Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008917.1 Hibiscus syriacus cultivar Beakdansim tig00112221_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 766343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:489820 original size:42 final size:40
Alignment explanation
Indices: 489753--489860 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 40
489743 TTCTTGGTGA
* * *
489753 GTAAGTCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATG
1 GTAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGATG
489794 CGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATG
1 -GTAAGTCCTTCGGGCCATC-ATAAGTCTTTCGAGCAAGATG
* *
489836 ATAAGTCCTTCGGACCATCCATAAG
1 GTAAGTCCTTCGGGCCAT-CATAAG
489861 ACATTTGGGC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 21 0.36
42 37 0.63
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (40 bp):
GTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCAAGATG
Found at i:489821 original size:20 final size:20
Alignment explanation
Indices: 489796--489860 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
489786 GCATGATGCG
489796 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGGGCCATCTA
* * * **
489816 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGGGCCATCT-A
* *
489837 TAAGTCCTTCGGACCATCCA
1 TAAGTCCTTCGGGCCATCTA
489857 TAAG
1 TAAG
489861 ACATTTGGGC
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCTA
Found at i:489854 original size:41 final size:42
Alignment explanation
Indices: 489774--489860 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
489764 GGGTCATCAG
* * * *
489774 TAAGTCTTTCGAGCATGATGCGTAAGTCCTTCGGGCCATCTA
1 TAAGTCTTTCGAGCAAGATGCATAAGTCCTTCGGACCATCCA
489816 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGGACCATCCA
1 TAAGTCTTTCGAGCAAGATGCATAAGTCCTTCGGACCATCCA
489857 TAAG
1 TAAG
489861 ACATTTGGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 22 0.54
42 19 0.46
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGCATAAGTCCTTCGGACCATCCA
Found at i:490051 original size:42 final size:42
Alignment explanation
Indices: 490005--490118 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 42
489995 AAGGGTTTCT
*
490005 TGATGAGTAAGTCTTTTGGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCTTTCGGGCCATCTA-TAAGTCTTTCGAGCA
* *
490047 TGATGCGTAAGT-TCTCCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCT-TTCGGGCCATCTATAAGTCTTTCGAGCA
* * *
490089 AGATGA-TAAGTCCTTCGGGCCATCCATAAG
1 TGATGAGTAAGTCTTTCGGGCCATCTATAAG
490119 ACCCTCGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 21 0.34
42 39 0.64
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (42 bp):
TGATGAGTAAGTCTTTCGGGCCATCTATAAGTCTTTCGAGCA
Found at i:490344 original size:36 final size:34
Alignment explanation
Indices: 490304--490372 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
490294 GTTTCTTTTA
*
490304 AAACGAATTTTGTTTCTCTTGAGACAGTTTCCCTTG
1 AAACGAATTTTG--TCGCTTGAGACAGTTTCCCTTG
* *
490340 AAACGAGTTTTGTCGCTTGAGACAGTTTTCCTT
1 AAACGAATTTTGTCGCTTGAGACAGTTTCCCTT
490373 CTAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 19 0.63
36 11 0.37
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (34 bp):
AAACGAATTTTGTCGCTTGAGACAGTTTCCCTTG
Found at i:490961 original size:132 final size:132
Alignment explanation
Indices: 490723--491237 Score: 657
Period size: 132 Copynumber: 3.9 Consensus size: 132
490713 TCAATTGTTT
* * * * *
490723 GCTCGATTCTATCACAGAAAG-AGGTAGATCAGCATCAACATCTCATTCGATTCCATCACAGAAT
1 GCTCGATTCTATAACAG-AAGTAGGTAGATCAACACCAACATCTCGTTTGATTCCATCACAGAAT
* * * * * * *
490787 AAGGTGGATCGACATTTTTATTTTGCTCAAATCAATCGCAGAAGAAGTTGGATCAGTGTTAACTT
65 GAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACTT
490852 TTA
130 TTA
* *
490855 GCTCGATTCTATAACAGAAGTAGGTAGATCAACACCAACATCCCGTTTGAATT-CATCATAGGAA
1 GCTCGATTCTATAACAGAAGTAGGTAGATCAACACCAACATCTCGTTTG-ATTCCATCACA-GAA
490919 -GAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACT
64 TGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACT
490983 TTTA
129 TTTA
* * *
490987 GCTCGATTATATCACAGAA-TGAGGTAGATCAGCACCAACATCTCGTTTGATTCCATCACAGAAT
1 GCTCGATTCTATAACAGAAGT-AGGTAGATCAACACCAACATCTCGTTTGATTCCATCACAGAAT
* * *
491051 GAGGTGGATCGACATTTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATTAGCGTCGACTT
65 GAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACTT
491116 TTA
130 TTA
* ** * *
491119 GCTCGATTCTATCAA-AGAAGGAGGTAGATCAACACCAACATCTCGTTCAATTCCATCATAGAAG
1 GCTCGATTCTAT-AACAGAAGTAGGTAGATCAACACCAACATCTCGTTTGATTCCATCACAGAAT
* * * * * *
491183 GAGGTGGATCGACA--TTTACTTCGATTAAATCCATCGCATACGGAGTTGGATCAGC
65 GAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGC
491238 ATCGTCAACA
Statistics
Matches: 337, Mismatches: 38, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
130 33 0.10
131 10 0.03
132 287 0.85
133 7 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (132 bp):
GCTCGATTCTATAACAGAAGTAGGTAGATCAACACCAACATCTCGTTTGATTCCATCACAGAATG
AGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACTTT
TA
Found at i:491193 original size:264 final size:262
Alignment explanation
Indices: 490723--491237 Score: 748
Period size: 264 Copynumber: 2.0 Consensus size: 262
490713 TCAATTGTTT
* *
490723 GCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCAACATCTCATTCGATTCCATCACAGAATA
1 GCTCGATTATATCACAGAAAGAGGTAGATCAGCACCAACATCTCATTCGATTCCATCACAGAATA
* * * * *
490788 AGGTGGATCGACATTTTTATTTTGCTCAAATCAATCGCAGAAGAAGTTGGATCAGTGTTAACTTT
66 AGGTGGATCGACATTTTAATTTCGCTCAAATCAATCACAGAAGAAGTTGGATCAGCGTCAACTTT
* *
490853 TAGCTCGATTCTATAACAGAAGTAGGTAGATCAACACCAACATCCCGTTTGAATTCATCATAGGA
131 TAGCTCGATTCTATAACAGAAGGAGGTAGATCAACACCAACATCCCGTTTCAATTCATCATAGGA
* *
490918 AGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACT
196 AGAGGTGGATCGACA--TTTACTTCGATCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACT
490983 TTTA
259 TTTA
* * * *
490987 GCTCGATTATATCACAGAATGAGGTAGATCAGCACCAACATCTCGTTTGATTCCATCACAGAATG
1 GCTCGATTATATCACAGAAAGAGGTAGATCAGCACCAACATCTCATTCGATTCCATCACAGAATA
* * * *
491052 AGGTGGATCGACATTTTAATTTCGCTCAAATCCATCACAGAAGGAGTTGGATTAGCGTCGACTTT
66 AGGTGGATCGACATTTTAATTTCGCTCAAATCAATCACAGAAGAAGTTGGATCAGCGTCAACTTT
*
491117 TAGCTCGATTCTATCAA-AGAAGGAGGTAGATCAACACCAACATCTCG-TTCAATTCCATCATA-
131 TAGCTCGATTCTAT-AACAGAAGGAGGTAGATCAACACCAACATCCCGTTTCAATT-CATCATAG
* * * *
491179 GAAGGAGGTGGATCGACATTTACTTCGATTAAATCCATCGCATACGGAGTTGGATCAGC
194 GAA-GAGGTGGATCGACATTTACTTCGATCAAATCCATCACAGAAGGAGTTGGATCAGC
491238 ATCGTCAACA
Statistics
Matches: 224, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
262 35 0.16
263 9 0.04
264 178 0.79
265 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (262 bp):
GCTCGATTATATCACAGAAAGAGGTAGATCAGCACCAACATCTCATTCGATTCCATCACAGAATA
AGGTGGATCGACATTTTAATTTCGCTCAAATCAATCACAGAAGAAGTTGGATCAGCGTCAACTTT
TAGCTCGATTCTATAACAGAAGGAGGTAGATCAACACCAACATCCCGTTTCAATTCATCATAGGA
AGAGGTGGATCGACATTTACTTCGATCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACTTT
TA
Found at i:492489 original size:22 final size:21
Alignment explanation
Indices: 492467--492521 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
492457 CTGATATTGT
492467 TTTATTTTAATTTAG-TCACTG
1 TTTATTTTAATTTAGCT-ACTG
* *
492488 TTAATTTCTGATTTAGCTACTG
1 TTTATTT-TAATTTAGCTACTG
492510 -TTATTTTAATTT
1 TTTATTTTAATTT
492522 TTGCATTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 11 0.39
23 1 0.04
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTATTTTAATTTAGCTACTG
Found at i:494304 original size:18 final size:18
Alignment explanation
Indices: 494262--494304 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
494252 TATTATTGAA
494262 TAAAAAATATAAAAAAAT
1 TAAAAAATATAAAAAAAT
** * *
494280 TCTAAAATATATAATAAT
1 TAAAAAATATAAAAAAAT
494298 TAAAAAA
1 TAAAAAA
494305 ATTTAAAGGA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAATATAAAAAAAT
Found at i:501111 original size:17 final size:16
Alignment explanation
Indices: 501091--501231 Score: 76
Period size: 17 Copynumber: 8.4 Consensus size: 16
501081 GAATTTAACC
*
501091 TTTTGTTATTATTATT
1 TTTTTTTATTATTATT
501107 TTTTTCTTCATT-TTATT
1 TTTTT-TT-ATTATTATT
*
501124 TCGTTTTTATTTATTATT
1 T-TTTTTTA-TTATTATT
* *
501142 ATTATTTATT-TTATT
1 TTTTTTTATTATTATT
501157 TTATTATTTATTATTATT
1 TT-TT-TTTATTATTATT
* *
501175 TTTCTTTT-TTACTCAAT
1 TTT-TTTTATTA-TTATT
*
501192 TTTATTTATT-TT-TT
1 TTTTTTTATTATTATT
*
501206 ATTTTTTATATTAATATT
1 -TTTTTT-TATTATTATT
501224 TTATTTTT
1 TT-TTTTT
501232 TTCATATTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
14 1 0.01
15 12 0.13
16 18 0.19
17 39 0.41
18 25 0.26
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTTTTATTATTATT
Found at i:501122 original size:23 final size:21
Alignment explanation
Indices: 501096--501182 Score: 68
Period size: 23 Copynumber: 3.9 Consensus size: 21
501086 TAACCTTTTG
501096 TTATTATTATTTTTTTCTTCATT
1 TTATTATTATTTTTTT-TT-ATT
** *
501119 TTATT-TCGTTTTTATTTATT
1 TTATTATTATTTTTTTTTATT
*
501139 ATTATTATTTATTTTATTTTATTAT
1 -TTATTA-TTATTTTTTTTTA-T-T
501164 TTATTATTATTTTTCTTTT
1 TTATTATTATTTTT-TTTT
501183 TTACTCAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 3 0.06
21 7 0.14
22 7 0.14
23 21 0.42
24 11 0.22
25 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (21 bp):
TTATTATTATTTTTTTTTATT
Found at i:501142 original size:3 final size:3
Alignment explanation
Indices: 501134--501174 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
501124 TCGTTTTTAT
501134 TTA TTA TTA TTA TTTA TT- TTA TT- TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
501175 TTTCTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:501143 original size:10 final size:10
Alignment explanation
Indices: 501137--501175 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
501127 TTTTTATTTA
501137 TTATTATTAT
1 TTATTATTAT
501147 TTATT-TTA-
1 TTATTATTAT
501155 TT-TTATTAT
1 TTATTATTAT
501164 TTATTATTAT
1 TTATTATTAT
501174 TT
1 TT
501176 TTCTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 5 0.19
9 5 0.19
10 14 0.54
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTATTAT
Found at i:501170 original size:20 final size:20
Alignment explanation
Indices: 501128--501243 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 20
501118 TTTATTTCGT
501128 TTTTA-TTTATTATTATTATTTA
1 TTTTATTTTATTA-T-TTA-TTA
501150 TTTTATTTTATTATTTATTA
1 TTTTATTTTATTATTTATTA
* * * *
501170 TTAT-TTTTCTTTTTTACTCAA
1 TTTTATTTTATTATTTA-T-TA
*
501191 TTTTA-TTTATTTTTTATT-
1 TTTTATTTTATTATTTATTA
* * *
501209 TTTTATATTAATATTTTATTT
1 TTTTATTTTATTA-TTTATTA
501230 TTTTCATATTTATT
1 TTTT-AT-TTTATT
501244 TCTATTTTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
18 5 0.07
19 14 0.19
20 14 0.19
21 21 0.29
22 8 0.11
23 11 0.15
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATTTTATTATTTATTA
Found at i:501223 original size:22 final size:22
Alignment explanation
Indices: 501202--501251 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
501192 TTTATTTATT
501202 TTTTA-TTTTTT-ATATTAATA
1 TTTTATTTTTTTCATATTAATA
501222 TTTTATTTTTTTCATATT--TA
