Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:421682 original size:42 final size:42
Alignment explanation
Indices: 421635--421717 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
421625 ACAAATTTCT
*
421635 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCC
1 CGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCC
*
421677 CGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 CGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGC
421718 AGTTACTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (42 bp):
CGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCC
Found at i:421685 original size:20 final size:20
Alignment explanation
Indices: 421657--421717 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
421647 TCATCATGCT
421657 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
421677 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
421699 CGAAAGACTTACTGATGGC
1 CGAAAGACTTACTGATGGC
421718 AGTTACTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 2 0.06
22 12 0.38
23 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:431144 original size:18 final size:19
Alignment explanation
Indices: 431121--431156 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
431111 CTTCTGTGTG
*
431121 TTCCCCC-CTTTTGTTTTC
1 TTCCCCCTCTTTTATTTTC
431139 TTCCCCCTCTTTTATTTT
1 TTCCCCCTCTTTTATTTT
431157 TTCTCCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.03, C:0.36, G:0.03, T:0.58
Consensus pattern (19 bp):
TTCCCCCTCTTTTATTTTC
Found at i:436228 original size:3 final size:3
Alignment explanation
Indices: 436220--436277 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
436210 GTTTATTAAT
436220 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
436268 TTA TT- TTA TT
1 TTA TTA TTA TT
436278 GATTGTATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:443703 original size:37 final size:36
Alignment explanation
Indices: 443662--443743 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
443652 ACAAAGTGTC
* * *
443662 GTCTCGCTAGAGATAATTTTTC-TTAGAAACAAATTTT
1 GTCTCGCTA-AGACAA-TTTTCACTAAAAACAAATTTT
443699 GTCTCGCTTAAGACAATTTTCACTAAAAACAAATTTT
1 GTCTCGC-TAAGACAATTTTCACTAAAAACAAATTTT
*
443736 GTATCGCT
1 GTCTCGCT
443744 TGAAACAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 6 0.15
37 31 0.79
38 2 0.05
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCGCTAAGACAATTTTCACTAAAAACAAATTTT
Found at i:444200 original size:68 final size:66
Alignment explanation
Indices: 444091--444305 Score: 209
Period size: 68 Copynumber: 3.2 Consensus size: 66
444081 TTGGAAATTG
* * ** * * *
444091 TTTCTCTTAAAACATAGAAAAACTGAGATTGTTTCTCTTGAAACAAGTTTTGTCTCGCTTGAGAC
1 TTTCTCTTGAAACATA-CAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGAC
444156 TGT
65 -GT
* * *
444159 TTTCTCTTGAAATATA-AAGTATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTTAGA
1 TTTCTCTTGAAACATACAA--ATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGA
*
444223 CAT
64 CGT
* * * * * *
444226 ATTCTCTTAAAACATACAACTTTAAGATCGTTTCCCTTGAAACAAATTTTGTCTCACTGGAGACA
1 TTTCTCTTGAAACATACAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGAC-
444291 G-
65 GT
*
444292 TTTATCTTGAAACA
1 TTTCTCTTGAAACA
444306 AATTATCCCT
Statistics
Matches: 121, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
66 52 0.43
67 14 0.12
68 55 0.45
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (66 bp):
TTTCTCTTGAAACATACAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGACG
T
Found at i:444305 original size:66 final size:66
Alignment explanation
Indices: 444116--444305 Score: 213
Period size: 66 Copynumber: 2.8 Consensus size: 66
444106 AGAAAAACTG
* * * * *
444116 AGATTGTTTCTCTTGAAACAAGTTTTGTCTCGCTTGAGACTGTTTTCTCTTGAAATATAAAGTAT
1 AGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAG-TTTCTCTTGAAACATAAAG-AT
*
444181 TTG
64 TTA
* * * *
444184 AGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTTAGACA-TATTCTCTTAAAACATACAA-CT
1 AGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGT-TTCTCTTGAAACATA-AAGAT
444247 TTA
64 TTA
* * *
444250 AGATCGTTTCCCTTGAAACAAATTTTGTCTCACTGGAGACAGTTTATCTTGAAACA
1 AGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
444306 AATTATCCCT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
66 52 0.50
67 14 0.13
68 38 0.37
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (66 bp):
AGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAAGATTT
A
Found at i:445083 original size:411 final size:412
Alignment explanation
Indices: 444353--445128 Score: 947
Period size: 411 Copynumber: 1.9 Consensus size: 412
444343 AGGAACCATG
* * * *
444353 TCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCACGAGATCCTTAGATAACCAGACTTCCT
1 TCATCCACCGACCAAATCTCCTCATCACATAGGAGCCACGACACCCTTAGATAACCAGACTTCCT
* *
444418 CATCACGTAGGAACCATATTATTTCCATTATCCCTAAAGATGGCCAAGACGTCCTCATCACGTAA
66 CATCACGTAGGAACCATATTATCTCCATTATCCCTAAAGATGGCCAAGACATCCTCATCACGTAA
* **
444483 GAACAAAGTCATCCACCATCCAGATCTCCTCATCACATAGGAGCCATGTCATCCTTAGATAGTCA
131 GAACAAAGTAATCCACCATCCAGATCTCCTCATCACATAGGAGCCATGTCATCCTTAGATAACCA
* * * * * * * *
444548 AACTTCCTCATCGCGTAGGAATCATGTTATCTTCATTATCCCTAAAGATGGCCTGATGTCTTAAT
196 AACTTCCACATCACGTAGGAATCATGTTATCTCCATTATCCCTAAAGACGACCAGACGTCCTAAT
* * *
444613 CACGTAGGAACCGTGTCATCTACCGACCAGATCTCCTTATCACGTAAGAGAAGCGTCACCCTTAG
261 CACGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAAGAGAAGCGTCACCCTTAG
* *
444678 ATAGA-CATACTTCCCCATCACGTAGGAACCATGTTATCTCTATTATTCCTAAAGATGGCCAGTC
326 ATA-ACCAGACTTCCCCATCACATAGGAACCATGTTATCTCTATTATTCCTAAAGATGGCCAGTC
444742 GTACTCATAGCGTAGGATTTTCA
390 GTACTCATAGCGTAGGATTTTCA
** * * **
444765 TCATCCACCGACCAAATCTCCTTGTCATATAGGAG-CAGCGTCACCCTTAGATAGTCAGACTTCC
1 TCATCCACCGACCAAATCTCCTCATCACATAGGAGCCA-CGACACCCTTAGATAACCAGACTTCC
* * * * * * * * **
444829 TCATCACGTAGGAATCGTTTTATCTCTATTTTGCCTAAATATGGTC-ATCCATCCTCATCACGTA
65 TCATCACGTAGGAACCATATTATCTCCATTATCCCTAAAGATGGCCAAGACATCCTCATCACGTA
* *** * **
444893 TGAACCGTGTAATCCACCGA-CCAGATCTCCTCATCACGTAGGAG-CA-GTTTTACCTTTAGATA
130 AGAACAAAGTAATCCACC-ATCCAGATCTCCTCATCACATAGGAGCCATGTCAT-CC-TTAGATA
* * * *
444955 ACCAGACTTCCACATCACGTAGTAA-CTGTGTTATCTCCATTATCCCTAAAGACGACCAGCCGTC
192 ACCAAACTTCCACATCACGTAGGAATC-ATGTTATCTCCATTATCCCTAAAGACGACCAGACGTC
* *
445019 CTCATCACGTAGGAATCGTGTCATCCACCGACCAAATCTCCTCATCACGTAAGAGCAA-CGTCAC
256 CTAATCACGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAAGAG-AAGCGTCAC
* * *
445083 CCTTAGATAACCAGATTTCCTCATCACATAGGAACCGTGTTATCTC
320 CCTTAGATAACCAGACTTCCCCATCACATAGGAACCATGTTATCTC
445129 CAAATTTACC
Statistics
Matches: 303, Mismatches: 54, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
409 3 0.01
410 6 0.02
411 203 0.67
412 91 0.30
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (412 bp):
TCATCCACCGACCAAATCTCCTCATCACATAGGAGCCACGACACCCTTAGATAACCAGACTTCCT
CATCACGTAGGAACCATATTATCTCCATTATCCCTAAAGATGGCCAAGACATCCTCATCACGTAA
GAACAAAGTAATCCACCATCCAGATCTCCTCATCACATAGGAGCCATGTCATCCTTAGATAACCA
AACTTCCACATCACGTAGGAATCATGTTATCTCCATTATCCCTAAAGACGACCAGACGTCCTAAT
CACGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAAGAGAAGCGTCACCCTTAG
ATAACCAGACTTCCCCATCACATAGGAACCATGTTATCTCTATTATTCCTAAAGATGGCCAGTCG
TACTCATAGCGTAGGATTTTCA
Found at i:445128 original size:137 final size:137
Alignment explanation
Indices: 444307--445130 Score: 839
Period size: 137 Copynumber: 6.0 Consensus size: 137
444297 CTTGAAACAA
* * * *
444307 ATTATCCCTAAAGGTGGCCAGCCATCCTCATCATGTAGGAACCATGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* ** * *
444372 CCTCATCACGTAGGAGCCACGAGATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATAT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
*
444437 TATTTCC
131 TATCTCC
* * ***
444444 ATTATCCCTAAAGATGGCCAAGACGTCCTCATCACGTAAGAACAAAGTCATCCACC-ATCCAGAT
1 ATTATCCCTAAAGATGGCC-AGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGA-CCAGAT
* * * * ** * * *
444508 CTCCTCATCACATAGGAGCCATGTCATCCTTAGATAGTCAAACTTCCTCATCGCGTAGGAATCAT
64 CTCCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCAT
*
444573 GTTATCTTC
129 GTTATCTCC
* ** * * *
444582 ATTATCCCTAAAGATGGCCTGATGTCTTAATCACGTAGGAACCGTGTCATCTACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * *
444647 CCTTATCACGTAAGAG-AAGCGTCACCCTTAGATAGA-CATACTTCCCCATCACGTAGGAACCAT
66 CCTCATCACGTAGGAGCAA-CGTCACCCTTAGATA-ACCAGACTTCCTCATCACGTAGGAACCAT
*
444710 GTTATCTCT
129 GTTATCTCC
* * * *** * *
444719 ATTATTCCTAAAGATGGCCAGTCGTACTCAT-AGCGTAGG-ATTTTCATCATCCACCGACCAAAT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCA-CGTAGGAACCGT-GTCATCCACCGACCAGAT
** ** * ** * *
444782 CTCCTTGTCATATAGGAGCAGCGTCACCCTTAGATAGTCAGACTTCCTCATCACGTAGGAATCGT
64 CTCCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCAT
* *
444847 TTTATCTCT
129 GTTATCTCC
* * * * * * * *
444856 ATTTTGCCTAAATATGGTCATCCATCCTCATCACGTATGAACCGTGTAATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
*** * * * * **
444921 CCTCATCACGTAGGAGCAGTTTTACCTTTAGATAACCAGACTTCCACATCACGTAGTAACTGTGT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
444986 TATCTCC
131 TATCTCC
* * * *
444993 ATTATCCCTAAAGACGACCAGCCGTCCTCATCACGTAGGAATCGTGTCATCCACCGACCAAATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * *
445058 CCTCATCACGTAAGAGCAACGTCACCCTTAGATAACCAGATTTCCTCATCACATAGGAACCGTGT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
445123 TATCTCC
131 TATCTCC
445130 A
1 A
445131 AATTTACCAA
Statistics
Matches: 557, Mismatches: 119, Indels: 22
0.80 0.17 0.03
Matches are distributed among these distances:
136 4 0.01
137 431 0.77
138 122 0.22
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
TATCTCC
Found at i:445338 original size:3 final size:3
Alignment explanation
Indices: 445330--445373 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
445320 GTATATTAAT
*
445330 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
445374 ATTTTATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:449942 original size:29 final size:30
Alignment explanation
Indices: 449873--449931 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
449863 CAATTTAAGG
449873 CAAAATGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
*
449903 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
449932 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTAAATTGAATTTA
Found at i:450037 original size:21 final size:21
Alignment explanation
Indices: 450011--450087 Score: 145
Period size: 21 Copynumber: 3.7 Consensus size: 21
450001 AGGGTGTCAA
450011 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCATCCCTAC
*
450032 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTAC
450053 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCATCCCTAC
450074 AGTGCATCCATGCA
