Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold318
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: 411206
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:153002 original size:60 final size:59
Alignment explanation
Indices: 152932--153686 Score: 912
Period size: 60 Copynumber: 12.5 Consensus size: 59
152922 TAAGTGGCAC
* * *
152932 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
* * *
152991 CCATTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTATGACATTTT
1 CC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
153051 CCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTT
1 CC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA--TT-TT
* *
153114 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGATATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
* * * * * *
153172 CCTTTTAAAAGCCCAGACAAGTTGGTAGTACC-TTCTAGTCCTTAAAGAGCTGGACACCTTCT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACA--TTTT
* * * * *
153234 CCTTTTAAAGCCCACACAAGTTGATGGTACCTTTCAGTCCTCAAAGTGGAGGATATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
*
153293 CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTCT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--CATTTT
*
153355 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
* * *
153414 CCTTTTTAAAGCCCACACAAGTTGGTGGAACCTTTCAGTCCTCAAAGAGCAAGGCGCCTTTT
1 CC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC-AGG-ACATTTT
* *
153476 CCTTTTTAAAGACCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAACAGGACATCTTTT
1 CC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA--TTTT
** * *
153538 CCTTTTTAAAGCCCACACAAGTTATTAGCACC-TTCTAGTCCTCAAAGAGTAGGACATCTTTT
1 CC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACA--TTTT
* * * * *
153600 CTTTTTAAAGCCCACACAAGTTGTTGGCACC-TTCTAGTCCCCAAAGAGTAGGACGCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGAC-ATTTT
*
153660 --TTTTCAAAG-CCACACAAATTGGTGGCA
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA
153687 ACCCTTTGTC
Statistics
Matches: 618, Mismatches: 57, Indels: 43
0.86 0.08 0.06
Matches are distributed among these distances:
58 22 0.04
59 31 0.05
60 237 0.38
61 193 0.31
62 133 0.22
63 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (59 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACATTTT
Found at i:153171 original size:121 final size:121
Alignment explanation
Indices: 152934--153686 Score: 959
Period size: 121 Copynumber: 6.2 Consensus size: 121
152924 AGTGGCACCC
* * * *
152934 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATA--TTTTCCATTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTT-CTTTT
* * * *
152997 TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTATGACATTTTCCT
65 TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
153054 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTTC-TTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTT-TTCTTTT
*
153118 TAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGATATTTTCCT
65 TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
* * * * * * * *
153175 TTTAAAAGCCCAGACAAGTTGGTAGTACC-TTCTAGTCCTTAAAGAGCTGGACACCTTCTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACACCTTTTCTTTT
* * * *
153239 TAAAGCCCACACAAGTTGATGGTACCTTTCAGTCCTCAAAGTGGAGGATATTTTCCT
65 TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
* * * * *
153296 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTCTCCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCTTTTT
153361 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
66 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
* *
153417 TTTTAAAGCCCACACAAGTTGGTGGAACCTTTCAGTCCTCAAAGAGCAAGG-CGCCTTTTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC-AGGACACCTTTT-CTTT
* * *
153481 TTAAAGACCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAACAGGACATCTTTTCCT
64 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGG--ATATTTTCCT
** * * *
153541 TTTTAAAGCCCACACAAGTTATTAGCACC-TTCTAGTCCTCAAAGAGTAGGACATCTTTTCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACACCTTTTCTTTT
* * * **
153605 TAAAGCCCACACAAGTTGTTGGCACC-TTCTAGTCCCCAAAGAGTAGGACGCTTTT--T
65 TAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGA-TATTTTCCT
* *
153661 TTTCAAAG-CCACACAAATTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
153687 ACCCTTTGTC
Statistics
Matches: 561, Mismatches: 58, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
119 14 0.02
120 63 0.11
121 314 0.56
122 66 0.12
123 51 0.09
124 53 0.09
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (121 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCTTTTT
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATATTTTCCT
Found at i:153805 original size:32 final size:32
Alignment explanation
Indices: 153766--153838 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
153756 AAAGCCATAG
*
153766 AAGTTGGTGGCAACCTTTCTC-AAAGCCTACAC
1 AAGTTGGTGGCAA-CTTTCTCTAAAGCCCACAC
153798 AAGTTGGTGGCAACTTTCTCTAAAGCCCACAC
1 AAGTTGGTGGCAACTTTCTCTAAAGCCCACAC
*
153830 AAGTCGGTG
1 AAGTTGGTG
153839 ATAACTCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 7 0.18
32 31 0.82
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (32 bp):
AAGTTGGTGGCAACTTTCTCTAAAGCCCACAC
Found at i:153809 original size:90 final size:91
Alignment explanation
Indices: 153606--153809 Score: 286
Period size: 91 Copynumber: 2.3 Consensus size: 91
153596 TTTTCTTTTT
* * ** *
153606 AAAGCCCACACAAGTTGTTGGCACCTTCTAGTCCCCAAAGAGTAGGACGCTTTTTTTTCAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCCCAAAAACCAGGACGATTTTTTTTCAAAGCC
*
153671 ACACAAATTGGTGGCAACCCTTTGTC
66 ACACAAATTGGTGGCAACCCTTTCTC
*
153697 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTGCCCAAAAACCAGGAC-ATTTTTCTTTCAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCCCAAAAACCAGGACGATTTTT-TTTCAAAGC
* * *
153761 CATAGAAGTTGGTGGCAA-CCTTTCTC
65 CACACAAATTGGTGGCAACCCTTTCTC
*
153787 AAAGCCTACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTTGGTGGCA
153810 ACTTTCTCTA
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
90 34 0.34
91 67 0.66
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (91 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCCCAAAAACCAGGACGATTTTTTTTCAAAGCC
ACACAAATTGGTGGCAACCCTTTCTC
Found at i:154013 original size:62 final size:61
Alignment explanation
Indices: 153947--154171 Score: 197
Period size: 62 Copynumber: 3.6 Consensus size: 61
153937 GCACATTGGT
* * * *
153947 ACCTTTATCGTTCTTTTCATTTTTCAAGCCTAATATCGTTGGCTGTGAATTAGTATATCGAC
1 ACCTTTATCATTCTTTTCATCTTT-AAGCCTAATATCATTGGCTGTGAATCAGTATATCGAC
* * *
154009 ACCTTTATCATT-TTTTGGCATCTTTAGGTCTAATATCATTGG-TCGTGAATCAGTATATCAAC
1 ACCTTTATCATTCTTTT--CATCTTTAAGCCTAATATCATTGGCT-GTGAATCAGTATATCGAC
* * * * * * *
154071 ACTTTTATCATTTCTTTGCATCTTTAGGTCC-AATATCACTGGCCT-TGAATCAGCATATTGGC
1 ACCTTTATCA-TTCTTTTCATCTTTAAG-CCTAATATCATTGG-CTGTGAATCAGTATATCGAC
* * * *
154133 ACTTTTATCATTCTTTTCATTTTTAAGTCTAATGTCATT
1 ACCTTTATCATTCTTTTCATCTTTAAGCCTAATATCATT
154172 AACCTTGAAT
Statistics
Matches: 133, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
60 1 0.01
61 26 0.20
62 93 0.70
63 9 0.07
64 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (61 bp):
ACCTTTATCATTCTTTTCATCTTTAAGCCTAATATCATTGGCTGTGAATCAGTATATCGAC
Found at i:154192 original size:61 final size:62
Alignment explanation
Indices: 154070--154198 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 62
154060 AGTATATCAA
* ** *
154070 CACTTTTATCATTTCTTTGCATCTTTAGGTCCAATATCACTGGCCTTGAATCAGCATATTGG
1 CACTTTTATCATTTCTTTGCATCTTTAAGTCCAATATCACTAACCTTGAATCAGCACATTGG
* * * * * *
154132 CACTTTTATCA-TTCTTTTCATTTTTAAGTCTAATGTCATTAACCTTGAATTAGCACATTGG
1 CACTTTTATCATTTCTTTGCATCTTTAAGTCCAATATCACTAACCTTGAATCAGCACATTGG
*
154193 TACTTT
1 CACTTT
154199 CCTTATCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
61 45 0.80
62 11 0.20
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (62 bp):
CACTTTTATCATTTCTTTGCATCTTTAAGTCCAATATCACTAACCTTGAATCAGCACATTGG
Found at i:155109 original size:17 final size:18
Alignment explanation
Indices: 155087--155134 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
155077 GATTTTTTAT
*
155087 ATAAAATTAAAATAAT-A
1 ATAAAATAAAAATAATCA
* *
155104 ATAAAATGAAAACAATCA
1 ATAAAATAAAAATAATCA
*
155122 AAAAAATAAAAAT
1 ATAAAATAAAAAT
155135 CAAAAACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
ATAAAATAAAAATAATCA
Found at i:155135 original size:15 final size:16
Alignment explanation
Indices: 155112--155150 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
155102 TAATAAAATG
*
155112 AAAACAATCAAAAA-A
1 AAAAAAATCAAAAACA
*
155127 ATAAAAATCAAAAACA
1 AAAAAAATCAAAAACA
155143 AAAAAAAT
1 AAAAAAAT
155151 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAATCAAAAACA
Found at i:155179 original size:28 final size:27
Alignment explanation
Indices: 155129--155200 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
155119 TCAAAAAAAT
** *
155129 AAAAATCAAAAACAAAAAAAATTAATTA
1 AAAAATCAAAAA-AAATCAAATTAATAA
**
155157 AAATTTCTAAAAAAAATCAAATTAATAA
1 AAAAATC-AAAAAAAATCAAATTAATAA
155185 AAAAATCAAAAAAAAT
1 AAAAATCAAAAAAAAT
155201 ATGAAAATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 9 0.25
28 22 0.61
29 5 0.14
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (27 bp):
AAAAATCAAAAAAAATCAAATTAATAA
Found at i:157877 original size:79 final size:78
Alignment explanation
Indices: 157670--158111 Score: 457
Period size: 79 Copynumber: 5.6 Consensus size: 78
157660 TCATTCACGT
** *
157670 TTTTATTTCTAAAATATCGATTTTCCACCATC-GGGATACTCCAACCCCATTATTTCCG-AGGAG
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAAGGA-
157733 ATACTCCAACCCTGA
65 ATACTCCAACCC-GA
* * * * *
157748 TTTTATTTCCAAAACATCGA-TTTCCACAATCGAGGATACTCAAACCCTGTTATTTCTGAAGGAA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAAGGAA
*
157812 TACTCGAATCCCGA
66 TACTCCAA-CCCGA
* * * *
157826 TTTTATTTCTAAAATA-CTAATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCCGAGGGG
1 TTTTATTTCTAAAATATC-GATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAAGGA
*
157890 ATACTCTAACCC-A
65 ATACTCCAACCCGA
* ** * * **
157903 GTTTTATTTCCAAAGCATTGATTTTTCATAATCGGGGATACTCCAACCCTGTTATTTCTGAGAGG
1 -TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGA-AGG
*
157968 -ATACTCTAACCCCGA
64 AATACTCCAA-CCCGA
* * * * * * * *
157983 TTTTATTTCTAAAATACCAATTTTTCACTATCGGGGATGCTCTAACCCTATTATTTCTGAAGGGA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAAGGAA
*
158048 TACTCCAACCGCGG
66 TACTCCAACC-CGA
* *
158062 TTTTGTTT-TCAAAATATCGATTTTCCACCATCAGGGATACTCCAACCCTG
1 TTTTATTTCT-AAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTG
158112 ATTTTGTTTC
Statistics
Matches: 300, Mismatches: 51, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
77 12 0.04
78 132 0.44
79 155 0.52
80 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAAGGAA
TACTCCAACCCGA
Found at i:157942 original size:157 final size:157
Alignment explanation
Indices: 157670--158111 Score: 577
Period size: 157 Copynumber: 2.8 Consensus size: 157
