Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008015.1 Hibiscus syriacus cultivar Beakdansim tig00110481_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: 961110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:663360 original size:26 final size:26
Alignment explanation
Indices: 663301--663352 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
663291 TTGAGACTTT
*
663301 ACCCGCCCCGCATCCGCCCCGCATCC
1 ACCCGCCCCGCATCCGCCCCGCACCC
663327 ACCCGCCCCGCATCCG-CCCGC-CCC
1 ACCCGCCCCGCATCCGCCCCGCACCC
663351 AC
1 AC
663353 ATCCGCCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.16
25 5 0.20
26 16 0.64
ACGTcount: A:0.12, C:0.67, G:0.15, T:0.06
Consensus pattern (26 bp):
ACCCGCCCCGCATCCGCCCCGCACCC
Found at i:675385 original size:29 final size:30
Alignment explanation
Indices: 675313--675386 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
675303 GGATTTAACG
*
675313 GTTCAGTGGTATAATTGAAACGAAAATCAAA
1 GTTCAGTGGTATAATTG-AACGAAAATAAAA
*
675344 GTTCAGTGCTATAATTG-AC-AAAATTAAAA
1 GTTCAGTGGTATAATTGAACGAAAA-TAAAA
*
675373 GTTCAATGGTATAA
1 GTTCAGTGGTATAA
675387 ACGATACAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 18 0.47
31 16 0.42
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (30 bp):
GTTCAGTGGTATAATTGAACGAAAATAAAA
Found at i:693275 original size:2 final size:2
Alignment explanation
Indices: 693268--693319 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
693258 CGATAGAAGC
693268 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
693310 AT AT AT AT AT
1 AT AT AT AT AT
693320 GCTATTCGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:705034 original size:130 final size:130
Alignment explanation
Indices: 704886--705156 Score: 461
Period size: 130 Copynumber: 2.1 Consensus size: 130
704876 GCATATATAT
* * *
704886 ATATATATATATGGATGGATTCGAGGAAGCGGAATCACGACTCTTAAAAAATTTAAATTTTTAGT
1 ATATATATAGATGGATGGATTCGAGGAAGCGGAATCACGACTCTTAAAAAAATTAAATTCTTAGT
* * *
704951 TTAAGTATTTTCTTTGTTCCTAAATATTTAAATTTATCTCTAAGATAAAATTTTACGTTCATTAC
66 TTAAGTATTTTCTTTGTTCCTAAATATTTAAATTTATCTCTAACATAAAATTTTACATTCATAAC
* *
705016 ATATATATGGATGGATGGATTTGAGGAAGCGGAATCACGACTCTTAAAAAAATTAAATTCTTAGT
1 ATATATATAGATGGATGGATTCGAGGAAGCGGAATCACGACTCTTAAAAAAATTAAATTCTTAGT
*
705081 TTAAGTATTTTCTTTGTTCCTAAATATTTAAATTTATCTCTAACATAAAATTTTACATTCATAAT
66 TTAAGTATTTTCTTTGTTCCTAAATATTTAAATTTATCTCTAACATAAAATTTTACATTCATAAC
705146 ATATATATAGA
1 ATATATATAGA
705157 GAGAGAGAGA
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (130 bp):
ATATATATAGATGGATGGATTCGAGGAAGCGGAATCACGACTCTTAAAAAAATTAAATTCTTAGT
TTAAGTATTTTCTTTGTTCCTAAATATTTAAATTTATCTCTAACATAAAATTTTACATTCATAAC
Found at i:706904 original size:28 final size:27
Alignment explanation
Indices: 706859--706912 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
706849 CAAATGAGCG
706859 AAATTATTTTTTTCAAGTTCAAGGGTC
1 AAATTATTTTTTTCAAGTTCAAGGGTC
*
706886 AAATTGATTTTTTTTAAGTTCAAGGGT
1 AAATT-ATTTTTTTCAAGTTCAAGGGT
706913 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (27 bp):
AAATTATTTTTTTCAAGTTCAAGGGTC
Found at i:707411 original size:14 final size:16
Alignment explanation
Indices: 707381--707417 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
707371 TTTTATAGTA
707381 AATATTTATTAATTTT
1 AATATTTATTAATTTT
707397 AATATTTA-T-ATTTT
1 AATATTTATTAATTTT
707411 AATATTT
1 AATATTT
707418 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTTATTAATTTT
Found at i:715946 original size:4 final size:4
Alignment explanation
Indices: 715937--715967 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
715927 TTATTCTTAT
715937 TAAA TAAA TAAA TAAA TAAA TAAA T-AA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
715968 AAGGATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:719217 original size:6 final size:6
Alignment explanation
Indices: 719206--719242 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
719196 GTGTCGAAGA
719206 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC C
719243 CGAGCCGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:724324 original size:19 final size:18
Alignment explanation
Indices: 724270--724330 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
724260 ATTCTATTGA
724270 TTATATTTTTAAAAAATAT
1 TTATATTTTTAAAAAAT-T
* **
724289 TTAT-TATTTAATTAATT
1 TTATATTTTTAAAAAATT
724306 TTATATTCTTTAAAAAATT
1 TTATATT-TTTAAAAAATT
*
724325 TAATAT
1 TTATAT
724331 ATATATTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 5 0.15
18 10 0.30
19 18 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTTTTAAAAAATT
Found at i:728749 original size:16 final size:16
Alignment explanation
Indices: 728728--728760 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
728718 AGCCGATAGA
728728 TGGCGTGCCCACGCCT
1 TGGCGTGCCCACGCCT
728744 TGGCGTGCCCACGCCT
1 TGGCGTGCCCACGCCT
728760 T
1 T
728761 AACTGGAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.42, G:0.30, T:0.21
Consensus pattern (16 bp):
TGGCGTGCCCACGCCT
Found at i:728832 original size:54 final size:54
Alignment explanation
Indices: 728747--728869 Score: 178
Period size: 54 Copynumber: 2.3 Consensus size: 54
728737 CACGCCTTGG
* * *
728747 CGTGCCCACGCCTTAACTGGAGACTTTTTCTGTGGTAGCTC-AGGATGGATAAGA-
1 CGTGCCCACGCCTTAACTGAAGACTTCTTCTGTGGTAGCTCGA-GATGAATAA-AC
*
728801 CGTGCCCACGCCTTAACTGAAGACTTCTTCTGTGTTAGCTCGAGATGAATAAAC
1 CGTGCCCACGCCTTAACTGAAGACTTCTTCTGTGGTAGCTCGAGATGAATAAAC
728855 CGTGCCCACGCCTTA
1 CGTGCCCACGCCTTA
728870 TGTTAGAGCC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
53 1 0.02
54 61 0.97
55 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (54 bp):
CGTGCCCACGCCTTAACTGAAGACTTCTTCTGTGGTAGCTCGAGATGAATAAAC
Found at i:737042 original size:18 final size:17
Alignment explanation
Indices: 737015--737058 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
737005 GGATAATGCA
*
737015 TTTTATGATAAAATTAGAT
1 TTTTA-GATAAAA-TACAT
*
737034 TTTTAGATAACATACAT
1 TTTTAGATAAAATACAT
737051 TTTTAGAT
1 TTTTAGAT
737059 GTATTAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 6 0.26
19 5 0.22
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (17 bp):
TTTTAGATAAAATACAT
Found at i:738773 original size:36 final size:38
Alignment explanation
Indices: 738724--738800 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
738714 ATAATATTAC
738724 AAATTCTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTCTAAAATATTTATATAATTTTCTTTAAAAAATT
* * *
738761 AAATTC-ATAATATTTATATAATTTTTTTTACAAAATT
1 AAATTCTAAAATATTTATATAATTTTCTTTAAAAAATT
738798 AAA
1 AAA
