Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397286.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_459.0, 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: 854433
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 16369 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:340891 original size:15 final size:14
Alignment explanation
Indices: 340825--340882 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 14
340815 TTGATTGAGG
340825 ATGAAGAAGATGAC
1 ATGAAGAAGATGAC
* *
340839 ATGCAAAAAGATGAAG
1 ATG-AAGAAGATG-AC
340855 ATGAAGAAGATGAC
1 ATGAAGAAGATGAC
340869 ATGGAAGAAGATGA
1 AT-GAAGAAGATGA
340883 AAATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.16
15 27 0.73
16 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.14
Consensus pattern (14 bp):
ATGAAGAAGATGAC
Found at i:348055 original size:22 final size:23
Alignment explanation
Indices: 348005--348050 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
347995 AATTTTGTTA
*
348005 ATTTAATTTTTCTTCTTAACGGC
1 ATTTAATTTTTCTTCTTAACCGC
*
348028 ATTTAATTTTGTCTTGTTAACCG
1 ATTTAATTTT-TCTTCTTAACCG
348051 ATTAAGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (23 bp):
ATTTAATTTTTCTTCTTAACCGC
Found at i:349135 original size:14 final size:14
Alignment explanation
Indices: 349116--349161 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
349106 ATTTTTTTAA
349116 AAAATAAATAAAAT
1 AAAATAAATAAAAT
*
349130 AAAATACATAAATAT
1 AAAATAAATAAA-AT
349145 AAATATAAATATAAAT
1 AAA-ATAAATA-AAAT
349161 A
1 A
349162 TTTTATAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.41
15 5 0.19
16 9 0.33
17 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:349148 original size:6 final size:6
Alignment explanation
Indices: 349119--349162 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
349109 TTTTTAAAAA
349119 ATAAAT A-AAAT A-AAAT ACATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT --ATAAAT ATAAAT ATAAAT ATAAAT AT
349163 TTTATAGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.26
6 21 0.60
7 1 0.03
8 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:349158 original size:18 final size:18
Alignment explanation
Indices: 349113--349162 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
349103 TTAATTTTTT
349113 TAAAA-AATAAATA-AAA
1 TAAAATAATAAATATAAA
349129 TAAAATACATAAATATAAA
1 TAAAATA-ATAAATATAAA
349148 TATAAAT-ATAAATAT
1 TA-AAATAATAAATAT
349163 TTTATAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 15 0.50
19 5 0.17
20 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATAATAAATATAAA
Found at i:352452 original size:17 final size:17
Alignment explanation
Indices: 352430--352477 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
352420 TATTGATAAG
352430 ATTTTAGTAA-TATTTAT
1 ATTTTA-TAATTATTTAT
*
352447 ATTTTATAATTTTTTAT
1 ATTTTATAATTATTTAT
* *
352464 ATTTCAAAATTATT
1 ATTTTATAATTATT
352478 ATCACATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTATAATTATTTAT
Found at i:354392 original size:17 final size:17
Alignment explanation
Indices: 354370--354425 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
354360 GTTAGAATTG
354370 ATTAAAAATATTATTTA
1 ATTAAAAATATTATTTA
*
354387 ATTAAAATTATTAATTT-
1 ATTAAAAATATT-ATTTA
*
354404 ATT--AAATATTAATTA
1 ATTAAAAATATTATTTA
354419 A-TAAAAA
1 ATTAAAAA
354426 GTATCATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 4 0.12
15 7 0.22
16 3 0.09
17 14 0.44
18 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAAAATATTATTTA
Found at i:354731 original size:2 final size:2
Alignment explanation
Indices: 354720--354748 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
354710 TCACAGATAG
354720 AT AT -T 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
354749 GAAAAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:354776 original size:38 final size:38
Alignment explanation
Indices: 354733--354820 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
354723 TTATATATAT
*
354733 ATATATATATATATATGAAAAGATATCACTTTCTCATG
1 ATATATACATATATATGAAAAGATATCACTTTCTCATG
354771 ATATATACATATATATGAAAAGATATCACTTTCTCATG
1 ATATATACATATATATGAAAAGATATCACTTTCTCATG
354809 ATATATACATAT
1 ATATATACATAT
354821 GCCAGTAGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (38 bp):
ATATATACATATATATGAAAAGATATCACTTTCTCATG
Found at i:365277 original size:12 final size:13
Alignment explanation
Indices: 365258--365293 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
365248 CAGAATAGTT
365258 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
365271 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
365282 TCTTGCTGCCTC
1 TCTTGCTGCCTC
365294 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:365976 original size:21 final size:22
Alignment explanation
Indices: 365941--365984 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
365931 CTCTTAAAGT
365941 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
365963 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
365984 A
1 A
365985 TTATCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:371223 original size:31 final size:31
Alignment explanation
Indices: 371167--371245 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
371157 CAAGGGCTAC
* * * *
371167 ATTGAATAAAATTGTAGAATGCATG-ATCTAA
1 ATTGAACAAAATTCTATAATACATGAAT-TAA
*
371198 ATTGAACAAAATTCTATAATACATGAATTAT
1 ATTGAACAAAATTCTATAATACATGAATTAA
*
371229 ATTGAACAAAACTCTAT
1 ATTGAACAAAATTCTAT
371246 TGTATAGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (31 bp):
ATTGAACAAAATTCTATAATACATGAATTAA
Found at i:373980 original size:23 final size:23
Alignment explanation
Indices: 373932--373980 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
373922 TCTGTTGAGG
* *
373932 AAGGTTGCAGCGCTGAGGAAGCC
1 AAGGCTGCAGCGCTGAGGAAGAC
*
373955 AAGGCTGCAGTGCTGA-GAAGAAC
1 AAGGCTGCAGCGCTGAGGAAG-AC
373978 AAG
1 AAG
373981 ACTGTAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.33, C:0.18, G:0.37, T:0.12
Consensus pattern (23 bp):
AAGGCTGCAGCGCTGAGGAAGAC
Found at i:382560 original size:6 final size:6
Alignment explanation
Indices: 382551--382600 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
382541 TACATTTAGC
* * * * *
382551 TATAGG TATAGG TATAAG TATAAG TATAGG TAGAGG TAGAGG TAGAGG
1 TATAGG TATAGG TATAGG TATAGG TATAGG TATAGG TATAGG TATAGG
382599 TA
1 TA
382601 GAAGACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (6 bp):
TATAGG
Found at i:385623 original size:34 final size:33
Alignment explanation
Indices: 385572--385642 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
385562 TTCAATATTT
** * * *
385572 CAACAATTTTGTGTTCAATATTTTAACAACTTA
1 CAACAATTTTGCATTCAATATTTCAAAAACTCA
385605 CAACAACTTTTGCATTCAATATTTCAAAAACTCA
1 CAACAA-TTTTGCATTCAATATTTCAAAAACTCA
385639 CAAC
1 CAAC
385643 TTTTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (33 bp):
CAACAATTTTGCATTCAATATTTCAAAAACTCA
Found at i:386122 original size:101 final size:102
Alignment explanation
Indices: 385946--386236 Score: 327
Period size: 100 Copynumber: 2.9 Consensus size: 102
385936 TAAAGGTAAA
* * * * * * * * * *
385946 ATCCATTTCTGGTTCTTGAAATAATCTTTTTCCTCCATTACTTTCATCATCTCTTACTTTT-TGG
1 ATCCATCTATGGTTCTTCAAACAATCATTTTACTCAATTAATTTCATCAT-TTTTTCTTTTGTGG
* *
386010 AGTGCCAAAAATCATCAAGAAATTTGAATTTTTAGCTT
65 AGTGTCAAAAATCATCAAGAAATCTGAATTTTTAGCTT
*
386048 ATCCATCTATGGTTCTTCAAACAATCATTTTACTCAATTAATTTCGTCATTTTTT-TTTTGTGGA
1 ATCCATCTATGGTTCTTCAAACAATCATTTTACTCAATTAATTTCATCATTTTTTCTTTTGTGGA
* *
386112 GTGTCAAAAAT-ATAAAAAAATCTGAATTTTTAGCTT
66 GTGTCAAAAATCATCAAGAAATCTGAATTTTTAGCTT
* * * ** * *
386148 ATCCATCTATGGTTCTTCAAATAATCTTTTTTCTTGATTAGTTTCATCATTTTTTCTTTTGTGGG
1 ATCCATCTATGGTTCTTCAAACAATCATTTTACTCAATTAATTTCATCATTTTTTCTTTTGTGGA
* * *
386213 GTATAAAAAATCAGCAAGAAATCT
66 GTGTCAAAAATCATCAAGAAATCT
386237 AGAGCCTTTT
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
100 74 0.47
101 34 0.22
102 50 0.32
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (102 bp):
ATCCATCTATGGTTCTTCAAACAATCATTTTACTCAATTAATTTCATCATTTTTTCTTTTGTGGA
GTGTCAAAAATCATCAAGAAATCTGAATTTTTAGCTT
Found at i:396387 original size:12 final size:13
Alignment explanation
Indices: 396360--396392 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
396350 TTATCAACCT
396360 TTAATTTAATTTAA
1 TTAA-TTAATTTAA
396374 TTAATTAA-TTAA
1 TTAATTAATTTAA
396386 TTAATTA
1 TTAATTA
396393 TAACAGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTAATTTAA
Found at i:404994 original size:27 final size:28
Alignment explanation
Indices: 404964--405016 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
404954 TGTTATAAAC
404964 AAATAAA-TACA-CTAAACATAAATAAGT
1 AAATAAATTACATC-AAACATAAATAAGT
*
404991 AAATAAATTACATCAATCATAAATAA
1 AAATAAATTACATCAAACATAAATAA
405017 AGTTTTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 15 0.65
29 1 0.04
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATAAATTACATCAAACATAAATAAGT
Found at i:407751 original size:21 final size:22
Alignment explanation
Indices: 407726--407769 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
407716 AAGTGATTAA
407726 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
407747 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
407769 T
1 T
407770 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:410229 original size:18 final size:19
Alignment explanation