1 AGTGCATCCATGCA
450088 CCTGCACTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTAC
Found at i:450179 original size:20 final size:20
Alignment explanation
Indices: 450154--450217 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
450144 GCACTTAGTA
450154 CATCGATGCAT-CAATCCATG
1 CATCGATGCATGC-ATCCATG
*
450174 CATCGATGCATGCATCGATG
1 CATCGATGCATGCATCCATG
*
450194 CATC-CTGCCATGCATCCATG
1 CATCGATG-CATGCATCCATG
450214 CATC
1 CATC
450218 AAGGCTGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
CATCGATGCATGCATCCATG
Found at i:450190 original size:12 final size:12
Alignment explanation
Indices: 450159--450196 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
450149 TAGTACATCG
* *
450159 ATGCATCAATCC
1 ATGCATCGATGC
450171 ATGCATCGATGC
1 ATGCATCGATGC
450183 ATGCATCGATGC
1 ATGCATCGATGC
450195 AT
1 AT
450197 CCTGCCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (12 bp):
ATGCATCGATGC
Found at i:450356 original size:20 final size:22
Alignment explanation
Indices: 450318--450357 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
450308 TTTTAGTAGA
450318 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
450340 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
450358 ATATAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:453361 original size:29 final size:29
Alignment explanation
Indices: 453294--453350 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
453284 AATTTAAGGT
453294 AAAATGTTTTTGGACTTAATTGAATTTAC
1 AAAATGTTTTTGGACTTAATTGAATTTAC
*
453323 AAAATATTTTTGGACTTAATTGAATTTA
1 AAAATGTTTTTGGACTTAATTGAATTTA
453351 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (29 bp):
AAAATGTTTTTGGACTTAATTGAATTTAC
Found at i:453542 original size:8 final size:8
Alignment explanation
Indices: 453543--453590 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
453533 TCGATGCATC
453543 CATCCATG
1 CATCCATG
*
453551 CATCGATG
1 CATCCATG
453559 CATCC-TG
1 CATCCATG
453566 ---CCATG
1 CATCCATG
453571 CATCCATG
1 CATCCATG
453579 CATCCATG
1 CATCCATG
453587 CATC
1 CATC
453591 AAGGGTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 2 0.06
8 28 0.82
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.25
Consensus pattern (8 bp):
CATCCATG
Found at i:453554 original size:20 final size:21
Alignment explanation
Indices: 453529--453587 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
453519 ATGCACTTAG
453529 TGCATCGATGCATCCAT-CCA
1 TGCATCGATGCATCCATGCCA
453549 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCATGCCA
*
453569 TGCATCCATGCATCCATGC
1 TGCATCGATGCATCCATGC
453588 ATCAAGGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.89
21 3 0.08
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCATCCATGCCA
Found at i:453561 original size:28 final size:28
Alignment explanation
Indices: 453529--453591 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
453519 ATGCACTTAG
*
453529 TGCATCGATG-CATCCATCCATGCATCGA
1 TGCATC-ATGCCATCCATCCATGCATCCA
* *
453557 TGCATCCTGCCATGCATCCATGCATCCA
1 TGCATCATGCCATCCATCCATGCATCCA
453585 TGCATCA
1 TGCATCA
453592 AGGGTGCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (28 bp):
TGCATCATGCCATCCATCCATGCATCCA
Found at i:453842 original size:28 final size:29
Alignment explanation
Indices: 453811--453874 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
453801 TTGATATAAC
* *
453811 AATTTAAGGT-AAAATGTTTTTGGACTTA
1 AATTGAAGGTAAAAATATTTTTGGACTTA
**
453839 AATTGAATTTACAAAATATTTTTGGACTT-
1 AATTGAAGGTA-AAAATATTTTTGGACTTA
453868 AATTGAA
1 AATTGAA
453875 TTTATTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 7 0.23
30 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (29 bp):
AATTGAAGGTAAAAATATTTTTGGACTTA
Found at i:453889 original size:29 final size:30
Alignment explanation
Indices: 453821--453878 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
453811 AATTTAAGGT
453821 AAAATGTTTTTGGACTTAAATTGAATTTAC
1 AAAATGTTTTTGGACTTAAATTGAATTTAC
*
453851 AAAATATTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTAAATTGAATTTA
453879 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTAAATTGAATTTAC
Found at i:454086 original size:20 final size:21
Alignment explanation
Indices: 454057--454115 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
454047 ATGCACTTAG
454057 TGCATCGATGCATCCAT-CCA
1 TGCATCGATGCATCCATGCCA
*
454077 TGCATTGATGCATCC-TGCCA
1 TGCATCGATGCATCCATGCCA
*
454097 TGCATCCATGCATCCATGC
1 TGCATCGATGCATCCATGC
454116 ATCAAGGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.88
21 3 0.09
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCATGCCA
Found at i:454089 original size:28 final size:28
Alignment explanation
Indices: 454057--454119 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
454047 ATGCACTTAG
**
454057 TGCATCGATG-CATCCATCCATGCATTGA
1 TGCATC-ATGCCATCCATCCATGCATCCA
* *
454085 TGCATCCTGCCATGCATCCATGCATCCA
1 TGCATCATGCCATCCATCCATGCATCCA
454113 TGCATCA
1 TGCATCA
454120 AGGTTGCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (28 bp):
TGCATCATGCCATCCATCCATGCATCCA
Found at i:454105 original size:8 final size:8
Alignment explanation
Indices: 454094--454118 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
454084 ATGCATCCTG
454094 CCATGCAT
1 CCATGCAT
454102 CCATGCAT
1 CCATGCAT
454110 CCATGCAT
1 CCATGCAT
454118 C
1 C
454119 AAGGTTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (8 bp):
CCATGCAT
Found at i:454220 original size:528 final size:528
Alignment explanation
Indices: 453218--454805 Score: 2874
Period size: 528 Copynumber: 3.0 Consensus size: 528
453208 GGGTTTTGCC
453218 AAAACAA--TTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
1 AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
453281 AACAATTTAAGGTAAAATGTTTTTGGACTT-AATTGAATTTACAAAATATTTTTGGACTTAATTG
66 AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
*
453345 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCAGATTTGAGGC
131 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGGC
*
453410 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGCACTAA
196 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTACACTAA
453475 TGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTTAGTGCATCGATGC
261 TGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTTAGTGCATCGATGC
*
453540 ATCCATCCATGCATCGATGCATCCTGCCATGCATCCATGCATCCATGCATCAAGGGTGCAACGGC
326 ATCCATCCATGCATCGATGCATCCTGCCATGCATCCATGCATCCATGCATCAAGGCTGCAACGGC
453605 TAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCGATGCACCATGTTA
391 TAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCGATGCACCATGTTA
453670 TGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCCCAATGGCTATATA
456 TGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCCCAATGGCTATATA
453735 CAACATCA
521 CAACATCA
453743 AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
1 AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
453808 AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
66 AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
*
453873 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATTGGATTTGAGGC
131 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGGC
*
453938 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTACAATAA
196 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTACACTAA
454003 TGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTTAGTGCATCGATGC
261 TGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTTAGTGCATCGATGC
* *
454068 ATCCATCCATGCATTGATGCATCCTGCCATGCATCCATGCATCCATGCATCAAGGTTGCAACGGC
326 ATCCATCCATGCATCGATGCATCCTGCCATGCATCCATGCATCCATGCATCAAGGCTGCAACGGC
454133 TAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCGATGCACCATGTTA
391 TAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCGATGCACCATGTTA
454198 TGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCCCAATGGCTATATA
456 TGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCCCAATGGCTATATA
454263 CAACATCA
521 CAACATCA
454271 AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
1 AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
454336 AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
66 AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
*
454401 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGGA
131 AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGGC
454466 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCTTGCAGTGCATCCAT
196 AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCAT-C---CA-TGCA-CC-T
454531 GCACCTGCACTAATGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTT
254 --A----CACTAATGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTT
454596 AGTGCATCGATGCATCCATCCATGCATCGATGCA---T-CC-TG---CCATGCATCCATGCATCA
313 AGTGCATCGATGCATCCATCCATGCATCGATGCATCCTGCCATGCATCCATGCATCCATGCATCA
* *
454653 AGGCTGCAACGGCTAGTTTATTTGAATTTAATGAAGGGGTATCGATGTACCATGATAGTGCACCG
378 AGGCTGCAACGGCTAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCG
* *
454718 ATGCACCATGTTATGTGAAGTCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAATATCCC
443 ATGCACCATGTTATGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCC
454783 CAATGGCTATATACAACATCA
508 CAATGGCTATATACAACATCA
454804 AA
1 AA
454806 CACATTCCAA
Statistics
Matches: 1032, Mismatches: 15, Indels: 24
0.96 0.01 0.02
Matches are distributed among these distances:
525 7 0.01
527 86 0.08
528 667 0.65
529 1 0.00
532 2 0.00
533 170 0.16
534 2 0.00
535 1 0.00
536 2 0.00
537 3 0.00
538 1 0.00
541 90 0.09
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (528 bp):
AAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGAACTATGTTTTGATAT
AACAATTTAAGGTAAAATGTTTTTGGACTTAAATTGAATTTACAAAATATTTTTGGACTTAATTG
AATTTATTCAAAGTTTTAAAAGGTTTCAAAAATAATTCAAAGTCCATTAAAATCGGATTTGAGGC
AAAATGCTAAAGGGTGTCAAAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTACACTAA
TGCATCGATACATCATGCAATGCATCCATGCACTCAAACATCGAATGCACTTAGTGCATCGATGC
ATCCATCCATGCATCGATGCATCCTGCCATGCATCCATGCATCCATGCATCAAGGCTGCAACGGC
TAGTTTATTTGAATTTAATGAAGGGGTATCAATGCACCATGATAGTGCACCGATGCACCATGTTA
TGTGAAGCCTTTTTGAGTAGAAAATCATCCCCAAACGGCTCCAAAACATCCCCAATGGCTATATA
CAACATCA
Found at i:454370 original size:28 final size:29
Alignment explanation
Indices: 454339--454402 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
454329 TTGATATAAC
* *
454339 AATTTAAGGT-AAAATGTTTTTGGACTTA
1 AATTGAAGGTAAAAATATTTTTGGACTTA
**
454367 AATTGAATTTACAAAATATTTTTGGACTT-
1 AATTGAAGGTA-AAAATATTTTTGGACTTA
454396 AATTGAA
1 AATTGAA
454403 TTTATTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 7 0.23
30 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (29 bp):
AATTGAAGGTAAAAATATTTTTGGACTTA
Found at i:454417 original size:29 final size:30