738801 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 12 0.33
37 24 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (38 bp):
AAATTCTAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:740985 original size:2 final size:2
Alignment explanation
Indices: 740978--741032 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
740968 TTGTTTGTAT
* *
740978 TA TA TA TA -A T- TA -A TA TA AA AA TA TA -A TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
741015 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
741033 ATCGGGGCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:741004 original size:13 final size:14
Alignment explanation
Indices: 740978--741034 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
740968 TTGTTTGTAT
*
740978 TATATATAAT-TAA
1 TATATAAAATATAA
740991 TATA-AAAATATAA
1 TATATAAAATATAA
*
741004 TATATATAATATATA
1 TATATAAAATATA-A
*
741019 TATATATATATATAA
1 TATATA-AAATATAA
741034 T
1 T
741035 CGGGGCAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 11 0.31
14 7 0.19
15 9 0.25
16 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAAAATATAA
Found at i:741010 original size:17 final size:18
Alignment explanation
Indices: 740981--741030 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
740971 TTTGTATTAT
740981 ATATAAT-TAATATAA-AA
1 ATATAATAT-ATATAATAA
*
740998 ATATAATATATATAATAT
1 ATATAATATATATAATAA
741016 ATATATATATATATA
1 ATATA-ATATATATA
741031 TAATCGGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.45
18 7 0.24
19 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATATATATAATAA
Found at i:741028 original size:26 final size:25
Alignment explanation
Indices: 740978--741034 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
740968 TTGTTTGTAT
740978 TATATATAATTAATATAAAAATATA
1 TATATATAATTAATATAAAAATATA
* *
741003 -ATATAT-A-TAATATATATATATA
1 TATATATAATTAATATAAAAATATA
741025 TATATATAAT
1 TATATATAAT
741035 CGGGGCAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 13 0.48
23 7 0.26
24 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TATATATAATTAATATAAAAATATA
Found at i:743293 original size:29 final size:29
Alignment explanation
Indices: 743245--743312 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
743235 CGTACATCAT
* * * *
743245 TCATTATTTGTTAATTGATCGATCGTTGC
1 TCATTGTTTGTTAATCGATCAACCGTTGC
*
743274 TCATTGTTTGTTTATCGATCAACCGTTGC
1 TCATTGTTTGTTAATCGATCAACCGTTGC
*
743303 TCATGGTTTG
1 TCATTGTTTG
743313 ATTGAAGCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (29 bp):
TCATTGTTTGTTAATCGATCAACCGTTGC
Found at i:743541 original size:15 final size:15
Alignment explanation
Indices: 743492--743543 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
743482 TATTGTTTTA
743492 TATATTAATATTATT
1 TATATTAATATTATT
* *
743507 TATTATATAAGAGTATTT
1 TA-TAT-TAATATTA-TT
743525 TATATTAATATTATT
1 TATATTAATATTATT
743540 TATA
1 TATA
743544 GTATCTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 8 0.27
16 9 0.30
17 9 0.30
18 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TATATTAATATTATT
Found at i:744522 original size:2 final size:2
Alignment explanation
Indices: 744515--744543 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
744505 ATTAATTATG
744515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
744544 GTATGCACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:747314 original size:21 final size:21
Alignment explanation
Indices: 747290--747335 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
747280 TCTATTATTC
747290 TTTAACCTTAAATTTATCGTT
1 TTTAACCTTAAATTTATCGTT
747311 TTTAACCTTAAATTTATCGTT
1 TTTAACCTTAAATTTATCGTT
747332 TTTA
1 TTTA
747336 TTGACTGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAACCTTAAATTTATCGTT
Found at i:753790 original size:33 final size:33
Alignment explanation
Indices: 753748--753811 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
753738 TTTATCCACC
753748 ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
1 ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
753781 ATCTGTGCAAGACAAAGGGAAACAGAGCACA
1 ATCTGTGCAAGACAAAGGGAAACAGAGCACA
753812 GCAAACGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.09
Consensus pattern (33 bp):
ATCTGTGCAAGACAAAGGGAAACAGAGCACACA
Found at i:754358 original size:43 final size:43
Alignment explanation
Indices: 754311--754653 Score: 201
Period size: 44 Copynumber: 8.0 Consensus size: 43
754301 ATAAAAGTAT
*
754311 GATTAAAAAAATTAGGGGTCTCAATTTTAAAGATAAAAAATGA
1 GATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
** * * * * *
754354 GATTAAAAAAAATTAGATGCCTTAATTTTAAAGGTAAAAAGTGA
1 GATT-AAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
* * * * * **
754398 -ATTAAAAAAAATATGGGCCTCAATTGTAAAGGTAAAATGTGA
1 GATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
* * *
754440 TATTGAAAAAAATTATGAGT-TCAATTATAAAGATAAAAAATGA
1 GATT-AAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
* * * *
754483 GTTTGAAAAAATTA-GGGTCATCAATTATAAATATAAAAAATTA
1 GATTAAAAAAATTAGGGGTC-TCAATTATAAAGATAAAAAATGA
* *** * * * *
754526 GGATTGAAAAAATTAATAGTCCCAATTATCAAGATAAAAAGTGT
1 -GATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
* * *** * * *
754570 GACT-ACAAAATTAGGAACCTTAATTATAAATATAAAAAATAA
1 GATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
* * * ** *
754612 AATTGAAGAAAATGA-AAGTACTCAATTATAAAAATAAAAAAT
1 GATT-AAAAAAATTAGGGGT-CTCAATTATAAAGATAAAAAAT
754654 AGAGTCCTTA
Statistics
Matches: 233, Mismatches: 57, Indels: 19
0.75 0.18 0.06
Matches are distributed among these distances:
41 3 0.01
42 69 0.30
43 56 0.24
44 102 0.44
45 3 0.01
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (43 bp):
GATTAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAATGA
Found at i:754392 original size:86 final size:82
Alignment explanation
Indices: 754309--754565 Score: 216
Period size: 86 Copynumber: 3.0 Consensus size: 82
754299 TTATAAAAGT
* *
754309 ATGATTAAAAAAATTAGGGGTCTCAATTTTAAAGATAAAAAATGAGATTAAAAAAAATTA-GATG
1 ATGATTAAAAAAATTA-GGGTCTCAATTATAAAGATAAAAAATGAGATTGAAAAAAATTATGA-G
* *
754373 CCTT-AATTTTAAAGGTAAAA
64 --TTCAATTATAAAGATAAAA
* * * * ** *
754393 AGTGAATTAAAAAAAATATGGGCCTCAATTGTAAAGGTAAAATGTGATATTGAAAAAAATTATGA
1 A-TG-ATTAAAAAAATTA-GGGTCTCAATTATAAAGATAAAAAATGAGATTGAAAAAAATTATGA
754458 GTTCAATTATAAAGATAAAAA
63 GTTCAATTATAAAGAT-AAAA
* * *
754479 ATGAGTTTGAAAAAATTAGGGTCATCAATTATAAATATAAAAAATTAGGATTG-AAAAAATTAAT
1 ATGA--TTAAAAAAATTAGGGTC-TCAATTATAAAGATAAAAAATGA-GATTGAAAAAAATT-AT
* *
754543 -AGTCCCAATTATCAAGATAAAA
61 GAGT-TCAATTATAAAGATAAAA
754565 A