Indices: 410202--410245 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
410192 CGTAATAGCC
*
410202 TAAAAGAATATTTTA-GAA
1 TAAAATAATATTTTATGAA
*
410220 TAAAATAATATTTTATTAA
1 TAAAATAATATTTTATGAA
410239 TAAAATA
1 TAAAATA
410246 TTAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAAATAATATTTTATGAA
Found at i:410247 original size:11 final size:11
Alignment explanation
Indices: 410233--410260 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
410223 AATAATATTT
410233 TATTAATAAAA
1 TATTAATAAAA
410244 TATTAATAAAA
1 TATTAATAAAA
410255 TATTAA
1 TATTAA
410261 CATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:411065 original size:21 final size:25
Alignment explanation
Indices: 411016--411065 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 25
411006 AGAGGAAAGG
*
411016 AAGAAAGGAAGGAAAGAGATAAAAG
1 AAGAAAGGAAGGAAAGAGATAAAAA
411041 AAGAAAGG-AGG-AAGA-A-AAAAA
1 AAGAAAGGAAGGAAAGAGATAAAAA
411062 AAGA
1 AAGA
411066 GGAAAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 4 0.17
24 3 0.12
25 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (25 bp):
AAGAAAGGAAGGAAAGAGATAAAAA
Found at i:419887 original size:16 final size:16
Alignment explanation
Indices: 419866--419904 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
419856 TTCGTTGTTG
419866 TTAATTTAATCTCACT
1 TTAATTTAATCTCACT
419882 TTAATTT-ATCTCACT
1 TTAATTTAATCTCACT
*
419897 TTACTTTA
1 TTAATTTA
419905 GGAAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATTTAATCTCACT
Found at i:422793 original size:48 final size:48
Alignment explanation
Indices: 422741--422842 Score: 204
Period size: 48 Copynumber: 2.1 Consensus size: 48
422731 CCTTTAGTAA
422741 AAAGAAATATATGTCAAAATGTATACGAATATGCAAAGGTTAAGTGAG
1 AAAGAAATATATGTCAAAATGTATACGAATATGCAAAGGTTAAGTGAG
422789 AAAGAAATATATGTCAAAATGTATACGAATATGCAAAGGTTAAGTGAG
1 AAAGAAATATATGTCAAAATGTATACGAATATGCAAAGGTTAAGTGAG
422837 AAAGAA
1 AAAGAA
422843 TGGTAATTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (48 bp):
AAAGAAATATATGTCAAAATGTATACGAATATGCAAAGGTTAAGTGAG
Found at i:443101 original size:16 final size:17
Alignment explanation
Indices: 443082--443119 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
443072 TTTAAGGTGT
*
443082 TAATG-AGTTAAATATA
1 TAATGAAGTTAAATAAA
*
443098 TAATGAAGTTAATTAAA
1 TAATGAAGTTAAATAAA
443115 TAATG
1 TAATG
443120 TAATGTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (17 bp):
TAATGAAGTTAAATAAA
Found at i:449423 original size:23 final size:23
Alignment explanation
Indices: 449380--449447 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
449370 ATTTAGATAC
*
449380 AAAAGTAAATAGTAAATTTTTTAA
1 AAAAGTAAATAATAAA-TTTTTAA
*
449404 AAAAGTAAATAATAAATTTTTTA
1 AAAAGTAAATAATAAATTTTTAA
* *
449427 AAAATTATAT-AT-AATTTTTAA
1 AAAAGTAAATAATAAATTTTTAA
449448 TTGGTTTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.21
22 2 0.05
23 14 0.36
24 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AAAAGTAAATAATAAATTTTTAA
Found at i:449441 original size:25 final size:24
Alignment explanation
Indices: 449380--449430 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
449370 ATTTAGATAC
*
449380 AAAAGTAAATAGTAAATTTTTTAA
1 AAAAGTAAATAATAAATTTTTTAA
449404 AAAAGTAAATAATAAATTTTTTAA
1 AAAAGTAAATAATAAATTTTTTAA
449428 AAA
1 AAA
449431 TTATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
AAAAGTAAATAATAAATTTTTTAA
Found at i:449697 original size:21 final size:21
Alignment explanation
Indices: 449673--449715 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
449663 ATGAAGAAAC
449673 TAATAAAAAATTAAATAAAAT
1 TAATAAAAAATTAAATAAAAT
* * *
449694 TAATATAAAGTTAAATTAAAT
1 TAATAAAAAATTAAATAAAAT
449715 T
1 T
449716 CATTTATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAATAAAAAATTAAATAAAAT
Found at i:458400 original size:20 final size:21
Alignment explanation
Indices: 458377--458424 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
458367 GGATTGTACG
458377 AAGAAA-AAATTGAACCTTAA
1 AAGAAATAAATTGAACCTTAA
***
458397 AAGAAATGGCTTGAACCTTAA
1 AAGAAATAAATTGAACCTTAA
458418 AAGAAAT
1 AAGAAAT
458425 GGCTTGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (21 bp):
AAGAAATAAATTGAACCTTAA
Found at i:458412 original size:21 final size:21
Alignment explanation
Indices: 458386--458433 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
458376 GAAGAAAAAA
458386 TTGAACCTTAAAAGAAATGGC
1 TTGAACCTTAAAAGAAATGGC
458407 TTGAACCTTAAAAGAAATGGC
1 TTGAACCTTAAAAGAAATGGC
458428 TTGAAC
1 TTGAAC
458434 TATGATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (21 bp):
TTGAACCTTAAAAGAAATGGC
Found at i:466345 original size:13 final size:12
Alignment explanation
Indices: 466317--466341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
466307 CCGAGGCTCC
466317 ATAACTTTAAAA
1 ATAACTTTAAAA
466329 ATAACTTTAAAA
1 ATAACTTTAAAA
466341 A
1 A
466342 ATAAACAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTTAAAA
Found at i:466412 original size:102 final size:102
Alignment explanation
Indices: 466079--466656 Score: 471
Period size: 102 Copynumber: 5.7 Consensus size: 102
466069 TTCGAAACTT
* * * ** * *
466079 TTTTGAAAAAGATAAACAACTCCTTATCGGAGGCTTTACAACTTT-AAAATCAGTTTGAAAAATA
1 TTTTG-AAAATATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAAAT-AATTTAAAAAAT-
* * *
466143 AAAAAACTCTTCATCTAAGGCTTAAACAACTTTAAAATCA
63 AAACAACTCCTCATCTGAGGCTTAAACAACTTTAAAATCA
** * * *** ** * * * *
466183 GATT-AAAAAATAAACAACTCCTTATTTAAGGCTTAAACAACATTAAAATTAGTTTGAAAAATAA
1 TTTTGAAAATATAAACAACTCCTCATCCGAGGC-TCCACAACTTTAAAAATAATTTAAAAAATAA
*
466247 ACAACTCCTCA--T-AGGCTTAAACAATTTTAAAATCA
65 ACAACTCCTCATCTGAGGCTTAAACAACTTTAAAATCA
* * * *
466282 -ATTCAAAAAATAAACAACTCCTCATCCGAGGCTCCATAACTTTAAAAATAACTTTAAAAAATAA
1 TTTTGAAAATATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAAATAA-TTTAAAAAATAA
* * *
466346 ACAACTCCTTATCTGAGGCGTAGACAACTTTAAAATCA
65 ACAACTCCTCATCTGAGGCTTAAACAACTTTAAAATCA
* * * *
466384 TTTTGAAAATA-AAACAACTCTTCATCCGAGGCTCCACAACTTT-AAAATCATTTGGAAAAATAG
1 TTTTGAAAATATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAAATAATTT-AAAAAATAA
* * *
466447 ACAACTCCTTATCCGAGGCTCT--ACAACTTTAAAATTAA
65 ACAACTCCTCATCTGAGGCT-TAAACAACTTTAAAA-TCA
* * * * *
466485 TTTTGAAAAACATAAACAACTCTTCATCCG-GTCTCCACAACTTTAAAAACAATTCAAAAAAATA
1 TTTTG-AAAATATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAAATAATT-TAAAAAATA
* *
466549 AACAACTCCTCATATGAGGTTTAAACAACTTTAAAAAT-A
64 AACAACTCCTCATCTGAGGCTTAAACAACTTT-AAAATCA
* ** ** * * *
466588 CTTT-AAAATATAAACAACTCCTCATCTAAGGCTTAGACAACTTTAAAAACATTTTGAAAAATAA
1 TTTTGAAAATATAAACAACTCCTCATCCGAGGC-TCCACAACTTTAAAAATAATTTAAAAAATAA
*
466652 GCAAC
65 ACAAC
466657 ATCTAGGTGT
Statistics
Matches: 392, Mismatches: 62, Indels: 42
0.79 0.12 0.08
Matches are distributed among these distances:
98 16 0.04
99 67 0.17
100 16 0.04
101 59 0.15
102 119 0.30
103 96 0.24
104 15 0.04
105 4 0.01
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (102 bp):
TTTTGAAAATATAAACAACTCCTCATCCGAGGCTCCACAACTTTAAAAATAATTTAAAAAATAAA
CAACTCCTCATCTGAGGCTTAAACAACTTTAAAATCA
Found at i:466425 original size:50 final size:51
Alignment explanation
Indices: 466079--466656 Score: 409
Period size: 51 Copynumber: 11.4 Consensus size: 51
466069 TTCGAAACTT
* **
466079 TTTTGAAAAAGATAAACAACTCCTT-ATCGGAGGCTTTACAACTTTAAAATCA
1 TTTTGAAAAA-ATAAACAACT-CTTCATCTGAGGCTAAACAACTTTAAAATCA
* * *
466131 GTTTG-AAAAATAAAAAAACTCTTCATCTAAGGCTTAAACAACTTTAAAATCA
1 TTTTGAAAAAAT-AAACAACTCTTCATCTGAGGC-TAAACAACTTTAAAATCA
** * * * *
466183 GATT-AAAAAATAAACAACTCCTT-ATTTAAGGCTTAAACAACATTAAAATTA
1 TTTTGAAAAAATAAACAACT-CTTCATCTGAGGC-TAAACAACTTTAAAATCA
* * *
466234 GTTTG-AAAAATAAACAACTCCTCA--T-AGGCTTAAACAATTTTAAAATCA
1 TTTTGAAAAAATAAACAACTCTTCATCTGAGGC-TAAACAACTTTAAAATCA
* * * * ** * *
466282 -ATTCAAAAAATAAACAACTCCTCATCCGAGGCTCCATAACTTTAAAAATAA
1 TTTTGAAAAAATAAACAACTCTTCATCTGAGGCTAAACAACTTT-AAAATCA
* *
466333 CTTT-AAAAAATAAACAACTCCTT-ATCTGAGGCGTAGACAACTTTAAAATCA
1 TTTTGAAAAAATAAACAACT-CTTCATCTGAGGC-TAAACAACTTTAAAATCA
* * **
466384 TTTTGAAAATA-AAACAACTCTTCATCCGAGGCTCCACAACTTTAAAATCA
1 TTTTGAAAAAATAAACAACTCTTCATCTGAGGCTAAACAACTTTAAAATCA
* * * ** *
466434 -TTTGGAAAAATAGACAACTCCTT-ATCCGAGGCTCTACAACTTTAAAATTAA
1 TTTTGAAAAAATAAACAACT-CTTCATCTGAGGCTAAACAACTTTAAAA-TCA
* * ** *
466485 TTTTGAAAAACATAAACAACTCTTCATCCG-GTCTCCACAACTTTAAAAACA
1 TTTTGAAAAA-ATAAACAACTCTTCATCTGAGGCTAAACAACTTTAAAATCA
* ** * * *
466536 ATTCAAAAAAATAAACAACTCCTCATATGAGGTTTAAACAACTTTAAAAAT-A
1 TTTTGAAAAAATAAACAACTCTTCATCTGAGG-CTAAACAACTTT-AAAATCA
* * * * * *
466588 CTTT-AAAATATAAACAACTCCTCATCTAAGGCTTAGACAACTTTAAAAACA
1 TTTTGAAAAAATAAACAACTCTTCATCTGAGGC-TAAACAACTTTAAAATCA
*
466639 TTTTG-AAAAATAAGCAAC
1 TTTTGAAAAAATAAACAAC
466657 ATCTAGGTGT
Statistics
Matches: 428, Mismatches: 69, Indels: 59
0.77 0.12 0.11
Matches are distributed among these distances:
47 2 0.00
48 39 0.09
49 9 0.02
50 83 0.19
51 189 0.44
52 88 0.21
53 18 0.04
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (51 bp):
TTTTGAAAAAATAAACAACTCTTCATCTGAGGCTAAACAACTTTAAAATCA
Found at i:467485 original size:9 final size:10
Alignment explanation
Indices: 467465--467508 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
467455 TGAATCCCTC
467465 TTCTTCTTTTT
1 TTCTT-TTTTT
467476 TTCTTTTTTT
1 TTCTTTTTTT
467486 TTCTTTTTTT
1 TTCTTTTTTT
*
467496 CTTCCTTTTTT
1 -TTCTTTTTTT
467507 TT
1 TT
467509 AGGCATACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 17 0.55