Alignment explanation
Indices: 454349--454406 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
454339 AATTTAAGGT
454349 AAAATGTTTTTGGACTTAAATTGAATTTAC
1 AAAATGTTTTTGGACTTAAATTGAATTTAC
*
454379 AAAATATTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTAAATTGAATTTA
454407 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTAAATTGAATTTAC
Found at i:454514 original size:13 final size:13
Alignment explanation
Indices: 454496--454533 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
454486 AGTGCATCCA
*
454496 TGCATCCCTGCAG
1 TGCATCCATGCAG
*
454509 TGCATCCTTGCAG
1 TGCATCCATGCAG
454522 TGCATCCATGCA
1 TGCATCCATGCA
454534 CCTGCACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.26
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:454623 original size:20 final size:20
Alignment explanation
Indices: 454598--454651 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
454588 ATGCACTTAG
454598 TGCATCGATGCATCCAT-CCA
1 TGCATCGATGCATCC-TGCCA
454618 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
454638 TGCATCCATGCATC
1 TGCATCGATGCATC
454652 AAGGCTGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:455046 original size:34 final size:32
Alignment explanation
Indices: 455007--455076 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
454997 TTTTGTAAAG
* *
455007 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
455041 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
455073 GGGA
1 GGGA
455077 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:456686 original size:2 final size:2
Alignment explanation
Indices: 456679--456757 Score: 54
Period size: 2 Copynumber: 39.0 Consensus size: 2
456669 GTATAACACG
* * *
456679 TA TA TA TA TA TA TA TG CA TCA TA CA TA TA TCA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA TA TA TA
* * * *
456723 TG TA TA CA TA TA T- TA AA CT- TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
456758 AGTATAACAT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
1 2 0.03
2 52 0.90
3 4 0.07
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:456755 original size:27 final size:27
Alignment explanation
Indices: 456684--456755 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
456674 ACACGTATAT
* *
456684 ATATATATATGCATCATACATATATCAT
1 ATATATATATACAT-ATACATATATCAA
** *
456712 ATATATATATATGTATACATATATTAA
1 ATATATATATACATATACATATATCAA
456739 ACT-TATATATACATATA
1 A-TATATATATACATATA
456756 TAAGTATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 24 0.67
28 12 0.33
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.42
Consensus pattern (27 bp):
ATATATATATACATATACATATATCAA
Found at i:456781 original size:18 final size:17
Alignment explanation
Indices: 456754--456792 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
456744 TATATACATA
*
456754 TATAAGTATAACATACG
1 TATAAGTATAACATAAG
*
456771 TATAAGTTATAGCATAAG
1 TATAAG-TATAACATAAG
456789 TATA
1 TATA
456793 TATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (17 bp):
TATAAGTATAACATAAG
Found at i:462533 original size:5 final size:5
Alignment explanation
Indices: 462523--462573 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
462513 TTTTCACTTT
* *
462523 TTTTA TTTTA TTTTCA TTTTTA TTTTTA TTTTC GTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTT-A -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
462570 TTTT
1 TTTT
462574 CTATGAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.10
5 24 0.60
6 8 0.20
7 4 0.10
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:462536 original size:20 final size:20
Alignment explanation
Indices: 462500--462574 Score: 77
Period size: 19 Copynumber: 4.0 Consensus size: 20
462490 CTCCACATTT
* *
462500 CTTTTTTTCTTCT-TTTTCA
1 CTTTTTTTATTTTATTTTCA
462519 CTTTTTTTATTTTATTTTCA
1 CTTTTTTTATTTTATTTTCA
*
462539 -TTTTTAT-TTTTATTTTC-
1 CTTTTTTTATTTTATTTTCA
* *
462556 GTTTATTTATTTTATTTTC
1 CTTTTTTTATTTTATTTTC
462575 TATGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
18 15 0.31
19 27 0.56
20 6 0.12
ACGTcount: A:0.12, C:0.11, G:0.01, T:0.76
Consensus pattern (20 bp):
CTTTTTTTATTTTATTTTCA
Found at i:462541 original size:6 final size:6
Alignment explanation
Indices: 462522--462554 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
462512 TTTTTCACTT
*
462522 TTTTTA -TTTTA TTTTCA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
462555 CGTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:462638 original size:16 final size:16
Alignment explanation
Indices: 462605--462635 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
462595 AGAATTTAAC
462605 ATGTTGTTATTTTTTT
1 ATGTTGTTATTTTTTT
462621 ATGTT-TTATTTTTTT
1 ATGTTGTTATTTTTTT
462636 TATTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (16 bp):
ATGTTGTTATTTTTTT
Found at i:462670 original size:32 final size:32
Alignment explanation
Indices: 462625--462690 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
462615 TTTTTTATGT
**
462625 TTTATTTTTTTTATTTATTT-TCTTATTTTTCC
1 TTTATTTCCTTTATTTATTTAT-TTATTTTTCC
462657 TTTATTTCCTTTATTTATTTATTTATTTTTCC
1 TTTATTTCCTTTATTTATTTATTTATTTTTCC
462689 TT
1 TT
462691 CGTTTCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTATTTCCTTTATTTATTTATTTATTTTTCC
Found at i:462707 original size:32 final size:31
Alignment explanation
Indices: 462634--462712 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
462624 TTTTATTTTT
*
462634 TTTATTTATTTTCTTATTTTTCCTTTATTTCC
1 TTTATTTATTTT-TTATTTTTCCTTCATTTCC
* *
462666 TTTATTTATTTATTTATTTTTCCTTCGTTTCT
1 TTTATTTATTT-TTTATTTTTCCTTCATTTCC
462698 TATTA-TTATTTTTTA
1 T-TTATTTATTTTTTA
462713 CGAAATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.10
32 34 0.81
33 4 0.10
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.72
Consensus pattern (31 bp):
TTTATTTATTTTTTATTTTTCCTTCATTTCC
Found at i:462814 original size:28 final size:27
Alignment explanation
Indices: 462777--462832 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
462767 ATACTAACAT
*
462777 TTTTTCCTTTCTTTTTTATTTATATTTA
1 TTTTTACTTTCTTTTTTATTTAT-TTTA
*
462805 TTTTTACTTTGTTTTTTATTTATTTTA
1 TTTTTACTTTCTTTTTTATTTATTTTA
462832 T
1 T
462833 CTATCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTTACTTTCTTTTTTATTTATTTTA
Found at i:462913 original size:12 final size:13
Alignment explanation
Indices: 462891--462919 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
462881 TGAATCGGAT
462891 TTTTAAATTTTAA
1 TTTTAAATTTTAA
462904 TTTT-AATTTTAA
1 TTTTAAATTTTAA
462916 TTTT
1 TTTT
462920 CACAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:465473 original size:100 final size:97
Alignment explanation
Indices: 465358--465709 Score: 450
Period size: 95 Copynumber: 3.6 Consensus size: 97
465348 ATATTACATA
* * * *
465358 TATATAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAATGCCCTGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC-GGCTTTATGGATAAG
*
465423 ATTCAGATAAGCCTGATAAAGGTGGTTATAATATC
65 ATTCAG-T-AGCCTGATAAAGGTGATTATAATATC
* *
465458 TATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCCGGCTTTATGGATAAG
*
465523 ATTCAGTTAGCCTGGTAAAGGTGATTAT-A-A--
65 ATTCAG-TAGCCTGATAAAGGTGATTATAATATC
* *
465553 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGGCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAC-GCCCGGCTTTATGGATAAG
*
465618 ATTCAGCTAGCCTGATAAAGGTGATTAAAATATC
65 ATTCAG-TAGCCTGATAAAGGTGATTATAATATC
* * *
465652 TATACAATGATA--TTAAGTTGTCCCTCTAGAGCAATTGGTTAAACACCC--CTTTATGGAT
1 TATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGGAT
465710 TCAGCTAGCC
Statistics
Matches: 227, Mismatches: 18, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
95 94 0.41
96 2 0.01
97 5 0.02
98 31 0.14
99 26 0.11
100 66 0.29
101 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (97 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGGATAAGA
TTCAGTAGCCTGATAAAGGTGATTATAATATC
Found at i:466983 original size:41 final size:42
Alignment explanation
Indices: 466881--466984 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 42
466871 AATGGGTTAT
* * *
466881 CACGATTTCAGCTCCACGACGGAGGATATCGTACCCATAAATC
1 CACGATTTCAACTCCATGACAGAGGATATCGTACCCA-AAATC
* * *
466924 TACGATTTCAACTCCATGACAGAGGATATCGTGCCC-ACATC
1 CACGATTTCAACTCCATGACAGAGGATATCGTACCCAAAATC
* *
466965 CACGATTTTAACTTCATGAC
1 CACGATTTCAACTCCATGAC
466985 GAACAATATC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 21 0.40
43 31 0.60
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (42 bp):
CACGATTTCAACTCCATGACAGAGGATATCGTACCCAAAATC
Found at i:467303 original size:124 final size:124
Alignment explanation
Indices: 467142--467475 Score: 526
Period size: 124 Copynumber: 2.7 Consensus size: 124
467132 TACAAGCTTA
* * *
467142 GATTTTAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAATGAAGGGCCCATGCA
1 GATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGCCCATCCA
*
467207 CGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGATTG
66 CGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTCAGATTG
* *
467266 GATTTTAACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACAATGAAGGGGCCATCCA
1 GATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGCCCATCCA
* *
467331 CGGTTTCAACTTCATGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTCATATTG
66 CGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTCAGATTG
* * *
467390 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACCTCACAACGAAGGGGCCC-TCC
1 GATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAA-GGGCCCATCC
* * *
467454 ATGATTTCAACTTCACTACGAA
65 ACGGTTTCAACTTCACGACGAA
467476 TGATATCATG
Statistics
Matches: 192, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
124 187 0.97
125 5 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (124 bp):
GATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGCCCATCCA
CGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTCAGATTG
Found at i:467817 original size:80 final size:81
Alignment explanation
Indices: 467487--468173 Score: 842
Period size: 80 Copynumber: 8.4 Consensus size: 81
467477 GATATCATGT
* * * * * *
467487 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATC-TGC-AC-AAAGACCTTCGAGTTCGATTA
* * *
467552 CGCTCAGTTCCAAGGCACA
63 CACTCAGCTCAAAGGCACA
** * * * * *
467571 TCATTTGCAATATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGGCCTTAGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG-C-AC-AAAGACCTTCGAGTTCGATTA
*
467636 CACTCAGCTCCAAGGCACA
63 CACTCAGCTCAAAGGCACA
* * * * * *
467655 TAATTTGCAACATAGCTCAAGGCAATAAGGGCTATTTGCCAACAAAAGATCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG-C-AC-AAAGACCTTCGAGTTCGATTA
467720 CACTCAGCTCAAAGGCACA
63 CACTCAGCTCAAAGGCACA
* *