1 A
754566 GTGTGACTAC
Statistics
Matches: 139, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
84 4 0.03
85 18 0.13
86 97 0.70
87 20 0.14
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.29
Consensus pattern (82 bp):
ATGATTAAAAAAATTAGGGTCTCAATTATAAAGATAAAAAATGAGATTGAAAAAAATTATGAGTT
CAATTATAAAGATAAAA
Found at i:760282 original size:18 final size:18
Alignment explanation
Indices: 760259--760297 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
760249 TATAAGTATA
* *
760259 ATTTAAGAATATATTACT
1 ATTTAAAAATATATTAAT
760277 ATTTAAAAATATATTAAT
1 ATTTAAAAATATATTAAT
760295 ATT
1 ATT
760298 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTAAAAATATATTAAT
Found at i:760860 original size:20 final size:20
Alignment explanation
Indices: 760823--760874 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
760813 ATTCGCGTTG
760823 CATTTCGCGTTGAGA-TTTT
1 CATTTCGCGTTGAGATTTTT
760842 CTATTTCGCGTTGTA-ATTTTT
1 C-ATTTCGCGTTG-AGATTTTT
*
760863 CATTTCACGTTG
1 CATTTCGCGTTG
760875 CGATAGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 22 0.76
21 6 0.21
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (20 bp):
CATTTCGCGTTGAGATTTTT
Found at i:760916 original size:22 final size:21
Alignment explanation
Indices: 760870--760984 Score: 92
Period size: 22 Copynumber: 5.4 Consensus size: 21
760860 TTTCATTTCA
* *
760870 CGTTGCGATAGT-TGAAAATCG
1 CGTTGCGATAGTCT-ACAATTG
*
760891 CGTTGCGATAGTCTACATTTCG
1 CGTTGCGATAGTCTACAATT-G
* *
760913 CGTTGCGGTAGTCTACAGTTG
1 CGTTGCGATAGTCTACAATTG
** *
760934 TCGTTGCGATTTTCCA-AATT-
1 -CGTTGCGATAGTCTACAATTG
*
760954 CGTTGCGATAGTCTACAGTTG
1 CGTTGCGATAGTCTACAATTG
760975 TCGTTGCGAT
1 -CGTTGCGAT
760985 TTTCCAAATT
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.16
20 3 0.04
21 19 0.26
22 40 0.54
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAATTG
Found at i:760958 original size:19 final size:19
Alignment explanation
Indices: 760934--761002 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
760924 TCTACAGTTG
760934 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
760953 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
760974 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
760994 TCGTTGCGA
1 TCGTTGCGA
761003 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:760966 original size:41 final size:41
Alignment explanation
Indices: 760913--761002 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
760903 CTACATTTCG
*
760913 CGTTGCGGTAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
760954 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
760995 CGTTGCGA
1 CGTTGCGA
761003 AAATTCGTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:761730 original size:19 final size:19
Alignment explanation
Indices: 761706--761815 Score: 67
Period size: 19 Copynumber: 5.5 Consensus size: 19
761696 CAACGAATTT
761706 TCGCAACGAATTTAGAAAA
1 TCGCAACGAATTTAGAAAA
* **
761725 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTAGAAAA
* * **
761747 TCGCAACAAAAAATGTAGACTA
1 TCGCAAC---GAATTTAGAAAA
*
761769 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTAGAAAA
* * *
761788 TCGCCATGAATTTGGAAAA
1 TCGCAACGAATTTAGAAAA
761807 TCGCAACGA
1 TCGCAACGA
761816 CAACAGTAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
19 39 0.54
21 2 0.03
22 29 0.40
23 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTAGAAAA
Found at i:761749 original size:22 final size:22
Alignment explanation
Indices: 761724--761778 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
761714 AATTTAGAAA
* *
761724 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGAAAAATGTAGACT
*
761746 ATCGCAACAAAAAATGTAGACT
1 ATCGCAACGAAAAATGTAGACT
761768 ATCGCAACGAA
1 ATCGCAACGAA
761779 TTTGGAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (22 bp):
ATCGCAACGAAAAATGTAGACT
Found at i:763080 original size:35 final size:36
Alignment explanation
Indices: 763040--763117 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 36
763030 CATAATGATA
763040 ATATTTTAATTAAATAAAAGCGAAAGT-A-TATATTTT
1 ATATTTTAATTAAA-AAAA-CGAAAGTGACTATATTTT
*
763076 -TATTTAAATTAAAAAAACGAAAGTGACTATATTTT
1 ATATTTTAATTAAAAAAACGAAAGTGACTATATTTT
763111 ATATTTT
1 ATATTTT
763118 TCGAAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 7 0.19
34 5 0.14
35 20 0.54
36 5 0.14
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (36 bp):
ATATTTTAATTAAAAAAACGAAAGTGACTATATTTT
Found at i:763083 original size:30 final size:34
Alignment explanation
Indices: 763043--763116 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 34
763033 AATGATAATA
* *
763043 TTTTAATTAAA-T-AAAAGCGAAAGT-A-TATAT
1 TTTTATTTAAATTAAAAAACGAAAGTGACTATAT
763073 TTTTATTTAAATTAAAAAAACGAAAGTGACTATAT
1 TTTTATTTAAATT-AAAAAACGAAAGTGACTATAT
763108 TTTATATTT
1 TTT-TATTT
763117 TTCGAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 10 0.28
31 1 0.03
33 11 0.31
34 1 0.03
35 8 0.22
36 5 0.14
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (34 bp):
TTTTATTTAAATTAAAAAACGAAAGTGACTATAT
Found at i:765197 original size:27 final size:27
Alignment explanation
Indices: 765155--765222 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
765145 GTGTAGGAAT
765155 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
765180 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
765207 TATAGAGATATGATTT
1 TATAGAGATATGATTT
765223 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:768120 original size:27 final size:27
Alignment explanation
Indices: 768090--768146 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
768080 GAAAAGAAGG
768090 ACTTGTGATCAAC-CAAAGAAAATATGT
1 ACTTGTGATCAACTCAAA-AAAATATGT
**
768117 AC-T-TGATTTACTCAAAAAAATATGT
1 ACTTGTGATCAACTCAAAAAAATATGT
768142 ACTTG
1 ACTTG
768147 ATTTATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
25 17 0.68
26 6 0.24
27 2 0.08
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (27 bp):
ACTTGTGATCAACTCAAAAAAATATGT
Found at i:768136 original size:25 final size:26
Alignment explanation
Indices: 768103--768161 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 26
768093 TGTGATCAAC
768103 CAAAGAAAATATGTACTTGATTTACT
1 CAAAGAAAATATGTACTTGATTTACT
*
768129 CAAA-AAAATATGTACTTGATTTATT
1 CAAAGAAAATATGTACTTGATTTACT
768154 CAAAGAAA
1 CAAAGAAA
768162 CTGGTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (26 bp):
CAAAGAAAATATGTACTTGATTTACT
Found at i:768985 original size:27 final size:27
Alignment explanation
Indices: 768943--769037 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