1 TTTTATTTTTTTCATATTAATA
501242 TTTCTATTTT
1 TTT-TATTTT
501252 CTAACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTTTCATATTAATA
Found at i:501240 original size:31 final size:32
Alignment explanation
Indices: 501128--501249 Score: 80
Period size: 30 Copynumber: 3.9 Consensus size: 32
501118 TTTATTTCGT
501128 TTTTATTTATTATTATTATTTATTT-TATT--T-
1 TTTTATTTATT-TTA-TATTTATTTATATTAATA
* * * *
501158 TATTATTTATTATTATTTTTCTTT-T-TTACTCAA
1 TTTTATTTATT-TTATATTTATTTATATTAAT--A
*
501191 TTTTATTTATTTTTTATTT-TTTATATTAATA
1 TTTTATTTATTTTATATTTATTTATATTAATA
*
501222 TTTTATTT-TTTTCATATTTATTTCTATT
1 TTTTATTTATTTT-ATATTTATTTATATT
501250 TTCTAACATT
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.03
29 8 0.11
30 19 0.26
31 17 0.23
32 14 0.19
33 14 0.19
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTATTTATTTTATATTTATTTATATTAATA
Found at i:501242 original size:46 final size:45
Alignment explanation
Indices: 501127--501251 Score: 121
Period size: 46 Copynumber: 2.7 Consensus size: 45
501117 TTTTATTTCG
* *
501127 TTTTTATTTATTATTATTATTTATTTTATTTTATTATTTATTATTA
1 TTTTTATTTTTTATCA-TATTTATTTTATTTTATTATTTATTATTA
* * *
501173 TTTTTCTTTTTTACTCA-ATTTTATTTATTTTTTATTTTTTA-TATTAA
1 TTTTTATTTTTTA-TCATA-TTTATTT-TATTTTATTATTTATTATT-A
501220 TATTTTATTTTTT-TCATATTTATTTCTATTTT
1 T-TTTTATTTTTTATCATATTTATTT-TATTTT
501252 CTAACATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
45 1 0.02
46 37 0.57
47 17 0.26
48 10 0.15
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (45 bp):
TTTTTATTTTTTATCATATTTATTTTATTTTATTATTTATTATTA
Found at i:501244 original size:20 final size:20
Alignment explanation
Indices: 501194--501251 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
501184 TACTCAATTT
*
501194 TATTTATTTT-TTATTTTTTA
1 TATTTATTTTATT-TTTTTCA
501214 TATTAATATTTTATTTTTTTCA
1 TATT--TATTTTATTTTTTTCA
501236 TATTTATTTCTATTTT
1 TATTTATTT-TATTTT
501252 CTAACATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 9 0.27
21 6 0.18
22 16 0.48
23 2 0.06
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTATTTTATTTTTTTCA
Found at i:501893 original size:137 final size:137
Alignment explanation
Indices: 501719--501967 Score: 367
Period size: 137 Copynumber: 1.8 Consensus size: 137
501709 TGTTGTTCCA
* * *
501719 ACTCCTTATGTGATGAAAACGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
1 ACTCCATATGCGATGAAAACGAGCTAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCT-CC
*
501784 TCATCGGATGAG-TTCTCATTACGAACTCTCACATTGGAAATGTTGATCCCTCAAGTGAGGTGTT
65 TCATCGGATGAGTTTCTCATTACGAACTCTC-CACTGGAAATGTTGATCCCTCAAGTGAGGTGTT
501848 GCTGATTGG
129 GCTGATTGG
* * *
501857 ACTCCATATGCGATG-AATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTT
1 ACTCCATATGCGATGAAAACGAGCTAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCT
* *
501921 TATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
66 CATCGGATGAG-T-TTCTCATTACGAACTCTCCACTGGAAATGTTGA
501968 CTAGTTTATC
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
136 12 0.12
137 43 0.43
138 27 0.27
139 17 0.17
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (137 bp):
ACTCCATATGCGATGAAAACGAGCTAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCT
CATCGGATGAGTTTCTCATTACGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGTTGC
TGATTGG
Found at i:502795 original size:57 final size:57
Alignment explanation
Indices: 502596--502917 Score: 236
Period size: 54 Copynumber: 5.8 Consensus size: 57
502586 ATGGACTTAC
* * * * * * *
502596 TCATCAAAAAACCCTTGAAAATCA-AGCTTAGTTTCTTAAAAACTTTCGTTT-ACAGTTA
1 TCATCAAGAAACCCCTGAAAATCAGA-CTTAGCTTCTTAAAAA-ATTCATTTGA-AATAA
* * * * *
502654 TCATCAAGAAATCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTG--A-AA
1 TCATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAATAA
* * * * * *
502708 GCATTAAGAAACCCCTTAAAATCAGGCTTAGTTTCTTAAAAAATTCATTGGAAATAA
1 TCATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAATAA
*
502765 TCATCAATAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTG-AA-AA
1 TCATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAATAA
* * * ** *
502820 -CATCAAGAAACTTCC-GAAAATCGGATTTAGCTTCTT-TCAAATTCATTT-AAAAAA
1 TCATCAAGAAAC-CCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAATAA
* * ** * *
502874 TAATAAAGAAACTTCT-AAATATCAGACTTAGTTTCTAAAAAAAT
1 TCATCAAGAAACCCCTGAAA-ATCAGACTTAGCTTCTTAAAAAAT
502918 AGAATTAGCC
Statistics
Matches: 210, Mismatches: 42, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
53 12 0.06
54 80 0.38
55 26 0.12
56 7 0.03
57 52 0.25
58 33 0.16
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (57 bp):
TCATCAAGAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAATAA
Found at i:502808 original size:111 final size:113
Alignment explanation
Indices: 502597--502830 Score: 296
Period size: 111 Copynumber: 2.1 Consensus size: 113
502587 TGGACTTACT
* * * * * *
502597 CATCAA-AAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAAACTTTCGTTTACAGTTATCATCAA
1 CATCAAGAAACCCCTTGAAAATCAAGCTTAGTTTCTTAAAAACATTCATTGACAATAATCATCAA
* * * * *
502661 GAAATCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAG
66 GAAACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
* *
502709 CATTAAGAAACCCCTT-AAAATCAGGCTTAGTTTCTTAAAAA-ATTCATTGGA-AATAATCATCA
1 CATCAAGAAACCCCTTGAAAATCAAGCTTAGTTTCTTAAAAACATTCATT-GACAATAATCATCA
* *
502771 ATAAACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
65 AGAAACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
502820 CATCAAGAAAC
1 CATCAAGAAAC
502831 TTCCGAAAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
111 66 0.63
112 30 0.29
113 8 0.08
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (113 bp):
CATCAAGAAACCCCTTGAAAATCAAGCTTAGTTTCTTAAAAACATTCATTGACAATAATCATCAA
GAAACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
Found at i:502855 original size:111 final size:111
Alignment explanation
Indices: 502597--502917 Score: 283
Period size: 111 Copynumber: 2.9 Consensus size: 111
502587 TGGACTTACT
* * * * * * * * *
502597 CATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAAACTTTCGTT-TACAGTTATCATCAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTAAAAA-ATTCATTGGA-AATAATCATCAA
* * * * *
502661 GAAATCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAG
64 GAAACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
* * * *
502709 CATTAAGAAACCCCTTAAAATCAGGCTTAGTTTCTTAAAAAATTCATTGGAAATAATCATCAATA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTAAAAAATTCATTGGAAATAATCATCAAGA
*
502774 AACCCCTGAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
66 AACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
* * ** * * * *
502820 CATCAAGAAACTTCC-GAAAATC-GGATTTAGCTTCTT-TCAAATTCATT-TAAAAAATAATAAA
1 CATCAAGAAAC-CCCTGAAAATCAGG-CTTAGCTTCTTAAAAAATTCATTGGAAATAATCATCAA
** * * *
502881 GAAACTTCTAAATATCAGACTTAGTTTCTAAAAAAAT
64 GAAACCCCTAAAAATCAGACTTAGCTTCTTAAAAAAT
502918 AGAATTAGCC
Statistics
Matches: 171, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
109 40 0.23
110 11 0.06
111 81 0.47
112 39 0.23
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (111 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTAAAAAATTCATTGGAAATAATCATCAAGA
AACCCCTAAAAATCAGACTTAGCTTCTTAAAAAATTCATTTGAAAA
Found at i:504991 original size:16 final size:16
Alignment explanation
Indices: 504962--505026 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
504952 TTCAAGTGTT
*
504962 TTTTTTTCTATTTTTC
1 TTTTTCTCTATTTTTC
*
504978 TTTTTCTCTCTTTTT-
1 TTTTTCTCTATTTTTC
*
504993 TTCTATTCT-T-TCTTT-
1 TT-T-TTCTCTATTTTTC
505008 TTTTTCTCTA-TTTTC
1 TTTTTCTCTATTTTTC
505023 TTTT
1 TTTT
505027 ATATTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.10
14 5 0.12
15 12 0.30
16 15 0.38
17 4 0.10
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTCTATTTTTC
Found at i:505012 original size:18 final size:19
Alignment explanation
Indices: 504988--505066 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
504978 TTTTTCTCTC
504988 TTTTTTTCTAT-TCTTTCT
1 TTTTTTTCTATATCTTTCT
*
505006 TTTTTTTCTCTAT-TTTCT
1 TTTTTTTCTATATCTTTCT
505024 TTTATATTT-T-T-TC-TTCT
1 TTT-T-TTTCTATATCTTTCT
*
505041 TCTTTTTGCTATATCTCTTCT
1 T-TTTTTTCTATATCT-TTCT
505062 TTTTT
1 TTTTT
505067 CTCTCTGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
16 2 0.04
17 8 0.16
18 22 0.45
19 5 0.10
20 7 0.14
21 5 0.10
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTTTCTATATCTTTCT
Found at i:506332 original size:20 final size:20
Alignment explanation
Indices: 506304--506341 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
506294 CGATGTATAG
*
506304 ATGCTAATGCAAAGATGCTC
1 ATGCAAATGCAAAGATGCTC
506324 ATGCAAATGCAAAGATGC
1 ATGCAAATGCAAAGATGC
506342 AAAAATGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
ATGCAAATGCAAAGATGCTC
Found at i:507854 original size:9 final size:8
Alignment explanation
Indices: 507800--507852 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
507790 AATGATATAA
*
507800 AATAAAAT
1 AATAAAAG
507808 AA-AAAAG
1 AATAAAAG
507815 AATAAAAG
1 AATAAAAG
507823 AATAAAAG
1 AATAAAAG
*
507831 AATTGAAAG
1 AA-TAAAAG
507840 AAATCAAAAG
1 -AAT-AAAAG
507850 AAT
1 AAT
507853 CATTAGCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 6 0.16
8 17 0.45
9 9 0.24
10 6 0.16
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (8 bp):
AATAAAAG
Found at i:509272 original size:15 final size:15
Alignment explanation
Indices: 509254--509283 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
509244 GTGCTATAAT
*
509254 TAAAGGACTGAAATA
1 TAAAGAACTGAAATA
509269 TAAAGAACTGAAATA
1 TAAAGAACTGAAATA
509284 AAAAATAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
TAAAGAACTGAAATA
Found at i:510570 original size:43 final size:42
Alignment explanation
Indices: 510521--511353 Score: 564
Period size: 43 Copynumber: 19.7 Consensus size: 42
510511 TAGGGTCAAA
* * *
510521 AATTATAAAAGTAAAAAGTTAGATTGGAAAAAGTAGGGGACTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTA-GGGACTC
* * *
510564 ACTTATAAAGGT-AAAAGTGAGATT-AAAAAATTAGGCACTTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGAC-TC
*
510605 AATTATAAAGGTAGAAAA-TGAGATTGAAAAAATTAGGGACCTC
1 AATTATAAAAGTA-AAAAGTGAGATTGAAAAAATTAGGGA-CTC
* * * *
510648 AATTAT-ACAGTAAAAAGTAAGATTGAAAAAATAATAAGGGCCAC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAAT--T-AGGGACTC
* * * *
510692 AATTATAAATGAAAAAAGTTAGATT-AAAAAATTTAGGGGCTCC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAA-TTAGGGACT-C
* * * * *
510735 AATTATAAAGGTAAAAGGTGAAATTGAAAAAAAATAGGGTCTC
1 AATTATAAAAGTAAAAAGTGAGATTG-AAAAAATTAGGGACTC
*
510778 AATTAT-AAAGTTAAAAAGTGAGATT--AAAAATTAGGGGCTTC
1 AATTATAAAAG-TAAAAAGTGAGATTGAAAAAATTAGGGAC-TC
** * * * * *
510819 AATTGCAAAAGTAGAATGTGAGATTAAAAAAATGAGGGGCCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTA-GGGACTC
* * * * *
510862 AATTACAAAGGTAAAAGGTG-GATTGAAAAAATTAGGAGCCTT
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGG-GACTC
* * **
510904 AGTTATAAATGTAAAAAGTGAGACTT--AAAAATTAGGGTTTTC
1 AATTATAAAAGTAAAAAGTGAGA-TTGAAAAAATTAGGG-ACTC
* * * *
510946 AATTAT-AAAGATAGAAAG-GAGACTGAAAAAATTATGGGGCTT
