Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008177.1 Hibiscus syriacus cultivar Beakdansim tig00110773_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: 1003138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:379443 original size:187 final size:182
Alignment explanation
Indices: 379119--379508 Score: 586
Period size: 187 Copynumber: 2.1 Consensus size: 182
379109 ATTAAATTTT
* *
379119 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
379184 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAAAA-TTTT
* *
379249 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATT-AA
* ** *
379304 AAATATTATATATATATTATATATAACATTTGGGCTAAGCCTTAACAATTTAAAACTCAATTAAT
1 AAATATTA-A-ATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAAT
* * *
379369 AATTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-
64 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTA--TAAAAT
379433 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
127 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
* *
379489 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
379509 AATTAGAAAA
Statistics
Matches: 188, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
182 8 0.04
183 2 0.01
184 1 0.01
185 17 0.09
186 11 0.06
187 145 0.77
189 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAAAATTTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
Found at i:396214 original size:288 final size:287
Alignment explanation
Indices: 395698--396270 Score: 957
Period size: 288 Copynumber: 2.0 Consensus size: 287
395688 TGAAGCCATA
* *
395698 AAGCATCATTCACATTAAGAGAATAGAAATGCTATTAGCATTAGAAATATCCAAGGGTTAGAGTT
1 AAGCATCATTCACATTAAGAGAAGAGAAATGCTATTAGCATTAGAAATACCCAAGGGTTAGAGTT
* * * *
395763 GAGTCTTCGTTGTCAAGATCTCAGGTTGAAATCCAAATAAAGGGGAGGCAGATGGTATACAAGAG
66 GAGTCTTCATTGTCAAGATCTCAAGTTGAAATCCAAATAAAGGGGAGGCAGAAGGGATACAAGAG
* * * * *
395828 GGCAGCCTCTCATTATGTGAATGAAAACCATTAGTTAGCCCCAACAGAAAATTGAAAGAAAAGAT
131 AGCAGCCTCTCAATATGTGAATCAAAACCATTAGGTAACCCCAACAGAAAATTGAAAGAAAAGAT
* *
395893 GAAAATTCTAGCTTACATGATGCCTAATTTACCATCCGACGGATCAGAAAAAGGTTCAGGACCTT
196 GAAAATTCTAGCTTACATGATGCCTAATTTACCATCCGACAGATCAGAAAAAGGTTCAAGACCTT
*
395958 CAAGTTGACAAACCAAATACATTAAGTG
261 CAAGTTGACAAACCAAAAAC-TTAAGTG
395986 AAGCATCATTCACATTAAGAGAAGAGAAATGCTATTAGCATTAGAAATACCCAAGGGTTAGAGTT
1 AAGCATCATTCACATTAAGAGAAGAGAAATGCTATTAGCATTAGAAATACCCAAGGGTTAGAGTT
* * *
396051 GAGTCTTCATTGTCAAGATCTCAAGTTGAAATCCAAATATAGGGGAGGTAGAAGGGGTACAAGAG
66 GAGTCTTCATTGTCAAGATCTCAAGTTGAAATCCAAATAAAGGGGAGGCAGAAGGGATACAAGAG
* *
396116 AGCAGCCTTTCAATATGTGAATCAAAACCATTAGGTAACCCCGACAGAAAATTGAAAGAAAAGAT
131 AGCAGCCTCTCAATATGTGAATCAAAACCATTAGGTAACCCCAACAGAAAATTGAAAGAAAAGAT
396181 GAAAATTCTAGCTTACATGATGCCTAATTTACCATCCGACAGATCAGAAAAAGGTTCAAGACCTT
196 GAAAATTCTAGCTTACATGATGCCTAATTTACCATCCGACAGATCAGAAAAAGGTTCAAGACCTT
*
396246 CCAGTTGACAAACCAAAAACTTAAG
261 CAAGTTGACAAACCAAAAACTTAAG
396271 GAAAGTCAAA
Statistics
Matches: 265, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
287 5 0.02
288 260 0.98
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (287 bp):
AAGCATCATTCACATTAAGAGAAGAGAAATGCTATTAGCATTAGAAATACCCAAGGGTTAGAGTT
GAGTCTTCATTGTCAAGATCTCAAGTTGAAATCCAAATAAAGGGGAGGCAGAAGGGATACAAGAG
AGCAGCCTCTCAATATGTGAATCAAAACCATTAGGTAACCCCAACAGAAAATTGAAAGAAAAGAT
GAAAATTCTAGCTTACATGATGCCTAATTTACCATCCGACAGATCAGAAAAAGGTTCAAGACCTT
CAAGTTGACAAACCAAAAACTTAAGTG
Found at i:398080 original size:38 final size:38
Alignment explanation
Indices: 398029--398127 Score: 171
Period size: 38 Copynumber: 2.6 Consensus size: 38
398019 CAAAGAGATT
398029 GAAGTCTTGAACCAGTCATTATGGGCCTCTCTGAACGG
1 GAAGTCTTGAACCAGTCATTATGGGCCTCTCTGAACGG
* * *
398067 GAAGTCTTGAACCAGTTATTATGGGCTTCTCTGAACTG
1 GAAGTCTTGAACCAGTCATTATGGGCCTCTCTGAACGG
398105 GAAGTCTTGAACCAGTCATTATG
1 GAAGTCTTGAACCAGTCATTATG
398128 AGCTACCAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (38 bp):
GAAGTCTTGAACCAGTCATTATGGGCCTCTCTGAACGG
Found at i:398883 original size:86 final size:86
Alignment explanation
Indices: 398769--399065 Score: 304
Period size: 86 Copynumber: 3.5 Consensus size: 86
398759 CATTTTTTAT
* * **
398769 AGGGTATCTAATTTTTTCAATCATACATTTTATCTTTATAACTGAATTTCCTA-TTTTTTCTAAT
1 AGGGTCTCTAATTTTTTCAATCATACATTTTACCTTTATAACTG-ATCCCCTATTTTTTTC-AAT
* ***
398833 TTTGTTTTTTACCTTTATAATTA
64 CTCACTTTTTACCTTTATAATTA
* *
398856 A-GGTCTCTAATTTTTGCAAT-ATCACATTTTACCTTTATAATTGATCCCCTATTTTTTTCAATC
1 AGGGTCTCTAATTTTTTCAATCAT-ACATTTTACCTTTATAACTGATCCCCTATTTTTTTCAATC
398919 TCACTTTTTACCTTTATAATTA
65 TCACTTTTTACCTTTATAATTA
* * *
398941 AGGGTC-CTAATTTTTTCAATCCTAC-TTTTACATTTATCAA-TGAGACCCCTGATTTTTTTCAA
1 AGGGTCTCTAATTTTTTCAATCATACATTTTACCTTTAT-AACTGA-TCCCCT-ATTTTTTTCAA
** *
399003 TCTCACTTCCTACCTTTATAATTG
63 TCTCACTTTTTACCTTTATAATTA
* * * *
399027 A-GGCCTCTAA-TTTTTCAATCACACTTTTTACATTTATAA
1 AGGGTCTCTAATTTTTTCAATCATACATTTTACCTTTATAA
399066 TTGAGGTCTT
Statistics
Matches: 181, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
84 14 0.08
85 70 0.39
86 96 0.53
87 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (86 bp):
AGGGTCTCTAATTTTTTCAATCATACATTTTACCTTTATAACTGATCCCCTATTTTTTTCAATCT
CACTTTTTACCTTTATAATTA
Found at i:398929 original size:42 final size:43
Alignment explanation
Indices: 398838--399071 Score: 235
Period size: 42 Copynumber: 5.5 Consensus size: 43
398828 CTAATTTTGT
* * * * *
398838 TTTTTACCTTTATAATTAAGGTCTCTAATTTTTGCAATATCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
* * *
398881 ATTTTACCTTTATAATTGA-TCCCCTATTTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
* **
398923 TTTTTACCTTTATAATTAAGGGTCCTAATTTTTTCAATC-CTAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTC-AC
* * *
398966 -TTTTACATTTATCAA-TGAGACCCCTGATTTTTTTCAATCTCAC
1 TTTTTACCTTTAT-AATTGAGGCCCCT-AATTTTTTCAATCTCAC
** * *
399009 TTCCTACCTTTATAATTGAGGCCTCTAA-TTTTTCAATCACAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
*
399051 TTTTTACATTTATAATTGAGG
1 TTTTTACCTTTATAATTGAGG
399072 TCTTTAATTT
Statistics
Matches: 154, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
42 83 0.54
43 53 0.34
44 18 0.12
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
Found at i:420060 original size:2 final size:2
Alignment explanation
Indices: 420055--420079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
420045 TTCATTTTTT
420055 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
420080 GTTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:425526 original size:31 final size:31
Alignment explanation
Indices: 425488--425558 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
425478 GTCGGAAACA
* *
425488 ATATTGCAAATGGAGTAAATGTAGGGGGACC
1 ATATTGCAAATGGACTAAATGTAGAGGGACC
* *
425519 ATATTGCAAATGGACTAAATGTTGAGGGACT
1 ATATTGCAAATGGACTAAATGTAGAGGGACC
*
425550 GTATTGCAA
1 ATATTGCAA
425559 GTTTTAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (31 bp):
ATATTGCAAATGGACTAAATGTAGAGGGACC
Found at i:426322 original size:23 final size:24
Alignment explanation
Indices: 426277--426331 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
426267 TTATCAAATA
*
426277 ATTTAATTATATTCAATATTCAAT
1 ATTTAATTATATTCAATAATCAAT
*
426301 -TTTAATTATACTTTAA-AATCAAT
1 ATTTAATTATA-TTCAATAATCAAT
426324 ATTTAATT
1 ATTTAATT
426332 TTTCATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAATTATATTCAATAATCAAT
Found at i:426459 original size:10 final size:10
Alignment explanation
Indices: 426446--426515 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
426436 ATAAAGAAAC
426446 AATAAATAAT
1 AATAAATAAT
426456 AATAAATAAT
1 AATAAATAAT
*
426466 AAAACAATAA-
1 AATA-AATAAT
*
426476 AA-ACATATAT
1 AATAAATA-AT
*
426486 AA-AATTAAT
1 AATAAATAAT
* *
426495 AATAAAAAAC
1 AATAAATAAT
426505 AATAAATAAT
1 AATAAATAAT
426515 A
1 A
426516 GGGTAAAGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
8 3 0.06
9 6 0.13
10 33 0.70
11 5 0.11
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (10 bp):
AATAAATAAT
Found at i:427007 original size:74 final size:72
Alignment explanation
Indices: 426929--427099 Score: 177
Period size: 72 Copynumber: 2.3 Consensus size: 72
426919 TATGAGTCTA
* * * * *
426929 ATTTTTTTTAATACTTTTTATTAGATGTCCAATTTTTTTAATATTTATTATTTAT-GAGC-ACAC
1 ATTTTTTTTAATACTTTTTATTAG-GGACCAATTTTTTCAATACTTAATA-TTATGGAGCTAC-C
426992 TCTTAAAATTT
