Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003694.1 Hibiscus syriacus cultivar Beakdansim tig00007895_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: 787758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:282322 original size:22 final size:21
Alignment explanation
Indices: 282283--282325 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
282273 GATATTTTTA
**
282283 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
282304 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
282326 ACATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:293703 original size:33 final size:28
Alignment explanation
Indices: 293665--293758 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 28
293655 ATTATGCTTG
293665 AAGAAAAGAAAAAAAAAGAAAAAATGATGAATA
1 AAGAAAAGAAAAAAAAAGAAAAAA--A--AA-A
* *
293698 AAGAAAAGAAAAAAAGAGAATAAAAAAA
1 AAGAAAAGAAAAAAAAAGAAAAAAAAAA
* * *
293726 AAG-AAAGAAAAAAAAAGAGAGAAGAAA
1 AAGAAAAGAAAAAAAAAGAAAAAAAAAA
293753 AAGAAA
1 AAGAAA
293759 GGGGGTCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
27 22 0.42
28 6 0.11
29 2 0.04
31 1 0.02
33 22 0.42
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (28 bp):
AAGAAAAGAAAAAAAAAGAAAAAAAAAA
Found at i:293708 original size:23 final size:23
Alignment explanation
Indices: 293673--293736 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
293663 TGAAGAAAAG
*
293673 AAAAAAAAAGAAAAAATGATGAAT
1 AAAAAAAAAGAAAAAAAGA-GAAT
*
293697 -AAAGAAAAGAAAAAAAGAGAAT
1 AAAAAAAAAGAAAAAAAGAGAAT
293719 AAAAAAAAAGAAAGAAAA
1 AAAAAAAAAGAAA-AAAA
293737 AAAAAGAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.11
23 27 0.77
24 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (23 bp):
AAAAAAAAAGAAAAAAAGAGAAT
Found at i:293725 original size:14 final size:13
Alignment explanation
Indices: 293697--293756 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
293687 AATGATGAAT
293697 AAAGA-AAAGAAAA
1 AAAGAGAAA-AAAA
293710 AAAGAGAATAAAAAA
1 AAAGAG-A-AAAAAA
*
293725 AAAGAAAGAAAAAA
1 AAAGAGA-AAAAAA
* *
293739 AAAGAGAGAAGAA
1 AAAGAGAAAAAAA
293752 AAAGA
1 AAAGA
293757 AAGGGGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 14 0.36
14 13 0.33
15 10 0.26
16 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAA
Found at i:293741 original size:31 final size:32
Alignment explanation
Indices: 293665--293759 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 32
293655 ATTATGCTTG
* ** *
293665 AAGAAAAGAAAAAAAAAGAA-AAAATGATGAATA
1 AAGAAAAGAAAAAAAGAGAAGAAAA--AAAAAGA
*
293698 AAGAAAAGAAAAAAAGAGAATAAAAAAAAAGA
1 AAGAAAAGAAAAAAAGAGAAGAAAAAAAAAGA
* *
293730 AAGAAAA-AAAAAGAGAGAAGAAAAAGAAAG
1 AAGAAAAGAAAAAAAGAGAAGAAAAAAAAAG
293760 GGGGTCAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 20 0.37
32 11 0.20
33 19 0.35
34 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (32 bp):
AAGAAAAGAAAAAAAGAGAAGAAAAAAAAAGA
Found at i:293753 original size:13 final size:14
Alignment explanation
Indices: 293669--293759 Score: 71
Period size: 14 Copynumber: 6.3 Consensus size: 14
293659 TGCTTGAAGA
293669 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
293683 AAA-AAATGATGAATAAAG
1 AAAGAAA--A--AA-AAAG
*
293701 AAA-AGAAAAAAAG
1 AAAGAAAAAAAAAG
*
293714 AGAATAAAAAAAAAG
1 A-AAGAAAAAAAAAG
293729 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
* *
293743 AGAG-AAGAAAAAG
1 AAAGAAAAAAAAAG
293756 AAAG
1 AAAG
293760 GGGGTCAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
13 19 0.30
14 22 0.34
15 11 0.17
16 1 0.02
17 2 0.03
18 9 0.14
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:293759 original size:27 final size:27
Alignment explanation
Indices: 293663--293758 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 27
293653 ATATTATGCT
*
293663 TGAAG-AAAAGAAAAAAAAAGAAA-AAA
1 TGAAGAAAAAGAAAAAAAAA-AAAGAGA
* *
293689 TGATGAATAAAGAAAAGAAAAAAAGAGAA
1 TGAAGAA-AAAGAAAAAAAAAAAAGAG-A
* *
293718 TAAAAAAAAAGAAAGAAAAAAAAAGAGA
1 TGAAGAAAAAGAAA-AAAAAAAAAGAGA
293746 -GAAGAAAAAGAAA
1 TGAAGAAAAAGAAA
293759 GGGGGTCAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.07
27 15 0.27
28 21 0.38
29 16 0.29
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (27 bp):
TGAAGAAAAAGAAAAAAAAAAAAGAGA
Found at i:294103 original size:16 final size:17
Alignment explanation
Indices: 294084--294129 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
294074 CTATTTCAAG
*
294084 TTCAATTTATTT-GAGA
1 TTCAATTTATTTGGAAA
294100 TTCAATTTACTTTTGGAAA
1 TTCAATTTA--TTTGGAAA
294119 TTCAATTTATT
1 TTCAATTTATT
294130 CTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 3 0.12
19 12 0.46
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (17 bp):
TTCAATTTATTTGGAAA
Found at i:294829 original size:84 final size:84
Alignment explanation
Indices: 294688--295335 Score: 1226
Period size: 84 Copynumber: 7.7 Consensus size: 84
294678 AACCTTTTAT
*
294688 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
294753 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
294772 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
294837 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* *
294856 ATGTGCCCAATAGCATCTTCTAGAAGTTTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
294921 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
294940 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
295005 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
295024 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
295089 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
295108 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
295173 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
*
295192 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAACTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
295257 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* * *
295276 ATGTG-CCAAAAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAAC
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
295336 TTACAGAACC
Statistics
Matches: 554, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 51 0.09
84 503 0.91
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (84 bp):
ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAATTTAGAAGATGA
Found at i:296114 original size:113 final size:113
Alignment explanation
Indices: 295946--296791 Score: 1495
Period size: 113 Copynumber: 7.5 Consensus size: 113
295936 TGCAAGGTAG
295946 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296011 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
*
296059 AGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296124 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGA-AA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
296171 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
296236 AACCTTTT-GCTCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAA
66 AACCTTTTACCT-GAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
296284 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296349 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
296397 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296462 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGA-AA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
296509 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
296574 AACCTTTT-GCTCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAA
66 AACCTTTTACCT-GAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
296622 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296687 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAG-A
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
* * *
296734 AGTTCATAATGAGAAGAATTCATCTGAAGAAGAAAGAAAAAGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
296792 CTCATCAAGA
Statistics
Matches: 698, Mismatches: 29, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
111 4 0.01
112 261 0.37
113 429 0.61
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAA
Found at i:296337 original size:225 final size:226
Alignment explanation
Indices: 295946--296791 Score: 1495
Period size: 225 Copynumber: 3.8 Consensus size: 226
295936 TGCAAGGTAG
295946 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296011 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
*
296076 ACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
296141 CATCATTTGATGGATCATCTTTTCCAGA-AA
196 CATCATTTGATGGATCATCTTTTCCAGAGAA
296171 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
296236 AACCTTTT-GCTCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAG
66 AACCTTTTACCT-GAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
296300 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
130 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
296365 CCATCATTTGATGGATCATCTTTTCCAGAGAA
195 CCATCATTTGATGGATCATCTTTTCCAGAGAA
296397 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296462 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
* *
296526 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCAAAT
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT-GAAT
* * * *
296590 CTATCACTTGATGGATTATTTTTTCCAGAGAA
195 CCATCATTTGATGGATCATCTTTTCCAGAGAA
296622 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296687 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
* * *
296751 ATTCATCTGAAGAAGAAAGAAAAAGTTCATAATGAGAAGAA
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
296792 CTCATCAAGA
Statistics
Matches: 594, Mismatches: 22, Indels: 10
0.95 0.04 0.02
Matches are distributed among these distances:
224 4 0.01
225 485 0.82