11 14 0.45
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:467485 original size:11 final size:11
Alignment explanation
Indices: 467465--467508 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
467455 TGAATCCCTC
*
467465 TTCTTCTTTTT
1 TTCTTTTTTTT
467476 TTC-TTTTTTT
1 TTCTTTTTTTT
467486 TTCTTTTTTTCT
1 TTCTTTTTTT-T
*
467498 TCCTTTTTTTT
1 TTCTTTTTTTT
467509 AGGCATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.31
11 10 0.34
12 10 0.34
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:467495 original size:21 final size:21
Alignment explanation
Indices: 467465--467508 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
467455 TGAATCCCTC
* *
467465 TTCTTCTTTTTTTCTTTTTTT
1 TTCTTCTTTTCTTCCTTTTTT
*
467486 TTCTTTTTTTCTTCCTTTTTT
1 TTCTTCTTTTCTTCCTTTTTT
467507 TT
1 TT
467509 AGGCATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTCTTCTTTTCTTCCTTTTTT
Found at i:467504 original size:18 final size:18
Alignment explanation
Indices: 467468--467505 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
467458 ATCCCTCTTC
**
467468 TTCTTTTTTTCTTTTTTT
1 TTCTTTTTTTCTTCCTTT
467486 TTCTTTTTTTCTTCCTTT
1 TTCTTTTTTTCTTCCTTT
467504 TT
1 TT
467506 TTTAGGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTCTTTTTTTCTTCCTTT
Found at i:471561 original size:25 final size:26
Alignment explanation
Indices: 471522--471571 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
471512 TCCATTCCTT
*
471522 TTTTTTTCTTCTTC-TTCTTTTCTTCA
1 TTTTTCTCTTCTTCTTTC-TTTCTTCA
471548 TTTTTCTCTT-TTCTTTCTTTCTTC
1 TTTTTCTCTTCTTCTTTCTTTCTTC
471572 CTTTCCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTCTCTTCTTCTTTCTTTCTTCA
Found at i:471575 original size:17 final size:16
Alignment explanation
Indices: 471525--471575 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
471515 ATTCCTTTTT
471525 TTTTCTTC-TTCTT-C
1 TTTTCTTCTTTCTTCC
471539 TTTTCTTCATTT-TTCTC
1 TTTTCTTC-TTTCTTC-C
471556 TTTTCTTTCTTTCTTCC
1 TTTTC-TTCTTTCTTCC
471573 TTT
1 TTT
471576 CCTCTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 8 0.26
15 2 0.06
16 2 0.06
17 13 0.42
18 6 0.19
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTTCTTTCTTCC
Found at i:475961 original size:14 final size:14
Alignment explanation
Indices: 475942--475968 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
475932 TTAGTTTAAA
475942 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
475956 TTTTAGTTAATTA
1 TTTTAGTTAATTA
475969 ATTAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:482455 original size:12 final size:12
Alignment explanation
Indices: 482435--482467 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
482425 GTTTAGTATT
482435 ATAAGTAATTAA
1 ATAAGTAATTAA
*
482447 ATAATTAATTAA
1 ATAAGTAATTAA
482459 ATAAGTAAT
1 ATAAGTAAT
482468 ATTATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (12 bp):
ATAAGTAATTAA
Found at i:483140 original size:14 final size:15
Alignment explanation
Indices: 483093--483138 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
483083 CTTCCCTTCT
* *
483093 AAATATTTAGGAAGG
1 AAATATTTTGGAGGG
483108 AAATATTTTGGAGGG
1 AAATATTTTGGAGGG
483123 AAATA-TTTGG-GGG
1 AAATATTTTGGAGGG
483136 AAA
1 AAA
483139 ATTGACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 18 0.62
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.28
Consensus pattern (15 bp):
AAATATTTTGGAGGG
Found at i:509456 original size:35 final size:35
Alignment explanation
Indices: 509406--509486 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
509396 TAAATTGTTG
509406 TAAAATTTGCATGGTTTATACTCTT-TAAGTTGCTA
1 TAAAATTTGCATGGTTTATACT-TTCTAAGTTGCTA
** * *
509441 TAAAATTTGTGTGGTTTATACTTTCTAGGTTGCTG
1 TAAAATTTGCATGGTTTATACTTTCTAAGTTGCTA
509476 TAAAATTTGCA
1 TAAAATTTGCA
509487 CACTTTGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 2 0.05
35 37 0.95
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (35 bp):
TAAAATTTGCATGGTTTATACTTTCTAAGTTGCTA
Found at i:509880 original size:18 final size:18
Alignment explanation
Indices: 509857--509899 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
509847 ACCATTGAAC
509857 TTAAAAAAATTTATAAAT-
1 TTAAAAAAATTT-TAAATA
*
509875 TTAAAAAAATTTTAATTA
1 TTAAAAAAATTTTAAATA
509893 TTAAAAA
1 TTAAAAA
509900 TTAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAAAATTTTAAATA
Found at i:509899 original size:19 final size:18
Alignment explanation
Indices: 509859--509913 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
509849 CATTGAACTT
*
509859 AAAAAAATTTATAAATTT
1 AAAAAAATTTATAAATTA
509877 AAAAAAATTT-T-AATTA
1 AAAAAAATTTATAAATTA
** *
509893 TTAAAAA-TTAAAAATTA
1 AAAAAAATTTATAAATTA
509910 AAAA
1 AAAA
509914 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.07
16 9 0.31
17 8 0.28
18 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAAATTTATAAATTA
Found at i:509905 original size:6 final size:7
Alignment explanation
Indices: 509892--509920 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
509882 AATTTTAATT
509892 ATTAAAA
1 ATTAAAA
509899 ATTAAAA
1 ATTAAAA
509906 ATTAAAA
1 ATTAAAA
509913 ATTAAAA
1 ATTAAAA
509920 A
1 A
509921 AATTCCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATTAAAA
Found at i:519818 original size:21 final size:21
Alignment explanation
Indices: 519793--519841 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
519783 CCATTTCCAA
*
519793 ATGACATTGCAATGCTTGAGG
1 ATGACACTGCAATGCTTGAGG
**
519814 ATGACACTGTGATGCTTGAGG
1 ATGACACTGCAATGCTTGAGG
519835 ATGACAC
1 ATGACAC
519842 AACGATGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (21 bp):
ATGACACTGCAATGCTTGAGG
Found at i:519848 original size:21 final size:21
Alignment explanation
Indices: 519804--519860 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
519794 TGACATTGCA
***
519804 ATGCTTGAGGATGACACTGTG
1 ATGCTTGAGGATGACACAACG
519825 ATGCTTGAGGATGACACAACG
1 ATGCTTGAGGATGACACAACG
**
519846 ATGCTCAAGGATGAC
1 ATGCTTGAGGATGAC
519861 TATGCATCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (21 bp):
ATGCTTGAGGATGACACAACG
Found at i:519992 original size:61 final size:61
Alignment explanation
Indices: 519897--520012 Score: 232
Period size: 61 Copynumber: 1.9 Consensus size: 61
519887 TTTTTTACTA
519897 GTGAAGTAGTTTTGATGATAAGTCACATGGTGGGCCAAATGGCTATGCCCATAAGTTTCCG
1 GTGAAGTAGTTTTGATGATAAGTCACATGGTGGGCCAAATGGCTATGCCCATAAGTTTCCG
519958 GTGAAGTAGTTTTGATGATAAGTCACATGGTGGGCCAAATGGCTATGCCCATAAG
1 GTGAAGTAGTTTTGATGATAAGTCACATGGTGGGCCAAATGGCTATGCCCATAAG
520013 CTTCAGGCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (61 bp):
GTGAAGTAGTTTTGATGATAAGTCACATGGTGGGCCAAATGGCTATGCCCATAAGTTTCCG
Found at i:526406 original size:16 final size:16
Alignment explanation
Indices: 526385--526418 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
526375 CATGACGATT
*
526385 TGCCTTGAATAAGAGA
1 TGCCTTGAATAAAAGA
526401 TGCCTTGAATAAAAGA
1 TGCCTTGAATAAAAGA
526417 TG
1 TG
526419 GCACTACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (16 bp):
TGCCTTGAATAAAAGA
Found at i:534630 original size:61 final size:62
Alignment explanation
Indices: 534536--535256 Score: 695
Period size: 61 Copynumber: 11.7 Consensus size: 62
534526 ATGACTAGAA
* ** **
534536 TTAAACATCTTGGATGCCAGTTTGGTTGGGCTTAAACT-TTTTCCCGCCAATGTAATTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * * * * * * *
534597 TTAAACATCTTGGATACCA-TTGTGCTTGTGCTTAAACTCCTTTT-GTGCCAGCATAACTAGAC
1 TTAAACATCTTGGATGCCAGTT-TGATTGGGCTTAAACT-ATTTTCATGCCAACATAATTGGAC
* * * * *
534659 TTAAACATCTTGGATCCCAATTTGATTGGGCTTAAAC-A-TTTCATGCCAACCTAACTAGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * * * *
534719 TTAAACATCTTAGACGCCAATTTGATTGGACTTAAACTATTTTCATGCCAACATAACTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * *
534781 TTAAGCATCTTGGATGCCAGTTTGATTAGGCTTAAACT-TTTTCATGCTAACATAATTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * ** ** * *
534842 TTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTTGTGCCAATGTAACTGGAT
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * * * * *
534904 TTAAACATATTGGATGCCAATTTGATTAGGCTCAAA-TGTTTTCGTGCCAACATAATTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
** **
534965 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACT-TTTTTGTGCCAATGTAATTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* ** * *
535026 TTATATGTCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTAATTGGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * * ** * * *
535088 TTAAACATCTTGGATACCAATTTGATTGGGCTTTAAC-GCTTTCATGCTAACATAACTAGAC
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
* * * * ** ** ** * *
535149 TTAAACATCTTGGATGTCAGTTTGATTAGACTTAAACTTCTCTTTTTGTGTAAATGTAACTGGAA
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAA---CTATTTTCATGCCAACATAATTGGAC
* *
535214 TTAAACAACTTGGATGCCAGTTTGATTGGGCTTAAACTCTTTT
1 TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTT
535257 TATGTCATTA
Statistics
Matches: 545, Mismatches: 101, Indels: 27
0.81 0.15 0.04
Matches are distributed among these distances:
59 3 0.01
60 50 0.09
61 241 0.44
62 198 0.36
63 6 0.01
64 1 0.00
65 46 0.08
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (62 bp):
TTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTATTTTCATGCCAACATAATTGGAC
Found at i:534630 original size:123 final size:121
Alignment explanation
Indices: 534453--535286 Score: 758