157660 TCATTCACGT
* * *
157670 TTTTATTTCTAAAATA-TCGATTTTCCACCATC-GGGATACTCCAACCCCATTATTTCCGAGGAG
1 TTTTATTTCTAAAATACT-AATTTTCCACCATCGGGGATACTCCAACCCTATTATTTCCGAGGGG
* * *
157733 ATACTCCAACCCTGATTTTATTTCCAAAACATCGA-TTTCCACAATCGAGGATACTCAAACCCTG
65 ATACTCCAACCCAG-TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCTG
*
157797 TTATTTCTGA-AGGAATACTCGAATCCCGA
129 TTATTTCTGAGAGG-ATACTCGAACCCCGA
*
157826 TTTTATTTCTAAAATACTAATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAATACTAATTTTCCACCATCGGGGATACTCCAACCCTATTATTTCCGAGGGGA
* * * * *
157891 TACTCTAACCCAGTTTTATTTCCAAAGCATTGATTTTTCATAATCGGGGATACTCCAACCCTGTT
66 TACTCCAACCCAGTTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCTGTT
*
157956 ATTTCTGAGAGGATACTCTAACCCCGA
131 ATTTCTGAGAGGATACTCGAACCCCGA
* * * * * * *
157983 TTTTATTTCTAAAATACCAATTTTTCACTATCGGGGATGCTCTAACCCTATTATTTCTGAAGGGA
1 TTTTATTTCTAAAATACTAATTTTCCACCATCGGGGATACTCCAACCCTATTATTTCCGAGGGGA
* * * * * *
158048 TACTCCAACCGCGGTTTTGTTTTCAAAATATCGATTTTCCACCATCAGGGATACTCCAACCCTG
66 TACTCCAACC-CAGTTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCTG
158112 ATTTTGTTTC
Statistics
Matches: 248, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
156 47 0.19
157 155 0.62
158 46 0.19
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (157 bp):
TTTTATTTCTAAAATACTAATTTTCCACCATCGGGGATACTCCAACCCTATTATTTCCGAGGGGA
TACTCCAACCCAGTTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCTGTT
ATTTCTGAGAGGATACTCGAACCCCGA
Found at i:158151 original size:51 final size:51
Alignment explanation
Indices: 158043--158161 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 51
158033 TTATTTCTGA
* * *
158043 AGGGATACTCCAACCGC-GGTTTTGTTTTCAAAATATCGATTTTCCACCATC
1 AGGGATACTCCAACC-CTGATTTTGTTTCCAAAATATCGATTTTCCACAATC
* *
158094 AGGGATACTCCAACCCTGATTTTGTTTCCAAAATATCGATTTTTCATAATC
1 AGGGATACTCCAACCCTGATTTTGTTTCCAAAATATCGATTTTCCACAATC
*
158145 -GAGGATATTCCAACCCT
1 AG-GGATACTCCAACCCT
158162 ATTCCTCTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (51 bp):
AGGGATACTCCAACCCTGATTTTGTTTCCAAAATATCGATTTTCCACAATC
Found at i:161283 original size:41 final size:40
Alignment explanation
Indices: 161238--161314 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
161228 TTTCTCATAT
*
161238 TTGAATTTTGATA-T-AATTTTTATTTTTCAATTATTTTCGTA
1 TTGAATTATGATATTCAA-TTTT-TTTTT-AATTATTTTCGTA
161279 TTGAATTATGATATTCAATTTTTTTTTAATTATTTT
1 TTGAATTATGATATTCAATTTTTTTTTAATTATTTT
161315 AACATACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
40 9 0.27
41 17 0.52
42 5 0.15
43 2 0.06
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (40 bp):
TTGAATTATGATATTCAATTTTTTTTTAATTATTTTCGTA
Found at i:166625 original size:19 final size:20
Alignment explanation
Indices: 166589--166626 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
166579 GGAAGTCATA
*
166589 TTTTATCCATTTGGTTTTTT
1 TTTTATCCATTTGCTTTTTT
*
166609 TTTTTTCCA-TTGCTTTTT
1 TTTTATCCATTTGCTTTTT
166627 GTATCCACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTATCCATTTGCTTTTTT
Found at i:167703 original size:26 final size:26
Alignment explanation
Indices: 167650--167703 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
167640 TCATTTTTTT
*
167650 TTTTTTTAACAAAACAAAATCTTAGA
1 TTTTTTTAACAAAACAAAATATTAGA
** * *
167676 TTTTTTTAATGAAATAAAATATTGGA
1 TTTTTTTAACAAAACAAAATATTAGA
167702 TT
1 TT
167704 GCTTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTTTTAACAAAACAAAATATTAGA
Found at i:171473 original size:13 final size:13
Alignment explanation
Indices: 171455--171479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171445 CATAAAGTGT
171455 TGTATCGATACAA
1 TGTATCGATACAA
171468 TGTATCGATACA
1 TGTATCGATACA
171480 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:171492 original size:19 final size:19
Alignment explanation
Indices: 171433--171498 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
171423 ATTTCAACGA
171433 TTTT-TATCGATACATAAAG
1 TTTTGTATCGATACAT-AAG
*
171452 TGTTGTATCGATAC--AA-
1 TTTTGTATCGATACATAAG
171468 ---TGTATCGATACATAAG
1 TTTTGTATCGATACATAAG
171484 TTTTGTATCGATACA
1 TTTTGTATCGATACA
171499 ATGTAAGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 15 0.38
20 9 0.23
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTTGTATCGATACATAAG
Found at i:171495 original size:32 final size:33
Alignment explanation
Indices: 171437--171503 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
171427 CAACGATTTT
171437 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
*
171470 TATCGATACAT-AAGTTTTGTATCGATACAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
171502 TA
1 TA
171504 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (33 bp):
TATCGATACATAAAGTGTTGTATCGATACAATG
Found at i:171559 original size:13 final size:13
Alignment explanation
Indices: 171541--171565 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171531 ATTACTCAAA
171541 TGTATCGATACAT
1 TGTATCGATACAT
171554 TGTATCGATACA
1 TGTATCGATACA
171566 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:171630 original size:52 final size:52
Alignment explanation
Indices: 171574--171702 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
171564 CACTGATCTT
171574 TGTATCGATACATGTAGGCAAATTTACCCAGATGCATCGATACACTATAAAA
1 TGTATCGATACATGTAGGCAAATTTACCCAGATGCATCGATACACTATAAAA
* * * *
171626 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGTAGGCAAATTTACCCAGATGCATCGATACACTATAAAA
*
171678 TGTATCGATACATGTAGGTAAATTT
1 TGTATCGATACATGTAGGCAAATTT
171703 TTCATATTTC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGTAGGCAAATTTACCCAGATGCATCGATACACTATAAAA
Found at i:178642 original size:83 final size:83
Alignment explanation
Indices: 178503--178669 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
178493 CAAGTCGAGA
* *
178503 ATATGTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAGAATATAATCTTTCAACAATTAAAG
1 ATATGTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAA
178568 GGAGTCCAACAATTTTAT
66 GGAGTCCAACAATTTTAT
178586 ATATGTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAA
1 ATATGTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAA
*
178651 TGAGTCCAACAATTTTAT
66 GGAGTCCAACAATTTTAT
178669 A
1 A
178670 CGAGGGTAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (83 bp):
ATATGTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAA
GGAGTCCAACAATTTTAT
Found at i:180782 original size:28 final size:28
Alignment explanation
Indices: 180742--180820 Score: 158
Period size: 28 Copynumber: 2.8 Consensus size: 28
180732 TCATGGTCAT
180742 GGACCTCATTTATGCAAATTGGCAGTTG
1 GGACCTCATTTATGCAAATTGGCAGTTG
180770 GGACCTCATTTATGCAAATTGGCAGTTG
1 GGACCTCATTTATGCAAATTGGCAGTTG
180798 GGACCTCATTTATGCAAATTGGC
1 GGACCTCATTTATGCAAATTGGC
180821 TGCTGACCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (28 bp):
GGACCTCATTTATGCAAATTGGCAGTTG
Found at i:180918 original size:21 final size:22
Alignment explanation
Indices: 180888--180937 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
180878 ATGTAAAAAG
*
180888 TTAAAATTAAATT-ATTTTAAT
1 TTAAAATTAAATTGATTTAAAT
*
180909 TTAAATTTAAATTGATTTAAAT
1 TTAAAATTAAATTGATTTAAAT
180931 TTAAAAT
1 TTAAAAT
180938 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAAATTAAATTGATTTAAAT
Found at i:180926 original size:16 final size:16
Alignment explanation
Indices: 180904--180955 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
180894 TTAAATTATT
180904 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
180920 TTGATTTAAATTTAAA
1 TTAATTTAAATTTAAA
* *
180936 ATAATTTAAAATTAAA
1 TTAATTTAAATTTAAA
180952 TTAA
1 TTAA
180956 ATATAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:180964 original size:32 final size:32
Alignment explanation
Indices: 180905--180965 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
180895 TAAATTATTT
* * *
180905 TAATTTAAATTTAAATTGATTTAAATTTAAAA
1 TAATTTAAAATTAAATTAATATAAATTTAAAA
180937 TAATTTAAAATTAAATTAA-ATATAATTTA
1 TAATTTAAAATTAAATTAATATA-AATTTA
180966 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
TAATTTAAAATTAAATTAATATAAATTTAAAA
Found at i:181438 original size:16 final size:16
Alignment explanation
Indices: 181409--181451 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
181399 AAAATTACAT
181409 TTAATAAAATAATAAAAA
1 TTAA-AAAA-AATAAAAA
181427 TTAAAAAAAATAAAAA
1 TTAAAAAAAATAAAAA
*
181443 ATAAAAAAA
1 TTAAAAAAA
181452 TTAACAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.67
17 4 0.17
18 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TTAAAAAAAATAAAAA
Found at i:185885 original size:52 final size:51
Alignment explanation
Indices: 185744--185892 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
185734 CGAAATATGA
* *
185744 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTAGGC
* *
185796 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTAGGC
**
185848 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
185893 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
Found at i:185899 original size:13 final size:13
Alignment explanation
Indices: 185881--185905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185871 CAAAGATCAG
185881 TGTATCGATACAA
1 TGTATCGATACAA
185894 TGTATCGATACA
1 TGTATCGATACA
185906 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:185986 original size:13 final size:13
Alignment explanation
Indices: 185968--185992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185958 CAAAAAAATA
185968 TGTATCGATACAT
1 TGTATCGATACAT
185981 TGTATCGATACA
1 TGTATCGATACA
185993 AATCGTTGAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:186893 original size:55 final size:52
Alignment explanation
Indices: 186798--187077 Score: 223
Period size: 43 Copynumber: 5.6 Consensus size: 52
186788 TGATAAAGAA
* * * * * **
186798 TGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAGG
* *
186852 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
* *
186905 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
* * * *
186948 TGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
* * * * *
186997 TGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-GG-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
* *
187045 TGCCAATATGCTGATTCAAGGCCAACTATATTG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTG
187078 GGCTTAAAAG
Statistics
Matches: 192, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
43 38 0.20
44 1 0.01
46 1 0.01
47 2 0.01
48 36 0.19
49 38 0.20
51 1 0.01
52 32 0.17
53 6 0.03
54 1 0.01
55 36 0.19
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
Found at i:187030 original size:92 final size:95
Alignment explanation
Indices: 186846--187085 Score: 315
Period size: 92 Copynumber: 2.5 Consensus size: 95
186836 AAAGATGAGA
* *
186846 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAA
*
186911 TATGCTGATTCAAGGCCAGCTATATTGGACTT
64 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
186943 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATA
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
*
187005 TGCTGATTTAAGGCCAGCGATATTGGACTT