63 -CTTAAAATTT
* *
427003 ATTTTTCTTTAAT-TTTTTTATTAGGGACCCATTTTTTCAATACTTAATATTATGGAGCTACCCT
1 ATTTTT-TTTAATACTTTTTATTAGGGACCAATTTTTTCAATACTTAATATTATGGAGCTACCCT
427067 TAAAATTT
65 TAAAATTT
* * * *
427075 ATTATTTTCAACACTTGTTATTAGG
1 ATTTTTTTTAATACTTTTTATTAGG
427100 AACAATTATT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
71 4 0.05
72 29 0.36
73 24 0.30
74 18 0.22
75 6 0.07
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.52
Consensus pattern (72 bp):
ATTTTTTTTAATACTTTTTATTAGGGACCAATTTTTTCAATACTTAATATTATGGAGCTACCCTT
AAAATTT
Found at i:433548 original size:16 final size:17
Alignment explanation
Indices: 433527--433559 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
433517 AAGAAGTTGT
*
433527 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
433543 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
433560 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:447261 original size:14 final size:16
Alignment explanation
Indices: 447230--447268 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
447220 AAAAATATTT
447230 AAATATAAAACAAATA
1 AAATATAAAACAAATA
447246 AAAT-TAAAAC-AATAA
1 AAATATAAAACAAAT-A
447261 AAATATAA
1 AAATATAA
447269 TTAGAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATATAAAACAAATA
Found at i:448375 original size:10 final size:10
Alignment explanation
Indices: 448348--448386 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
448338 TCGGTTGGGG
448348 CGTGGCAGCGA
1 CGTGG-AGCGA
448359 C-TGGAGCGA
1 CGTGGAGCGA
448368 CGTGGAGCGA
1 CGTGGAGCGA
*
448378 CATGGAGCG
1 CGTGGAGCG
448387 GTGGCAGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 6 0.23
10 19 0.73
11 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.46, T:0.10
Consensus pattern (10 bp):
CGTGGAGCGA
Found at i:448378 original size:19 final size:21
Alignment explanation
Indices: 448348--448394 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
448338 TCGGTTGGGG
448348 CGTGGCAGCGAC-TGGAGCGA
1 CGTGGCAGCGACATGGAGCGA
448368 CGTGG-AGCGACATGGAGCG-
1 CGTGGCAGCGACATGGAGCGA
448387 -GTGGCAGC
1 CGTGGCAGC
448395 TGGTGTAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.19, C:0.23, G:0.47, T:0.11
Consensus pattern (21 bp):
CGTGGCAGCGACATGGAGCGA
Found at i:448610 original size:3 final size:3
Alignment explanation
Indices: 448602--448649 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
448592 AATTATTTTT
* *
448602 TAA TAA TAA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
448650 AATGAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:448622 original size:15 final size:15
Alignment explanation
Indices: 448602--448649 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
448592 AATTATTTTT
448602 TAATAATAATAATTA
1 TAATAATAATAATTA
448617 TAATAATAATAATTA
1 TAATAATAATAATTA
*
448632 TAATAATAATAATAA
1 TAATAATAATAATTA
448647 TAA
1 TAA
448650 AATGAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:449154 original size:112 final size:113
Alignment explanation
Indices: 448880--449559 Score: 793
Period size: 112 Copynumber: 6.0 Consensus size: 113
448870 GAGTCATTCC
* * * * * *
448880 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * * *
448945 ATGAACTTTCTCTGGAAAGGTTGATGCTAACAT-ATATGTGATAAAATTATG--TA
66 ATGAACTCGAACTGGAAAAGCTGAT-C---CATCA-A-GTGAT-GAATT-TGAATA
* * * * *
448998 AAAGGTTGAACATGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * *
449062 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAATA
66 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAATA
*
449110 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * * *
449174 ATGAACTTTCTCTGGAAATGTTGATCTATCAAGTGATGAATTTGAATA
66 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAATA
*
449222 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTGAA-TTCTTCTCAT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCAT
**
449286 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGCA
65 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAATA
* *
449335 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG--AA-TTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
* **
449397 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAATA
* * *
449445 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTC
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATAAGTTCTTCTC
*
449510 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAAT
63 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAAT
449560 CTTTGCTAAA
Statistics
Matches: 520, Mismatches: 31, Indels: 24
0.90 0.05 0.04
Matches are distributed among these distances:
110 109 0.21
111 4 0.01
112 156 0.30
113 109 0.21
114 3 0.01
115 1 0.00
116 57 0.11
117 44 0.08
118 37 0.07
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAATA
Found at i:450392 original size:94 final size:92
Alignment explanation
Indices: 450233--450420 Score: 286
Period size: 94 Copynumber: 2.0 Consensus size: 92
450223 CGATCATGCA
* * * * **
450233 ATTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACTGAACCAAATCAGATAACTCAAAG
1 ATTCATCTTTCAAGTCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAG
450298 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATGAGCAC
* *
450325 ATTCATCTTTCAAGTCCAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAGTCCAATGATTGG-TTCT-GGGGTTCATACCAAACCAAATCAGATAACTCAA
450390 AGAACACTTCCAGAAGATGCTATGAGCAC
64 AGAACACTTCCAGAAGATGCTATGAGCAC
450419 AT
1 AT
450421 GGCATTTGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 24 0.28
93 3 0.03
94 59 0.69
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (92 bp):
ATTCATCTTTCAAGTCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCAC
Found at i:451683 original size:7 final size:6
Alignment explanation
Indices: 451667--451734 Score: 72
Period size: 6 Copynumber: 11.3 Consensus size: 6
451657 CTTGACCCCC
451667 CTTTTT CTTTTT CCTTTTT C-TTTT CTTTTT -TTCTTT CTTTTT -TTCTTT
1 CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT CTT-TTT
451715 CTTTTT -TTCTTT CTTTTT CT
1 CTTTTT CTT-TTT CTTTTT CT
451735 CTTCTAGCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
5 11 0.20
6 31 0.57
7 12 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:451699 original size:20 final size:20
Alignment explanation
Indices: 451669--451731 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
451659 TGACCCCCCT
*
451669 TTTTC-TTTTTCCTTT-TTC
1 TTTTCTTTTTTTCTTTCTTC
*
451687 TTTTCTTTTTTTCTTTCTTT
1 TTTTCTTTTTTTCTTTCTTC
451707 TTTTCTTTCTTTT-TTTCTTTC
1 TTTTCTTT-TTTTCTTTC-TTC
451728 TTTT
1 TTTT
451732 TCTCTTCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 5 0.13
19 9 0.24
20 14 0.37
21 10 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTTTCTTTCTTC
Found at i:451703 original size:12 final size:12
Alignment explanation
Indices: 451668--451737 Score: 97
Period size: 12 Copynumber: 5.7 Consensus size: 12
451658 TTGACCCCCC
451668 TTTTTCTTT-TT
1 TTTTTCTTTCTT
451679 CCTTTTTCTTTTCTT
1 --TTTTTC-TTTCTT
451694 TTTTTCTTTCTT
1 TTTTTCTTTCTT
451706 TTTTTCTTTCTT
1 TTTTTCTTTCTT
451718 TTTTTCTTTCTT
1 TTTTTCTTTCTT
*
451730 TTTCTCTT
1 TTTTTCTT
451738 CTAGCATAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
12 37 0.69
13 12 0.22
14 3 0.06
15 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:451705 original size:4 final size:4
Alignment explanation
Indices: 451683--451730 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
451673 CTTTTTCCTT
* * *
451683 TTTC TTTTC TTTT TTTC TTTC TTTT TTTC TTTC TTTT TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
451731 TTCTCTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:451737 original size:8 final size:7
Alignment explanation
Indices: 451668--451726 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
451658 TTGACCCCCC
451668 TTTTTC-
1 TTTTTCT
*
451674 TTTTTCC
1 TTTTTCT
451681 TTTTTCT
1 TTTTTCT
*
451688 TTTCT-T
1 TTTTTCT
451694 TTTTTCT
1 TTTTTCT
*
451701 TTCTTTTT
1 TT-TTTCT
451709 TTCTTTCTT
1 TT-TTTC-T
451718 TTTTTCT
1 TTTTTCT
451725 TT
1 TT
451727 CTTTTTCTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
6 11 0.25
7 16 0.36
8 14 0.32
9 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:456442 original size:10 final size:10
Alignment explanation
Indices: 456427--456453 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
456417 TGGCAGCGGC
