AAAAAT-ATATT-TAAAA-ATTTC
18132874 AAAA
1 AAAA
18132878 TTTTTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 5 0.22
23 5 0.22
24 7 0.30
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATATATTTAAAAATTTC
Found at i:18140125 original size:26 final size:26
Alignment explanation
Indices: 18140102--18140153 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18140092 TTGAAAGAGG
* * *
18140102 AAAAAGAAGAAAAATAAAGGAAGAAA
1 AAAAAGAAAAAAAACAAAAGAAGAAA
18140128 AAAAAGAAAAAAAACAAAAGAAGAAA
1 AAAAAGAAAAAAAACAAAAGAAGAAA
18140154 GGGAAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAAAACAAAAGAAGAAA
Found at i:18140126 original size:14 final size:13
Alignment explanation
Indices: 18140102--18140167 Score: 55
Period size: 14 Copynumber: 5.0 Consensus size: 13
18140092 TTGAAAGAGG
18140102 AAAAA-GAAGAAA
1 AAAAAGGAAGAAA
18140114 AATAAAGGAAGAAA
1 AA-AAAGGAAGAAA
*
18140128 AAAAA-GAAAAAA
1 AAAAAGGAAGAAA
*
18140140 AACAAAAGAAGAAA
1 AA-AAAGGAAGAAA
**
18140154 GGGAAAGGAAGAAA
1 -AAAAAGGAAGAAA
18140168 TTGACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
12 10 0.23
13 9 0.20
14 25 0.57
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAAGGAAGAAA
Found at i:18144149 original size:23 final size:20
Alignment explanation
Indices: 18144114--18144155 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 20
18144104 AAAATATTTT
18144114 TATATAAATTTAATTATAAAC
1 TATATAAATTTAA-TATAAAC
18144135 TATATAAAATATTAATATAAA
1 TATAT-AAAT-TTAATATAAA
18144156 ATACTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAAATTTAATATAAAC
Found at i:18147762 original size:20 final size:18
Alignment explanation
Indices: 18147733--18147769 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
18147723 TGAAAAATAA
18147733 TTTTTAGAAAATGATTTAT
1 TTTTTAG-AAATGATTTAT
18147752 TTTTCTAGAAATGATTTA
1 TTTT-TAGAAATGATTTA
18147770 CTCTGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTTTAGAAATGATTTAT
Found at i:18148841 original size:56 final size:56
Alignment explanation
Indices: 18148781--18148893 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
18148771 AAGAACAAGT
18148781 AAAAAACAATTGAAATATACTTAAAAAATATATAAATATATTACCATCACTACTGC
1 AAAAAACAATTGAAATATACTTAAAAAATATATAAATATATTACCATCACTACTGC
18148837 AAAAAACAATTGAAATATACTTAAAAAATATATAAATATATTACCATCACTACTGC
1 AAAAAACAATTGAAATATACTTAAAAAATATATAAATATATTACCATCACTACTGC
18148893 A
1 A
18148894 TCATATGTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.28
Consensus pattern (56 bp):
AAAAAACAATTGAAATATACTTAAAAAATATATAAATATATTACCATCACTACTGC
Found at i:18153710 original size:8 final size:8
Alignment explanation
Indices: 18153697--18153723 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
18153687 AGATTTGCCT
18153697 GAGAAAGA
1 GAGAAAGA
18153705 GAGAAAGA
1 GAGAAAGA
18153713 GAGAAAGA
1 GAGAAAGA
18153721 GAG
1 GAG
18153724 GAAACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:18153809 original size:25 final size:26
Alignment explanation
Indices: 18153772--18153820 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
18153762 AAGCTAGAAG
18153772 ATGAAAAAAGGAAGAAGGA-AAAGGA
1 ATGAAAAAAGGAAGAAGGAGAAAGGA
* *
18153797 ATGAAGAATGGAAGAAGGAGAAAG
1 ATGAAAAAAGGAAGAAGGAGAAAG
18153821 ACTTACCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (26 bp):
ATGAAAAAAGGAAGAAGGAGAAAGGA
Found at i:18154516 original size:13 final size:13
Alignment explanation
Indices: 18154498--18154561 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
18154488 AGTTTGACAA
18154498 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
18154511 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
18154524 TGC-TGTGAAAAAA
1 TGCTTTTG-AAAAG
* *
18154537 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
18154550 TGTTTTTGAAAA
1 TGCTTTTGAAAA
18154562 TTTTGATTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 3 0.08
13 34 0.85
14 3 0.08
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:18171915 original size:22 final size:22
Alignment explanation
Indices: 18171887--18171931 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
18171877 CTCCATATGA
18171887 CATTTTCATTAAATTGTAAAAC
1 CATTTTCATTAAATTGTAAAAC
* *
18171909 CATTTTCCTTCAATTGTAAAAC
1 CATTTTCATTAAATTGTAAAAC
18171931 C
1 C
18171932 TTTAGGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (22 bp):
CATTTTCATTAAATTGTAAAAC
Found at i:18178608 original size:10 final size:10
Alignment explanation
Indices: 18178573--18178623 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
18178563 TAAAATTCTA
18178573 AAAGATAAAT
1 AAAGATAAAT
*
18178583 AATAAATAAAT
1 AA-AGATAAAT
* *
18178594 GAAGATAATT
1 AAAGATAAAT
18178604 AAAGATAAAT
1 AAAGATAAAT
18178614 AAAGATAAAT
1 AAAGATAAAT
18178624 GAAATTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:18178632 original size:20 final size:20
Alignment explanation
Indices: 18178573--18178633 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
18178563 TAAAATTCTA
18178573 AAAGATAAATAATAAATAAAT
1 AAAGATAAATAA-AAATAAAT
* * *
18178594 GAAGATAATTAAAGATAAAT
1 AAAGATAAATAAAAATAAAT
* *
18178614 AAAGATAAATGAAATTAAAT
1 AAAGATAAATAAAAATAAAT
18178634 CCTAAAATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAAATAAAT
Found at i:18181773 original size:29 final size:28
Alignment explanation
Indices: 18181708--18181773 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
18181698 CTCTTCATAA
* *
18181708 ATTTGAAATTTAGTCTATATACTTTTAT
1 ATTTGAAATTTAATCGATATACTTTTAT
* * *
18181736 TTTTAGAAATTTAATCGCTCTACTTTTCAT
1 ATTT-GAAATTTAATCGATATACTTTT-AT
18181766 ATTTGAAA
1 ATTTGAAA
18181774 ATCCATATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.10
29 22 0.73
30 5 0.17
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (28 bp):
ATTTGAAATTTAATCGATATACTTTTAT
Found at i:18182372 original size:26 final size:30
Alignment explanation
Indices: 18182351--18182415 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 30
18182341 TATTATGTTA
18182351 TAAAA-AATA-TTATATTAATTATATATAT
1 TAAAATAATATTTATATTAATTATATATAT
*
18182379 TAAAATAATATTTATATATATTTATATTTATAT
1 TAAAATAATATTTATAT-TAATTATA--TATAT
18182412 TAAA
1 TAAA
18182416 TCACTAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 5 0.16
29 4 0.13
30 6 0.19
31 7 0.23
33 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATAATATTTATATTAATTATATATAT
Found at i:18187753 original size:15 final size:15
Alignment explanation
Indices: 18187733--18187762 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18187723 TGTTGTATGA
18187733 TAGTTATTCATCGAG
1 TAGTTATTCATCGAG
18187748 TAGTTATTCATCGAG
1 TAGTTATTCATCGAG
18187763 ATACTATAGC
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:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TAGTTATTCATCGAG