768933 GTGTAGGAAT
768943 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
768968 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
768995 TATAGAGATATGATTTGTTACAATTCC
1 TATAGAGATATGATTTGTTACCATTCC
769022 TATAGAGATATGATTT
1 TATAGAGATATGATTT
769038 TGTAAATAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
25 7 0.10
27 60 0.90
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:772770 original size:27 final size:27
Alignment explanation
Indices: 772728--772795 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
772718 GTGTAGGAAT
772728 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
772753 TATAGAGATATGATTTGTTACCTTTCC
1 TATAGAGATATGATTTGTTACCATTCC
772780 TATAGAGATATGATTT
1 TATAGAGATATGATTT
772796 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:775993 original size:16 final size:16
Alignment explanation
Indices: 775970--776013 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
775960 TAAAATAAAT
775970 ATTTTTT-AAAGAGTA
1 ATTTTTTAAAAGAGTA
775985 ATTTGTTTAAAAGAGT-
1 ATTT-TTTAAAAGAGTA
*
776001 ATTATTTAAAAGA
1 ATTTTTTAAAAGA
776014 ACACAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 6 0.23
17 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (16 bp):
ATTTTTTAAAAGAGTA
Found at i:784134 original size:4 final size:4
Alignment explanation
Indices: 784127--784157 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
784117 CCAAAACTAA
784127 CTTT CTTT CTTT CTTT CTTT C-TT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
784158 TCGTCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:784159 original size:12 final size:12
Alignment explanation
Indices: 784127--784157 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
784117 CCAAAACTAA
784127 CTTTCTTTCTTT
1 CTTTCTTTCTTT
784139 CTTTCTTTC-TT
1 CTTTCTTTCTTT
784150 CTTTCTTT
1 CTTTCTTT
784158 TCGTCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTCTTTCTTT
Found at i:784531 original size:26 final size:26
Alignment explanation
Indices: 784502--784566 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
784492 TATACATAAT
784502 ATTTATATTTAATAACTTATGGA-ATA
1 ATTTATATTTAATAACTTAT-GATATA
*
784528 ATTTATTATTT-ATAATTTATGATATA
1 ATTTA-TATTTAATAACTTATGATATA
* *
784554 TTTTATTTTTAAT
1 ATTTATATTTAAT
784567 TATTCTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 6 0.18
26 22 0.67
27 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (26 bp):
ATTTATATTTAATAACTTATGATATA
Found at i:793377 original size:19 final size:18
Alignment explanation
Indices: 793353--793394 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
793343 TTTGGTTCAC
793353 AGAATGTAAGATTACCATG
1 AGAATGTAAGATTACCA-G
*
793372 AGAATGTAAGATTATCAG
1 AGAATGTAAGATTACCAG
793390 AGAAT
1 AGAAT
793395 AGAATTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (18 bp):
AGAATGTAAGATTACCAG
Found at i:795666 original size:36 final size:36
Alignment explanation
Indices: 795612--795722 Score: 172
Period size: 36 Copynumber: 3.1 Consensus size: 36
795602 CAAATTTGAA
795612 AAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
795647 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
795683 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
795719 AAAA
1 AAAA
795723 ATGATAATAG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 11 0.15
36 31 0.44
37 29 0.41
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:800260 original size:36 final size:36
Alignment explanation
Indices: 800206--800315 Score: 149
Period size: 35 Copynumber: 3.2 Consensus size: 36
800196 CAACTTTGAA
800206 AAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
800241 AAAATGGTTTTTCAAAGTTTGGTAAATG-TTCTTTG
1 AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
800276 AAAAAT-ATTTTTCAAAG-TTGGTAGATGTTT-GTTG
1 -AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
800310 AAAATG
1 AAAATG
800316 ATAATGGGAA
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
33 5 0.07
34 12 0.18
35 26 0.38
36 25 0.37
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
AAAATGGTTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:800304 original size:34 final size:35
Alignment explanation
Indices: 800199--800313 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 35
800189 TGGTAACCAA
800199 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAT--TTTTCAAAGTTTGGTAAATG-TT
*
800236 CTTTG-AAAATGGTTTTTCAAAGTTTGGTAAATGTT
1 CTTTGAAAAAT-ATTTTTCAAAGTTTGGTAAATGTT
*
800271 CTTTGAAAAATATTTTTCAAAG-TTGGTAGATGTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTT
800305 -TGTTGAAAA
1 CT-TTGAAAA
800314 TGATAATGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 11
0.84 0.04 0.13
Matches are distributed among these distances:
33 1 0.01
34 18 0.25
35 17 0.24
36 29 0.41
37 5 0.07
38 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (35 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTT
Found at i:801411 original size:24 final size:25
Alignment explanation
Indices: 801366--801412 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
801356 TTTAAGAATT
*
801366 AAAAAAGAGGTTAAATTTATGATTG
1 AAAAAAGAGGTTAAATTCATGATTG
801391 AAAAAAGAGGTTAAA-TCATGAT
1 AAAAAAGAGGTTAAATTCATGAT
801413 AAACTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.28
Consensus pattern (25 bp):
AAAAAAGAGGTTAAATTCATGATTG
Found at i:809731 original size:19 final size:20
Alignment explanation
Indices: 809707--809757 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
809697 AATGACCAAT
809707 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
809726 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
809746 AAAATCGCAACG
1 AAAATCGCAACG
809758 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:809751 original size:20 final size:20
Alignment explanation
Indices: 809707--809946 Score: 108
Period size: 20 Copynumber: 11.8 Consensus size: 20
809697 AATGACCAAT
* *
809707 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
809726 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
809746 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
809766 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
809786 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
809807 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
809830 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
809850 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
809870 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
809890 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
809910 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