66 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
187035 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAA
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
187086 AGGAGACGCC
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
92 40 0.31
94 2 0.02
95 40 0.31
96 5 0.04
97 40 0.31
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (95 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:187162 original size:28 final size:28
Alignment explanation
Indices: 187131--187228 Score: 115
Period size: 28 Copynumber: 3.4 Consensus size: 28
187121 GTTTGCATCA
* *
187131 ACTTGTGTGCTTTTGAAGGTTGCTACTG
1 ACTTGTGAGCTTTTGAAGGTTGCCACTG
* *
187159 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGAGCTTTTGAAGGTTGCCACTG
* *
187187 ACTTGTGAGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGAGCTTTTG--AAGGTTGCCACTG
*
187217 ACTTGTGGGCTT
1 ACTTGTGAGCTT
187229 AAAAAGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 38 0.63
30 22 0.37
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (28 bp):
ACTTGTGAGCTTTTGAAGGTTGCCACTG
Found at i:187213 original size:30 final size:30
Alignment explanation
Indices: 187131--187448 Score: 197
Period size: 30 Copynumber: 10.6 Consensus size: 30
187121 GTTTGCATCA
* * *
187131 ACTTGTGTGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
187159 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
187187 ACTTGTGAGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
187217 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** * *
187251 AGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGG
1 ACTTGTGGGCTT----TTG-AAAAGGGTGCCACTG
* * * * *
187286 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
187315 ACTTGTGGGCTTTAGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
187345 ATTTGTGGGC-TTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
187372 ACTTGTGGGCTTTTGAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG-AAAAGGGTGCCACTG
* *
187403 ACTTGTGGGC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
187432 ACTTGTGGACTTTTGAA
1 ACTTGTGGGCTTTTGAA
187449 GGGTGAGGAA
Statistics
Matches: 237, Mismatches: 37, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
27 21 0.09
28 42 0.18
29 49 0.21
30 54 0.23
31 21 0.09
33 2 0.01
34 20 0.08
35 28 0.12
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:187289 original size:35 final size:34
Alignment explanation
Indices: 187202--187292 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
187192 TGAGCTTTTG
* * *
187202 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* *
187236 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
187271 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
187293 GACTTTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 21 0.45
35 25 0.53
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:187320 original size:29 final size:29
Alignment explanation
Indices: 187271--187444 Score: 181
Period size: 29 Copynumber: 5.9 Consensus size: 29
187261 TTACAAAAGA
* * *
187271 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
187301 AAAAGATGCCACCGACTTGTGGGCTTTAG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
187330 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
187359 -AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAAAGATGCCACTGACTTGTGGGC-TTTG-G
* *
187389 AAAAAATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
*
187418 AAAAGATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
187445 TGAAGGGTGA
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.15
28 5 0.04
29 50 0.41
30 30 0.24
31 20 0.16
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:188843 original size:16 final size:16
Alignment explanation
Indices: 188824--188869 Score: 69
Period size: 15 Copynumber: 3.0 Consensus size: 16
188814 ATCTAGACCC
188824 TTTTTTTTGTTTTTGT
1 TTTTTTTTGTTTTTGT
188840 TTTTTTTTG-TTTTGT
1 TTTTTTTTGTTTTTGT
*
188855 TTGTTTTT-TTTTTGT
1 TTTTTTTTGTTTTTGT
188870 GGAGGACGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTTGTTTTTGT
Found at i:200023 original size:52 final size:52
Alignment explanation
Indices: 199967--200147 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
199957 CACTGATCTT
* **
199967 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
200019 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
200071 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
200123 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
200148 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
Found at i:206413 original size:52 final size:52
Alignment explanation
Indices: 206335--206483 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 52
206325 CGAAATATGA
* * *
206335 AAATTTGCTTGCATGTATTGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
** *
206387 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
** *
206439 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACA
206484 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 85 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
Found at i:206460 original size:32 final size:32
Alignment explanation
Indices: 206419--206528 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 32
206409 ACATTTTATA
206419 ATGTATCGATACATCTAGGCAAATTTGCCTGC
1 ATGTATCGATACATCTAGGCAAATTTGCCTGC
* *** * * *
206451 ATGTATCGATACA--AAGATTAGTGTAT-CGATAC
1 ATGTATCGATACATCTAGGCAAAT-T-TGC-CTGC
206483 AATGTATCGATACATCTAGGCAAATTTGCCTGC
1 -ATGTATCGATACATCTAGGCAAATTTGCCTGC
206516 ATGTATCGATACA
1 ATGTATCGATACA
206529 AAGATTAGTG
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
30 4 0.07
31 2 0.04
32 29 0.51
33 16 0.28
34 2 0.04
35 4 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACATCTAGGCAAATTTGCCTGC
Found at i:206490 original size:13 final size:13
Alignment explanation
Indices: 206472--206496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206462 CAAAGATTAG
206472 TGTATCGATACAA
1 TGTATCGATACAA
206485 TGTATCGATACA
1 TGTATCGATACA
206497 TCTAGGCAAA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:206522 original size:65 final size:65
Alignment explanation
Indices: 206418--206548 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
206408 TACATTTTAT
206418 AATGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
1 AATGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
206483 AATGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
1 AATGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
206548 A
1 A
206549 TTTAAGTGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (65 bp):
AATGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
Found at i:206629 original size:13 final size:13
Alignment explanation
Indices: 206611--206635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206601 CAAAAAAATA
206611 TGTATCGATACAT
1 TGTATCGATACAT
206624 TGTATCGATACA
1 TGTATCGATACA
206636 ATACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:216608 original size:26 final size:26
Alignment explanation
Indices: 216579--216630 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
216569 ATATATATAT
216579 ATATAAAAATATAAAACAAGAAATCA
1 ATATAAAAATATAAAACAAGAAATCA
* *
216605 ATATATAAATATAAAGCAAGAAATCA
1 ATATAAAAATATAAAACAAGAAATCA
216631 TGTGAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.21
Consensus pattern (26 bp):
ATATAAAAATATAAAACAAGAAATCA
Found at i:222526 original size:13 final size:13
Alignment explanation
Indices: 222504--222540 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
222494 AACTTACTCA
222504 GTATCGATATAGT
1 GTATCGATATAGT
*
222517 GTATCAATATAGT
1 GTATCGATATAGT
222530 GTATCGATATA
1 GTATCGATATA
222541 TGGTGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (13 bp):
GTATCGATATAGT
Found at i:223037 original size:32 final size:29
Alignment explanation
Indices: 222995--223117 Score: 124
Period size: 32 Copynumber: 4.0 Consensus size: 29
222985 AAGTGATTGA
222995 GAGGTTCTATCTTAGCCTTG-AAAGATAG
1 GAGGTTCTATCTTAGCCTTGAAAAGATAG
223023 TGTACAGGTTCTATCTTAGCCTTTGTAAAAGATAGG
1 -G---AGGTTCTATCTTAGCC-TTG-AAAAGATA-G
* *
223059 GAGTTTCTATCTTAGCCCGTGAAAAGATAAG
1 GAGGTTCTATCTTAG-CCTTGAAAAGAT-AG
223090 GAGGTTTCTATCTTAGCCTTG-AAAGATA
1 GAGG-TTCTATCTTAGCCTTGAAAAGATA
223118 ATGTTGTAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
29 2 0.03
30 6 0.08
31 15 0.19
32 43 0.54
33 5 0.06
35 8 0.10
36 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (29 bp):
GAGGTTCTATCTTAGCCTTGAAAAGATAG
Found at i:223548 original size:20 final size:20
Alignment explanation
Indices: 223525--223576 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
223515 AAAAATGATT
223525 AAAAATTGATTTTTATGACC
1 AAAAATTGATTTTTATGACC
*
223545 AAAAATTGATTTTTATGGCC
1 AAAAATTGATTTTTATGACC
223565 AAAAATTGATTT
1 AAAAATTGATTT
223577 ACTACACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (20 bp):
AAAAATTGATTTTTATGACC
Found at i:224338 original size:15 final size:15
Alignment explanation
Indices: 224300--224339 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
224290 GTTCTTCTTA
*
224300 TTATCTTTCTTTTTC
1 TTATCTTTTTTTTTC
224315 TTATCTTTTTTTTTC
1 TTATCTTTTTTTTTC
224330 TT-TCTTTTTT
1 TTATCTTTTTT
224340 CTCTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATCTTTTTTTTTC
Found at i:226354 original size:52 final size:52
Alignment explanation
Indices: 226290--226473 Score: 160
Period size: 52 Copynumber: 3.6 Consensus size: 52
226280 ATTTAACTGG
*
226290 ATGTATCGATAC-ATTAAAGAATGTATCGATACATTTGATTCAAAAATCCAAA
1 ATGTATCGATACAATTAAA-AATGTATCGATACATTTGAGTCAAAAATCCAAA
** * * * * * *
226342 ATGTATCGATACAATTACTAATCTATCGGTACCTTCGGGTCAAAAATCCAGA
1 ATGTATCGATACAATTAAAAATGTATCGATACATTTGAGTCAAAAATCCAAA
* * * * * * * *
226394 ATGTATTGACACAATGAAAAATGTATCGATACATTTG-GAC-CAAAGCTAGA
1 ATGTATCGATACAATTAAAAATGTATCGATACATTTGAGTCAAAAATCCAAA
* *
226444 ATGCATTGATACAA-TAAAAATGTATCGATA
1 ATGTATCGATACAATTAAAAATGTATCGATA
226474 TAATTTCTTT
Statistics
Matches: 106, Mismatches: 25, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
49 15 0.14
50 19 0.18
51 2 0.02
52 66 0.62
53 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATTAAAAATGTATCGATACATTTGAGTCAAAAATCCAAA
Found at i:230842 original size:153 final size:153
Alignment explanation
Indices: 230615--231006 Score: 482
Period size: 154 Copynumber: 2.6 Consensus size: 153
230605 ATTACATCGA
* * * * *
230615 ACTTGATTCTATAAAAATTACCAAAATACCCCTTAGGTATACCTTCGACGTGAAAGTATCTTGAT
1 ACTTGATTCTAAAAAAATTACCAAAATGCCCCTTGGGTATACTTTCGACGTGAAAGTATCTTGGT
* * * *
230680 AGCCTTAAAGGA-ACGAAAAGATCGAAAAAAGATAAACCTATCCTAAGTGTAGAAC-TTTGACGT
66 AACCCTAAAGGACACGAAAAGATCGAAAAAAGATAAACCTATACTAAGTGTAG-ACTTTTGACAT
* * *
230743 AAAAGTGACCAAATGACTACTTAAG
130 AAAAGT-AACAAATGACCACCTAAG
* *
230768 ACTTGGTTCTAAAAAAATTACCAAAATGCCCCTTGGGTATACTTTCGACGTGAAAGTATCTCGGT
1 ACTTGATTCTAAAAAAATTACCAAAATGCCCCTTGGGTATACTTTCGACGTGAAAGTATCTTGGT
* * * * * *
230833 AACCCTAAAGGACACGAAAAGATTGTAAAAGGGTGAACCTATACTAAGTGTAGACTTTTGGCATA
66 AACCCTAAAGGACACGAAAAGATCGAAAAAAGATAAACCTATACTAAGTGTAGACTTTTGACATA
*