Found at i:18196813 original size:5 final size:5
Alignment explanation
Indices: 18196805--18196835 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
18196795 TTACTTTTTC
18196805 TTTAA TTTAA TTTAA TTTAA TTTAA TATTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA T-TTAA
18196836 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:18227066 original size:18 final size:18
Alignment explanation
Indices: 18227043--18227109 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
18227033 TATTAAAGAC
* *
18227043 TGACTGCTACTGAATAAT
1 TGACTGTTACTGAATAAA
*
18227061 TGACTGTTACTGAGTAAA
1 TGACTGTTACTGAATAAA
* *
18227079 CGACTGATACTGAATAAA
1 TGACTGTTACTGAATAAA
*
18227097 TGATTGTTACTGA
1 TGACTGTTACTGA
18227110 TTAACCTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (18 bp):
TGACTGTTACTGAATAAA
Found at i:18232457 original size:29 final size:28
Alignment explanation
Indices: 18232403--18232457 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
18232393 TGAGTAAAAT
* **
18232403 GGACTAAATTGTGAAATTTATAAATGAG
1 GGACTAAAATGTGAAATAAATAAATGAG
18232431 GGACTAAAATGTGAAATAAATGAAATG
1 GGACTAAAATGTGAAATAAAT-AAATG
18232458 TGTGAACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (28 bp):
GGACTAAAATGTGAAATAAATAAATGAG
Found at i:18234141 original size:19 final size:19
Alignment explanation
Indices: 18234117--18234154 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18234107 TGACTTGTAG
18234117 TTGTTTGAAAAATGTTTAA
1 TTGTTTGAAAAATGTTTAA
18234136 TTGTTTGAAAAATGTTTAA
1 TTGTTTGAAAAATGTTTAA
18234155 GTTTTGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGTTTGAAAAATGTTTAA
Found at i:18234160 original size:18 final size:19
Alignment explanation
Indices: 18234118--18234160 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
18234108 GACTTGTAGT
*
18234118 TGTTTGAAAAATGTTTAAT
1 TGTTTGAAAAATGTTTAAG
18234137 TGTTTGAAAAATGTTTAAG
1 TGTTTGAAAAATGTTTAAG
18234156 T-TTTG
1 TGTTTG
18234161 GGAAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (19 bp):
TGTTTGAAAAATGTTTAAG
Found at i:18234166 original size:19 final size:19
Alignment explanation
Indices: 18234117--18234168 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
18234107 TGACTTGTAG
*
18234117 TTGTTTGAAAAATGTTTAA
1 TTGTTGGAAAAATGTTTAA
*
18234136 TTGTTTGAAAAATGTTTAA
1 TTGTTGGAAAAATGTTTAA
18234155 GTT-TTGGGAAAAAT
1 -TTGTT-GGAAAAAT
18234169 TTGTATGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGTTGGAAAAATGTTTAA
Found at i:18241276 original size:40 final size:40
Alignment explanation
Indices: 18241221--18241296 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
18241211 ACAGTACCTC
* *
18241221 ATGGTGTGTAGGGATGGATGGGTCGATTTTATCCCCTTAT
1 ATGGTGTGCAGGGATGGATAGGTCGATTTTATCCCCTTAT
*
18241261 ATGGTGTGCAGGGATGGTTAGGTCGATTTTATCCCC
1 ATGGTGTGCAGGGATGGATAGGTCGATTTTATCCCC
18241297 ACATAGTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (40 bp):
ATGGTGTGCAGGGATGGATAGGTCGATTTTATCCCCTTAT
Found at i:18251334 original size:15 final size:15
Alignment explanation
Indices: 18251293--18251363 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
18251283 TTTATATACT
*
18251293 TTTAATT-AAATCTA
1 TTTAATTAAAATTTA
* * *
18251307 ATTAATCATAATTTA
1 TTTAATTAAAATTTA
18251322 TTTAATTAAAATTTA
1 TTTAATTAAAATTTA
** *
18251337 AATAATTAAAAATTAA
1 TTTAATT-AAAATTTA
18251353 TTATAATTAAA
1 TT-TAATTAAA
18251364 CAATTTAGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
14 5 0.12
15 22 0.52
16 10 0.24
17 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATTAAAATTTA
Found at i:18253220 original size:24 final size:24
Alignment explanation
Indices: 18253175--18253220 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
18253165 GGTAGGAAAA
* **
18253175 AGAAAAATAAAATGAGGGAAAATG
1 AGAAAAATAAAATAAAAGAAAATG
*
18253199 AGAAAAATAAAATAAAATAAAA
1 AGAAAAATAAAATAAAAGAAAA
18253221 GGTGGGCCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (24 bp):
AGAAAAATAAAATAAAAGAAAATG
Found at i:18254955 original size:11 final size:11
Alignment explanation
Indices: 18254939--18254977 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18254929 AACATTTTCA
18254939 TAATAAAATAT
1 TAATAAAATAT
18254950 TAATAAAA-ATT
1 TAATAAAATA-T
18254961 TAATTAAAATAT
1 TAA-TAAAATAT
18254973 TAATA
1 TAATA
18254978 TTATAACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.04
11 14 0.56
12 9 0.36
13 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:18257226 original size:23 final size:23
Alignment explanation
Indices: 18257179--18257226 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
18257169 ATTTTTTTTC
*
18257179 ACATTAATAATTCTTTTCATTTA
1 ACATTAATAATTCTTTTCATCTA
18257202 ACATT-ATAATT-TTTTACATACTA
1 ACATTAATAATTCTTTT-CAT-CTA
18257225 AC
1 AC
18257227 TCATTACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (23 bp):
ACATTAATAATTCTTTTCATCTA
Found at i:18266962 original size:44 final size:44
Alignment explanation
Indices: 18266899--18266988 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
18266889 CGCCAACAGG
18266899 TATGTTGCTACTTGCAATAAATGCCAACGAACAGGTAATATCTC
1 TATGTTGCTACTTGCAATAAATGCCAACGAACAGGTAATATCTC
18266943 TATGTTGCTACTTGCAATAAATGCCAACGAACAGGTAATATCTC
1 TATGTTGCTACTTGCAATAAATGCCAACGAACAGGTAATATCTC
18266987 TA
1 TA
18266989 AACGTGACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (44 bp):
TATGTTGCTACTTGCAATAAATGCCAACGAACAGGTAATATCTC
Found at i:18272978 original size:30 final size:30
Alignment explanation
Indices: 18272943--18273000 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
18272933 TAGGCACTTC
*
18272943 CACACGGGTAGTCCACATGCCCGTGTGTGA
1 CACACGGGTAGACCACATGCCCGTGTGTGA
18272973 CACACGGGTAGACCACATGCCCGTGTGT
1 CACACGGGTAGACCACATGCCCGTGTGT
18273001 CATGGCTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (30 bp):
CACACGGGTAGACCACATGCCCGTGTGTGA
Found at i:18275520 original size:42 final size:43
Alignment explanation
Indices: 18275422--18275542 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
18275412 AACAAGTACA
* * * * *
18275422 ATGCCGACGTCCCAAACGTGATCTTACATGTAATTCAATATCG
1 ATGCCGATGTCCCAAACATGGTCTTACACGTAAATCAATATCG
** *
18275465 ATGCCTCTGTCCCAAACATGGTTTTACACG-AAATCAGATA-CG
1 ATGCCGATGTCCCAAACATGGTCTTACACGTAAATCA-ATATCG
* *
18275507 ATGCCGATGTCCCAGACATGGTCTTATACGTAAATC
1 ATGCCGATGTCCCAAACATGGTCTTACACGTAAATC
18275543 TCAATTGAGG
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 32 0.51
43 31 0.49
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGCCGATGTCCCAAACATGGTCTTACACGTAAATCAATATCG
Found at i:18279890 original size:15 final size:15
Alignment explanation
Indices: 18279870--18279900 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18279860 AGCCGAAGCT
18279870 ATCTCGATCTCACAC
1 ATCTCGATCTCACAC
*
18279885 ATCTCGATTTCACAC
1 ATCTCGATCTCACAC