809930 AGAGTCGCAACGCGATT
1 AAAATCGCAACGCGATT
809947 GACGTTGAAA
Statistics
Matches: 180, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.09
20 135 0.75
21 14 0.08
23 14 0.08
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:809947 original size:20 final size:20
Alignment explanation
Indices: 809832--809948 Score: 189
Period size: 20 Copynumber: 5.8 Consensus size: 20
809822 TTTAGAAGAA
809832 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
809852 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
809872 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
* *
809892 AATCGCAATGCGATTTATAT
1 AATCGCAATGCGATTGATAG
*
809912 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* *
809932 AGTCGCAACGCGATTGA
1 AATCGCAATGCGATTGA
809949 CGTTGAAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:810032 original size:6 final size:6
Alignment explanation
Indices: 810021--810058 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
810011 GACACGTCTT
810021 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
810059 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:810770 original size:6 final size:6
Alignment explanation
Indices: 810749--810803 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
810739 TCTCGTCTCG
810749 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
810795 GGTCGT GGT
1 GGTCGT GGT
810804 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:810898 original size:20 final size:20
Alignment explanation
Indices: 810866--810983 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 20
810856 TTAAGAAACA
*
810866 AATCGCGTTGCGATTCTCTC
1 AATCGCATTGCGATTCTCTC
* * *
810886 AGTCGCATCGCGATTTTCTTCTA
1 AATCGCATTGCGA--TTC-TCTC
* *
810909 AATCGCGTTGCGACTCTCTC
1 AATCGCATTGCGATTCTCTC
* * *
810929 AATCGCATTGCGATTATATA
1 AATCGCATTGCGATTCTCTC
*
810949 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTCTC
810969 AATCGCATTGCGATT
1 AATCGCATTGCGATT
810984 TTCTTCTAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
20 61 0.77
21 2 0.03
22 3 0.04
23 13 0.16
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTCTCTC
Found at i:810927 original size:43 final size:43
Alignment explanation
Indices: 810865--811004 Score: 196
Period size: 43 Copynumber: 3.3 Consensus size: 43
810855 CTTAAGAAAC
* *
810865 AAATCGCGTTGCGATTCTCTCAGTCGCATCGCGATTTTCTTCT
1 AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCT
* * *
810908 AAATCGCGTTGCGACTCTCTCAATCGCATTGCGA--TT-ATAT
1 AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCT
* *
810948 AAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCT
1 AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCT
810991 AAATCGCGTTGCGA
1 AAATCGCGTTGCGA
811005 ACTTGGAAGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 33 0.40
41 2 0.02
42 2 0.02
43 46 0.55
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (43 bp):
AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCT
Found at i:811081 original size:20 final size:20
Alignment explanation
Indices: 810865--811108 Score: 107
Period size: 20 Copynumber: 11.9 Consensus size: 20
810855 CTTAAGAAAC
*
810865 AAATCGCGTTGCGATTCTCT
1 AAATCGCGTTGCGATTTTCT
* * * *
810885 CAGTCGCATCGCGATTTTCTTCT
1 AAATCGCGTTGCGA--TT-TTCT
* *
810908 AAATCGCGTTGCGACTCTCT
1 AAATCGCGTTGCGATTTTCT
* * * *
810928 CAATCGCATTGCGATTATAT
1 AAATCGCGTTGCGATTTTCT
* * *
810948 AAATCGCATTGCGATTCTAT
1 AAATCGCGTTGCGATTTTCT
* *
810968 CAATCGCATTGCGATTTTCTTCT
1 AAATCGCGTTGCGA--TT-TTCT
** **
810991 AAATCGCGTTGCGAACTTGG
1 AAATCGCGTTGCGATTTTCT
*
811011 AAGCTCGCGTTGCGATTTTCT
1 AA-ATCGCGTTGCGATTTTCT
* *
811032 --TTTGACCGTTGCGATTTTCT
1 AAATCG--CGTTGCGATTTTCT
*** **
811052 TTTTAACGTTGCGATTTTCT
1 AAATCGCGTTGCGATTTTCT
*
811072 AAATCGCGTTGCGATTTT-G
1 AAATCGCGTTGCGATTTTCT
* *
811091 ATATCGCGTTGCAATTTT
1 AAATCGCGTTGCGATTTT
811109 ATTGGTCATT
Statistics
Matches: 169, Mismatches: 44, Indels: 23
0.72 0.19 0.10
Matches are distributed among these distances:
18 2 0.01
19 16 0.09
20 104 0.62
21 14 0.08
22 6 0.04
23 27 0.16
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
AAATCGCGTTGCGATTTTCT
Found at i:811098 original size:19 final size:20
Alignment explanation
Indices: 811058--811108 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
811048 TTCTTTTTAA
*
811058 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
811078 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
*
811097 CGTTGCAATTTT
1 CGTTGCGATTTT
811109 ATTGGTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:820986 original size:33 final size:32
Alignment explanation
Indices: 820949--821017 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
820939 TATCTTTTAT
820949 TATTATAATATAATTAAATATATAATAAT-AATA
1 TATTATAATATAATTAAA-AT-TAATAATCAATA
* * *
820982 TATTATTATATTATTAAAATTATTAATCAATA
1 TATTATAATATAATTAAAATTAATAATCAATA
821014 TATT
1 TATT
821018 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.19
32 10 0.31
33 16 0.50
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (32 bp):
TATTATAATATAATTAAAATTAATAATCAATA
Found at i:820992 original size:23 final size:23
Alignment explanation
Indices: 820926--820992 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
820916 TAATATTAAA
* *
820926 AATAATAATATAATATCT-TTTAT
1 AATAATAATATATTAT-TATATAT
* * *
820949 TATTATAATATAATTA-AATATAT
1 AATAATAATAT-ATTATTATATAT
820972 AATAATAATATATTATTATAT
1 AATAATAATATATTATTATAT
820993 TATTAAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 4 0.12
23 26 0.79
24 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAATAATATATTATTATATAT
Found at i:824293 original size:15 final size:16
Alignment explanation
Indices: 824275--824327 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
824265 ATGATACTTC
824275 TGATGA-ACTTGAAAA
1 TGATGATACTTGAAAA
*
824290 TGATGATACTT----C
1 TGATGATACTTGAAAA
824302 TGATGA-ACTTGAAAA
1 TGATGATACTTGAAAA
824317 TGATGATACTT
1 TGATGATACTT
824328 CTGATGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
15 12 0.40
16 8 0.27
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (16 bp):
TGATGATACTTGAAAA
Found at i:824297 original size:27 final size:27
Alignment explanation
Indices: 824262--824350 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
824252 CCTGCAAAAG
824262 ATGATGATACTTCTGATGAACTTGAAA
1 ATGATGATACTTCTGATGAACTTGAAA
824289 ATGATGATACTTCTGATGAACTTGAAA
1 ATGATGATACTTCTGATGAACTTGAAA
*
824316 ATGATGATACTTCTGATGAA-TTCGAAG
1 ATGATGATACTTCTGATGAACTT-GAAA
824343 ATGATGAT
1 ATGATGAT
