Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008489.1 Hibiscus syriacus cultivar Beakdansim tig00111331_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: 1108073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:198699 original size:29 final size:27
Alignment explanation
Indices: 198662--198717 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
198652 TAGTAATATG
*
198662 AAAATATAATATAATATAAAAAAACCAAA
1 AAAAAATAA-ATAA-ATAAAAAAACCAAA
* *
198691 AAAAAATAAATAAATATATAAACCAAA
1 AAAAAATAAATAAATAAAAAAACCAAA
198718 TATAAAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.50
28 4 0.17
29 8 0.33
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAAAATAAATAAATAAAAAAACCAAA
Found at i:198878 original size:2 final size:2
Alignment explanation
Indices: 198871--198904 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
198861 AATATTTAAA
*
198871 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
198905 GTATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:199531 original size:37 final size:37
Alignment explanation
Indices: 199438--199539 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
199428 GTGCTTGTAG
* * * * *
199438 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
199475 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
199512 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
199540 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:200559 original size:106 final size:106
Alignment explanation
Indices: 200241--201297 Score: 1481
Period size: 106 Copynumber: 10.0 Consensus size: 106
200231 GCATTGTTCC
* * ** * *
200241 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
200305 ACCAGTC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
200347 GAGTCCAATATCCTTCGCTGTGAAGTTGAAACTGACTCTG-AA-T--GAAA-T-TTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * ** *
200406 TCAGCCGCCCCTTCGTCGTGAAGTTGGGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
200448 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
200512 CAAGTGGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
200553 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
200618 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
200659 GAGTCCAATATCCTTCACTGCGAAGTTGAAACTGGCTCTGAAATTGGGAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
200723 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
200764 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGA-TGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTTATTGACA
200828 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
200870 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
200935 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
200976 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCAAAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
201041 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
201082 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
201147 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
201188 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
201253 CCAGTC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
201294 GAGT
1 GAGT
201298 GACACGATAT
Statistics
Matches: 851, Mismatches: 86, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
99 1 0.00
100 75 0.09
101 5 0.01
102 5 0.01
104 3 0.00
105 98 0.12
106 662 0.78
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:201076 original size:423 final size:420
Alignment explanation
Indices: 200241--201297 Score: 1579
Period size: 423 Copynumber: 2.5 Consensus size: 420
200231 GCATTGTTCC
* ** *
200241 GAGTCCAATATCC-TCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-GTTGTTGACA
* *
200305 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
63 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
* * * * *
200370 AGTTGAAACTGACTCTG-AA-T-GAA-AT-TTTGTTGATAATCAGCCGCCCCTTCGTCGTGAAGT
128 AGTTGAAATTGGCTCTGAAATTGGAAGATGTTTGTTGACAACCAG-CGTCCCTTCGTCGTGAAGT
** *
200430 TGGGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGG
192 TGAACTTGTGTTGTC-TGGAGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTATGAAATTGG
* * *
200494 GAAGTTGTTTATTAACAACAAGTGGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTGGAGTCC
256 GAAGTTATTTATTAACAACAAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* ** *
200559 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTAACAACCAGCG
321 AATATCCTTCGTTGTGAAGTTAAAATTGACTCAAAAATTAGGAAATTGTTTATTAACAACCAGCG
200624 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
386 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
200659 GAGTCCAATATCCTTCACTGCGAAGTTGAAACTGGCTCTGAAATTGGGAAATTGTTGTTGACAAC
1 GAGTCCAATATCCTTC-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAAC
* *
200724 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
200789 TTGAAATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTG-GAAGATGTTTGTTGACAACCAGC-GTCCCTTCGTCGTGAAGTT
* * *
200854 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGA
193 GAACTTGTGTTGTCTGGAGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTATGAAATTGGGA
* * * *
200919 AGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAA
258 AGTTATTTATTAACAACAAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
* *
200984 TATCCTTCGTTGTGAAGTTAAAATTGGCTCAAAAATTAGGAAATTGTTTATTGACAACCAGCGGT
323 TATCCTTCGTTGTGAAGTTAAAATTGACTCAAAAATTAGGAAATTGTTTATTAACAACCAGCGGT
201049 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
388 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
201082 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTC-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAA
* * * *
201147 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
64 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
*
201212 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTCGTGAAGT
129 GTTGAAATTGGCTCTGAAATT-GGAAGATGTTTGTTGACAACCAG-CGTCCCTTCGTCGTGAAGT
*
201277 TGAACTTGTGTTGTCTCGAGT
192 TGAACTTGTGTTGTCTGGAGT
201298 GACACGATAT
Statistics
Matches: 579, Mismatches: 47, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
417 85 0.15
418 44 0.08
419 4 0.01
420 1 0.00
421 3 0.01
422 6 0.01
423 287 0.50
424 147 0.25
425 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (420 bp):
GAGTCCAATATCCTTCCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAAATTGGAAGATGTTTGTTGACAACCAGCGTCCCTTCGTCGTGAAGTTGAA
CTTGTGTTGTCTGGAGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTATGAAATTGGGAAGT
TATTTATTAACAACAAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
CCTTCGTTGTGAAGTTAAAATTGACTCAAAAATTAGGAAATTGTTTATTAACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:201838 original size:18 final size:19
Alignment explanation
Indices: 201809--201845 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
201799 TATTGAATCC
201809 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
201828 CCAAA-AATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
201846 TTGATGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.19
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:202891 original size:20 final size:19
Alignment explanation
Indices: 202855--202949 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 19
202845 TTGCATGTGC
*
202855 TTTTTGTCCATTT-TTTTTT
1 TTTTTGTTC-TTTCTTTTTT
202874 ATTTTTGTTCTTTCTTTTTT
1 -TTTTTGTTCTTTCTTTTTT
*
202894 TCTTTTGTT-TCTC-TTTTT
1 T-TTTTGTTCTTTCTTTTTT
* *
202912 TCTTTGTT-TTT-TTTCTT
1 TTTTTGTTCTTTCTTTTTT
*
202929 CTTTTGCTTCTTTTCTTTTTT
1 TTTTTG-TTC-TTTCTTTTTT
202950 GTTCTTGATT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
17 16 0.27
18 8 0.13
19 7 0.12
20 24 0.40
21 5 0.08
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTTGTTCTTTCTTTTTT
Found at i:202891 original size:21 final size:19
Alignment explanation
Indices: 202876--202939 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 19
202866 TTTTTTTTAT
*
202876 TTTTGTTCTTTCTTTTTTTC
1 TTTTGTT-TCTCTTTTTTTC
202896 TTTTGTTTCTC-TTTTTTC
1 TTTTGTTTCTCTTTTTTTC
*
202914 -TTTGTTT-T-TTTTCTTC
1 TTTTGTTTCTCTTTTTTTC
*
202930 TTTTGCTTCT
1 TTTTGTTTCT
202940 TTTCTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 7 0.18
17 13 0.34
18 8 0.21
19 3 0.08
20 7 0.18
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTGTTTCTCTTTTTTTC
Found at i:202910 original size:17 final size:17
Alignment explanation
Indices: 202884--202952 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
202874 ATTTTTGTTC
202884 TTTCTTTTT-TTCTTTTG
1 TTTCTTTTTCTT-TTTTG
*
202901 TTTCTCTTTT-TTCTTTG
1 TTTCT-TTTTCTTTTTTG
202918 TTT-TTTTTCTTCTTTTG
1 TTTCTTTTTCTT-TTTTG
*
202935 CTTC-TTTTCTTTTTTG
1 TTTCTTTTTCTTTTTTG
202951 TT
1 TT
202953 CTTGATTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 4 0.09
16 9 0.20
17 25 0.57
18 6 0.14
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTTG
Found at i:202913 original size:9 final size:8
Alignment explanation
Indices: 202884--202955 Score: 58