18279900 A
1 A
18279901 CTAAATGCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (15 bp):
ATCTCGATCTCACAC
Found at i:18281640 original size:13 final size:13
Alignment explanation
Indices: 18281622--18281657 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
18281612 ATATCTCTAT
18281622 AAATATTTACTAA
1 AAATATTTACTAA
18281635 AAATATTTACTAA
1 AAATATTTACTAA
18281648 AAATATTTAC
1 AAATATTTAC
18281658 GGACCCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATTTACTAA
Found at i:18289965 original size:5 final size:5
Alignment explanation
Indices: 18289955--18289998 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
18289945 AAGAATTAAG
18289955 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
18289999 ATAAAAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:18290767 original size:24 final size:24
Alignment explanation
Indices: 18290740--18290786 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
18290730 ATTGAAATGG
18290740 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
18290764 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
18290787 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:18290799 original size:17 final size:15
Alignment explanation
Indices: 18290763--18290814 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
18290753 GTGATGAATT
18290763 TATTGAATTTATAT-
1 TATTGAATTTATATA
18290777 TGATTGAATTGGTATATA
1 T-ATTGAATT--TATATA
*
18290795 TATTGAATATATATA
1 TATTGAATTTATATA
18290810 TATTG
1 TATTG
18290815 GTTATTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 19 0.58
17 12 0.36
18 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TATTGAATTTATATA
Found at i:18292502 original size:13 final size:13
Alignment explanation
Indices: 18292484--18292508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18292474 GTAAGTGATT
18292484 TTGATGATTTTTC
1 TTGATGATTTTTC
18292497 TTGATGATTTTT
1 TTGATGATTTTT
18292509 ACATTTTGGG
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:18293475 original size:47 final size:49
Alignment explanation
Indices: 18293307--18293480 Score: 151
Period size: 49 Copynumber: 3.6 Consensus size: 49
18293297 AAGATGTGCT
* * * ** *
18293307 AGTGTAAGGCCATGTCAGGGATATGGCATCGGCACGGATATGT-GA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-ACTCA-AT-TCGATGAGCC
* * *
18293357 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCAATTTCGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCAA-TTCGATGAGCC
* ** *
18293406 AGTGTAAGACCATGTTTGGGACATGGCATC-GACTTGA-TGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCAATTCGATGAGCC
*
18293453 AGTGTAAGACCATGTCTAGGACATGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCA
18293481 CCGGTATTAT
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
46 4 0.04
47 29 0.28
48 6 0.06
49 35 0.34
50 28 0.27
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGACTCAATTCGATGAGCC
Found at i:18294449 original size:13 final size:13
Alignment explanation
Indices: 18294431--18294466 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18294421 GCCGTGTCAG
18294431 GGACACGGGCCAT
1 GGACACGGGCCAT
* *
18294444 GGACACGAGCTAT
1 GGACACGGGCCAT
18294457 GGACACGGGC
1 GGACACGGGC
18294467 GTGTGATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.25, C:0.28, G:0.39, T:0.08
Consensus pattern (13 bp):
GGACACGGGCCAT
Found at i:18304588 original size:29 final size:28
Alignment explanation
Indices: 18304552--18304629 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
18304542 TCATGAGATT
18304552 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
18304582 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
18304609 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
18304630 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:18304903 original size:173 final size:174
Alignment explanation
Indices: 18304582--18304908 Score: 566
Period size: 173 Copynumber: 1.9 Consensus size: 174
18304572 AAATTGTACA
* *
18304582 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
18304647 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
18304712 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
18304756 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
18304821 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
18304885 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
18304909 ACCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 80 0.56
174 64 0.44
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:18312717 original size:29 final size:28
Alignment explanation
Indices: 18312681--18312758 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
18312671 TCATGAGATT
18312681 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
18312711 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
18312738 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
18312759 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:18313031 original size:173 final size:172
Alignment explanation
Indices: 18312711--18313035 Score: 553
Period size: 173 Copynumber: 1.9 Consensus size: 172
18312701 AAATTGTACA
* *
18312711 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
18312776 TGTGCGAACCCAATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATT
66 TGTGCGAACCCAATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAATT
18312841 TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
18312883 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
18312948 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCA--ATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
18313012 TTTTGGACAGCGGAAAAGGTAAGT
129 TTTTGGACAGCGGAAAAGGTAAGT
18313036 ACCTTGAGTT
Statistics
Matches: 143, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
171 6 0.04
172 64 0.45
173 73 0.51
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (172 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAATT
TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:18315366 original size:392 final size:391
Alignment explanation
Indices: 18314642--18315429 Score: 914
Period size: 392 Copynumber: 2.0 Consensus size: 391
18314632 CATTGGTATC
* * * * *
18314642 ACTGAATTTGGGTTTGGATTTTGGATTTTTAGGTTCTGGAGTACTCGTGGTTGCTTTAGCATCAT
1 ACTGAATTCGAGTTTGGATTATGAATTTTTAGGTTCTAGAGTACTCGTGGTTGCTTTAGCATCAT
* * * *
18314707 TTTGATACTAGGTGTGTACCTAAAAACACAGAAAACAAGAAGCGACGAAAGCTGAAAAACGAATC
66 TTTGATACTAGGTGTGTACCCAAAAACACAAAAAACAAGAAGCGACAAAAGCTAAAAAACGAATC
* * * * *
18314772 TATCGATGCCACACGGCCATGTGGTCGCCCGTGTGGTAGGCCGTGTGATAGCACTTATGATCGAT
131 TATCAACGCCACACGGCCATGTGGTCACCCGTGTGGTAGGCCGTGTGACAGCACTTATGATCGAC
* * * * ** *
18314837 GAGCCAAGCCGTGAGAACAAGATATGGGCATATAACACAGCTGTGTGTTGGTCGGTGAGACCATG
196 GAGCCAAGCCGTGAG-ACAAGAAACGAGCACATAACACAGCTGTGTGTTGACCGGTAAGACCATG