824351 GATGAAACCT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 2 0.03
27 58 0.97
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (27 bp):
ATGATGATACTTCTGATGAACTTGAAA
Found at i:826717 original size:60 final size:58
Alignment explanation
Indices: 826653--826765 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 58
826643 GAATAGTCGG
*
826653 GAGACTATTTTGTAACTTTTAATAGTCGAGGTACTT-AACAAAATAACATCTTATAGTTGA
1 GAGACTATTTTGTAACTTTTAATAGTCG-GG-A-TTCAACAAAATAACACCTTATAGTTGA
* * *
826713 GAGACTATTTTGTTATTTTTAATAGTCGGGATTCAACAAAGTAACACCTTATA
1 GAGACTATTTTGTAACTTTTAATAGTCGGGATTCAACAAAATAACACCTTATA
826766 ATTGGGGACC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 2 0.04
58 18 0.38
59 2 0.04
60 26 0.54
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (58 bp):
GAGACTATTTTGTAACTTTTAATAGTCGGGATTCAACAAAATAACACCTTATAGTTGA
Found at i:834553 original size:28 final size:28
Alignment explanation
Indices: 834513--834593 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
834503 GAATGACCAC
834513 TATGTCCTGAAGGACCACATAGAACACA
1 TATGTCCTGAAGGACCACATAGAACACA
834541 TATGTCCTGAAGGACCACATAGAACACA
1 TATGTCCTGAAGGACCACATAGAACACA
* *
834569 TATGTCCCGAAAGACCACATAGAAC
1 TATGTCCTGAAGGACCACATAGAAC
834594 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (28 bp):
TATGTCCTGAAGGACCACATAGAACACA
Found at i:836018 original size:8 final size:8
Alignment explanation
Indices: 836005--836036 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
835995 GGAGCTTCAC
836005 GGGGAAGA
1 GGGGAAGA
836013 GGGGAAGA
1 GGGGAAGA
836021 GGGGAAGA
1 GGGGAAGA
*
836029 GGGAAAGA
1 GGGGAAGA
836037 AGAGAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
GGGGAAGA
Found at i:836373 original size:22 final size:21
Alignment explanation
Indices: 836343--836383 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
836333 TTTTTGTATT
* *
836343 ATATTATATTTTATATAAATAA
1 ATATCATA-TTTATAAAAATAA
836365 ATATCATATTTATAAAAAT
1 ATATCATATTTATAAAAAT
836384 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATCATATTTATAAAAATAA
Found at i:841958 original size:25 final size:25
Alignment explanation
Indices: 841930--842008 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 25
841920 AAGAGTTTAA
* *
841930 AGATGAAAGGAATGTGTTGTATAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
841955 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
* *
841980 AGATGAAAAGAGTGTGTTATGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
842005 AGAT
1 AGAT
842009 TGAAGATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTGTGTAAG
Found at i:842588 original size:17 final size:17
Alignment explanation
Indices: 842566--842621 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
842556 ACTATTAATT
842566 TAATTTTAAAAATAAAA
1 TAATTTTAAAAATAAAA
***
842583 TAA-TTTATTCATAATAA
1 TAATTTTAAAAATAA-AA
842600 T-ATTTTAAAAATAAAA
1 TAATTTTAAAAATAAAA
842616 TAATTT
1 TAATTT
842622 ATTTATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTTAAAAATAAAA
Found at i:842596 original size:16 final size:16
Alignment explanation
Indices: 842576--842629 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
842566 TAATTTTAAA
842576 AATAAAATAATTTATT
1 AATAAAATAATTTATT
* * **
842592 CATAATAATATTTTAAA
1 AATAA-AATAATTTATT
842609 AATAAAATAATTTATT
1 AATAAAATAATTTATT
*
842625 TATAA
1 AATAA
842630 TAAGTTATTC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAAATAATTTATT
Found at i:842610 original size:33 final size:33
Alignment explanation
Indices: 842568--842632 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
842558 TATTAATTTA
842568 ATTTTAAAAATAAAATAATTTATTCATAATAAT
1 ATTTTAAAAATAAAATAATTTATTCATAATAAT
*
842601 ATTTTAAAAATAAAATAATTTATTTATAATAA
1 ATTTTAAAAATAAAATAATTTATTCATAATAA
842633 GTTATTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (33 bp):
ATTTTAAAAATAAAATAATTTATTCATAATAAT
Found at i:842631 original size:19 final size:19
Alignment explanation
Indices: 842571--842632 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
842561 TAATTTAATT
*
842571 TTAAAAATAAAATAATTTA
1 TTAATAATAAAATAATTTA
*
842590 TTCATAAT--AAT-A-TT-
1 TTAATAATAAAATAATTTA
*
842604 TTAAAAATAAAATAATTTA
1 TTAATAATAAAATAATTTA
*
842623 TTTATAATAA
1 TTAATAATAA
842633 GTTATTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
14 6 0.19
15 2 0.06
16 4 0.12
17 4 0.12
18 2 0.06
19 14 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATAATAAAATAATTTA
Found at i:851181 original size:32 final size:33
Alignment explanation
Indices: 851117--851181 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
851107 GCAGACTATG
*
851117 CTGCTTGAATCCGAGTCACCATTGGAGAATAAA
1 CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
*
851150 CTGCTTGAATCCGGGAT-ACCA-GGGAGAATAAA
1 CTGCTTGAATCCGAG-TCACCATGGGAGAATAAA
851182 ATTTGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 18 0.62
34 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (33 bp):
CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
Found at i:851474 original size:33 final size:33
Alignment explanation
Indices: 851403--851467 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
851393 GCAGACTATG
*
851403 CTGCTTGAATCCGAGTCACCATTGGAGAATAAA
1 CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
*
851436 CTGCTTGAATCCGGGAT-ACCA-GGGAGAATAAA
1 CTGCTTGAATCCGAG-TCACCATGGGAGAATAAA
851468 TTTGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 18 0.62
34 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (33 bp):
CTGCTTGAATCCGAGTCACCATGGGAGAATAAA
Found at i:851609 original size:286 final size:286
Alignment explanation
Indices: 851097--851669 Score: 1121
Period size: 286 Copynumber: 2.0 Consensus size: 286
851087 ATCTAAACTC
851097 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
1 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
*
851162 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTTTAATTTCAGA
66 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
851227 TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
131 TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
851292 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
196 TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
851357 AATTATATCTAAAAAATAGAATTACA
261 AATTATATCTAAAAAATAGAATTACA
851383 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
1 ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
851448 GGGATACCAGGGAGAAT-AAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
66 GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