Period size: 123 Copynumber: 6.8 Consensus size: 121
534443 CCTAAAATTC
* * * * * * **
534453 TTTCATGCGAACATAACTGGGCCT-AACATCTTGGATGCTAACTAAATTGGGCTTAAACTCTCTT
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGC-CATTTGATTGGGCTTAAACTCT-TT
* * * * *
534517 TGTGCCGATATGACTAGAATTAAACATCTTGGATGCCAGTTTGGTTGGGCTTAAACTT
64 TGTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
** ** * * *
534575 TTTCCCGCCAATGTAATTGGACTTAAACATCTTGGATACCATTGTGCTTGTGCTTAAACTCCTTT
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCATT-TGATTGGGCTTAAACT-CTTT
** * * * *
534640 TGTGCCAGCATAACTAGACTTAAACATCTTGGATCCCAATTTGATTGGGCTTAAAC-A
64 TGTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
* * * * * * *
534697 TTTCATGCCAACCTAACTAGACTTAAACATCTTAGACGCCAATTTGATTGGACTTAAACTATTTT
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCC-ATTTGATTGGGCTTAAACTCTTTT
* * * *
534762 CATGCCAACATAACTGGACTTAAGCATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
65 -GTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
* * * *
534820 TTTCATGCTAACATAATTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTT
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCA-TTTGATTGGGCTTAAACT-CTTT
* * * * * *
534885 TGTGCCAATGTAACTGGATTTAAACATATTGGATGCCAATTTGATTAGGCTCAAA-TGT
64 TGTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACT-T
* *
534943 TTTCGTGCCAACATAATTGGACTTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTTTTTT
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCA-TTTGATTGGGCTTAAACTCTTTT
* * * * ** * *
535008 GTGCCAATGTAATTGGACTTATATGTCTTGGATGCTAGTTTGATTGGGCTTAAACTAT
65 GTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACT-T
* * * * *
535066 TTTCATGCCAACGTAATTGGACTTAAACATCTTGGATACCAATTTGATTGGGCTTTAACGCTTTC
1 TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCC-ATTTGATTGGGCTTAAACTCTTTT
* * * * *
535131 ATGCTAACATAACTAGACTTAAACATCTTGGATGTCAGTTTGATTAGACTTAAACTT
65 GTGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
** ** * * *
535188 CTCTTTTTGTGTAA-ATGTAACTGGAATTAAACAACTTGGATGCCAGTTTGATTGGGCTTAAACT
1 -T-TTCATG-CCAACA--TAATTGGACTTAAACATCTTGGATGCCA-TTTGATTGGGCTTAAACT
* * * * *
535252 CTTTTTATGTCATTATAAATAGACTTATACATCTT
60 C-TTTTGTGCCAATATAACTAGACTTAAACATCTT
535287 AAATGCCAAC
Statistics
Matches: 578, Mismatches: 116, Indels: 31
0.80 0.16 0.04
Matches are distributed among these distances:
121 4 0.01
122 162 0.28
123 332 0.57
124 11 0.02
125 3 0.01
126 40 0.07
127 26 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (121 bp):
TTTCATGCCAACATAATTGGACTTAAACATCTTGGATGCCATTTGATTGGGCTTAAACTCTTTTG
TGCCAATATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGGCTTAAACTT
Found at i:534792 original size:184 final size:183
Alignment explanation
Indices: 534529--535256 Score: 766
Period size: 184 Copynumber: 3.9 Consensus size: 183
534519 TGCCGATATG
* * * ** ** *
534529 ACTAGAATTAAACATCTTGGATGCCAGTTTGGTTGGGCTTAAACT-TTTTCCCGCCAATGTAATT
1 ACTAGACTTAAACATCTTGGATGCCAATTTGATTGGGCTTAAACTGTTTTCATGCCAACATAACT
* * * * *
534593 GGACTTAAACATCTTGGATACCA-TTGTGCTTGTGCTTAAACTCCTTTTGTGCCAGCATAACTAG
66 GGACTTAAACATCTTGGATGCCAGTT-TGATTG-GCTTAAACT--TTTTGTGCCAACATAATTGG
* * * * *
534657 ACTTAAACATCTTGGATCCCAATTTGATTGGGCTTAAAC-A-TTTCATGCCAACCTA
127 ACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTA
* * * *
534712 ACTAGACTTAAACATCTTAGACGCCAATTTGATTGGACTTAAACTATTTTCATGCCAACATAACT
1 ACTAGACTTAAACATCTTGGATGCCAATTTGATTGGGCTTAAACTGTTTTCATGCCAACATAACT
* * *
534777 GGACTTAAGCATCTTGGATGCCAGTTTGATTAGGCTTAAACTTTTTCATGCTAACATAATTGGAC
66 GGACTTAAACATCTTGGATGCCAGTTTGATT-GGCTTAAACTTTTT-GTGCCAACATAATTGGAC
** *
534842 TTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTTGTGCCAATGTA
129 TTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTA
* * * * * * *
534897 ACTGGATTTAAACATATTGGATGCCAATTTGATTAGGCTCAAA-TGTTTTCGTGCCAACATAATT
1 ACTAGACTTAAACATCTTGGATGCCAATTTGATTGGGCTTAAACTGTTTTCATGCCAACATAACT
**
534961 GGACTTAAACATCTTGGATGCCAGTTTGATTGGGCTTAAACTTTTTTGTGCCAATGTAATTGGAC
66 GGACTTAAACATCTTGGATGCCAGTTTGATT-GGCTTAAAC-TTTTTGTGCCAACATAATTGGAC
**
535026 TTATATGTCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTA
129 TTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTA
* * * * * *
535081 ATTGGACTTAAACATCTTGGATACCAATTTGATTGGGCTTTAAC-GCTTTCATGCTAACATAACT
1 ACTAGACTTAAACATCTTGGATGCCAATTTGATTGGGCTTAAACTGTTTTCATGCCAACATAACT
* * * ** ** *
535145 AGACTTAAACATCTTGGATGTCAGTTTGATTAGACTTAAACTTCTCTTTTTGTGTAAATGTAACT
66 GGACTTAAACATCTTGGATGCCAGTTTGATT-GGCTTAAA-----CTTTTTGTGCCAACATAATT
* * * * *
535210 GGAATTAAACAACTTGGATGCCAGTTTGATTGGGCTTAAACTCTTTT
125 GGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTT
535257 TATGTCATTA
Statistics
Matches: 458, Mismatches: 74, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
182 4 0.01
183 85 0.19
184 258 0.56
185 54 0.12
188 56 0.12
189 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (183 bp):
ACTAGACTTAAACATCTTGGATGCCAATTTGATTGGGCTTAAACTGTTTTCATGCCAACATAACT
GGACTTAAACATCTTGGATGCCAGTTTGATTGGCTTAAACTTTTTGTGCCAACATAATTGGACTT
ATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCAACGTA
Found at i:535023 original size:30 final size:30
Alignment explanation
Indices: 534866--535093 Score: 102
Period size: 31 Copynumber: 7.4 Consensus size: 30
534856 TGCTAGTTTG
* *
534866 ATTGGGCTTAAACTATTTTTGTGCCAATGTA
1 ATTGGACTTAAACT-TTTTGGTGCCAATGTA
* * * * * *
534897 ACTGGATTTAAACATATTGGATGCCAATTTG
1 ATTGGACTTAAACTTTTTGG-TGCCAATGTA
* * **
534928 ATTAGG-CTCAAA-TGTTTTCGTGCCAACATA
1 ATT-GGACTTAAACT-TTTTGGTGCCAATGTA
* * * * *
534958 ATTGGACTTAAACATCTTGGATGCCAGTTTG
1 ATTGGACTTAAACTTTTTGG-TGCCAATGTA
* *
534989 ATTGGGCTTAAACTTTTTTGTGCCAATGTA
1 ATTGGACTTAAACTTTTTGGTGCCAATGTA
* * * * * *
535019 ATTGGACTTATA-TGTCTTGGATGCTAGTTTG
1 ATTGGACTTAAACT-TTTTGG-TGCCAATGTA
* ** *
535050 ATTGGGCTTAAACTATTTTCATGCCAACGTA
1 ATTGGACTTAAACT-TTTTGGTGCCAATGTA
535081 ATTGGACTTAAAC
1 ATTGGACTTAAAC
535094 ATCTTGGATA
Statistics
Matches: 136, Mismatches: 52, Indels: 18
0.66 0.25 0.09
Matches are distributed among these distances:
29 3 0.02
30 44 0.32
31 83 0.61
32 6 0.04
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (30 bp):
ATTGGACTTAAACTTTTTGGTGCCAATGTA
Found at i:535329 original size:93 final size:93
Alignment explanation
Indices: 535209--535380 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
535199 TAAATGTAAC
* * *
535209 TGGAATTAAACAACTTGGATGCCAGTTTGATTGGGCTT-AAACTCTTTTTATGTCATTATAAATA
1 TGGAATTAAACAACTTGGATGCCAGTTTGATTAGGCTTAAAAC-CTTTTTATGCCAATATAAATA
535273 GACTTATACATCTTAAATGCCAACATAAG
65 GACTTATACATCTTAAATGCCAACATAAG
* * * * *
535302 TGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTTTGCCAATATAACTAG
1 TGGAATTAAACAACTTGGATGCCAGTTTGATTAGGCTTAAAACCTTTTTATGCCAATATAAATAG
535367 ACTTATACATCTTA
66 ACTTATACATCTTA
535381 GAAACCAGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
93 66 0.94
94 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (93 bp):
TGGAATTAAACAACTTGGATGCCAGTTTGATTAGGCTTAAAACCTTTTTATGCCAATATAAATAG
ACTTATACATCTTAAATGCCAACATAAG
Found at i:535453 original size:61 final size:60
Alignment explanation
Indices: 535290--535528 Score: 237
Period size: 61 Copynumber: 3.9 Consensus size: 60
535280 ACATCTTAAA
* * * * * *
535290 TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTT
1 TGCCAATATAACTAGACTTAAACATCTTGGATACCAGTTTGATTAGGCTT-AAA-CTTTTCT
* * *
535352 TGCCAATATAACTAGACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTATTTCT
1 TGCCAATATAACTAGACTTAAACATCTTGGATACCAGTTTGATTAGGCTTAAACT-TTTCT
* * * * ** * *
535413 TGCCAATGTAATTGGACATAAACATCTTGGATACTGGTTTGATTGGGTTTAAA-TGCTTTCT
1 TGCCAATATAACTAGACTTAAACATCTTGGATACCAGTTTGATTAGGCTTAAACT--TTTCT
* * * *
535474 TACCAACATAACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACT
1 TGCCAATATAACTAGACTTAAACATCTTGGATACCAGTTTGATTAGGCTTAAACT
535529 CCCCTTTTTG
Statistics
Matches: 141, Mismatches: 33, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
60 3 0.02
61 95 0.67
62 43 0.30
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
TGCCAATATAACTAGACTTAAACATCTTGGATACCAGTTTGATTAGGCTTAAACTTTTCT
Found at i:535525 original size:122 final size:123
Alignment explanation
Indices: 535302--535528 Score: 312
Period size: 122 Copynumber: 1.9 Consensus size: 123
535292 CCAACATAAG
* * * * *
535302 TGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTTTGCCAATATAACTAG
1 TGGACATAAACATCTTGGATACTAGTTTGATTAGGCTTAAAACCTTTTCTTACCAACATAACTAG
* *
535367 ACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTATTTCTTGCCAATGTAAT
66 ACTTAAACATCTTAGAAACCAGTTTGATTAGACTTAAACTATTTCTTGCCAATGTAAT
* * * **
535425 TGGACATAAACATCTTGGATACTGGTTTGATTGGGTTTAAATGC-TTTCTTACCAACATAACTAG
1 TGGACATAAACATCTTGGATACTAGTTTGATTAGGCTTAAAACCTTTTCTTACCAACATAACTAG
* **
535489 ACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACT
66 ACTTAAACATCTTAGAAACCAGTTTGATTAGACTTAAACT
535529 CCCCTTTTTG
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
122 52 0.58
123 37 0.42
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (123 bp):
TGGACATAAACATCTTGGATACTAGTTTGATTAGGCTTAAAACCTTTTCTTACCAACATAACTAG
ACTTAAACATCTTAGAAACCAGTTTGATTAGACTTAAACTATTTCTTGCCAATGTAAT
Found at i:535578 original size:342 final size:343
Alignment explanation
Indices: 534948--535703 Score: 1036
Period size: 342 Copynumber: 2.2 Consensus size: 343
534938 AATGTTTTCG
* * *