230898 AAAGTAACTAATGACCACCTAAG
131 AAAGTAACAAATGACCACCTAAG
* * ** * * * *
230921 ACTCGATTCTAGGAAAAATTATTAAAATGCCTCTTGAGTATACTTTCGACATGAAAGAATCTTGG
1 ACTTGATTCTA-AAAAAATTACCAAAATGCCCCTTGGGTATACTTTCGACGTGAAAGTATCTTGG
230986 TAACCCTAAAGGACACGAAAA
65 TAACCCTAAAGGACACGAAAA
231007 TACTATGAAA
Statistics
Matches: 205, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
153 93 0.45
154 112 0.55
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (153 bp):
ACTTGATTCTAAAAAAATTACCAAAATGCCCCTTGGGTATACTTTCGACGTGAAAGTATCTTGGT
AACCCTAAAGGACACGAAAAGATCGAAAAAAGATAAACCTATACTAAGTGTAGACTTTTGACATA
AAAGTAACAAATGACCACCTAAG
Found at i:231218 original size:58 final size:57
Alignment explanation
Indices: 231060--231307 Score: 172
Period size: 58 Copynumber: 4.3 Consensus size: 57
231050 AAAACTGCGC
* * * * * *
231060 ATTGACCATTAAACCTTTCAAACTTACATTTTG-TTCCTAAACTCCTCAAAATTACAT
1 ATTGACCCTTAAACTTTTCAAAATTACA-ATTGATTCCTAAACTTCTTAAAATTACAT
* * * * *
231117 ATTGACCCTTAGACATTTT-AAAACTACGAATT-AGCTCCCAAACTTCTTGAAATTACAT
1 ATTGACCCTTAAAC-TTTTCAAAATTAC-AATTGA-TTCCTAAACTTCTTAAAATTACAT
* * *
231175 TTTGACCCTTAAACTTTTCACAATTACACATTGATTCCTAAACTT-TTAAAAAT-CAT
1 ATTGACCCTTAAACTTTTCAAAATTACA-ATTGATTCCTAAACTTCTTAAAATTACAT
* * *
231231 AGATTGACCCTTAAACTTTTTAAAATTACGAATT-A-ACCTTAAAACTT-TTAAAGAATTACAC
1 --ATTGACCCTTAAACTTTTCAAAATTAC-AATTGATTCC-T-AAACTTCTT-AA-AATTACAT
231292 ATTGACCC-TAAACTTT
1 ATTGACCCTTAAACTTT
231308 AAAAAATATA
Statistics
Matches: 151, Mismatches: 25, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
56 5 0.03
57 33 0.22
58 96 0.64
59 12 0.08
60 3 0.02
61 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (57 bp):
ATTGACCCTTAAACTTTTCAAAATTACAATTGATTCCTAAACTTCTTAAAATTACAT
Found at i:231254 original size:30 final size:29
Alignment explanation
Indices: 231176--231459 Score: 188
Period size: 29 Copynumber: 9.7 Consensus size: 29
231166 AAATTACATT
* * * *
231176 TTGACCCTTAAACTTTTCACAATTACACA
1 TTGACCCTTAAACTTTTAAAAATTATAGA
* *
231205 TTGATTCC-TAAACTTTTAAAAATCATAGA
1 TTGA-CCCTTAAACTTTTAAAAATTATAGA
* *
231234 TTGACCCTTAAACTTTTTAAAATTA-CGAA
1 TTGACCCTTAAACTTTTAAAAATTATAG-A
* * *
231263 TT-AACCTTAAAACTTTTAAAGAATTACACA
1 TTGACCCTT-AAACTTTTAAA-AATTATAGA
*
231293 TTGACCC-TAAAC-TTTAAAAAATATAGA
1 TTGACCCTTAAACTTTTAAAAATTATAGA
* * *
231320 TTTAACCC-TAAACTTTTTTAAAATTATAGG
1 -TTGACCCTTAAAC-TTTTAAAAATTATAGA
**
231350 TTGACCC-TAAACATTTTAAAAATTACGGA
1 TTGACCCTTAAAC-TTTTAAAAATTATAGA
* * *
231379 TTG-CGCTCTAAACTTTTTCAAAATTATGGA
1 TTGACCCT-TAAAC-TTTTAAAAATTATAGA
** ** *
231409 TTGACCCCAAAACTTTTAAAAAATTACGGC
1 TTGACCCTTAAACTTTT-AAAAATTATAGA
*
231439 TTGACCCTAAAACTTTTAAAA
1 TTGACCCTTAAACTTTTAAAA
231460 TGGTTGGAAT
Statistics
Matches: 202, Mismatches: 39, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
27 6 0.03
28 27 0.13
29 90 0.45
30 74 0.37
31 5 0.02
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (29 bp):
TTGACCCTTAAACTTTTAAAAATTATAGA
Found at i:231314 original size:58 final size:56
Alignment explanation
Indices: 231176--231459 Score: 223
Period size: 58 Copynumber: 4.9 Consensus size: 56
231166 AAATTACATT
* * ** *
231176 TTGACCCTTAAACTTTTCACAATTAC-ACATTGATTCCTAAACTTTTAAAAATCATAGA
1 TTGACCC-TAAACTTTTAAAAATTACGA-ATT-AACCCTAAACTTTTAAAAATTATAGA
* * * *
231234 TTGACCCTTAAACTTTTTAAAATTACGAATTAACCTTAAAACTTTTAAAGAATTACACA
1 TTGACCC-TAAACTTTTAAAAATTACGAATTAACCCT-AAACTTTTAAA-AATTATAGA
* * * *
231293 TTGACCCTAAACTTTAAAAAATATA-GATTTAACCCTAAACTTTTTTAAAATTATAGG
1 TTGACCCTAAACTTTTAAAAAT-TACGAATTAACCCTAAAC-TTTTAAAAATTATAGA
* * * *
231350 TTGACCCTAAACATTTTAAAAATTACGGATT-GCGCTCTAAACTTTTTCAAAATTATGGA
1 TTGACCCTAAAC-TTTTAAAAATTACGAATTAAC-C-CTAAAC-TTTTAAAAATTATAGA
* ** *
231409 TTGACCCCAAAACTTTTAAAAAATTACGGCTTGACCCTAAAACTTTTAAAA
1 TTGA-CCCTAAACTTTT-AAAAATTACGAATTAACCCT-AAACTTTTAAAA
231460 TGGTTGGAAT
Statistics
Matches: 186, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
57 28 0.15
58 79 0.42
59 53 0.28
60 25 0.13
61 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (56 bp):
TTGACCCTAAACTTTTAAAAATTACGAATTAACCCTAAACTTTTAAAAATTATAGA
Found at i:231394 original size:87 final size:87
Alignment explanation
Indices: 231179--231375 Score: 217
Period size: 87 Copynumber: 2.3 Consensus size: 87
231169 TTACATTTTG
* * * * * *
231179 ACCCTTAAACTTTT-CACAATTACACATTGATTCCTAAACTTTTAAAAATCATAGATTGACCCTT
1 ACCCTAAAACTTTTAAAGAATTACACATTGA-CCCTAAACTTTAAAAAATCATAGATTAACCCTT
*
231243 AAACTTTTTAAAATTACGAATTA
65 AAACTTTTTAAAATTAAGAATTA
*
231266 ACCTTAAAACTTTTAAAGAATTACACATTGACCCTAAACTTTAAAAAAT-ATAGATTTAACCC-T
1 ACCCTAAAACTTTTAAAGAATTACACATTGACCCTAAACTTTAAAAAATCATAGA-TTAACCCTT
* *
231329 AAACTTTTTTAAAATTATAG-GTTG
65 AAAC-TTTTTAAAATTA-AGAATTA
231353 ACCCT-AAACATTTTAAA-AATTAC
1 ACCCTAAAAC-TTTTAAAGAATTAC
231376 GGATTGCGCT
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
86 20 0.21
87 59 0.63
88 15 0.16
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.36
Consensus pattern (87 bp):
ACCCTAAAACTTTTAAAGAATTACACATTGACCCTAAACTTTAAAAAATCATAGATTAACCCTTA
AACTTTTTAAAATTAAGAATTA
Found at i:232427 original size:23 final size:23
Alignment explanation
Indices: 232375--232421 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
232365 CATTACTAAC
*
232375 TAAATCAACCAAATCAAGAAACT
1 TAAATCAACAAAATCAAGAAACT
232398 TAAATCAACAAAATCAAGAAACT
1 TAAATCAACAAAATCAAGAAACT
232421 T
1 T
232422 TGATCATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.19
Consensus pattern (23 bp):
TAAATCAACAAAATCAAGAAACT
Found at i:232949 original size:21 final size:21
Alignment explanation
Indices: 232925--232969 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
232915 AAAATAAAAT
* *
232925 AAAATAAATAAAGTAAATTTA
1 AAAATAAAAAAAGTAAAATTA
*
232946 AAAATAAAAAAATTAAAATTA
1 AAAATAAAAAAAGTAAAATTA
232967 AAA
1 AAA
232970 TCAATTCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAAAAAAAGTAAAATTA
Found at i:233461 original size:167 final size:165
Alignment explanation
Indices: 233076--233679 Score: 768
Period size: 168 Copynumber: 3.6 Consensus size: 165
233066 TAATATATAC
* * * * * *
233076 AAAAAATTTAAAAATTCATG-AAAT-AATTTGAATTTCTCAAAACTGACTTAATGTGAATTTAAT
1 AAAAAATTCAAAAATTCATGAAAATGAA--TGAATTTCTAAAAACTAATTTAATATGAATTAAAT
* * * * * * * * *
233139 GACAATATTAGATGAATTTTTAAATTTTAAATCAAGAAAAATCCCCCCG-AAAAAATTTACGGAG
64 AATAATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCCTCTGAAAAAAATTTACGGAG
* * * * *
233203 AAAAAAATTCAGT-TTTTTAGAAAAGAGAAATATCAAGG
129 AAGAAAACTCCGTATTTTGA-AAAAGAG-AATTTCAAGG
* * * * *
233241 AAAAAA-TAAAAAACTCATGAAAATGAATGAATTTTTAAAAATTAATTTAATATGAATTAAATAT
1 AAAAAATTCAAAAATTCATGAAAATGAATGAATTTCTAAAAACTAATTTAATATGAATTAAATAA
* * * *
233305 TAATATCTGATGAATTTTAAAAAATAAAAACAAGAAAAATCCTTCTGAAAAAAATTTACAGAGAA
66 TAATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCCTCTGAAAAAAATTTACGGAGAA
233370 GAAAACTCCGTATTTTCGAAACAAGAGAATTTCAAGG
131 GAAAACTCCGTATTTT-GAAA-AAGAGAATTTCAAGG
* *
233407 AAAAAATTCAAAAATTCATGAAAATGAATGAATTTCTAAAAAATAATATAATATGAATTAAATAA
1 AAAAAATTCAAAAATTCATGAAAATGAATGAATTTCTAAAAACTAATTTAATATGAATTAAATAA
233472 TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCTGAAAAAAATTTACGGAGA
66 TAATATTTGATGAATTTTAAAAATTAAAAA-CAAGAAAAATCCCTCTGAAAAAAATTTACGGAGA
*
233537 AGAAAACTCCGTATTTTGAAAATAGAAAAATTTCAAGG
130 AGAAAACTCCGTATTTTGAAAA-AG-AGAATTTCAAGG
* *
233575 AAAAAATTCAAAAATTCAAGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAATTAAATAA
1 AAAAAATTCAAAAATTCATGAAAATGAATGAATTTCTAAAAACTAATTTAATATGAATTAAATAA
*
233640 TATTATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAA
66 TAATATTTGATGAATTTTAAAAATTAAAAAC-AAGAAAAA
233680 CCTCCCCGAA
Statistics
Matches: 384, Mismatches: 44, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
164 75 0.20
165 34 0.09
166 24 0.06
167 93 0.24
168 158 0.41
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (165 bp):
AAAAAATTCAAAAATTCATGAAAATGAATGAATTTCTAAAAACTAATTTAATATGAATTAAATAA
TAATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCCTCTGAAAAAAATTTACGGAGAA
GAAAACTCCGTATTTTGAAAAAGAGAATTTCAAGG
Found at i:234594 original size:49 final size:50
Alignment explanation
Indices: 234508--234634 Score: 177
Period size: 49 Copynumber: 2.6 Consensus size: 50
234498 AGTCAGTTGC
* * * * *
234508 TCACTTTATTCGGTTATGTGAAAGATCAATAGGGTTAGTT-TTCTTTTG-
1 TCACTTCATTCGATTATGTGAAAGATCGATAGAGTTAGTTGTCCTTTTGT
234556 TCAGCTTCATTCGATTATGTGAAAGATCGATAGAGTTAGTTGTCCTTTTGT
1 TCA-CTTCATTCGATTATGTGAAAGATCGATAGAGTTAGTTGTCCTTTTGT
*
234607 TTACTTCATTCGATTATGTGAAAGATCG
1 TCACTTCATTCGATTATGTGAAAGATCG
234635 GTAAGGGTGA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
48 3 0.04
49 33 0.47
50 32 0.46
51 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (50 bp):
TCACTTCATTCGATTATGTGAAAGATCGATAGAGTTAGTTGTCCTTTTGT
Found at i:234897 original size:24 final size:24
Alignment explanation
Indices: 234865--234910 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
234855 TCTTAGTCAT
234865 TGCCTAGTTCATGAGTTCTCAGAA
1 TGCCTAGTTCATGAGTTCTCAGAA
234889 TGCCTAGTTCATGAGTTCTCAG
1 TGCCTAGTTCATGAGTTCTCAG
234911 CAATAGCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (24 bp):
TGCCTAGTTCATGAGTTCTCAGAA
Found at i:239671 original size:99 final size:99
Alignment explanation
Indices: 239539--239726 Score: 295
Period size: 99 Copynumber: 1.9 Consensus size: 99
239529 TGATCCACAC
* ** * **
239539 AAGTAACTTGCAAAACCTTCACAAGGTGGGGATTGTGTTTTAGCTGGAAGCCATGCTAGTGGCTT
1 AAGTAACTTGCAAAACCTTCACAAGATAAGGATTATGTTTTAGCCAGAAGCCATGCTAGTGGCTT
*
239604 AGGTTTCCTAAACATTCCCTTGAATGAAAGCCAT
66 AGGTTCCCTAAACATTCCCTTGAATGAAAGCCAT
**
239638 AAGTAACTTGCAAAACCTTCACAAGATAAGGATTATGTTTTAGCCAGAAGCTGTGCTAGTGGCTT
1 AAGTAACTTGCAAAACCTTCACAAGATAAGGATTATGTTTTAGCCAGAAGCCATGCTAGTGGCTT
239703 AGGTTCCCTAAACATTCCCTTGAA
66 AGGTTCCCTAAACATTCCCTTGAA
239727 CAAAAGCCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (99 bp):
AAGTAACTTGCAAAACCTTCACAAGATAAGGATTATGTTTTAGCCAGAAGCCATGCTAGTGGCTT
AGGTTCCCTAAACATTCCCTTGAATGAAAGCCAT
Found at i:240588 original size:32 final size:32
Alignment explanation
Indices: 240552--240622 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
240542 TTCAACGATT
240552 TGTATCGATAAATAAGTGTTGTATCGATACAA
1 TGTATCGATAAATAAGTGTTGTATCGATACAA
* * *
240584 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATAAATAAGTGTTGTATCGATACAA
240616 TGTATCG
1 TGTATCG
240623 CTATGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATAAATAAGTGTTGTATCGATACAA
Found at i:240589 original size:13 final size:13
Alignment explanation
Indices: 240571--240595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240561 AAATAAGTGT
240571 TGTATCGATACAA
1 TGTATCGATACAA
240584 TGTATCGATACA
1 TGTATCGATACA
240596 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:240721 original size:52 final size:52
Alignment explanation
Indices: 240661--240815 Score: 213
Period size: 52 Copynumber: 3.0 Consensus size: 52
240651 TGATACATTA
*** *
240661 CCCAAATGTATCGATACACTGAT-CTTTGTATCGATACATGCAAGCAAATTTG
1 CCCAAATGTATCGATACACT-ATAAAATGTATCGATACATGCAGGCAAATTTG
*
240713 CCCAAATGTATCGATACACTATAAAATGTATCGATACATACAGGCAAATTTG