456427 TGGAGCGACG
1 TGGAGCGACG
456437 TGGAGCGACG
1 TGGAGCGACG
456447 TGGAGCG
1 TGGAGCG
456454 GCGGCAGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.52, T:0.11
Consensus pattern (10 bp):
TGGAGCGACG
Found at i:456677 original size:3 final size:3
Alignment explanation
Indices: 456669--456716 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
456659 AATTATTTTT
* * *
456669 TAA TAA TAA TAA TTA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
456717 AATGAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:457226 original size:112 final size:113
Alignment explanation
Indices: 456947--457627 Score: 807
Period size: 113 Copynumber: 6.0 Consensus size: 113
456937 GAGTCATTCC
* * * * * *
456947 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * * * *
457012 ATGAACTTTCTCTGGAAAGGTTGATGCTAACAT-ATATGTGATAAAATT-ATGTA
66 ATGAACTCGAACTGGAAAAGCTGAT-C---CATCA-A-GTGATGAATTTGA-GTA
* * * * * *
457065 AAAGGTTGAACATGCTCTTATCATTGTGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * * * *
457129 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTAAATA
66 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGTA
*
457177 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
**** * * *
457241 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAATA
66 ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGTA
457289 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCAT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCAT
*
457353 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGCA
65 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGTA
* *
457402 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCAT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCAT
* *
457466 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
65 TATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGTA
* * *
457515 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTC
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATAAGTTCTTCTC
*
457580 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
63 ATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
457628 ATCTTTGCTA
Statistics
Matches: 524, Mismatches: 31, Indels: 18
0.91 0.05 0.03
Matches are distributed among these distances:
112 158 0.30
113 221 0.42
114 3 0.01
115 2 0.00
116 60 0.11
117 44 0.08
118 36 0.07
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGTA
Found at i:458464 original size:94 final size:94
Alignment explanation
Indices: 458305--458586 Score: 478
Period size: 94 Copynumber: 3.0 Consensus size: 94
458295 CGATCATGCA
* * * * * *
458305 ATTCATCTTTTAATTCCAATGATTGGTTCTAT--GGTTCCTACCGAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAGTCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
*
458368 AGAACACTTTCAGAAGATGCTATGAGCAC
66 AGAACACTTCCAGAAGATGCTATGAGCAC
458397 ATTCATCTTTCAAGTCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAGTCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
458462 AGAACACTTCCAGAAGATGCTATGAGCAC
66 AGAACACTTCCAGAAGATGCTATGAGCAC
*
458491 ATTCATCTTTCAAGTCCAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTTCAAGTCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
458556 AGAACACTTCCAGAAGATGCTATGAGCAC
66 AGAACACTTCCAGAAGATGCTATGAGCAC
458585 AT
1 AT
458587 GGCATTTGTT
Statistics
Matches: 180, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
92 28 0.16
94 152 0.84
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (94 bp):
ATTCATCTTTCAAGTCCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAGATGCTATGAGCAC
Found at i:459852 original size:12 final size:11
Alignment explanation
Indices: 459834--459878 Score: 65
Period size: 12 Copynumber: 4.0 Consensus size: 11
459824 TTGACCCCCC
459834 TTTTTCTTTTT
1 TTTTTCTTTTT
459845 TCTTTTCTTTTT
1 T-TTTTCTTTTT
459857 TTCTTTC-TTTT
1 TT-TTTCTTTTT
459868 TTTTTCTTTTT
1 TTTTTCTTTTT
459879 CTCTTCAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.13
11 12 0.39
12 15 0.48
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:459869 original size:14 final size:13
Alignment explanation
Indices: 459835--459877 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
459825 TGACCCCCCT
459835 TTTTC-TTTTTTC
1 TTTTCTTTTTTTC
459847 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
*
459860 TTTCTTTTTTTTTC
1 TTT-TCTTTTTTTC
459874 TTTT
1 TTTT
459878 TCTCTTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 5 0.18
13 11 0.39
14 12 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:469163 original size:15 final size:15
Alignment explanation
Indices: 469140--469171 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
469130 TGAAATGAAT
469140 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
469155 AATGTATGTATGCAA
1 AATGAATGTATGCAA
469170 AA
1 AA
469172 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:474597 original size:3 final size:3
Alignment explanation
Indices: 474589--474676 Score: 135
Period size: 3 Copynumber: 30.0 Consensus size: 3
474579 AATTATTTTT
* * *
474589 TAA TAA TAA TTA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
474637 TAA TAA T-A TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
474677 AATGAGTAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
2 4 0.05
3 75 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:476102 original size:16 final size:16
Alignment explanation
Indices: 476081--476112 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
476071 GTTGAAGAAG
476081 GTCAATTAGATCACCT
1 GTCAATTAGATCACCT
476097 GTCAATTAGATCACCT
1 GTCAATTAGATCACCT
476113 TTACAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
GTCAATTAGATCACCT
Found at i:486131 original size:20 final size:20
Alignment explanation
Indices: 486108--486146 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
486098 TTTGAAACTT
486108 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
486128 AAATTCGTAACACGAAAAT
1 AAATTCGCAACACGAAAAT
486147 CGCAATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:487248 original size:21 final size:21
Alignment explanation
Indices: 487179--487277 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
487169 TTCGATGTTT
487179 GGATGCATGGATGCATTGCA-
1 GGATGCATGGATGCATTGCAG
* * *
487199 TGATTCATCGATGCATT--AG
1 GGATGCATGGATGCATTGCAG
487218 TGCAGATGCATGGATGCATTGCAG
1 -G--GATGCATGGATGCATTGCAG
*
487242 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCATTGCAG
487263 GGATGCATGGATGCA
1 GGATGCATGGATGCA
487278 CTTTGACACC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
20 14 0.21
21 34 0.52
22 14 0.21
23 1 0.02
24 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAG
Found at i:487380 original size:29 final size:29
Alignment explanation
Indices: 487359--487416 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
487349 AAACTTTGAA
487359 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
487388 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
487417 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:487406 original size:30 final size:30
Alignment explanation
Indices: 487359--487418 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
487349 AAACTTTGAA
487359 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
487388 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
487419 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:490630 original size:8 final size:8
Alignment explanation
Indices: 490617--490850 Score: 65
Period size: 8 Copynumber: 31.8 Consensus size: 8
490607 TTGCAGCCTT
490617 GATGCATG
1 GATGCATG
490625 GATGCAT-
1 GATGCATG
490632 G--GCA-G
1 GATGCATG
490637 GATGCATG
1 GATGCATG
490645 GATGCAT-
1 GATGCATG
490652 GA--CAT-
1 GATGCATG
*
490657 GATGCATC
1 GATGCATG
490665 GATGCATG
1 GATGCATG
*
490673 G-T--AAG
1 GATGCATG
*
490678 GATGCATC
1 GATGCATG
490686 GATGCATAG
1 GATGCAT-G
*
490695 CAAGATGCATC
1 ---GATGCATG
490706 GATGCACT-
1 GATGCA-TG
* *
490714 AATTGCATTC
1 GA-TGCA-TG
**
490724 GATGTTTG
1 GATGCATG
490732 GATGCATG
1 GATGCATG
490740 GATGCAT-
1 GATGCATG
490747 --TGCAT-
1 GATGCATG
*
490752 GATGCATC
1 GATGCATG
490760 GATGCAT-
1 GATGCATG
*
490767 TAGTGCA--
1 GA-TGCATG
490774 GATGCATG
1 GATGCATG
490782 GATGCAT-
1 GATGCATG
*
490789 --TGCAGG
1 GATGCATG
490795 GATGCATG
1 GATGCATG
490803 GATGCA--
1 GATGCATG
* *
490809 -CTGCAGG