467739 TCATTTGCAGCATAGCTCAAGGCAAGAATGGTTATCTGC-CAAAGACCTTCGAGTTTGATTACAC
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCGATTACAC
467803 TCAGCTCAAAGGCACA
66 TCAGCTCAAAGGCACA
* * *
467819 TCATTTGTAGCATAGCTCAAGGCAACAAGGGTTATCTGC-CAAAGACCTTCGAGTTCGATTAAAC
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCGATTACAC
467883 TCAGCTCAAAGGCACA
66 TCAGCTCAAAGGCACA
* * * *
467899 TCATTTGCAGCATAACTCAAGGTAAAAAGGGCTATCTGC-CAAAGACCTTCGAGTTCGATTACAC
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCGATTACAC
467963 TCAGCTCAAAGGCACA
66 TCAGCTCAAAGGCACA
467979 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGC-CAAAGACCTTCGAGTTCGATTACAC
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCGATTACAC
*
468043 TCAGCTCAAAGGCGCA
66 TCAGCTCAAAGGCACA
* *
468059 TCATTTGCAGTATAACTCAAGGCAAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTCGATTAC
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG-CA-CAAAGACCTTCGAGTTCGATTAC
* * * *
468124 ATTCAACTCAGAGGCAAA
64 ACTCAGCTCAAAGGCACA
* * * *
468142 TCAAATTTACAGCATAACTCAATGAAAGAAGG
1 TC--ATTTGCAGCATAGCTCAAGGCAAGAAGG
468174 ACTATCTGTT
Statistics
Matches: 543, Mismatches: 54, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
80 298 0.55
81 2 0.00
83 40 0.07
84 179 0.33
85 24 0.04
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (81 bp):
TCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCGATTACAC
TCAGCTCAAAGGCACA
Found at i:469938 original size:19 final size:18
Alignment explanation
Indices: 469914--469949 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
469904 CTCCACATTT
*
469914 CTTTTTTTCTTCTTTTTCA
1 CTTTTTTT-TTCATTTTCA
469933 CTTTTTTTTTCATTTTC
1 CTTTTTTTTTCATTTTC
469950 GTTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTTTTTTTTCATTTTCA
Found at i:470018 original size:7 final size:7
Alignment explanation
Indices: 470008--470085 Score: 54
Period size: 7 Copynumber: 11.0 Consensus size: 7
469998 TAACCTGTTG
470008 TTATTTT
1 TTATTTT
*
470015 TTATGTT
1 TTATTTT
470022 TTATTTAAT
1 TTATTT--T
*
470031 TT-TTAAT
1 TTATT-TT
470038 TTATTTT
1 TTATTTT
*
470045 ATTTTTTT
1 -TTATTTT
470053 TTATTTT
1 TTATTTT
470060 TTA--TT
1 TTATTTT
* *
470065 TTCTCTT
1 TTATTTT
470072 TTATTTT
1 TTATTTT
470079 TTATTTT
1 TTATTTT
470086 CCTTCGTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
5 4 0.07
7 38 0.69
8 10 0.18
9 3 0.05
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (7 bp):
TTATTTT
Found at i:470039 original size:26 final size:24
Alignment explanation
Indices: 470010--470066 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
470000 ACCTGTTGTT
470010 ATTTTTTATGTTTTATTTAATTTTTA
1 ATTTTTTAT-TTTT-TTTAATTTTTA
* *
470036 ATTTATTTTATTTTTTTTTATTTTTT
1 A-TT-TTTTATTTTTTTTAATTTTTA
470062 ATTTT
1 ATTTT
470067 CTCTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 2 0.07
25 2 0.07
26 11 0.41
27 6 0.22
28 6 0.22
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (24 bp):
ATTTTTTATTTTTTTTAATTTTTA
Found at i:470085 original size:12 final size:12
Alignment explanation
Indices: 470013--470085 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
470003 TGTTGTTATT
*
470013 TTTTATGTTTTA
1 TTTTATTTTTTA
*
470025 -TTTAATTTTTA
1 TTTTATTTTTTA
*
470036 ATTTA--TTTTA
1 TTTTATTTTTTA
*
470046 TTTT-TTTTTATT
1 TTTTATTTTT-TA
* *
470058 TTTTATTTTCTC
1 TTTTATTTTTTA
470070 TTTTATTTTTTA
1 TTTTATTTTTTA
470082 TTTT
1 TTTT
470086 CCTTCGTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 8 0.17
11 12 0.25
12 24 0.50
13 4 0.08
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:470085 original size:19 final size:18
Alignment explanation
Indices: 470012--470086 Score: 80
Period size: 19 Copynumber: 4.0 Consensus size: 18
470002 CTGTTGTTAT
* **
470012 TTTTTATGTTTTATTTAA
1 TTTTTATTTTTTATTTTC
470030 TTTTTAATTTATTTTATTTT-
1 TTTTT-A-TT-TTTTATTTTC
470050 TTTTTATTTTTTATTTTC
1 TTTTTATTTTTTATTTTC
470068 TCTTTTATTTTTTATTTTC
1 T-TTTTATTTTTTATTTTC
470087 CTTCGTTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.18
18 8 0.16
19 19 0.38
20 6 0.12
21 8 0.16
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (18 bp):
TTTTTATTTTTTATTTTC
Found at i:470218 original size:10 final size:10
Alignment explanation
Indices: 470188--470233 Score: 58
Period size: 9 Copynumber: 4.4 Consensus size: 10
470178 TTTCCTTTCT
470188 TTTTTTATTTA
1 TTTTTT-TTTA
470199 TATTTATTTTTA
1 T-TTT-TTTTTA
470211 TTTTTTTTT-
1 TTTTTTTTTA
470220 TTTTTTTTTA
1 TTTTTTTTTA
470230 TTTT
1 TTTT
470234 ATCTAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.28
10 9 0.28
11 4 0.12
12 8 0.25
13 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:481420 original size:45 final size:46
Alignment explanation
Indices: 481371--481470 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 46
481361 AATGGATGTT
* *
481371 ATAAAGGAAAACGTA-AACAG-AACATAAAAGGCATGAAGGGATGCC
1 ATAAAGGAAAACGTATAACAGTAA-ATAAAAGGCATGAAAGGAAGCC
* * * *
481416 ATAAATG-AAATGTATAATAGTGAATAAAAGGCATGAAAGGAAGCC
1 ATAAAGGAAAACGTATAACAGTAAATAAAAGGCATGAAAGGAAGCC
*
481461 ATAATGGAAA
1 ATAAAGGAAA
481471 TGGTTTATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
44 6 0.14
45 35 0.80
46 3 0.07
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (46 bp):
ATAAAGGAAAACGTATAACAGTAAATAAAAGGCATGAAAGGAAGCC
Found at i:485700 original size:20 final size:20
Alignment explanation
Indices: 485671--485721 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
485661 ATAATCAGTA
*
485671 GGTATCGATACCAACAGGTG
1 GGTATCGATACCAACAAGTG
*
485691 GGTATAGATACCAACAAGTG
1 GGTATCGATACCAACAAGTG
485711 GGTATCGATAC
1 GGTATCGATAC
485722 TCAGGGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCAACAAGTG
Found at i:486674 original size:20 final size:20
Alignment explanation
Indices: 486645--486695 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
486635 ATAATCAGTA
*
486645 GGTATCGATACCAACAGGTG
1 GGTATCGATACCAACAAGTG
*
486665 GGTATAGATACCAACAAGTG
1 GGTATCGATACCAACAAGTG
486685 GGTATCGATAC
1 GGTATCGATAC
486696 TCAGGGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCAACAAGTG
Found at i:489000 original size:20 final size:20
Alignment explanation
Indices: 488977--489037 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
488967 GTTTTTTTAT
*
488977 TATCGATATTGTTCACACAG
1 TATCGATATTATTCACACAG
* * *
488997 TATCGGTATTATTCATACAT
1 TATCGATATTATTCACACAG
* * *
489017 TATCGCTACTATTCATACAG
1 TATCGATATTATTCACACAG
489037 T
1 T
489038 GCAATACTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (20 bp):
TATCGATATTATTCACACAG
Found at i:491568 original size:15 final size:15
Alignment explanation
Indices: 491548--491579 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
491538 GTTTACCGGT
491548 TGTGAATCTTCAATA
1 TGTGAATCTTCAATA
491563 TGTGAATCTTCAATA
1 TGTGAATCTTCAATA
491578 TG
1 TG
491580 ATAGGCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (15 bp):
TGTGAATCTTCAATA
Found at i:509733 original size:39 final size:38
Alignment explanation
Indices: 509633--509734 Score: 91
Period size: 39 Copynumber: 2.6 Consensus size: 38
509623 ATCCTCAAAT
* *
509633 TATTTCACTCTAACATTCTAAAATCCTAATTTCTTAAA
1 TATTTCACTATAACATTCTAAATTCCTAATTTCTTAAA
* * * * *
509671 T-TTTAACGCTATAATATTTTAAATTCTTGATTTCTTAAA
1 TATTT--CACTATAACATTCTAAATTCCTAATTTCTTAAA
509710 TCATTTCAC-ATTAACATTCTAAATT
1 T-ATTTCACTA-TAACATTCTAAATT
509735 ATTTTTAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
37 3 0.06
38 2 0.04
39 41 0.84
41 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (38 bp):
TATTTCACTATAACATTCTAAATTCCTAATTTCTTAAA
Found at i:509928 original size:18 final size:18
Alignment explanation
Indices: 509895--509934 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
509885 TTATATATTT
*
509895 TTTAAAAAATAATATAA-
1 TTTAAAAAAAAATATAAC
509912 TTTAAAGAAAAAATATAAC
1 TTTAAA-AAAAAATATAAC
509931 TTTA
1 TTTA
509935 TATATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTAAAAAAAAATATAAC
Found at i:509974 original size:25 final size:27
Alignment explanation
Indices: 509941--510009 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
509931 TTTATATATA
*
509941 TTAACTTAAAATATTTTTA-TAATAAC
1 TTAATTTAAAATATTTTTACTAATAAC
* *
509967 TT-ATTTAATATA-TTTTACTATTAAC
1 TTAATTTAAAATATTTTTACTAATAAC
509992 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
510010 ATTTTTACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 5 0.14
25 16 0.46
26 6 0.17
27 5 0.14
28 3 0.09
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTACTAATAAC
Found at i:510025 original size:27 final size:27
Alignment explanation
Indices: 509948--510033 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
509938 ATATTAACTT
*
509948 AAAATATTTTTA-TAATAACTT-ATTT-
1 AAAATA-TTTTACTATTAACTTAATTTA
*
509973 AATATATTTTACTATTAACTTAATTTA
1 AAAATATTTTACTATTAACTTAATTTA
* * * * *
510000 AAAATATTTTATTTTTACCTTCATTTC
1 AAAATATTTTACTATTAACTTAATTTA
510027 AAAATAT
1 AAAATAT
510034 ATAATTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 5 0.10
25 13 0.26
26 4 0.08
27 28 0.56
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATTTTACTATTAACTTAATTTA
Found at i:523333 original size:12 final size:12
Alignment explanation
Indices: 523316--523351 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
523306 GAATGGGTAC
523316 CAATACCCCTAT
1 CAATACCCCTAT
523328 CAATA-CCCTAT
1 CAATACCCCTAT
523339 CAATACCTCCTAT
1 CAATACC-CCTAT
523352 GAACGGGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 6 0.27
13 5 0.23
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (12 bp):
CAATACCCCTAT
Found at i:523373 original size:22 final size:22
Alignment explanation
Indices: 523290--523397 Score: 87
Period size: 22 Copynumber: 4.9 Consensus size: 22
523280 AATATTAATA
* *
523290 GGTACCGATA-CCCTATGAATG
1 GGTACCAATACCCCTATGAACG
*
523311 GGTACCAATACCCCTATCAATAC-
1 GGTACCAATACCCCTAT-GA-ACG
** *
523334 CCTATCAATACCTCCTATGAACG
1 GGTACCAATACC-CCTATGAACG
* *
523357 GGTACCGATACCCCTATGAATG
1 GGTACCAATACCCCTATGAACG
*
523379 GGTATCAATA-CCCTATGAA
1 GGTACCAATACCCCTATGAA
523398 GGCTCAAATT
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
21 18 0.26
22 25 0.37
23 19 0.28
24 6 0.09
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (22 bp):
GGTACCAATACCCCTATGAACG
Found at i:525551 original size:83 final size:82
Alignment explanation
Indices: 525394--525555 Score: 193
Period size: 83 Copynumber: 2.0 Consensus size: 82
525384 ATACTTTGAT
* ***
525394 TTTAAATGCAAATGATATATCGCTAACAATTGATATCAAAATTTTAAATTTTTTAACATAAATTT
1 TTTAAATGAAAATGATATATCGCTAACAATTGATATCAAAATTTTAAATTGCATAACAT-AATTT
**
525459 AAATGTTTATGCATGTGA
65 AAAACTTTATGCATGTGA
* * *
525477 TTTAAATGAAAATGATATCTCTCTAACAATTGATATCAAAATTTTCAAA-TGCATAACAT-TTTT
1 TTTAAATGAAAATGATATATCGCTAACAATTGATATCAAAATTTT-AAATTGCATAACATAATTT