1 AATTATAAAAG-TAAAAAGTGAGATTGAAAAAATTA-GGGACTC
* *
510988 AATTATAAATGTAAAAAGTGAGATTAAAAAAATTA-GGACATC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGAC-TC
* *
511030 AATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGGGGCTTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGAC-TC
* * * ** * *
511072 AATTAT-AGAGCTATAATGCAAGATTGGAAAAATTATGGGCCTC
1 AATTATAAAAG-TAAAAAGTGAGATTGAAAAAATTA-GGGACTC
* * * * *
511115 AATTATAAAGGCAGAAAGTGGGATTGAAAAAATTAGGGGTCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTA-GGGACTC
* *
511158 AATTATAAAATGTAAAAAGTGTGA-T--AAAAATTAGAGACCTC
1 AATTATAAAA-GTAAAAAGTGAGATTGAAAAAATTAGGGA-CTC
* *
511199 AATTATAAAGGTAAAAAGTGAGA-T-AAAAATTTAGGGATCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGA-CTC
* * * * *
511240 AATTATAAAAATAAAAGGTGGGATTAAAAAAATTAGGGATCCC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGA-CTC
* * * ***
511283 AGTTATAAAAG-AAAAA-TAAAATT-AAAAAATTAAATACATC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGAC-TC
* *
511323 AATTATAAAAATAAAATGT-ATGATTGAAAAA
1 AATTATAAAAGTAAAAAGTGA-GATTGAAAAA
511354 TTATGGGTCT
Statistics
Matches: 627, Mismatches: 117, Indels: 92
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.00
40 51 0.08
41 127 0.20
42 178 0.28
43 200 0.32
44 45 0.07
45 25 0.04
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (42 bp):
AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACTC
Found at i:511289 original size:84 final size:83
Alignment explanation
Indices: 510521--511291 Score: 590
Period size: 84 Copynumber: 9.1 Consensus size: 83
510511 TAGGGTCAAA
* * * * * *
510521 AATTATAAAAGTAAAAAGTTAGATTGGAAAAAGTAGGGGACTCACTTATAAAGGT-AAAAGTGAG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGG-CTCAATTATAAAAGTAAAAAGTGAG
510585 ATT-AAAAAATTA-GGCACTTC
65 ATTAAAAAAATTAGGGC-C--C
* * *
510605 AATTATAAAGGTAGAAAA-TGAGATTGAAAAAATTAGGGACCTCAATTAT-ACAGTAAAAAGTAA
1 AATTATAAAGGTA-AAAAGTGAGATTGAAAAAATTAGGG-GCTCAATTATAAAAGTAAAAAGTGA
*
510668 GATTGAAAAAATAATAAGGGCCAC
64 GATT--AAAAA-AATTAGGGCC-C
* * * * *
510692 AATTATAAATGAAAAAAGTTAGATT-AAAAAATTTAGGGGCTCCAATTATAAAGGTAAAAGGTGA
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAA-TTAGGGGCT-CAATTATAAAAGTAAAAAGTGA
* * *
510756 AATTGAAAAAAAATAGGGTCTC
64 GATT-AAAAAAATTAGGG-CCC
* ** * *
510778 AATTATAAAGTTAAAAAGTGAGATT--AAAAATTAGGGGCTTCAATTGCAAAAGTAGAATGTGAG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGGC-TCAATTATAAAAGTAAAAAGTGAG
*
510841 ATTAAAAAAATGAGGGGCCTC
65 ATTAAAAAAATTA-GGGCC-C
* * * * * *
510862 AATTACAAAGGTAAAAGGTG-GATTGAAAAAATTAGGAGCCTTAGTTATAAATGTAAAAAGTGAG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGG-GGCTCAATTATAAAAGTAAAAAGTGAG
**
510926 ACTT--AAAAATTAGGGTTTTC
65 A-TTAAAAAAATTAGGG--CCC
* * * * *
510946 AATTATAAAGATAGAAAG-GAGACTGAAAAAATTATGGGGCTTAATTATAAATGTAAAAAGTGAG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTA-GGGGCTCAATTATAAAAGTAAAAAGTGAG
* *
511010 ATTAAAAAAATTAGGACATC
65 ATTAAAAAAATTAGGGC-CC
* * * **
511030 AATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGGGGCTTCAATTAT-AGAGCTATAATGCAA
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGGC-TCAATTATAAAAG-TAAAAAGTGA
**
511093 GATTGGAAAAATTATGGGCCTC
64 GATTAAAAAAATTA-GGGCC-C
* * * *
511115 AATTATAAAGGCAGAAAGTGGGATTGAAAAAATTAGGGGTCTCAATTATAAAATGTAAAAAGTGT
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGG-CTCAATTATAAAA-GTAAAAAGTGA
*
511180 GA-T--AAAAATTAGAGACCTC
64 GATTAAAAAAATTAG-GGCC-C
* * * * *
511199 AATTATAAAGGTAAAAAGTGAGA-T-AAAAATTTAGGGATCTCAATTATAAAAATAAAAGGTGGG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGG-GCTCAATTATAAAAGTAAAAAGTGAG
511262 ATTAAAAAAATTAGGGATCCC
65 ATTAAAAAAATTAGGG--CCC
*
511283 AGTTATAAA
1 AATTATAAA
511292 AGAAAAATAA
Statistics
Matches: 550, Mismatches: 94, Indels: 86
0.75 0.13 0.12
Matches are distributed among these distances:
81 10 0.02
82 25 0.05
83 32 0.06
84 261 0.47
85 83 0.15
86 66 0.12
87 51 0.09
88 19 0.03
89 3 0.01
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (83 bp):
AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGGCTCAATTATAAAAGTAAAAAGTGAGA
TTAAAAAAATTAGGGCCC
Found at i:511899 original size:2 final size:2
Alignment explanation
Indices: 511892--511937 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
511882 ATCTATTTTC
511892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
511934 AT AT
1 AT AT
511938 CAATTGATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512734 original size:20 final size:21
Alignment explanation
Indices: 512709--512758 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
512699 GCTTTGGATA
512709 TCGCAACGCGATTTTC-AAAT
1 TCGCAACGCGATTTTCAAAAT
*
512729 TCGCAACGTGATTTTCAAAAT
1 TCGCAACGCGATTTTCAAAAT
512750 TCGCAACGC
1 TCGCAACGC
512759 TAATTACCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (21 bp):
TCGCAACGCGATTTTCAAAAT
Found at i:512821 original size:57 final size:58
Alignment explanation
Indices: 512729--512837 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 58
512719 ATTTTCAAAT
*
512729 TCGCAACGTGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
512787 TCGCAACGCGATTTTC-AAATTTGCAACGCTAATTACCGATATAGGTAAACA
1 TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACA
512838 CAATTATCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 34 0.69
58 15 0.31
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (58 bp):
TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:512846 original size:57 final size:58
Alignment explanation
Indices: 512729--512850 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
512719 ATTTTCAAAT
* **
512729 TCGCAACGTGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
* *
512787 TCGCAACGCGATTTTC-AAATTTGCAACGCTAATTACCGATATAGGTAAACACAATTA
1 TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
512844 TCGCAAC
1 TCGCAAC
512851 AAAAATTTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 44 0.75
58 15 0.25
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (58 bp):
TCGCAACGCGATTTTCAAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
Found at i:512959 original size:92 final size:92
Alignment explanation
Indices: 512776--512961 Score: 255
Period size: 92 Copynumber: 2.0 Consensus size: 92
512766 CGATATAGGT
* *
512776 AAACAGTACTATCGCAACGCGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACACAA
1 AAACAATACTATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAA
* ***
512841 TTATCGCAACAAAAATTTCGTTTTCGC
66 CTATCGCAACAAAAATTTCAAATTCGC
**
512868 AAACAATACTATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTA
1 AAACAATACTATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAA
* *** *
512933 CTATCGTAACGCGATTTTCAAATTCGC
66 CTATCGCAACAAAAATTTCAAATTCGC
512960 AA
1 AA
512962 TGCGATTTTC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (92 bp):
AAACAATACTATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAA
CTATCGCAACAAAAATTTCAAATTCGC
Found at i:512968 original size:20 final size:20
Alignment explanation
Indices: 512943--512981 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
512933 CTATCGTAAC
512943 GCGATTTTCAAATTCGCAAT
1 GCGATTTTCAAATTCGCAAT
*
512963 GCGATTTTCAAATTTGCAA
1 GCGATTTTCAAATTCGCAA
512982 CGCTAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (20 bp):
GCGATTTTCAAATTCGCAAT
Found at i:513010 original size:77 final size:77
Alignment explanation
Indices: 512879--513047 Score: 284
Period size: 77 Copynumber: 2.2 Consensus size: 77
512869 AACAATACTA
* *
512879 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGTAACG
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
512944 CGATTTTCAAAT
66 CGATTTTCAAAT
* *
512956 TCGCAATGCGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAATAGTACTATCGCAACG
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
513021 CGATTTTCAAAT
66 CGATTTTCAAAT
**
513033 TCGCGTTGCGATTTT
1 TCGCAATGCGATTTT
513048 GGAGAATCGC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 86 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (77 bp):
TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
CGATTTTCAAAT
Found at i:513061 original size:16 final size:16
Alignment explanation
Indices: 513040--513074 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
513030 AATTCGCGTT
*
513040 GCGATTTTGGAGAATC
1 GCGATTTTGAAGAATC
513056 GCGATTTTGAAGAATC
1 GCGATTTTGAAGAATC
513072 GCG
1 GCG
513075 TTGCGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (16 bp):
GCGATTTTGAAGAATC
Found at i:513469 original size:13 final size:13
Alignment explanation
Indices: 513451--513479 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
513441 TTTTTACCAC
513451 TGAAATCACTTAA
1 TGAAATCACTTAA
513464 TGAAATCACTTAA
1 TGAAATCACTTAA
513477 TGA
1 TGA
513480 TTCTTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (13 bp):
TGAAATCACTTAA
Found at i:513797 original size:26 final size:27
Alignment explanation
Indices: 513768--513827 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
513758 CTTCTTCAAA
*
513768 ACATTTTAGATTGTAA-CGAAAATGTT
1 ACATTTTAGATTATAACCGAAAATGTT
*
513794 ACATTTTAGGTTATAACCGAAAATGTT
1 ACATTTTAGATTATAACCGAAAATGTT
*
513821 ATATTTT
1 ACATTTT
513828 TAATAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (27 bp):
ACATTTTAGATTATAACCGAAAATGTT
Found at i:520335 original size:24 final size:26
Alignment explanation
Indices: 520286--520336 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
520276 ACTGAATTGC
520286 AAGGTGTGTTCCTTGTGTGCTATATA
1 AAGGTGTGTTCCTTGTGTGCTATATA
*
520312 AAGGTGTGTTCCTTGTGTCCTATAT
1 AAGGTGTGTTCCTTGTGTGCTATAT
520337 GATTGTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (26 bp):
AAGGTGTGTTCCTTGTGTGCTATATA
Found at i:521657 original size:26 final size:26
Alignment explanation
Indices: 521621--521672 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
521611 CTGAATTGCG
*
521621 AGGTGTGTTCCTTGTGTGCTATATGA
1 AGGTGTGTTCCTTGTGTCCTATATGA
521647 AGGTGTGTTCCTTGTGTCCTATATGA
1 AGGTGTGTTCCTTGTGTCCTATATGA
521673 CTGTTTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.29, T:0.42
Consensus pattern (26 bp):
AGGTGTGTTCCTTGTGTCCTATATGA
Found at i:522167 original size:13 final size:14
Alignment explanation
Indices: 522135--522161 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
522125 TGTTTTATTG
522135 AAAATGTTTTCCGA
1 AAAATGTTTTCCGA
522149 AAAATGTTTTCCG
1 AAAATGTTTTCCG
522162 TAAATGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Found at i:522191 original size:14 final size:14
Alignment explanation
Indices: 522174--522206 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
522164 AATGAATTAT
522174 ATTTTCT-GAAAAAC
1 ATTTTCTAG-AAAAC
522188 ATTTTCTAGAAAAC
1 ATTTTCTAGAAAAC
522202 ATTTT
1 ATTTT
522207 ACGATGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTTTCTAGAAAAC
Found at i:522438 original size:31 final size:29
Alignment explanation
Indices: 522370--522500 Score: 74
Period size: 33 Copynumber: 4.3 Consensus size: 29
522360 AAATATTTTT
*
522370 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