534948 TGCCAACATAATTGGACTTAAACATCTTGGATGCCAGTTTGATTGGGCTT-AAA-CTTTTTTGTG
1 TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTT-TG
* * * ** * ** * *
535011 CCAATGTAATTGGACTTATATGTCTTGGATGCTAGTTTGATTGGGCTTAAACTATTTTCATGCCA
65 CCAATATAACTAGACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTATTTTCATGCCA
* * *
535076 ACGTAATTGGACTTAAACATCTTGGATACCAATTTGATTGGGCTTTAACGCTTTCATGCTAACAT
130 ACGTAATTGGACATAAACATCTTGGATACCAATTTGATTGGGCTTTAACGCTTTCATACCAACAT
* * * * *
535141 AACTAGACTTAAACATCTTGGATGTCAGTTTGATTAGACTTAAACTTCTCTTTTTGTGTAAATGT
195 AACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACTCCCCTTTTTGTGCAAACGT
*
535206 AACTGGAATTAAACAACTTGGATGCCAGTTTGATTGGGCTTAAACTCTTTTTATGTCATTATAAA
260 AACTGGAATTAAACAACTTGGATGCCAGTTTGATTGGGATTAAACTCTTTTTATGTCATTATAAA
535271 TAGACTTATACATCTTAAA
325 TAGACTTATACATCTTAAA
535290 TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTTTGC
1 TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTTTGC
*
535355 CAATATAACTAGACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTA-TTTCTTGCCAA
66 CAATATAACTAGACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTATTTTCATGCCAA
* *** * *
535419 TGTAATTGGACATAAACATCTTGGATACTGGTTTGATTGGG-TTTAAATGCTTTCTTACCAACAT
131 CGTAATTGGACATAAACATCTTGGATACCAATTTGATTGGGCTTT-AACGCTTTCATACCAACAT
**
535483 AACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACTCCCCTTTTTGTGCCCACGT
195 AACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACTCCCCTTTTTGTGCAAACGT
* * * *
535548 AGCTGGAATTAAACACCTTGGAAT-CCAGTTTGATTGGGATTTAACTCTTTTTGTGTCATTATAA
260 AACTGGAATTAAACAACTTGG-ATGCCAGTTTGATTGGGATTAAACTCTTTTTATGTCATTATAA
* * **
535612 TTGGACTTATACATCTTGGA
324 ATAGACTTATACATCTTAAA
* * * * * *
535632 TACCAACATAAGTGGACTTAAACATCTTAGATGCTAGCTTGATCAGGCTTAAACTCCTTTTTTTA
1 TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAA-ACCTTTTTTTG
535697 CCAATAT
65 CCAATAT
535704 TATTAGGCAT
Statistics
Matches: 364, Mismatches: 45, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
341 3 0.01
342 287 0.79
343 67 0.18
344 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (343 bp):
TGCCAACATAAGTGGACTTAAACATCTTGGATGCTAGTTTGATTAGGCTTAAAACCTTTTTTTGC
CAATATAACTAGACTTATACATCTTAGAAACCAGTTTGATTAGGCTTAAACTATTTTCATGCCAA
CGTAATTGGACATAAACATCTTGGATACCAATTTGATTGGGCTTTAACGCTTTCATACCAACATA
ACTAGACTTAAACATCTTGGATGCCAGTTTGATTAGACTTAAACTCCCCTTTTTGTGCAAACGTA
ACTGGAATTAAACAACTTGGATGCCAGTTTGATTGGGATTAAACTCTTTTTATGTCATTATAAAT
AGACTTATACATCTTAAA
Found at i:537758 original size:28 final size:28
Alignment explanation
Indices: 537718--537776 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
537708 TATTGAAGAA
*
537718 CAATTCCTAAAAGG-GAAACATTTTAGAG
1 CAATTCCTAAAAGGAAAAAC-TTTTAGAG
537746 CAATTCCTAAAAGGAAAAACTTTTAGAG
1 CAATTCCTAAAAGGAAAAACTTTTAGAG
537774 CAA
1 CAA
537777 AGGTTGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (28 bp):
CAATTCCTAAAAGGAAAAACTTTTAGAG
Found at i:543814 original size:73 final size:73
Alignment explanation
Indices: 543659--543820 Score: 252
Period size: 73 Copynumber: 2.2 Consensus size: 73
543649 TATTCAATGC
* * * *
543659 CATTGTGGAAAGCATGAGTTGCTAGAAAATGATAGGTGATTTGAATACCTATTTGAGAATGATCA
1 CATTGTGGAAAGCATGAATGGCTAGAAAATGATAGGTGATTTCAATACCTATTTGAAAATGATCA
543724 TACTCTGT
66 TACTCTGT
* * * *
543732 AACTATGGAAAACATGAATGGCTAGAAAATGATAGGTGATTTCAATACCTATTTGAAAATGATCA
1 CATTGTGGAAAGCATGAATGGCTAGAAAATGATAGGTGATTTCAATACCTATTTGAAAATGATCA
543797 TACTCTGT
66 TACTCTGT
543805 CATTGTGGAAAGCATG
1 CATTGTGGAAAGCATG
543821 GGCTGGAAGG
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (73 bp):
CATTGTGGAAAGCATGAATGGCTAGAAAATGATAGGTGATTTCAATACCTATTTGAAAATGATCA
TACTCTGT
Found at i:543844 original size:73 final size:72
Alignment explanation
Indices: 543659--543845 Score: 189
Period size: 73 Copynumber: 2.6 Consensus size: 72
543649 TATTCAATGC
* * ** * * *
543659 CATTGTGGAAAGCATGAGTTGCTAGAAAATGATAGGTGATTTGAATACCTATTTGAGAATGATCA
1 CATTGTGGAAAGCATGGGCTGGAAGAAAGT-ATAGGTGATTTCAATACCTATTTGAAAATGATCA
543724 TACTCTGT
65 TACTCTGT
* * * * * *
543732 AACTATGGAAAACATGAATGGCTAGAA-AATG-ATAGGTGATTTCAATACCTATTTGAAAATGAT
1 CATTGTGGAAAGCATG---GGCTGGAAGAAAGTATAGGTGATTTCAATACCTATTTGAAAATGAT
543795 CATACTCTGT
63 CATACTCTGT
*
543805 CATTGTGGAAAGCATGGGCTGGAAGGAAAGTATACGTGATT
1 CATTGTGGAAAGCATGGGCTGGAA-GAAAGTATAGGTGATT
543846 ATGAATGCAA
Statistics
Matches: 88, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
70 7 0.08
72 3 0.03
73 73 0.83
75 2 0.02
76 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (72 bp):
CATTGTGGAAAGCATGGGCTGGAAGAAAGTATAGGTGATTTCAATACCTATTTGAAAATGATCAT
ACTCTGT
Found at i:546195 original size:20 final size:20
Alignment explanation
Indices: 546172--546211 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
546162 CAAAATCAAT
546172 GGATGTTTAAATGCATGATG
1 GGATGTTTAAATGCATGATG
*
546192 GGATGTTTAAATGTATGATG
1 GGATGTTTAAATGCATGATG
546212 AGTGACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (20 bp):
GGATGTTTAAATGCATGATG
Found at i:551114 original size:21 final size:21
Alignment explanation
Indices: 551090--551134 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
551080 CAAAAGAGGG
*
551090 AAGAAAGGAGAAAGAAGAAAA
1 AAGAAAAGAGAAAGAAGAAAA
*
551111 AAGAAAAGAGAAATAAGAAAA
1 AAGAAAAGAGAAAGAAGAAAA
551132 AAG
1 AAG
551135 CTTGGAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
AAGAAAAGAGAAAGAAGAAAA
Found at i:555542 original size:10 final size:9
Alignment explanation
Indices: 555516--555573 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
555506 GCCCTTAGTT
555516 TTTTCTTTTC
1 TTTT-TTTTC
* *
555526 ATTTTTTCC
1 TTTTTTTTC
555535 TTTTTTTTC
1 TTTTTTTTC
*
555544 TTCTTTTTAC
1 TT-TTTTTTC
* *
555554 TTTTCTTTG
1 TTTTTTTTC
555563 TTTTTTTTC
1 TTTTTTTTC
555572 TT
1 TT
555574 GCTTCTCTCT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
9 26 0.70
10 11 0.30
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:555550 original size:19 final size:19
Alignment explanation
Indices: 555528--555571 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
555518 TTCTTTTCAT
*
555528 TTTTTCCTTTTTTTTCTTC
1 TTTTTCCTTTTCTTTCTTC
* * *
555547 TTTTTACTTTTCTTTGTTT
1 TTTTTCCTTTTCTTTCTTC
555566 TTTTTC
1 TTTTTC
555572 TTGCTTCTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTCCTTTTCTTTCTTC
Found at i:555570 original size:13 final size:12
Alignment explanation
Indices: 555514--555573 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
555504 CCGCCCTTAG
555514 TTTTTTCTTTTCAT
1 TTTTTTCTTTT--T
*
555528 TTTTTCCTTTTT
1 TTTTTTCTTTTT
*
555540 TTTCTTCTTTTT
1 TTTTTTCTTTTT
**
555552 ACTTTTCTTTGTT
1 TTTTTTCTTT-TT
555565 TTTTTTCTT
1 TTTTTTCTT
555574 GCTTCTCTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 18 0.49
13 9 0.24
14 10 0.27
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:555746 original size:10 final size:10
Alignment explanation
Indices: 555731--555765 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
555721 TGTCAACTGG
555731 TTTTTTTAAT
1 TTTTTTTAAT
555741 TTTTTTTAAT
1 TTTTTTTAAT
555751 TTTTTTTAAT
1 TTTTTTTAAT
555761 TTTTT
1 TTTTT
555766 CAAAATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:556537 original size:15 final size:16
Alignment explanation
Indices: 556508--556537 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
556498 AAGACCAAGT
556508 AGTAATTACATGAAAA
1 AGTAATTACATGAAAA
556524 AGTAATTA-ATGAAA
1 AGTAATTACATGAAA
556538 TTGGTCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.03, G:0.13, T:0.27
Consensus pattern (16 bp):
AGTAATTACATGAAAA
Found at i:560687 original size:35 final size:35
Alignment explanation
Indices: 560639--560830 Score: 179
Period size: 35 Copynumber: 5.4 Consensus size: 35
560629 TACTAAGTAC
* *
560639 TTGATTAACATTGTTTAATTAAGTTTTTGGGCGTAA
1 TTGATTAA-ATTGTTTAATTAAGTTATTGGGCCTAA
* * * * *
560675 TTAATTAAATTGTTTAATTAAGTCATAGGACCTAC
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * * **
560710 TTGATTAAAATTATTTAGTTAAGTCATTACGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* * **
560746 TTGATTAAAATTATTTAATTAAGTTGTTGGGATTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* *
560782 TT-ACTTAAATTGTTTAATTAAGTTATTGGGCTTGA
1 TTGA-TTAAATTGTTTAATTAAGTTATTGGGCCTAA
560817 TTGATTAAATTGTT
1 TTGATTAAATTGTT
560831 AACTGGGCTT
Statistics
Matches: 127, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
35 64 0.50
36 63 0.50
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:560732 original size:36 final size:36
Alignment explanation
Indices: 560639--560769 Score: 131
Period size: 36 Copynumber: 3.7 Consensus size: 36
560629 TACTAAGTAC
* * ** ** *
560639 TTGATTAACATTGTTTAATTAAGTTTTTGGGCGTAA
1 TTGATTAAAATTATTTAATTAAGTCATTACGCCTAA
* * * *
560675 TTAATT-AAATTGTTTAATTAAGTCA-TAGGACCTAC
1 TTGATTAAAATTATTTAATTAAGTCATTACG-CCTAA
*
560710 TTGATTAAAATTATTTAGTTAAGTCATTACGCCTAA
1 TTGATTAAAATTATTTAATTAAGTCATTACGCCTAA
560746 TTGATTAAAATTATTTAATTAAGT
1 TTGATTAAAATTATTTAATTAAGT
560770 TGTTGGGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
34 3 0.04
35 24 0.30
36 49 0.62
37 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (36 bp):
TTGATTAAAATTATTTAATTAAGTCATTACGCCTAA
Found at i:560747 original size:71 final size:72
Alignment explanation
Indices: 560636--560769 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 72
560626 GCTTACTAAG
* * ** ** * *
560636 TACTTGATTAACATTGTTTAATTAAGTTTTTGGGCGTAATTAATT-AAATTGTTTAATTAAGTCA