* ** * *
18314902 TGGGATAAACGGGCTCGACCCATTGGGCCGTGTGGGCCACACAAGCGTGTGAGCCCACACAGGTA
260 TGGGATAAACGGACTCGACCCATCAGGCCGTGTGGGCCACACAAGCGTGTGAGACCACACAGGCA
* * * * *
18314967 GGCCACATGGGCATGTGAGCCCATTTTTTTGAAATAATCTATAAGGTTGCACGGGTTGCCCAAGT
325 GGCCACATAGGCATGTGAGCCCATTTTTCTAAAATAATCTATAAAGTTGCACGGGTCGCCCAAGT
18315032 CG
390 CG
* *
18315034 ACTGAATTCGAGTTTGGATTATGAATTTTTAGGTTCTAGAGTGCTTGTGGTTGCTTTAGCATCAT
1 ACTGAATTCGAGTTTGGATTATGAATTTTTAGGTTCTAGAGTACTCGTGGTTGCTTTAGCATCAT
* *
18315099 TTTGATACCTA-GTGTGTACCCGAAAACACAAAAAACAAGAAGCGACAAAAG-TCAAAAAATGAA
66 TTTGATA-CTAGGTGTGTACCCAAAAACACAAAAAACAAGAAGCGACAAAAGCT-AAAAAACGAA
* *
18315162 TCTGTCAACGCCACACGGCCGTGTGGTCACCCGTGTGGTA-GCCTGTGTGACAGCACATGGGCGT
129 TCTATCAACGCCACACGGCCATGTGGTCACCCGTGTGGTAGGCC-GTGTGACAGCAC-T-----T
* * ** * *
18315226 GTGATTGACGAGCCAAGCC-TGTACG-CAAGAAACGAGCACATTGCACGGCTTTGTGTTGACCGG
187 ATGATCGACGAGCCAAGCCGTG-A-GACAAGAAACGAGCACATAACACAGCTGTGTGTTGACCGG
* * * * *
18315289 TAAGGCCATGTGTGATACACGGACTCGGCCACA-CAGG-CGTGTGGGCC-CACATG-G-GTGA-A
250 TAAGACCATGTGGGATAAACGGACTCGACC-CATCAGGCCGTGTGGGCCACACAAGCGTGTGAGA
* ** *
18315348 CCACACGGGCAGGCCACATAGGCATGTGAGCTTATTTTTCTAAAATAATCTATAAAGTTGCATGG
314 CCACACAGGCAGGCCACATAGGCATGTGAGCCCATTTTTCTAAAATAATCTATAAAGTTGCACGG
18315413 GTCGCCCAAGTCG
379 GTCGCCCAAGTCG
18315426 ACTG
1 ACTG
18315430 TGACCAACCA
Statistics
Matches: 332, Mismatches: 52, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
391 4 0.01
392 227 0.68
393 8 0.02
394 1 0.00
395 5 0.02
396 10 0.03
397 56 0.17
398 20 0.06
399 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (391 bp):
ACTGAATTCGAGTTTGGATTATGAATTTTTAGGTTCTAGAGTACTCGTGGTTGCTTTAGCATCAT
TTTGATACTAGGTGTGTACCCAAAAACACAAAAAACAAGAAGCGACAAAAGCTAAAAAACGAATC
TATCAACGCCACACGGCCATGTGGTCACCCGTGTGGTAGGCCGTGTGACAGCACTTATGATCGAC
GAGCCAAGCCGTGAGACAAGAAACGAGCACATAACACAGCTGTGTGTTGACCGGTAAGACCATGT
GGGATAAACGGACTCGACCCATCAGGCCGTGTGGGCCACACAAGCGTGTGAGACCACACAGGCAG
GCCACATAGGCATGTGAGCCCATTTTTCTAAAATAATCTATAAAGTTGCACGGGTCGCCCAAGTC
G
Found at i:18320136 original size:21 final size:21
Alignment explanation
Indices: 18320112--18320174 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
18320102 GAAAATTTGA
18320112 GATAGATTGAAGATAGCTTTT
1 GATAGATTGAAGATAGCTTTT
** *
18320133 GATAGACAGAA-AT--C--AT
1 GATAGATTGAAGATAGCTTTT
18320149 -ATAGATTGAAGATAGCTTTT
1 GATAGATTGAAGATAGCTTTT
18320169 GATAGA
1 GATAGA
18320175 CAGAAATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 8 0.27
16 3 0.10
18 2 0.07
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (21 bp):
GATAGATTGAAGATAGCTTTT
Found at i:18320154 original size:36 final size:36
Alignment explanation
Indices: 18320113--18320186 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
18320103 AAAATTTGAG
18320113 ATAGATTGAAGATAGCTTTTGATAGACAGAAATCAT
1 ATAGATTGAAGATAGCTTTTGATAGACAGAAATCAT
18320149 ATAGATTGAAGATAGCTTTTGATAGACAGAAATCAT
1 ATAGATTGAAGATAGCTTTTGATAGACAGAAATCAT
18320185 AT
1 AT
18320187 GTAGATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (36 bp):
ATAGATTGAAGATAGCTTTTGATAGACAGAAATCAT
Found at i:18321021 original size:5 final size:5
Alignment explanation
Indices: 18321011--18321115 Score: 185
Period size: 5 Copynumber: 20.8 Consensus size: 5
18321001 GAATTAAGTA
18321011 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
18321061 TATAT TATAT TATTATT TATAT TATAT TATA- TATAT TATAT TATAT TATAT
1 TATAT TATAT TA-TA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT
18321112 TATA
1 TATA
18321116 ATAAAAAACA
Statistics
Matches: 97, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.04
5 86 0.89
6 4 0.04
7 3 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:18321922 original size:13 final size:13
Alignment explanation
Indices: 18321904--18321928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18321894 GATTGAATTG
18321904 TATATATATTGAA
1 TATATATATTGAA
18321917 TATATATATTGA
1 TATATATATTGA
18321929 TTATTTGAAT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TATATATATTGAA
Found at i:18325125 original size:49 final size:49
Alignment explanation
Indices: 18325056--18325347 Score: 452
Period size: 49 Copynumber: 6.1 Consensus size: 49
18325046 GAAATGATAG
18325056 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
18325105 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
18325152 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
18325201 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
18325250 TAGGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
18325297 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
18325344 TAAG
1 TAAG
18325348 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
47 95 0.42
48 1 0.00
49 132 0.58
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:18325220 original size:96 final size:96
Alignment explanation
Indices: 18325056--18325347 Score: 462
Period size: 96 Copynumber: 3.0 Consensus size: 96
18325046 GAAATGATAG
*
18325056 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
*
18325121 ATGTGATGAATGTGAAAGTGTATATACGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
18325152 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
18325217 ATGTGATGAATGTGAAAGTGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTG--TATATATGTGA
* * * * *
18325250 TAGGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATATATATGTGACAGGGCCGAGTGGCCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
* * *
18325313 ACGTGATGGATGTGAAAGTGTATAAATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
18325344 TAAG
1 TAAG
18325348 TCCCGAAGGG
Statistics
Matches: 183, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
94 13 0.07
96 128 0.70
98 42 0.23
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (96 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:18325326 original size:145 final size:143
Alignment explanation
Indices: 18325059--18325345 Score: 466
Period size: 145 Copynumber: 2.0 Consensus size: 143
18325049 ATGATAGTAA
18325059 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
* * * * *
18325124 TGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTATATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
18325189 ATATATATGTGATAG
131 ATA-A-ATGTGATAG
*
18325204 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
* * * *
18325269 TGATGAATGTGAAAGTATATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGT
66 TGATGAATGTGAAAGTATATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
18325334 ATAAATGTGATA
131 ATAAATGTGATA
18325346 AGTCCCGAAG
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 8 0.06
144 1 0.01
145 123 0.93
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (143 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
TGATGAATGTGAAAGTATATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGT
ATAAATGTGATAG
Found at i:18327387 original size:41 final size:40
Alignment explanation
Indices: 18327337--18327450 Score: 126
Period size: 41 Copynumber: 2.9 Consensus size: 40
18327327 TTCGACTTCA
18327337 ATTCGATGAGACACTAGGTGTCAAATTATTACTTCGGATAT
1 ATTCGATGAGACACTAGGTGTCAAATTATTACTTCGG-TAT
* * * * *
18327378 ATTCAATGAGGCACTAGGTG-CCAA-T-TTACTTCAGTTT
1 ATTCGATGAGACACTAGGTGTCAAATTATTACTTCGGTAT
** *
18327415 AGCCGATGAGACACTGGGTGTCAAATTATTACTTCG
1 ATTCGATGAGACACTAGGTGTCAAATTATTACTTCG
18327451 AATTATCCGA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
37 17 0.29
38 11 0.19
39 2 0.03
40 10 0.17
41 18 0.31
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (40 bp):
ATTCGATGAGACACTAGGTGTCAAATTATTACTTCGGTAT
Found at i:18327461 original size:40 final size:40
Alignment explanation
Indices: 18327340--18327464 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
18327330 GACTTCAATT
* *
18327340 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAAT-TATC
* * * * *
18327381 CAATGAGGCACTAGGTG-CCAA-T-TTACTTC-AGTTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGA-ATTATC
*
18327418 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
18327458 CGATGAG
1 CGATGAG
18327465 GCATTGGGTG
Statistics
Matches: 66, Mismatches: 13, Indels: 11
0.73 0.14 0.12
Matches are distributed among these distances:
37 16 0.24
38 11 0.17
39 2 0.03
40 21 0.32
41 16 0.24
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
Found at i:18327473 original size:40 final size:40
Alignment explanation
Indices: 18327340--18327479 Score: 126
Period size: 40 Copynumber: 3.5 Consensus size: 40
18327330 GACTTCAATT
* * * *
18327340 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAAT-TATC
* * * * *
18327381 CAATGAGGCACTAGGTG-CCAA-T-TTACTTC-AGTTTAGC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGA-ATTATC
*
18327418 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
* *
18327458 CGATGAGGCATTGGGTGCCAAA
1 CGATGAGGCACTGGGTGTCAAA
18327480 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 11
0.74 0.15 0.10
Matches are distributed among these distances:
37 16 0.21
38 11 0.14
39 2 0.03
40 33 0.42
41 16 0.21
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (40 bp):
CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:18339826 original size:18 final size:18
Alignment explanation
Indices: 18339803--18339837 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18339793 AAATATATCA
18339803 TTTTAT-ATTAACATTTAT
1 TTTTATAATTAA-ATTTAT
18339821 TTTTATAATTAAATTTA
1 TTTTATAATTAAATTTA
18339838 AATAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAATTAAATTTAT
Found at i:18341170 original size:17 final size:17
Alignment explanation
Indices: 18341148--18341182 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18341138 ATTACATTAT
18341148 CATATCTTCT-AAGATTG
1 CATATCTT-TGAAGATTG
18341165 CATATCTTTGAAGATTG
1 CATATCTTTGAAGATTG
18341182 C
1 C
18341183 GTACCATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (17 bp):
CATATCTTTGAAGATTG
Found at i:18348985 original size:29 final size:29
Alignment explanation
Indices: 18348940--18349003 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
18348930 GTTAAAAAAA
* *
18348940 TTTTA-AAGATCAGAATTGTAAATCAAATT
1 TTTTAGAAAATCAGAATTAT-AATCAAATT
* *
18348969 TTTTAGAAAATCA-AATTATATTTAAATT
1 TTTTAGAAAATCAGAATTATAATCAAATT
18348997 TTTTAGA
1 TTTTAGA
18349004 GTGATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.47
29 10 0.33
30 6 0.20
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTTAGAAAATCAGAATTATAATCAAATT
Found at i:18352575 original size:3 final size:3
Alignment explanation
Indices: 18352567--18352633 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
18352557 AAGGACCCAA
* * *
18352567 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AGT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18352615 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
18352634 CAAATAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:18353187 original size:20 final size:20
Alignment explanation
Indices: 18353162--18353236 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
18353152 AAGGTTTAAA
18353162 ATTTTTAAAAGAAAATTTTG
1 ATTTTTAAAAGAAAATTTTG
***
18353182 ATTTTT--AAGAAAAGTAGAG
1 ATTTTTAAAAGAAAA-TTTTG
*
18353201 AATTTTTAAAAGAAAATTTTA
1 -ATTTTTAAAAGAAAATTTTG
18353222 ATTTTGTAAAA-AAAA
1 ATTTT-TAAAAGAAAA
18353237 AAAATTCCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 21 0.49
21 6 0.14
22 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
ATTTTTAAAAGAAAATTTTG
Found at i:18355736 original size:118 final size:119
Alignment explanation
Indices: 18355555--18355776 Score: 299
Period size: 118 Copynumber: 1.9 Consensus size: 119
18355545 TCCTCGTTCA
*
18355555 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
18355620 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
18355674 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
18355736 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
18355777 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 66 0.73
119 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:18355776 original size:40 final size:40
Alignment explanation
Indices: 18355553--18355776 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
18355543 GCTCCTCGTT
* *
18355553 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
18355593 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
18355633 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
18355673 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
18355711 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
18355752 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18355777 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 24 0.15
39 21 0.13
40 107 0.65
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:18363489 original size:40 final size:39
Alignment explanation
Indices: 18363445--18363616 Score: 202
Period size: 40 Copynumber: 4.3 Consensus size: 39
18363435 GCTCCTCGTT
* * *
18363445 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
**
18363485 CAAATGCCTTCGGGACTTAACCCAAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGTTTAGTAACTCGCA
18363525 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
* * ** * *
18363565 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAACCC-GGTTTAGTAACTCGCA
18363604 CAAATGCCTTCGG
1 CAAATGCCTTCGG
18363617 ATCTTAGTCT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 30 0.26
40 83 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:18363653 original size:79 final size:80
Alignment explanation
Indices: 18363445--18363669 Score: 244