522400 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* *
522433 TTATATTAATTATTTATTAAAGAA-A-TAAT-G
1 TTATATT--TTA-TTAATAAA-AATATTAATAA
* * *
522463 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
522491 GTATATTTTA
1 TTATATTTTA
522501 AATATCTTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
25 2 0.02
26 6 0.07
27 6 0.07
28 10 0.12
30 8 0.10
31 15 0.19
32 13 0.16
33 19 0.23
34 2 0.02
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:522519 original size:23 final size:23
Alignment explanation
Indices: 522470--522520 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
522460 ATGTTATATT
**
522470 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
522493 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
522516 ATATT
1 ATATT
522521 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:522588 original size:27 final size:29
Alignment explanation
Indices: 522534--522588 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
522524 AGATTATTAT
522534 ATTATTTATATATATAAATAATATTATTC
1 ATTATTTATATATATAAATAATATTATTC
*
522563 ATTATTTATA-AT-TTAATAATATTATT
1 ATTATTTATATATATAAATAATATTATT
522589 TCCATGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.52
28 2 0.08
29 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTATTTATATATATAAATAATATTATTC
Found at i:522749 original size:23 final size:24
Alignment explanation
Indices: 522718--522771 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
522708 TATAATATTT
522718 TATTATTAAAAATATTAATAAAT-A
1 TATT-TTAAAAATATTAATAAATAA
* * *
522742 TATTTTAAATATTTTAATAATTAA
1 TATTTTAAAAATATTAATAAATAA
522766 TATTTT
1 TATTTT
522772 GATTATAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTAAAAATATTAATAAATAA
Found at i:538485 original size:19 final size:19
Alignment explanation
Indices: 538461--538508 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
538451 AAAGAAGTAA
538461 ATAAGTGATTGGGAGCCTT
1 ATAAGTGATTGGGAGCCTT
538480 ATAAGTGATTGGGAGCCTT
1 ATAAGTGATTGGGAGCCTT
538499 ATAAGTGATT
1 ATAAGTGATT
538509 AAAAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.33
Consensus pattern (19 bp):
ATAAGTGATTGGGAGCCTT
Found at i:540194 original size:20 final size:18
Alignment explanation
Indices: 540155--540189 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
540145 AATTTTTTCC
*
540155 AAAAAATTAATATAAATT
1 AAAAAATTAAAATAAATT
540173 AAAAAATTAAAATAAAT
1 AAAAAATTAAAATAAAT
540190 ATTAATCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATTAAAATAAATT
Found at i:540803 original size:2 final size:2
Alignment explanation
Indices: 540796--540832 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
540786 TTTGTACCCT
540796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
540833 CAAAGTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560382 original size:24 final size:24
Alignment explanation
Indices: 560355--560628 Score: 169
Period size: 24 Copynumber: 11.3 Consensus size: 24
560345 ACGCAATGGT
560355 ACTAATACAGGAGTGCACAAATGC
1 ACTAATACAGGAGTGCACAAATGC
* * * *
560379 ACTAATACTGGAGTACACATATGT
1 ACTAATACAGGAGTGCACAAATGC
* ** *
560403 AATAGA-ATCAGGAGTGCATGAATGA
1 ACTA-ATA-CAGGAGTGCACAAATGC
* * *
560428 ACTAATTCAGGAGTG-AAAAATTAC
1 ACTAATACAGGAGTGCACAAA-TGC
* **
560452 ACTAATACAGGAGTGTATGAATGC
1 ACTAATACAGGAGTGCACAAATGC
* *
560476 ACTAATATAGGAGTGTA-AGAATGC
1 ACTAATACAGGAGTGCACA-AATGC
*
560500 ACTAATACAGGAGTGCACAAAGGC
1 ACTAATACAGGAGTGCACAAATGC
* * * *
560524 ACTAATACAAGATTGCACAATTGG
1 ACTAATACAGGAGTGCACAAATGC
* * *
560548 ACTAATACAAGAGTGCATAATTGC
1 ACTAATACAGGAGTGCACAAATGC
* * * * *
560572 ACTGAA-ACATGAGTACCCAAAGGT
1 ACT-AATACAGGAGTGCACAAATGC
* * * *
560596 ACCAATAAAGGTGTGCAAGAAATGC
1 ACTAATACAGGAGTGC-ACAAATGC
560621 ACTAATAC
1 ACTAATAC
560629 GATGGGCTTT
Statistics
Matches: 188, Mismatches: 52, Indels: 19
0.73 0.20 0.07
Matches are distributed among these distances:
23 5 0.03
24 152 0.81
25 31 0.16
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.22
Consensus pattern (24 bp):
ACTAATACAGGAGTGCACAAATGC
Found at i:560383 original size:48 final size:47
Alignment explanation
Indices: 560289--560628 Score: 177
Period size: 48 Copynumber: 7.0 Consensus size: 47
560279 TACATAATGC
* * * * * *
560289 CAAGAGTACACTAATGTACTAAATACATGATTACACAAAGGTACTAACA
1 CAAGAGTACAC-AATGTACT-AATACAGGAGTGCACAAATGCACTAATA
*
560338 CAAGAGTACGCAATGGTACTAATACAGGAGTGCACAAATGCACTAATA
1 CAAGAGTACACAAT-GTACTAATACAGGAGTGCACAAATGCACTAATA
** * ** * *
560386 CTGGAGTACACATATGTAATAGA-ATCAGGAGTGCATGAATGAACTAATT
1 CAAGAGTACACA-ATGTACTA-ATA-CAGGAGTGCACAAATGCACTAATA
* * * **
560435 CAGGAGTGA-AAAAT-TACACTAATACAGGAGTGTATGAATGCACTAATA
1 CAAGAGT-ACACAATGT--ACTAATACAGGAGTGCACAAATGCACTAATA
* * * * *
560483 TAGGAGTGTA-AGAATGCACTAATACAGGAGTGCACAAAGGCACTAATA
1 CA--AGAGTACACAATGTACTAATACAGGAGTGCACAAATGCACTAATA
* * * * * *
560531 CAAGATTGCACAATTGGACTAATACAAGAGTGCATAATTGCACTGAA-A
1 CAAGAGTACACAA-TGTACTAATACAGGAGTGCACAAATGCACT-AATA
* * * * * * *
560579 CATGAGTACCCAAAGGTACCAATAAAGGTGTGCAAGAAATGCACTAATA
1 CAAGAGTACAC-AATGTACTAATACAGGAGTGC-ACAAATGCACTAATA
560628 C
1 C
560629 GATGGGCTTT
Statistics
Matches: 222, Mismatches: 52, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
46 3 0.01
47 4 0.02
48 141 0.64
49 70 0.32
50 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.21
Consensus pattern (47 bp):
CAAGAGTACACAATGTACTAATACAGGAGTGCACAAATGCACTAATA
Found at i:563085 original size:15 final size:15
Alignment explanation
Indices: 563048--563078 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
563038 CTTGGATTCT
563048 GGTTTGGTATATCTA
1 GGTTTGGTATATCTA
563063 GGTTTGGTATATCTA
1 GGTTTGGTATATCTA
563078 G
1 G
563079 TTGTGGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.45
Consensus pattern (15 bp):
GGTTTGGTATATCTA
Found at i:564562 original size:59 final size:59
Alignment explanation
Indices: 564459--564572 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
564449 AATAGATGGA
** *
564459 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGTTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGAAAAACTCAATAATATGGTTC
* *
564518 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGCAAAGAAAAACTCAATAATATG
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGAAAAACTCAATAATATG
564573 ACTCTAACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGAAAAACTCAATAATATGGTTC
Found at i:573307 original size:58 final size:59
Alignment explanation
Indices: 573217--573336 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 59
573207 AATAGGTGGA
* * *
573217 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATG-AATGGTAAACTCGATAATATGGATC
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAAATCGATAATATGGATC
* * *
573275 TAAGTGTCCTATCGAACCCTTCTAGTTC-CAATGAAAAGGAAAAATCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAG-TCGCAATGAAAAGGAAAAATCGATAATATGGATC
573334 TAA
1 TAA
573337 CCAACCCTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
58 28 0.52
59 26 0.48
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAAATCGATAATATGGATC
Found at i:581657 original size:2 final size:2
Alignment explanation
Indices: 581650--581718 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
581640 ATTGACACTT
581650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
581692 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
581719 CAAAATATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:602378 original size:15 final size:15
Alignment explanation
Indices: 602358--602395 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
602348 GAAGAAGCAA
602358 TGACATCACCAGATT
1 TGACATCACCAGATT
602373 TGACATCACCAGATT
1 TGACATCACCAGATT
602388 TGACATCA
1 TGACATCA
602396 AATCACCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (15 bp):
TGACATCACCAGATT
Found at i:602600 original size:21 final size:21
Alignment explanation
Indices: 602562--602602 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
602552 TTGGTTTCTT
* *
602562 TAAATAAAATGGTTTTATAAA
1 TAAATAAAATGCTATTATAAA
*
602583 TAAATAAAATTCTATTATAA
1 TAAATAAAATGCTATTATAA
602603 CATGTGTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAATAAAATGCTATTATAAA
Found at i:605238 original size:31 final size:30
Alignment explanation
Indices: 605176--605243 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
605166 CAAAATACAT
* *
605176 AAATTTTAAAAATTATACTTTTGGTCCCTA
1 AAATTTTAAAAATTATACTTCTGCTCCCTA
* * *
605206 AAATTTTGGAAAATTATTCTTCTGCTCTCTA
1 AAATTTT-AAAAATTATACTTCTGCTCCCTA
*
605237 AATTTTT
1 AAATTTT
605244 CTAAAATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.47
Consensus pattern (30 bp):
AAATTTTAAAAATTATACTTCTGCTCCCTA
Found at i:609186 original size:27 final size:26
Alignment explanation
Indices: 609155--609240 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 26
609145 TTTTTCTTAT
609155 AATATTCTAAATTTAAGATAAAAATAA
1 AATATT-TAAATTTAAGATAAAAATAA
*
609182 AATATAGTTATTGAAGTTAAGATAAAAATAA
1 AATAT--TTA---AATTTAAGATAAAAATAA
* * *
609213 TATATATATATATTAAGATAAAAATAA
1 AATATTTAAAT-TTAAGATAAAAATAA
609240 A
1 A
609241 TTGCACATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 2 0.04
29 3 0.06
31 21 0.45
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (26 bp):
AATATTTAAATTTAAGATAAAAATAA
Found at i:609202 original size:31 final size:27
Alignment explanation
Indices: 609167--609240 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 27
609157 TATTCTAAAT
609167 TTAAGATAAAAATAAAATATAGT-TATTGAA
1 TTAAGATAAAAATAAAATATA-TATA-T--A
*
609197 GTTAAGATAAAAATAATATATATATATA
1 -TTAAGATAAAAATAAAATATATATATA
609225 TTAAGATAAAAATAAA
1 TTAAGATAAAAATAAA
609241 TTGCACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 15 0.38
28 1 0.03
30 2 0.05
31 22 0.55
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (27 bp):
TTAAGATAAAAATAAAATATATATATA
Found at i:609287 original size:29 final size:27
Alignment explanation
Indices: 609249--609309 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
609239 AATTGCACAT
609249 TTTTAAGTTAAAATAAGAATAAATATATA
1 TTTTAAGTTAAAATAA-AATAAA-ATATA
* ** *
609278 TTTTATGTTACGATAAATTAAAATATA
1 TTTTAAGTTAAAATAAAATAAAATATA
609305 TTTTA
1 TTTTA
609310 CCTTAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.36
28 5 0.18
29 13 0.46
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (27 bp):
TTTTAAGTTAAAATAAAATAAAATATA
Found at i:609442 original size:33 final size:33
Alignment explanation
Indices: 609404--609513 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
609394 AAGTTCAAAT
* *
609404 AAAAATATATTTTTAAAAGTTAAGATAAGAGTA
1 AAAAATATATTTTTATAAGTTAAGATAAGAATA
* ** *
609437 AAAAATA-CTTTAGATTAAGTTAAAATAAGAATA
1 AAAAATATATTTTTA-TAAGTTAAGATAAGAATA
609470 AAATATATATATTTTT-TAAG-TAAGATAAGAATA
1 AAA-A-ATATATTTTTATAAGTTAAGATAAGAATA
*
609503 AATATATATAT
1 AA-AAATATAT
609514 ATATATATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
32 10 0.16
33 39 0.64
34 6 0.10
35 3 0.05
36 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.35
Consensus pattern (33 bp):
AAAAATATATTTTTATAAGTTAAGATAAGAATA
Found at i:609510 original size:34 final size:34
Alignment explanation