1 TACTTGATTAAAATTATTTAATTAAGTCATTACGCCTAATTAATTAAAATTATTTAATTAAGTCA
560700 TAGGACC
66 TAGGACC
* *
560707 TACTTGATTAAAATTATTTAGTTAAGTCATTACGCCTAATTGATTAAAATTATTTAATTAAGT
1 TACTTGATTAAAATTATTTAATTAAGTCATTACGCCTAATTAATTAAAATTATTTAATTAAGT
560770 TGTTGGGATT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
71 36 0.69
72 16 0.31
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (72 bp):
TACTTGATTAAAATTATTTAATTAAGTCATTACGCCTAATTAATTAAAATTATTTAATTAAGTCA
TAGGACC
Found at i:579123 original size:16 final size:16
Alignment explanation
Indices: 579092--579125 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
579082 TTCCAAGCTA
**
579092 TTTTTCTTTTTTTTCT
1 TTTTTCTTTTACTTCT
579108 TTTTTCTTTTACTTCT
1 TTTTTCTTTTACTTCT
579124 TT
1 TT
579126 ACTTGGCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTACTTCT
Found at i:583984 original size:52 final size:53
Alignment explanation
Indices: 583924--584036 Score: 149
Period size: 53 Copynumber: 2.2 Consensus size: 53
583914 ATTGTTACTT
* * * *
583924 GACTAAGAGCTTATTGCTAGAAACTGA-GTTCAG-AGACAAAAATGACTTAATC
1 GACTAAGAGCTCAATGCCA-AAACTGAGGTTCAGAAGACAAAAACGACTTAATC
* *
583976 GACTAAGAGCTCAATGCCAAAAGTTAGGTTCAGAAGACAAAAACGACTTAATC
1 GACTAAGAGCTCAATGCCAAAACTGAGGTTCAGAAGACAAAAACGACTTAATC
584029 GACTAAGA
1 GACTAAGA
584037 AGCATGTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 5 0.09
52 22 0.42
53 26 0.49
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (53 bp):
GACTAAGAGCTCAATGCCAAAACTGAGGTTCAGAAGACAAAAACGACTTAATC
Found at i:596919 original size:21 final size:21
Alignment explanation
Indices: 596893--596947 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
596883 AAAGACATCT
596893 ATCAATAGATAGAGAATATCA
1 ATCAATAGATAGAGAATATCA
596914 ATCAATAGATAGAGAATATCA
1 ATCAATAGATAGAGAATATCA
596935 ATCAATAGATAGA
1 ATCAATAGATAGA
596948 CTCTGGTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (21 bp):
ATCAATAGATAGAGAATATCA
Found at i:599019 original size:19 final size:19
Alignment explanation
Indices: 598985--599024 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
598975 ATAGTGGTAT
**
598985 TGATGTGTGGTTACATGGA
1 TGATGTGTGGAGACATGGA
*
599004 TGATGTGTGGAGACATTGA
1 TGATGTGTGGAGACATGGA
599023 TG
1 TG
599025 CAGAAGGCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.35
Consensus pattern (19 bp):
TGATGTGTGGAGACATGGA
Found at i:604096 original size:16 final size:16
Alignment explanation
Indices: 604060--604097 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
604050 TATTGATTGG
604060 TAAAATATTTTTTATT
1 TAAAATATTTTTTATT
604076 T-AAATATTTTTCT-TT
1 TAAAATATTTTT-TATT
604091 TAAAATA
1 TAAAATA
604098 GAAAATATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAAATATTTTTTATT
Found at i:612996 original size:22 final size:22
Alignment explanation
Indices: 612969--613014 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
612959 AAGCCAAACC
*
612969 TTCCTTCCTTT-CTCTCTTTTCT
1 TTCCTT-CTTTCCTCTCCTTTCT
612991 TTCCTTCTTTCCTCTCCTTTCT
1 TTCCTTCTTTCCTCTCCTTTCT
613013 TT
1 TT
613015 TTCTTCTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (22 bp):
TTCCTTCTTTCCTCTCCTTTCT
Found at i:621277 original size:68 final size:68
Alignment explanation
Indices: 621187--621375 Score: 216
Period size: 68 Copynumber: 2.8 Consensus size: 68
621177 ATATCAAGCC
* * * * * **
621187 CTCAAACTCATATCATATGGTATGTGGAAACTACGTCACATACATAGCATCATATCATTCAACAT
1 CTCAATCTCATATCATATGGTATGTGGAAATTACATCACATACTTAGCAACATAGAATTCAACAT
621252 GTA
66 GTA
* ** * * **
621255 CTCATTCTCATATCATGGGGTATGTGGGATTTACATCACATACTTAATAACATAGAATTCAACAT
1 CTCAATCTCATATCATATGGTATGTGGAAATTACATCACATACTTAGCAACATAGAATTCAACAT
621320 GTA
66 GTA
* * * *
621323 CTCAATCTGATGTCTTATGGTATGTGGAAATTATATCACATACTTAGCAACAT
1 CTCAATCTCATATCATATGGTATGTGGAAATTACATCACATACTTAGCAACAT
621376 GTTTTACACC
Statistics
Matches: 96, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (68 bp):
CTCAATCTCATATCATATGGTATGTGGAAATTACATCACATACTTAGCAACATAGAATTCAACAT
GTA
Found at i:622779 original size:62 final size:62
Alignment explanation
Indices: 622693--622845 Score: 157
Period size: 62 Copynumber: 2.4 Consensus size: 62
622683 AATCTACCTT
* * *
622693 AAATAAAGAAAGTTCGATTCTTGCAAGTTAGAATAGCTTTTGGATTA-AAAGAATTGATTCTTA-
1 AAATAAAG-AAGTT-GATTCTTGCAAGTTAGAAAAGCTTTTAGACTAGAAAG-ATTGATTC-TAG
622756 G
62 G
* * ** * *
622757 AAATTAAGAAGTTGATTTTTGCAAGGCAGAAAAGTTTTTAGACTAGAATGATTGATTCTAGG
1 AAATAAAGAAGTTGATTCTTGCAAGTTAGAAAAGCTTTTAGACTAGAAAGATTGATTCTAGG
* *
622819 AAATCAAGAAGTTGGTTCTTGCAAGTT
1 AAATAAAGAAGTTGATTCTTGCAAGTT
622846 TGGGATTCCA
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
61 2 0.03
62 56 0.77
63 8 0.11
64 7 0.10
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (62 bp):
AAATAAAGAAGTTGATTCTTGCAAGTTAGAAAAGCTTTTAGACTAGAAAGATTGATTCTAGG
Found at i:623870 original size:73 final size:72
Alignment explanation
Indices: 623733--623871 Score: 165
Period size: 73 Copynumber: 1.9 Consensus size: 72
623723 AAAGTGGTGG
* * * *
623733 ATGTGGATGATAAAATGCCTACAAACAAAGTTATGAGAGTGGATGAGTAAGTCTCTACCACTTAA
1 ATGTGGATGATAAAATGCCCACAAAAAAAATTATGAGAGTGGATGAGCAAGTCTCTACCACTTAA
623798 TTATTAA
66 TTATTAA
* * * *
623805 ATGTGGATGGTTAAATGCCCACAAAAATAAATTATGA-AGGTTGATGAGCAAGTGTAC-ACCACT
1 ATGTGGATGATAAAATGCCCACAAAAA-AAATTATGAGA-GTGGATGAGCAAGTCT-CTACCACT
623868 TAAT
63 TAAT
623872 GATTTTGGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
72 24 0.43
73 31 0.55
74 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (72 bp):
ATGTGGATGATAAAATGCCCACAAAAAAAATTATGAGAGTGGATGAGCAAGTCTCTACCACTTAA
TTATTAA
Found at i:630549 original size:15 final size:17
Alignment explanation
Indices: 630529--630565 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
630519 GTAGAAATAT
630529 AAATAA-ATAAAAGA-A
1 AAATAACATAAAAGAGA
*
630544 AAATAACTTAAAAGAGA
1 AAATAACATAAAAGAGA
630561 AAATA
1 AAATA
630566 TGAGTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 7 0.37
17 6 0.32
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (17 bp):
AAATAACATAAAAGAGA
Found at i:634283 original size:14 final size:14
Alignment explanation
Indices: 634264--634290 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
634254 GCAATGATAT
634264 TTGATCAAAAGGTA
1 TTGATCAAAAGGTA
634278 TTGATCAAAAGGT
1 TTGATCAAAAGGT
634291 TGAATATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (14 bp):
TTGATCAAAAGGTA
Found at i:665893 original size:13 final size:13
Alignment explanation
Indices: 665872--665914 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
665862 TAAATAATCA
*
665872 AAATCAATTAACT
1 AAATTAATTAACT
665885 AAATTAATTAACT
1 AAATTAATTAACT
* *
665898 AAAACTAATTAAAT
1 -AAATTAATTAACT
665912 AAA
1 AAA
665915 ATTTCAGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAATTAACT
Found at i:665908 original size:14 final size:14
Alignment explanation
Indices: 665877--665915 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
665867 AATCAAAATC
*
665877 AATTAACT-AAATT
1 AATTAACTAAAACT
665890 AATTAACTAAAACT
1 AATTAACTAAAACT
*
665904 AATTAAATAAAA
1 AATTAACTAAAA
665916 TTTCAGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTAACTAAAACT
Found at i:693417 original size:73 final size:73
Alignment explanation
Indices: 693283--693455 Score: 224
Period size: 73 Copynumber: 2.4 Consensus size: 73
693273 ACTAGGTTCG
* * *
693283 GAGACAAAAATGACTTAATCGACTAAGAAGTTTTGTTAGTTGACTAAAAGCTTACTACCAGAAA-
1 GAGACAGAAATGACTTAATCGACTAAGAAGTTTTGTTAGTCGACTAAAAGCTCACTACCAGAAAC
*
693347 TTAGGTTTA
66 TGA-GTTTA
* * * *
693356 GAGATAGAAATGACTTAATCGACTAATAAGTTTTGTTAGTCGACTACGAA-CTCACTGCCAGAAA
1 GAGACAGAAATGACTTAATCGACTAAGAAGTTTTGTTAGTCGACTA-AAAGCTCACTACCAGAAA
693420 CTGAGTTTA
65 CTGAGTTTA
* *
693429 GAGACAGAGATGACTTAATAGACTAAG
1 GAGACAGAAATGACTTAATCGACTAAG
693456 TAGCAATGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 82 0.95
74 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (73 bp):
GAGACAGAAATGACTTAATCGACTAAGAAGTTTTGTTAGTCGACTAAAAGCTCACTACCAGAAAC
TGAGTTTA
Found at i:698206 original size:12 final size:12
Alignment explanation
Indices: 698189--698218 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
698179 TTTTATTTTA
698189 TAAAATAAATAT
1 TAAAATAAATAT
698201 TAAAAT-AATAT
1 TAAAATAAATAT
698212 TAAAATA
1 TAAAATA
698219 TTAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAATAAATAT
Found at i:701605 original size:16 final size:17
Alignment explanation
Indices: 701584--701616 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
701574 GGCACAAATA
701584 TCTTAC-TTATGATTTT
1 TCTTACATTATGATTTT
701600 TCTTACAATTATGATTT
1 TCTTAC-ATTATGATTT
701617 GATTATTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (17 bp):
TCTTACATTATGATTTT
Found at i:703945 original size:20 final size:20
Alignment explanation
Indices: 703909--703946 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
703899 GAAGAAACTG
*
703909 AGAGAAAAGGAACAAAAATC
1 AGAGAAAAGGAAAAAAAATC
703929 AGAGAAGAA-GAAAAAAAA
1 AGAGAA-AAGGAAAAAAAA
703947 AGGAAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.03
Consensus pattern (20 bp):
AGAGAAAAGGAAAAAAAATC
Found at i:705787 original size:14 final size:15
Alignment explanation
Indices: 705760--705790 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
705750 TTTGTTTTAA
705760 TTGTTGATAGATATT
1 TTGTTGATAGATATT
705775 TTGTTGA-AGATATT
1 TTGTTGATAGATATT
705789 TT
1 TT
705791 AATGCTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (15 bp):