Period size: 8 Copynumber: 8.8 Consensus size: 8
202874 ATTTTTGTTC
202884 TTTCTTTT
1 TTTCTTTT
202892 TTTCTTTT
1 TTTCTTTT
202900 GTTTCTCTTT
1 -TTTCT-TTT
202910 TTTCTTTGT
1 TTTCTTT-T
202919 TTT-TTTT
1 TTTCTTTT
*
202926 CTTCTTTT
1 TTTCTTTT
*
202934 GCTTCTTTT
1 -TTTCTTTT
*
202943 CTT-TTTT
1 TTTCTTTT
*
202950 GTTCTT
1 TTTCTT
202956 GATTGGATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
7 9 0.16
8 22 0.39
9 22 0.39
10 3 0.05
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (8 bp):
TTTCTTTT
Found at i:202947 original size:22 final size:21
Alignment explanation
Indices: 202885--202947 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
202875 TTTTTGTTCT
* *
202885 TTCTTTTTTTCTTTTGTTTCTC
1 TTCTTTTCTTCTTTTCTTT-TC
*
202907 TT-TTTTCTT-TGTTTTTTTTC
1 TTCTTTTCTTCT-TTTCTTTTC
202927 TTCTTTTGCTTCTTTTCTTTT
1 TTCTTTT-CTTCTTTTCTTTT
202948 TTGTTCTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 5 0.15
21 16 0.47
22 12 0.35
23 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (21 bp):
TTCTTTTCTTCTTTTCTTTTC
Found at i:204114 original size:8 final size:8
Alignment explanation
Indices: 204101--204136 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
204091 GTAGATGAAT
204101 ATGCAAAA
1 ATGCAAAA
204109 ATGCAAAA
1 ATGCAAAA
204117 ATGC-AAA
1 ATGCAAAA
*
204124 ATGCAAGA
1 ATGCAAAA
204132 ATGCA
1 ATGCA
204137 TGAAATGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:204126 original size:15 final size:15
Alignment explanation
Indices: 204101--204136 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
204091 GTAGATGAAT
204101 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
204117 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
204132 ATGCA
1 ATGCA
204137 TGAAATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:207453 original size:16 final size:16
Alignment explanation
Indices: 207416--207456 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
207406 AAAAATGAAG
*
207416 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
207432 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
207447 AATAAATAAA
1 AATAAATAAA
207457 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:207563 original size:14 final size:16
Alignment explanation
Indices: 207509--207561 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
207499 GTAAAATAGA
* *
207509 AAAATAATAATCATAAC
1 AAAATAATAATAAT-AT
207526 AATAATAATAATAATAT
1 AA-AATAATAATAATAT
207543 GAAAATAAT-ATAATAT
1 -AAAATAATAATAATAT
207559 AAA
1 AAA
207562 TACAAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 3 0.09
16 7 0.22
17 9 0.28
18 13 0.41
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATAATAATAATAT
Found at i:207762 original size:2 final size:2
Alignment explanation
Indices: 207755--207807 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
207745 ATATTTAAAA
207755 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
*
207797 AT AT AA AT AT A
1 AT AT AT AT AT A
207808 GTATTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:208439 original size:37 final size:37
Alignment explanation
Indices: 208354--208449 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
208344 GGATCCTATC
* * *
208354 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
*
208391 TTTAGGAGTTTGAATCCTAGTAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
*
208428 TTTAGGAGTTTGAATTCTAGTA
1 TTTAGGAGTTTGAATCCTAGTA
208450 GGACGAAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
Found at i:209120 original size:23 final size:22
Alignment explanation
Indices: 209088--209132 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
209078 ACCGTATTAA
*
209088 CAAATATAAAATGTAGAAACAAT
1 CAAATAT-AAATGCAGAAACAAT
*
209111 CAAATGTAAATGCAGAAACAAT
1 CAAATATAAATGCAGAAACAAT
209133 ACCGGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (22 bp):
CAAATATAAATGCAGAAACAAT
Found at i:209420 original size:38 final size:37
Alignment explanation
Indices: 209343--209425 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
209333 CTTTTTATAT
*
209343 TTTTAATTTTGTAAAAAAATAATATAAATATTATGAA
1 TTTTAATTTTGTAAAAAAATAATATAAATATTATCAA
* * *
209380 TTTTATTTTTTTAAAGAAAAT-ATATAAATATTTTACAA
1 TTTTAATTTTGTAAA-AAAATAATATAAATATTAT-CAA
209418 TTTGTAAT
1 TTT-TAAT
209426 ATTATACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
37 25 0.66
38 10 0.26
39 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTTAATTTTGTAAAAAAATAATATAAATATTATCAA
Found at i:209602 original size:20 final size:20
Alignment explanation
Indices: 209566--209603 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
209556 ATCCTATTCC
**
209566 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
209586 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
209604 ATGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:210134 original size:16 final size:16
Alignment explanation
Indices: 210113--210144 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
210103 CTTTTGAGTT
210113 TTATAAATTTATAGTC
1 TTATAAATTTATAGTC
210129 TTATAAATTTATAGTC
1 TTATAAATTTATAGTC
210145 ATTAGATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTATAAATTTATAGTC
Found at i:210482 original size:20 final size:20
Alignment explanation
Indices: 210444--210482 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
210434 AGTTTCCAAA
**
210444 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAATCCAT
210464 TTCGCGTTGCGATAATCCA
1 TTCGCGTTGCGATAATCCA
210483 AAATCGCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAATCCAT
Found at i:210497 original size:41 final size:41
Alignment explanation
Indices: 210464--210616 Score: 243
Period size: 41 Copynumber: 3.7 Consensus size: 41
210454 GATTTTCCAT
* *
210464 TTCGCGTTGCGATAATCCAAAATCGCAACGCGATTTGCAGA
1 TTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTGCAGA
* *
210505 TTCGCGTTGCAATAGTCCAAAATCGCAACGCGATTTGCAGA
1 TTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTGCAGA
* * *
210546 TTCACATTGCGATAGTCAAAAATCGCAACGCGATTTTCAGA
1 TTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTGCAGA
210587 TTCGCATTGCGATAGTCCAAAATCGCAACG
1 TTCGCATTGCGATAGTCCAAAATCGCAACG
210617 GTAAAGCGAT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTGCAGA
Found at i:210598 original size:20 final size:20
Alignment explanation
Indices: 210534--210599 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
210524 AAATCGCAAC
* *
210534 GCGATTTGCAGATTCACATT
1 GCGATTTTCAGATTCGCATT
** * * **
210554 GCGATAGTCAAAAATCGCAAC
1 GCGATTTTC-AGATTCGCATT
210575 GCGATTTTCAGATTCGCATT
1 GCGATTTTCAGATTCGCATT
210595 GCGAT
1 GCGAT
210600 AGTCCAAAAT
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
GCGATTTTCAGATTCGCATT
Found at i:211650 original size:6 final size:6
Alignment explanation
Indices: 211639--211663 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
211629 ATCTCGGGTA
211639 GCGGTC GCGGTC GCGGTC GCGGTC G
1 GCGGTC GCGGTC GCGGTC GCGGTC G
211664 TGGTAATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.52, T:0.16
Consensus pattern (6 bp):
GCGGTC
Found at i:211843 original size:20 final size:20
Alignment explanation
Indices: 211779--211844 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
211769 ACTATCACAA
*
211779 TGCGAATCTGCAAATTGCGT
1 TGCGAATCTGCAAATCGCGT
* * * * **
211799 TGCGATTTTGGACTATCGCAA
1 TGCGAATCTGCA-AATCGCGT
211820 TGCGAATCTGCAAATCGCGT
1 TGCGAATCTGCAAATCGCGT
211840 TGCGA
1 TGCGA
211845 TTTTGGACTA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TGCGAATCTGCAAATCGCGT
Found at i:211858 original size:21 final size:21
Alignment explanation
Indices: 211795--211858 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
211785 TCTGCAAATT
211795 GCGTTGCGATTTTGGACTATC
1 GCGTTGCGATTTTGGACTATC
** * * * *
211816 GCAATGCGAATCTGCA-AATC
1 GCGTTGCGATTTTGGACTATC
211836 GCGTTGCGATTTTGGACTATC
1 GCGTTGCGATTTTGGACTATC
211857 GC
1 GC
211859 AACACGAATT
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
GCGTTGCGATTTTGGACTATC
Found at i:211867 original size:41 final size:41
Alignment explanation
Indices: 211755--211860 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
211745 GTCGCTTTAC
* * *
211755 CGTTACGATTTTGGACTATCACAATGCGAATCTGCAAATTG
1 CGTTGCGATTTTGGACTATCGCAATGCGAATCTGCAAATCG
211796 CGTTGCGATTTTGGACTATCGCAATGCGAATCTGCAAATCG
1 CGTTGCGATTTTGGACTATCGCAATGCGAATCTGCAAATCG
211837 CGTTGCGATTTTGGACTATCGCAA
1 CGTTGCGATTTTGGACTATCGCAA
211861 CACGAATTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (41 bp):
CGTTGCGATTTTGGACTATCGCAATGCGAATCTGCAAATCG
Found at i:211896 original size:14 final size:14
Alignment explanation
Indices: 211877--211909 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
211867 TTTGGAAACT
211877 GAGTTGCGAAGTTG
1 GAGTTGCGAAGTTG
211891 GAGTTGCGAAGTTG
1 GAGTTGCGAAGTTG
211905 GAGTT
1 GAGTT
211910 CGCGTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.42, T:0.30
Consensus pattern (14 bp):
GAGTTGCGAAGTTG
Found at i:212167 original size:18 final size:19