226 103 0.17
227 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (226 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
CATCATTTGATGGATCATCTTTTCCAGAGAA
Found at i:296348 original size:338 final size:338
Alignment explanation
Indices: 295946--296791 Score: 1649
Period size: 338 Copynumber: 2.5 Consensus size: 338
295936 TGCAAGGTAG
295946 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296011 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
*
296076 ACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
296141 CATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
196 CATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
296206 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAT
261 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAT
296271 TTTTTCCAGAGAA
326 TTTTTCCAGAGAA
296284 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296349 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
296414 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
296479 CATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
196 CATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
296544 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAT
261 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAT
296609 TTTTTCCAGAGAA
326 TTTTTCCAGAGAA
296622 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
296687 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGA
66 AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
* * *
296751 ATTCATCTGAAGAAGAAAGAAAAAGTTCATAATGAGAAGAA
131 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
296792 CTCATCAAGA
Statistics
Matches: 504, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
337 56 0.11
338 448 0.89
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (338 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTACCTGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
CATCATTTGATGGATCATCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAT
TTTTTCCAGAGAA
Found at i:297048 original size:3 final size:3
Alignment explanation
Indices: 297040--297119 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
297030 TTTTTATCCA
* *
297040 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
297088 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
297120 AATATATTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:297159 original size:20 final size:19
Alignment explanation
Indices: 297118--297162 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
297108 CTATTATTAT
* *
297118 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
297137 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
297157 TAAATA
1 TAAATA
297163 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:298573 original size:22 final size:21
Alignment explanation
Indices: 298534--298576 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
298524 GATATTTTTA
**
298534 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
298555 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
298577 ACATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:300325 original size:99 final size:100
Alignment explanation
Indices: 300147--300346 Score: 341
Period size: 100 Copynumber: 2.0 Consensus size: 100
300137 AATAAATTTA
* *
300147 ATAATCAATCAAATTTTATAAATTTAAAAAATCTTCATGAGTCTAATAATTTTTTTGGGGGTGCT
1 ATAATCAATCAAATTTTATAAATTTAAAAAATCTTCATGAGTATAATAAATTTTTTGGGGGTGCT
*
300212 TACAAGCCTAAAAATTCATCTTCAATTAAATGTCT
66 TACAAGCCTAAAAATTCACCTTCAATTAAATGTCT
*
300247 ATAATCAATCAAATTTTATAAATTTAAAAAGTCTTCATGAGTAATAA-AAATTTTTT-GGGGTGC
1 ATAATCAATCAAATTTTATAAATTTAAAAAATCTTCATGAGT-ATAATAAATTTTTTGGGGGTGC
300310 TTACAAGCCTAAAAATTCACCTTCAATTAAATGTCT
65 TTACAAGCCTAAAAATTCACCTTCAATTAAATGTCT
300346 A
1 A
300347 CTAAACCTGG
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
99 43 0.45
100 49 0.52
101 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (100 bp):
ATAATCAATCAAATTTTATAAATTTAAAAAATCTTCATGAGTATAATAAATTTTTTGGGGGTGCT
TACAAGCCTAAAAATTCACCTTCAATTAAATGTCT
Found at i:300706 original size:2 final size:2
Alignment explanation
Indices: 300694--300736 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
300684 TATTTTACTT
* * *
300694 TA TA CA TA TA TA TA TA TA TA TA TC TA TA CA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
300735 TA
1 TA
300737 GTTCGCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:300938 original size:32 final size:33
Alignment explanation
Indices: 300863--300952 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
300853 TTTTAAAAAA
*
300863 AAAACATTTTTTGAAAAC-ATATAATATAGTTTT
1 AAAACA-TTTTTGAAAACTATATAATACAGTTTT
*
300896 AAAACGTTTTTGAAAACTATA-ACATACAG-TTT
1 AAAACATTTTTGAAAACTATATA-ATACAGTTTT
* *
300928 GAAACATTTTT-AAAATTATATAATA
1 AAAACATTTTTGAAAACTATATAATA
300953 TATGATTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 11 0.22
32 25 0.51
33 13 0.27
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.39
Consensus pattern (33 bp):
AAAACATTTTTGAAAACTATATAATACAGTTTT
Found at i:301052 original size:9 final size:8
Alignment explanation
Indices: 301038--301092 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
301028 TATTATTTTG
301038 TTTTATTCT
1 TTTTATT-T
301047 TTTTATTT
1 TTTTATTT
301055 TTTTATTT
1 TTTTATTT
301063 ATTTTATTT
1 -TTTTATTT
301072 TTGTT-TTT
1 TT-TTATTT
*
301080 ATTTATTT
1 TTTTATTT
*
301088 ATTTA
1 TTTTA
301093 ATCGTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
7 2 0.05
8 23 0.55
9 17 0.40
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:301060 original size:17 final size:17
Alignment explanation
Indices: 301038--301092 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
301028 TATTATTTTG
301038 TTTTATTCT-TTTTATTT
1 TTTTATT-TATTTTATTT
301055 TTTTATTTATTTTATTT
1 TTTTATTTATTTTATTT
301072 TTGTT-TTTA-TTTATTT
1 TT-TTATTTATTTTATTT
*
301088 ATTTA
1 TTTTA
301093 ATCGTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 21 0.62
18 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATTTATTTTATTT
Found at i:301100 original size:21 final size:21
Alignment explanation
Indices: 301054--301101 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
301044 TCTTTTTATT
*
301054 TTTTTATTTATTTTATTTTTG
1 TTTTTATTTATTTTATTTTCG
301075 TTTTTATTTA-TTTATTTAATCG
1 TTTTTATTTATTTTATTT--TCG
301097 TTTTT
1 TTTTT
301102 TGGTGTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 10 0.42
22 7 0.29
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTATTTATTTTATTTTCG
Found at i:301101 original size:29 final size:28
Alignment explanation
Indices: 301030--301103 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
301020 TCATATCATA
* *
301030 TTATTT-T-GTTTTATTCTTTTTATTTTT
1 TTATTTATCGTTTT-TTGTTTTTATTTAT
**
301057 TTATTTATTTTATTTTTGTTTTTATTTAT
1 TTATTTATCGT-TTTTTGTTTTTATTTAT
301086 TTATTTAATCGTTTTTTG
1 TTATTT-ATCGTTTTTTG
301104 GTGTTTGTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 6 0.16
28 1 0.03
29 25 0.66
30 6 0.16
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (28 bp):
TTATTTATCGTTTTTTGTTTTTATTTAT
Found at i:302143 original size:4 final size:4
Alignment explanation
Indices: 302127--302159 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
302117 CATTAATCCT
*
302127 TTTA TTCA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
302160 ATATATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:306396 original size:106 final size:105
Alignment explanation
Indices: 306195--307396 Score: 1604
Period size: 106 Copynumber: 11.4 Consensus size: 105
306185 TCCAATTTCA
* * * * *
306195 TTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
306260 CGACGAAGGGACCGCTGGTTGTTAATAAACAATTTTCCAC
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCAAT
* *
306300 TTCTAGAGCCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCATACAACGCATA-TTCAACTT
1 TTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA-AGTTCAACTT
* * *
306364 CATGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAAT
64 CACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
* *
306407 TTCAGAGCCAATTTC-A---CA-A-CGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
306466 CGACGAAGGGACTGCTGGTTGTCAACAAACAATTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTT-TCAAT
*
306507 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
306572 CGACGAAGGGACCGCTGGTTGTCAATAAATAATTTTCCAC
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCAAT
* * *
306612 TTCTAGAGCCAATTTTAACTTCACAGCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTC
1 TTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * *
306677 ATGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAAT
65 ACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
* *
306719 TTCAGAGCCAATTTC-A---CA-A-CGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
306778 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
* *
306819 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* **
306884 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
*
306925 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
306990 CGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
** * * * *
307031 TTCAGAGCTGATTTAAAACTTCAAAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTCAGAGCCAATTT-CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * *
307096 ACGACGAAGGGACCGCTGGTTGTCAAAAAAAAAAACAACTTCCTAAT
65 ACGACGAAGGGACCGCTGGTTGTC-----AACAAACAATTTTC-AAT
307143 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
307208 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTTCAAT
** *
307249 TTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCATG-CAACACAAGTTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA-GACAACGCAAGTTCAACTTC
* * *
307313 ACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCAGT
65 ACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTT-CAAT
* * * *
307355 TCCAGAGTCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
307397 GGAACAATAC
Statistics
Matches: 977, Mismatches: 91, Indels: 57
0.87 0.08 0.05
Matches are distributed among these distances:
99 2 0.00
100 176 0.18
101 4 0.00
102 4 0.00
104 4 0.00
105 16 0.02
106 588 0.60
107 88 0.09
111 72 0.07
112 23 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCAAT
Found at i:306582 original size:206 final size:208
Alignment explanation
Indices: 306228--307396 Score: 1583
Period size: 206 Copynumber: 5.6 Consensus size: 208
306218 AGCGAAGAAA
*
306228 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAA-
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* * * * *
306292 TTTTCCACTTCTAGAGCCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCATACAACGCATA-
66 TTCTCAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA-AG
* *
306356 TTCAACTTCATGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA-T-
129 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTA
*
306419 TTCACAACGAATGAT
194 TTCACAACGAAGGAT
* * * *
306434 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
*
306499 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
* * * * *
306564 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAA-TTTTCCACTTCTAGAGCCAATTTT
131 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC-AGAGCCAA--TT
*
306628 AACTTCACAGCGAAGGAT
193 -A-TTCACAACGAAGGAT
* * * * *
306646 AGTGGACTCCAGACAACGCATGTTCAACTTCATGACGAAGGGACCACTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* *
306711 TTCTCAATTTCAGAGCCAATTTC-A---CA-A-CGAATGATATTGGACTCCAGACAACGCATGTT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
306770 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
131 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA-TT--
306835 ACTTCACAACGAAGGAT
193 A-TTCACAACGAAGGAT
*
306852 ATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* *
306917 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
* * *
306982 CAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTCAGAGCTGATTTAA
131 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGC-CAATT--
* *
307047 AACTTCAAAACGAAAGAT
193 -A-TTCACAACGAAGGAT
*
307065 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAAAA
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-----AATAA
307130 ACAACTTC-CTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
61 ACAACTTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
307194 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
125 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
307259 ATTTCAACTTCACAATGAAGGAT
190 A-TT--A-TTCACAACGAAGGAT
* *
307282 ATTGGACTCCATG-CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAA
1 ATTGGACTCCA-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
* * * * * *
307346 -TTTTCCAGTTCCAGAGTCAATTTCAACTTCACGGCGGAGGATATTGGACTC
65 CTTCT-CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
307397 GGAACAATAC
Statistics
Matches: 869, Mismatches: 65, Indels: 52
0.88 0.07 0.05
Matches are distributed among these distances:
205 12 0.01
206 327 0.38
207 18 0.02
208 2 0.00
209 1 0.00
210 2 0.00
211 4 0.00
212 233 0.27
213 72 0.08
217 68 0.08
218 130 0.15
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (208 bp):
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTATT
CACAACGAAGGAT
Found at i:306760 original size:312 final size:312
Alignment explanation
Indices: 306195--307345 Score: 1761
Period size: 312 Copynumber: 3.7 Consensus size: 312
306185 TCCAATTTCA
* * * * * *
306195 TTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
306260 CGACGAAGGGACCGCTGGTTGTTAATAAACAATTTTCCACTTCTAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCACTTCTAGAGCCAATTTCAACTTCACA
* * *
306325 GCGAAGGATAGTGGACTCCATACAACGCATATTCAACTTCATGACGAAGGGACCACTGGTTGTCA
131 GCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCACTGGTTGTCA
306390 ACAAACAACTTCTCAATTTCAGAGCCAATTTCACAACGAATGATATTGGACTCCAGACAACGCAT
196 ACAAACAACTTCTCAATTTCAGAGCCAATTTCACAACGAATGATATTGGACTCCAGACAACGCAT
* *
306455 GTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAATTTCTCAAT
261 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
306507 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
306572 CGACGAAGGGACCGCTGGTTGTCAATAAATAATTTTCCACTTCTAGAGCCAATTTTAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCACTTCTAGAGCCAATTTCAACTTCACA
*
306637 GCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCATGACGAAGGGACCACTGGTTGTCA
131 GCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCACTGGTTGTCA
306702 ACAAACAACTTCTCAATTTCAGAGCCAATTTCACAACGAATGATATTGGACTCCAGACAACGCAT
196 ACAAACAACTTCTCAATTTCAGAGCCAATTTCACAACGAATGATATTGGACTCCAGACAACGCAT
306767 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
261 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
*
306819 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
306884 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATT-TCAGAGCCAATTTCAACTTCAC
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCACTTCT-AGAGCCAATTTCAACTTCAC
* * *
306948 AGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTAGTTGTC
130 AGCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCACTGGTTGTC
* * * *
307013 AACAAACAACTTCTCAATTTCAGAGCTGATTTAAAACTTCAAAACGAAAGATATTGGACTCCAGA
195 AACAAACAACTTCTCAATTTCAGAGC-------CAATTTCACAACGAATGATATTGGACTCCAGA
* *
307078 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAAAAACAACTTC-CTAA
253 CAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-----AACAAACAACTTCTC-AA
307142 T
312 T
*
307143 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
307208 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC-AGAGCCAATTTCAACTTCAC
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTCCACTTCTAGAGCCAATTTCAACTTCAC
** * * * * *
307272 AATGAAGGATATTGGACTCCATG-CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGT
130 AGCGAAGGATAGTGGACTCCA-GACAACGCATGTTCAACTTCACGACGAAGGGACCACTGGTTGT
*
307336 CAATAAACAA
194 CAACAAACAA
307346 TTTTCCAGTT
Statistics
Matches: 778, Mismatches: 44, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
311 1 0.00
312 507 0.65
319 69 0.09
323 1 0.00
324 194 0.25
325 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (312 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCACTTCTAGAGCCAATTTCAACTTCACA
GCGAAGGATAGTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCACTGGTTGTCA
ACAAACAACTTCTCAATTTCAGAGCCAATTTCACAACGAATGATATTGGACTCCAGACAACGCAT
GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
Found at i:307995 original size:2 final size:2
Alignment explanation
Indices: 307983--308052 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
307973 TATTTTACTT
*
307983 TA TA CA 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
* *
308025 TA TA TA TA TA TC TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
308053 GTTCGCAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:308258 original size:32 final size:33
Alignment explanation
Indices: 308183--308272 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
308173 TTTTTAAAAA
*
308183 AAAACATTTTTTGAAAAC-ATATAATATAGTTTT
1 AAAACA-TTTTTGAAAACTATATAATACAGTTTT
*
308216 AAAACGTTTTTGAAAACTATA-ACATACAG-TTT
1 AAAACATTTTTGAAAACTATATA-ATACAGTTTT
* *
308248 GAAACATTTTT-AAAATTATATAATA
1 AAAACATTTTTGAAAACTATATAATA
308273 TATGATTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 11 0.22
32 25 0.51
33 13 0.27
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.39
Consensus pattern (33 bp):
AAAACATTTTTGAAAACTATATAATACAGTTTT
Found at i:308378 original size:8 final size:9
Alignment explanation
Indices: 308358--308391 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
308348 TATTATTTTG
308358 TTTTATTCT
1 TTTTATTCT
308367 TTTTATTCT
1 TTTTATTCT
308376 TTTTATT-T
1 TTTTATTCT
308384 ATTTTATT
1 -TTTTATT
308392 TTTGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 1 0.04
9 23 0.96
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTCT
Found at i:309470 original size:2 final size:2
Alignment explanation
Indices: 309463--309487 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
309453 TTCATTTATT
309463 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 T
309488 GCTGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:328021 original size:21 final size:21
Alignment explanation
Indices: 327995--328054 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
327985 CATAGTCGAC
327995 TATCGCAATGCGAACTTGGAA
1 TATCGCAATGCGAACTTGGAA
* * *
328016 TATCGCAACGCGAACTTCGAC
1 TATCGCAATGCGAACTTGGAA
328037 TATCGCAATGCGAACTTG
1 TATCGCAATGCGAACTTG
328055 CGAACTTGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (21 bp):
TATCGCAATGCGAACTTGGAA
Found at i:328205 original size:21 final size:21
Alignment explanation
Indices: 328153--328228 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
328143 CGTTGCGATT
*
328153 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
328172 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
328195 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
328216 TTCGACTATCGCA
1 TTGGACTATCGCA
328229 TTGCGATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.12
21 33 0.67
23 10 0.20