Period size: 80 Copynumber: 2.8 Consensus size: 80
18363435 GCTCCTCGTT
* * * *
18363445 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-CACAAATGCCTTCGGGACTTAACCCA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACT-AGCACAAA-GCCTTCGGGACTTAGCCCA
18363509 -AATTTAGTAACTCGCA
64 GAATTTAGTAACTCGCA
* * *
18363525 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCAG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCAG
* *
18363589 AA-TTAGTATCTCGTA
65 AATTTAGTAACTCGCA
** * * *
18363604 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCA
18363668 GA
64 GA
18363670 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.02
79 56 0.46
80 60 0.49
81 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCAGA
ATTTAGTAACTCGCA
Found at i:18366308 original size:10 final size:10
Alignment explanation
Indices: 18366289--18366348 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
18366279 TGACATTCTA
18366289 AAAGATAAAT
1 AAAGATAAAT
18366299 ACAA-ATAAAT
1 A-AAGATAAAT
*
18366309 AAAGATAATT
1 AAAGATAAAT
18366319 AAAGATAAAT
1 AAAGATAAAT
18366329 AAAGATAAAT
1 AAAGATAAAT
18366339 GAAA-ATAAAT
1 -AAAGATAAAT
18366349 CCTAGAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:18366991 original size:21 final size:21
Alignment explanation
Indices: 18366967--18367006 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18366957 TTAATACCTC
* * *
18366967 ATTTTTTTTCTTTTTTTTTTA
1 ATTTTATTTATTTATTTTTTA
18366988 ATTTTATTTATTTATTTTT
1 ATTTTATTTATTTATTTTT
18367007 ACTTAGGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
ATTTTATTTATTTATTTTTTA
Found at i:18367167 original size:96 final size:97
Alignment explanation
Indices: 18366998--18367184 Score: 313
Period size: 96 Copynumber: 1.9 Consensus size: 97
18366988 ATTTTATTTA
* * *
18366998 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
18367063 CCCCGGTTACTCAGCCCAACACATTCCTAATT
66 CCCCGGTTACTCAGCCCAACACATTCCTAATT
*
18367095 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
* *
18367159 CCCTGGTTACTTAGCCCAACACATTC
66 CCCCGGTTACTCAGCCCAACACATTC
18367185 TTAAAAATTA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 75 0.89
97 9 0.11
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
CCCCGGTTACTCAGCCCAACACATTCCTAATT
Found at i:18367958 original size:18 final size:15
Alignment explanation
Indices: 18367925--18367965 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
18367915 TTAATATCTG
18367925 AAAATAATAAATAAT
1 AAAATAATAAATAAT
*
18367940 AAAATAAT-AA-GAT
1 AAAATAATAAATAAT
18367953 AAAATAA-AAATAA
1 AAAATAATAAATAA
18367966 AAATTGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:18371920 original size:21 final size:21
Alignment explanation
Indices: 18371896--18371937 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18371886 CTTATGAATG
*
18371896 CCTTGGT-TTTCTGTTGGAAAT
1 CCTTGGTCTCTCT-TTGGAAAT
*
18371917 CCTTTGTCTCTCTTTGGAAAT
1 CCTTGGTCTCTCTTTGGAAAT
18371938 TAAGAGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (21 bp):
CCTTGGTCTCTCTTTGGAAAT
Found at i:18374327 original size:10 final size:10
Alignment explanation
Indices: 18374308--18374366 Score: 77
Period size: 10 Copynumber: 6.0 Consensus size: 10
18374298 TGAAATTCTA
18374308 AAAGATAAAT
1 AAAGATAAAT
18374318 ACAA-ATAAAT
1 A-AAGATAAAT
*
18374328 AAAGATAATT
1 AAAGATAAAT
18374338 AAAGATAAA-
1 AAAGATAAAT
18374347 AAAGATAAAT
1 AAAGATAAAT
*
18374357 AAAAATAAAT
1 AAAGATAAAT
18374367 CCTAGAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 11 0.26
10 30 0.70
11 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:18375501 original size:23 final size:20
Alignment explanation
Indices: 18375475--18375524 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
18375465 TTTTTTTTAG
18375475 TATTTGTGCATATTAGATTTATT
1 TATTTGTGC--ATTA-ATTTATT
*
18375498 TATTCGTGCATTAATTTATT
1 TATTTGTGCATTAATTTATT
*
18375518 TAATTGT
1 TATTTGT
18375525 CTAATGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
23 8 0.33
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
TATTTGTGCATTAATTTATT
Found at i:18380474 original size:27 final size:27
Alignment explanation
Indices: 18380444--18380647 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
18380434 ATATTGAGTC
* * *
18380444 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
18380471 CGCACACTTAGTGCTACGTAATC-AAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
18380497 CGCACACTTAGTGCTACATAATCAATCT
1 CGCACACTTAGTGCTACATAATCAA-AT
* ** *
18380525 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
18380552 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
18380579 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
18380606 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
18380633 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18380648 GTACAATTTA
Statistics
Matches: 156, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
26 25 0.16
27 107 0.69
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:18384102 original size:7 final size:7
Alignment explanation
Indices: 18384092--18384205 Score: 104
Period size: 7 Copynumber: 15.9 Consensus size: 7
18384082 CCCTAAATTT
18384092 TAAACCC
1 TAAACCC
*
18384099 TAAAACCT
1 T-AAACCC
*
18384107 TAAAACCT
1 T-AAACCC
*
18384115 TAAAATCC
1 T-AAACCC
*
18384123 TAAACCT
1 TAAACCC
**
18384130 TAAACAT
1 TAAACCC
18384137 TAAACCC
1 TAAACCC
18384144 TAAACCC
1 TAAACCC
18384151 TAAACCC
1 TAAACCC
18384158 TAAACCC
1 TAAACCC
18384165 TAAATCCC
1 TAAA-CCC
18384173 -AAACCC
1 TAAACCC
18384179 TAAACCC
1 TAAACCC
***
18384186 TAAATTT
1 TAAACCC
18384193 TAAACCC
1 TAAACCC
18384200 TAAACC
1 TAAACC
18384206 ACATGCTACC
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
6 3 0.03
7 64 0.71
8 23 0.26
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:18384110 original size:8 final size:8
Alignment explanation
Indices: 18384093--18384133 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
18384083 CCTAAATTTT
*
18384093 AAACCCTA
1 AAACCTTA
18384101 AAACCTTA
1 AAACCTTA
18384109 AAACCTTA
1 AAACCTTA
18384117 AAATCC-T-
1 AAA-CCTTA
18384124 AAACCTTA
1 AAACCTTA
18384132 AA
1 AA
18384134 CATTAAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
6 2 0.07
7 4 0.14
8 21 0.72
9 2 0.07
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (8 bp):
AAACCTTA
Found at i:18384464 original size:11 final size:11
Alignment explanation
Indices: 18384448--18384473 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18384438 AAATCCAGGG
18384448 TTTTAAAATTA
1 TTTTAAAATTA
18384459 TTTTAAAATTA
1 TTTTAAAATTA
18384470 TTTT
1 TTTT
18384474 TAGTGCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:18385873 original size:50 final size:50
Alignment explanation
Indices: 18385791--18385927 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 50