1 CCCAAATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTG
* * * *
240765 CCCAGATGTATCAATATACTATGAAATGTATCGATACATGCAGGCAAATTT
1 CCCAAATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
240816 TCATATTTTG
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 2 0.02
52 90 0.98
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (52 bp):
CCCAAATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTG
Found at i:241747 original size:19 final size:21
Alignment explanation
Indices: 241705--241747 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
241695 AACCCATGAA
*
241705 TCATGCATTTTTAGCTATGCT
1 TCATGCATTTATAGCTATGCT
241726 TCATGCATTTATAGC-ATG-T
1 TCATGCATTTATAGCTATGCT
241745 TCA
1 TCA
241748 GCACCTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 14 0.67
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (21 bp):
TCATGCATTTATAGCTATGCT
Found at i:243147 original size:13 final size:13
Alignment explanation
Indices: 243129--243154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243119 ACATTTGGTC
243129 ATGTATCGATACA
1 ATGTATCGATACA
243142 ATGTATCGATACA
1 ATGTATCGATACA
243155 TCTTGTATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:243149 original size:33 final size:32
Alignment explanation
Indices: 243107--243174 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
243097 CGTTACAAGC
243107 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
243140 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
243172 CAA
1 CAA
243175 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:250426 original size:20 final size:21
Alignment explanation
Indices: 250384--250434 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
250374 TTCAATAATT
250384 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
250405 TGTATCGATAC-ATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
250425 TGTATCGATA
1 TGTATCGATA
250435 TATTCTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:253228 original size:20 final size:20
Alignment explanation
Indices: 253165--253240 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
253155 GCCAAGGAAA
253165 TGTATCGATACATTAAT-AAA-
1 TGTATCGATACATT--TCAAAT
253185 TGTATCGATACATGTTTCAAAT
1 TGTATCGATACA--TTTCAAAT
**
253207 TGTATCGATACATTTCCCAT
1 TGTATCGATACATTTCAAAT
*
253227 TGTATTGATACATT
1 TGTATCGATACATT
253241 CTGGGTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
20 32 0.65
21 3 0.06
22 14 0.29
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTCAAAT
Found at i:257504 original size:21 final size:21
Alignment explanation
Indices: 257452--257512 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
257442 GCCTTGTATC
*
257452 GATATATTGTATCGATACAT-
1 GATAAATTGTATCGATACATG
*
257472 -ATTCAA-TGTATCGATACATG
1 GA-TAAATTGTATCGATACATG
257492 GATAAATTGTATCGATACATG
1 GATAAATTGTATCGATACATG
257513 AAATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 14 0.41
20 5 0.15
21 15 0.44
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
GATAAATTGTATCGATACATG
Found at i:257578 original size:13 final size:13
Alignment explanation
Indices: 257557--257587 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
257547 CGATACATGG
*
257557 TACAATGTATCGA
1 TACATTGTATCGA
257570 TACATTGTATCGA
1 TACATTGTATCGA
257583 TACAT
1 TACAT
257588 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:257597 original size:33 final size:33
Alignment explanation
Indices: 257541--257607 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
257531 CTATCACTAT
*
257541 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGAAACA
257574 TTGTATCGATACATGAAG-A-AATGTATCGAAACA
1 TTGTATCGATACATG--GTACAATGTATCGAAACA
257607 T
1 T
257608 GAAGAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGGTACAATGTATCGAAACA
Found at i:257600 original size:20 final size:20
Alignment explanation
Indices: 257575--257627 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
257565 ATCGATACAT
257575 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
*
257595 TGTATCGAAACATGAAGAAA
1 TGTATCGATACATGAAGAAA
257615 TGTATCGATACAT
1 TGTATCGATACAT
257628 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAA
Found at i:261536 original size:27 final size:27
Alignment explanation
Indices: 261506--261573 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
261496 AAAAGAAGTC
*
261506 AAAAGCAAAAGCACGAAAAAT-GAAAAA
1 AAAAGCAAAAGCAAGAAAAATCG-AAAA
*
261533 AAAAG-AAAAGAAAAGAAAAATCGAAAA
1 AAAAGCAAAAG-CAAGAAAAATCGAAAA
*
261560 AAATGCAAAAGCAA
1 AAAAGCAAAAGCAA
261574 AATAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 5 0.15
27 23 0.68
28 6 0.18
ACGTcount: A:0.72, C:0.09, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAGCAAAAGCAAGAAAAATCGAAAA
Found at i:261569 original size:23 final size:23
Alignment explanation
Indices: 261543--261609 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 23
261533 AAAAGAAAAG
*
261543 AAAAGAAAAATCGAAAAAAATGC
1 AAAAGAAAAATCGAAAAAAAGGC
* *
261566 AAAAGCAAAAT--AAAAAAAGGG
1 AAAAGAAAAATCGAAAAAAAGGC
* *
261587 ATAACAAAAATCGAAAAACAAGG
1 AAAAGAAAAATCGAAAAA-AAGG
261610 ACATGACTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 16 0.46
23 15 0.43
24 4 0.11
ACGTcount: A:0.69, C:0.09, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAAGAAAAATCGAAAAAAAGGC
Found at i:261569 original size:28 final size:28
Alignment explanation
Indices: 261520--261581 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
261510 GCAAAAGCAC
261520 GAAAAATGAAAAAAAAAGAAAAG-AAAA
1 GAAAAATGAAAAAAAAAGAAAAGCAAAA
*
261547 GAAAAATCG-AAAAAAATGCAAAAGCAAAA
1 GAAAAAT-GAAAAAAAAAG-AAAAGCAAAA
*
261576 TAAAAA
1 GAAAAA
261582 AAGGGATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 15 0.50
28 6 0.20
29 9 0.30
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.06
Consensus pattern (28 bp):
GAAAAATGAAAAAAAAAGAAAAGCAAAA
Found at i:262874 original size:29 final size:29
Alignment explanation
Indices: 262751--262893 Score: 112
Period size: 29 Copynumber: 4.8 Consensus size: 29
262741 TATTTTTCTA
*
262751 AAAGCCCACGACTCCGTGGCACCCTTCCT
1 AAAGCCCACGACTTCGTGGCACCCTTCCT
* * * *
262780 AAAGTCTATGAC-TCAGTGGCATCTCTTCTCT
1 AAAGCCCACGACTTC-GTGGCA-CCCTTC-CT
* * *
262811 -AAGTCCACGACTTAGTGGCACCTTTCTTCCA
1 AAAGCCCACGACTTCGTGGCACC---CTTCCT
*
262842 AAAGCCCACAACTTCGTGGCACCCTTCCT
1 AAAGCCCACGACTTCGTGGCACCCTTCCT
*
262871 AAAGCCCACAAC-TCTGTGGCACC
1 AAAGCCCACGACTTC-GTGGCACC
262894 TTTTTTCCTT
Statistics
Matches: 91, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.03
29 41 0.45
30 20 0.22
31 4 0.04
32 23 0.25
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAGCCCACGACTTCGTGGCACCCTTCCT
Found at i:262952 original size:26 final size:27
Alignment explanation
Indices: 262923--262984 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
262913 CAACTCTGTC
*
262923 GCACCTTTT-AACTCCATAA-TGTCGTG
1 GCACCTTTTCAACTCCACAACT-TCGTG
*
262949 GCACCTTTTCAAGTCCACAACTTCGTG
1 GCACCTTTTCAACTCCACAACTTCGTG
262976 GCACCTTTT
1 GCACCTTTT
262985 TCTTTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 9 0.28
27 22 0.69
28 1 0.03
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.34
Consensus pattern (27 bp):
GCACCTTTTCAACTCCACAACTTCGTG
Found at i:262974 original size:27 final size:26
Alignment explanation
Indices: 262900--262984 Score: 93
Period size: 26 Copynumber: 3.2 Consensus size: 26
262890 CACCTTTTTT
* *
262900 CCTTTTAAGTTCACAAC-TCTGTCGCA
1 CCTTTTAAGTCCACAACTTC-GTGGCA
* *
262926 CCTTTTAACTCCATAA-TGTCGTGGCA
1 CCTTTTAAGTCCACAACT-TCGTGGCA
262952 CCTTTTCAAGTCCACAACTTCGTGGCA
1 CCTTTT-AAGTCCACAACTTCGTGGCA
262979 CCTTTT
1 CCTTTT
262985 TCTTTTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 24 0.49
27 24 0.49
28 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (26 bp):
CCTTTTAAGTCCACAACTTCGTGGCA
Found at i:263013 original size:34 final size:34
Alignment explanation
Indices: 262953--263340 Score: 330
Period size: 34 Copynumber: 11.9 Consensus size: 34
262943 GTCGTGGCAC
* *
262953 CTTTTC-AAGTCCACAACTTCGTGGCACCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* *
262986 CTTTTCAAAACCCATAACTCCGTGGCACCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
*
263020 CTTTTCAAAACCCACAACTCCGTGGCACCTTTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACC--TTTTT
* * *
263056 CTTTT--AAGTCCACAACTTCATGGCACC-----
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* **
263083 CTTTT--AAGTCCACAACTTTGTGGCACCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* * *
263115 CATTTCAAAGCCTACAACT-CTTGGCACCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* * *
263148 CTTTTCAAAGCCCATAACTCCATGGCACTTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
*
263182 CTTTTCAAAGCCCACAACTCCAGTGTCACC-----
1 CTTTTCAAAGCCCACAACTCC-GTGGCACCTTTTT
* *
263212 CTTTT--AAGTCCACAACTCCATGGCACCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* * **
263244 TTTTTCAAAGCCTACAACTCAATGGCATCCTTTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTTT
* * * *
263279 CCTTTT--AAGTCCACAACTTCGTGGCAACTATTT
1 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
*
263312 CTTTTCAAAGCCCACAACTCCGTAGCACC
1 CTTTTCAAAGCCCACAACTCCGTGGCACC
263341 CCTTTTCCTT
Statistics
Matches: 288, Mismatches: 44, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
27 31 0.11
28 13 0.05
30 5 0.02
32 13 0.05
33 39 0.14
34 161 0.56
35 12 0.04
36 14 0.05
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.35
Consensus pattern (34 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:263044 original size:68 final size:66
Alignment explanation
Indices: 262953--263391 Score: 373
Period size: 68 Copynumber: 6.7 Consensus size: 66
262943 GTCGTGGCAC
* * *
262953 CTTTTCAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAACCCATAACTCCGTGGCACCTTT
1 CTTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
263018 TT
65 TT
** * * *
263020 CTTTTCAAAACCCACAACTCCGTGGCACCTTTTTTTCTTTT--AAGTCCACAACTTCATGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACC--TTTTTCTTTTCAAAGCCCACAACTCCGTGGCACC
263083 -----
62 TTTTT
** * * *
263083 CTTTTAAGTCCACAACTTTGTGGCACCTTTTTCATTTCAAAGCCTACAACT-CTTGGCACCTTTT
1 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
263147 T
66 T
* * * * *
263148 CTTTTCAAAGCCCATAACTCCATGGCACTTTTTTCTTTTCAAAGCCCACAACTCCAGTGTCACC-
1 CTTTT--AAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCC-GTGGCACCT
263212 ----
63 TTTT
* * * **
263212 CTTTTAAGTCCACAACTCCATGGCACCTTTTTTTTTTCAAAGCCTACAACTCAATGGCATCCTTT
1 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTT
263277 TT
65 TT
* * * *
263279 CCTTTTAAGTCCACAACTTCGTGGCAACTATTTCTTTTCAAAGCCCACAACTCCGTAGCACCCCT
1 -CTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCA--CCT
*
263344 TTTC
63 TTTT
* ** * * *
263348 CTTTTAAGTCCATAACTCTATGGCACATTTTCCTTCTCAAAGCC
1 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCC
263392 TATATAAGTT
Statistics
Matches: 295, Mismatches: 55, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
59 9 0.03
60 8 0.03
61 32 0.11
62 44 0.15
63 5 0.02
64 5 0.02
65 5 0.02
67 43 0.15
68 122 0.41