Alignment explanation
Indices: 212125--212167 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
212115 TTGGTTCACA
*
212125 GAATATAAGATTACCAGTG
1 GAATAAAAGATTACCAGTG
*
212144 GAAATAAAAGATTACTAG-G
1 G-AATAAAAGATTACCAGTG
212163 GAATA
1 GAATA
212168 GGATTACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 3 0.14
20 14 0.67
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (19 bp):
GAATAAAAGATTACCAGTG
Found at i:213783 original size:20 final size:20
Alignment explanation
Indices: 213758--213888 Score: 113
Period size: 20 Copynumber: 6.5 Consensus size: 20
213748 GGGAAAATCA
213758 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
*
213778 CAATGCGATACTTACTATCG
1 CAATGCGATACTGACTATCG
* *
213798 CAATGCGATAAT-ACAAAATCG
1 CAATGCGATACTGAC--TATCG
* * *
213819 CAACGAGATACTGACTTTCG
1 CAATGCGATACTGACTATCG
* * *
213839 CAACGCGATTCTGACTTTCG
1 CAATGCGATACTGACTATCG
* *
213859 CAACGCGATAAT-ACATAATCG
1 CAATGCGATACTGAC-T-ATCG
213880 CAATGCGAT
1 CAATGCGAT
213889 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 62 0.67
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:213798 original size:61 final size:61
Alignment explanation
Indices: 213751--213878 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
213741 GCGAATTGGG
* * * * *
213751 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
213812 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
213873 ATAATC
1 AAAATC
213879 GCAATGCGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (61 bp):
AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:213879 original size:61 final size:61
Alignment explanation
Indices: 213764--213882 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
213754 ATCACAATGC
* * *
213764 GATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
* * * *
213825 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATCGCAA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAA
213883 TGCGATTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
Found at i:214086 original size:22 final size:22
Alignment explanation
Indices: 214058--214101 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
214048 CTCTCTCACC
214058 CATCTCCGACGAAATCCGTCTA
1 CATCTCCGACGAAATCCGTCTA
214080 CATCTCCGACGAAATCCGTCTA
1 CATCTCCGACGAAATCCGTCTA
214102 TCTCCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCTA
Found at i:214414 original size:20 final size:20
Alignment explanation
Indices: 214360--214418 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
214350 GCGATTCTCT
**
214360 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
214380 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
214400 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
214419 AGTAACGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:216030 original size:19 final size:20
Alignment explanation
Indices: 215976--216042 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
215966 TAGTTTACTT
* *
215976 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
215996 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
216016 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
216035 TCGCAACG
1 TCGCAACG
216043 AGAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:216038 original size:39 final size:34
Alignment explanation
Indices: 215995--216082 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 34
215985 GAAAATGACT
215995 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATG-AA
*
216034 ATCGCAACGAGAAA--ATCGCAATGCGAAATGAA
1 ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
216066 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
216083 AAATCGCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
32 15 0.33
33 16 0.36
34 1 0.02
38 4 0.09
39 9 0.20
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
Found at i:216047 original size:19 final size:19
Alignment explanation
Indices: 216015--216093 Score: 107
Period size: 18 Copynumber: 4.5 Consensus size: 19
216005 GGAAATGGCT
216015 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
216034 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
216048 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
216066 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
216085 ATCGCAATG
1 ATCGCAATG
216094 AGATTTGTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
14 11 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.35
19 18 0.35
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:216073 original size:32 final size:33
Alignment explanation
Indices: 216015--216079 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
216005 GGAAATGGCT
216015 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
216048 ATCGCAATGCGAAATG-AAATCGCAACGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
216080 TGAAAATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:216127 original size:14 final size:14
Alignment explanation
Indices: 216108--216165 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
216098 TTGTGTTTCG
216108 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
216122 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
216138 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
216154 CGTTGCGATTTT
1 CGTTGCGATTTT
216166 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:216139 original size:32 final size:33
Alignment explanation
Indices: 216103--216178 Score: 136
Period size: 32 Copynumber: 2.3 Consensus size: 33
216093 GAGATTTGTG
*
216103 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
216135 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
216168 TTTCGCATTGC
1 TTTCGCATTGC
216179 ATTAGCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 26 0.62
33 16 0.38
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:216208 original size:20 final size:19
Alignment explanation
Indices: 216154--216221 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
216144 GCGATTTTGT
**
216154 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
216173 CATTGC-ATTAGCCATTTCCG
1 CGTTGCGA-TAGTCATTT-CG
216193 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
216213 TGTTGCGAT
1 CGTTGCGAT
216222 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.29
20 22 0.58
21 4 0.11
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:216647 original size:21 final size:22
Alignment explanation
Indices: 216587--216647 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
216577 GACTCACCGG
216587 TCATCCCTCAAGAGTCCCCTCA
1 TCATCCCTCAAGAGTCCCCTCA
* ** *
216609 -AATCGTTCAAGAGGCCCCT-A
1 TCATCCCTCAAGAGTCCCCTCA
*
216629 TCATCCCTCAAGATTCCCC
1 TCATCCCTCAAGAGTCCCC
216648 CCCCCCACCG
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.25, C:0.41, G:0.11, T:0.23
Consensus pattern (22 bp):
TCATCCCTCAAGAGTCCCCTCA
Found at i:218115 original size:14 final size:14
Alignment explanation
Indices: 218096--218131 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
218086 ATTGTTTAAT
218096 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
218110 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
218124 TGATTTGT
1 TGATTTGT
218132 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:218239 original size:20 final size:20
Alignment explanation
Indices: 218214--218252 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
218204 ATGTTGAAGG
218214 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
218234 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
218253 GAGAGAATCG
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:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:218264 original size:14 final size:14
Alignment explanation
Indices: 218245--218298 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
218235 AAAACTGACT
*
218245 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
218259 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
218278 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
218292 ATCGCAA
1 ATCGCAA
218299 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:218282 original size:19 final size:17
Alignment explanation
Indices: 218258--218303 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
218248 GCAACGAGAG
218258 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
218277 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
218291 AATCGCAATGCGA
1 AATCGCAATGCGA
218304 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:218368 original size:20 final size:20
Alignment explanation
Indices: 218329--218398 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
218319 GCGATTTTAT
*
218329 CGTTGCGATAGGCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
218348 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
218368 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
218388 CGTTGCGATAG
1 CGTTGCGATAG
218399 TCAAATGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 13 0.27
20 36 0.73