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:328269 original size:21 final size:21
Alignment explanation
Indices: 328243--328296 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
328233 GATTTACATA
328243 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
328264 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
328285 TTCGCGTTGCGA
1 TTCGCATTGCGA
328297 ATCTGAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:331716 original size:17 final size:17
Alignment explanation
Indices: 331694--331727 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
331684 GATTATGGTG
*
331694 TGGGTAATCTTAAGTTA
1 TGGGTAAGCTTAAGTTA
*
331711 TGGGTAAGCTTATGTTA
1 TGGGTAAGCTTAAGTTA
331728 CTTTGGCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.41
Consensus pattern (17 bp):
TGGGTAAGCTTAAGTTA
Found at i:332942 original size:2 final size:2
Alignment explanation
Indices: 332935--332998 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
332925 GTTTAGTTTC
332935 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
332977 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
332999 TGATTTTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334708 original size:39 final size:36
Alignment explanation
Indices: 334665--334738 Score: 94
Period size: 39 Copynumber: 2.0 Consensus size: 36
334655 TAAAGTTTAG
* * *
334665 TTTTTGTTTTATTTTATTACCCATCGTCAAAACTTTAAT
1 TTTTTATTTCATTTTAGTACCCAT--TCAAAA-TTTAAT
334704 TTTTTATTTCATTTTAGTACCCATTCAAAATTTAA
1 TTTTTATTTCATTTTAGTACCCATTCAAAATTTAA
334739 CGTTAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 6 0.19
39 21 0.66
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (36 bp):
TTTTTATTTCATTTTAGTACCCATTCAAAATTTAAT
Found at i:334924 original size:20 final size:21
Alignment explanation
Indices: 334873--334917 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
334863 TAATTTTGAA
* *
334873 AAAATTAAAAGTTTAGGTACT
1 AAAATGAATAGTTTAGGTACT
*
334894 AAAATGAATAGTTTATGTACT
1 AAAATGAATAGTTTAGGTACT
334915 AAA
1 AAA
334918 TGCATAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (21 bp):
AAAATGAATAGTTTAGGTACT
Found at i:334996 original size:14 final size:15
Alignment explanation
Indices: 334969--334997 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
334959 TTATCATAAA
334969 AATAAAAAATATTAT
1 AATAAAAAATATTAT
334984 AATAAAAAA-ATTAT
1 AATAAAAAATATTAT
334998 TTTGTGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAAAATATTAT
Found at i:336449 original size:23 final size:23
Alignment explanation
Indices: 336423--336469 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
336413 AAATTAATTC
336423 AATAAAAAT-TAAAAATTTAAAGT
1 AATAAAAATATAAAAA-TTAAAGT
* *
336446 AATAAATATATATAAATTAAAGT
1 AATAAAAATATAAAAATTAAAGT
336469 A
1 A
336470 TTTTTTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AATAAAAATATAAAAATTAAAGT
Found at i:336810 original size:2 final size:2
Alignment explanation
Indices: 336803--336828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
336793 ATACTACGAA
336803 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
336829 ATCTATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:336920 original size:2 final size:2
Alignment explanation
Indices: 336913--336942 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
336903 TCCATATACA
336913 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
336943 TCGCCATTGC
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):
AT
Found at i:341241 original size:18 final size:18
Alignment explanation
Indices: 341213--341276 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
341203 GAAGGGTTGG
* *
341213 CTTCATTGCCGACGAATC
1 CTTCATCGCCGATGAATC
* *
341231 CTTCGTCGCCGATGACTC
1 CTTCATCGCCGATGAATC
*
341249 CTTCATCCCCGATGAATC
1 CTTCATCGCCGATGAATC
*
341267 CTTCCTCGCC
1 CTTCATCGCC
341277 AAGGAATAGG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.28
Consensus pattern (18 bp):
CTTCATCGCCGATGAATC
Found at i:353038 original size:40 final size:40
Alignment explanation
Indices: 352994--353088 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
352984 TTTGTTTCCT
*
352994 TTAA-TATTTTTAACATTCTTAATAAATTTTATTTTTCTAA
1 TTAATTATTTTTAA-AATCTTAATAAATTTTATTTTTCTAA
* *
353034 TTAATTTTTTTTAAAATCTTATTAAATTTTATTTTT-TAAA
1 TTAATTATTTTTAAAATCTTAATAAATTTTATTTTTCT-AA
* *
353074 TAAATTAATTTTAAA
1 TTAATTATTTTTAAA
353089 TTTTAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 38 0.81
41 8 0.17
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (40 bp):
TTAATTATTTTTAAAATCTTAATAAATTTTATTTTTCTAA
Found at i:353083 original size:22 final size:22
Alignment explanation
Indices: 353058--353100 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
353048 AATCTTATTA
**
353058 AATTTTATTTTTTAAATAAATT
1 AATTTTAAATTTTAAATAAATT
353080 AATTTTAAATTTTAAATAAAT
1 AATTTTAAATTTTAAATAAAT
353101 CTCCAAATTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTAAATTTTAAATAAATT
Found at i:359412 original size:54 final size:55
Alignment explanation
Indices: 359347--359456 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 55
359337 TCGTCTTTTA
* *
359347 TGATAATTTTTGATAAAAATTTTCAAAAATCCCT-TGTAATTTTAAATTTAA-AAT
1 TGATAATTTTTGATAAAAATTCTCAAAAAT-CCTGTATAATTTTAAATTTAATAAT
* ** *
359401 TGATAATTTTTGGTAAAAATTCTCGTAAATTCTGTATAATTTTAAATTTAATAAT
1 TGATAATTTTTGATAAAAATTCTCAAAAATCCTGTATAATTTTAAATTTAATAAT
359456 T
1 T
359457 ATTTTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.04
54 42 0.88
55 4 0.08
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (55 bp):
TGATAATTTTTGATAAAAATTCTCAAAAATCCTGTATAATTTTAAATTTAATAAT
Found at i:377504 original size:23 final size:23
Alignment explanation
Indices: 377478--377521 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
377468 TTCATTTAGC
* *
377478 GTTCACAAATATGTTCGTTTAAT
1 GTTCACAAACATATTCGTTTAAT
*
377501 GTTCGCAAACATATTCGTTTA
1 GTTCACAAACATATTCGTTTA
377522 GCATTCGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (23 bp):
GTTCACAAACATATTCGTTTAAT
Found at i:378282 original size:19 final size:19
Alignment explanation
Indices: 378219--378307 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
378209 AGAAATTTTA
*
378219 AATAATTTTTATAA-AATG
1 AATAATTTTTATAATAATT
* * *
378237 AAT-ATATTTTA-ATTTATA
1 AATAAT-TTTTATAATAATT
*
378255 AATATATTTTTATAATATTT
1 AATA-ATTTTTATAATAATT
* * *
378275 TATAATTTATATTATAATT
1 AATAATTTTTATAATAATT
378294 AATAATTTTTATAA
1 AATAATTTTTATAA
378308 AATAGAATTG
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
17 3 0.06
18 13 0.25
19 28 0.54
20 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
AATAATTTTTATAATAATT
Found at i:380422 original size:37 final size:38
Alignment explanation
Indices: 380376--380449 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
380366 GTGATAGTAC
*
380376 ATTGTTTAGTG-ATATATATGCTATTGTCTTGTACAGA
1 ATTGGTTAGTGAATATATATGCTATTGTCTTGTACAGA
380413 ATTGGTTAGTGATATATATATGCTATTGTCTTGTACA
1 ATTGGTTAGTGA-ATATATATGCTATTGTCTTGTACA
380450 TAAAGCAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 10 0.29
39 24 0.71
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (38 bp):
ATTGGTTAGTGAATATATATGCTATTGTCTTGTACAGA
Found at i:392452 original size:15 final size:15
Alignment explanation
Indices: 392411--392452 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
392401 AAATAATGCA
392411 TAAATTTTATAGATT
1 TAAATTTTATAGATT
**
392426 TAACGTTTATAG-TT
1 TAAATTTTATAGATT
392440 TAAATTTTGATAG
1 TAAATTTT-ATAG
392453 CAAATATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TAAATTTTATAGATT
Found at i:392526 original size:20 final size:20
Alignment explanation
Indices: 392503--392540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
392493 GATCATTTTG
392503 TAATAATTT-GATAAATTTAA
1 TAATAATTTAG-TAAATTTAA
*
392523 TAATTATTTAGTAAATTT
1 TAATAATTTAGTAAATTT
392541 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATAATTTAGTAAATTTAA
Found at i:408133 original size:24 final size:23
Alignment explanation
Indices: 408106--408158 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
408096 CGAACTAAAA
* *
408106 AAAATAGAAGTTCGATTGAAGCCT
1 AAAATAG-AGCTCAATTGAAGCCT
*
408130 AAAATTTGAGCTCAATTGAAGCCT
1 AAAA-TAGAGCTCAATTGAAGCCT
408154 AAAAT
1 AAAAT
408159 TTGAGCTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 22 0.88
25 2 0.08
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
AAAATAGAGCTCAATTGAAGCCT
Found at i:408159 original size:24 final size:24
Alignment explanation
Indices: 408120--408166 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
408110 TAGAAGTTCG
408120 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
408144 ATTGAAGCCTAAAATTTGAGCTC
1 ATTGAAGCCTAAAATTTGAGCTC
408167 GAAAGAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:417410 original size:36 final size:36
Alignment explanation
Indices: 417368--417444 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
417358 AAGCTAGATT
417368 ATATAGATGCTAACACTGGAATAAATAAAAACAATA
1 ATATAGATGCTAACACTGGAATAAATAAAAACAATA
417404 ATATAGATGCTAACACTGGAATAAATAAAAACAATA
1 ATATAGATGCTAACACTGGAATAAATAAAAACAATA
417440 ATATA
1 ATATA
417445 AGACGAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (36 bp):
ATATAGATGCTAACACTGGAATAAATAAAAACAATA
Found at i:421999 original size:27 final size:27
Alignment explanation
Indices: 421961--422018 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
421951 ACCTGTGTAT
421961 CTGCTACGCGTTAGAAAGGCGCGCTCC
1 CTGCTACGCGTTAGAAAGGCGCGCTCC
421988 CTGCTACGCGTTAGAAAGGCGCGCTCC
1 CTGCTACGCGTTAGAAAGGCGCGCTCC
422015 CTGC
1 CTGC
422019 CCCGCACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.19