TTGTTGATAGATATT
Found at i:706541 original size:73 final size:73
Alignment explanation
Indices: 706459--706695 Score: 253
Period size: 73 Copynumber: 3.2 Consensus size: 73
706449 CTAGAGACAG
* * *
706459 TGTTTGTCGACTAAGAGCTTATTGCCAAAAACTAGGTTCAGAGACAAAAACGACTTAATCGACTA
1 TGTTAGTCGACTAAGAGCTTAATGCCAGAAACTAGGTTCAGAGACAAAAACGACTTAATCGACTA
706524 AGAAGTTT
66 AGAAGTTT
* * * * *
706532 TGTTAGTCGACTAAGAGCTTAATGCTAGAAATTAGGTTCAAAGACAAAAACGAATTAATCGATTA
1 TGTTAGTCGACTAAGAGCTTAATGCCAGAAACTAGGTTCAGAGACAAAAACGACTTAATCGACTA
*
706597 AGAAGCTT
66 AGAAGTTT
* * * * * * *
706605 TGTTAGTCAACTAAGAGCTTACT-CTCAGAAACT-GAGTTCAGAGATAGAGACGACTTAATTGGC
1 TGTTAGTCGACTAAGAGCTTAATGC-CAGAAACTAG-GTTCAGAGACAAAAACGACTTAATCGAC
* * **
706668 AAAGTAGTAA
64 TAAGAAGTTT
*
706678 TGTTAGTTGACTAAGAGC
1 TGTTAGTCGACTAAGAGC
706696 ATTCGTTTGA
Statistics
Matches: 134, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
72 2 0.01
73 132 0.99
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGCTTAATGCCAGAAACTAGGTTCAGAGACAAAAACGACTTAATCGACTA
AGAAGTTT
Found at i:712328 original size:35 final size:35
Alignment explanation
Indices: 712287--712458 Score: 191
Period size: 35 Copynumber: 4.9 Consensus size: 35
712277 GAAGCCTAAT
** *
712287 TAACTTAATTGTTTAATTTAATCAATTAGGCCCAG
1 TAACTTAATTAATTAATTTAATCAATTAGGCCCAA
** *
712322 TAACTTAATTAAACAATTTAATCAATTAGGACCAA
1 TAACTTAATTAATTAATTTAATCAATTAGGCCCAA
* ** *
712357 TAACTTGATTAAACAAATTTAATCAATTAGGCCTAA
1 TAACTTAATT-AATTAATTTAATCAATTAGGCCCAA
* *
712393 TAACTTAATTATTTAATTTAATTAATTAGGCCCAA
1 TAACTTAATTAATTAATTTAATCAATTAGGCCCAA
* ** *
712428 TGACTTAATTAAACAATTTAATGAATTAGGC
1 TAACTTAATTAATTAATTTAATCAATTAGGC
712459 ACAACTTAAT
Statistics
Matches: 114, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 84 0.74
36 30 0.26
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.37
Consensus pattern (35 bp):
TAACTTAATTAATTAATTTAATCAATTAGGCCCAA
Found at i:712379 original size:71 final size:69
Alignment explanation
Indices: 712301--712485 Score: 230
Period size: 71 Copynumber: 2.7 Consensus size: 69
712291 TTAATTGTTT
*
712301 AATTTAATCAATTAGGCCCAGTAACTTAATTAAACAATTTAATCAATTAGGACCAATAACTTGAT
1 AATTTAATCAATTAGGCCCA-TAACTTAATTAAACAATTTAATCAATTAGGACCAATAACTTAAT
712366 TAAAC
65 TAAAC
* *** * * *
712371 AAATTTAATCAATTAGGCCTAATAACTTAATTATTTAATTTAATTAATTAGGCCCAATGACTTAA
1 -AATTTAATCAATTAGGCC-CATAACTTAATTAAACAATTTAATCAATTAGGACCAATAACTTAA
712436 TTAAAC
64 TTAAAC
* *
712442 AATTTAATGAATTAGG--CACAACTTAATTAAACAATTGTAATCAA
1 AATTTAATCAATTAGGCCCATAACTTAATTAAACAATT-TAATCAA
712486 GTGCTTGCGA
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
67 15 0.15
68 6 0.06
70 15 0.15
71 60 0.62
72 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (69 bp):
AATTTAATCAATTAGGCCCATAACTTAATTAAACAATTTAATCAATTAGGACCAATAACTTAATT
AAAC
Found at i:712401 original size:106 final size:104
Alignment explanation
Indices: 712280--712485 Score: 299
Period size: 106 Copynumber: 2.0 Consensus size: 104
712270 TCCTTAAGAA
* *
712280 GCCTAATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAGTAACTTAATTAAACAATTTAATC
1 GCCTAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATC
* *
712345 AATTAGGACCAATAACTTGATTAAACAAATT-TAATCAATTAG
66 AATTAGG--C-ACAACTTAATTAAAC-AATTGTAATCAATTAG
* * *
712387 GCCTAA-TAACTTAATTATTTAATTTAATTAATTAGGCCCAATGACTTAATTAAACAATTTAATG
1 GCCTAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATC
712451 AATTAGGCACAACTTAATTAAACAATTGTAATCAA
66 AATTAGGCACAACTTAATTAAACAATTGTAATCAA
712486 GTGCTTGCGA
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
102 4 0.04
103 20 0.22
104 1 0.01
106 60 0.66
107 6 0.07
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (104 bp):
GCCTAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATC
AATTAGGCACAACTTAATTAAACAATTGTAATCAATTAG
Found at i:725151 original size:21 final size:21
Alignment explanation
Indices: 725124--725177 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
725114 GAACATATAG
*
725124 ATATATAGATATGTGT-ATAT
1 ATATATATATATGTGTAATAT
* *
725144 ATGATATATATGTGTTTAATAT
1 AT-ATATATATATGTGTAATAT
725166 ATATATATATAT
1 ATATATATATAT
725178 ATGATTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.71
22 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (21 bp):
ATATATATATATGTGTAATAT
Found at i:725156 original size:19 final size:19
Alignment explanation
Indices: 725119--725173 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
725109 TGGTAGAACA
*
725119 TATAGATATATAGATATGTG
1 TATA-ATATATATATATGTG
725139 TAT-ATATGATATATATGTG
1 TATAATAT-ATATATATGTG
*
725158 TTTAATATATATATAT
1 TATAATATATATATAT
725174 ATATATGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.13
19 20 0.65
20 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
TATAATATATATATATGTG
Found at i:730295 original size:16 final size:16
Alignment explanation
Indices: 730265--730294 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
730255 CCAAAATTTA
730265 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
730281 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
730295 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:750627 original size:35 final size:35
Alignment explanation
Indices: 750600--750700 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 35
750590 TAAATTGTTT
* **
750600 AATTAAGTCATTAGGTCTAATTAATTAAATTAAAC
1 AATTAAGTTATTAGACCTAATTAATTAAATTAAAC
750635 AATTAAGTTATTAGACCTAATTAATTAAATTAAAC
1 AATTAAGTTATTAGACCTAATTAATTAAATTAAAC
*
750670 AATTAAGTTATTAGACCTAATTGATTAAATT
1 AATTAAGTTATTAGACCTAATTAATTAAATT
750701 TGTTTAATCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (35 bp):
AATTAAGTTATTAGACCTAATTAATTAAATTAAAC
Found at i:759779 original size:16 final size:17
Alignment explanation
Indices: 759753--759788 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
759743 TTATGAGAGA
*
759753 CTTATGAATATAATGTC
1 CTTATGAATATAATGGC
759770 CTTA-GAATATAATGGC
1 CTTATGAATATAATGGC
759786 CTT
1 CTT
759789 GCAAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (17 bp):
CTTATGAATATAATGGC
Found at i:765529 original size:20 final size:21
Alignment explanation
Indices: 765493--765532 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
765483 AAAATATTAT
*
765493 AAAATGTTATAATTAAAATAA
1 AAAATGTTATAAATAAAATAA
765514 AAAATGTTA-AAATAAAATA
1 AAAATGTTATAAATAAAATA
765533 TATAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAATGTTATAAATAAAATAA
Found at i:765557 original size:33 final size:32
Alignment explanation
Indices: 765491--765695 Score: 113
Period size: 33 Copynumber: 6.3 Consensus size: 32
765481 TAAAAATATT
* *
765491 ATAAAATGTTATAAT-TAAAATAAAAAATGTTAAA
1 ATAAAAT-ATATAATATAAAATTAAAAA--TTAAA
765525 ATAAAATATATAATATAAGAATTAAAAATTAAA
1 ATAAAATATATAATATAA-AATTAAAAATTAAA
* *
765558 ATAAAATA-A-AATATAAAAAATT-AAAATTTAT
1 ATAAAATATATAATAT--AAAATTAAAAATTAAA
* ** *
765589 ATAATATAGGTAAAAT-AAATT-AAAA-TAAA
1 ATAAAATATATAATATAAAATTAAAAATTAAA
* * * *
765618 ATATATAATATA-AAAATTATATTAAAAAATGAAA
1 ATA-A-AATATATAATATAAAATT-AAAAATTAAA
* * *
765652 ATAAAATATATCATATTATAA-TAATAAATGAAA
1 ATAAAATATATAATA-TAAAATTAA-AAATTAAA
765685 ATAAAATATAT
1 ATAAAATATAT
765696 GACATTAAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
29 5 0.04
30 15 0.11
31 26 0.19
32 13 0.09
33 52 0.38
34 18 0.13
35 8 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (32 bp):
ATAAAATATATAATATAAAATTAAAAATTAAA
Found at i:765667 original size:28 final size:28
Alignment explanation
Indices: 765636--765706 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 28
765626 TATAAAAATT
765636 ATATTAAAAAATGAAAATAAAATATATC
1 ATATTAAAAAATGAAAATAAAATATATC
*
765664 ATATTATAATAATAAATGAAAATAAAATATATG
1 ATA-T-T-A-AA-AAATGAAAATAAAATATATC
*
765697 ACATTAAAAA
1 ATATTAAAAA
765707 TATATTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
28 5 0.14
29 3 0.08
30 2 0.06
31 2 0.06
32 3 0.08
33 21 0.58
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (28 bp):
ATATTAAAAAATGAAAATAAAATATATC
Found at i:765917 original size:54 final size:54
Alignment explanation
Indices: 765835--765940 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
765825 TTGTAAACCA
*
765835 AATGCTGAAATGTTATCTTCTCTGCATTTTAATCATTATTTTGCTTATATACGG
1 AATGCTGAAATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATACGG
* * *
765889 AATGCTGCAATGTTATCTTCTTTTCATTTTAATCATTATGTTGCTTATATAC
1 AATGCTGAAATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATAC
765941 CAAACACTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (54 bp):
AATGCTGAAATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATACGG
Found at i:765955 original size:54 final size:54
Alignment explanation
Indices: 765843--765968 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
765833 CAAATGCTGA
* ** **
765843 AATGTTATCTTCTCTGCATTTTAATCATTATTTTGCTTATATACGGAATGCTGC
1 AATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATACCAAACACTGC
* * *
765897 AATGTTATCTTCTTTTCATTTTAATCATTATGTTGCTTATATACCAAACACTGT
1 AATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATACCAAACACTGC
* *
765951 AATGTTATTTTCCCTGCA
1 AATGTTATCTTCTCTGCA
765969 ATGACATTGC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (54 bp):
AATGTTATCTTCTCTGCATTTTAATCATTATGTTGCTTATATACCAAACACTGC
Found at i:773063 original size:28 final size:28
Alignment explanation
Indices: 772995--773185 Score: 202