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:218636 original size:20 final size:20
Alignment explanation
Indices: 218611--218661 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
218601 AAATGATTGC
*
218611 CTTTCGTAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
218631 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
218651 CTTTCGCAACG
1 CTTTCGCAACG
218662 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:219433 original size:24 final size:24
Alignment explanation
Indices: 219406--219459 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
219396 GTATTCGAAA
*
219406 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
219430 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
219454 TTTGAT
1 TTTGAT
219460 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:219651 original size:12 final size:12
Alignment explanation
Indices: 219634--219658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
219624 ATATAATCCT
219634 GAAGAAGAAAAA
1 GAAGAAGAAAAA
219646 GAAGAAGAAAAA
1 GAAGAAGAAAAA
219658 G
1 G
219659 TCCCCAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:222014 original size:52 final size:52
Alignment explanation
Indices: 221958--222060 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
221948 TCGTAATGCG
*
221958 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCA
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCA
*
222010 AAATGAAAATCGCAACGAGGGAATCGCAACGCGAAATGAAAATCGCAACGC
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
222061 GAATTTAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (52 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCA
Found at i:222074 original size:19 final size:19
Alignment explanation
Indices: 221927--222063 Score: 105
Period size: 19 Copynumber: 7.7 Consensus size: 19
221917 CTTAATATCT
* **
221927 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
* *
221947 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
221966 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
221980 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
221999 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
222018 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
222032 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
222051 ATCGCAACGCGAA
1 ATCGCAACGCGAA
222064 TTTAATTTCG
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 3 0.03
18 2 0.02
19 54 0.59
20 8 0.09
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:222081 original size:19 final size:19
Alignment explanation
Indices: 222059--222100 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
222049 AAATCGCAAC
222059 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
222078 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
222097 GCGA
1 GCGA
222101 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:222101 original size:19 final size:19
Alignment explanation
Indices: 222068--222134 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
222058 CGCGAATTTA
222068 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
222087 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
* *
222104 ---CCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
222120 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
222135 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.24
16 3 0.08
17 3 0.08
19 23 0.61
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:222261 original size:14 final size:14
Alignment explanation
Indices: 222242--222277 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
222232 CATCAATTAA
*
222242 ACAAATCAACTTTT
1 ACAAATCAACCTTT
222256 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
222269 ACAAATCAA
1 ACAAATCAA
222278 TTAAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:223673 original size:42 final size:41
Alignment explanation
Indices: 223614--223817 Score: 144
Period size: 42 Copynumber: 4.9 Consensus size: 41
223604 GTGAATCGGG
* *
223614 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
223656 CTCTTGAACGGTGGGAGGAAACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGG-GACTCTTCAAGG-ATGACAGTGGC
* * * * * *
223698 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
223740 CTCTTGAAC-GTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
223781 CTCTTCAACGATAGGAGTGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAG
223818 GCGAGTCGGG
Statistics
Matches: 121, Mismatches: 33, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
40 3 0.02
41 43 0.36
42 70 0.58
43 5 0.04
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:223782 original size:83 final size:83
Alignment explanation
Indices: 223644--223817 Score: 305
Period size: 83 Copynumber: 2.1 Consensus size: 83
223634 CCTCTTCAAC
*
223644 GATGACAGTGGCCTCTTGAACGGTGGGAGGAAACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGAAACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
223709 TAGGAGTGGACTCTTGAGG
66 TAGGAGT-GACTCTTGAGG
**
223728 GATGACAGTGGCCTCTTGAAC-GTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGAAACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
223792 TAGGAGTGACTCTTGAGG
66 TAGGAGTGACTCTTGAGG
223810 GATGACAG
1 GATGACAG
223818 GCGAGTCGGG
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
82 19 0.22
83 47 0.54
84 21 0.24
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (83 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGAAACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGACTCTTGAGG
Found at i:223803 original size:41 final size:41
Alignment explanation
Indices: 223676--223814 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
223666 GTGGGAGGAA
*
223676 ACTCTCGAGGAATGATAGGGGCCTCTTCAATGATAGGAGTGG
1 ACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGT-G
* * * * * * *
223718 ACTCTTGAGGGATGACAGTGGCCTCTTGAACG-TGGGAGGGG
1 ACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGA-GTG
223759 ACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
1 ACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
* *
223800 ACTCTTGAGGGATGA
1 ACTCTCGAGGAATGA
223815 CAGGCGAGTC
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
41 47 0.60
42 31 0.40
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.23
Consensus pattern (41 bp):
ACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
Found at i:224201 original size:92 final size:90
Alignment explanation
Indices: 224033--224220 Score: 263
Period size: 92 Copynumber: 2.0 Consensus size: 90
224023 ATATTTCAAA
* *
224033 ACTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
224098 GCAGAATTGGCAGCAATCGAATAAAATTT
63 GCAGAATTGGCAGCAACCGAAT-AAATTT
224127 ACTTCAACCAAAAGACAAAACAAAAAAGACAAATACT-ACTTCACAGTGTT-AATAAACAGTTTA
1 ACTTCAACCAAAAGACAAAAC---AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTA
*
224190 GCAGTATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
224218 ACT
1 ACT
224221 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
91 9 0.10
92 32 0.37
94 20 0.23
96 13 0.15
97 13 0.15
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:224429 original size:61 final size:62
Alignment explanation
Indices: 224353--224470 Score: 204
Period size: 61 Copynumber: 1.9 Consensus size: 62
224343 GACACCTCAT
224353 ACGCCATGGCACCATCGTTATCGCGTAGAGTACCGAT-CTCAACGCAAGGCATTGACCTCCAC
1 ACGCCATGGCACCATCGTTATCGCGTAGAGTACCGATCCTC-ACGCAAGGCATTGACCTCCAC
224415 ACGCCAT-GCACCATCGTTATCGCGTAGAGTACCGATCCCTCACGCAAGGCATTGAC
1 ACGCCATGGCACCATCGTTATCGCGTAGAGTACCGAT-CCTCACGCAAGGCATTGAC
224471 TCATCACGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
61 29 0.54
62 22 0.41
63 3 0.06
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.19
Consensus pattern (62 bp):
ACGCCATGGCACCATCGTTATCGCGTAGAGTACCGATCCTCACGCAAGGCATTGACCTCCAC
Found at i:225930 original size:19 final size:18
Alignment explanation
Indices: 225901--226022 Score: 116
Period size: 19 Copynumber: 7.0 Consensus size: 18
225891 TTGAAATGAT
225901 AATGAGAATCGCAACGCGA
1 AATGA-AATCGCAACGCGA
*
225920 AATGACTATCGCAA--CGA
1 AATGA-AATCGCAACGCGA
*
225937 GA-G-AATCGCAACGCGA
1 AATGAAATCGCAACGCGA
225953 AATGAAAATCGCAACGCGA
1 AATG-AAATCGCAACGCGA
225972 AATGAAAATCGCAA--CGA
1 AATG-AAATCGCAACGCGA
*
225989 GA-G-AATCGCAACGCGA
1 AATGAAATCGCAACGCGA
*
226005 AATGAAATCGCAATGCGA
1 AATGAAATCGCAACGCGA
226023 TTTTGGTTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
14 15 0.17
16 10 0.12
17 10 0.12
18 12 0.14
19 39 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.11
Consensus pattern (18 bp):
AATGAAATCGCAACGCGA
Found at i:225946 original size:33 final size:33
Alignment explanation
Indices: 225904--225968 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
225894 AAATGATAAT
**
225904 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
225937 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
225969 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:225983 original size:52 final size:52
Alignment explanation