Consensus pattern (27 bp):
CTGCTACGCGTTAGAAAGGCGCGCTCC
Found at i:422225 original size:23 final size:22
Alignment explanation
Indices: 422186--422230 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
422176 TTATTATATT
*
422186 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
422209 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
422231 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:422237 original size:17 final size:18
Alignment explanation
Indices: 422200--422238 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
422190 ATATTTTGTA
422200 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
422218 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
422235 TTTA
1 TTTA
422239 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:424681 original size:25 final size:25
Alignment explanation
Indices: 424653--424704 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
424643 TGAAGCCATC
*
424653 GTGTCAAATGGAAATTGCACAGATG
1 GTGTCAAATGGAAATTACACAGATG
424678 GTGTCAAATGGAAATTACACAGATG
1 GTGTCAAATGGAAATTACACAGATG
424703 GT
1 GT
424705 TGCGTCGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (25 bp):
GTGTCAAATGGAAATTACACAGATG
Found at i:425566 original size:14 final size:15
Alignment explanation
Indices: 425532--425570 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
425522 TCAAATAATC
425532 ATAATAAACAATAAGT
1 ATAATAAA-AATAAGT
*
425548 ATAATAAAAA-AATT
1 ATAATAAAAATAAGT
425562 ATAATAAAA
1 ATAATAAAA
425571 TTACCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:425853 original size:51 final size:51
Alignment explanation
Indices: 425770--425922 Score: 256
Period size: 51 Copynumber: 3.0 Consensus size: 51
425760 CACTGTGCCT
* *
425770 TATATAATTATATCAG--TTAAAGGTATGGCGCGGCCCCTGCCCCACGCTA
1 TATATAATTATGTCAGAATTAAAGGTAAGGCGCGGCCCCTGCCCCACGCTA
425819 TATATAATTATGTCAGAATTAAAGGTAAGGCGCGGCCCCTGCCCCACGCTA
1 TATATAATTATGTCAGAATTAAAGGTAAGGCGCGGCCCCTGCCCCACGCTA
* *
425870 TATATAATTATGTCAGAATTAAAGGTAAGGTGCGGCCCCTGCCCCGCGCTA
1 TATATAATTATGTCAGAATTAAAGGTAAGGCGCGGCCCCTGCCCCACGCTA
425921 TA
1 TA
425923 CCCACGTGTA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
49 15 0.15
51 83 0.85
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (51 bp):
TATATAATTATGTCAGAATTAAAGGTAAGGCGCGGCCCCTGCCCCACGCTA
Found at i:435889 original size:42 final size:42
Alignment explanation
Indices: 435830--435911 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
435820 TACGTTGATC
435830 GTTAATTAACTAGCAATTTTCATATAATAGGATTTATTTTTG
1 GTTAATTAACTAGCAATTTTCATATAATAGGATTTATTTTTG
435872 GTTAATTAACTAGCAATTTTCATATAATAGGATTTATTTT
1 GTTAATTAACTAGCAATTTTCATATAATAGGATTTATTTT
435912 GACCAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (42 bp):
GTTAATTAACTAGCAATTTTCATATAATAGGATTTATTTTTG
Found at i:437168 original size:3 final size:3
Alignment explanation
Indices: 437160--437185 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
437150 ATCTTCATAC
437160 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
437186 GAATTGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:439269 original size:14 final size:14
Alignment explanation
Indices: 439248--439323 Score: 80
Period size: 14 Copynumber: 5.0 Consensus size: 14
439238 CGCTGGGCAT
439248 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
439262 CTGAGGCCATCCGA
1 CCGAGGCCATCCGA
439276 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
*
439295 TCCGAGGTCATCCGA
1 -CCGAGGCCATCCGA
439310 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
439324 ACGAACTATG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 37 0.71
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 11 0.21
ACGTcount: A:0.22, C:0.38, G:0.29, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:439346 original size:23 final size:23
Alignment explanation
Indices: 439311--439362 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
439301 GTCATCCGAC
* *
439311 CGAGGCCATCCGAACGAACTATG
1 CGAGGGCAACCGAACGAACTATG
* *
439334 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAACGAACTATG
439357 CGAGGG
1 CGAGGG
439363 AATCCGAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (23 bp):
CGAGGGCAACCGAACGAACTATG
Found at i:439369 original size:23 final size:24
Alignment explanation
Indices: 439318--439370 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
439308 GACCGAGGCC
*
439318 ATCCGAACGAACTATGCGAGGGCA
1 ATCCGAGCGAACTATGCGAGGGCA
*
439342 A-CCGAGCGAGCTATGCGAGGG-A
1 ATCCGAGCGAACTATGCGAGGGCA
439364 ATCCGAG
1 ATCCGAG
439371 GGAAGCCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.34, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAACTATGCGAGGGCA
Found at i:439421 original size:29 final size:29
Alignment explanation
Indices: 439388--439443 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
439378 GAGCGAGGGT
439388 AGGTCGCCCGGAGTG-CATGGCGACCTACA
1 AGGTCGCCCGGAG-GACATGGCGACCTACA
439417 AGGTCGCCCGGAGGACATGGCGACCTA
1 AGGTCGCCCGGAGGACATGGCGACCTA
439444 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGACATGGCGACCTACA
Found at i:439544 original size:29 final size:29
Alignment explanation
Indices: 439502--439558 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
439492 GAACAAGGGT
*
439502 AGGTCGCCTGGAGTGCATGGCAACCTACA
1 AGGTCGCCCGGAGTGCATGGCAACCTACA
*
439531 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCAACCTAC
439559 GGCCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCAACCTACA
Found at i:441463 original size:15 final size:14
Alignment explanation
Indices: 441424--441459 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
441414 AAAATAATTA
441424 AAATGATATATTTT
1 AAATGATATATTTT
*
441438 ATAATTATATATTTT
1 A-AATGATATATTTT
441453 AAATGAT
1 AAATGAT
441460 TATAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
AAATGATATATTTT
Found at i:441799 original size:11 final size:11
Alignment explanation
Indices: 441783--441807 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
441773 AAATTAAGAG
441783 CTCAATTGAAA
1 CTCAATTGAAA
441794 CTCAATTGAAA
1 CTCAATTGAAA
441805 CTC
1 CTC
441808 GATTCAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (11 bp):
CTCAATTGAAA
Found at i:441819 original size:11 final size:11
Alignment explanation
Indices: 441805--441831 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
441795 TCAATTGAAA
441805 CTCGATTCAAG
1 CTCGATTCAAG
441816 CTCGATTCAAG
1 CTCGATTCAAG
441827 CTCGA
1 CTCGA
441832 ATTGCCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:443222 original size:21 final size:21
Alignment explanation
Indices: 443196--443242 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
443186 AATGTTGTTC
*
443196 AAACTCTAAATCATAAATCCT
1 AAACTCTAAATCATAAACCCT
*
443217 AAACTCTAAATTATAAACCCT
1 AAACTCTAAATCATAAACCCT
443238 AAACT
1 AAACT
443243 ATAGACCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACTCTAAATCATAAACCCT
Found at i:443233 original size:14 final size:14
Alignment explanation
Indices: 443216--443283 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
443206 TCATAAATCC
* *
443216 TAAACTCTAAATTA
1 TAAACCCTAAACTA
443230 TAAACCCTAAACTA
1 TAAACCCTAAACTA
* *
443244 TAGACCCTAAACTC
1 TAAACCCTAAACTA
443258 T-AACCCTTAAACCT-
1 TAAACCC-TAAA-CTA
*
443272 TAAACCTTAAAC
1 TAAACCCTAAAC
443284 CCTAAACTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.11
14 34 0.76
15 6 0.13
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:443240 original size:7 final size:7
Alignment explanation
Indices: 443230--443290 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
443220 CTCTAAATTA
443230 TAAACCC
1 TAAACCC
**
443237 TAAACTA
1 TAAACCC
*
443244 TAGACCC
1 TAAACCC
*
443251 TAAACTC
1 TAAACCC
443258 T-AACCC
1 TAAACCC
*
443264 TTAAACCT
1 -TAAACCC
*
443272 TAAACCT
1 TAAACCC
443279 TAAACCC
1 TAAACCC
443286 TAAAC
1 TAAAC
443291 TCTATCACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 4 0.10
7 34 0.81
8 4 0.10
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:443253 original size:35 final size:35
Alignment explanation
Indices: 443209--443294 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
443199 CTCTAAATCA
* *
443209 TAAATCCTAAACTCTAA-ATTATAAACCCTAAA-CT
1 TAAACCCTAAACTCTAACACT-TAAACCCTAAACCT
* * *
443243 ATAGACCCTAAACTCTAACCCTTAAACCTTAAACCT
1 -TAAACCCTAAACTCTAACACTTAAACCCTAAACCT
443279 TAAACCCTAAACTCTA
1 TAAACCCTAAACTCTA
443295 TCACATAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
35 40 0.93
36 3 0.07
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (35 bp):
TAAACCCTAAACTCTAACACTTAAACCCTAAACCT
Found at i:444111 original size:11 final size:11
Alignment explanation
Indices: 444090--444157 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
444080 TAGGTGTACT
444090 ATATAATTTTTA
1 ATAT-ATTTTTA
444102 ATATATTTTTA
1 ATATATTTTTA
444113 A-A-ATTTTATA
1 ATATATTTT-TA
* ***
444123 AT-CATCAATA
1 ATATATTTTTA
*
444133 ATTTATTTTTA
1 ATATATTTTTA
444144 ATATATTTTTA
1 ATATATTTTTA
444155 ATA
1 ATA
444158 ATGTAATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.11
10 8 0.18
11 27 0.61
12 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:450120 original size:21 final size:21
Alignment explanation
Indices: 450096--450145 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
450086 GAGTATTGTT
450096 GAGCTTGACTCGAAAGCTCAA
1 GAGCTTGACTCGAAAGCTCAA
450117 GAGCTTGACTCGAAAGCTCAA
1 GAGCTTGACTCGAAAGCTCAA
450138 GAGCTTGA
1 GAGCTTGA
450146 AATTGTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGCTTGACTCGAAAGCTCAA
Found at i:450535 original size:21 final size:21
Alignment explanation