18385781 AGGGAGATAG
* * ** * *
18385791 GAGAGCTAGTGTAAGACAATGTCTGGGACATGGCATTGGCAC-CGATAAAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTCAATAAAC
* *
18385841 GCGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCAATAAAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAATAAAC
* *
18385891 GAGAGTCAGTGTAAGACCATGTCTCGGACATGGCATC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
18385928 GACTTTGATG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 73 0.99
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (50 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCAATAAAC
Found at i:18404803 original size:39 final size:39
Alignment explanation
Indices: 18404757--18404885 Score: 195
Period size: 39 Copynumber: 3.3 Consensus size: 39
18404747 ATTATATCTG
18404757 GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCA
1 GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCA
*
18404796 GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCG
1 GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCA
* * ** *
18404835 GACTTCAGGTCCGCAGGCTACGTGCTGGAAATATATCCA
1 GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCA
*
18404874 GGCTTAAAGTCC
1 GACTTAAAGTCC
18404886 CGAAGGCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (39 bp):
GACTTAAAGTCCGCAGGCTATATGCGGGAAATATATCCA
Found at i:18414138 original size:13 final size:13
Alignment explanation
Indices: 18414117--18414166 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
18414107 AGTAATTGAA
18414117 CACGGGCGTGTGC
1 CACGGGCGTGTGC
*
18414130 CATGGGCGTGTGC
1 CACGGGCGTGTGC
*
18414143 CACGGCCGTGTGC
1 CACGGGCGTGTGC
18414156 CACGGGCGTGT
1 CACGGGCGTGT
18414167 ACCTGCCGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.08, C:0.30, G:0.44, T:0.18
Consensus pattern (13 bp):
CACGGGCGTGTGC
Found at i:18416423 original size:40 final size:40
Alignment explanation
Indices: 18416379--18416602 Score: 262
Period size: 40 Copynumber: 5.6 Consensus size: 40
18416369 GCTCCTCGTT
*
18416379 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
18416419 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
18416459 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
18416499 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTATCTCGCA
* * * * *
18416539 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ATC-TCGCA
18416580 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
18416603 ACATCATTCA
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 4 0.02
40 146 0.89
41 14 0.09
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:18424386 original size:40 final size:40
Alignment explanation
Indices: 18424297--18424520 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
18424287 GCTCCTCGTT
*
18424297 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAA-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
18424336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
18424376 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
18424416 CAAATGCCTTC-GGATCTTAGTCCGGA-TTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
18424455 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
18424496 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18424521 CATCATTCAA
Statistics
Matches: 167, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
39 71 0.43
40 85 0.51
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:18424397 original size:79 final size:78
Alignment explanation
Indices: 18424297--18424520 Score: 260
Period size: 79 Copynumber: 2.8 Consensus size: 78
18424287 GCTCCTCGTT
* *
18424297 CAAATGCCTTCGGGACATAGCCCGGTTATAGTA-ATCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGG
18424361 ATTTAGTAACTCGCA
65 A-TTAGTAACTCGCA
* *
18424376 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATC-TCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTA-CATCGCACAAATGCCTTCGGGA-CTTAGCCC
*
18424439 GGATTAGTATCTCGCA
63 GGATTAGTAACTCGCA
* * * *
18424455 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGT-ACATCGCACAAATGCCTTCGGGACTTAGCCC
18424518 GGA
63 GGA
18424521 CATCATTCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
78 4 0.03
79 84 0.67
80 38 0.30
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTAGTAACTCGCA
Found at i:18428228 original size:21 final size:23
Alignment explanation
Indices: 18428189--18428247 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
18428179 CTTTAACCAT
*
18428189 TTTTATTTTTATTGCAATT-TAA-
1 TTTT-TTTTTATTTCAATTATAAC
*
18428211 TTTTTTTTTATTTTAATTACTAAC
1 TTTTTTTTTATTTCAATTA-TAAC
*
18428235 TTTTCTTTTATTT
1 TTTTTTTTTATTT
18428248 ACTTTTGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 4 0.13
23 3 0.10
24 12 0.39
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTATTTCAATTATAAC
Found at i:18431208 original size:16 final size:17
Alignment explanation
Indices: 18431187--18431225 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
18431177 TTACCCCACC
18431187 CTTTCTTTC-CCTTTTT
1 CTTTCTTTCTCCTTTTT
18431203 CTTTCTTTCTTCCTTTTT
1 CTTTCTTTC-TCCTTTTT
*
18431221 GTTTC
1 CTTTC
18431226 CCTTTATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (17 bp):
CTTTCTTTCTCCTTTTT
Found at i:18436716 original size:14 final size:14
Alignment explanation
Indices: 18436697--18436754 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
18436687 AAAAATTGTT
18436697 TTACTTTTCATATA
1 TTACTTTTCATATA
18436711 TTACTTTTCATATA
1 TTACTTTTCATATA
*
18436725 TTA--TTTCATGTA
1 TTACTTTTCATATA
*
18436737 TTAAACATTTCATATA
1 TT--ACTTTTCATATA
18436753 TT
1 TT
18436755 TTCATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 10 0.26
14 18 0.47
16 10 0.26
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (14 bp):
TTACTTTTCATATA
Found at i:18436776 original size:13 final size:14
Alignment explanation
Indices: 18436758--18436789 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
18436748 ATATATTTTC
18436758 ATTATTTTATAT-T
1 ATTATTTTATATAT
18436771 ATTA-TTTATATAT
1 ATTATTTTATATAT
18436784 ATTATT
1 ATTATT
18436790 ATCCTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATATAT
Found at i:18436839 original size:36 final size:35
Alignment explanation
Indices: 18436799--18436878 Score: 81
Period size: 36 Copynumber: 2.2 Consensus size: 35
18436789 TATCCTTAAC
*
18436799 TATTATATTTTATTAATCAAT-TGCTTATATACTATA
1 TATTATATTTTA--AATCAATATACTTATATACTATA
* * * *
18436835 TATTACGATTTTAAATCCATATACTTTTATATTATA
1 TATTA-TATTTTAAATCAATATACTTATATACTATA
18436871 TATTATAT
1 TATTATAT
18436879 AATTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
35 8 0.22
36 22 0.61
37 6 0.17
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (35 bp):
TATTATATTTTAAATCAATATACTTATATACTATA