1 GATGCATG
490816 GATGCATG
1 GATGCATG
490824 GATGCA--
1 GATGCATG
* *
490830 -CTGCAGG
1 GATGCATG
490837 GATGCATG
1 GATGCATG
490845 GATGCA
1 GATGCA
490851 CTTTGACACC
Statistics
Matches: 170, Mismatches: 24, Indels: 64
0.66 0.09 0.25
Matches are distributed among these distances:
5 29 0.17
6 5 0.03
7 17 0.10
8 103 0.61
9 8 0.05
10 1 0.01
12 7 0.04
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (8 bp):
GATGCATG
Found at i:490692 original size:41 final size:40
Alignment explanation
Indices: 490616--490711 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 40
490606 GTTGCAGCCT
* * *
490616 TGATGCATGGATGCATGGCAGGATGCATGGATGCAT-GACA
1 TGATGCATCGATGCATGGAAGGATGCATCGATGCATAG-CA
490656 TGATGCATCGATGCATGGTAAGGATGCATCGATGCATAGCA
1 TGATGCATCGATGCATGG-AAGGATGCATCGATGCATAGCA
*
490697 AGATGCATCGATGCA
1 TGATGCATCGATGCA
490712 CTAATTGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 17 0.34
41 32 0.64
42 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (40 bp):
TGATGCATCGATGCATGGAAGGATGCATCGATGCATAGCA
Found at i:490753 original size:95 final size:97
Alignment explanation
Indices: 490636--490810 Score: 250
Period size: 95 Copynumber: 1.8 Consensus size: 97
490626 ATGCATGGCA
*
490636 GGATGCATGGATGCATGACATGATGCATCGATGCA-TGGT-AAGGATGCATCGATGCATAGCA-A
1 GGATGCATGGATGCATGACATGATGCATCGATGCATTAGTGAA-GATGCATCGATGCATAGCAGA
490698 GATGCATCGATGCACTAATTGCATTCGATGTTT
65 GATGCATCGATGCACTAATTGCATTCGATGTTT
* * * *
490731 GGATGCATGGATGCATTG-CATGATGCATCGATGCATTAGTGCAGATGCATGGATGCATTGCAGG
1 GGATGCATGGATGCA-TGACATGATGCATCGATGCATTAGTGAAGATGCATCGATGCATAGCAGA
*
490795 GATGCATGGATGCACT
65 GATGCATCGATGCACT
490811 GCAGGGATGC
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
95 32 0.46
96 22 0.31
97 16 0.23
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (97 bp):
GGATGCATGGATGCATGACATGATGCATCGATGCATTAGTGAAGATGCATCGATGCATAGCAGAG
ATGCATCGATGCACTAATTGCATTCGATGTTT
Found at i:490757 original size:12 final size:13
Alignment explanation
Indices: 490734--490801 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
490724 GATGTTTGGA
490734 TGCATGGATGCAT
1 TGCATGGATGCAT
490747 TGCAT-GATGCAT
1 TGCATGGATGCAT
* *
490759 CGATGCAT-TAGTGCAGA
1 ---TGCATGGA-TGCA-T
490776 TGCATGGATGCAT
1 TGCATGGATGCAT
*
490789 TGCAGGGATGCAT
1 TGCATGGATGCAT
490802 GGATGCACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 7 0.16
13 17 0.39
14 9 0.20
15 7 0.16
16 4 0.09
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (13 bp):
TGCATGGATGCAT
Found at i:490800 original size:21 final size:21
Alignment explanation
Indices: 490731--490850 Score: 156
Period size: 21 Copynumber: 5.7 Consensus size: 21
490721 TTCGATGTTT
490731 GGATGCATGGATGCATTGCA-
1 GGATGCATGGATGCATTGCAG
* *
490751 TGATGCATCGATGCATT--AG
1 GGATGCATGGATGCATTGCAG
490770 TGCAGATGCATGGATGCATTGCAG
1 -G--GATGCATGGATGCATTGCAG
*
490794 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCATTGCAG
*
490815 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCATTGCAG
490836 GGATGCATGGATGCA
1 GGATGCATGGATGCA
490851 CTTTGACACC
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.01
20 15 0.17
21 55 0.62
22 15 0.17
23 1 0.01
24 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAG
Found at i:490979 original size:30 final size:30
Alignment explanation
Indices: 490932--490991 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
490922 AAACTTTGAA
490932 TAAATTAAATTAAGTCCAAAAA-CATTTTG
1 TAAATTAAATTAAGTCCAAAAACCATTTTG
*
490961 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTAAATT-AAGTCCAAAAACCATTTTG
490992 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTAAATTAAGTCCAAAAACCATTTTG
Found at i:492272 original size:93 final size:93
Alignment explanation
Indices: 492113--492298 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
492103 CGAGAGCCAT
492113 CACCTGATCGAGCTGATTATACACCTCCACACCGAGAGCCATCACCTATTCCATCACATCATCGA
1 CACCTGATCGAGCTGATTATACACCTCCACACCGAGAGCCATCACCTATTCCATCACATCATCGA
492178 GCCTCTTCTCCACCATCACCTCATGATA
66 GCCTCTTCTCCACCATCACCTCATGATA
*
492206 CACCTGATCGAGCTGATTATACACCTCCACACCGAGAGCCATCACCTATTTCATCACATCATCGA
1 CACCTGATCGAGCTGATTATACACCTCCACACCGAGAGCCATCACCTATTCCATCACATCATCGA
492271 GCCTCTTCTCCACCATCACCTCATGATA
66 GCCTCTTCTCCACCATCACCTCATGATA
492299 GGCGACCGAC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.27, C:0.38, G:0.11, T:0.24
Consensus pattern (93 bp):
CACCTGATCGAGCTGATTATACACCTCCACACCGAGAGCCATCACCTATTCCATCACATCATCGA
GCCTCTTCTCCACCATCACCTCATGATA
Found at i:492413 original size:42 final size:41
Alignment explanation
Indices: 492367--492466 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
492357 GTTAGGGGAG
*
492367 TTACGTGATGAGGTCAGTGCTTTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGGT-AGTGCTTGGCGTGATGAGGTACGGT-CT
* ** *
492409 TTACGTGACGACAATGGTGCTTGGCGTGATGAGGTACGGTCT
1 TTACGTGATGA-GGTAGTGCTTGGCGTGATGAGGTACGGTCT
*
492451 TTACGTGGTGAGGTAG
1 TTACGTGATGAGGTAG
492467 ATGTTTTACG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 2 0.04
42 39 0.85
43 5 0.11
ACGTcount: A:0.18, C:0.14, G:0.37, T:0.31
Consensus pattern (41 bp):
TTACGTGATGAGGTAGTGCTTGGCGTGATGAGGTACGGTCT
Found at i:492457 original size:21 final size:22
Alignment explanation
Indices: 492367--492528 Score: 97
Period size: 21 Copynumber: 7.7 Consensus size: 22
492357 GTTAGGGGAG
*
492367 TTACGTGATGAGGT-CAGTGCT
1 TTACGTGATGAGGTACGGTGCT
* *
492388 TTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGGTACGGTGCT
* ** *
492409 TTACGTGACGA-CAATGGTGCT
1 TTACGTGATGAGGTACGGTGCT
**
492430 TGGCGTGATGAGGTACGGT-CT
1 TTACGTGATGAGGTACGGTGCT
* * *
492451 TTACGTGGTGAGGTA-GATGTT
1 TTACGTGATGAGGTACGGTGCT
* ** *
492472 TTACGCGATGA-CAATGGTGCT
1 TTACGTGATGAGGTACGGTGCT
* *
492493 TTACGTGGTGAGGTATC--TACT
1 TTACGTGATGAGGTA-CGGTGCT
492514 TTACGTGATGAGGTA
1 TTACGTGATGAGGTA
492529 GCCGCTCTAC
Statistics
Matches: 102, Mismatches: 33, Indels: 12
0.69 0.22 0.08
Matches are distributed among these distances:
20 3 0.03
21 94 0.92
22 5 0.05
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.33
Consensus pattern (22 bp):
TTACGTGATGAGGTACGGTGCT
Found at i:492475 original size:63 final size:63
Alignment explanation
Indices: 492408--492529 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
492398 AGGTCGGTAC
* * *
492408 TTTACGTGACGACAATGGTGCTTGGCGTGATGAGGTA-CGGT-CTTTACGTGGTGAGGTAGATGT
1 TTTACGCGACGACAATGGTGCTTGACGTGATGAGGTATC--TACTTTACGTGATGAGGTAGATGT
* * *
492471 TTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAG
1 TTTACGCGACGACAATGGTGCTTGACGTGATGAGGTATCTACTTTACGTGATGAGGTAG
492530 CCGCTCTACG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 1 0.02
63 49 0.96
64 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.33
Consensus pattern (63 bp):
TTTACGCGACGACAATGGTGCTTGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGATGT
Found at i:492852 original size:21 final size:21
Alignment explanation
Indices: 492826--492896 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
492816 CCTGTCATCA
492826 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
* ** *
492847 TTCAAGAGGCCCATGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
* *
492868 TTCAAGAGGTCTCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
492889 TTCAAGAG
1 TTCAAGAG
492897 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:497000 original size:24 final size:24
Alignment explanation
Indices: 496963--497016 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
496953 CTGGAACATC
* *
496963 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATAGACCAAG
*
496987 ATCAAAGTCCGAGTATAGACCAAG
1 ATCAAAATCCGAGTATAGACCAAG
497011 ATCAAA
1 ATCAAA
497017 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATAGACCAAG
Found at i:497794 original size:14 final size:15
Alignment explanation
Indices: 497758--497795 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
497748 GAAATCATTG
497758 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
497773 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
497788 AAAAATTA
1 AAAAATTA
497796 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:497833 original size:22 final size:22
Alignment explanation
Indices: 497808--497856 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
497798 GATGGGGAAA
497808 GATGTCGTTGGATATAGGAACG
1 GATGTCGTTGGATATAGGAACG