Indices: 450509--450552 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
450499 ATTCCTCACC
450509 GACTCGAAAGCTCAAGAGCTT
1 GACTCGAAAGCTCAAGAGCTT
450530 GACTCGAAAGCTCAAGAGCTT
1 GACTCGAAAGCTCAAGAGCTT
450551 GA
1 GA
450553 AATTGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (21 bp):
GACTCGAAAGCTCAAGAGCTT
Found at i:450897 original size:407 final size:407
Alignment explanation
Indices: 450102--450918 Score: 1577
Period size: 407 Copynumber: 2.0 Consensus size: 407
450092 TGTTGAGCTT
450102 GACTCGAAAGCTCAAGAGCTTGACTCGAAAGCTCAAGAGCTTGAAATTGTCAAGCTAAAAAAAAT
1 GACTCGAAAGCTCAAGAGCTTGACTCGAAAGCTCAAGAGCTTGAAATTGTCAAGCTAAAAAAAAT
450167 TTGAACTCAAAATTTTCAGACTTAGCTCGAATTCGAACTCAATTTAAGCTCGAACCTGAACCTGA
66 TTGAACTCAAAATTTTCAGACTTAGCTCGAATTCGAACTCAATTTAAGCTCGAACCTGAACCTGA
450232 AGTACATGAAAACTTTGTATTATATATTTTTTAAAACAACACATATATGTTAATATTATTAATAA
131 AGTACATGAAAACTTTGTATTATATATTTTTTAAAACAACACATATATGTTAATATTATTAATAA
450297 TTTAATTGAAAAAATAAAATAAAATATATTACTTTTTTCGATTTGATCACGAACTTATCAAGTTA
196 TTTAATTGAAAAAATAAAATAAAATATATTA-TTTTTTCGATTTGATCACGAACTTATCAAGTTA
450362 GATATCAAATAACTCACTTCGATTCGTTTAGAACTAGAGTTAAGCTCAAATCAAGTCATTTGATT
260 GATATCAAATAACTCACTTCGATTCGTTTAGAACTAGAGTTAAGCTCAAATCAAGTCATTTGATT
450427 TGAGTGTTGACCGAACTTTGACCGAGTCAAACTCGAATAGATTAAAATTGTATGTCGTCATTTAC
325 TGAGTGTTGACCGAACTTTGACCGAGTCAAACTCGAATAGATTAAAATTGTATGTCGTCATTTAC
450492 AACCCTAAT-TCCTCACC
390 AACCCTAATCTCCTCACC
450509 GACTCGAAAGCTCAAGAGCTTGACTCGAAAGCTCAAGAGCTTGAAATTGTCAAGCTAAAAAAAAT
1 GACTCGAAAGCTCAAGAGCTTGACTCGAAAGCTCAAGAGCTTGAAATTGTCAAGCTAAAAAAAAT
450574 TTGAACTCAAAATTTTCAGACTTAGCTCGAATTCGAACTCAATTTAAGCTCGAACCTGAACCTGA
66 TTGAACTCAAAATTTTCAGACTTAGCTCGAATTCGAACTCAATTTAAGCTCGAACCTGAACCTGA
450639 AGTACATGAAAACTTTGTATTATATATTTTTTAAAACAACACATATATGTTAATATTATTAATAA
131 AGTACATGAAAACTTTGTATTATATATTTTTTAAAACAACACATATATGTTAATATTATTAATAA
450704 TTTAATTGAAAAAATAAAATAAAATATA-T-TTTTTTCGATTTGATCACGAACTTATCAAGTTAG
196 TTTAATTGAAAAAATAAAATAAAATATATTATTTTTTCGATTTGATCACGAACTTATCAAGTTAG
450767 ATATCAAATAACTCACTTCGATTCGTTTAGAACTAGAGTTAAGCTCAAATCAAGTCATTTGATTT
261 ATATCAAATAACTCACTTCGATTCGTTTAGAACTAGAGTTAAGCTCAAATCAAGTCATTTGATTT
450832 GAGTGTTGACCGAACTTTGACCGAGTCAAACTCGAATAGATTAAAATTTGTATGTCGTCTCATTT
326 GAGTGTTGACCGAACTTTGACCGAGTCAAACTCGAATAGATTAAAA-TTGTATGTCG--TCATTT
450897 ACAACCCTAATCTCCTCACC
388 ACAACCCTAATCTCCTCACC
450917 GA
1 GA
450919 AGTCAATTCT
Statistics
Matches: 406, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
404 145 0.36
405 10 0.02
406 1 0.00
407 240 0.59
408 10 0.02
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (407 bp):
GACTCGAAAGCTCAAGAGCTTGACTCGAAAGCTCAAGAGCTTGAAATTGTCAAGCTAAAAAAAAT
TTGAACTCAAAATTTTCAGACTTAGCTCGAATTCGAACTCAATTTAAGCTCGAACCTGAACCTGA
AGTACATGAAAACTTTGTATTATATATTTTTTAAAACAACACATATATGTTAATATTATTAATAA
TTTAATTGAAAAAATAAAATAAAATATATTATTTTTTCGATTTGATCACGAACTTATCAAGTTAG
ATATCAAATAACTCACTTCGATTCGTTTAGAACTAGAGTTAAGCTCAAATCAAGTCATTTGATTT
GAGTGTTGACCGAACTTTGACCGAGTCAAACTCGAATAGATTAAAATTGTATGTCGTCATTTACA
ACCCTAATCTCCTCACC
Found at i:462792 original size:2 final size:2
Alignment explanation
Indices: 462785--462810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
462775 AGATGATCAG
462785 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
462811 TTAGTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474543 original size:54 final size:54
Alignment explanation
Indices: 474482--474586 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
474472 TTCCTGTATC
474482 ACACAACCAACCGCATAAAATTCAGCAAGAACATTTTCATCCTTGGTAAGTGAT
1 ACACAACCAACCGCATAAAATTCAGCAAGAACATTTTCATCCTTGGTAAGTGAT
474536 ACACAACCAACCGCATAAAATTCAGCAAGAACATTTTCATCCTTGGTAAGT
1 ACACAACCAACCGCATAAAATTCAGCAAGAACATTTTCATCCTTGGTAAGT
474587 TTACTGATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (54 bp):
ACACAACCAACCGCATAAAATTCAGCAAGAACATTTTCATCCTTGGTAAGTGAT
Found at i:488975 original size:16 final size:16
Alignment explanation
Indices: 488956--489010 Score: 110
Period size: 16 Copynumber: 3.4 Consensus size: 16
488946 AACAATATAT
488956 ATATACACAAACATAC
1 ATATACACAAACATAC
488972 ATATACACAAACATAC
1 ATATACACAAACATAC
488988 ATATACACAAACATAC
1 ATATACACAAACATAC
489004 ATATACA
1 ATATACA
489011 GCCAGATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (16 bp):
ATATACACAAACATAC
Found at i:489183 original size:6 final size:6
Alignment explanation
Indices: 489172--489198 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
489162 TTCTTGAGAA
489172 TTTTGT TTTTGT TTTTGT TTTTGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTT
489199 CAGAATCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:494063 original size:2 final size:2
Alignment explanation
Indices: 494056--494084 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
494046 AACCAAGTGG
494056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
494085 CTTTTTGTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:495200 original size:216 final size:214
Alignment explanation
Indices: 494761--495200 Score: 758
Period size: 216 Copynumber: 2.0 Consensus size: 214
494751 TTTTTTAATA
494761 ATATTATTTGTAATATTTAACATTAAATTTCTTTTATTTTGTTGCGTTTGATTTCGCCGTTGAAG
1 ATATTATTTGTAATATTTAACATTAAATTTCTTTTATTTTGTTGCGTTTGATTTCGCCGTTGAAG
494826 GACTGTCGGACACGAATGCGTTTGTCAGTGGTTGAAGAACGGCTGACATCAATCGAGTTGAGCAA
66 GACTGTCGGACACGAATGCGTTTGTCAGTGGTTGAAGAACGGCTGACATCAATCGAGTTGAGCAA
494891 ATCGATGTTGATATCAAAAGGTTTGCTGGTTTGGGTGAATTAGTGAGTCCGGTTCGAGTTAGACG
131 ATCGATGTTGATATCAAAAGGTTTGCTGGTTTGGGTGAATTAGTGAGTCCGGTTCGAGTTAGACG
** ***
494956 ATATTCTCATCCTTTTTTAAT
196 ATATTCTCAAAC--TAACAAT
494977 ATATTATTTGTAATATTTAACATTAAATTTCTTTTATTTTGTTGCGTTTGATTTCGCCGTTGAAG
1 ATATTATTTGTAATATTTAACATTAAATTTCTTTTATTTTGTTGCGTTTGATTTCGCCGTTGAAG
495042 GACTGTCGGACACGAATGCGTTTGTCAGTGGTTGAAGAACGGCTGACATCAATCGAGTTTGAAGC
66 GACTGTCGGACACGAATGCGTTTGTCAGTGGTTGAAGAACGGCTGACATCAATCGAG-TTG-AGC
495107 AAACTCGATGTTGATATCAAAAGGTTTGCTGGTTTGGGTGAATTAGTGAGTCCGGTTCGAGTTAG
129 AAA-TCGATGTTGATATCAAAAGGTTTGCTGGTTTGGGTGAATTAGTGAGTCCGGTTCGAGTTAG
*
495172 ACGATTATTCTCAAAC-AACGAT
193 ACGA-TATTCTCAAACTAACAAT
495194 -TATTATT
1 ATATTATT
495201 CTAAATTTTT
Statistics
Matches: 214, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
216 129 0.60
217 5 0.02
218 6 0.03
219 65 0.30
220 9 0.04
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (214 bp):
ATATTATTTGTAATATTTAACATTAAATTTCTTTTATTTTGTTGCGTTTGATTTCGCCGTTGAAG
GACTGTCGGACACGAATGCGTTTGTCAGTGGTTGAAGAACGGCTGACATCAATCGAGTTGAGCAA
ATCGATGTTGATATCAAAAGGTTTGCTGGTTTGGGTGAATTAGTGAGTCCGGTTCGAGTTAGACG
ATATTCTCAAACTAACAAT
Found at i:495608 original size:60 final size:60
Alignment explanation
Indices: 495444--495614 Score: 173
Period size: 60 Copynumber: 2.9 Consensus size: 60
495434 ATGAAATTGG
* * * * ** * **
495444 AATATATAAAAATTTTGGGATCAATTTAGAATGAGGGTCATAGTATGAGGATGGAATTGG
1 AATATTTAAAAATTTAGAGACCAATTTAGAATGAGAATCATAGTTTGAGGATGGAATTAA
* * * * *
495504 AATGTTTAAAAGTTTAAAGACCAATATAGAATGAGTATCATAGTTTGAGGAT-GAAGTTAA
1 AATATTTAAAAATTTAGAGACCAATTTAGAATGAGAATCATAGTTTGAGGATGGAA-TTAA
* * *
495564 AATATTTAAAAATTTAGAGACCAATTTAAAATAAGAATCATAGTTTAAGGA
1 AATATTTAAAAATTTAGAGACCAATTTAGAATGAGAATCATAGTTTGAGGA
495615 CATGCGATGC
Statistics
Matches: 89, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
59 3 0.03
60 86 0.97
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (60 bp):
AATATTTAAAAATTTAGAGACCAATTTAGAATGAGAATCATAGTTTGAGGATGGAATTAA
Found at i:504285 original size:30 final size:30
Alignment explanation
Indices: 504219--504285 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
504209 ATCAATTTTA
504219 TTTAAATTATTAAATTGAAAGAATAAAGAG
1 TTTAAATTATTAAATTGAAAGAATAAAGAG
504249 -TTAAATTCA-TAAGATT-AAA-AATAGAAGAG
1 TTTAAATT-ATTAA-ATTGAAAGAATA-AAGAG
504278 TTTAAATT
1 TTTAAATT
504286 TCAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
28 4 0.12
29 18 0.55
30 11 0.33
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTAAATTATTAAATTGAAAGAATAAAGAG
Found at i:512230 original size:33 final size:34
Alignment explanation
Indices: 512163--512230 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
512153 GTTGAAAAAT
* *
512163 ATTTATATATTTTTTAAAAAATTTAAATTCATAA
1 ATTTATATATTTTTTAAAAAATTAAAAATCATAA
*
512197 ATTTATA-ATTTTTTTATAAAATTAAAAAT-ATAA
1 ATTTATATA-TTTTTTAAAAAATTAAAAATCATAA
512230 A
1 A
512231 GGTTTAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.20
34 24 0.80
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTTATATATTTTTTAAAAAATTAAAAATCATAA
Found at i:512925 original size:26 final size:26
Alignment explanation
Indices: 512898--512946 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
512888 TATAATTTTA
*
512898 AAAAATAA-AATTTATATACTAAAAT
1 AAAAATAATAATTTAAATACTAAAAT
*
512923 AAAAATAATAGTTTAAATACTAAA
1 AAAAATAATAATTTAAATACTAAA
512947 CATGTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAATAATAATTTAAATACTAAAAT
Found at i:520370 original size:18 final size:18
Alignment explanation
Indices: 520347--520439 Score: 63
Period size: 18 Copynumber: 5.5 Consensus size: 18
520337 CATTCCTCCA
520347 ATTCTTCTTCTCCTTCAG
1 ATTCTTCTTCTCCTTCAG
*
520365 ATTCTTCTGCTCCTTC--
1 ATTCTTCTTCTCCTTCAG
*
520381 -TTC-TC--CTCCTTCAA
1 ATTCTTCTTCTCCTTCAG
* * * *
520395 ATGCTTCCTCGCCTTCCG
1 ATTCTTCTTCTCCTTCAG
* * *
520413 ATTCTTCGTCTTCTTCGG
1 ATTCTTCTTCTCCTTCAG
520431 ATTCTTCTT
1 ATTCTTCTT
520440 GACCTGATCC
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
12 7 0.12
14 2 0.03
15 5 0.09
16 2 0.03
18 42 0.72
ACGTcount: A:0.09, C:0.35, G:0.09, T:0.47
Consensus pattern (18 bp):
ATTCTTCTTCTCCTTCAG
Found at i:520410 original size:30 final size:30