69 12 0.04
70 10 0.03
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.36
Consensus pattern (66 bp):
CTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
T
Found at i:263094 original size:27 final size:27
Alignment explanation
Indices: 263056--263114 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
263046 ACCTTTTTTT
263056 CTTTTAAGTCCACAACTTCATGGCACC
1 CTTTTAAGTCCACAACTTCATGGCACC
**
263083 CTTTTAAGTCCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTTCATGGCACC
*
263110 TTTTT
1 CTTTT
263115 CATTTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTTCATGGCACC
Found at i:263109 original size:129 final size:129
Alignment explanation
Indices: 262946--263346 Score: 458
Period size: 129 Copynumber: 3.1 Consensus size: 129
262936 CCATAATGTC
* * * *
262946 GTGGCA-CCTTTTCAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAACCCATAACTCCGTG
1 GTGGCACCCTTTT-AAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCTACAACTCCATG
* * *
263010 GCACCTTTTTCTTTTCAAAACCCACAACTCCGTGGCACCTTTTTTTCTTTT-AAGTCCACAACTT
65 GCACCTTTTTCTTTTCAAAACCCACAACTCCATGGCA-C-TTTTTTCTTTTAAAGCCCACAACTC
263074 CA
128 CA
* * *
263076 -TGGCACCCTTTTAAGTCCACAACTTTGTGGCACCTTTTTCATTTCAAAGCCTACAACT-CTTGG
1 GTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCTACAACTCCATGG
* *
263139 CACCTTTTTCTTTTCAAAGCCCATAACTCCATGGCACTTTTTTCTTTTCAAAGCCCACAACTCCA
66 CACCTTTTTCTTTTCAAAACCCACAACTCCATGGCACTTTTTTCTTTT-AAAGCCCACAACTCCA
* * * * *
263204 GTGTCACCCTTTTAAGTCCACAACTCCATGGCACCTTTTTTTTTTCAAAGCCTACAACTCAATGG
1 GTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCTACAACTCCATGG
** * * *
263269 CATCCTTTTTCCTTTT--AAGTCCACAACTTCGTGGCAAC-TATTTCTTTTCAAAGCCCACAACT
66 CA-CCTTTTT-CTTTTCAAAACCCACAACTCCATGGC-ACTTTTTTCTTTT-AAAGCCCACAACT
263331 CC-
127 CCA
*
263333 GTAGCACCCCTTTT
1 GTGGCA-CCCTTTT
263347 CCTTTTAAGT
Statistics
Matches: 236, Mismatches: 26, Indels: 18
0.84 0.09 0.06
Matches are distributed among these distances:
126 11 0.05
127 1 0.00
128 50 0.21
129 102 0.43
130 58 0.25
131 9 0.04
132 5 0.02
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.35
Consensus pattern (129 bp):
GTGGCACCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCTACAACTCCATGG
CACCTTTTTCTTTTCAAAACCCACAACTCCATGGCACTTTTTTCTTTTAAAGCCCACAACTCCA
Found at i:263198 original size:162 final size:154
Alignment explanation
Indices: 262871--263216 Score: 421
Period size: 162 Copynumber: 2.2 Consensus size: 154
262861 CACCCTTCCT
* *
262871 AAAGCCCACAACTCTGTGGCACCTTTTTTCCTTTTAAGTTCACAACTCTGTCGCACCTTTTAACT
1 AAAGCCCACAACTCCGTGGCACCTTTTTTCCTTTTAAGTCCACAACTCTG-CGCACCTTTTAACT
*
262936 CCATAATGTCGTGGCACCTTTTCAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAACCCAT
65 CCACAATGTCGTGGCACCTTTTCAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAACCCAT
*
263001 AACTCCGTGGCACCTTTTTCTTTTC
130 AACTCCATGGCACCTTTTTCTTTTC
* *
263026 AAAACCCACAACTCCGTGGCACCTTTTTTTCTTTTAAGTCCACAACTTCATG-GCACCCTTTTAA
1 AAAGCCCACAACTCCGTGGCACCTTTTTTCCTTTTAAGTCCACAAC-TC-TGCGCA-CCTTTTAA
* * *
263090 GTCCACAACT-TTGTGGCACCTTTTTCATTTCAAAG-CCTACAAC-TCTTGGCACCTTTTTCTTT
63 CTCCACAA-TGTCGTGGCACC----T--TTTC-AAGTCC-ACAACTTCGTGGCACCTTTTTCTTT
* *
263152 TCAAAGCCCATAACTCCATGGCACTTTTTTCTTTTC
119 TCAAAACCCATAACTCCATGGCACCTTTTTCTTTTC
* *
263188 AAAGCCCACAACTCCAGTGTCACCCTTTT
1 AAAGCCCACAACTCC-GTGGCACCTTTTT
263217 AAGTCCACAA
Statistics
Matches: 164, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
155 45 0.27
156 25 0.15
157 3 0.02
160 1 0.01
162 71 0.43
163 19 0.12
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.36
Consensus pattern (154 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTTCCTTTTAAGTCCACAACTCTGCGCACCTTTTAACTC
CACAATGTCGTGGCACCTTTTCAAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAACCCATA
ACTCCATGGCACCTTTTTCTTTTC
Found at i:263528 original size:32 final size:31
Alignment explanation
Indices: 263397--263535 Score: 120
Period size: 32 Copynumber: 4.4 Consensus size: 31
263387 AAGCCTATAT
* * * * *
263397 AAGTTGATTGCAACCTCTTCTAAATCCTAC-T
1 AAGTCGATGGCAACCT-TTCTAAAGCCCACAC
*
263428 AAGTCGGTGGCAACCTCTTCTAAAGCCCACAC
1 AAGTCGATGGCAACCT-TTCTAAAGCCCACAC
* *
263460 AAG-CTAGTGGCAACCTTTCTTAAAGCCCACAA
1 AAGTCGA-TGGCAACCTTTC-TAAAGCCCACAC
* *
263492 AAGTCGATGGCAACCCTTTCAAAAGCTCACAC
1 AAGTCGATGGCAA-CCTTTCTAAAGCCCACAC
*
263524 AAGTCGGTGGCA
1 AAGTCGATGGCA
263536 TCTTCTAAGC
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
31 29 0.33
32 52 0.58
33 8 0.09
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (31 bp):
AAGTCGATGGCAACCTTTCTAAAGCCCACAC
Found at i:263971 original size:156 final size:155
Alignment explanation
Indices: 263799--264323 Score: 681
Period size: 156 Copynumber: 3.4 Consensus size: 155
263789 GCACCTTTCT
* * * *
263799 CATCCTTAAGTCCAATATCGCTATCCTTGAATCAGCATATTGCCATCTTTAACATTCCTAAGCCC
1 CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCC
* * * * *
263864 AATGTCGCTGATCATGAATCAGCACATTGGCGTTTTTCTCATCTTCAAGTCTAATATTGCTGGTC
66 AATGTCGCTGATCTTGAATCAGCACATTGGCGCTCTTCTCATCTTCAAGTCTAATGTCGCTGG-C
*
263929 GTGAATCAGCACATTGGCATTCTTCG
130 GTGAATTAGCACATTGGCATTCTTCG
* * *
263955 CATCTTTAAGCTCAATATCGCTAGCCTTGAATCAGTATATTGGCATCTTTAACATTCTTAAGCCC
1 CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCC
* * * * *
264020 GATGTCGCTGATCTTGAATAAGCACATTGGTGCTCTTCTCACCTTCAAGTCTAATGTCGTTGGCT
66 AATGTCGCTGATCTTGAATCAGCACATTGGCGCTCTTCTCATCTTCAAGTCTAATGTCGCTGGC-
* *
264085 GTGAATTAGCATATTGGAATTCTTCG
130 GTGAATTAGCACATTGGCATTCTTCG
* * * * *
264111 CATCTTTAAGCCCAATATCCCTAGCCTTGAATTAGCATATCGGCATCTTTAACTTTCCTAAGCTC
1 CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCC
* *
264176 AATGTCGCTGATCTTGAATCAACACATTGGCACTCTTCTCATCTTCAAGTCTAATGTCGCTGGCC
66 AATGTCGCTGATCTTGAATCAGCACATTGGCGCTCTTCTCATCTTCAAGTCTAATGTCGCTGG-C
* ** *
264241 GTAAATTAGCACATTAACAGTCTTCG
130 GTGAATTAGCACATTGGCATTCTTCG
* * * ** * *
264267 CATTTTTAAGCCCAATATTGCTGGCCTTGAATCAATATATTGGCACCTTTATCATTC
1 CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAACATTC
264324 TTCTCATCTT
Statistics
Matches: 315, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
155 1 0.00
156 313 0.99
157 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (155 bp):
CATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCC
AATGTCGCTGATCTTGAATCAGCACATTGGCGCTCTTCTCATCTTCAAGTCTAATGTCGCTGGCG
TGAATTAGCACATTGGCATTCTTCG
Found at i:264028 original size:52 final size:52
Alignment explanation
Indices: 263595--264325 Score: 317
Period size: 52 Copynumber: 14.0 Consensus size: 52
263585 CAAACCATCT
* * * * * *
263595 TTAAGCCCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTTTCTTTC
1 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * *
263647 TTAAGTCTAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTTGTTA-TC
1 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * * * *
263698 TTTAAGTCTAATGTCACTGGTCCTTGAATCAGCAAATTGGCACCTTTTTCTTTC
1 -TTAAGTCCAATATCGCTAG-CCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * *
263752 TTAAGTCCAATATCGCTAGCCTTGAATTAGTATATTAGCACCTTTCTCATCC
1 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * **
263804 TTAAGTCCAATATCGCTATCCTTGAATCAGCATATTGCCATCTTTAACATTC
1 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * * * ***
263856 CTAAGCCCAATGTCGCT-GATCATGAATCAGCACATTGGCGTTTTTCTCA-TC
1 TTAAGTCCAATATCGCTAG-CCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * * * * *
263907 TTCAAGTCTAATATTGCTGGTCGTGAATCAGCACATTGGCA-TTCTTCGCA-TC
1 TT-AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCT-TTCTCATTC
* * **
263959 TTTAAG-CTCAATATCGCTAGCCTTGAATCAGTATATTGGCATCTTTAACATTC
1 -TTAAGTC-CAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * * * ** *
264012 TTAAGCCCGATGTCGCT-GATCTTGAATAAGCACATTGG-TGCTCTTCTCA-CC
1 TTAAGTCCAATATCGCTAG-CCTTGAATCAGCATATTGGCACCT-TTCTCATTC
* * * * * ** *
264063 TTCAAGTCTAATGTCG-TTGGCTGTGAATTAGCATATTGG-AATTCTTCGCA-TC
1 TT-AAGTCCAATATCGCTAGCCT-TGAATCAGCATATTGGCACCT-TTCTCATTC
* * * * * ** *
264115 TTTAAGCCCAATATCCCTAGCCTTGAATTAGCATATCGGCATCTTTAACTTTC
1 -TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
* * * * *
264168 CTAAG-CTCAATGTCGCT-GATCTTGAATCAACACATTGGCA-CTCTTCTCA-TC
1 TTAAGTC-CAATATCGCTAG-CCTTGAATCAGCATATTGGCACCT-TTCTCATTC
* * * * * * * ** * * *
264219 TTCAAGTCTAATGTCGCTGGCCGTAAATTAGCACATTAACA-GTCTTCGCATTT
1 TT-AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCT-TTCTCATTC
* * * ** *
264272 TTAAGCCCAATATTGCTGGCCTTGAATCAATATATTGGCACCTTTATCATTC
1 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
264324 TT
1 TT
264326 CTCATCTTTA
Statistics
Matches: 510, Mismatches: 140, Indels: 58
0.72 0.20 0.08
Matches are distributed among these distances:
51 24 0.05
52 421 0.83
53 63 0.12
54 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (52 bp):
TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATTC
Found at i:264359 original size:61 final size:61
Alignment explanation
Indices: 264261--264393 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 61
264251 ACATTAACAG
* * * * * *
264261 TCTTCGCATTTTTAAGCCCAATATTGCTGGCCTTGAATCAATATATTGGCACCTTTATCAT
1 TCTTCTCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTGTATCAT
* * * * *
264322 TCTTCTCATCTTTAAGCTCAATATCGCTGGTCGTGAATTAGCATATTGGTACCTGTATCAT
1 TCTTCTCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTGTATCAT
*
264383 TCCTCTCATCT
1 TCTTCTCATCT
264394 CTAACGTCAC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (61 bp):
TCTTCTCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTGTATCAT
Found at i:265277 original size:20 final size:20
Alignment explanation
Indices: 265252--265289 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
265242 TTTTGACCCA
265252 AATGTATCGATACATTCTTT
1 AATGTATCGATACATTCTTT
265272 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
265290 ATATGCAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTCTTT
Found at i:281834 original size:32 final size:32
Alignment explanation
Indices: 281798--281904 Score: 94
Period size: 32 Copynumber: 3.3 Consensus size: 32
281788 AGGCATTTAA
*
281798 ACTCACGTGCAATCACACTCATCTATATTCAT
1 ACTCACATGCAATCACACTCATCTATATTCAT
* ** * *
281830 ACTCACATGCATTGTCATTCAT-TAGCATTTGCAT
1 ACTCACATGCAATCACACTCATCTA-TA-TT-CAT
**
281864 --TCATGTGCAATCACACTCATCTATATTCAT
1 ACTCACATGCAATCACACTCATCTATATTCAT
281894 ACTCACATGCA
1 ACTCACATGCA
281905 TTCTCATTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
30 3 0.06
31 4 0.07
32 40 0.74
33 4 0.07
34 3 0.06
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (32 bp):
ACTCACATGCAATCACACTCATCTATATTCAT
Found at i:281891 original size:64 final size:64
Alignment explanation
Indices: 281800--282000 Score: 257
Period size: 64 Copynumber: 3.1 Consensus size: 64
281790 GCATTTAAAC
*
281800 TCACGTGCAATCACACTCATCTATATTCATACTCACATGCATTGTCATTCATTAGCATTTGCAT
1 TCACGTGCAATCACACTCATCTATATTCATACTCACATGCATTCTCATTCATTAGCATTTGCAT
*
281864 TCATGTGCAATCACACTCATCTATATTCATACTCACATGCATTCTCATTCATTAGCATTTGCAT
1 TCACGTGCAATCACACTCATCTATATTCATACTCACATGCATTCTCATTCATTAGCATTTGCAT
* * * * ** *