Found at i:18449105 original size:206 final size:206
Alignment explanation
Indices: 18448743--18449344 Score: 954
Period size: 206 Copynumber: 2.9 Consensus size: 206
18448733 GCAGATCTGG
* * * * *
18448743 CTGAAGCAAGATCCAATATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATTGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCT
* *
18448808 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGAATCTCTATATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * *
18448873 AGAACAAATCAAAGTTTGGAGTCTCCATATTCGATGGAGAGTAGATACATAGCAGATCTGGCCTT
130 AAAACAAATCGAAGTTTGGAGTCTCCATATTCGATGGAGAGAAGATACATAGCAGATCTAGCCTT
18448938 CAGATGTTTATA
195 CAGATGTTTATA
*
18448950 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAACTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
*
18449015 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGTTTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
18449080 AAACAAATCGAATTTTGGAGTCTCCATATTCGATGGAGAGAAGATACATAGCAGATCTAGCCTTC
131 AAACAAATCGAAGTTTGGAGTCTCCATATTCGATGGAGAGAAGATACATAGCAGATCTAGCCTTC
18449145 AGATGTTTATA
196 AGATGTTTATA
* * *
18449156 TTGAAGCAAATCCAAGATGATTTGGCATCCTTGTGTTAACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
* *
18449221 ATTTGGCCTTCACGTGCTTACGATGAAGCAAATCTAGGATGATTTGGCATCTCTGTATTGTCA-A
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * * * *
18449285 AGAACAAATCGAAGTTTGGCGTCTTCATATTCGACGGAGGGCAGACACATAGCAGATCTA
131 A-AACAAATCGAAGTTTGGAGTCTCCATATTCGATGGAGAGAAGATACATAGCAGATCTA
18449345 AGATGGTTTG
Statistics
Matches: 366, Mismatches: 28, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
205 2 0.01
206 357 0.98
207 7 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
AAACAAATCGAAGTTTGGAGTCTCCATATTCGATGGAGAGAAGATACATAGCAGATCTAGCCTTC
AGATGTTTATA
Found at i:18451294 original size:16 final size:17
Alignment explanation
Indices: 18451273--18451307 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
18451263 AAAAATTGTT
18451273 TTACTTTTC-TATATTA
1 TTACTTTTCATATATTA
18451289 TTACTTTTCATATATTA
1 TTACTTTTCATATATTA
18451306 TT
1 TT
18451308 TCATGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TTACTTTTCATATATTA
Found at i:18451354 original size:13 final size:14
Alignment explanation
Indices: 18451336--18451367 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
18451326 ATATATTTTC
18451336 ATTATTTTATAT-T
1 ATTATTTTATATAT
18451349 ATTA-TTTATATAT
1 ATTATTTTATATAT
18451362 ATTATT
1 ATTATT
18451368 ATCCTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATATAT
Found at i:18456190 original size:20 final size:20
Alignment explanation
Indices: 18456152--18456191 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18456142 CCAAAATGTA
*
18456152 TATATACATATGTTAAACAT
1 TATATACATATGATAAACAT
18456172 TATATACATAT-ATAGAACAT
1 TATATACATATGATA-AACAT
18456192 GGAACACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TATATACATATGATAAACAT
Found at i:18458077 original size:21 final size:20
Alignment explanation
Indices: 18458049--18458088 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
18458039 AGGTATAATA
18458049 GCCAAGCTTA-ATCATATTCG
1 GCCAAGCTTATAT-ATATTCG
18458069 GCCATAGCTTATATATATTC
1 GCCA-AGCTTATATATATTC
18458089 ACACATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GCCAAGCTTATATATATTCG
Found at i:18461935 original size:41 final size:41
Alignment explanation
Indices: 18461876--18462037 Score: 177
Period size: 41 Copynumber: 4.0 Consensus size: 41
18461866 CGGGGTTTAA
* * *
18461876 AACCGAGCTTGGTATCGAAGGGCTTTTGAGCCAGTGCTAAT
1 AACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGCTAAT
* *
18461917 AACCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTG-TCAT
1 AACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGCTAAT
* * * *
18461957 AACCGGACTTAGTTCCGAAGGGCCTTCGAGCCAGTGGTCTAAT
1 AACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGT-G-CTAAT
* * *
18462000 --CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 AACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGCTAA
18462038 GAATCGGGCT
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
39 4 0.04
40 35 0.35
41 59 0.58
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
AACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGCTAAT
Found at i:18462582 original size:13 final size:13
Alignment explanation
Indices: 18462564--18462589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18462554 CGAAATGTTT
18462564 ATTCTCTGTTTTA
1 ATTCTCTGTTTTA
18462577 ATTCTCTGTTTTA
1 ATTCTCTGTTTTA
18462590 TAGATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTCTCTGTTTTA
Found at i:18464421 original size:43 final size:42
Alignment explanation
Indices: 18464374--18464524 Score: 175
Period size: 43 Copynumber: 3.6 Consensus size: 42
18464364 CCTCAGACGT
* *
18464374 GGTCTTACATGTAATCACATATCGATGCCACTGTCCTAGACAG
1 GGTCTTACACGTAATCACATATCGATGCCA-TGTCCCAGACAG
* * *
18464417 GGTCTTACACG-AATCAAATA-CGATGTCGATGTCCCAGACAT
1 GGTCTTACACGTAATCACATATCGATG-CCATGTCCCAGACAG
18464458 GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC-G
1 GGTCTTACACGTAATCACATATCGATGCC-ATGTCCCAGACAG
*
18464500 TGGTCTTACACG-AGAACACATATCG
1 -GGTCTTACACGTA-ATCACATATCG
18464525 GAAATCCTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
41 26 0.28
42 20 0.22
43 47 0.51
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGTAATCACATATCGATGCCATGTCCCAGACAG
Found at i:18465128 original size:15 final size:15
Alignment explanation
Indices: 18465105--18465134 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18465095 TCAAAAATTC
18465105 TAATACAAAACATAT
1 TAATACAAAACATAT
*
18465120 TAATCCAAAACATAT
1 TAATACAAAACATAT
18465135 CTTTCATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATACAAAACATAT
Found at i:18470866 original size:13 final size:13
Alignment explanation
Indices: 18470848--18470872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18470838 AACTAGTATA
18470848 ATTATTTCATACC
1 ATTATTTCATACC
18470861 ATTATTTCATAC
1 ATTATTTCATAC
18470873 ATGAATCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATTTCATACC
Found at i:18472602 original size:41 final size:43
Alignment explanation
Indices: 18472520--18472630 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 43
18472510 TCCTAGACGT
* * * * *
18472520 GGTCTTACATGTAATCACATATCAAT-CCCATTGTCTCAGACAG
1 GGTCTTACACGTAATCAAATATCGATGTCGA-TGTCTCAGACAG
* *
18472563 GGTCTTACATG-AATCAAATA-CGATGTCGATGTCTCAGACAT
1 GGTCTTACACGTAATCAAATATCGATGTCGATGTCTCAGACAG
*
18472604 GGTCTTACACGTAATCACATATCGATG
1 GGTCTTACACGTAATCAAATATCGATG
18472631 CCAACGTCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 24 0.41
42 18 0.31
43 16 0.28
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATATCGATGTCGATGTCTCAGACAG
Done.