Indices: 609451--609515 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
609441 ATACTTTAGA
609451 TTAAGTTAAAATAAGAATAAAATATATATATTTT
1 TTAAGTTAAAATAAGAATAAAATATATATATTTT
*
609485 TTAAG-TAAGATAAGAATAAATATATATATAT
1 TTAAGTTAAAATAAGAATAAA-ATATATATAT
609516 ATATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (34 bp):
TTAAGTTAAAATAAGAATAAAATATATATATTTT
Found at i:609511 original size:2 final size:2
Alignment explanation
Indices: 609504--609548 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
609494 ATAAGAATAA
609504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
609546 AT A
1 AT A
609549 ATTAATATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:610324 original size:32 final size:30
Alignment explanation
Indices: 610285--610348 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
610275 TCGTTAAAAA
*
610285 TAGGTGCTTAATGTTTTCTCCGTTACACTTTT
1 TAGGTGCTTAATATTTT-TCCGTTACA-TTTT
*
610317 TAGGTGCTTAATATTTTTCCGTTATATTTT
1 TAGGTGCTTAATATTTTTCCGTTACATTTT
610347 TA
1 TA
610349 AATGTCTACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.20
31 8 0.27
32 16 0.53
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (30 bp):
TAGGTGCTTAATATTTTTCCGTTACATTTT
Found at i:613143 original size:527 final size:527
Alignment explanation
Indices: 612150--613201 Score: 2104
Period size: 527 Copynumber: 2.0 Consensus size: 527
612140 AAGAAGACAA
612150 TGGGATAAAGGAAATGGAAGAAGATAAGAAAAATGAAGAGAAAGTTGAGACTGAGAAGATGGATG
1 TGGGATAAAGGAAATGGAAGAAGATAAGAAAAATGAAGAGAAAGTTGAGACTGAGAAGATGGATG
612215 ATCAACTGGTCGAGGAAGACAAGGAAAGCAAAGAAGTGGAAAGTGAAACAAAGGAGGAACCTAAA
66 ATCAACTGGTCGAGGAAGACAAGGAAAGCAAAGAAGTGGAAAGTGAAACAAAGGAGGAACCTAAA
612280 ACTGATGCAATGGAAGAAGATGCCAAGAAAATTGAGGAGGAAAACAAAGATGAGGCGGGTGAGAA
131 ACTGATGCAATGGAAGAAGATGCCAAGAAAATTGAGGAGGAAAACAAAGATGAGGCGGGTGAGAA
612345 AGTTGAGGGGATCTTGCCATGGCTTGGATCAACAAGACCAAATAAGCCACGAGCATAAAAAAGCA
196 AGTTGAGGGGATCTTGCCATGGCTTGGATCAACAAGACCAAATAAGCCACGAGCATAAAAAAGCA
612410 ACATTCTAGCTATGTCGGAGTGACCATGGAGTTCACTGATTGCCTTGGGGAAAACCGGACACCCC
261 ACATTCTAGCTATGTCGGAGTGACCATGGAGTTCACTGATTGCCTTGGGGAAAACCGGACACCCC
612475 AAAGCTCGTTCTTAAATGAAACGGTTGGTTTCTGTGAATATACAAGCATGGCTAGCCGAACCATT
326 AAAGCTCGTTCTTAAATGAAACGGTTGGTTTCTGTGAATATACAAGCATGGCTAGCCGAACCATT
612540 TTTGAACTACTCAAATGCATTCGTCGAGAAGTTTTCAGAAAGCAAATATTGGAGACTGAACTGCA
391 TTTGAACTACTCAAATGCATTCGTCGAGAAGTTTTCAGAAAGCAAATATTGGAGACTGAACTGCA
612605 CTGAAGATGATATGCGTATGGTTGGCTCTGTTTTGAACGTAGACTCCTTTTATGCATTCCGGGAT
456 CTGAAGATGATATGCGTATGGTTGGCTCTGTTTTGAACGTAGACTCCTTTTATGCATTCCGGGAT
612670 TGTTCAC
521 TGTTCAC
612677 TGGGATAAAGGAAATGGAAGAAGATAAGAAAAATGAAGAGAAAGTTGAGACTGAGAAGATGGATG
1 TGGGATAAAGGAAATGGAAGAAGATAAGAAAAATGAAGAGAAAGTTGAGACTGAGAAGATGGATG
612742 ATCAACTGGTCGAGGAAGACAAGGAAAGCAAAGAAGTGGAAAGTGAAACAAAGGAGGAACCTAAA
66 ATCAACTGGTCGAGGAAGACAAGGAAAGCAAAGAAGTGGAAAGTGAAACAAAGGAGGAACCTAAA
612807 ACTGATGCAATGGAAGAAGATGCCAAGAAAATTGAGGAGGAAAACAAAGATGAGGCGGGTGAGAA
131 ACTGATGCAATGGAAGAAGATGCCAAGAAAATTGAGGAGGAAAACAAAGATGAGGCGGGTGAGAA
612872 AGTTGAGGGGATCTTGCCATGGCTTGGATCAACAAGACCAAATAAGCCACGAGCATAAAAAAGCA
196 AGTTGAGGGGATCTTGCCATGGCTTGGATCAACAAGACCAAATAAGCCACGAGCATAAAAAAGCA
612937 ACATTCTAGCTATGTCGGAGTGACCATGGAGTTCACTGATTGCCTTGGGGAAAACCGGACACCCC
261 ACATTCTAGCTATGTCGGAGTGACCATGGAGTTCACTGATTGCCTTGGGGAAAACCGGACACCCC
613002 AAAGCTCGTTCTTAAATGAAACGGTTGGTTTCTGTGAATATACAAGCATGGCTAGCCGAACCATT
326 AAAGCTCGTTCTTAAATGAAACGGTTGGTTTCTGTGAATATACAAGCATGGCTAGCCGAACCATT
613067 TTTGAACTACTCAAATGCATTCGTCGAGAAGTTTTCAGAAAGCAAATATTGGAGACTGAACTGCA
391 TTTGAACTACTCAAATGCATTCGTCGAGAAGTTTTCAGAAAGCAAATATTGGAGACTGAACTGCA
613132 CTGAAGATGATATGCGTATGGTTGGCTCTGTTTTGAACGTAGACTCCTTTTATGCATTCCGGGAT
456 CTGAAGATGATATGCGTATGGTTGGCTCTGTTTTGAACGTAGACTCCTTTTATGCATTCCGGGAT
613197 TGTTC
521 TGTTC
613202 CGGTAACAAG
Statistics
Matches: 525, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
527 525 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (527 bp):
TGGGATAAAGGAAATGGAAGAAGATAAGAAAAATGAAGAGAAAGTTGAGACTGAGAAGATGGATG
ATCAACTGGTCGAGGAAGACAAGGAAAGCAAAGAAGTGGAAAGTGAAACAAAGGAGGAACCTAAA
ACTGATGCAATGGAAGAAGATGCCAAGAAAATTGAGGAGGAAAACAAAGATGAGGCGGGTGAGAA
AGTTGAGGGGATCTTGCCATGGCTTGGATCAACAAGACCAAATAAGCCACGAGCATAAAAAAGCA
ACATTCTAGCTATGTCGGAGTGACCATGGAGTTCACTGATTGCCTTGGGGAAAACCGGACACCCC
AAAGCTCGTTCTTAAATGAAACGGTTGGTTTCTGTGAATATACAAGCATGGCTAGCCGAACCATT
TTTGAACTACTCAAATGCATTCGTCGAGAAGTTTTCAGAAAGCAAATATTGGAGACTGAACTGCA
CTGAAGATGATATGCGTATGGTTGGCTCTGTTTTGAACGTAGACTCCTTTTATGCATTCCGGGAT
TGTTCAC
Found at i:614636 original size:17 final size:17
Alignment explanation
Indices: 614614--614646 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
614604 TTTAAATATG
614614 ATTTAAAAAGATATCAT
1 ATTTAAAAAGATATCAT
614631 ATTTAAAAAGATATCA
1 ATTTAAAAAGATATCA
614647 ACTAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTTAAAAAGATATCAT
Found at i:617624 original size:3 final size:3
Alignment explanation
Indices: 617618--617650 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
617608 CGTCGTCGTT
617618 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
617651 AAATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:618651 original size:60 final size:60
Alignment explanation
Indices: 618578--618723 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
618568 CCATTAGGGT
* * * *
618578 AAAG-TATAAAAATGGTCCCTCGACTATAGGGTACTACTTTATTAAGTCTCTCGACTATTA
1 AAAGTTAT-AAAATGGTCCCTCGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
* * * * *
618638 AAAGTTATAAAATGGT-CCTCCAACAATAGAGTTCTACTTTGTTGAGTCCCTCAACTATCA
1 AAAGTTATAAAATGGTCCCT-CGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
* *
618698 AAAGTTACAAAATGGTCACTCGACTA
1 AAAGTTATAAAATGGTCCCTCGACTA
618724 GTCATTATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
59 3 0.04
60 62 0.89
61 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCCCTCGACTATAGAGTACTACTTTATTAAGTCCCTCAACTATCA
Found at i:618856 original size:25 final size:25
Alignment explanation
Indices: 618828--618877 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
618818 GATTCTGAAG
618828 TTAGATTTTATCATATCATATTCAA
1 TTAGATTTTATCATATCATATTCAA
618853 TTAGATTTTATCATATCATATTCAA
1 TTAGATTTTATCATATCATATTCAA
618878 CAAGTTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (25 bp):
TTAGATTTTATCATATCATATTCAA
Found at i:624617 original size:24 final size:24
Alignment explanation
Indices: 624590--624637 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
624580 GCATGACATG
624590 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
* *
624614 GTACGTAGATGTTTTATATATCAT
1 GTACATAGATGTTTTATACATCAT
624638 CAGGAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:624998 original size:40 final size:40
Alignment explanation
Indices: 624954--625063 Score: 193
Period size: 40 Copynumber: 2.8 Consensus size: 40
624944 AGGACACTAA
*
624954 GTGTATATGGTGGGCACGACCTTATGTGTAATGCACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
624994 GTGTATATGGTGGGCACGACCGTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
625034 GTGTATATGGTGGGCATGACCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
625064 GCACTACGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:625223 original size:44 final size:45
Alignment explanation
Indices: 625168--625254 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 45
625158 GTAACCATGC
*
625168 AAATAATCTTACAAGCTTATGGAAT-AATGGCAAGTACATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGGTA
* * * *
625212 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGG
1 AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGG
625255 AAAGAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 22 0.59
45 15 0.41
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGCAAGTACATTGGTA
Found at i:627865 original size:13 final size:12
Alignment explanation
Indices: 627846--627926 Score: 83
Period size: 13 Copynumber: 6.4 Consensus size: 12
627836 CTTAAAATAT
627846 AAAAAAGAAGAA
1 AAAAAAGAAGAA
627858 AGAAAAAGAAGAA
1 A-AAAAAGAAGAA
*
627871 AAAGAAAAAAGAA
1 AAA-AAAGAAGAA
*
627884 AAAGAAA-AATAA
1 AAA-AAAGAAGAA
*
627896 GAAAAAGAAGAGGA
1 AAAAAAGAAGA--A
627910 AAAAAAGAAGAA
1 AAAAAAGAAGAA
627922 AAAAA
1 AAAAA
627927 TATGAGAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
11 3 0.05
12 18 0.31
13 27 0.46
14 11 0.19
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:627872 original size:22 final size:21
Alignment explanation
Indices: 627846--627926 Score: 103
Period size: 22 Copynumber: 3.9 Consensus size: 21
627836 CTTAAAATAT
627846 AAAAAAGAAGAAAGAAAAAGA
1 AAAAAAGAAGAAAGAAAAAGA
*
627867 AGAAAAAGAAAAAAGAAAAAGA
1 A-AAAAAGAAGAAAGAAAAAGA
* *
627889 AAAATAAGAA-AAAGAAGAGGA
1 AAAA-AAGAAGAAAGAAAAAGA
627910 AAAAAAGAAGAAA-AAAA
1 AAAAAAGAAGAAAGAAAA
627927 TATGAGAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
20 8 0.15
21 20 0.38
22 25 0.47
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (21 bp):
AAAAAAGAAGAAAGAAAAAGA
Found at i:627914 original size:28 final size:28
Alignment explanation
Indices: 627846--627904 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
627836 CTTAAAATAT
627846 AAAAAAGAAGAAAGAAAAAGAAGAAAAAG
1 AAAAAAGAA-AAAGAAAAAGAAGAAAAAG
*
627875 AAAAAAGAAAAAGAAAAATAAGAAAAAG
1 AAAAAAGAAAAAGAAAAAGAAGAAAAAG
627903 AA
1 AA
627905 GAGGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (28 bp):
AAAAAAGAAAAAGAAAAAGAAGAAAAAG
Found at i:627917 original size:11 final size:11
Alignment explanation
Indices: 627846--627926 Score: 73
Period size: 11 Copynumber: 7.5 Consensus size: 11
627836 CTTAAAATAT
627846 AAAAAAGAAGA
1 AAAAAAGAAGA
*
627857 AAGAAA-AAGA
1 AAAAAAGAAGA
627867 AGAAAAAGAA-A
1 A-AAAAAGAAGA
627878 AAAGAAA-AAGA
1 AAA-AAAGAAGA
627889 AAAATAAG-A-A
1 AAAA-AAGAAGA
* *
627899 AAAGAAGAGGA
1 AAAAAAGAAGA
627910 AAAAAAGAAGA
1 AAAAAAGAAGA
627921 AAAAAA
1 AAAAAA
627927 TATGAGAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
9 3 0.05
10 14 0.25
11 37 0.66
12 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:627924 original size:9 final size:9
Alignment explanation
Indices: 627857--627906 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
627847 AAAAAGAAGA
627857 AAGAAAAAG
1 AAGAAAAAG
627866 AAGAAAAAG
1 AAGAAAAAG
* *
627875 AAAAAAGAAA
1 AAGAAA-AAG
*
627885 AAGAAAAAT
1 AAGAAAAAG
627894 AAGAAAAAG
1 AAGAAAAAG
627903 AAGA
1 AAGA
627907 GGAAAAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:631145 original size:97 final size:98
Alignment explanation
Indices: 630965--631147 Score: 210
Period size: 97 Copynumber: 1.9 Consensus size: 98
630955 ATAAAAAAAT
* * * *
630965 ATTTATTTATTTAAAAATATCAGAAAAGAACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTTGAT
1 ATTTATTTATTTAAAAATATCAGAAAAGAACATCCAGGTGCATTAAGACAGCTCTTTTCTTCGAT
* * *
631030 ATTGATAAATATTAATTTAAATAATATTGTTTA
66 ATTAAAAAATAATAATTTAAATAATATTGTTTA
* * * * * *
631063 ATTT-TTTATTTTAAAATATCAGAATAGGACATCCAGTTGTATTAAGACTG-TCTTTTTCTTCGA
1 ATTTATTTATTTAAAAATATCAGAAAAGAACATCCAGGTGCATTAAGACAGCTC-TTTTCTTCGA
631126 TATTAAAAAATAA-ATATTTAAA
65 TATTAAAAAATAATA-ATTTAAA