Indices: 225901--226022 Score: 201
Period size: 52 Copynumber: 2.4 Consensus size: 52
225891 TTGAAATGAT
* **
225901 AATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
225953 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
*
226005 AATG-AAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
226023 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 13 0.20
52 53 0.80
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.11
Consensus pattern (52 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:226040 original size:19 final size:19
Alignment explanation
Indices: 226018--226062 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
226008 GAAATCGCAA
*
226018 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
226037 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
226056 TGCGATT
1 TGCGATT
226063 CTCTCGTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:226449 original size:20 final size:20
Alignment explanation
Indices: 226425--226538 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
226415 CGCTATGTAA
* *
226425 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
226445 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
226465 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
226486 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
226506 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
226526 ATCGCATTGCGAT
1 ATCGCATTGCGAT
226539 TTTCCCAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:226523 original size:61 final size:61
Alignment explanation
Indices: 226425--226541 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
226415 CGCTATGTAA
* * * *
226425 ATCGCATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
226486 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
226542 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:226557 original size:61 final size:61
Alignment explanation
Indices: 226425--226559 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
226415 CGCTATGTAA
* * * * * ** *
226425 ATCGCATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* *
226486 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
226548 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
226560 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:226737 original size:20 final size:20
Alignment explanation
Indices: 226712--226759 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
226702 TTTGGCGAAT
* *
226712 TTGCGATAATGGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
226732 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
226751 TTGCGATAA
1 TTGCGATAA
226760 GGCATTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:227881 original size:56 final size:56
Alignment explanation
Indices: 227774--227882 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
227764 TTTTTTATAT
*
227774 ATTAATTTAAAAAAAATAATTTTTATACTAAATTATTAAATATATTTTATTATTAA
1 ATTAATTTAAAAAAAATAATTTTTATACTAAATTATTAAATATATTATATTATTAA
** * * *
227830 ATTAATTTAAAAAATTTTATTTTTAT-TTAAA-TATATATATATATATATATTAT
1 ATTAATTTAAAAAAAATAATTTTTATACTAAATTAT-TAAATATAT-TATATTAT
227883 AATAAAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 3 0.07
55 12 0.27
56 30 0.67
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (56 bp):
ATTAATTTAAAAAAAATAATTTTTATACTAAATTATTAAATATATTATATTATTAA
Found at i:227940 original size:30 final size:30
Alignment explanation
Indices: 227897--228009 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 30
227887 AAATATTTTG
227897 AAGTTAAAATAAAAATAAAATATATTTAAT
1 AAGTTAAAATAAAAATAAAATATATTTAAT
* * * *
227927 AAGTTATAGTAAAAATATAATATATTTAGT
1 AAGTTAAAATAAAAATAAAATATATTTAAT
* * *
227957 AAATTAAGAT-AGAAT---ATATACTTTGAA-
1 AAGTTAAAATAAAAATAAAATATA-TTT-AAT
*
227984 AAGTTAAAATAATAAT-AAATATATTT
1 AAGTTAAAATAAAAATAAAATATATTT
228010 TTTAAAGTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
26 5 0.08
27 11 0.17
28 5 0.08
29 7 0.11
30 37 0.57
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (30 bp):
AAGTTAAAATAAAAATAAAATATATTTAAT
Found at i:228064 original size:26 final size:27
Alignment explanation
Indices: 228031--228085 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
228021 GACAAGAATA
*
228031 AAATTAAA-TAAAAATAAAACATTTTT
1 AAATTAAATTAAAAATAAAACATATTT
* *
228057 AAATTAAATTAATAATAAAATATATTT
1 AAATTAAATTAAAAATAAAACATATTT
228084 AA
1 AA
228086 TTAGCTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATTAAATTAAAAATAAAACATATTT
Found at i:228118 original size:24 final size:25
Alignment explanation
Indices: 228044--228121 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 25
228034 TTAAATAAAA
* * *
228044 ATAAAACATTTTTAAATTAAATTAAT
1 ATAAAAAATATTT-AATTAAGTTAAT
* *
228070 AATAAAATATATTTAATT-AGCTAAT
1 -ATAAAAAATATTTAATTAAGTTAAT
*
228095 ATAAAAAATATTT-CTTAAGTTAAT
1 ATAAAAAATATTTAATTAAGTTAAT
228119 ATA
1 ATA
228122 TATAACATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 2 0.05
24 21 0.49
25 5 0.12
26 4 0.09
27 11 0.26
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (25 bp):
ATAAAAAATATTTAATTAAGTTAAT
Found at i:232554 original size:59 final size:59
Alignment explanation
Indices: 232462--232579 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
232452 CTTTCAATTA
232462 CAGATTTACAAAGAGGACTTGTAAATTATAGTATAAGCTTGAGCTGGAATAGTTTTTTG
1 CAGATTTACAAAGAGGACTTGTAAATTATAGTATAAGCTTGAGCTGGAATAGTTTTTTG
232521 CAGATTTACAAAGAGGACTTGTAAATTATAGTATAAGCTTGAGCTGGAATAGTTTTTTG
1 CAGATTTACAAAGAGGACTTGTAAATTATAGTATAAGCTTGAGCTGGAATAGTTTTTTG
232580 TACTTCGATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (59 bp):
CAGATTTACAAAGAGGACTTGTAAATTATAGTATAAGCTTGAGCTGGAATAGTTTTTTG
Found at i:235535 original size:20 final size:20
Alignment explanation
Indices: 235512--235553 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
235502 GAATCCTTCG
235512 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
235532 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
235552 TC
1 TC
235554 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:235806 original size:103 final size:105
Alignment explanation
Indices: 235610--236229 Score: 1070
Period size: 103 Copynumber: 6.0 Consensus size: 105
235600 CGTTGTGAAG
* * *
235610 CTGAAATTGGGTAATG-TTATTGACAACCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
235673 C--GAGTCCAATATCCTTCGTTGTGAAGTTG-AA-TGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
235709 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
235774 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
235814 CTGAAATTGAGAAATGTTTGTTGACAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAAATGTTTGTTGAC-AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
235879 TCTGGAGTCCAATATCCTTCG-T-TGAAGTTGCAACTGG--
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
235916 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTC-TCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
235980 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
236020 CTGAAATTGAGAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
236085 CTGGAGTCCAATAT-CTTCGTTGTGAAGTTG-AATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
236123 CTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
236188 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-T
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
236227 CTG
1 CTG
236230 GGTAAAACCT
Statistics
Matches: 497, Mismatches: 10, Indels: 23
0.94 0.02 0.04
Matches are distributed among these distances:
99 14 0.03
100 60 0.12
101 47 0.09
102 38 0.08
103 113 0.23
104 91 0.18
105 74 0.15
106 60 0.12
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:236148 original size:207 final size:208
Alignment explanation
Indices: 235629--236229 Score: 1078
Period size: 207 Copynumber: 2.9 Consensus size: 208
235619 GGTAATGTTA
235629 TTGACAACCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTC--GAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
235691 TTGTGAAGTTGAATGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
66 TTGTGAAGTTGAATGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
235756 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
131 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
*
235821 TGAGAAATGTTTG
196 TGAGAAACGTTTG
235834 TTGACAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 TTGAC-AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
235899 G-T-TGAAGTTGCAACTGG--CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTC-TC
65 GTTGTGAAGTTG-AA-TGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
235959 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
128 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
236024 AATTGAGAAACGTTTG
193 AATTGAGAAACGTTTG
236040 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT-CTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
236104 TTGTGAAGTTGAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGT
66 TTGTGAAGTTGAA-TGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
236169 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TCTG
130 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
236230 GGTAAAACCT
Statistics
Matches: 382, Mismatches: 3, Indels: 20
0.94 0.01 0.05
Matches are distributed among these distances:
204 5 0.01
205 65 0.17
206 105 0.27
207 123 0.32
208 64 0.17
209 20 0.05
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (208 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAATGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
TGAGAAACGTTTG
Found at i:236654 original size:38 final size:38
Alignment explanation
Indices: 236603--236679 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
236593 AATGGTCTTT
236603 ATTCATAAGGGAGGAGAAGAACAAATAATACATGGCAA
1 ATTCATAAGGGAGGAGAAGAACAAATAATACATGGCAA
236641 ATTCATAAGGGAGGAGAAGAACAAATAATACATGGCAA
1 ATTCATAAGGGAGGAGAAGAACAAATAATACATGGCAA
236679 A
1 A
236680 CATTCTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.16
Consensus pattern (38 bp):
ATTCATAAGGGAGGAGAAGAACAAATAATACATGGCAA
Found at i:237058 original size:50 final size:55
Alignment explanation
Indices: 236980--237083 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 55
236970 ACCTTATTTT
* ** *
236980 CTTTTTTCTTTTTTCTTTTTCAATTTAGGGTGCCCTTTCGGG-TTTCA-CCTAAA
1 CTTTTTTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAA
237033 CTTTTTT-TTTTTT-TTTTT-AACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 CTTTTTTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
237084 GCGAAGTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 17 0.38
51 10 0.22
52 11 0.24
53 7 0.16
ACGTcount: A:0.13, C:0.21, G:0.12, T:0.53
Consensus pattern (55 bp):
CTTTTTTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAA
Found at i:249336 original size:12 final size:12
Alignment explanation
Indices: 249310--249354 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
249300 AAGAAAAATG
249310 TAATA-AATATA
1 TAATATAATATA
*
249321 TAATATAATTTA
1 TAATATAATATA
249333 TAATATAAATATA
1 TAATAT-AATATA
249346 TATATATAA
1 TA-ATATAA
249355 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:251885 original size:45 final size:45
Alignment explanation
Indices: 251819--252015 Score: 277
Period size: 46 Copynumber: 4.3 Consensus size: 45
251809 AATATATTTA
* * * * *
251819 CCATTTATCCCATAAGTTCGTAAGCTTATTTTACCAACATACTTA
1 CCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
* *
251864 TCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
1 CCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
* *
251909 CCATTTAATACCATTAGCTCGTAGGCTTATTTTACCAATACACTTG
1 CCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
*
251955 CCATTTAATACCATAAGCTCGTAATCTTATTTTACCAATACACTTG
1 CCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
*
252001 CCATTTATCCCATAA
1 CCATTTATACCATAA
252016 ACCATATACC
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 52 0.38
46 85 0.62
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (45 bp):
CCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACACTTG
Found at i:251920 original size:22 final size:22
Alignment explanation
Indices: 251895--251967 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
251885 AAGCTTATTT
251895 TACCAATACACTTGCCATTTAA
1 TACCAATACACTTGCCATTTAA
* * * *
251917 TACCATTAGCTCGTAGGCTTATTT--
1 TACCAATA-CAC-T-TGC-CATTTAA
251941 TACCAATACACTTGCCATTTAA
1 TACCAATACACTTGCCATTTAA
251963 TACCA
1 TACCA
251968 TAAGCTCGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 4 0.11
21 2 0.05
22 13 0.35
23 4 0.11
24 8 0.22
25 2 0.05
26 4 0.11
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (22 bp):
TACCAATACACTTGCCATTTAA
Found at i:251990 original size:92 final size:91
Alignment explanation
Indices: 251819--252015 Score: 272
Period size: 91 Copynumber: 2.2 Consensus size: 91
251809 AATATATTTA
* * * * *
251819 CCATTT-ATCCCATAAGTTCGTAAGCTTATTTTACCAACATACTTATCATTTATTCCATAAGCTC
1 CCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAACACACTTACCATTTATACCATAAGCTC
251883 GTAAGCTTATTTTACCAATACACTTG
66 GTAAGCTTATTTTACCAATACACTTG
* * * *
251909 CCATTTAATACCATTAGCTCGTAGGCTTATTTTACCAATACACTTGCCATTTAATACCATAAGCT
1 CCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAACACACTTACCATTT-ATACCATAAGCT
*
251974 CGTAATCTTATTTTACCAATACACTTG
65 CGTAAGCTTATTTTACCAATACACTTG
*
252001 CCATTT-ATCCCATAA
1 CCATTTAATACCATAA
252016 ACCATATACC
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 6 0.06
91 44 0.47
92 43 0.46
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (91 bp):
CCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAACACACTTACCATTTATACCATAAGCTC
GTAAGCTTATTTTACCAATACACTTG
Found at i:252008 original size:24 final size:24
Alignment explanation
Indices: 251889--252008 Score: 67
Period size: 24 Copynumber: 5.2 Consensus size: 24
251879 GCTCGTAAGC
251889 TTATTTTACCAATACACTTGCCAT
1 TTATTTTACCAATACACTTGCCAT
* * * * *
251913 TTA--ATACCATTAGCTCGTAGGC--
1 TTATTTTACCAATA-CAC-TTGCCAT
251935 TTATTTTACCAATACACTTGCCAT
1 TTATTTTACCAATACACTTGCCAT
* * **
251959 TTA--ATACC-ATA-AGCTCGTAAT
1 TTATTTTACCAATACA-CTTGCCAT
251980 CTTATTTTACCAATACACTTGCCAT
1 -TTATTTTACCAATACACTTGCCAT
252005 TTAT
1 TTAT
252009 CCCATAAACC
Statistics
Matches: 66, Mismatches: 18, Indels: 24
0.61 0.17 0.22
Matches are distributed among these distances:
20 1 0.02
21 8 0.12
22 20 0.30
23 4 0.06
24 24 0.36
25 8 0.12
26 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (24 bp):
TTATTTTACCAATACACTTGCCAT
Found at i:258992 original size:24 final size:24
Alignment explanation
Indices: 258914--258993 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
258904 ATTTCCGACT
* *
258914 TGAATTCTGTTATGATA-CATTACC
1 TGAATTCTGTTCTGATATC-TTATC
* * *
258938 TGAATTCTGTTCTGATTTCTGATT
1 TGAATTCTGTTCTGATATCTTATC
*
258962 TGGATTCTGTTCTGATATCTTATC
1 TGAATTCTGTTCTGATATCTTATC
*
258986 TAAATTCT
1 TGAATTCT
258994 ATTTTTATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATC
Found at i:258992 original size:48 final size:48
Alignment explanation
Indices: 258900--259008 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
258890 AAATATTTTA
* * * *
258900 TCTGATTTCCGACTTGAATTCTGTTATGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTATGATACATTACCTAAATTCTAT
* * *
258948 TCTGATTTCTGATTTGGATTCTGTTCTGATATC-TTATCTAAATTCTAT
1 TCTGATTTCTGATTTGAATTCTGTTATGATA-CATTACCTAAATTCTAT
* *
258996 TTTTATTTCTGAT
1 TCTGATTTCTGAT
259009 ATCTCCGTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATTTGAATTCTGTTATGATACATTACCTAAATTCTAT
Found at i:262377 original size:136 final size:132
Alignment explanation
Indices: 262135--262388 Score: 332
Period size: 136 Copynumber: 1.9 Consensus size: 132
262125 TAAATTATTT
* *
262135 TAAAATAAAAGGTAAACTACATAAATGATCATTTATCTTTTGTTTACACTTATACTCACTAAATC
1 TAAAATAAAAGGTAAACTACATAAATGATCACTTATCTTTTGTTTACACTTATACTCACCAAATC
*
262200 CAATAACATTAAATTTTAGTCTTTTACGTTATCGTTTTATTAAGTTTTAGTTACTAGGACGACAT
66 CAATAACATTAAATTTTAGTCTCTTACGTTATCGTTTTATTAAGTTTTAGTTACTAGGACGACAT
262265 TC
131 TC
* * *
262267 TAAAATAAAAGGTAAACTACATGAATGATCACTTATCTTTTATTTTTGTACACTTGTGA-TCACC
1 TAAAATAAAAGGTAAACTACATAAATGATCACTTATC--TT-TTGTT-TACACTTAT-ACTCACC
** * * * *
262331 AAATTTAATAATATTAAATTTTAGT-TACTTAGGTTATTGTTTTATTAAGTTTTGGTTA
61 AAATCCAATAACATTAAATTTTAGTCT-CTTACGTTATCGTTTTATTAAGTTTTAGTTA
262389 TTGAGACGTT
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
132 35 0.34
134 2 0.02
135 5 0.05
136 61 0.59
137 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (132 bp):
TAAAATAAAAGGTAAACTACATAAATGATCACTTATCTTTTGTTTACACTTATACTCACCAAATC
CAATAACATTAAATTTTAGTCTCTTACGTTATCGTTTTATTAAGTTTTAGTTACTAGGACGACAT
TC
Found at i:262749 original size:14 final size:15
Alignment explanation
Indices: 262732--262819 Score: 78
Period size: 15 Copynumber: 6.1 Consensus size: 15
262722 GTGAAATTCT
*
262732 AATTA-TTAAATAAA
1 AATTATTTATATAAA
262746 AATTATTTATATAAAA
1 AATTATTTATAT-AAA
262762 AATTATTTATATAAA
1 AATTATTTATATAAA
* * *
262777 AA--A-TCATCT-AT
1 AATTATTTATATAAA
*
262788 AATATATTTAAATAAA
1 AAT-TATTTATATAAA
262804 AATTATTTATATAAA
1 AATTATTTATATAAA
262819 A
1 A
262820 TTCATCGATA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.05
12 4 0.07
13 1 0.02
14 6 0.10
15 25 0.43
16 19 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:262788 original size:16 final size:16
Alignment explanation
Indices: 262743--262780 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
262733 ATTATTAAAT
262743 AAAAATTATTTATATA
1 AAAAATTATTTATATA
262759 AAAAATTATTTATATA
1 AAAAATTATTTATATA
262775 AAAAAT
1 AAAAAT
262781 CATCTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATTATTTATATA
Found at i:262813 original size:42 final size:42
Alignment explanation
Indices: 262749--262833 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
262739 AAATAAAAAT
* *
262749 TATTTATATAAAAAATTATTTATATAAAAAATCATCTATAATA
1 TATTTAAATAAAAAATTATTTATAT-AAAAATCATCGATAATA