525540 GGAAAACTTTATGCAT
65 --AAAACTTTATGCAT
525556 ATGCACTTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
81 3 0.04
83 61 0.91
84 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (82 bp):
TTTAAATGAAAATGATATATCGCTAACAATTGATATCAAAATTTTAAATTGCATAACATAATTTA
AAACTTTATGCATGTGA
Found at i:525922 original size:18 final size:19
Alignment explanation
Indices: 525899--525955 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 19
525889 TATATTTTCC
*
525899 AACAATTAGTATCTTTTT-
1 AACAATTGGTATCTTTTTA
525917 AACAATTGGTATTCTTTTGTA
1 AACAATTGGTA-TCTTTT-TA
525938 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
525956 CATTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 10 0.29
19 7 0.20
20 7 0.20
21 11 0.31
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTA
Found at i:529018 original size:3 final size:3
Alignment explanation
Indices: 529005--529055 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
528995 GATCTAAAAC
*
529005 AAT AAT AAAT AAT ATT ACAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
529051 AAT AA
1 AAT AA
529056 CCCGAACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 37 0.86
4 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:552875 original size:14 final size:15
Alignment explanation
Indices: 552839--552879 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
552829 AATAAACGAA
*
552839 AATATAAAGTAAACT
1 AATATAAAATAAACT
*
552854 -ATAAAAAATAAA-T
1 AATATAAAATAAACT
552867 AATATAAAATAAA
1 AATATAAAATAAA
552880 ATGCTCTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (15 bp):
AATATAAAATAAACT
Found at i:556354 original size:15 final size:16
Alignment explanation
Indices: 556334--556363 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
556324 ATTGTTTAAA
556334 AAATTCAAAA-AATTT
1 AAATTCAAAATAATTT
556349 AAATTCAAAATAATT
1 AAATTCAAAATAATT
556364 ATGATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTCAAAATAATTT
Found at i:560275 original size:19 final size:19
Alignment explanation
Indices: 560231--560297 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
560221 GAATATCAAG
560231 TTAAAATTAAGCATCAAAA
1 TTAAAATTAAGCATCAAAA
* * *
560250 TTGAAATTAATG-ATTAATA
1 TTAAAATTAA-GCATCAAAA
* *
560269 TTAAAATTTACGTATCAAAA
1 TTAAAA-TTAAGCATCAAAA
*
560289 TTAATATTA
1 TTAAAATTA
560298 TCATGATTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 23 0.62
20 14 0.38
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (19 bp):
TTAAAATTAAGCATCAAAA
Found at i:560905 original size:12 final size:12
Alignment explanation
Indices: 560888--560912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
560878 TAATATAATA
560888 TTTTTCGACGAG
1 TTTTTCGACGAG
560900 TTTTTCGACGAG
1 TTTTTCGACGAG
560912 T
1 T
560913 CAAAGTCACT
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:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TTTTTCGACGAG
Found at i:563968 original size:21 final size:21
Alignment explanation
Indices: 563931--563970 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
563921 TATTGAATTT
*
563931 GTATATAAATAATTTTGTTGA
1 GTATATAAATAAATTTGTTGA
563952 GTATAT-AATGAAATTTGTT
1 GTATATAAAT-AAATTTGTT
563971 TCAATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (21 bp):
GTATATAAATAAATTTGTTGA
Found at i:567788 original size:60 final size:60
Alignment explanation
Indices: 567680--567794 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
567670 TCCACGATAC
* * * * *
567680 CGACATTTAGTTCGAACAAGCTGGTAGTTGAGTGCATTCCCCTTGAACTTGAAGGCATCT
1 CGACATTGAGGTCGAACAAGCTCGTAGTTGAATGCACTCCCCTTGAACTTGAAGGCATCT
*
567740 CGACATTGAGGTCGAAGAAGCTCGTAGTTGAATGC-CTCCCCTTGGAACTTGAAGG
1 CGACATTGAGGTCGAACAAGCTCGTAGTTGAATGCACTCCCCTT-GAACTTGAAGG
567795 AATCGTTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 7 0.15
60 41 0.85
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (60 bp):
CGACATTGAGGTCGAACAAGCTCGTAGTTGAATGCACTCCCCTTGAACTTGAAGGCATCT
Found at i:568651 original size:12 final size:14
Alignment explanation
Indices: 568634--568707 Score: 50
Period size: 14 Copynumber: 5.3 Consensus size: 14
568624 TTTTACAATC
568634 ATAAAAT-A-TAAT
1 ATAAAATAATTAAT
568646 ATAAAATAATTAAT
1 ATAAAATAATTAAT
*
568660 ATAATAA-AATCT-GT
1 ATAA-AATAAT-TAAT
*
568674 -TCAAATAATTAAAT
1 ATAAAATAATT-AAT
568688 ATAAAATAAATATAAT
1 ATAAAAT-AAT-TAAT
568704 ATAA
1 ATAA
568708 GAAAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
12 10 0.21
13 6 0.12
14 13 0.27
15 8 0.17
16 10 0.21
17 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (14 bp):
ATAAAATAATTAAT
Found at i:569792 original size:9 final size:9
Alignment explanation
Indices: 569780--569804 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
569770 AAAATTAAAA
569780 AAAAAAACT
1 AAAAAAACT
569789 AAAAAAACT
1 AAAAAAACT
569798 AAAAAAA
1 AAAAAAA
569805 GGTTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAACT
Found at i:571451 original size:15 final size:15
Alignment explanation
Indices: 571431--571484 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
571421 TAGAGGAGAG
*
571431 AACAGGTGATATAGT
1 AACAGGTGAGATAGT
571446 AACAGGTGAGATAGT
1 AACAGGTGAGATAGT
571461 AACAGGTGAGATAGT
1 AACAGGTGAGATAGT
*
571476 AACGGGTGA
1 AACAGGTGA
571485 AGGGATGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
AACAGGTGAGATAGT
Found at i:573188 original size:16 final size:16
Alignment explanation
Indices: 573164--573203 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
573154 GAAAGAGAAA
* *
573164 CCTCTCTCTCCCTCTT
1 CCTCCCTCTCCCTCTC
*
573180 CCTCCCTCTCTCTCTC
1 CCTCCCTCTCCCTCTC
573196 CCTCCCTC
1 CCTCCCTC
573204 CCTCCCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (16 bp):
CCTCCCTCTCCCTCTC
Found at i:573189 original size:20 final size:20
Alignment explanation
Indices: 573165--573207 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
573155 AAAGAGAAAC
573165 CTCTCTCTCCCTCTTCCTCCCT
1 CTCTCTCTCCCTC--CCTCCCT
573187 CTCTCTCTCCCTCCCTCCCT
1 CTCTCTCTCCCTCCCTCCCT
573207 C
1 C
573208 CCTCATGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (20 bp):
CTCTCTCTCCCTCCCTCCCT
Found at i:576120 original size:311 final size:311
Alignment explanation
Indices: 575529--576126 Score: 724
Period size: 311 Copynumber: 1.9 Consensus size: 311
575519 TCTTTTTCTT
* * ** * *
575529 AAGCTTCTTGGTAATTGGTTTTGTCACTGACTTATCCTTTCCTCCTTCAAGCACATTCAAGTTAG
1 AAGCTTCTTGCTAACTAATTTTGTCACCGACTTATCATTTCCTCCTTCAAGCACATTCAAGTTAG
* * * * *
575594 AAGGGTTATGGGAACCTTCATTTCCAGGCCTTCTTCATCAAGTGAAGGAACCTCAACATCTTGCT
66 AAGGGCTATGAGAACCTTCATTCCCAGGCCTTCTTCATCAAATGAAGGAACCTCAACAACTTGCT
* * * * **
575659 GCTTATTCTTCAGCTCATCGTGCTCTCCAACAACTTGTAGTTGTTCTAAGCCGTACTCTTTGATA
131 GCTTATTCTGCAGCTCACCGTGCTCTCCAACAACTTGTAGCTGTTCTAAGCCGTAATCTTCAATA
* * *
575724 TTTGATCTGCTTGCAGAGGAGCTCTCTCTTAATCCCTTGAAGGACATTTGGGGTGATTTCTCACA
196 TTTGATCTGCTTGCAGAGGAGCGCTCTCTTAATCCCGTGAAGGACATTTGGGGTGACTTCTCACA
** *
575789 GGCATTCTCACTTTGCATATCTGGCTTGTTCACTTGTTTTGTCAGTTTTGC
261 ACCAATCTCACTTTGCATATCTGGCTTGTTCACTTGTTTTGTCAGTTTTGC
*
575840 AAGCTTCTTGCTAACTAATTTTGTCACCGACTTATCATTTCCTCCTTCAAGCAC-TTCCATGTTA
1 AAGCTTCTTGCTAACTAATTTTGTCACCGACTTATCATTTCCTCCTTCAAGCACATT-CAAGTTA
* ** **
575904 GAAGGGCTGTGAGAATTTTCATTCCGCA-GTTTTCTTTCATCAAATGAAGGAACCTCAACAACTT
65 GAAGGGCTATGAGAACCTTCATTCC-CAGGCCTTC-TTCATCAAATGAAGGAACCTCAACAACTT
** * ** *
575968 GCTGCTTATTCTGCAGCTCACC-TGGCTCTCCGCCTACTTGT-GCCTGTTCTTGGCTGTAATCTT
128 GCTGCTTATTCTGCAGCTCACCGT-GCTCTCCAACAACTTGTAG-CTGTTCTAAGCCGTAATCTT
* * * *
576031 CAATA-TTGATCTGCTTGCAGGGGTGGGCTCTCTTAATCCCGTGTAA-GACATTTGTGGTGACTT
191 CAATATTTGATCTGCTTGCAGAGGAGCGCTCTCTTAATCCCGTG-AAGGACATTTGGGGTGACTT
*
576094 CTCATAACCAATCTCA-TTTCGCATATCTGGCTT
255 CTCACAACCAATCTCACTTT-GCATATCTGGCTT
576127 ACCTGCAAAG
Statistics
Matches: 240, Mismatches: 40, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
310 5 0.02
311 152 0.63
312 83 0.35
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (311 bp):
AAGCTTCTTGCTAACTAATTTTGTCACCGACTTATCATTTCCTCCTTCAAGCACATTCAAGTTAG
AAGGGCTATGAGAACCTTCATTCCCAGGCCTTCTTCATCAAATGAAGGAACCTCAACAACTTGCT
GCTTATTCTGCAGCTCACCGTGCTCTCCAACAACTTGTAGCTGTTCTAAGCCGTAATCTTCAATA
TTTGATCTGCTTGCAGAGGAGCGCTCTCTTAATCCCGTGAAGGACATTTGGGGTGACTTCTCACA
ACCAATCTCACTTTGCATATCTGGCTTGTTCACTTGTTTTGTCAGTTTTGC
Found at i:578288 original size:123 final size:124
Alignment explanation
Indices: 577983--578358 Score: 350
Period size: 123 Copynumber: 3.0 Consensus size: 124
577973 TCTAAGAGTA
* * * * *
577983 ACACAACTCCTACGTGATG-GGAGATCTGGTCAGGG-GATGACACTGCTCATACGTGATGAAGAG
1 ACACAACTCCTACGTGATGAGGAGATCAGGTC-GGGTGATGACACGGTTCCTACGTGATGAGGA-
* * * *
578046 TTCTTGGCCATCTTTAGGAAGGGTGATAACTCAGTTTCTACGTGATGAGGACGACTGGTTATATG
64 TTGTAGGCCA-C-TT---AAGGGTGATAACAC-GGTTCTACGTGATGAGGACGACTGGTTATA--
578111 GGTTG
121 -GTTG
* * *
578116 ACACAACTCCTACATAAT-ATGGAAAT-ATGGTCGGGTGATGACACGGTTCCTACGTGATGAGGA
1 ACACAACTCCTACGTGATGA-GGAGATCA-GGTCGGGTGATGACACGGTTCCTACGTGATGAGGA
*
578179 TTGTAGGCCACTTAAGGGTGATAACACGGTTCTACATGATGAGGACGACTGGTTATA-TTG
64 TTGTAGGCCACTTAAGGGTGATAACACGGTTCTACGTGATGAGGACGACTGGTTATAGTTG
* ** * * *
578239 AGACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTATGCGATGAGGACT
1 ACACAACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGAGGATT
* * * ** *
578304 GCAGG-AAATCTAAGGGTGATAACATAGTTCCTACGTGATGAGGATGACTGGTTAT
66 GTAGGCCACT-TAAGGGTGATAACACGGTT-CTACGTGATGAGGACGACTGGTTAT
578359 CTAGGGTTGA
Statistics
Matches: 206, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
122 2 0.01
123 76 0.37
124 25 0.12
127 28 0.14
128 13 0.06
131 2 0.01
132 1 0.00
133 27 0.13
134 32 0.16
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (124 bp):
ACACAACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGAGGATT
GTAGGCCACTTAAGGGTGATAACACGGTTCTACGTGATGAGGACGACTGGTTATAGTTG
Found at i:578471 original size:251 final size:247
Alignment explanation
Indices: 578064--578825 Score: 658
Period size: 249 Copynumber: 3.1 Consensus size: 247
578054 CATCTTTAGG
* *
578064 AAGGGTGATAAC-TCAGTTTCTACGTGATGAGGACGACTGGTTATAT-GGGTTGACACAACTCCT
1 AAGGGTGATAACAT-AGTTCCTACGTGATGAGGA-GACTGGTTATCTAGGGTTGACAC-ACTCCT
* * * * * ** * * *
578127 ACATAATATGGA-AATATGGTCGGGTGATGACACGGTTCCTACGTGATGAGGATTGTAGGCCA-C
63 ACATAATAAGGAGATTA-GGTCGGGTGATGACACTGCTCATAC-T-ATGATAAGTCTTGGCCATC
* * * *
578190 TTAAGGGTGATAACACGGTTC-TAC-ATGATGAGGA-CGACTGGTTAT-A-TTGAGACGGCTCCT
125 -TAATGGTGATAACACTGCTCATACTATGATGA--ATC--CTGGTTATCAGTTGACACGGCTCCT
* * * *
578250 ACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTATGCGATGAGGACTGC-AGGAAATC
185 ACGTGATGAGGAGATCAGGTCGAGTGATGACACGGCT-C-ATACGATGAGAACT-CTAGGAAATC
578314 T
247 T
*
578315 AAGGGTGATAACATAGTTCCTACGTGATGAGGATGACTGGTTATCTAGGGTTGAAACGACTCCTA
1 AAGGGTGATAACATAGTTCCTACGTGATGAGGA-GACTGGTTATCTAGGGTTGACAC-ACTCCTA