281928 TCACGTGC-ATC-CTTATTCA-C-ATGCCTTCACACTTATGTGCATTCTCATTCATGAGCATTTG
1 TCACGTGCAATCAC--ACTCATCTAT--ATTCATACTCACATGCATTCTCATTCATTAGCATTTG
281989 CAT
62 CAT
281992 TCACGTGCA
1 TCACGTGCA
282001 TCTTCATTCA
Statistics
Matches: 122, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 115 0.94
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.36
Consensus pattern (64 bp):
TCACGTGCAATCACACTCATCTATATTCATACTCACATGCATTCTCATTCATTAGCATTTGCAT
Found at i:281937 original size:32 final size:32
Alignment explanation
Indices: 281832--282010 Score: 118
Period size: 32 Copynumber: 5.6 Consensus size: 32
281822 ATATTCATAC
* *
281832 TCACATGCATTGTCATTCATTAGCATTTGCAT
1 TCACGTGCATTCTCATTCATTAGCATTTGCAT
* * * * *
281864 TCATGTGCAATCACACTCATCTA-TA-TT-CAT
1 TCACGTGCATTCTCATTCAT-TAGCATTTGCAT
*
281894 ACTCACATGCATTCTCATTCATTAGCATTTGCAT
1 --TCACGTGCATTCTCATTCATTAGCATTTGCAT
* * * * **
281928 TCACGTGCATCCTTATTCA-CATGCCTTCACACT
1 TCACGTGCATTCTCATTCATTA-GCATTTGCA-T
* *
281961 T-ATGTGCATTCTCATTCATGAGCATTTGCAT
1 TCACGTGCATTCTCATTCATTAGCATTTGCAT
281992 TCACGTGCA-TCTTCATTCA
1 TCACGTGCATTC-TCATTCA
282011 CATGCCTTCA
Statistics
Matches: 108, Mismatches: 28, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
30 3 0.03
31 9 0.08
32 86 0.80
33 7 0.06
34 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (32 bp):
TCACGTGCATTCTCATTCATTAGCATTTGCAT
Found at i:282001 original size:16 final size:15
Alignment explanation
Indices: 281964--282011 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
281954 TCACACTTAT
*
281964 GTGCATTCTCATTCAT
1 GTGCATT-TCATTCAC
*
281980 GAGCATTTGCATTCAC
1 GTGCATTT-CATTCAC
281996 GTGCATCTTCATTCAC
1 GTGCAT-TTCATTCAC
282012 ATGCCTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.89
17 2 0.07
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (15 bp):
GTGCATTTCATTCAC
Found at i:282002 original size:64 final size:64
Alignment explanation
Indices: 281901--282035 Score: 227
Period size: 64 Copynumber: 2.1 Consensus size: 64
281891 CATACTCACA
* *
281901 TGCATTCTCATTCATTAGCATTTGCATTCACGTGCATCCTT-ATTCACATGCCTTCACACTTATG
1 TGCATTCTCATTCATGAGCATTTGCATTCACGTGCAT-CTTCATTCACATGCCTTCACACTCATG
281965 TGCATTCTCATTCATGAGCATTTGCATTCACGTGCATCTTCATTCACATGCCTTCACACTCATG
1 TGCATTCTCATTCATGAGCATTTGCATTCACGTGCATCTTCATTCACATGCCTTCACACTCATG
*
282029 TGTATTC
1 TGCATTC
282036 CTCTTTATGT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 3 0.04
64 64 0.96
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.39
Consensus pattern (64 bp):
TGCATTCTCATTCATGAGCATTTGCATTCACGTGCATCTTCATTCACATGCCTTCACACTCATG
Found at i:282143 original size:32 final size:32
Alignment explanation
Indices: 282095--282178 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
282085 CACTCATCTT
282095 ATTTGCACTCATGTGCATTCTTATTCACAAGC
1 ATTTGCACTCATGTGCATTCTTATTCACAAGC
* * *
282127 ATTTGCATTCACGTGCATTCTTATTCACATGC
1 ATTTGCACTCATGTGCATTCTTATTCACAAGC
* *
282159 CTTTACACTCATGTGCATTC
1 ATTTGCACTCATGTGCATTC
282179 GCATTCATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (32 bp):
ATTTGCACTCATGTGCATTCTTATTCACAAGC
Found at i:283416 original size:52 final size:52
Alignment explanation
Indices: 283360--283608 Score: 159
Period size: 52 Copynumber: 4.8 Consensus size: 52
283350 TTGATGCCTG
* * *
283360 TATAGGGAAGTCAAGCCCTATAGAACCCAAAGTCTATATTAGTCGGTAGTTA
1 TATAGGGAAGTCAAGCCTTATAGAACCCAAAGTCTATATTAGTCGGCAATTA
* * * * * * *
283412 TATAGAGAAGTCAAGCTTTATGGAACCCTATGTCTATATTAGTTGGCACTTA
1 TATAGGGAAGTCAAGCCTTATAGAACCCAAAGTCTATATTAGTCGGCAATTA
* * * * * *
283464 TTTA-GGAAGCTTAAGCCTTATAGAATCC-AAGTCTACATTA-ACTGGCATTTA
1 TATAGGGAAG-TCAAGCCTTATAGAACCCAAAGTCTATATTAGTC-GGCAATTA
** * * * * ** *
283515 TATACAG-AGCTCAAGCCTTCTAGAACCCAAAGCCCATTTTAG-C-TAACATCTG
1 TATAGGGAAG-TCAAGCCTTATAGAACCCAAAGTCTATATTAGTCGGCA-AT-TA
* * *
283567 TATAGGGAGGTCAAGCCCTATAGAACCCAAAGTCCATATTAG
1 TATAGGGAAGTCAAGCCTTATAGAACCCAAAGTCTATATTAG
283609 CTAGCATCTG
Statistics
Matches: 149, Mismatches: 40, Indels: 16
0.73 0.20 0.08
Matches are distributed among these distances:
50 1 0.01
51 43 0.29
52 104 0.70
53 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (52 bp):
TATAGGGAAGTCAAGCCTTATAGAACCCAAAGTCTATATTAGTCGGCAATTA
Found at i:283609 original size:52 final size:52
Alignment explanation
Indices: 283525--283639 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
283515 TATACAGAGC
* * * * *
283525 TCAAGCCTTCTAGAACCCAAAGCCCATTTTAGCTAACATCTGTATAGGGAGG
1 TCAAGCCCTATAGAACCCAAAGCCCATATTAGCTAACATCTGTATAAGAAGG
* *
283577 TCAAGCCCTATAGAACCCAAAGTCCATATTAGCTAGCATCTGTATAAGAAGG
1 TCAAGCCCTATAGAACCCAAAGCCCATATTAGCTAACATCTGTATAAGAAGG
*
283629 TTAAGCCCTAT
1 TCAAGCCCTAT
283640 GAATCTAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (52 bp):
TCAAGCCCTATAGAACCCAAAGCCCATATTAGCTAACATCTGTATAAGAAGG
Found at i:284375 original size:110 final size:111
Alignment explanation
Indices: 284182--284397 Score: 267
Period size: 110 Copynumber: 2.0 Consensus size: 111
284172 TAAGGTAATC
* * ** *
284182 ATAAATTATTTAATTTAAGGCCAAGTCTAATACAAAATATTTATTAGATAAAATAAGTCCAACTT
1 ATAAATTATTTAATTTAAGGCCAAGCCTAATACAAAAAATACATTAGATAAAATAAGTCCAACAT
*
284247 GCTTATTCAACTAATTTATTTGGACCT-ATTTTATTTAATTTAGTT
66 GCATATTCAACTAATTTATTTGGACCTAATTTTATTTAATTTAGTT
* * **
284292 ATAAATTATTTAATTTGAGGCCAAGCCTTATA-AAATAAATACATTAGATAAAATAAAG-CCCTC
1 ATAAATTATTTAATTTAAGGCCAAGCCTAATACAAA-AAATACATTAGATAAAAT-AAGTCCAAC
* * **
284355 ATGCATATTTAATTAATTTATTTGGGGCTAATTTTATTTAATT
64 ATGCATATTCAACTAATTTATTTGGACCTAATTTTATTTAATT
284398 ATGATTGGGC
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
109 3 0.03
110 70 0.79
111 16 0.18
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (111 bp):
ATAAATTATTTAATTTAAGGCCAAGCCTAATACAAAAAATACATTAGATAAAATAAGTCCAACAT
GCATATTCAACTAATTTATTTGGACCTAATTTTATTTAATTTAGTT
Found at i:284399 original size:24 final size:25
Alignment explanation
Indices: 284362--284414 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
284352 CTCATGCATA
284362 TTTAATTAATTTAT-TTGGGGCTAAT
1 TTTAATTAATTTATATT-GGGCTAAT
*
284387 TTTATTTAA-TTATGATTGGGCTAAT
1 TTTAATTAATTTAT-ATTGGGCTAAT
284412 TTT
1 TTT
284415 TCAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 4 0.16
25 19 0.76
26 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (25 bp):
TTTAATTAATTTATATTGGGCTAAT
Found at i:287014 original size:179 final size:179
Alignment explanation
Indices: 286676--287196 Score: 733
Period size: 179 Copynumber: 2.9 Consensus size: 179
286666 CGACCATATT
* * * ** * * *
286676 TTTTTAAAATATTAATTTTAAGGAAATTAAATTTTCCTAAATTTTTTAATTTAACTTCTAAATTT
1 TTTTAAAAATATTGA-TTTAAGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCT-AATTT
* * * *
286741 CGAAAATTATGTTTCGTACCTGACGAAAAATCAGAGAATATGAAATGTATTAAAAAATTTTCATA
64 CGAAAATTATGTTTCGTACCTGACGAAAAATCAGAGGATACGAAAGGTGTTAAAAAATTTTCATA
286806 CCCTTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCT-
129 CCCTTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCTC
*
286856 TTATTAAAAATATTGATTTAAGAAAACCGAATTTTTCTAAATTCTTAAATTTAACTTCTAATTTC
1 TT-TTAAAAATATTGATTTAAGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTTC
* * * *
286921 GAAAATTATGTTTCATACCTGATGAAAAA-CTAGGGGATACGAAGGGTGTTAAAAAATTTTCATA
65 GAAAATTATGTTTCGTACCTGACGAAAAATC-AGAGGATACGAAAGGTGTTAAAAAATTTTCATA
* * *
286985 CCCTTACAGAAAACGATAGGGACATGAAAACATAAACGACCTCATATTCTC
129 CCCTTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCTC
* *
287036 TTTTTAAAATATTGATTTAGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTTCG
1 TTTTAAAAATATTGATTTAAGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTTCG
* * *
287101 AAAATTATGTTTCGTACCCGACGGAAAAATCAGAGGATACAAAAGGTGTT-AAAAATTTTCATTC
66 AAAATTATGTTTCGTACCTGAC-GAAAAATCAGAGGATACGAAAGGTGTTAAAAAATTTTCATAC
* *
287165 CCCTACGGAAAACCATAGGAATATGAAAACAT
130 CCTTACGGAAAACCATAGGGATATGAAAACAT
287197 GACTCGAGTG
Statistics
Matches: 301, Mismatches: 35, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
178 1 0.00
179 226 0.75
180 62 0.21
181 12 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (179 bp):
TTTTAAAAATATTGATTTAAGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTTCG
AAAATTATGTTTCGTACCTGACGAAAAATCAGAGGATACGAAAGGTGTTAAAAAATTTTCATACC
CTTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCTC
Found at i:288103 original size:61 final size:62
Alignment explanation
Indices: 288038--288180 Score: 209
Period size: 61 Copynumber: 2.3 Consensus size: 62
288028 GTTTTCTTTG
*
288038 TTTTCTTCTTGTTTCGATTCTTG-TTTTTCTTGCTTTCTCTCTTTTTTTGCTGTTTCATCTT
1 TTTTCTGCTTGTTTCGATTCTTGATTTTTCTTGCTTTCTCTCTTTTTTTGCTGTTTCATCTT
* **
288099 TTTTCTGCTTGTTTCGATTC-TGATTTTTCTTGCTTTCTCTCTTTTTTTGTTGTTTTGTCTT
1 TTTTCTGCTTGTTTCGATTCTTGATTTTTCTTGCTTTCTCTCTTTTTTTGCTGTTTCATCTT
* * *
288160 TGTTCTGCTAGTTTCGGTTCT
1 TTTTCTGCTTGTTTCGATTCT
288181 GTTCTCTCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 2 0.03
61 71 0.97
ACGTcount: A:0.03, C:0.18, G:0.13, T:0.65
Consensus pattern (62 bp):
TTTTCTGCTTGTTTCGATTCTTGATTTTTCTTGCTTTCTCTCTTTTTTTGCTGTTTCATCTT
Found at i:288181 original size:61 final size:60
Alignment explanation
Indices: 288023--288183 Score: 200
Period size: 61 Copynumber: 2.6 Consensus size: 60
288013 TTTGTTTCGG
* *
288023 TTGCTGTTT--TCTTTGTTTTCTTCTTGTTTCGATTCTTGTTTTTCTTGCTTTCTCTCTTTTT
1 TTGCTGTTTCATCTTTG--TTCTGCTAGTTTCGATTC-TGTTTTTCTTGCTTTCTCTCTTTTT
* *
288084 TTGCTGTTTCATCTTTTTTCTGCTTGTTTCGATTCTGATTTTTCTTGCTTTCTCTCTTTTT
1 TTGCTGTTTCATCTTTGTTCTGCTAGTTTCGATTCTG-TTTTTCTTGCTTTCTCTCTTTTT
* ** *
288145 TTGTTGTTTTGTCTTTGTTCTGCTAGTTTCGGTTCTGTT
1 TTGCTGTTTCATCTTTGTTCTGCTAGTTTCGATTCTGTT
288184 CTCTCCTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
60 4 0.04
61 80 0.90
63 5 0.06
ACGTcount: A:0.03, C:0.17, G:0.14, T:0.65
Consensus pattern (60 bp):
TTGCTGTTTCATCTTTGTTCTGCTAGTTTCGATTCTGTTTTTCTTGCTTTCTCTCTTTTT
Found at i:288723 original size:14 final size:14
Alignment explanation
Indices: 288704--288825 Score: 69
Period size: 14 Copynumber: 8.9 Consensus size: 14
288694 GGCGTGAAAC
288704 ATGCATGAAATGTA
1 ATGCATGAAATGTA
*
288718 ATGCATGCAA--T-
1 ATGCATGAAATGTA
*
288729 A--CATGAAATGAA
1 ATGCATGAAATGTA
*
288741 ATGCATGAAATGAA
1 ATGCATGAAATGTA
* * * *
288755 CATTACGTAAAATG-C
1 -A-TGCATGAAATGTA
288770 ATGCATGAAATGTA
1 ATGCATGAAATGTA
*
288784 ATGCATGAAATGAAA
1 ATGCATGAAATG-TA
* *
288799 ATTACATGAAATG-C
1 A-TGCATGAAATGTA
288813 ATGCATGAAATGT
1 ATGCATGAAATGT
288826 TAAATAAACG
Statistics
Matches: 82, Mismatches: 15, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
9 6 0.07
11 1 0.01
12 2 0.02
13 18 0.22
14 34 0.41
15 3 0.04
16 18 0.22
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:288767 original size:25 final size:23
Alignment explanation
Indices: 288739--288823 Score: 65
Period size: 25 Copynumber: 3.8 Consensus size: 23
288729 ACATGAAATG
288739 AAATGCATGAAATGAACATTACGT
1 AAATGCATGAAATGAA-ATTACGT
*
288763 AAAATGCATG-CATGAAA-T--GT
1 -AAATGCATGAAATGAAATTACGT
*
288783 -AATGCATGAAATGAAAATTACAT
1 AAATGCATGAAATG-AAATTACGT
*
288806 GAAATGCATG-CATGAAAT
1 -AAATGCATGAAATGAAAT
288824 GTTAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