497830 GATGTCGTTGGATATAGGAACG
1 GATGTCGTTGGATATAGGAACG
497852 GATGT
1 GATGT
497857 TGCCAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.29
Consensus pattern (22 bp):
GATGTCGTTGGATATAGGAACG
Found at i:497924 original size:27 final size:27
Alignment explanation
Indices: 497886--497947 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
497876 TGGAGATGGA
497886 ATGAGTTGCAATTTAGGGATTTAGGTT
1 ATGAGTTGCAATTTAGGGATTTAGGTT
497913 ATGAGTTGCAATTTAGGGATTTAGGTT
1 ATGAGTTGCAATTTAGGGATTTAGGTT
497940 ATGAGTTG
1 ATGAGTTG
497948 ATGCAGCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.40
Consensus pattern (27 bp):
ATGAGTTGCAATTTAGGGATTTAGGTT
Found at i:498028 original size:20 final size:21
Alignment explanation
Indices: 498000--498089 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 21
497990 AAATAAAACC
498000 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAAATTCAAAATTCG
*
498020 TGTTACG-AATTCGAAAA-TCG
1 TGTTGCGAAATTC-AAAATTCG
* *
498040 AGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATTCAAAATTCG
* * **
498060 AGTTACG-AATTTGAAATTCAG
1 TGTTGCGAAATTCAAAATTC-G
498081 TGTTGCGAA
1 TGTTGCGAA
498090 TTTGGAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 8 0.14
20 37 0.66
21 10 0.18
22 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTTGCGAAATTCAAAATTCG
Found at i:498065 original size:40 final size:40
Alignment explanation
Indices: 498001--498091 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
497991 AATAAAACCT
* *
498001 GTTGCGAAATTAAAATTCGTGTTACGAATTCGAAAATC-GA
1 GTTGCG-AATTAAAAATCGAGTTACGAATTCGAAAATCAGA
* * *
498041 GTTGCGAATTCAAAAATCGAGTTACGAATTTGAAATTCAGT
1 GTTGCGAATT-AAAAATCGAGTTACGAATTCGAAAATCAGA
498082 GTTGCGAATT
1 GTTGCGAATT
498092 TGGAAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
39 4 0.09
40 29 0.66
41 11 0.25
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (40 bp):
GTTGCGAATTAAAAATCGAGTTACGAATTCGAAAATCAGA
Found at i:498107 original size:20 final size:20
Alignment explanation
Indices: 498034--498210 Score: 85
Period size: 20 Copynumber: 8.8 Consensus size: 20
498024 ACGAATTCGA
* ***
498034 AAATCGAGTTGCGAATTCAA
1 AAATCGCGTTGCGAATTTGG
* *
498054 AAATCGAGTTACGAATTT-G
1 AAATCGCGTTGCGAATTTGG
*
498073 AAATTCAGTGTTGCGAATTTGG
1 AAA-TC-GCGTTGCGAATTTGG
498095 AAATCGCGTTGCGAATTT-G
1 AAATCGCGTTGCGAATTTGG
** * **
498114 ACTTCTGTGTTGCG-ATTTAC
1 AAATC-GCGTTGCGAATTTGG
* *
498134 ATATTCGCGTTGCAAATTTGG
1 A-AATCGCGTTGCGAATTTGG
* *
498155 AAAAT-GTGTTGCGAAATTGG
1 -AAATCGCGTTGCGAATTTGG
** *
498175 AGTTCGCGTTGCGAA-TTCG
1 AAATCGCGTTGCGAATTTGG
* *
498194 AGACCGCGTTGCGAATT
1 AAATCGCGTTGCGAATT
498211 CGTTGGTCAT
Statistics
Matches: 122, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
19 29 0.24
20 66 0.54
21 22 0.18
22 5 0.04
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
AAATCGCGTTGCGAATTTGG
Found at i:503299 original size:27 final size:29
Alignment explanation
Indices: 503246--503299 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
503236 GAGCGGCAAT
* *
503246 ACTTACATCTTACATCAATGCATCACAAA
1 ACTTACATCTGACAGCAATGCATCACAAA
503275 ACTTACAT-TGACAGCAA-GCATCACA
1 ACTTACATCTGACAGCAATGCATCACA
503300 TTATCATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 7 0.30
29 8 0.35
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (29 bp):
ACTTACATCTGACAGCAATGCATCACAAA
Found at i:503356 original size:2 final size:2
Alignment explanation
Indices: 503339--503439 Score: 186
Period size: 2 Copynumber: 51.0 Consensus size: 2
503329 CTTTATTCTC
*
503339 TA TA -A TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503422 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
503440 GTCAAGATTA
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 95 0.99
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:505079 original size:12 final size:12
Alignment explanation
Indices: 505041--505113 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
505031 GGAAAAAATG
*
505041 AAAA-AAATGAA
1 AAAATAAATAAA
* *
505052 AAAATGAAGAATA
1 AAAATAAATAA-A
*
505065 AAAATAAGTAAA
1 AAAATAAATAAA
505077 AAAATAAA-AGAA
1 AAAATAAATA-AA
505089 AAAATAAATAAA
1 AAAATAAATAAA
*
505101 TAAATAAATAAA
1 AAAATAAATAAA
505113 A
1 A
505114 TATTAAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
11 5 0.10
12 34 0.69
13 10 0.20
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:505099 original size:4 final size:4
Alignment explanation
Indices: 505066--505112 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
505056 TGAAGAATAA
* * *
505066 AAAT AAGT AAAA AAAT AAA- AGAAA AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAA
505113 ATATTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 1 0.03
4 34 0.94
5 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:505153 original size:31 final size:31
Alignment explanation
Indices: 505052--505154 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 31
505042 AAAAAATGAA
* * * *
505052 AAAAT-GAAGAATAAAAATAAGTAAAAAAAT
1 AAAATAGAAAAATATAAATAAATAAATAAAT
505082 -AAA-AGAAAAA-ATAAATAAATAAATAAAT
1 AAAATAGAAAAATATAAATAAATAAATAAAT
** * * * *
505110 AAAATATTAAAATATATATATATAAATGAGT
1 AAAATAGAAAAATATAAATAAATAAATAAAT
505141 AAAATAGAAAAATA
1 AAAATAGAAAAATA
505155 ATAATCATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
28 15 0.26
29 11 0.19
30 5 0.09
31 26 0.46
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (31 bp):
AAAATAGAAAAATATAAATAAATAAATAAAT
Found at i:505252 original size:29 final size:30
Alignment explanation
Indices: 505185--505252 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
505175 AGTAATATGA
*
505185 AAATAT-AATATAATATAAATAAAAAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
* * *
505214 AAA-ACCAAAAATAA-ATAAATATATAAACC
1 AAATA-TAAAAATAATATAAATAAAAAAACC
505243 AAATATAAAA
1 AAATATAAAA
505253 GTATACATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 23 0.74
30 7 0.23
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATATAAAAATAATATAAATAAAAAAACC
Found at i:505418 original size:19 final size:20
Alignment explanation
Indices: 505395--505443 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
505385 GTAAAATATT
*
505395 TTAAAAAAAGTATATATA-TA
1 TTAAAAAAA-TAAATATAGTA
505415 -TAAAAATAATAAATATAGTA
1 TTAAAAA-AATAAATATAGTA
505435 TTAAAAAAA
1 TTAAAAAAA
505444 ACCAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 13 0.52
20 6 0.24
21 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TTAAAAAAATAAATATAGTA
Found at i:506018 original size:37 final size:36
Alignment explanation
Indices: 505972--506073 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
505962 CTTGTGGATC
*
505972 CTATCTTTAGGAGTTTAAATCATAGTAGAACTCTA-T
1 CTATTTTTAGGAGTTTAAATC-TAGTAGAACTCTATT
* * * *
506008 CATATTTTTAGGAGTTTGAATCCTAGCAAAATTCTATT
1 C-TATTTTTAGGAGTTTAAAT-CTAGTAGAACTCTATT
* *
506046 CTATTTTTAGAAATTTAAATTCTAGTAG
1 CTATTTTTAGGAGTTTAAA-TCTAGTAG
506074 GACGAAAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
36 1 0.02
37 47 0.90
38 4 0.08
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (36 bp):
CTATTTTTAGGAGTTTAAATCTAGTAGAACTCTATT
Found at i:508566 original size:70 final size:70
Alignment explanation
Indices: 508453--508587 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
508443 ATATTTTCAG
* *
508453 TCTGAATTTGCATGTCTCGAAAAAGTCTAAGAGAATGAATAGATAAAGTTGGAGAGAAAAACACT
1 TCTGAATTTGCATATCTCGAAAAAGTATAAGAGAATGAATAGATAAAGTTGGAGAGAAAAACACT
508518 ATCTT
66 ATCTT
* * *
508523 TCTGAATTTGCATATCTCGAAAAAGTATGAGAGAATGAATAGATAAAGTTGGATAGAGAAACACT
1 TCTGAATTTGCATATCTCGAAAAAGTATAAGAGAATGAATAGATAAAGTTGGAGAGAAAAACACT
508588 CATCCAACAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (70 bp):
TCTGAATTTGCATATCTCGAAAAAGTATAAGAGAATGAATAGATAAAGTTGGAGAGAAAAACACT
ATCTT
Found at i:508638 original size:57 final size:57
Alignment explanation
Indices: 508550--508658 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
508540 CGAAAAAGTA
*
508550 TGAGAGAATGAATAGATAAAGTTGGATAGAGAAACACTCATCCAACACACAACGATC
1 TGAGAGAATGAATAGATAAAGTTGGAGAGAGAAACACTCATCCAACACACAACGATC
*
508607 TGAGAGAATGAATAGATAAAGTTGGAGAGAGAAACACTCTTCCAACACACAA
1 TGAGAGAATGAATAGATAAAGTTGGAGAGAGAAACACTCATCCAACACACAA
508659 ATTTCCAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (57 bp):
TGAGAGAATGAATAGATAAAGTTGGAGAGAGAAACACTCATCCAACACACAACGATC