631148 AATTATTATT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
96 3 0.04
97 63 0.90
98 4 0.06
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (98 bp):
ATTTATTTATTTAAAAATATCAGAAAAGAACATCCAGGTGCATTAAGACAGCTCTTTTCTTCGAT
ATTAAAAAATAATAATTTAAATAATATTGTTTA
Found at i:632633 original size:3 final size:3
Alignment explanation
Indices: 632625--632736 Score: 197
Period size: 3 Copynumber: 37.3 Consensus size: 3
632615 ATTTAATATT
*
632625 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
632673 TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
632721 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
632737 GATATGGGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:633188 original size:112 final size:112
Alignment explanation
Indices: 633057--633586 Score: 837
Period size: 112 Copynumber: 4.7 Consensus size: 112
633047 AGAGTCATTC
* * * *
633057 AAAAGGTTGAATAAATTCTTCTTATTATGAACTTCTTTTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
633122 TATGAACTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
633169 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
633234 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAAC-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
633282 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
633347 TATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
633394 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * ***
633459 CATTATGAAC-TCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAAC
63 CATTATGAACTTCT--CTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
* *
633510 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCA
633575 TTATGAACTTCT
65 TTATGAACTTCT
633587 TCTTCCTTCT
Statistics
Matches: 391, Mismatches: 19, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
112 158 0.40
113 112 0.29
114 21 0.05
115 23 0.06
116 77 0.20
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (112 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:633547 original size:225 final size:223
Alignment explanation
Indices: 633056--633586 Score: 803
Period size: 225 Copynumber: 2.3 Consensus size: 223
633046 CAGAGTCATT
* * * *
633056 CAAAAGGTTGAATAAATTCTTCTTATTATGAACTTCTTTTTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
633121 TTATGAACTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
64 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
*
633186 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
129 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGA
**
633251 AAAGATGATCCATCAAATGATGAATTCAGG
194 AAAGATGATCCATCAAATGATGAATTCAAA
*
633281 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
633346 TTATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
64 TTATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
*
633411 CTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-C
129 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TACTC
* * * *
633475 TGGCAATGTTGATCCATCAAATGATGAATTTAAA
190 TGGAAAAGATGATCCATCAAATGATGAATTCAAA
* *
633509 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGA-GTTCTTCTC
633574 ATTATGAACTTCT
63 ATTATGAACTTCT
633587 TCTTCCTTCT
Statistics
Matches: 283, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
225 157 0.55
228 102 0.36
229 24 0.08
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (223 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAA
AGATGATCCATCAAATGATGAATTCAAA
Found at i:633563 original size:24 final size:23
Alignment explanation
Indices: 633540--633612 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 23
633530 CTCATTATGA
633540 ACTTCTTCTTCCTTCTTCAGATG
1 ACTTCTTCTTCCTTCTTCAGATG
*
633563 A--TGTTCTT-C-TCATT---ATG
1 ACTTCTTCTTCCTTC-TTCAGATG
633580 AACTTCTTCTTCCTTCTTCAGATG
1 -ACTTCTTCTTCCTTCTTCAGATG
*
633604 AGTTCTTCT
1 ACTTCTTCT
633613 CATTATGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 2 0.05
20 9 0.24
21 9 0.24
22 2 0.05
23 9 0.24
24 3 0.08
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.49
Consensus pattern (23 bp):
ACTTCTTCTTCCTTCTTCAGATG
Found at i:633569 original size:41 final size:40
Alignment explanation
Indices: 633523--633626 Score: 199
Period size: 41 Copynumber: 2.6 Consensus size: 40
633513 AAGTTGAACA
633523 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
633563 ATGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 A-GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
633604 AGTTCTTCTCATTATGAACTTCT
1 AGTTCTTCTCATTATGAACTTCT
633627 CTGGAAAAGC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 23 0.37
41 40 0.63
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.48
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:634986 original size:330 final size:333
Alignment explanation
Indices: 634383--635090 Score: 1275
Period size: 330 Copynumber: 2.1 Consensus size: 333
634373 GTAGTTCCTA
* *
634383 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
*
634448 ATTTAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
634513 AACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
131 AACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
634578 CTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGAT
196 CTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGAT
* *
634643 CAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCAATGAT
261 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAACTCAATGAT
634707 TGGTTCTG-
325 TGGTTCTGT
634715 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-A-ACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634778 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
634843 AACACATTCATCTTCCACATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
131 AACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
*
634908 CTTCCAGAAGATGCTATGAACACATTCATCTTCCACATTCAATGATTGGTTCTGTCC-AACCAGA
196 CTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGA
* *
634972 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGAT
260 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAATGAT
635037 TGGTTCTGT
325 TGGTTCTGT
635046 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
635091 TGAGTCTCTT
Statistics
Matches: 364, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
330 311 0.85
331 7 0.02
332 46 0.13
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (333 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
AACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGAT
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAATGATT
GGTTCTGT
Found at i:635092 original size:83 final size:83
Alignment explanation
Indices: 634383--635090 Score: 1273
Period size: 83 Copynumber: 8.6 Consensus size: 83
634373 GTAGTTCCTA
* *
634383 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
*
634448 ATTTAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
634466 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634531 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
634549 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634614 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
634632 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634697 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
634715 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-A-ACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634778 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
634796 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634861 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
634879 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
634944 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
634962 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCC
*
635025 AAACTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
635045 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
635091 TGAGTCTCTT
Statistics
Matches: 612, Mismatches: 9, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
81 80 0.13
82 3 0.00
83 525 0.86
84 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:635906 original size:16 final size:16
Alignment explanation
Indices: 635885--635924 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
635875 GAATTTCCAA
635885 AAATAAATTG-ACTCTC
1 AAATAAATTGAACT-TC
*
635901 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
635917 AAATAAAT
1 AAATAAAT
635925 ATAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:639811 original size:18 final size:19
Alignment explanation
Indices: 639785--639821 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
639775 ATTTATGAAA
*
639785 TAAATAAATGTAAA-AATG
1 TAAAAAAATGTAAAGAATG
639803 TAAAAAAATGTAAAGAATG
1 TAAAAAAATGTAAAGAATG
639822 ATTGCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAAAAAATGTAAAGAATG
Found at i:649092 original size:3 final size:3
Alignment explanation
Indices: 649084--649177 Score: 161
Period size: 3 Copynumber: 31.3 Consensus size: 3
649074 TTAATATATT
* *
649084 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
649132 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
649178 GATATGGGTA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:651284 original size:54 final size:54
Alignment explanation
Indices: 650864--651263 Score: 545
Period size: 54 Copynumber: 7.4 Consensus size: 54
650854 CCAAAATTGA
* * * *
650864 AATTCATAAACTTATTATGAATTCCATGGATTGCACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* * *
650918 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACAGATAGTGCCAATAAGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
*
650972 AATTCACAAACTCATTATGAATTCCGTAGGTTGCACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* * * *
651026 AATTCACAAATTCATTATGAATACCGTGGGTTGCACACATAATGTCGATA-GGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
*
651079 AATTCA-ATAACTCATTATGAATGT-CGTGGGTTTCACACATAGTGCCGATATGGT
1 AATTCACA-AACTCATTATGAAT-TCCGTGGGTTGCACACATAGTGCCGATATGGT
* * * *
651133 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACACAGTACCGATATGAT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
* ** * * *
651187 AATTCACAAACACATTATGAATAACATGAGTTACACACATAGTGCCGATATGGT
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
*
651241 AATTTACAAACTCATTATGAATT
1 AATTCACAAACTCATTATGAATT
651264 TTGTGAGTTG
Statistics
Matches: 302, Mismatches: 39, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
52 1 0.00
53 46 0.15
54 254 0.84
55 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATATGGT
Found at i:651618 original size:20 final size:23
Alignment explanation
Indices: 651580--651634 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
651570 TTCAGACTGA
651580 ATAGTATCGATA-TCCCTC-T-T
1 ATAGTATCGATACTCCCTCTTCT
*
651600 ATAGTATCGATACT-TCTCTTCT
1 ATAGTATCGATACTCCCTCTTCT
*
651622 ATGGTATCGATAC
1 ATAGTATCGATAC
651635 CCACTTCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 15 0.50
21 2 0.07
22 13 0.43
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (23 bp):
ATAGTATCGATACTCCCTCTTCT
Found at i:657777 original size:54 final size:53