* *
578380 CATAACAAGGAGATTAGTTCGGGTGATGA-ACTGCTCATACTATGATAAGTCTTGGCCATCTAAT
64 CATAATAAGGAGATTAGGTCGGGTGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTAAT
* * *
578444 GGTGATAACACTGCTCACACTATGATGAATCTTGGTTATCAGGTTGACACTGCTCCTACGTGATG
129 GGTGATAACACTGCTCATACTATGATGAATCCTGGTTATCA-GTTGACACGGCTCCTACGTGATG
* * * * * * **
578509 AGGAGATCAGGTTGAGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCT
193 AGGAGATCAGGTCGAGTGATGACACGGCTCATACGATGAGAACTCTAGGAAATCT
* * * * * *
578564 ACGGGTGATAACACT-GCTCATAC-T-ATGATGA-ATCTTGGTTATCCAGGGTTGACACAATCCT
1 AAGGGTGATAACA-TAGTTCCTACGTGATGAGGAGA-C-TGGTTATCTAGGGTTGACACACTCCT
* * *
578625 ACATGATGAGGAGATCT-GGTCGGGTGATGACACTGCTCATACGATGATAAGTCTTGGCCATCT-
63 ACATAATAAGGAGAT-TAGGTCGGGTGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTA
* * *
578688 ATGGGTGATAACACTGCTCATACTATGATGAATCTTGGTTGTCCAGGGTTGACACGACTCCTACG
127 AT-GGTGATAACACTGCTCATACTATGATGAATCCTGGTTAT-CA--GTTGACACGGCTCCTACG
* * * * ** * * * * **
578753 TGATAAGGAGATCTGGTAGGGTGATGACACTACTCATACTATGATAAGTCTTGGCCATCT
188 TGATGAGGAGATCAGGTCGAGTGATGACACGGCTCATACGATGAGAACTCTAGGAAATCT
578813 AAGGGTGATAACA
1 AAGGGTGATAACA
578826 CTGCATACTA
Statistics
Matches: 433, Mismatches: 59, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
245 1 0.00
246 32 0.07
247 93 0.21
248 11 0.03
249 147 0.34
250 7 0.02
251 101 0.23
252 38 0.09
253 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (247 bp):
AAGGGTGATAACATAGTTCCTACGTGATGAGGAGACTGGTTATCTAGGGTTGACACACTCCTACA
TAATAAGGAGATTAGGTCGGGTGATGACACTGCTCATACTATGATAAGTCTTGGCCATCTAATGG
TGATAACACTGCTCATACTATGATGAATCCTGGTTATCAGTTGACACGGCTCCTACGTGATGAGG
AGATCAGGTCGAGTGATGACACGGCTCATACGATGAGAACTCTAGGAAATCT
Found at i:578587 original size:44 final size:43
Alignment explanation
Indices: 578400--578859 Score: 235
Period size: 44 Copynumber: 11.1 Consensus size: 43
578390 AGATTAGTTC
*
578400 GGGTGATGA-ACTGCTCATACTATGATAAGTCTTGGCCATCTAA
1 GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCT-A
* * * *
578443 TGGTGATAACACTGCTCACACTATGATGAA-TCTTGGTTATC-A
1 GGGTGATGACACTGCTCATACTATGAT-AAGTCTTGGTCATCTA
* * * ** * ** *
578485 -GGT--TGACACTGCTCCTAC-GTGATGAG--GAGATCAGGTT
1 GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCTA
*
578522 GAGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCTA
1 GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCTA
* * *
578565 CGGGTGATAACACTGCTCATACTATGATGAA-TCTTGGTTATCCA
1 -GGGTGATGACACTGCTCATACTATGAT-AAGTCTTGGTCATCTA
** *
578609 GGGT--TGACAC-AATCCTAC-ATGATGAGGAGATC-TGG---TC--
1 GGGTGATGACACTGCTCATACTATGAT-A--AG-TCTTGGTCATCTA
* *
578646 GGGTGATGACACTGCTCATACGATGATAAGTCTTGGCCATCTA
1 GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCTA
* ** *
578689 TGGGTGATAACACTGCTCATACTATGATGAA-TCTTGGTTGTCCA
1 -GGGTGATGACACTGCTCATACTATGAT-AAGTCTTGGTCATCTA
* * ** * *
578733 GGGT--TGACAC-GACTCCTAC-GTGATAAG--GAGATC-TGGTA
1 GGGTGATGACACTG-CTCATACTATGATAAGTCTTGGTCAT-CTA
* *
578771 GGGTGATGACACTACTCATACTATGATAAGTCTTGGCCATCTAA
1 GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCT-A
* * *
578815 GGGTGATAACACTG--CATACTATGATGAA-TCTTGGTTATCCA
1 GGGTGATGACACTGCTCATACTATGAT-AAGTCTTGGTCATCTA
578856 GGGT
1 GGGT
578860 TGACACGGCT
Statistics
Matches: 311, Mismatches: 66, Indels: 82
0.68 0.14 0.18
Matches are distributed among these distances:
36 3 0.01
37 8 0.03
38 18 0.06
39 29 0.09
40 42 0.14
41 45 0.14
42 24 0.08
43 27 0.09
44 109 0.35
45 6 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
GGGTGATGACACTGCTCATACTATGATAAGTCTTGGTCATCTA
Found at i:578680 original size:124 final size:125
Alignment explanation
Indices: 578352--578895 Score: 807
Period size: 123 Copynumber: 4.4 Consensus size: 125
578342 TGAGGATGAC
* * * * ** *
578352 TGGTTATCTAGGGTTGAAACGACTCCTACATAACAAGGAGAT-TAGTTCGGGTGATGA-ACTGCT
1 TGGTTATCCAGGGTTGACACGACTCCTACGTGATGAGGAGATCT-GGTCGGGTGATGACACTGCT
* *
578415 CATACTATGATAAGTCTTGGCCATCTAATGGTGATAACACTGCTCACACTATGATGAATCT
65 CATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCT
* * *
578476 TGGTTAT-CA-GGTTGACACTG-CTCCTACGTGATGAGGAGATCAGGTTGAGTGATGACACTGCT
1 TGGTTATCCAGGGTTGACAC-GACTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACTGCT
* *
578538 CATACTATGATAAGTCTTGGTCATCTACGGGTGATAACACTGCTCATACTATGATGAATCT
65 CATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCT
* *
578599 TGGTTATCCAGGGTTGACAC-AATCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTC
1 TGGTTATCCAGGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACTGCTC
* *
578663 ATACGATGATAAGTCTTGGCCATCTATGGGTGATAACACTGCTCATACTATGATGAATCT
66 ATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCT
* * * *
578723 TGGTTGTCCAGGGTTGACACGACTCCTACGTGATAAGGAGATCTGGTAGGGTGATGACACTACTC
1 TGGTTATCCAGGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACTGCTC
578788 ATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTG--CATACTATGATGAATCT
66 ATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCT
*
578846 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGG
1 TGGTTATCCAGGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGG
578896 AGAATTTGGT
Statistics
Matches: 379, Mismatches: 34, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
122 34 0.09
123 135 0.36
124 123 0.32
125 87 0.23
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (125 bp):
TGGTTATCCAGGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACTGCTC
ATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATCT
Found at i:578683 original size:247 final size:247
Alignment explanation
Indices: 578352--578895 Score: 821
Period size: 247 Copynumber: 2.2 Consensus size: 247
578342 TGAGGATGAC
* * * ** *
578352 TGGTTATCTAGGGTTGAAACGACTCCTACATAACAAGGAGAT-TAGTTCGGGTGATGAACTGCTC
1 TGGTTATCCAGGGTTGACACGACTCCTACATGATGAGGAGATCT-GGTCGGGTGATGAACTGCTC
*
578416 ATACTATGATAAGTCTTGGCCATCTAAT-GGTGATAACACTGCTCACACTATGATGAATCTTGGT
65 ATACGATGATAAGTCTTGGCCATCT-ATGGGTGATAACACTGCTCACACTATGATGAATCTTGGT
* * *
578480 TAT-CA-GGTTGACACTG-CTCCTACGTGATGAGGAGATCAGGTTGAGTGATGACACTGCTCATA
129 TATCCAGGGTTGACAC-GACTCCTACGTGATAAGGAGATCAGGTAGAGTGATGACACTACTCATA
* *
578542 CTATGATAAGTCTTGGTCATCTACGGGTGATAACACTGCTCATACTATGATGAATCT
193 CTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTG--CATACTATGATGAATCT
*
578599 TGGTTATCCAGGGTTGACAC-AATCCTACATGATGAGGAGATCTGGTCGGGTGATGACACTGCTC
1 TGGTTATCCAGGGTTGACACGACTCCTACATGATGAGGAGATCTGGTCGGGTGATGA-ACTGCTC
*
578663 ATACGATGATAAGTCTTGGCCATCTATGGGTGATAACACTGCTCATACTATGATGAATCTTGGTT
65 ATACGATGATAAGTCTTGGCCATCTATGGGTGATAACACTGCTCACACTATGATGAATCTTGGTT
* * *
578728 GTCCAGGGTTGACACGACTCCTACGTGATAAGGAGATCTGGTAGGGTGATGACACTACTCATACT
130 ATCCAGGGTTGACACGACTCCTACGTGATAAGGAGATCAGGTAGAGTGATGACACTACTCATACT
578793 ATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCATACTATGATGAATCT
195 ATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCATACTATGATGAATCT
* *
578846 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGG
1 TGGTTATCCAGGGTTGACACGACTCCTACATGATGAGGAGATCTGGTCGG
578896 AGAATTTGGT
Statistics
Matches: 270, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
246 31 0.11
247 124 0.46
248 29 0.11
249 86 0.32
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (247 bp):
TGGTTATCCAGGGTTGACACGACTCCTACATGATGAGGAGATCTGGTCGGGTGATGAACTGCTCA
TACGATGATAAGTCTTGGCCATCTATGGGTGATAACACTGCTCACACTATGATGAATCTTGGTTA
TCCAGGGTTGACACGACTCCTACGTGATAAGGAGATCAGGTAGAGTGATGACACTACTCATACTA
TGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCATACTATGATGAATCT
Found at i:579210 original size:32 final size:32
Alignment explanation
Indices: 579156--579244 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
579146 TCCGCATCAG
* * *
579156 GATGTTAAATCCCCGAAGATGCCCCAATATTC
1 GATGTTGAATCTCCAAAGATGCCCCAATATTC
* *
579188 GATGTTGAATCTCCAAATATGCCCCAATATTT
1 GATGTTGAATCTCCAAAGATGCCCCAATATTC
* **
579220 GCTGTTGAATCTTTAAAGATGCCCC
1 GATGTTGAATCTCCAAAGATGCCCC
579245 TATTGTTCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAATATTC
Found at i:586168 original size:20 final size:20
Alignment explanation
Indices: 586145--586187 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
586135 AATCCACCAC
*
586145 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
586165 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
586185 ATG
1 ATG
586188 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:595030 original size:27 final size:25
Alignment explanation
Indices: 594991--595040 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
594981 GAAAATGTTT
594991 AAAAATGAAATGCAGATGCAAAATG
1 AAAAATGAAATGCAGATGCAAAATG
*
595016 AAAAGATGCAAATGCATATGCAAAA
1 AAAA-ATG-AAATGCAGATGCAAAA
595041 ATATTAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 15 0.68
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.16
Consensus pattern (25 bp):
AAAAATGAAATGCAGATGCAAAATG
Found at i:597987 original size:3 final size:3
Alignment explanation
Indices: 597935--597974 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
597925 GTAGTGTTAG
* *
597935 ATA ATA ATTA ATA ATA ATA GTA ATA ATA ATA ATA ACA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
597975 GTATTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:599982 original size:12 final size:11
Alignment explanation
Indices: 599959--600006 Score: 69
Period size: 12 Copynumber: 4.2 Consensus size: 11
599949 TTAGTCCCTA
*
599959 AAAATAAAAAT
1 AAAATAATAAT
599970 AAAATTAATAAT
1 AAAA-TAATAAT
599982 AAAATAATATAT
1 AAAATAATA-AT
599994 AAAATAATAAT
1 AAAATAATAAT
600005 AA
1 AA
600007 GCTTAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
11 13 0.38
12 21 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:600018 original size:24 final size:24
Alignment explanation
Indices: 599959--600006 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
599949 TTAGTCCCTA
*
599959 AAAATAA-AAATAAAATTAATAAT
1 AAAATAATATATAAAATTAATAAT
599982 AAAATAATATATAAAA-TAATAAT
1 AAAATAATATATAAAATTAATAAT
600005 AA
1 AA
600007 GCTTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATAATATATAAAATTAATAAT
Found at i:600147 original size:13 final size:14
Alignment explanation
Indices: 600131--600159 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
600121 TATAAATACG
600131 TTTTCAAAA-TATA
1 TTTTCAAAATTATA
600144 TTTTCAAAATTATA
1 TTTTCAAAATTATA
600158 TT
1 TT
600160 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTCAAAATTATA
Found at i:600171 original size:80 final size:79
Alignment explanation
Indices: 600085--600232 Score: 187
Period size: 77 Copynumber: 1.9 Consensus size: 79
600075 TTTCGAAAAT
* * *
600085 TATATAT-TATATATTCTTCCAAGAAT-ATTTAAAAACTATA-A-ATACGTTTTCAAAATATATT
1 TATATATATATATATTTTTCCAAAAATGATTTAAAAACTATAGATATACGTTTTCAAAA-ATATA