851512 TTCTTGAATGAGAGATACAAGGTGATTTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGA
131 TTCTTGAATGAGAGATACAAGGTGA-TTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGA
851577 ATCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTG
195 ATCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTG
851642 GAATTATATCTAAAAAATAGAATTACA
260 GAATTATATCTAAAAAATAGAATTACA
851669 A
1 A
851670 AAGCTATACT
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
285 71 0.25
286 214 0.75
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (286 bp):
ACACACACGTGCAGACTATGCTGCTTGAATCCGAGTCACCATTGGAGAATAAACTGCTTGAATCC
GGGATACCAGGGAGAATAAAATTTGCTTTTACAACTTAGACCACTTAAAAGGTTCTAATTTCAGA
TTCTTGAATGAGAGATACAAGGTGATTTTTTCCTCTTCAAAATAAGCCATAGTTTGGGATCTGAA
TCGCATGGGTCACTCTTACTTCAATAAGCTCTATGGAATCATGCATGACGAAGAGTCAAACCTGG
AATTATATCTAAAAAATAGAATTACA
Found at i:865301 original size:44 final size:43
Alignment explanation
Indices: 865252--865349 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
865242 TGGTATATGG
* *
865252 TTATGGAATAATGACAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGACAAGTATATCGGT-AAATAAGCTTACGAGC
**
865296 TTATGGACA-AATGGTAAGTATATCGGTAAATAAGCTTACGAGC
1 TTATGGA-ATAATGACAAGTATATCGGTAAATAAGCTTACGAGC
*
865339 TTATGGGATAA
1 TTATGGAATAA
865350 ATGGTAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 24 0.51
44 21 0.45
45 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (43 bp):
TTATGGAATAATGACAAGTATATCGGTAAATAAGCTTACGAGC
Found at i:865968 original size:19 final size:19
Alignment explanation
Indices: 865940--865982 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
865930 TTAAGAAAAT
*
865940 AAATTTTAAATCACTTTT-G
1 AAATTGTAAAT-ACTTTTAG
*
865959 AAATTGTAAATAGTTTTAG
1 AAATTGTAAATACTTTTAG
865978 AAATT
1 AAATT
865983 TGGGTGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (19 bp):
AAATTGTAAATACTTTTAG
Found at i:866095 original size:23 final size:23
Alignment explanation
Indices: 866065--866161 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
866055 TCAAGGGTTT
* *
866065 TATGTGGTCCTTTGAGACAAATC
1 TATGTGGTCCTTCGAGACAAACC
*
866088 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGAGACAAACC
*
866111 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGAGACAAACC
*
866134 TATGTGGTCATTCGAGACAAA--
1 TATGTGGTCCTTCGAGACAAACC
866155 TATGTGG
1 TATGTGG
866162 CACTTTGGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
21 7 0.10
23 62 0.90
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
TATGTGGTCCTTCGAGACAAACC
Found at i:867410 original size:59 final size:60
Alignment explanation
Indices: 867334--867447 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
867324 CCCAGGTGAC
*
867334 CATTTTGTAACTGTTAATAGTCG-GGGACTTAACAAAACAACATTC-TATAGTCGAAGAAT
1 CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACA-TCATATAGTCGAAGAAT
* * * *
867393 CATTTTATAACTTTTAATAGTCGAGGGTCTTAATAAAACAATATCATATAGTCGA
1 CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACATCATATAGTCGA
867448 GGGACCATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTGTTAATAGTCGAGGGACTTAACAAAACAACATCATATAGTCGAAGAAT
Found at i:867466 original size:60 final size:59
Alignment explanation
Indices: 867332--867466 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 59
867322 AACCCAGGTG
** *
867332 ACCATTTTGTAACTGTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
1 ACCATTTCATAACTTTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
* * * * * * *
867391 ATCATTTTATAACTTTTAATAGTCGAGGGTCTTAATAAAACAATA-TCATATAGTCGAGGG
1 ACCATTTCATAACTTTTAATAGTCG-GGGACTTAACAAAACAACATTC-TATAGTCGAAGA
867451 ACCA-TTCATACACTTT
1 ACCATTTCATA-ACTTT
867467 ACCCTAAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 29 0.46
60 34 0.54
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (59 bp):
ACCATTTCATAACTTTTAATAGTCGGGGACTTAACAAAACAACATTCTATAGTCGAAGA
Found at i:868927 original size:17 final size:18
Alignment explanation
Indices: 868907--868940 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
868897 ACATTTATCG
*
868907 TTTTAGTTGTTT-TAATA
1 TTTTAATTGTTTGTAATA
868924 TTTTAATTGTTTGTAAT
1 TTTTAATTGTTTGTAAT
868941 GCGAATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTAATTGTTTGTAATA
Found at i:895217 original size:14 final size:13
Alignment explanation
Indices: 895195--895233 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
895185 AATGGGAAGT
*
895195 AATCCCTGCAAATA
1 AATCTCTGCAAA-A
895209 AATCTCTGCATAAA
1 AATCTCTGCA-AAA
895223 AATCTCTGCAA
1 AATCTCTGCAA
895234 TATAGACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
AATCTCTGCAAAA
Found at i:910988 original size:53 final size:53
Alignment explanation
Indices: 910930--911039 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 53
910920 TACAAATAAA
* * * *
910930 ATTTTAATGTGAGCACCATTAGTAAAATAAGTAACTAATC-GAAGAAAAATCAG
1 ATTTTAAGGTGAGCACCATCAATAAAATAAGTAACCAA-CAGAAGAAAAATCAG
* * * *
910983 ATTTTAGGGTGGGCACCGTCAATAAAATAAGTAACCAACAGAAGAAAACTCAG
1 ATTTTAAGGTGAGCACCATCAATAAAATAAGTAACCAACAGAAGAAAAATCAG
911036 ATTT
1 ATTT
911040 CACGATGAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (53 bp):
ATTTTAAGGTGAGCACCATCAATAAAATAAGTAACCAACAGAAGAAAAATCAG
Found at i:912953 original size:13 final size:14
Alignment explanation
Indices: 912930--912985 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
912920 GGGGACGTCC
912930 TTCTCTCTCTCTTT
1 TTCTCTCTCTCTTT
912944 TTCTTCTCTCTATCATTT
1 TTC-TCTCTC--TC-TTT
*
912962 TTCT-TCTTTCTTT
1 TTCTCTCTCTCTTT
912975 TTCT-TCTCTCT
1 TTCTCTCTCTCT
912986 AAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 13 0.36
14 5 0.14
15 6 0.17
16 3 0.08
17 3 0.08
18 6 0.17
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCTCTCTCTCTTT
Found at i:915421 original size:2 final size:2
Alignment explanation
Indices: 915414--915444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
915404 TTACTGCTGT
915414 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
915445 AATTGAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:920974 original size:2 final size:2
Alignment explanation
Indices: 920967--921008 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
920957 ATTTAAAAAT
920967 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
921009 AAGTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:924520 original size:8 final size:9
Alignment explanation
Indices: 924496--924521 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
924486 GAAATTCCTT
924496 TTGTTTTTG
1 TTGTTTTTG
924505 TTGTTTTTG
1 TTGTTTTTG
924514 TTGTTTTT
1 TTGTTTTT