Found at i:508735 original size:72 final size:72
Alignment explanation
Indices: 508590--508728 Score: 228
Period size: 72 Copynumber: 2.0 Consensus size: 72
508580 GAAACACTCA
** * *
508590 TCCAACACACAACGATCTGAGAGAATGAATAGATAAAGTTGGAGAGAGAAACACTCTTCCAACAC
1 TCCAACACACAACGATCTGAGAGAATGAATAGATAAAGTTAAAGAGAGAAACACTCATCAAACAC
508655 ACAAATT
66 ACAAATT
508662 TCCAACACACAACGATCTGAGAGAATGAATAGATAAA-TTAAAGAGAGAAA-ACTCATCAAACAC
1 TCCAACACACAACGATCTGAGAGAATGAATAGATAAAGTTAAAGAGAGAAACACTCATCAAACAC
508725 ACAA
66 ACAA
508729 CGATTTCATT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 15 0.24
71 11 0.17
72 37 0.59
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (72 bp):
TCCAACACACAACGATCTGAGAGAATGAATAGATAAAGTTAAAGAGAGAAACACTCATCAAACAC
ACAAATT
Found at i:516119 original size:3 final size:3
Alignment explanation
Indices: 516111--516161 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
516101 CCATTTTAAA
*
516111 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
516158 ATT A
1 ATT A
516162 AATTATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:526428 original size:22 final size:22
Alignment explanation
Indices: 526350--526428 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
526340 ACATCTACAT
* * *
526350 TCTTCAAAGATAATAGATT-TAT
1 TCTTCAAAGATGATAAATTCT-C
*
526372 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
526394 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
* *
526416 TTTTCAAAAATGA
1 TCTTCAAAGATGA
526429 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 50 0.98
23 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:527145 original size:42 final size:42
Alignment explanation
Indices: 527086--527610 Score: 689
Period size: 42 Copynumber: 12.3 Consensus size: 42
527076 CTATTTCCCA
* * *
527086 CATCTGTAAGACCTCCAGTGCAAGAT-TTGAAATCATTCAGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTT-AAATCCTTCGGGT
*
527128 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
*
527170 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
* * * *
527212 CATCCATAAGACCTCCAGTGTAGGATGTTTAAAATCCTTTGGGT
1 CATCTATAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGT
*
527256 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCC-TCTGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTC-GGGT
* *
527298 CATCAATAAGACCTCTAGTGCAAGATGTTAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
*
527340 CATCTATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGT
*
527384 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
* *
527426 CATCCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGT
*
527470 CATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
* * * * *
527512 CATCCATAAGA-CTCCAATGCATGATATTTAAAATCCTCCGGGT
1 CATCTATAAGACCTCCAGTGCAAGAT-GTT-AAATCCTTCGGGT
* * * *
527555 CATCTGTAAGACCTCTAGTGTAAGATGTTAAATCCTTCGGGC
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
527597 CATCCT-TAAGACCT
1 CAT-CTATAAGACCT
527611 TCAATGCAGA
Statistics
Matches: 427, Mismatches: 43, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
41 13 0.03
42 254 0.59
43 41 0.10
44 119 0.28
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (42 bp):
CATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGT
Found at i:527279 original size:86 final size:85
Alignment explanation
Indices: 527086--527610 Score: 718
Period size: 86 Copynumber: 6.2 Consensus size: 85
527076 CTATTTCCCA
* * * * *
527086 CATCTGTAAGACCTCCAGTGCAAGAT-TTGAAATCATTCAGGTCATCTGTAAGACCTCCAGTGCA
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGCA
527150 AGATGTTAAATCCTTCGGGT
66 AGATGTTAAATCCTTCGGGT
** *
527170 CATCTATAAGACCTCCAGTGCAAGATGTT-AAATCCTCCGGGTCATCCATAAGACCTCCAGTGTA
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGCA
* *
527234 GGATGTTTAAAATCCTTTGGGT
66 AGATG-TT-AAATCCTTCGGGT
* * ** *
527256 CATCTGTAAGACCTCCAGTGCAAGATGTT-AAATCCTCTGGGTCATCAATAAGACCTCTAGTGCA
1 CATCTATAAGACCTCCAGTGCAAGATGTTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGCA
527320 AGATGTTAAATCCTTCGGGT
66 AGATGTTAAATCCTTCGGGT
* *
527340 CATCTATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGC
1 CATCTATAAGACCTCCAGTGCAAGATG-TTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGC
527405 AAGATGTTAAATCCTTCGGGT
65 AAGATGTTAAATCCTTCGGGT
* * *
527426 CATCCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGC
1 CATCTATAAGACCTCCAGTGCAAGATG-TTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGC
527491 AAGATGTTAAATCCTTCGGGT
65 AAGATGTTAAATCCTTCGGGT
* * * * * *
527512 CATCCATAAGA-CTCCAATGCATGATATTTAAAATCCTCCGGGTCATCTGTAAGACCTCTAGTGT
1 CATCTATAAGACCTCCAGTGCAAGAT-GTTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGC
*
527576 AAGATGTTAAATCCTTCGGGC
65 AAGATGTTAAATCCTTCGGGT
527597 CATCCT-TAAGACCT
1 CAT-CTATAAGACCT
527611 TCAATGCAGA
Statistics
Matches: 401, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
84 95 0.24
85 82 0.20
86 224 0.56
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (85 bp):
CATCTATAAGACCTCCAGTGCAAGATGTTAAAATCCTCCGGGTCATCTGTAAGACCTCCAGTGCA
AGATGTTAAATCCTTCGGGT
Found at i:527343 original size:128 final size:128
Alignment explanation
Indices: 527092--527619 Score: 717
Period size: 128 Copynumber: 4.1 Consensus size: 128
527082 CCCACATCTG
* * * *
527092 TAAGACCTCCAGTGCAAGA--TTTGAAATCATTCAGGTCATCTGTAAGACCTCCAGTGCAAGATG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
*
527155 TTAAATCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTCCGGGTCATCCA
66 TTAAATCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
* *
527218 TAAGACCTCCAGTGTAGGATGTTTAAAATCCTTTGGGTCATCTGTAAGACCTCCAGTGCAAGATG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
* * *
527283 TTAAATCC-TCTGGGTCATCAATAAGACCTCTAGTGCAAGATGTTAAATCCTTCGGGTCATCTA
66 TTAAATCCTTC-GGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
527346 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
* * **
527411 TTAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTG
66 TTAAATCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATCCA
* ** * *
527476 TAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATCCATAAGA-CTCCAATGCATGATA
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGAT-
* * * * * * *
527538 TTTAAAATCCTCCGGGTCATCTGTAAGACCTCTAGTGTAAGATGTTAAATCCTTCGGGCCATCCT
65 GTT-AAATCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
* *
527603 TAAGACCTTCAATGCAG
1 TAAGACCTCCAGTGCAG
527620 AATATTTTCA
Statistics
Matches: 360, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
126 17 0.05
127 44 0.12
128 221 0.61
129 40 0.11
130 38 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (128 bp):
TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
TTAAATCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
Found at i:527941 original size:3 final size:3
Alignment explanation
Indices: 527933--527992 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
527923 CCATTTTAAA
* * *
527933 ATT ATT ATT ATT ATC ATT ATT ACT ATT ACT ATT ATT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
527980 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
527993 AATTATAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:530947 original size:16 final size:15
Alignment explanation
Indices: 530921--530958 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
530911 TTATAAGAGA
530921 AATGATATGAATACAT
1 AATGATATGAA-ACAT
530937 GAATG-TATGAAACAT
1 -AATGATATGAAACAT
530952 AATGATA
1 AATGATA
530959 ATGCCCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 6 0.30
17 4 0.20
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (15 bp):
AATGATATGAAACAT
Found at i:534559 original size:25 final size:25
Alignment explanation
Indices: 534511--534560 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
534501 GATTAAAGAT
* *
534511 AAGAGGTTTATAAGTGAAATTTTGA
1 AAGAGGGTTATAAGTGAAAATTTGA
534536 AAGAGGGTTAGTAAGT-AAAATTTGA
1 AAGAGGGTTA-TAAGTGAAAATTTGA
534561 TACTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (25 bp):
AAGAGGGTTATAAGTGAAAATTTGA
Found at i:535381 original size:19 final size:18
Alignment explanation
Indices: 535359--535403 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
535349 AGATAAGTGA
*
535359 TATAAATTATATGTTATGG
1 TATAAATTATATGATAT-G
**
535378 TATAGGTTATATGATATG
1 TATAAATTATATGATATG
535396 TATAAATT
1 TATAAATT