Alignment explanation
Indices: 520348--520410 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
520338 ATTCCTCCAA
* * * *
520348 TTCTTCTTCTCCTTCAGATTCTTCTGCTCC
1 TTCTTCTCCTCCTTCAAATGCTTCTGCGCC
520378 TTCTTCTCCTCCTTCAAATGCTTCCT-CGCC
1 TTCTTCTCCTCCTTCAAATGCTT-CTGCGCC
520408 TTC
1 TTC
520411 CGATTCTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.08, C:0.40, G:0.06, T:0.46
Consensus pattern (30 bp):
TTCTTCTCCTCCTTCAAATGCTTCTGCGCC
Found at i:523871 original size:23 final size:22
Alignment explanation
Indices: 523832--523874 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
523822 TTATAGGTTA
523832 TTTTTTTTGTTTTTTTCCTTTG
1 TTTTTTTTGTTTTTTTCCTTTG
523854 TTTTTTTAT-TTTTATTTCCTT
1 TTTTTTT-TGTTTT-TTTCCTT
523875 CCTCCAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTTTTGTTTTTTTCCTTTG
Found at i:532909 original size:21 final size:22
Alignment explanation
Indices: 532880--532934 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
532870 ATTCTGATTA
532880 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCTAAAT
*
532901 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
532922 TCGCAATGCGATT
1 TCGCATTGCGATT
532935 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:532943 original size:20 final size:20
Alignment explanation
Indices: 532918--533095 Score: 198
Period size: 20 Copynumber: 8.8 Consensus size: 20
532908 GCGATTTTCC
532918 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
532938 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
532958 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
* * *
532978 TAAATTGCAATACGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* *
532999 AAAATCGCAAAGCGATTACG
1 TAAATCGCAATGCGATTACG
*
533019 TAAATCGCAATGTGATTACG
1 TAAATCGCAATGCGATTACG
* *
533039 T-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
* * *
533059 T-AATCGCATTGCGACTTTCC
1 TAAATCGCAATGCGA-TTACG
* *
533079 TAATTCGCATTGCGATT
1 TAAATCGCAATGCGATT
533096 TACATAGCGT
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.07
20 99 0.73
21 27 0.20
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:533088 original size:21 final size:21
Alignment explanation
Indices: 532880--533098 Score: 107
Period size: 20 Copynumber: 10.8 Consensus size: 21
532870 ATTCTGATTA
532880 TCGCATTGCGATTT-CCTAAAT
1 TCGCATTGCGATTTACCT-AAT
* * *
532901 TCGCGTTGCGATTTTCCTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
532922 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
532942 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* *
532962 TCGCAATGCGA-TTACGTAAAT
1 TCGCATTGCGATTTACCT-AAT
* * * *** *
532983 T-GCAATACGAATTAGGAAAA
1 TCGCATTGCGATTTACCTAAT
** * *
533003 TCGCAAAGCGA-TTACGTAAA
1 TCGCATTGCGATTTACCTAAT
* * *
533023 TCGCAATGTGA-TTACGT-AT
1 TCGCATTGCGATTTACCTAAT
*
533042 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
533062 TCGCATTGCGACTTT-CCTAAT
1 TCGCATTGCGA-TTTACCTAAT
533083 TCGCATTGCGATTTAC
1 TCGCATTGCGATTTAC
533099 ATAGCGTCAT
Statistics
Matches: 168, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
19 10 0.06
20 101 0.60
21 54 0.32
22 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:533651 original size:20 final size:19
Alignment explanation
Indices: 533628--533699 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
533618 TTCTAAACTT
*
533628 AAAATCGCAACATTAAAATG
1 AAAATCGCAACA-GAAAATG
533648 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
533668 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
533689 AAAATCGCAAC
1 AAAATCGCAAC
533700 GAGAGAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:533689 original size:21 final size:21
Alignment explanation
Indices: 533643--533706 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
533633 CGCAACATTA
533643 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
533663 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
533684 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
533705 AA
1 AA
533707 TCATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:534545 original size:94 final size:94
Alignment explanation
Indices: 534330--534796 Score: 725
Period size: 94 Copynumber: 5.1 Consensus size: 94
534320 TAGATTGCTT
* *
534330 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
534391 ATTTGTCTTT-TGTTGTCTTTTGCTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
534418 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
534483 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
534512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
534577 ATTTGTCTTTGTTTTGTTTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
534606 AGTAAATTTCTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTTTTTAACACTGTGAATTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
534671 ATTTGTCTTTGTTTTATCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
534700 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
534765 ATTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
534792 AGTAA
1 AGTAA
534797 TGCAATCCAT
Statistics
Matches: 350, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
88 34 0.10
90 3 0.01
91 2 0.01
92 35 0.10
93 22 0.06
94 254 0.73
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:534913 original size:20 final size:20
Alignment explanation
Indices: 534888--534949 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
534878 TTTTGGTTGA
534888 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
534908 AATGAAAATTGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
534927 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
534947 AAT
1 AAT
534950 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:534935 original size:19 final size:19
Alignment explanation
Indices: 534886--534945 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
534876 TTTTTTGGTT
534886 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
534905 GAGAATGAAAATTGCAACGC
1 GA-AATGAAAATCGCAACGA
*
534925 GAAACGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
534944 GA
1 GA
534946 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.50, C:0.17, G:0.23, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:534995 original size:19 final size:19
Alignment explanation
Indices: 534973--535058 Score: 110
Period size: 19 Copynumber: 4.8 Consensus size: 19
534963 TATAATCGCG
534973 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTCCGCA
*
534992 TTGCGATTCTC--T-CG--
1 TTGCGATTTTCATTCCGCA
*
535006 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTCCGCA
*
535025 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTCCGCA
535044 TTGCGATTTTCATTC
1 TTGCGATTTTCATTC
535059 TCTCGTTGCG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
19 43 0.73
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTCCGCA
Found at i:535571 original size:21 final size:21
Alignment explanation
Indices: 535547--535613 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
535537 TCATTCCTCG
535547 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
535568 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
535589 AGATGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
535610 AGAG
1 AGAG
535614 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:535571 original size:42 final size:42
Alignment explanation
Indices: 535495--535613 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
535485 GACTCGCCTG
* * * * * *
535495 TCATCCCTCGAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
535537 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
535579 TCA-TCGTTGAAGATGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
535614 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 59 0.91
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:536995 original size:14 final size:14
Alignment explanation
Indices: 536960--536996 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
536950 GATTGTTTAA
*
536960 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
*
536974 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
536988 TTGATTTGT
1 TTGATTTGT
536997 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:537127 original size:19 final size:19
Alignment explanation
Indices: 537105--537194 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
537095 AAATGACTAG
537105 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
537124 CGCAAT--G--A-GAGAAT
1 CGCAATGCGAAATGAAAAT
*
537138 CACAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
537157 CGTAA--CG--A-GAAAAT
1 CGCAATGCGAAATGAAAAT
537171 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
537190 CGCAA
1 CGCAA
537195 CGACAAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
14 20 0.36
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 25 0.45
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
CGCAATGCGAAATGAAAAT
Found at i:537144 original size:33 final size:33
Alignment explanation
Indices: 537107--537215 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
537097 ATGACTAGCG
* *
537107 CAATGCGAAATGAAAATCGCAATGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
* *
537140 CAATGCGAAATGAAAATCGTAACGAGAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
* *
537173 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
*
537206 CAACGCGAAA
1 CAATGCGAAA
537216 CTAAATCCGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAAAATCA
Found at i:537182 original size:14 final size:14
Alignment explanation
Indices: 537151--537215 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
537141 AATGCGAAAT
*