Alignment explanation
Indices: 657694--657983 Score: 339
Period size: 54 Copynumber: 5.4 Consensus size: 53
657684 ATTCCATGGA
* *
657694 TTGCACACATAGTG-CTGATATGGTAATTCACAAACTCGTTATGAATGACGTGGG
1 TTGCACACATAGTGTC-GATACGGTAATTCACAAACTCATTATGAAT-ACGTGGG
** * * *
657748 TTGCTTACAGAGTGTCGATACAGTAATTCAAAAACTCATTATGAATACCGTGGG
1 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATA-CGTGGG
** * *
657802 TTAAACACATAGTGTCGATACGGTAATTCACAAATTCATTATGAATTCTGTGGG
1 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATAC-GTGGG
*
657856 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATAAATGACGTGGG
1 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAAT-ACGTGGG
* * * * * *
657910 TTGCACACATAGTGCCAATACGATAATTCAAAAACTCATTATGAATTATGTGAG
1 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAA-TACGTGGG
**
657964 TTGCACATTTAGTGTCGATA
1 TTGCACACATAGTGTCGATA
657984 GTACATATAG
Statistics
Matches: 199, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.01
54 194 0.97
55 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (53 bp):
TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATACGTGGG
Found at i:659281 original size:28 final size:28
Alignment explanation
Indices: 659241--659297 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
659231 TTTCACTATA
659241 ATCACTAACCCGATGTTTGGGGTATTAC
1 ATCACTAACCCGATGTTTGGGGTATTAC
*
659269 ATCACTGACCCGATGTTTGGGGTATTAC
1 ATCACTAACCCGATGTTTGGGGTATTAC
659297 A
1 A
659298 ATTTTCCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
ATCACTAACCCGATGTTTGGGGTATTAC
Found at i:680007 original size:19 final size:20
Alignment explanation
Indices: 679970--680009 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
679960 CAATCTTTAC
679970 TTTCTCTTGATTTTCCTTTT
1 TTTCTCTTGATTTTCCTTTT
679990 TTTCTC-TGATCTTT-CTTTT
1 TTTCTCTTGAT-TTTCCTTTT
680009 T
1 T
680010 CTTTCACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTCTCTTGATTTTCCTTTT
Found at i:686281 original size:21 final size:19
Alignment explanation
Indices: 686243--686289 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
686233 AATTAATCCT
686243 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
686263 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
686284 A-TAATA
1 ACTAATA
686290 ATTCAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:699943 original size:28 final size:24
Alignment explanation
Indices: 699867--699947 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 24
699857 TTGAAAATGG
* * *
699867 TATCGATACCATAAAAAAGTATCAA
1 TATCAATACCATAATATA-TATCAA
699892 TATCAATACCATAATATA-AT-AA
1 TATCAATACCATAATATATATCAA
*
699914 TATCAATACCATAGTATA-AT-AA
1 TATCAATACCATAATATATATCAA
699936 TATCAATACCAT
1 TATCAATACCAT
699948 GGTAGGGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 35 0.67
23 2 0.04
25 15 0.29
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.30
Consensus pattern (24 bp):
TATCAATACCATAATATATATCAA
Found at i:699958 original size:28 final size:22
Alignment explanation
Indices: 699890--699947 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
699880 AAAAAGTATC
*
699890 AATATCAATACCATAATATAAT
1 AATATCAATACCATAGTATAAT
699912 AATATCAATACCATAGTATAAT
1 AATATCAATACCATAGTATAAT
699934 AATATCAATACCAT
1 AATATCAATACCAT
699948 GGTAGGGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.31
Consensus pattern (22 bp):
AATATCAATACCATAGTATAAT
Found at i:700376 original size:54 final size:54
Alignment explanation
Indices: 700291--700920 Score: 809
Period size: 54 Copynumber: 11.8 Consensus size: 54
700281 CTATGTGTAC
* * * *
700291 TACAGGCATTATATGTGCAACCCACGTAATTCATCATGAGTTTATGAATAACCA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
* *
700345 TAGAGGCACTATGTGTGCAACCCACGAAATTCATCAGGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
* * *
700399 TATAGGCACTATGTGTGCAACCCA-AAGAATTCCTCATGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAACCA
* * * *
700453 TACAGGCACTATGTGTGCAATCCAC-AGAATTCATCATGAGTTGGTGAACAACCG
1 TACAGGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAACCA
* * * *
700507 TACAAGCACTATGTGTGCAACCCATGAAATTCATCATGAGTTAATAAATAACCA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
* * *
700561 TACAAGCACTATGTGTGTAACCCACTG-AATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAACCCAC-GAAATTCATCATGAGTTGATGAATAACCA
* * * *
700615 TACATGCACTA----TG----CCACGGAATTCATCATGAGTTGATGAAAAATCA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
*
700661 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
* * * *
700715 TACAGGCACTATGTGTGCAACCCATGGAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
* * * *
700769 TACATGCACTATTTGTGCAACCCAC-ATAATTCATCATGAGTTGATGAAAAACCG
1 TACAGGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAACCA
*
700823 TACAGGCACTATGTGTGCAACCCAC-AGAATTCATCATGAGTTGATGAACAACCA
1 TACAGGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAACCA
*
700877 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGTGTTGA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGA
700921 GAACGGCCGT
Statistics
Matches: 509, Mismatches: 52, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.00
46 38 0.07
50 4 0.01
53 1 0.00
54 462 0.91
55 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (54 bp):
TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCA
Found at i:700788 original size:262 final size:262
Alignment explanation
Indices: 700304--700889 Score: 802
Period size: 262 Copynumber: 2.2 Consensus size: 262
700294 AGGCATTATA
* * *
700304 TGTGCAACCCAC-GTAATTCATCATGAGTTTATGAATAACCATAGAGGCACTATGTGTGCAACCC
1 TGTGCAACCCACAG-AATTCATCATGAGTTGATGAACAACCATACAGGCACTA----TG----CC
* * *
700368 ACGAAATTCATCAGGAGTTGATGAATAACCATATAGGCACTATGTGTGCAACCCAAAGAATTCCT
57 ACGAAATTCATCAGGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCAAAGAATTCAT
* *
700433 CATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAATCCACAGAATTCATCATGAGTTGGT
122 CATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGAT
*
700498 GAACAACCGTACAAGCACTATGTGTGCAACCCATGA-AATTCATCATGAGTTAAT-AAATAACCA
187 GAACAACCGTACAAGCACTATGTGTGCAACCCA-CATAATTCATCATGAGTTAATGAAA-AACCA
700561 TACAAGCACTATG
250 TACAAGCACTATG
* * * * * *
700574 TGTGTAACCCACTGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGCCACGGAATTC
1 TGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACCATACAGGCACTATGCCACGAAATTC
* * *
700639 ATCATGAGTTGATGAAAAATCATACAGGCACTATGTGTGCAACCC-ACGAAATTCATCATGAGTT
66 ATCAGGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCAAAG-AATTCATCATGAGTT
* **
700703 GATGAATAACCGTACAGGCACTATGTGTGCAACCCATGGAATTCATCATGAGTTGATGAACAACC
130 GATGAATAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACC
* * * * *
700768 GTACATGCACTATTTGTGCAACCCACATAATTCATCATGAGTTGATGAAAAACCGTACAGGCACT
195 GTACAAGCACTATGTGTGCAACCCACATAATTCATCATGAGTTAATGAAAAACCATACAAGCACT
700833 ATG
260 ATG
700836 TGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACCATACAGGCACTATG
1 TGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACCATACAGGCACTATG
700890 TGTGCAACCC
Statistics
Matches: 284, Mismatches: 28, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
261 3 0.01
262 230 0.81
263 3 0.01
266 2 0.01
270 45 0.16
271 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (262 bp):
TGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACCATACAGGCACTATGCCACGAAATTC
ATCAGGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCAAAGAATTCATCATGAGTTG
ATGAATAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGATGAACAACCG
TACAAGCACTATGTGTGCAACCCACATAATTCATCATGAGTTAATGAAAAACCATACAAGCACTA
TG
Found at i:700891 original size:316 final size:316
Alignment explanation
Indices: 700312--700920 Score: 943
Period size: 316 Copynumber: 1.9 Consensus size: 316
700302 TATGTGCAAC
* * * *
700312 CCACGTAATTCATCATGAGTTTATGAATAACCATAGAGGCACTATGTGTGCAACCCACGAAATTC
1 CCACGGAATTCATCATGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCACGAAATTC
* *
700377 ATCAGGAGTTGATGAATAACCATATAGGCACTATGTGTGCAACCCAAAGAATTCCTCATGAGTTG
66 ATCAGGAGTTGATGAATAACCATACAGGCACTATGTGTGCAACCCAAAGAATTCATCATGAGTTG
* * * *
700442 ATGAATAACCATACAGGCACTATGTGTGCAATCCACAGAATTCATCATGAGTTGGTGAACAACCG
131 ATGAACAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGATGAAAAACCG
* *
700507 TACAAGCACTATGTGTGCAACCCATGAAATTCATCATGAGTTAATAAATAACCATACAAGCACTA
196 TACAAGCACTATGTGTGCAACCCAAGAAATTCATCATGAGTTAATAAACAACCATACAAGCACTA
*
700572 TGTGTGTAACCCACTG-AATTCATCATGAGTTGATGAATAACCGTACATGCACTATG
261 TGTGTGCAACCCAC-GAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATG
*
700628 CCACGGAATTCATCATGAGTTGATGAAAAATCATACAGGCACTATGTGTGCAACCCACGAAATTC
1 CCACGGAATTCATCATGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCACGAAATTC
* * **
700693 ATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAACCCATGGAATTCATCATGAGTTG
66 ATCAGGAGTTGATGAATAACCATACAGGCACTATGTGTGCAACCCAAAGAATTCATCATGAGTTG
* * * *
700758 ATGAACAACCGTACATGCACTATTTGTGCAACCCACATAATTCATCATGAGTTGATGAAAAACCG
131 ATGAACAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGATGAAAAACCG
* * * *
700823 TACAGGCACTATGTGTGCAACCCACAG-AATTCATCATGAGTTGATGAACAACCATACAGGCACT
196 TACAAGCACTATGTGTGCAACCCA-AGAAATTCATCATGAGTTAATAAACAACCATACAAGCACT
*
700887 ATGTGTGCAACCCACGAAATTCATCATGTGTTGA
260 ATGTGTGCAACCCACGAAATTCATCATGAGTTGA
700921 GAACGGCCGT
Statistics
Matches: 264, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
315 1 0.00
316 262 0.99
317 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (316 bp):
CCACGGAATTCATCATGAGTTGATGAAAAACCATACAGGCACTATGTGTGCAACCCACGAAATTC
ATCAGGAGTTGATGAATAACCATACAGGCACTATGTGTGCAACCCAAAGAATTCATCATGAGTTG
ATGAACAACCATACAGGCACTATGTGTGCAACCCACAGAATTCATCATGAGTTGATGAAAAACCG
TACAAGCACTATGTGTGCAACCCAAGAAATTCATCATGAGTTAATAAACAACCATACAAGCACTA
TGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATG
Found at i:701430 original size:25 final size:24
Alignment explanation
Indices: 701377--701429 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
701367 AAATTAAGAT
701377 GTTTTATAAAAGAAATTTTTTACA
1 GTTTTATAAAAGAAATTTTTTACA
701401 GTTTTATAAAAGAAATTTTTTACA
1 GTTTTATAAAAGAAATTTTTTACA
701425 GTTTT
1 GTTTT
701430 TCAAATGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
GTTTTATAAAAGAAATTTTTTACA
Found at i:707803 original size:54 final size:54
Alignment explanation
Indices: 707486--707829 Score: 435
Period size: 54 Copynumber: 6.4 Consensus size: 54
707476 CTATTTGTAC
* *
707486 TACATGCACTGTGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACTG
1 TACATGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
* *
707540 TACA-GACACTATGTGTACAACCCACGAAATTCATCATGAGTTGATGAATAACTG
1 TACATG-CACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
*
707594 TACA-GCACTATGTGTGCAACCCAC-ATAATTCATCATGAGTTGATGAATAATCG
1 TACATGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAACCG
* * * * *
707647 TACAGGCACTATGTGCGCAACCAACAAAATTCATCATCAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
* ** * *
707701 TATATGCACTATGTGTGCAACCCAAAAAATTCATCACT-AGTTGATGAACAACCA
1 TACATGCACTATGTGTGCAACCCACGAAATTCATCA-TGAGTTGATGAATAACCG