600146 TTCAAAATTATATTA
65 TTCAAAATTATATTA
* * * *
600161 TATATATATATATGTTTTTTCAAAAATGTTTTTAAAACTATAGATTATACGTTTTCAAAAATATA
1 TATATATATATATATTTTTCCAAAAATGATTTAAAAACTATAGA-TATACGTTTTCAAAAATATA
600226 TTCAAAA
65 TTCAAAA
600233 ACATATATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
76 7 0.12
77 15 0.25
78 12 0.20
79 1 0.02
80 11 0.18
81 14 0.23
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (79 bp):
TATATATATATATATTTTTCCAAAAATGATTTAAAAACTATAGATATACGTTTTCAAAAATATAT
TCAAAATTATATTA
Found at i:600222 original size:69 final size:69
Alignment explanation
Indices: 600177--600328 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
600167 TATATATGTT
*
600177 TTTTCAAAAATGTTTTTAAAACTATAGATTATACGTTTTCAAAAATATATTCAAAAACATATATT
1 TTTT-AAAAATGTTTTTAAAACCATAGATTATACGTTTTCAAAAATATATTCAAAAACATATATT
600242 ATACG
65 ATACG
* * * *
600247 TTTTAAAAATGTTTTTAAAACCATATATTATACGTTTTCAAAACTATTTTTAAAAAACTATATAT
1 TTTTAAAAATGTTTTTAAAACCATAGATTATACGTTTTCAAAAATA-TATTCAAAAAC-ATATAT
600312 TATACG
64 TATACG
600318 TTTTCAAAAAT
1 TTTT-AAAAAT
600329 AAGTTTCCAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
69 39 0.53
70 13 0.18
71 16 0.22
72 6 0.08
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (69 bp):
TTTTAAAAATGTTTTTAAAACCATAGATTATACGTTTTCAAAAATATATTCAAAAACATATATTA
TACG
Found at i:600313 original size:37 final size:36
Alignment explanation
Indices: 600177--600353 Score: 218
Period size: 35 Copynumber: 4.9 Consensus size: 36
600167 TATATATGTT
* *
600177 TTTTCAAAAATGTTTTT-AAAACTATAGATTATACG
1 TTTTCAAAAATATTTTTAAAAACTATATATTATACG
* *
600212 TTTTCAAAAATATATTCAAAAAC-ATATATTATACG
1 TTTTCAAAAATATTTTTAAAAACTATATATTATACG
* *
600247 TTTT-AAAAATGTTTTT-AAAACCATATATTATACG
1 TTTTCAAAAATATTTTTAAAAACTATATATTATACG
*
600281 TTTTCAAAACTATTTTTAAAAAACTATATATTATACG
1 TTTTCAAAAATATTTTT-AAAAACTATATATTATACG
**
600318 TTTTCAAAAATAAGTTTCCAAAAACTATATATTATA
1 TTTTCAAAAAT-A-TTTTTAAAAACTATATATTATA
600354 TATTTTTAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
33 5 0.04
34 25 0.20
35 39 0.32
36 5 0.04
37 27 0.22
38 18 0.15
39 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (36 bp):
TTTTCAAAAATATTTTTAAAAACTATATATTATACG
Found at i:602113 original size:14 final size:15
Alignment explanation
Indices: 602094--602122 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
602084 TTGGACCCAC
602094 CTTATTTTT-TTTTT
1 CTTATTTTTCTTTTT
602108 CTTATTTTTCTTTTT
1 CTTATTTTTCTTTTT
602123 TCTTTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTATTTTTCTTTTT
Found at i:612500 original size:6 final size:6
Alignment explanation
Indices: 612491--612523 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
612481 ACTTGGATCC
612491 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
612524 TGTAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:612805 original size:38 final size:36
Alignment explanation
Indices: 612701--612838 Score: 140
Period size: 38 Copynumber: 3.9 Consensus size: 36
612691 CAAAACTATA
* * * * * *
612701 TTAAAAAACATAAATTAAACATTTTGAAAAATGTTT
1 TTAAAAACCATATATTATACGTTTTCAAAAATTTTT
612737 TT-AAAACCATATATTATACGTTTT---AAATTTTT
1 TTAAAAACCATATATTATACGTTTTCAAAAATTTTT
*
612769 TTAAAAACCATATATTATATGTTTTCAAAACTATTTTT
1 TTAAAAACCATATATTATACGTTTTCAAAA--ATTTTT
* * *
612807 TAAAAAACTATATATTATACATTTTCAAAAAT
1 TTAAAAACCATATATTATACGTTTTCAAAAAT
612839 AAGTTTCCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.10
33 21 0.24
35 18 0.21
36 6 0.07
38 32 0.37
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (36 bp):
TTAAAAACCATATATTATACGTTTTCAAAAATTTTT
Found at i:612851 original size:38 final size:38
Alignment explanation
Indices: 612771--612877 Score: 124
Period size: 38 Copynumber: 2.8 Consensus size: 38
612761 AAATTTTTTT
* * * ** *
612771 AAAAACCATATATTATATGTTTTCAAAACTATTTTTTA
1 AAAAACTATATATTATATATTTTCAAAAATAAGTTTCA
* *
612809 AAAAACTATATATTATACATTTTCAAAAATAAGTTTCC
1 AAAAACTATATATTATATATTTTCAAAAATAAGTTTCA
* *
612847 AAAAACTCTATATTATATATTTTTAAAAATA
1 AAAAACTATATATTATATATTTTCAAAAATA
612878 TATTTGAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (38 bp):
AAAAACTATATATTATATATTTTCAAAAATAAGTTTCA
Found at i:613626 original size:10 final size:10
Alignment explanation
Indices: 613583--613660 Score: 66
Period size: 10 Copynumber: 7.3 Consensus size: 10
613573 GTTAGATGGT
*
613583 AAATAAAAAA
1 AAATAATAAA
613593 AATATCAACTAAA
1 AA-AT-AA-TAAA
613606 AAATAAATAAA
1 AAAT-AATAAA
*
613617 TAATAATAAA
1 AAATAATAAA
*
613627 AAAAAATAAA
1 AAATAATAAA
*
613637 AAATAAAAAA
1 AAATAATAAA
*
613647 TAAAAAATAAA
1 -AAATAATAAA
613658 AAA
1 AAA
613661 GGATGTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
10 27 0.49
11 17 0.31
12 6 0.11
13 5 0.09
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (10 bp):
AAATAATAAA
Found at i:613637 original size:31 final size:31
Alignment explanation
Indices: 613602--613660 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
613592 AAATATCAAC
*
613602 TAAAAAATAAATAAAT-AATAATAAAAAAAAA
1 TAAAAAATAAA-AAATAAAAAATAAAAAAAAA
613633 TAAAAAATAAAAAATAAAAAATAAAAAA
1 TAAAAAATAAAAAATAAAAAATAAAAAA
613661 GGATGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (31 bp):
TAAAAAATAAAAAATAAAAAATAAAAAAAAA
Found at i:613680 original size:7 final size:7
Alignment explanation
Indices: 613602--613660 Score: 82
Period size: 7 Copynumber: 8.0 Consensus size: 7
613592 AAATATCAAC
613602 TAAAAAA
1 TAAAAAA
613609 TAAATAAA
1 TAAA-AAA
613617 TAATAATAA
1 TAA-AA-AA
*
613626 AAAAAAA
1 TAAAAAA
613633 TAAAAAA
1 TAAAAAA
613640 TAAAAAA
1 TAAAAAA
613647 TAAAAAA
1 TAAAAAA
613654 TAAAAAA
1 TAAAAAA
613661 GGATGTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 33 0.70
8 9 0.19
9 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:614851 original size:3 final size:3
Alignment explanation
Indices: 614840--614880 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
614830 AAAAAATTAA
*
614840 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
614881 ATACATATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:615307 original size:86 final size:86
Alignment explanation
Indices: 615140--615303 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 86
615130 TTTTGTTGAC
* * * * * *
615140 AGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTCGATTTGCCTCTGAGTTGAATGTAATCGA
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATTCGATGTGCCTCTGAGCTGAATGTAATCGA
615205 ACTCGAAGGTCTTTGGTTGGT
66 ACTCGAAGGTCTTTGGTTGGT
* *
615226 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA-T-GATGGTGCCTTTGAGCTGAGTGTAATCG
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATTCGAT-GTGCCTCTGAGCTGAATGTAATCG
615289 AACTCGAAGGTCTTT
65 AACTCGAAGGTCTTT
615304 TGGTGAGTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 3 0.04
85 36 0.52
86 30 0.43
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (86 bp):
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATTCGATGTGCCTCTGAGCTGAATGTAATCGA
ACTCGAAGGTCTTTGGTTGGT
Found at i:615958 original size:106 final size:106
Alignment explanation
Indices: 615773--616432 Score: 884
Period size: 106 Copynumber: 6.5 Consensus size: 106
615763 TATTGTTCCA
* * * * * *
615773 AGTCCAATATCCTCCACCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * * *
615838 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
615879 AGTCCAATATCCTTCGCTGTGAAGTTGCAATTGGCTCTGAGATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
615944 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
615985 AGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTAACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * **
616038 CAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
616079 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
616144 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
616185 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
616250 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
616291 AGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
616344 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
616385 AGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTG-AATTGGGAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
616433 GCCCCTTCGT
Statistics
Matches: 494, Mismatches: 36, Indels: 49
0.85 0.06 0.08
Matches are distributed among these distances:
94 156 0.32
95 4 0.01
96 4 0.01
99 6 0.01
100 8 0.02
101 6 0.01
104 4 0.01
105 13 0.03
106 293 0.59
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:616081 original size:94 final size:94
Alignment explanation
Indices: 615920--616418 Score: 656
Period size: 94 Copynumber: 5.1 Consensus size: 94
615910 TGGCTCTGAG
* *
615920 ATTGGGAAATTGTTTATTGACAACCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
1 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
615985 AGTCCAATATCCTTCGTTGTGAAGTTGAA
66 AGTCCAATATCCTTCGTTGTGAAGTTGAA
* * * **
616014 ATTGGGAAATTGTTTATTAACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTGTCTGG
1 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
616079 AGTCCAATATCATTCGTTGTGAAGTTGAA
66 AGTCCAATATCCTTCGTTGTGAAGTTGAA
616108 ATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
1 A-----T-TG------GGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
616173 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
54 TGCGTTGTCTGGAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAA
* *
616226 ATTGGGAAATTGTTTATTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
1 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
616291 AGTCCAATATCCTTCGTTGTGAAGTTGAA
66 AGTCCAATATCCTTCGTTGTGAAGTTGAA
* *
616320 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGG
1 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
616385 AGTCCAATATCCCTCGCTGTGAAGTTGAA
66 AGTCCAATATCCTTCGTTGTGAAGTTGAA
616414 ATTGG
1 ATTGG
616419 CTCTGAATTG
Statistics
Matches: 359, Mismatches: 22, Indels: 48
0.84 0.05 0.11
Matches are distributed among these distances:
94 184 0.51
95 1 0.00
96 1 0.00
99 3 0.01
100 4 0.01
101 1 0.00
104 1 0.00
105 1 0.00
106 146 0.41
107 1 0.00
108 1 0.00
111 1 0.00
112 4 0.01
113 3 0.01
116 1 0.00
117 1 0.00
118 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (94 bp):
ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
AGTCCAATATCCTTCGTTGTGAAGTTGAA
Found at i:616166 original size:200 final size:198
Alignment explanation
Indices: 615816--616418 Score: 796
Period size: 200 Copynumber: 3.0 Consensus size: 198
615806 GCTCTGGAAC
* * * * * *
615816 TGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAG
1 TGGGAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
* *
615881 TCCAATATCCTTCGCTGTGAAGTTGCAATTGGCTCTGAGATTGGGAAATTGTTTATTGACAACCA