*
262792 TATTTAAAT-AAAAATTATTTATATAAAATTCATCGATAATA
1 TATTTAAATAAAAAATTATTTATATAAAAATCATCGATAATA
262833 T
1 T
262834 TTTTTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 16 0.41
42 15 0.38
43 8 0.21
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (42 bp):
TATTTAAATAAAAAATTATTTATATAAAAATCATCGATAATA
Found at i:265640 original size:2 final size:2
Alignment explanation
Indices: 265633--265662 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
265623 AAAACTACTT
265633 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
265663 AATTATTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:266536 original size:31 final size:31
Alignment explanation
Indices: 266498--266607 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
266488 TAAAAAAACA
*
266498 TAAGTTTTGGTTACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
*
266529 TATGTTTTGGTCACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
* *
266560 TAAGTTTTAGCCACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
*
266591 TAAGTTTTGGTAACTTA
1 TAAGTTTTGGTCACTTA
266608 GACGTTGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCATTTTAT
Found at i:266628 original size:62 final size:61
Alignment explanation
Indices: 266510--266628 Score: 134
Period size: 62 Copynumber: 1.9 Consensus size: 61
266500 AGTTTTGGTT
* * *** *
266510 ACTTACGTTATCATTTTATTATGTTTTGGTCACTTACGTTATCATTTTATTAAGTTTTAGCC
1 ACTTACGTTATCATTTTATTAAGTTTTGGTAACTTACGTTA-CATGCCACTAAGTTTTAGCC
266572 ACTTACGTTATCATTTTATTAAGTTTTGGTAACTTAGACGTTGA-ATGCCACT-AGTTT
1 ACTTACGTTATCATTTTATTAAGTTTTGGTAACTT--ACGTT-ACATGCCACTAAGTTT
266629 GATGACATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
62 38 0.79
63 4 0.08
64 5 0.10
65 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.48
Consensus pattern (61 bp):
ACTTACGTTATCATTTTATTAAGTTTTGGTAACTTACGTTACATGCCACTAAGTTTTAGCC
Found at i:269693 original size:30 final size:31
Alignment explanation
Indices: 269638--269698 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
269628 ATTTAAAATC
*
269638 ATGATCTTCAACGTCGAATAATTGTT-TTTT
1 ATGATCTTAAACGTCGAATAATTGTTCTTTT
**
269668 ATGATCTTAAACGTCGAATCTTTGTTCTTTT
1 ATGATCTTAAACGTCGAATAATTGTTCTTTT
269699 TCCCAAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (31 bp):
ATGATCTTAAACGTCGAATAATTGTTCTTTT
Found at i:270507 original size:31 final size:31
Alignment explanation
Indices: 270437--270510 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
270427 AATGGGCAAG
* * * *
270437 TGACAAAAAGTTAATAAAACGATAAAGTAAG
1 TGACCAAAACTTAATAAAACAATAAAGTAAA
* * *
270468 CGATCAAAACTTAATAAAACAATAACGTAAA
1 TGACCAAAACTTAATAAAACAATAAAGTAAA
270499 TGACCAAAACTT
1 TGACCAAAACTT
270511 GTGTTTTTTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACAATAAAGTAAA
Found at i:271369 original size:29 final size:31
Alignment explanation
Indices: 271308--271383 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
271298 AATCAAACAC
*
271308 TTTTATGATTTTT-AAAAATCATAATTTTATT
1 TTTTAT-ATTTTTAAAAAATCATAATATTATT
*
271339 TTTTATATTTTTAAAAAAT-ATAA-ATTCTT
1 TTTTATATTTTTAAAAAATCATAATATTATT
*
271368 TTATATATTTTTAAAA
1 TTTTATATTTTTAAAA
271384 TATTTTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 19 0.46
30 10 0.24
31 12 0.29
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTATATTTTTAAAAAATCATAATATTATT
Found at i:274273 original size:19 final size:19
Alignment explanation
Indices: 274249--274286 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
274239 TCCAAGTTTG
*
274249 CGTTGCGATTTTTCAAATT
1 CGTTGCGATTTTACAAATT
274268 CGTTGCGATTTTACAAATT
1 CGTTGCGATTTTACAAATT
274287 TACGTTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTACAAATT
Found at i:274328 original size:21 final size:21
Alignment explanation
Indices: 274303--274384 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
274293 AGTCTAAATT
274303 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
* *
274324 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCA
** *
274345 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCA
274364 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
274385 TGTTCGAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
19 16 0.32
21 34 0.68
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCA
Found at i:274369 original size:19 final size:19
Alignment explanation
Indices: 274230--274379 Score: 74
Period size: 21 Copynumber: 7.7 Consensus size: 19
274220 CAACGCGATT
* *
274230 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATTGTCCAA-ATT-CG
* *
274251 TTGCGATTTTTCAAATTCG
1 TTGCGATTGTCCAAATTCG
* *
274270 TTGCGATTTTACAAA-T--
1 TTGCGATTGTCCAAATTCG
* *
274286 TTACG-TTAGTCTAAATTCG
1 TTGCGATT-GTCCAAATTCG
* *
274305 TTGCGATAGTCCAAGTTCACG
1 TTGCGATTGTCCAAATT--CG
* * *
274326 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATTGTCCAAATT--CG
*
274347 TTGCGATTTTCCAAATTCG
1 TTGCGATTGTCCAAATTCG
*
274366 TTGCGATAGTCCAA
1 TTGCGATTGTCCAA
274380 GTTCATGTTC
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.02
16 8 0.08
17 1 0.01
18 1 0.01
19 41 0.41
20 3 0.03
21 45 0.45
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGCGATTGTCCAAATTCG
Found at i:274455 original size:40 final size:40
Alignment explanation
Indices: 274400--274494 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
274390 GAAGTTCGTA
** *
274400 TTGCGATTTTCCAAATTCGTTGTGATAGTCTTAGTTTACG
1 TTGCGATTTTCCAAATTCGTTGTGATAGTCGAAGTTCACG
* *
274440 TTGCGATTTTCCAAATTTGTTGTGATAGTCGAAGTTCGCG
1 TTGCGATTTTCCAAATTCGTTGTGATAGTCGAAGTTCACG
274480 TTGCGATTTTCCAAA
1 TTGCGATTTTCCAAA
274495 ATCGCAACGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (40 bp):
TTGCGATTTTCCAAATTCGTTGTGATAGTCGAAGTTCACG
Found at i:274986 original size:19 final size:19
Alignment explanation
Indices: 274937--274978 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
274927 TCAAACTCTT
274937 GCAACACATTTTAACTATC
1 GCAACACATTTTAACTATC
274956 GCAACACATTTTAACTATC
1 GCAACACATTTTAACTATC
274975 GCAA
1 GCAA
274979 TATATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (19 bp):
GCAACACATTTTAACTATC
Found at i:275014 original size:20 final size:21
Alignment explanation
Indices: 274991--275046 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
274981 TATTTTTTAA
*
274991 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
* *
275011 AATCACGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
*
275032 ATTCGCGTTGCGAAT
1 AATCGCGTTGCGAAT
275047 TTGAAAACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:276637 original size:21 final size:21
Alignment explanation
Indices: 276613--276686 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
276603 TATCGCAAAT
*
276613 TCGCGTTGAGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
276634 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
276654 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
276675 TCGCGTTGCGAT
1 TCGCGTTGCGAT
276687 TTTCCATTTG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:276669 original size:41 final size:41
Alignment explanation
Indices: 276612--276695 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
276602 CTATCGCAAA
276612 TTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
276653 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAT
276694 TT
1 TT
276696 GCGATTTTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:276699 original size:14 final size:14
Alignment explanation
Indices: 276680--276709 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
276670 GAAAATCGCG
276680 TTGCGATTTTCCAT
1 TTGCGATTTTCCAT
276694 TTGCGATTTTCCAT
1 TTGCGATTTTCCAT
276708 TT
1 TT
276710 CGCGTTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (14 bp):
TTGCGATTTTCCAT
Found at i:276741 original size:55 final size:55
Alignment explanation
Indices: 276639--276750 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
276629 GAAAATCGCG
*** *
276639 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTGTCCAT
*
276694 TTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAATCGCAACGCGATTGTCCAT
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTGTCCAT
276749 TT
1 TT
276751 CGCGTTGCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (55 bp):
TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTGTCCAT
Found at i:276753 original size:41 final size:41
Alignment explanation
Indices: 276696--276774 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
276686 TTTTCCATTT
* *
276696 GCGATTTTCCATTTCGCGTTGCTATAGTTGAAAATCGCAAC
1 GCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
276737 GCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGC
1 GCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGC
276775 GTTGCGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (41 bp):
GCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
Found at i:276776 original size:96 final size:96
Alignment explanation
Indices: 276612--276786 Score: 296
Period size: 96 Copynumber: 1.8 Consensus size: 96