* ***
707755 TACATGCACTATGTGTGCAACCCACGAAATTCATCATGTGTTGATGAACGTCCG
1 TACATGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
* * *
707809 TATAGGCACTACGTGTGCAAC
1 TACATGCACTATGTGTGCAAC
707830 TTAATAAATT
Statistics
Matches: 258, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.00
53 49 0.19
54 206 0.80
55 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (54 bp):
TACATGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACCG
Found at i:709700 original size:19 final size:20
Alignment explanation
Indices: 709660--709697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
709650 GAAGACATTG
709660 AGGAACAAATTTTCTTGCCA
1 AGGAACAAATTTTCTTGCCA
709680 AGGAA-AAATTTATCTTGC
1 AGGAACAAATTT-TCTTGC
709698 AAGTCTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
AGGAACAAATTTTCTTGCCA
Found at i:712716 original size:20 final size:20
Alignment explanation
Indices: 712691--712730 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
712681 TCGCAAAGCC
*
712691 ATAATTTATCCTTGAGAGCA
1 ATAATTCATCCTTGAGAGCA
712711 ATAATTCATCCTTGAGAGCA
1 ATAATTCATCCTTGAGAGCA
712731 TTAGAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATAATTCATCCTTGAGAGCA
Found at i:713674 original size:20 final size:21
Alignment explanation
Indices: 713649--713695 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
713639 ATTGCGAGAA
713649 GGGAGAATTCACGATGA-GGT
1 GGGAGAATTCACGATGAGGGT
713669 GGGAGAATTCACGATGAGGGT
1 GGGAGAATTCACGATGAGGGT
713690 GGGAGA
1 GGGAGA
713696 TCAAAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.30, C:0.09, G:0.45, T:0.17
Consensus pattern (21 bp):
GGGAGAATTCACGATGAGGGT
Found at i:740753 original size:42 final size:42
Alignment explanation
Indices: 740701--740782 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
740691 AAAAATAAGC
* *
740701 AAATCATTCGAGCCATCAGTAAATCTTTCAAGCATGATGATT
1 AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGATT
* * * *
740743 AAATCCTTCGAGTCATCAGTCATTCTCTCAAGCAAGATGA
1 AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGA
740783 CAAGTCCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (42 bp):
AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGATT
Found at i:741457 original size:44 final size:45
Alignment explanation
Indices: 741417--741558 Score: 200
Period size: 44 Copynumber: 3.2 Consensus size: 45
741407 TTTTTTGTTT
* * * *
741417 GATTCCATCATACAAGGAGTTGGATTAGCATCACTC-TTTTGGTC
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
* *
741461 GATTCCATCACATAAGGAGTTGGATCAACATCAC-CATTTCGCTC
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
*
741505 GATTCCATCACATAAGGAGTTGGATTAACATCA-TCATTTTGCTT
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
741549 GATTCCATCA
1 GATTCCATCA
741559 AAAAGGAAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.01
44 86 0.99
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
Found at i:744685 original size:20 final size:20
Alignment explanation
Indices: 744660--744732 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
744650 AAAAAAAAAT
*
744660 TGGTCTTCATACCGAGGGAC
1 TGGTCTCCATACCGAGGGAC
***
744680 TGGTCTCCATACCGAAAAAC
1 TGGTCTCCATACCGAGGGAC
744700 TGGTCTCCATACC-AGAGGAC
1 TGGTCTCCATACCGAG-GGAC
*
744720 TGGTATCCATACC
1 TGGTCTCCATACC
744733 AAAGATTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TGGTCTCCATACCGAGGGAC
Found at i:744698 original size:40 final size:39
Alignment explanation
Indices: 744654--744740 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
744644 CGTACCAAAA
* *
744654 AAAAATTGGTCTTCATACC-GAGGGACTGGTCTCCATACC
1 AAAAATTGGTCTCCATACCAGA-GGACTGGTATCCATACC
*
744693 GAAAAACTGGTCTCCATACCAGAGGACTGGTATCCATACC
1 -AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
*
744733 AAAGATTG
1 AAAAATTG
744741 AGTATACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 6 0.15
40 33 0.80
41 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (39 bp):
AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
Found at i:744751 original size:40 final size:41
Alignment explanation
Indices: 744667--744753 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 41
744657 AATTGGTCTT
* * *
744667 CATACC-GAGGGACTGGTCTCCATACCGAAAAACTGGTCTC
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
* *
744707 CATACCAGA-GGACTGGTATCCATACC-AAAGATTGAGTATA
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTG-GTATA
744747 CATACCA
1 CATACCA
744754 AAGGCTTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.15
40 32 0.80
41 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (41 bp):
CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
Found at i:745485 original size:18 final size:20
Alignment explanation
Indices: 745462--745507 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
745452 TTTTTGGTGC
745462 CGATACTCAA-GG-GAGTAT
1 CGATACTCAAGGGAGAGTAT
745480 CGATAC-CAAGGGTAGAGTAT
1 CGATACTCAAGGG-AGAGTAT
745500 CGATACTC
1 CGATACTC
745508 CCCATAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
20 12 0.50
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (20 bp):
CGATACTCAAGGGAGAGTAT
Found at i:745588 original size:19 final size:20
Alignment explanation
Indices: 745561--745605 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
745551 GCTAGTTTTT
* * *
745561 GTATTGATACTCAA-GGTGA
1 GTATCGATACCCAAGGGTCA
745580 GTATCGATACCCAAGGGTCA
1 GTATCGATACCCAAGGGTCA
745600 GTATCG
1 GTATCG
745606 TCACTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCAAGGGTCA
Found at i:746889 original size:30 final size:30
Alignment explanation
Indices: 746853--746982 Score: 242
Period size: 30 Copynumber: 4.3 Consensus size: 30
746843 GTAAGCCACT
* *
746853 AAACTTTCTAGGTTTACGGAAAATGTCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
746883 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
746913 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
746943 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
746973 AAACTTTCTA
1 AAACTTTCTA
746983 AATTTGTAAT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
AAACTTTCTAGGTTTATGGAAAATGGCTCC
Found at i:748856 original size:47 final size:46
Alignment explanation
Indices: 748780--748911 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 46
748770 AAAATAATAT
*
748780 AAAAT-CTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
1 AAAATACT-TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC
* *
748826 AAAATA-TTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATC
1 AAAATACTTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACC
*
748873 AATATACTTT-CCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 AAAATACTTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
748912 GCATACTTAC
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
43 20 0.26
44 3 0.04
45 9 0.12
46 8 0.10
47 34 0.44
48 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (46 bp):
AAAATACTTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC
Found at i:749810 original size:14 final size:14
Alignment explanation
Indices: 749791--749835 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
749781 AATTTTCATC
*
749791 TTTTTAAATTTATT
1 TTTTTAAATATATT
* * *
749805 TTTTTAAAAAAATA
1 TTTTTAAATATATT
749819 TTTTTAAATATATT
1 TTTTTAAATATATT
749833 TTT
1 TTT
749836 AGATATTTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAAATATATT
Found at i:750483 original size:21 final size:21
Alignment explanation
Indices: 750457--750715 Score: 241
Period size: 21 Copynumber: 12.4 Consensus size: 21
750447 TCGAAGTCCG
*
750457 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
*
750478 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
750499 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* * *
750520 CGTTGCGA--TAGTCGAAGTCCA
1 CGTTGCGATTTATTCCAAGT--T
*
750541 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
*
750562 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
750581 CGCGTTGCAATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
* *
750604 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
750623 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
*
750646 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* *
750665 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
750684 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
750707 CGTTGCGAT
1 CGTTGCGAT
750716 AGTCCAAAAT
Statistics
Matches: 198, Mismatches: 24, Indels: 32
0.78 0.09 0.13
Matches are distributed among these distances:
19 53 0.27
21 112 0.57
23 33 0.17
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:750516 original size:42 final size:40
Alignment explanation
Indices: 750457--750673 Score: 290
Period size: 42 Copynumber: 5.2 Consensus size: 40
750447 TCGAAGTCCG
* *
750457 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTT
* * *
750499 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT--T
750541 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
* * *
750581 CGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
750623 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
750665 CGTTGCGAT
1 CGTTGCGAT
750674 AGTCGAAGTT
Statistics
Matches: 157, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
40 16 0.10
42 141 0.90
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
Found at i:750587 original size:84 final size:82
Alignment explanation
Indices: 750446--750673 Score: 375
Period size: 84 Copynumber: 2.7 Consensus size: 82
750436 GTCCAAGTTC
* *
750446 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTA
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCGTTGCGATTTA
750511 TTCCAAGTTCGTTGCGATA
64 TTCCAAGTTCGTTGCGATA
* *
750530 GTCGAAGTCCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTA
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTA
750595 TTCCAAGTTCGTTGCGATA
64 TTCCAAGTTCGTTGCGATA
*
750614 GTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGAT
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGAT
750674 AGTCGAAGTT
Statistics
Matches: 135, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
82 17 0.13
84 118 0.87
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (82 bp):
GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATTTATT
CCAAGTTCGTTGCGATA
Found at i:750675 original size:61 final size:61
Alignment explanation
Indices: 750499--750722 Score: 258
Period size: 61 Copynumber: 3.6 Consensus size: 61
750489 ATTCCAAATT
* * * * * *
750499 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCACGTTGCGATTTATTCCAAATT--
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT--TCGTTGCGA--TAGTCGAAGTTCG
* * * *
750562 CGTTGCGA--TAGTCCAAGTTCGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
750625 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
750686 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
750723 AATCGCAACG
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
61 86 0.61
63 38 0.27
65 17 0.12
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (61 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
Done.