924522 TTACATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (9 bp):
TTGTTTTTG
Found at i:926920 original size:3 final size:3
Alignment explanation
Indices: 926912--926940 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
926902 TATTTTTCAC
926912 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
926941 CTTAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:927654 original size:41 final size:41
Alignment explanation
Indices: 927597--927684 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
927587 TATAAAGTGG
927597 TACCCGTCGTGGGTGGTGGGCGGGTAATGAGTTTGAGACAT
1 TACCCGTCGTGGGTGGTGGGCGGGTAATGAGTTTGAGACAT
* *
927638 TACCCTTCGTGGGTGGTGGGCGGGTAATGGGTTTGAGACAT
1 TACCCGTCGTGGGTGGTGGGCGGGTAATGAGTTTGAGACAT
927679 TACCCG
1 TACCCG
927685 CCCCGCATCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.16, C:0.17, G:0.40, T:0.27
Consensus pattern (41 bp):
TACCCGTCGTGGGTGGTGGGCGGGTAATGAGTTTGAGACAT
Found at i:927701 original size:15 final size:15
Alignment explanation
Indices: 927681--927717 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
927671 TGAGACATTA
*
927681 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
927696 CCCGCCCCACATCTG
1 CCCGCCCCACATCCG
927711 CCCGCCC
1 CCCGCCC
927718 AACTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:932086 original size:22 final size:22
Alignment explanation
Indices: 932061--932103 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
932051 ATAATACATT
*
932061 AAAAATAT-TACTTTTATTTAAC
1 AAAAATATATA-TTTAATTTAAC
932083 AAAAATATATATTTAATTTAA
1 AAAAATATATATTTAATTTAA
932104 AAATATAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATATATATTTAATTTAAC
Found at i:936495 original size:15 final size:15
Alignment explanation
Indices: 936475--936505 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
936465 AGTTTAGGTT
936475 GAGGAGGAAGAGGAA
1 GAGGAGGAAGAGGAA
*
936490 GAGGAGGAGGAGGAA
1 GAGGAGGAAGAGGAA
936505 G
1 G
936506 GTTAACTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (15 bp):
GAGGAGGAAGAGGAA
Found at i:939399 original size:29 final size:29
Alignment explanation
Indices: 939356--939438 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
939346 CTCACCTAAC
*
939356 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
939386 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
939415 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
939439 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:942973 original size:15 final size:15
Alignment explanation
Indices: 942937--942973 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
942927 GCATATCCTT
*
942937 GAGTTGAAGCTTGAG
1 GAGTTGCAGCTTGAG
942952 GAGTTGCAGCTTGAG
1 GAGTTGCAGCTTGAG
942967 GAGTTGC
1 GAGTTGC
942974 TCAGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.41, T:0.27
Consensus pattern (15 bp):
GAGTTGCAGCTTGAG
Found at i:944161 original size:29 final size:29
Alignment explanation
Indices: 944118--944200 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
944108 CTCACCTAAC
* *
944118 TAAATTGATGTAAGCAATGCCATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
944148 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
944177 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
944201 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:945056 original size:73 final size:73
Alignment explanation
Indices: 944934--945083 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
944924 GGGAATGCTA
*
944934 CCGGATTTCGTTCTTTGTATCGGGGAAGACAGGTCGGACGAGGATATGTTTGAGGTCATCATACG
1 CCGGATTTCGTTCTTTGTATCGGGGAAGACAGGTCGGACGAGGACATGTTTGAGGTCATCATACG
*
944999 AGCAATGT
66 AGCAATGC
*
945007 CCGGATTTCGTTCTTTGTATCGGGGACGACAGGTCGGACGAGGACATGTTTGAGGTCATCATACG
1 CCGGATTTCGTTCTTTGTATCGGGGAAGACAGGTCGGACGAGGACATGTTTGAGGTCATCATACG
945072 AGCAATGC
66 AGCAATGC
945080 CCGG
1 CCGG
945084 CCCCTATCTC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (73 bp):
CCGGATTTCGTTCTTTGTATCGGGGAAGACAGGTCGGACGAGGACATGTTTGAGGTCATCATACG
AGCAATGC
Found at i:945318 original size:22 final size:22
Alignment explanation
Indices: 945270--945312 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
945260 GCTATCATTG
* *
945270 ATAATATACATATTCTATTGAC
1 ATAATATACATATGCTATAGAC
945292 ATAATATACATATGCTATAGA
1 ATAATATACATATGCTATAGA
945313 TGTAATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
ATAATATACATATGCTATAGAC
Found at i:952303 original size:12 final size:12
Alignment explanation
Indices: 952286--952322 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
952276 GATATTCTCT
952286 TCATCTTCTTCA
1 TCATCTTCTTCA
*
952298 TCATCTTCTTCT
1 TCATCTTCTTCA
*
952310 TCTTCTTCTTCA
1 TCATCTTCTTCA
952322 T
1 T
952323 GTACGAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.57
Consensus pattern (12 bp):
TCATCTTCTTCA
Found at i:952970 original size:64 final size:65
Alignment explanation
Indices: 952858--953014 Score: 167
Period size: 64 Copynumber: 2.4 Consensus size: 65
952848 TTGAAGGTGT
* * * ** * *
952858 ATCGATGCACAGGAAGTGCATCGATGCA-CTCTTTTAAAATAAATACATCGAATGTAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCTCTAGTAAAATAAATACATCGAATGCAATTCATGC
* * *
952922 ATCGATGCATAAGTAGTGCATCGATGCATC-CTAGTAATAATACA-ACATCGAATGCATTTTATG
1 ATCGATGCATAAGTAGTGCATCGATGCATCTCTAGTAA-AATAAATACATCGAATGCAATTCATG
952985 C
65 C
* * *
952986 ACCGATACATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
953015 ACCTTCATTA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 72 0.92
65 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (65 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCTCTAGTAAAATAAATACATCGAATGCAATTCATGC
Found at i:953709 original size:31 final size:31
Alignment explanation
Indices: 953671--953795 Score: 225
Period size: 31 Copynumber: 4.0 Consensus size: 31
953661 AGGGTCGAGG
953671 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
953702 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
953733 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
953764 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
953795 G
1 G
953796 GTTCTTCGGG
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
31 91 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:955639 original size:14 final size:15
Alignment explanation
Indices: 955603--955636 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
955593 ATGTTTAATT
955603 TTTTTAAATAATATA
1 TTTTTAAATAATATA
955618 TTTTTAAATAATATA
1 TTTTTAAATAATATA
955633 TTTT
1 TTTT
955637 AAAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAAATAATATA
Done.