18 8 0.16
19 3 0.06
20 5 0.10
21 1 0.02
22 1 0.02
23 6 0.12
24 8 0.16
25 17 0.35
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (23 bp):
AAATGCATGAAATGAAATTACGT
Found at i:288825 original size:43 final size:43
Alignment explanation
Indices: 288730--288825 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
288720 GCATGCAATA
* * *
288730 CATGAAATGAAATGCATGAAATGAACATTACGTAAAATGCATG
1 CATGAAATGTAATGCATGAAATGAAAATTACATAAAATGCATG
*
288773 CATGAAATGTAATGCATGAAATGAAAATTACATGAAATGCATG
1 CATGAAATGTAATGCATGAAATGAAAATTACATAAAATGCATG
288816 CATGAAATGT
1 CATGAAATGT
288826 TAAATAAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (43 bp):
CATGAAATGTAATGCATGAAATGAAAATTACATAAAATGCATG
Found at i:288857 original size:4 final size:4
Alignment explanation
Indices: 288848--288914 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
288838 AAATTTGAGT
* * *
288848 TTTA TTTA TTAA TTT- TTTA TTTC TTTA -TT- TTTA TATA TATT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
*
288893 TTTA TTTA TTTTA TTTT TTTA T
1 TTTA TTTA -TTTA TTTA TTTA T
288915 AAATGTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
3 9 0.18
4 35 0.71
5 5 0.10
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:288896 original size:16 final size:13
Alignment explanation
Indices: 288847--288914 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
288837 GAAATTTGAG
*
288847 TTTTATTTATTAATT
1 TTTTATTTATT--TA
*
288862 TTTTATTTCTTTA
1 TTTTATTTATTTA
* *
288875 TTTT-TATATATA
1 TTTTATTTATTTA
288887 TTTTTATTTATTTA
1 -TTTTATTTATTTA
*
288901 TTTTATTTTTTTA
1 TTTTATTTATTTA
288914 T
1 T
288915 AAATGTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 5 0.12
13 22 0.51
14 6 0.14
15 10 0.23
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:292186 original size:28 final size:28
Alignment explanation
Indices: 292145--292365 Score: 302
Period size: 28 Copynumber: 7.8 Consensus size: 28
292135 TTCATGAAAA
292145 CCCACAAGTCAGTGGCACCTTTTCAAAG
1 CCCACAAGTCAGTGGCACCTTTTCAAAG
* *
292173 CCCACATGTTAGTGGCATCC-TTTCAAAG
1 CCCACAAGTCAGTGGCA-CCTTTTCAAAG
*
292201 CCCATAAGTCAGTGGCACCTTTTCAAAG
1 CCCACAAGTCAGTGGCACCTTTTCAAAG
* *
292229 CCCACAAGTTAATGGCACCTTTTCAAAG
1 CCCACAAGTCAGTGGCACCTTTTCAAAG
*
292257 CCCACAAGTCAATGGCACCTTTTCAAAG
1 CCCACAAGTCAGTGGCACCTTTTCAAAG
* *
292285 CCCACAAGTTAGTGGCATCTTTTCAAAG
1 CCCACAAGTCAGTGGCACCTTTTCAAAG
292313 CCCACAAGTCAGTGGCATCCTTTT-AAAG
1 CCCACAAGTCAGTGGCA-CCTTTTCAAAG
* *
292341 CCCACACAAGTCGGTGGCAACTTTT
1 -CC-CACAAGTCAGTGGCACCTTTT
292366 TTTTAAAGCC
Statistics
Matches: 172, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
27 2 0.01
28 142 0.83
29 14 0.08
30 14 0.08
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCACCTTTTCAAAG
Found at i:293459 original size:32 final size:32
Alignment explanation
Indices: 293395--293473 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
293385 TGAACAATAC
293395 ATGTATCGATACA--TTCTATTTTTTACCCAG
1 ATGTATCGATACATTTTCTATTTTTTACCCAG
* * *
293425 ATGTATCGATACATTTTGTTTTTTTTACCTAG
1 ATGTATCGATACATTTTCTATTTTTTACCCAG
293457 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
293474 TTCAATGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 13 0.30
32 31 0.70
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (32 bp):
ATGTATCGATACATTTTCTATTTTTTACCCAG
Found at i:303395 original size:12 final size:12
Alignment explanation
Indices: 303378--303416 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
303368 GTCGAGAATG
*
303378 TTTGTCAAAAAC
1 TTTGTCAAGAAC
*
303390 TTTGTCAAGAAT
1 TTTGTCAAGAAC
*
303402 TTTGTGAAGAAC
1 TTTGTCAAGAAC
303414 TTT
1 TTT
303417 CCCATTTCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTGTCAAGAAC
Found at i:303414 original size:24 final size:25
Alignment explanation
Indices: 303365--303416 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
303355 GTTAAGCACT
*
303365 TTTGTCGAGAATGTTTGTCAAAAAC
1 TTTGTCAAGAATGTTTGTCAAAAAC
* *
303390 TTTGTCAAGAAT-TTTGTGAAGAAC
1 TTTGTCAAGAATGTTTGTCAAAAAC
303414 TTT
1 TTT
303417 CCCATTTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (25 bp):
TTTGTCAAGAATGTTTGTCAAAAAC
Found at i:309368 original size:446 final size:446
Alignment explanation
Indices: 308533--309424 Score: 1739
Period size: 446 Copynumber: 2.0 Consensus size: 446
308523 TTCTAAAGCC
308533 TATCGAGTGTTTAACAAAAGAACCTTAGTGGTTGAAGAATCAATCCATGTTATTTTTGATGATTC
1 TATCGAGTGTTTAACAAAAGAACCTTAGTGGTTGAAGAATCAATCCATGTTATTTTTGATGATTC
308598 TAACACTTCCGAAAGGAAAGTATCTTTTGTTGACAATGATGTAGAGATTTTTGAAGAAAATCTAG
66 TAACACTTCCGAAAGGAAAGTATCTTTTGTTGACAATGATGTAGAGATTTTTGAAGAAAATCTAG
308663 AACAAGCATCACACAAGGAGCAAGACAAAAGTGTCCAAATTGAGGAAGCTCAAAATGAAGAAGCT
131 AACAAGCATCACACAAGGAGCAAGACAAAAGTGTCCAAATTGAGGAAGCTCAAAATGAAGAAGCT
308728 CCAAACGAATTTGATGAACGAGAGTCAACCCAAACCAAAAAGAAATATTCAAGAGAGTTGACATA
196 CCAAACGAATTTGATGAACGAGAGTCAACCCAAACCAAAAAGAAATATTCAAGAGAGTTGACATA
*
308793 TGTACAAGAAGGTGAGATCATCGGTAATCTAAGCCATGAGGTAAGAACTAGATCTTCCCTTAGAA
261 TGTACAAGAAGGTGAGATCATCGGTAATCCAAGCCATGAGGTAAGAACTAGATCTTCCCTTAGAA
*
308858 ATACTTGCGATTATGTAGCCTTTCTCTCTCAAATAGAACCTAAAAGCATAGACGAAGCAATATTA
326 ATACTTGCGATTATGTAGCCTTTCTCTCTCAAATAAAACCTAAAAGCATAGACGAAGCAATATTA
308923 GATGAAAATTGGATTTTGGCTATGCAAGAGGAATTAAATCAATTTGAGAGAAGCAA
391 GATGAAAATTGGATTTTGGCTATGCAAGAGGAATTAAATCAATTTGAGAGAAGCAA
308979 TATCGAGTGTTTAACAAAAGAACCTTAGTGGTTGAAGAATCAATCCATGTTATTTTTGATGATTC
1 TATCGAGTGTTTAACAAAAGAACCTTAGTGGTTGAAGAATCAATCCATGTTATTTTTGATGATTC
309044 TAACACTTCCGAAAGGAAAGTATCTTTTGTTGACAATGATGTAGAGATTTTTGAAGAAAATCTAG
66 TAACACTTCCGAAAGGAAAGTATCTTTTGTTGACAATGATGTAGAGATTTTTGAAGAAAATCTAG
309109 AACAAGCATCACACAAGGAGCAAGACAAAAGTGTCCAAATTGAGGAAGCTCAAAATGAAGAAGCT
131 AACAAGCATCACACAAGGAGCAAGACAAAAGTGTCCAAATTGAGGAAGCTCAAAATGAAGAAGCT
*
309174 CCAAACGAATTTGATGAACGAGAGTCAACCCAAACCGAAAAGAAATATTCAAGAGAGTTGACATA
196 CCAAACGAATTTGATGAACGAGAGTCAACCCAAACCAAAAAGAAATATTCAAGAGAGTTGACATA
*
309239 TGTATAAGAAGGTGAGATCATCGGTAATCCAAGCCATGAGGTAAGAACTAGATCTTCCCTTAGAA
261 TGTACAAGAAGGTGAGATCATCGGTAATCCAAGCCATGAGGTAAGAACTAGATCTTCCCTTAGAA
*
309304 ATACTTGCGATTATGTAGCCTTTCTCTCTCAAATAAAACCTAAAAGCATAGACGAAGTAATATTA
326 ATACTTGCGATTATGTAGCCTTTCTCTCTCAAATAAAACCTAAAAGCATAGACGAAGCAATATTA
309369 GATGAAAATTGGATTTTGGCTATGCAAGAGGAATTAAATCAATTTGAGAGAAGCAA
391 GATGAAAATTGGATTTTGGCTATGCAAGAGGAATTAAATCAATTTGAGAGAAGCAA
309425 AGTTTGGTCT
Statistics
Matches: 441, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
446 441 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (446 bp):
TATCGAGTGTTTAACAAAAGAACCTTAGTGGTTGAAGAATCAATCCATGTTATTTTTGATGATTC
TAACACTTCCGAAAGGAAAGTATCTTTTGTTGACAATGATGTAGAGATTTTTGAAGAAAATCTAG
AACAAGCATCACACAAGGAGCAAGACAAAAGTGTCCAAATTGAGGAAGCTCAAAATGAAGAAGCT
CCAAACGAATTTGATGAACGAGAGTCAACCCAAACCAAAAAGAAATATTCAAGAGAGTTGACATA
TGTACAAGAAGGTGAGATCATCGGTAATCCAAGCCATGAGGTAAGAACTAGATCTTCCCTTAGAA
ATACTTGCGATTATGTAGCCTTTCTCTCTCAAATAAAACCTAAAAGCATAGACGAAGCAATATTA
GATGAAAATTGGATTTTGGCTATGCAAGAGGAATTAAATCAATTTGAGAGAAGCAA
Found at i:311265 original size:13 final size:13
Alignment explanation
Indices: 311247--311285 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
311237 ACATTTTTCT
311247 TTGTATCGATACA
1 TTGTATCGATACA
311260 TTGTATCGATACA
1 TTGTATCGATACA
*
311273 CTGTATCGATACA
1 TTGTATCGATACA
311286 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:311449 original size:20 final size:20
Alignment explanation
Indices: 311406--311451 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
311396 AAATCTTTTG
311406 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
311427 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
311447 CAAAA
1 CAAAA
311452 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:313159 original size:12 final size:12
Alignment explanation
Indices: 313142--313166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
313132 GGGAGAATGC
313142 ATAAATTTGCTA
1 ATAAATTTGCTA
313154 ATAAATTTGCTA
1 ATAAATTTGCTA
313166 A
1 A
313167 AATTACCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATAAATTTGCTA
Found at i:313757 original size:18 final size:19
Alignment explanation
Indices: 313736--313776 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
313726 AATTGTCAAA
313736 ACAC-TTAAAAGTATCGAT
1 ACACATTAAAAGTATCGAT
*
313754 ACACAATTCAAAGTATCGAT
1 ACAC-ATTAAAAGTATCGAT
313774 ACA
1 ACA
313777 TGTTGCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (19 bp):
ACACATTAAAAGTATCGAT
Found at i:313887 original size:13 final size:13
Alignment explanation
Indices: 313869--313894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
313859 ACACCAAAGT
313869 ATGTATCGATACA
1 ATGTATCGATACA
313882 ATGTATCGATACA
1 ATGTATCGATACA
313895 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:313892 original size:33 final size:33
Alignment explanation
Indices: 313850--313914 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
313840 TAGCCAAACT
* *
313850 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
313883 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
313915 CAAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:313908 original size:20 final size:20
Alignment explanation
Indices: 313883--313934 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
313873 ATCGATACAA
313883 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
313903 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
*
313923 TGTATTGATACA
1 TGTATCGATACA
313935 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACAAAAAAT
Found at i:315876 original size:16 final size:18
Alignment explanation
Indices: 315855--315888 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
315845 AGCCATTACA
315855 CCTTTTC-TAAAA-TTTT
1 CCTTTTCTTAAAACTTTT
315871 CCTTTTCTTAAAACTTTT
1 CCTTTTCTTAAAACTTTT
315889 AGTCCAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTTTCTTAAAACTTTT
Found at i:319734 original size:32 final size:32
Alignment explanation
Indices: 319679--319779 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
319669 TTCATCGATT
* *
319679 TGTATCGATACATAAAGTGTTGTATCAATACAG
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
319712 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
319744 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
319776 TGTA
1 TGTA
319780 AGCTACTACC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:319736 original size:19 final size:19
Alignment explanation
Indices: 319678--319774 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
319668 TTTCATCGAT
319678 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
*
319698 TTGTATCAATAC---A--G
1 TTGTATCGATACATAAGTG
319712 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
319730 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
319744 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
319762 TTGTATCGATACA
1 TTGTATCGATACA
319775 ATGTAAGCTA
Statistics
Matches: 63, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 1 0.02
15 2 0.03
16 2 0.03
17 2 0.03
18 1 0.02
19 23 0.37
20 11 0.17
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Done.