66 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GGAAATTGTTTATTGACAACCA
* *
615946 GCAGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
129 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
616011 GAAAT
194 GAAAT
* * *
616016 TGGGAAATTGTTTATTAACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTGTCTGGAG
1 TGGGAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
*
616081 TCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCA
66 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATT-GGAAATTGTTTATTGACAACCA
616146 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
129 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-T-T---G-T
616211 GAAATTGGCTCTGAAAT
188 G-AA---G-T-TGAAAT
**
616228 TGGGAAATTGTTTATTGAA-AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGA
1 TGGGAAATTGTTTATT-AACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGA
616292 GTCCAATATCCTTCGTTGTGAAGTTGAAA-----T-TG----GGAAATTGTTTATTGACAACCAG
65 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAAATTGTTTATTGACAACCAG
* * * *
616347 CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGGAGTCCAATATCCCTCGCTGTGAAGTTG
130 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
616412 AAAT
195 AAAT
616416 TGG
1 TGG
616419 CTCTGAATTG
Statistics
Matches: 364, Mismatches: 25, Indels: 40
0.85 0.06 0.09
Matches are distributed among these distances:
188 9 0.02
189 1 0.00
190 1 0.00
193 2 0.01
194 2 0.01
195 1 0.00
198 1 0.00
200 242 0.66
201 2 0.01
202 1 0.00
205 1 0.00
206 4 0.01
207 3 0.01
210 1 0.00
211 1 0.00
212 90 0.25
213 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (198 bp):
TGGGAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAAATTGTTTATTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AAT
Found at i:616326 original size:306 final size:306
Alignment explanation
Indices: 615773--616425 Score: 1056
Period size: 306 Copynumber: 2.1 Consensus size: 306
615763 TATTGTTCCA
* * * * *
615773 AGTCCAATATC-CTCCACCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCACT-CGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTATTGACAA
* *
615837 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAGTCCAATATCCTTCGCTGTGAA
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCGAGTCCAATATCCTTCGCTGTGAA
* * * *
615902 GTTGCAATTGGCTCTGAGATTGGGAAATTGTTTATTGACAACCAGCAGTCCCTTCGTTGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAACCAGCAGTCCCTTCGTCGTGAAGT
*
615967 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATT
195 TGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATT
*
616032 AACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTGTCTGG
260 AACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTATCTGG
* * *
616079 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAAC
1 AGTCCAATATCACTCGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTATTGACAAC
* * * *
616144 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCGAGTCCAATATCCTTCGCTGTGAAG
*
616209 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAACCAGCAGTCCCTTCGTCGTGAAGTT
*
616274 GAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTG
196 GAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTA
* * *
616339 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGG
261 ACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTATCTGG
*
616385 AGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 AGTCCAATATCACTCGCTGTGAAGTTGAAATTGGCTCTGAA
616426 TTGGGAAGCC
Statistics
Matches: 318, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
306 317 1.00
307 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (306 bp):
AGTCCAATATCACTCGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTATTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAACCAGCAGTCCCTTCGTCGTGAAGTT
GAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTA
ACAACCAACGGTCCCTTCGCCGTGAAGTTGAACTTATGTTATCTGG
Found at i:620761 original size:7 final size:7
Alignment explanation
Indices: 620701--620741 Score: 55
Period size: 7 Copynumber: 5.4 Consensus size: 7
620691 ATCAACTAAT
620701 AAATAAA
1 AAATAAA
620708 TAAATAATA
1 -AAATAA-A
620717 ATAATAAA
1 A-AATAAA
620725 AAATAAA
1 AAATAAA
620732 AAATAAA
1 AAATAAA
620739 AAA
1 AAA
620742 GGATGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 16 0.52
8 9 0.29
9 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:628108 original size:14 final size:14
Alignment explanation
Indices: 628089--628115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
628079 AACAGAATTC
628089 ATATCATATATCAA
1 ATATCATATATCAA
628103 ATATCATATATCA
1 ATATCATATATCA
628116 GAACAGAATC
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATCATATATCAA
Found at i:628161 original size:24 final size:24
Alignment explanation
Indices: 628112--628168 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
628102 AATATCATAT
* *
628112 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATCCAGATAAAAA
* *
628136 ATCAGAACAGAATTCATATAAAAA
1 ATCAGAACAGAATCCAGATAAAAA
*
628160 ATTAGAACA
1 ATCAGAACA
628169 TATTTCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATAAAAA
Found at i:637611 original size:16 final size:17
Alignment explanation
Indices: 637590--637625 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
637580 TATATGATAA
*
637590 ATGTTGAA-TAGATGTT
1 ATGTTGAATTAAATGTT
637606 ATGTTGAATTAAATGTT
1 ATGTTGAATTAAATGTT
637623 ATG
1 ATG
637626 AGAACAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (17 bp):
ATGTTGAATTAAATGTT
Found at i:637697 original size:16 final size:15
Alignment explanation
Indices: 637673--637716 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
637663 CATGTTTTGT
*
637673 AAAACTGTTATATGTG
1 AAAA-TGTTATATCTG
*
637689 AAAAGTGTTCTATCTG
1 AAAA-TGTTATATCTG
637705 AAAATGTTATAT
1 AAAATGTTATAT
637717 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (15 bp):
AAAATGTTATATCTG
Found at i:648964 original size:4 final size:4
Alignment explanation
Indices: 648955--648982 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
648945 GGATTAAAAT
648955 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
648983 GAAAAGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:649153 original size:16 final size:17
Alignment explanation
Indices: 649118--649160 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
649108 AGAAACTTAA
*
649118 AGAAGCTTAAAGATAATT
1 AGAAGC-TAAAGAGAATT
649136 AGAAGCTAAAG-GAATT
1 AGAAGCTAAAGAGAATT
*
649152 AGGAGCTAA
1 AGAAGCTAA
649161 TGGTGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 5 0.22
18 6 0.26
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (17 bp):
AGAAGCTAAAGAGAATT
Found at i:661941 original size:20 final size:20
Alignment explanation
Indices: 661913--661958 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
661903 AGTTTTCATG
*
661913 AAAATAACATAATT-AAATCA
1 AAAACAACA-AATTCAAATCA
*
661933 AAAACAACAATTTCAAATCA
1 AAAACAACAAATTCAAATCA
661953 AAAACA
1 AAAACA
661959 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAACAACAAATTCAAATCA
Found at i:662383 original size:20 final size:20
Alignment explanation
Indices: 662345--662383 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
662335 TAAACCGACT
* *
662345 AGGGGTATCGGTACCCATTG
1 AGGGGTATCGATACACATTG
662365 AGGGGTATCGATACACATT
1 AGGGGTATCGATACACATT
662384 CAAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (20 bp):
AGGGGTATCGATACACATTG
Found at i:666486 original size:74 final size:76
Alignment explanation
Indices: 666361--666513 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 76
666351 TCCTTGGTAG
*
666361 TTGAACAAGATGATATTCTCCCGTATTCATCTGGTCCAAGTACACAGAAAAG-TGGATCTTTTGC
1 TTGAACAAGATGATATTCTCCCGTATTCATCTGGTCCAAGTACACAGAAAAGATGGATCTTTTGA
666425 GTTGAGCTGAA
66 GTTGAGCTGAA
666436 TTGAACAAGATGATATTCTCCCGTA-TCATCTGGTCCAAGTACACAGAAAAGAATATGGATCTTT
1 TTGAACAAGATGATATTCTCCCGTATTCATCTGGTCCAAGTACACAGAAAAG---ATGGATCTTT
666500 TGAGTTGAGCTGAA
63 TGAGTTGAGCTGAA
666514 ATAATCTCTT
Statistics
Matches: 73, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
74 26 0.36
75 25 0.34
78 22 0.30
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (76 bp):
TTGAACAAGATGATATTCTCCCGTATTCATCTGGTCCAAGTACACAGAAAAGATGGATCTTTTGA
GTTGAGCTGAA
Found at i:667374 original size:103 final size:103
Alignment explanation
Indices: 667195--667402 Score: 400
Period size: 103 Copynumber: 2.0 Consensus size: 103
667185 TATTGAAAGT
667195 AAAATGAATATTGAAAGGAATTTGGCTTGAATTGGTTAAACTTATGTTTGATGTTTTCTATCTTG
1 AAAATGAATATTGAAAGGAATTTGGCTTGAATTGGTTAAACTTATGTTTGATGTTTTCTATCTTG
667260 TTTTTCTTTTTTCAATTCTTGAAGATCAAAGGCTTTAG
66 TTTTTCTTTTTTCAATTCTTGAAGATCAAAGGCTTTAG
667298 AAAATGAATATTGAAAGGAATTTGGCTTGAATTGGTTAAACTTGATGTTTGATGTTTTCTATCTT
1 AAAATGAATATTGAAAGGAATTTGGCTTGAATTGGTTAAACTT-ATGTTTGATGTTTTCTATCTT
667363 GTTTTTC-TTTTTCAATTCTTGAAGATCAAAGGCTTTAG
65 GTTTTTCTTTTTTCAATTCTTGAAGATCAAAGGCTTTAG
667401 AA
1 AA
667403 CTTGTTTAAA
Statistics
Matches: 104, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 76 0.73
104 28 0.27
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (103 bp):
AAAATGAATATTGAAAGGAATTTGGCTTGAATTGGTTAAACTTATGTTTGATGTTTTCTATCTTG
TTTTTCTTTTTTCAATTCTTGAAGATCAAAGGCTTTAG
Found at i:668017 original size:19 final size:19
Alignment explanation
Indices: 667993--668029 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
667983 ATTCGAATAA
*
667993 TTGAATCGAATATATAATT
1 TTGAATCAAATATATAATT
*
668012 TTGAATTAAATATATAAT
1 TTGAATCAAATATATAAT
668030 ATTAAAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (19 bp):
TTGAATCAAATATATAATT
Found at i:672538 original size:21 final size:21
Alignment explanation
Indices: 672514--672553 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
672504 ATACAAATTC
672514 ATCCGATATAGATACCAACTT
1 ATCCGATATAGATACCAACTT
*
672535 ATCCGATATAGATATCAAC
1 ATCCGATATAGATACCAAC
672554 AATATCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (21 bp):
ATCCGATATAGATACCAACTT
Found at i:672562 original size:21 final size:21
Alignment explanation
Indices: 672514--672564 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
672504 ATACAAATTC
*
672514 ATCCGATATAGATACCAACTT
1 ATCCGATATAGATACCAACAT
*
672535 ATCCGATATAGATATCAACAAT
1 ATCCGATATAGATACCAAC-AT
672557 AT-CGATAT
1 ATCCGATAT
672565 CGACTTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (21 bp):
ATCCGATATAGATACCAACAT
Found at i:673335 original size:6 final size:6
Alignment explanation
Indices: 673320--673352 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
673310 AAGAAAAGAA
673320 AAGA-G AAGATG AAGATG AAGATG AAGATG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGA
673353 AGGAAATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (6 bp):
AAGATG
Done.