537151 GAAAATCGTAACGA
1 GAAAATCGCAACGA
537165 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
537183 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
537198 CAAAATCGCAACGC
1 GAAAATCGCAACGA
537212 GAAA
1 GAAA
537216 CTAAATCCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 25 0.60
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 11 0.26
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:537265 original size:33 final size:33
Alignment explanation
Indices: 537223--537332 Score: 184
Period size: 33 Copynumber: 3.3 Consensus size: 33
537213 AAACTAAATC
* *
537223 CGCATTGCGATTCTCTTGTTGCGGTTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
537256 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
* *
537289 CGCATTGCGATTCTCTCGTTACGATTTTCAGTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
537322 CGCATTGCGAT
1 CGCATTGCGAT
537333 AGTCATTTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:537298 original size:19 final size:19
Alignment explanation
Indices: 537241--537352 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
537231 GATTCTCTTG
*
537241 TTGCGGTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
537260 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
537274 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
537293 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
* *
537307 TTACGATTTTCAGTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
537326 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
537346 TTGCGAT
1 TTGCGAT
537353 AGACATTAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
14 11 0.16
16 14 0.20
17 13 0.19
19 22 0.31
20 10 0.14
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:537398 original size:20 final size:20
Alignment explanation
Indices: 537326--537398 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
537316 TCAGTTCGCA
**
537326 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
537346 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
537366 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
537387 TTGCGATAGTCA
1 TTGCGATAGTCA
537399 AATGAATGCC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:539895 original size:24 final size:24
Alignment explanation
Indices: 539861--539914 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
539851 CTGAAAAATC
539861 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
539885 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
539909 ATCAAA
1 ATCAAA
539915 TTTCGAATAC
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:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:540796 original size:20 final size:20
Alignment explanation
Indices: 540773--540839 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
540763 AGAATCTCGT
540773 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
540793 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
* ***
540813 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTTACTAAATCGCAA
540834 TGCGAT
1 TGCGAT
540840 AGTCAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 13 0.33
22 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (20 bp):
TGCGATTTACTAAATCGCAA
Found at i:540860 original size:41 final size:41
Alignment explanation
Indices: 540719--540860 Score: 105
Period size: 41 Copynumber: 3.5 Consensus size: 41
540709 TGTTGCGAAT
* * *
540719 TCAGAAATCGAGTTGCGAATTT--GAAATTCAGTATTGCGATAG
1 TCAG-AATCGCGTTGCGAATTTACGAAA-TC-GCAATGCGATAG
* *
540761 TCAGAATCTCGTTGCG-ATTTACTAAATCGCAATGCGATTACG
1 TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGA-TA-G
*** **
540803 T-A-AATCGCAACGCGAATTTGGGAAATCGCAATGCGATAG
1 TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGATAG
*
540842 TCAGAATCGCGTTACGAAT
1 TCAGAATCGCGTTGCGAAT
540861 CTGGAAACTG
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.03
40 22 0.29
41 44 0.57
42 9 0.12
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (41 bp):
TCAGAATCGCGTTGCGAATTTACGAAATCGCAATGCGATAG
Found at i:548741 original size:52 final size:53
Alignment explanation
Indices: 548672--548777 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 53
548662 AATATGTGTA
548672 TATATAGCTCAAATTCAGATAATGTTTACGTTTTGTTTAAA-AT-ATAGATTT
1 TATATAGCTCAAATTCAGATAATGTTTACGTTTTGTTTAAATATAATAGATTT
548723 TATATGAGCTCAAATTCAGATAATGTTTACGTTTTGTTTAAATATAATAGATTT
1 TATAT-AGCTCAAATTCAGATAATGTTTACGTTTTGTTTAAATATAATAGATTT
548777 T
1 T
548778 GTCACTAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 5 0.10
52 36 0.69
53 2 0.04
54 9 0.17
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (53 bp):
TATATAGCTCAAATTCAGATAATGTTTACGTTTTGTTTAAATATAATAGATTT
Found at i:564753 original size:289 final size:289
Alignment explanation
Indices: 564223--564769 Score: 753
Period size: 289 Copynumber: 1.9 Consensus size: 289
564213 CCTGCTTCCA
* * *
564223 AGTTTTTATAATTGTTTAAATTCTATTATTAGTTCTTCTATAATGTGAAAATTAAACATTTAGTC
1 AGTTTTTATAATTGTTCAAATTCTATTATTAGTCCTTCTATAATGTCAAAATTAAACATTTAGTC
* * * * * *
564288 TTTATAGACTAATTTGGTTAATTTTGATCTCTATTCTTTTATAACTTTAAACTTCAATCATTACT
66 CTTATACACTAATTTGATTAATTTTGATCCCTATACTTTTATAACTTTAAACTTCAATCATTACC
* * * *
564353 CAAATAGTATATTAACAATATTATTAAAAGCATAATGACTAAAAAATTATAAATTTGGAGAAAAA
131 CAAATAGTATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTATAAATATGGAGAAAAA
* * *
564418 TAATTAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTGCTAGAGCAGTAATTACT
196 TAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAATTACT
564483 GTGTGCAAAACCTAAATCCTCATTTTCTT
261 GTGTGCAAAACCTAAATCCTCATTTTCTT
* * **
564512 AGTTTTTATAGTT-TCTCAAATTCTATTATTAGTCCTTCTATAATG-CAATTATTTCACATTTAG
1 AGTTTTTATAATTGT-TCAAATTCTATTATTAGTCCTTCTATAATGTCAA-AATTAAACATTTAG
* *
564575 TCCTTATACACTAATTTGATTAATTTTTATCCCTATACTTTCT-TAACTTTAAATTTCAATCATT
64 TCCTTATACACTAATTTGATTAATTTTGATCCCTATACTTT-TATAACTTTAAACTTCAATCATT
*
564639 ACCCAAAT-GATATATTAACAATATGAATAAAAGTATAAGGACTAAAAAATTACTAAA-ATGGAG
128 ACCCAAATAG-TATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTA-TAAATATGGAG
* * ** * *
564702 AAAAATAAATAAGGGTGTATTTGGACATGATAGGTTGTGAGGATGTGTACTTACTAGAACAGTAA
191 AAAAATAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAA
564767 TTA
256 TTA
564770 TCGTGTCTTG
Statistics
Matches: 224, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
288 4 0.02
289 215 0.96
290 5 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (289 bp):
AGTTTTTATAATTGTTCAAATTCTATTATTAGTCCTTCTATAATGTCAAAATTAAACATTTAGTC
CTTATACACTAATTTGATTAATTTTGATCCCTATACTTTTATAACTTTAAACTTCAATCATTACC
CAAATAGTATATTAACAATATGAATAAAAGCATAAGGACTAAAAAATTATAAATATGGAGAAAAA
TAAATAAGGGTATATTTGGACATGATAGGCTGCAAGAATATGTACTTACTAGAACAGTAATTACT
GTGTGCAAAACCTAAATCCTCATTTTCTT
Found at i:565920 original size:2 final size:2
Alignment explanation
Indices: 565913--565948 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
565903 ACTAAGATCC
*
565913 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
565949 GATGAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:566090 original size:14 final size:14
Alignment explanation
Indices: 566071--566098 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
566061 GGATTGCTTT
566071 TTCTTATCAACCAC
1 TTCTTATCAACCAC
566085 TTCTTATCAACCAC
1 TTCTTATCAACCAC
566099 AAATTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCTTATCAACCAC
Found at i:574921 original size:18 final size:19
Alignment explanation
Indices: 574898--574942 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
574888 ATTTAAGTAG
574898 AAATAAAAACGATT-AAAT
1 AAATAAAAACGATTAAAAT
*
574916 AAATAAAAGCGATTAAAAT
1 AAATAAAAACGATTAAAAT
574935 AAA-AAAAA
1 AAATAAAAA
574943 TAAGAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (19 bp):
AAATAAAAACGATTAAAAT
Found at i:575827 original size:26 final size:26
Alignment explanation
Indices: 575798--575860 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
575788 AGGATGAAGT
*
575798 CTTCTAGAAACCGCTGTTGACTGGAC
1 CTTCTAGAAACCGCTGTTAACTGGAC
575824 CTTCTAGAAACCGCTGTTAACTGGAC
1 CTTCTAGAAACCGCTGTTAACTGGAC
575850 CTTCTAGAAAC
1 CTTCTAGAAAC
575861 TGCCACGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (26 bp):
CTTCTAGAAACCGCTGTTAACTGGAC
Found at i:583726 original size:20 final size:20
Alignment explanation
Indices: 583703--583745 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
583693 AATCCACCAC
*
583703 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
583723 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
583743 ATG
1 ATG
583746 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:591947 original size:19 final size:18
Alignment explanation
Indices: 591900--591947 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
591890 TGGTTTAAGT
591900 AGTAATAAAAAACGATTAA
1 AGTAA-AAAAAACGATTAA
**
591919 A-TAAATAAAAGTGATTAA
1 AGTAAA-AAAAACGATTAA
591937 AGTAAAAAAAA
1 AGTAAAAAAAA
591948 ATAAGAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.04
18 18 0.75
19 5 0.21
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (18 bp):
AGTAAAAAAAACGATTAA
Found at i:597542 original size:31 final size:32
Alignment explanation
Indices: 597507--597583 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
597497 AGACCTTTAT
597507 GAACTGGGAATTTCTTTCA-TTTTTAATCAAA
1 GAACTGGGAATTTCTTTCATTTTTTAATCAAA
* *
597538 GAACTGGGAGTTTCTTTCATTTTTTTATCAAA
1 GAACTGGGAATTTCTTTCATTTTTTAATCAAA
* *
597570 GAAGTGGTAATTTC
1 GAACTGGGAATTTC
597584 AGTAAAAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 18 0.45
32 22 0.55
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (32 bp):
GAACTGGGAATTTCTTTCATTTTTTAATCAAA
Done.