276602 CTATCGCAAA
*** *
276612 TTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
1 TTCGCGTTGAGATAGTTGAAAATCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATC
276677 GCGTTGCGATTTTCCATTTGCGATTTTCCAT
66 GCGTTGCGATTTTCCATTTGCGATTTTCCAT
**
276708 TTCGCGTTGCTATAGTTGAAAATCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATC
1 TTCGCGTTGAGATAGTTGAAAATCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATC
276773 GCGTTGCGATTTTC
66 GCGTTGCGATTTTC
276787 TACAGTTGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (96 bp):
TTCGCGTTGAGATAGTTGAAAATCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATC
GCGTTGCGATTTTCCATTTGCGATTTTCCAT
Found at i:276782 original size:41 final size:41
Alignment explanation
Indices: 276694--276783 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
276684 GATTTTCCAT
* *
276694 TTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAATCGCA
1 TTGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCA
** *
276735 ACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCG
1 TTGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCA
276776 TTGCGATT
1 TTGCGATT
276784 TTCTACAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TTGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCA
Found at i:276803 original size:22 final size:22
Alignment explanation
Indices: 276774--276830 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
276764 TTGAAAATCG
276774 CGTTGCGATTTTCTACAGTTGT
1 CGTTGCGATTTTCTACAGTTGT
* **
276796 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCTACAGTTGT
276818 CGTTGCGATTTTC
1 CGTTGCGATTTTC
276831 CAAATTCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.44
Consensus pattern (22 bp):
CGTTGCGATTTTCTACAGTTGT
Found at i:276988 original size:6 final size:6
Alignment explanation
Indices: 276925--276984 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
276915 AGACACGTAT
*
276925 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC GACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
* *
276973 GACCAC GACCAC
1 TACCAC TACCAC
276985 GACCCGAGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.50, G:0.05, T:0.12
Consensus pattern (6 bp):
TACCAC
Found at i:277489 original size:6 final size:6
Alignment explanation
Indices: 277480--277522 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
277470 CCGTCCCGTC
277480 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
277523 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:291409 original size:383 final size:378
Alignment explanation
Indices: 290861--291611 Score: 1133
Period size: 383 Copynumber: 2.0 Consensus size: 378
290851 CACTCCAATT
*
290861 ACAATAAAAATAAAACTCAAAATGGTTTTGTGAAATTTCTCATGCCACTATGTTGAAGCTTGTTT
1 ACAATAAAAATAAAACTCAAAATGGTTTTGTGAAATTTCTCATACCACTATGTTGAAGCTTGTTT
* *
290926 AAGGCCATAAACTTTTCAAGTCTACACATTTTACCTTCCATGATAGGTGCTTAAAAACCTGGTGG
66 AAGGCCATAAACTTTTCAAGTCTACACACTTTACCTTCCATGATAGGTGCTTAAAAACCTAGTGG
* * * * ** *
290991 TTGCTCCATTTACATTTTCTCATCTAGATCTCTATTTAAAAATTCAATCTTTATATCCATTTGAT
131 TTGCTCCATATACATATCCTCATCTAGACCTCTATTTAAAAATGAAATCTTTACATCCATTTGAT
* * * *
291056 GTACGTGTAACTTATGAATGGACGCTATCAAAAACAAGGCACGCATCATTTAGTTTTTTGTGATG
196 GTACGTGTAAATTATGAATAGACGCTATCAAAAACAAGGCAC-AATCATTGAGTTTTTTGTGATG
* * ** *
291121 GGAGAGTATGTATCAAAGAAGTCTATACCAAACTTCTTAGTAAACTTTTTGACTACTAGTCTTAC
260 GGAGAGTATGCATCAAAGAAGTCTATACCAAACTTCTGAGTAAACCCTTTGACTACTAATCTTAC
* * *
291186 ATTATATCTCTAGATTGACGTATCTGGTCTAAGTTTCTTTTTGAGGACCCATTC
325 ATTATATATCTAGATTGACATAGCTGGTCTAAGTTTCTTTTTGAGGACCCATTC
* ** * *
291240 ACAATAAAACTAAAACTCAAAATGGTTTTGTGAAATTTCTTGTACCACTGTTTTGAAGCTTGTTT
1 ACAATAAAAATAAAACTCAAAATGGTTTTGTGAAATTTCTCATACCACTATGTTGAAGCTTGTTT
** *
291305 AAGGCCATAAAGTGACTTTTTTAGTCTACACACTTTACCTTCCATGCTAGGTGCTTAAAAACCTA
66 AAGGCCAT-AA---ACTTTTCAAGTCTACACACTTTACCTTCCATGATAGGTGCTTAAAAACCTA
*
291370 GTGGTTGCTCCATATAGATATCCTCATCTAGACCTCTATTTAAAAATGAAATCTTTACATCCATT
127 GTGGTTGCTCCATATACATATCCTCATCTAGACCTCTATTTAAAAATGAAATCTTTACATCCATT
* * * *
291435 TGATGTACGTGTAAATTATGAATAGATGCTATCACAAATAAGGTACAATCATTGAGTTTTTTGTG
192 TGATGTACGTGTAAATTATGAATAGACGCTATCAAAAACAAGGCACAATCATTGAGTTTTTTGTG
*
291500 ATGGGAGAGTATGCATCAAAGAAGTTTATACCAAACTTCTGAGTAAACCCTTTGACTACTAATCT
257 ATGGGAGAGTATGCATCAAAGAAGTCTATACCAAACTTCTGAGTAAACCCTTTGACTACTAATCT
291565 TACATTATATATCTAGATTGACATAGCTGGTCTAAGTTTCTTTTTGA
322 TACATTATATATCTAGATTGACATAGCTGGTCTAAGTTTCTTTTTGA
291612 AGAACAATTT
Statistics
Matches: 332, Mismatches: 36, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
379 67 0.20
380 2 0.01
382 120 0.36
383 143 0.43
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (378 bp):
ACAATAAAAATAAAACTCAAAATGGTTTTGTGAAATTTCTCATACCACTATGTTGAAGCTTGTTT
AAGGCCATAAACTTTTCAAGTCTACACACTTTACCTTCCATGATAGGTGCTTAAAAACCTAGTGG
TTGCTCCATATACATATCCTCATCTAGACCTCTATTTAAAAATGAAATCTTTACATCCATTTGAT
GTACGTGTAAATTATGAATAGACGCTATCAAAAACAAGGCACAATCATTGAGTTTTTTGTGATGG
GAGAGTATGCATCAAAGAAGTCTATACCAAACTTCTGAGTAAACCCTTTGACTACTAATCTTACA
TTATATATCTAGATTGACATAGCTGGTCTAAGTTTCTTTTTGAGGACCCATTC
Found at i:293867 original size:108 final size:107
Alignment explanation
Indices: 293677--293896 Score: 329
Period size: 108 Copynumber: 2.0 Consensus size: 107
293667 ATTTTGTAAA
* *
293677 CTTTTGAAGATTTTAGACCAAAATTTAAAGTCCGTGAAAGTTCAAGGACTCGTTTCTTGATTTGA
1 CTTTTGAAGATTTTAGACCAAAATTTAAAGTCCGTGAAAGTTCAAGGACTCGTTCCCTGATTTGA
293742 CCATCGTTAGTCAACATAGAAAAAGAAGAAGGAAAAAGTGAGAT
66 CCATCGTTAGTCAACATAGAAAAA-AAGAAGG-AAAAGTGAGAT
293786 CTTTTGAAGATTTTAGACCAAAATTTAAAG-CAC-TGAAAGTTCAAGGACTCGTTCCCTGATTTG
1 CTTTTGAAGATTTTAGACCAAAATTTAAAGTC-CGTGAAAGTTCAAGGACTCGTTCCCTGATTTG
* * *
293849 ATCGTCGTT-GGCTAACATAGAAAAAAAGAAGGAAAAGTGAGAT
65 ACCATCGTTAGTC-AACATAGAAAAAAAGAAGGAAAAGTGAGAT
*
293892 ATTTT
1 CTTTT
293897 CAACGTGTGG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
106 15 0.15
107 9 0.09
108 48 0.47
109 31 0.30
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (107 bp):
CTTTTGAAGATTTTAGACCAAAATTTAAAGTCCGTGAAAGTTCAAGGACTCGTTCCCTGATTTGA
CCATCGTTAGTCAACATAGAAAAAAAGAAGGAAAAGTGAGAT
Found at i:294704 original size:15 final size:15
Alignment explanation
Indices: 294686--294733 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
294676 CCACTAAGTT
*
294686 AACTCGCACTGAGTC
1 AACTCACACTGAGTC
*
294701 AACTCACATTGAGTC
1 AACTCACACTGAGTC
* *
294716 AACTCACATTAAGTC
1 AACTCACACTGAGTC
294731 AAC
1 AAC
294734 CTAGTCTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.23
Consensus pattern (15 bp):
AACTCACACTGAGTC
Found at i:294767 original size:17 final size:16
Alignment explanation
Indices: 294745--294788 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
294735 TAGTCTGTTA
*
294745 ACTTTGATCCTACGTTG
1 ACTTTGA-CCAACGTTG
*
294762 ACTTTGACCAAGGTTG
1 ACTTTGACCAACGTTG
*
294778 ACTTTAACCAA
1 ACTTTGACCAA
294789 AAAGTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (16 bp):
ACTTTGACCAACGTTG
Found at i:294779 original size:16 final size:16
Alignment explanation
Indices: 294758--294788 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
294748 TTGATCCTAC
*
294758 GTTGACTTTGACCAAG
1 GTTGACTTTAACCAAG
294774 GTTGACTTTAACCAA
1 GTTGACTTTAACCAA
294789 AAAGTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (16 bp):
GTTGACTTTAACCAAG
Found at i:303072 original size:22 final size:22
Alignment explanation
Indices: 303044--303087 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
303034 CCTTTTAGTG
*
303044 ATACTGAAACTCTGCCCGTTTT
1 ATACTGAAACTCTACCCGTTTT
*
303066 ATACTGAACCTCTACCCGTTTT
1 ATACTGAAACTCTACCCGTTTT
303088 TCTTCGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (22 bp):
ATACTGAAACTCTACCCGTTTT
Found at i:303678 original size:21 final size:21
Alignment explanation
Indices: 303654--303747 Score: 120
Period size: 21 Copynumber: 4.4 Consensus size: 21
303644 ACCAAGGACT
*
303654 AGAAGACTATTCATCAAGACG
1 AGAAGACCATTCATCAAGACG
303675 AGAAGACCATTCATCAAGACG
1 AGAAGACCATTCATCAAGACG
*
303696 AGAAGACCATTCGTCAAGGACG
1 AGAAGACCATTCATCAA-GACG
*
303718 AGAAGACCCTTCAT-AATGAC-
1 AGAAGACCATTCATCAA-GACG
303738 ATGAAGACCA
1 A-GAAGACCA
303748 CTTCGCATTG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 48 0.74
22 16 0.25
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.16
Consensus pattern (21 bp):
AGAAGACCATTCATCAAGACG
Found at i:303725 original size:43 final size:41
Alignment explanation
Indices: 303654--303752 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 41
303644 ACCAAGGACT
* *
303654 AGAAGACTATTCATCAAGACGAGAAGACCATTCATCAA-GAC
1 AGAAGACCATTCGTCAAGACGAGAAGACCATTCAT-AATGAC
*
303695 GAGAAGACCATTCGTCAAGGACGAGAAGACCCTTCATAATGAC
1 -AGAAGACCATTCGTCAA-GACGAGAAGACCATTCATAATGAC
303738 ATGAAGACCACTTCG
1 A-GAAGACCA-TTCG
303753 CATTGGAGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
42 18 0.36
43 28 0.56
44 4 0.08
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
AGAAGACCATTCGTCAAGACGAGAAGACCATTCATAATGAC
Done.