Period size: 28 Copynumber: 6.6 Consensus size: 28
772985 TTTTGTCTTT
* * *
772995 AATTAAGACAAAAATATTTTATGTTGTCTA
1 AATTAAGACAAACAT-GTTT-TCTTGTCTA
* * *
773025 AATTGAGATAAATATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* * * *
773053 GATTAACATAAAACATATTTTTCTTGTCTTA
1 AATTAAGA-CAAACAT-GTTTTCTTGTC-TA
* *
773084 AATTAAGACAAACATATTTTCTTGTCCA
1 AATTAAGACAAACATGTTTTCTTGTCTA
*
773112 AATTAAGACCAAAAATGTTTTCTTGTCTA
1 AATTAAGA-CAAACATGTTTTCTTGTCTA
773141 AATTAAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
*
773169 AATTAAGACAATCATGT
1 AATTAAGACAAACATGT
773186 CTAAGCTGGC
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
28 57 0.42
29 43 0.32
30 28 0.21
31 8 0.06
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:773153 original size:57 final size:57
Alignment explanation
Indices: 772995--773179 Score: 237
Period size: 59 Copynumber: 3.2 Consensus size: 57
772985 TTTTGTCTTT
* * * *
772995 AATTAAGACAAAAATATTTTATGTTGTCTAAATTGAGATAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
* * * * *
773053 GATTAACATAAAACATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCCA
1 AATTAAGACAAAA-ATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGTCTA
*
773112 AATTAAGACCAAAAAT-GTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
1 AATTAAGA-CAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
773169 AATTAAGACAA
1 AATTAAGACAA
773180 TCATGTCTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.03
57 36 0.33
58 26 0.24
59 40 0.37
60 4 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (57 bp):
AATTAAGACAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
Found at i:778854 original size:20 final size:20
Alignment explanation
Indices: 778826--778874 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
778816 TTATAATTAG
*
778826 TTTATTTTTAAGTGAGTTAT
1 TTTAATTTTAAGTGAGTTAT
* * * *
778846 TTTAATTTTATGTTATTTTT
1 TTTAATTTTAAGTGAGTTAT
778866 TTTAATTTT
1 TTTAATTTT
778875 GTCAGTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTAATTTTAAGTGAGTTAT
Found at i:785020 original size:26 final size:27
Alignment explanation
Indices: 784970--785021 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
784960 AATTAGTTTC
*
784970 AAAAAAATTAAAAAAAAAGGGAAAAGA
1 AAAAAAATTAAAAAAAAAGGAAAAAGA
* *
784997 AAAAAAATTTAAAAATAA-GAAAAAG
1 AAAAAAATTAAAAAAAAAGGAAAAAG
785022 GTCAGCACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAAAAATTAAAAAAAAAGGAAAAAGA
Found at i:798445 original size:4 final size:4
Alignment explanation
Indices: 798436--798502 Score: 50
Period size: 4 Copynumber: 17.2 Consensus size: 4
798426 CCGCCATAAC
* ** * * *
798436 AAAG AAAG AAAA AAAG GGAG AAAG AAAG AAAG GAAG AAAG -GAG GAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
798483 -AAG AAA- AAAG AAAGG AAAG A
1 AAAG AAAG AAAG AAA-G AAAG A
798503 TCGGTTTGGG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
3 8 0.16
4 37 0.76
5 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:798459 original size:16 final size:16
Alignment explanation
Indices: 798437--798475 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
798427 CGCCATAACA
798437 AAGAAAGAAAAAAAGG
1 AAGAAAGAAAAAAAGG
* *
798453 GAGAAAGAAAGAAAGG
1 AAGAAAGAAAAAAAGG
798469 AAGAAAG
1 AAGAAAG
798476 GAGGAAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAAAGG
Found at i:812179 original size:36 final size:36
Alignment explanation
Indices: 812092--812179 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
812082 NNNNNNNNNN
* **
812092 ACAATTAAGTTATTGGGCCTAATTGATTAAATTTGT
1 ACAATTAAGTTATTGGCCCTAATTGATTAAATTTAA
** * *
812128 TTAATCAATTTATTGGCCCTAATTGATTAAA-TTAA
1 ACAATTAAGTTATTGGCCCTAATTGATTAAATTTAA
812163 ACAATTAAGTTCATTGG
1 ACAATTAAGTT-ATTGG
812180 GCTTCTTAAG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
35 9 0.22
36 31 0.77
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (36 bp):
ACAATTAAGTTATTGGCCCTAATTGATTAAATTTAA
Found at i:816700 original size:38 final size:38
Alignment explanation
Indices: 816649--816725 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
816639 TTGCTTTTAT
*
816649 TGATTAAGGATTTTTGTTAATCAATTAAGACTAATCTA
1 TGATTAAGAATTTTTGTTAATCAATTAAGACTAATCTA
816687 TGATTAAGAATTTTTGTTAATCAATTAAGACTAATCTA
1 TGATTAAGAATTTTTGTTAATCAATTAAGACTAATCTA
816725 T
1 T
816726 CTTCATTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (38 bp):
TGATTAAGAATTTTTGTTAATCAATTAAGACTAATCTA
Found at i:821090 original size:74 final size:73
Alignment explanation
Indices: 820972--821109 Score: 195
Period size: 74 Copynumber: 1.9 Consensus size: 73
820962 GTGCTTAAAT
* *
820972 TCAAATTTTTGACAGTGAGCTTTTAGTTGTCTAACCATACTTCTTAGTCAATTAAGTCTTCTCTG
1 TCAAATTTTTGACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCAATTAAGTCTTCTCTG
821037 TTTTGTAA
66 TTTTGTAA
* * * * **
821045 TCAAATTCTTTGACGGTGAGCTTTTAGCTGGCTAACTATATTTCTTATTTGATTAAGTCTTCTCT
1 TCAAATT-TTTGACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCAATTAAGTCTTCTCT
821110 ATCTTGCAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
73 7 0.12
74 49 0.88
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (73 bp):
TCAAATTTTTGACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCAATTAAGTCTTCTCTG
TTTTGTAA
Found at i:827897 original size:21 final size:19
Alignment explanation
Indices: 827861--827901 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
827851 ACATGTTGAA
827861 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
827880 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
827901 T
1 T
827902 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:831021 original size:18 final size:19
Alignment explanation
Indices: 830984--831022 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
830974 TTTATTTGTC
**
830984 TTTTTTCATATTTTTTAAA
1 TTTTTTCATATTTTCAAAA
831003 TTTTTT-ATATTTTCAAAA
1 TTTTTTCATATTTTCAAAA
831021 TT
1 TT
831023 CAATAAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTCATATTTTCAAAA
Found at i:831382 original size:38 final size:38
Alignment explanation
Indices: 831276--831386 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 38
831266 AAAAACTAAA
* * * *
831276 ACTCCTTATAT-GAAATGAGGCTACGTAACTTTAAAATG
1 ACTCCTTATCTAG-AATAAGGCTACATAACTTTAAAAGG
* * * *
831314 ACTCCTCATCTAGAATAAGGTTGCACAACTTTAAAAGG
1 ACTCCTTATCTAGAATAAGGCTACATAACTTTAAAAGG
*
831352 ACTCCTTATCTAGAATAAGGCTACTTAACTTTAAA
1 ACTCCTTATCTAGAATAAGGCTACATAACTTTAAA
831387 CTCTTCATCA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
38 58 0.98
39 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (38 bp):
ACTCCTTATCTAGAATAAGGCTACATAACTTTAAAAGG
Found at i:831489 original size:34 final size:34
Alignment explanation
Indices: 831364--831526 Score: 148
Period size: 34 Copynumber: 4.7 Consensus size: 34
831354 TCCTTATCTA
* * * **
831364 GAATAAGGCTACTTAACTTTAAACTCTTCATCAT
1 GAATGAGGCTACGTAACTTTAAACTCCTCATTTT
* * * *
831398 AAATGATGTTGCGTAACTTTAAACTCCTCA-TTT
1 GAATGAGGCTACGTAACTTTAAACTCCTCATTTT
*
831431 CAATGAGGCTACTACGTAACTTTAAACTCCTCATTTT
1 GAATGAGG---CTACGTAACTTTAAACTCCTCATTTT
* *
831468 GGATGAGGCTACGTAATTTTAAACTCCTCATTTT
1 GAATGAGGCTACGTAACTTTAAACTCCTCATTTT
* * * *
831502 GAATAAGGCTATGTGACCTTAAACT
1 GAATGAGGCTACGTAACTTTAAACT
831527 GTTACTTAAC
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
33 7 0.07
34 67 0.65
36 20 0.19
37 9 0.09
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (34 bp):
GAATGAGGCTACGTAACTTTAAACTCCTCATTTT
Found at i:833943 original size:23 final size:24
Alignment explanation
Indices: 833898--833944 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
833888 CAGAATAGTT
*
833898 TCTTGCTGCCTCCTTTTCTGCCTC
1 TCTTGCTGCCTCCTCTTCTGCCTC
833922 TCTTGCTGCCT-CTCTTCTGCCTC
1 TCTTGCTGCCTCCTCTTCTGCCTC
833945 AAAAATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.00, C:0.43, G:0.13, T:0.45
Consensus pattern (24 bp):
TCTTGCTGCCTCCTCTTCTGCCTC
Found at i:837095 original size:21 final size:21
Alignment explanation
Indices: 837062--837102 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
837052 TTATGAAGTC
* *
837062 TATCTATCGATAAATGTTCTT
1 TATCCATCAATAAATGTTCTT
837083 TATCCATCAATAAATGTTCT
1 TATCCATCAATAAATGTTCT
837103 CTGTTTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (21 bp):
TATCCATCAATAAATGTTCTT
Found at i:840096 original size:21 final size:21
Alignment explanation
Indices: 840070--840120 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
840060 TTCATTCAAT
840070 TCATGACAAAGACAGATGCCC
1 TCATGACAAAGACAGATGCCC
* **
840091 TCATGATAAAGACAGATGCTT
1 TCATGACAAAGACAGATGCCC
840112 TCATGACAA
1 TCATGACAA
840121 GGACTAATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (21 bp):
TCATGACAAAGACAGATGCCC
Found at i:842975 original size:75 final size:75
Alignment explanation
Indices: 842885--843036 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
842875 TTGTCAGGTA
* *
842885 AACCTCTACCTATGCAAGTATGCATATCGAAAAGATAATATAATGATAAGCAAAGAATTGACCCT
1 AACCTCTACCTATGCAAGTATGCATATCAAAAAGATAATATAATGATAAGCAAAGAACTGACCCT
842950 AAATTTTACT
66 AAATTTTACT
* *
842960 AACCTCTACCTATGCAAGTATGCATATCAAAAAGATAATATAATGGTAAGCAGAGAACTGACCCT
1 AACCTCTACCTATGCAAGTATGCATATCAAAAAGATAATATAATGATAAGCAAAGAACTGACCCT
843025 AAATTTTACT
66 AAATTTTACT
843035 AA
1 AA
843037 GTACAAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (75 bp):
AACCTCTACCTATGCAAGTATGCATATCAAAAAGATAATATAATGATAAGCAAAGAACTGACCCT
AAATTTTACT
Done.