535404 CAGGATAGTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (18 bp):
TATAAATTATATGATATG
Found at i:536507 original size:73 final size:72
Alignment explanation
Indices: 536422--536566 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 72
536412 ATACCTAAGT
* *
536422 CATAGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAAGCAGAATGCCAAACGGGTACT
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAA-CAGAATGCCAAACGGGTACC
536487 GATACCCC
65 GATACCCC
* * * *
536495 CATAGGTACCGATACCCTTGTGTTAATTTTGGCTTCGAGAAAAACAGAATGCCCAATGGGTACCG
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTACCG
536560 ATACCCC
66 ATACCCC
536567 TTAGAGGTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 25 0.38
73 41 0.62
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (72 bp):
CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTACCG
ATACCCC
Found at i:536575 original size:73 final size:73
Alignment explanation
Indices: 536425--536587 Score: 220
Period size: 73 Copynumber: 2.2 Consensus size: 73
536415 CCTAAGTCAT
* *
536425 AGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAAGCAGAATGCCAAACGGGTACTGAT
1 AGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAAGCAGAATGCCAAACGGGTACCGAT
*
536490 ACCCCCAT
66 ACCCCCAG
* * * *
536498 AGGTACCGATACCCTTGTGTTAATTTTGGCTTCGAGAAAAA-CAGAATGCCCAATGGGTACCGAT
1 AGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAAGCAGAATGCCAAACGGGTACCGAT
*
536562 ACCCCTTAG
66 ACCCC-CAG
* *
536571 AGGTACTGATATCCTTA
1 AGGTACCGATACCCTTA
536588 GTCTTTTAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 25 0.32
73 53 0.68
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (73 bp):
AGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAAGCAGAATGCCAAACGGGTACCGAT
ACCCCCAG
Found at i:538991 original size:19 final size:18
Alignment explanation
Indices: 538969--539012 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
538959 CCATCAGAAA
538969 ATTT-CCACAACATCTATTC
1 ATTTGCCACAACAT-T-TTC
538988 ATTTTGCCACAACATTTTC
1 A-TTTGCCACAACATTTTC
539007 ATTTGC
1 ATTTGC
539013 AAATAACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 4 0.17
21 9 0.39
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTTGCCACAACATTTTC
Found at i:543926 original size:3 final size:3
Alignment explanation
Indices: 543898--543985 Score: 85
Period size: 3 Copynumber: 30.0 Consensus size: 3
543888 CATTTGTTTT
* * * * *
543898 TTA TTT TTA ATA TTA TTT TTA ATA TTA TTA TTA TTA TT- TTA -TA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
543944 TTTA TTTA TT- TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA
1 -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
543986 CAAACAGGCC
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
2 8 0.11
3 57 0.80
4 6 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:543966 original size:14 final size:14
Alignment explanation
Indices: 543908--543981 Score: 85
Period size: 14 Copynumber: 4.9 Consensus size: 14
543898 TTATTTTTAA
* *
543908 TATTATTTTTAATAT
1 TATTATTATT-ATTT
543923 TATTATTATTATTT
1 TATTATTATTATTT
543937 TATACTATTTATTTATTT
1 TAT--TA-TTA-TTATTT
543955 TATTATTATTATTT
1 TATTATTATTATTT
543969 TATTATTATTATT
1 TATTATTATTATT
543982 ATTACAAACA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
14 25 0.47
15 12 0.23
16 4 0.08
17 3 0.06
18 9 0.17
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:543984 original size:35 final size:35
Alignment explanation
Indices: 543898--543984 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 35
543888 CATTTGTTTT
*
543898 TTATTTT-TAATATTATT-TTTAATATTATTATTA
1 TTATTTTATACTATTATTATTTAATATTATTATTA
*
543931 TTATTTTATACTA-T-TTATTT-ATTTTATTATTA
1 TTATTTTATACTATTATTATTTAATATTATTATTA
*
543963 TTATTTTATTATTATTATTATT
1 TTATTTTA-TACTATTATTATT
543985 ACAAACAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
32 21 0.46
33 15 0.33
34 5 0.11
35 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (35 bp):
TTATTTTATACTATTATTATTTAATATTATTATTA
Found at i:545042 original size:2 final size:2
Alignment explanation
Indices: 545035--545081 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
545025 TCCTTATCTG
545035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
545077 TA TA T
1 TA TA T
545082 TTAGGATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:545282 original size:39 final size:37
Alignment explanation
Indices: 545220--545295 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
545210 TTTAAATAAG
* *
545220 TTATAGTTTAATCCCTAATTTTAATTAATTATTTATTTT
1 TTATAGTTTAATCCCTAAGTTTAACT--TTATTTATTTT
*
545259 TTATATTTTAATACCCT-AGTTTAACTTTATTTATTTT
1 TTATAGTTTAAT-CCCTAAGTTTAACTTTATTTATTTT
545296 AGTCATTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 11 0.33
39 18 0.55
40 4 0.12
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (37 bp):
TTATAGTTTAATCCCTAAGTTTAACTTTATTTATTTT
Found at i:545339 original size:23 final size:22
Alignment explanation
Indices: 545308--545352 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
545298 TCATTGTTTA
545308 TTTATAT-TTTAATT-TTATATG
1 TTTATATATTTAATTATTAT-TG
545329 TTTATATATTTAATTATTATTG
1 TTTATATATTTAATTATTATTG
545351 TT
1 TT
545353 CTTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTATTATTG
Found at i:545735 original size:2 final size:2
Alignment explanation
Indices: 545730--545765 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
545720 TTTATAAAAA
545730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
545766 TTTCTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549589 original size:15 final size:15
Alignment explanation
Indices: 549569--549600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
549559 GATCAATACC
549569 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
549584 TTTTGCATACATTCA
1 TTTTGCATACATGCA
549599 TT
1 TT
549601 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:557365 original size:18 final size:18
Alignment explanation
Indices: 557342--557391 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
557332 TATCTTTTCA
557342 AAATTCAATTTATTTCCG
1 AAATTCAATTTATTTCCG
*
557360 AAATTCAATTTATTTCTG
1 AAATTCAATTTATTTCCG
557378 AAATTCAATTTATT
1 AAATTCAATTTATT
557392 CTTGCAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (18 bp):
AAATTCAATTTATTTCCG
Found at i:558028 original size:22 final size:22
Alignment explanation
Indices: 558000--558050 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
557990 TCTACATTCG
558000 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
* *
558022 TCAAAGATGATAGATTTTCTTT
1 TCAAAGATGATAGATTCTCTCT
558044 TCAAAGA
1 TCAAAGA
558051 AAAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:558443 original size:20 final size:20
Alignment explanation
Indices: 558381--558444 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
558371 TCCAGAGAAA
558381 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
558401 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
558420 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
558440 GTTCA
1 GTTCA
558445 ACCTTTGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:558510 original size:122 final size:122
Alignment explanation
Indices: 558360--558689 Score: 506
Period size: 122 Copynumber: 2.7 Consensus size: 122
558350 ATCACTCGAT
*
558360 GCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCA
1 GCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCA
* *
558425 TAATGAGAAGAACTTGTTCAACCTTTGCATGGCTCTATCACAGAAAGAGATATATCA
66 TAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCA
558482 GCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCA
1 GCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCA
* * *
558547 TAATGAGAATAACTTGTTCAACCTTTGCATGACTCTATCACATAATGAGATAGATCA
66 TAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCA
* * * * *
558604 GCATCAACATTTCTA-A-AAGTGTTCATAATGAGAATAACTCT-TCTGAAGAAGG-AGAAGAAAT
1 GCATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAAAACT-TATCTGAAG-AGGAAGAAGAAGT
558665 TCATAATGAGAAGAACTTGTTCAAC
63 TCATAATGAGAAGAACTTGTTCAAC
558690 ATTACCTTAA
Statistics
Matches: 193, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
120 2 0.01
121 58 0.30
122 133 0.69
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (122 bp):
GCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCA
Found at i:558681 original size:243 final size:235
Alignment explanation
Indices: 558249--558689 Score: 552
Period size: 243 Copynumber: 1.8 Consensus size: 235
558239 CATTCAATAG
* *
558249 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGGTAAAGTTCATAATGAGAAAAACTCATCTAAAGAAGGAAGAAGAAGTTCAT
* * * * * *
558314 AATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTCGATGCATCAACTTTTCCAGAGA
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAAATAATCAATAGATGCATCAACATTTCCAGAGA
*
558379 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
131 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
558444 AACCTTTGCATGGCTCTATCACAGAAAGAGATATATCAGC
196 AACCTTTGCATGGCTCTATCACAGAAAGAGATATATCAGC
* * *
558484 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAAAACTTATCTGAAG-AGGAAGAAGAAGTTCA
1 ATCAACATTTCCAG-GTAAAGTTCATAATGAGAAAAACTCATCTAAAGAAGGAAGAAGAAGTTCA
* * *
558547 TAATGAGAATAACTTGTTCAACCTTTGCATGACTCTATCACATAATGAGATAGATCAGCATCAAC
65 TAATGAGAAGAACTTGTTCAACCTTT---TG-CTCGA--A-ATAATCA-ATAGAT--GCATCAAC
* * *
558612 ATTTCTA-A-AAGTGTTCATAATGAGAATAACTCT-TCTGAAGAAGG-AGAAGAAATTCATAATG
120 ATTTCCAGAGAA-AGTTCATAATGAGAAGAACT-TATCTGAAG-AGGAAGAAGAAATTCATAATG
558673 AGAAGAACTTGTTCAAC
182 AGAAGAACTTGTTCAAC
558690 ATTACCTTAA
Statistics
Matches: 174, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
234 40 0.23
235 40 0.23
236 1 0.01
237 2 0.01
238 4 0.02
240 1 0.01
241 4 0.02
242 6 0.03
243 59 0.34
244 17 0.10
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (235 bp):
ATCAACATTTCCAGGTAAAGTTCATAATGAGAAAAACTCATCTAAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGAAATAATCAATAGATGCATCAACATTTCCAGAGA
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTGCATGGCTCTATCACAGAAAGAGATATATCAGC
Found at i:559057 original size:3 final size:3
Alignment explanation
Indices: 559051--559128 Score: 94
Period size: 3 Copynumber: 27.3 Consensus size: 3
559041 TTTTTTTTAA
* *
559051 TAT TAT TAT TAA TAT TAT TAT TAT T-T TA- TAC TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
559094 T-T TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
559129 CCAAACAGGC
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
2 10 0.15
3 53 0.80
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:559099 original size:14 final size:17
Alignment explanation
Indices: 559051--559128 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
559041 TTTTTTTTAA
559051 TATTATTATTAATATTAT
1 TATTATTATT-ATATTAT
*
559069 TATTATT-TTATACTAT
1 TATTATTATTATATTAT
*
559085 T-TTATTTATTTTATTAT
1 TATTA-TTATTATATTAT
559102 TATTA-TATTATTATTAT
1 TATTATTATTA-TATTAT
559119 TATTATTATT
1 TATTATTATT
559129 CCAAACAGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 3 0.06
16 13 0.25
17 21 0.41
18 14 0.27
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTATTATATTAT
Found at i:559890 original size:2 final size:2
Alignment explanation
Indices: 559883--559914 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
559873 TCCTTATCTG
559883 TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
559915 GGGCAGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:560563 original size:2 final size:2
Alignment explanation
Indices: 560551--560599 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
560541 AAAAATAAAA
560551 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
560592 -T A- AT AT AT
1 AT AT AT AT AT
560600 TTTCTTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:565996 original size:20 final size:22
Alignment explanation
Indices: 565944--565986 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
565934 AGTGTTGCAG
*
565944 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACTGATTCCCCCTTT-AAT
565967 GGGAACTGATTCCCCCTTTA
1 GGGAACTGATTCCCCCTTTA
565987 GGGAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (22 bp):
GGGAACTGATTCCCCCTTTAAT
Found at i:567959 original size:13 final size:13
Alignment explanation
Indices: 567941--567965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567931 ACCATGTCAC
567941 ATTGATTATGAAT
1 ATTGATTATGAAT
567954 ATTGATTATGAA
1 ATTGATTATGAA
567966 ACTAATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:570417 original size:17 final size:16
Alignment explanation
Indices: 570386--570419 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
570376 CACGTGAGGA
570386 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
570402 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
570419 T
1 T
570420 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:570819 original size:18 final size:19
Alignment explanation
Indices: 570798--570834 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
570788 TGCCAAAGCA
570798 TTTTA-TTTTGTTTTGTAT
1 TTTTATTTTTGTTTTGTAT
*
570816 TTTTATTTTTTTTTTGTAT
1 TTTTATTTTTGTTTTGTAT
570835 AGTTTACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTGTTTTGTAT
Found at i:576791 original size:19 final size:21
Alignment explanation
Indices: 576754--576796 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
576744 TAACTTTTTC
576754 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
576774 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
576794 TTT
1 TTT
576797 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:576802 original size:19 final size:20
Alignment explanation
Indices: 576753--576802 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
576743 TTAACTTTTT
*
576753 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
576773 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
576792 CTTTTACCTTT
1 CTTTTACCTTT
576803 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:580615 original size:17 final size:16
Alignment explanation
Indices: 580584--580617 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
580574 CACGTGAGGA
580584 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
580600 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
580617 T
1 T
580618 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:584399 original size:13 final size:13
Alignment explanation
Indices: 584368--584401 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
584358 AGGGGGAGTA
584368 ATTTTCAAAAAATG
1 ATTTTC-AAAAATG
584382 A-TTTCAAAAATG
1 ATTTTCAAAAATG
584394 ATTTTCAA
1 ATTTTCAA
584402 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 10 0.53
14 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:584771 original size:73 final size:72
Alignment explanation
Indices: 584685--584850 Score: 190
Period size: 73 Copynumber: 2.3 Consensus size: 72
584675 ATACCTAAGT
* *
584685 CATAGGTACCGATACCCTTATGTTGATTTT-GTCTCCAAGAAAAACAGAATGCCAAACGGGTACC
1 CATAGGTA-CGATACCCTTATGTTAATTTTGGT-TCCAAGAAAAACAGAATACCAAACGGGTACC
584749 GATACCCCC
64 GATACCCCC
* *** * * *
584758 CATAGGTATCGATACCCTTGTGTTAATTTTGGTTGTGAGAAAAATAGAATACCCAATGGGTACCG
1 CATAGGTA-CGATACCCTTATGTTAATTTTGGTTCCAAGAAAAACAGAATACCAAACGGGTACCG
584823 ATACCCCC
65 ATACCCCC
* *
584831 TAGAGGTACTGATACCCTTA
1 CATAGGTAC-GATACCCTTA
584851 GTTTTAACGG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
72 1 0.01
73 75 0.96
74 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (72 bp):
CATAGGTACGATACCCTTATGTTAATTTTGGTTCCAAGAAAAACAGAATACCAAACGGGTACCGA
TACCCCC
Found at i:590584 original size:24 final size:24
Alignment explanation
Indices: 590552--590606 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
590542 AGAGACTCCT
590552 AAGACTTATCATTTCTTATCATAA
1 AAGACTTATCATTTCTTATCATAA
590576 AAGACTTATCATTTCTTATCATAA
1 AAGACTTATCATTTCTTATCATAA
590600 AAGACTT
1 AAGACTT
590607 CTAAACAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (24 bp):
AAGACTTATCATTTCTTATCATAA
Found at i:596781 original size:11 final size:11
Alignment explanation
Indices: 596765--596795 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
596755 CAGCCTCGCA
596765 TAATCCCCTAT
1 TAATCCCCTAT
596776 TAATCCCCTAT
1 TAATCCCCTAT
596787 TAATCCCCT
1 TAATCCCCT
596796 GATCTGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATCCCCTAT
Found at i:600571 original size:99 final size:99
Alignment explanation
Indices: 600400--600597 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
600390 TTGCTGGTAG
600400 GGATCACTTACTAAGTTGCGAATCACACTATTATTTTTTGTGGTTGATATTGTTGAATGGTGCTT
1 GGATCACTTACTAAGTTGCGAATCACACTATTATTTTTTGTGGTTGATATTGTTGAATGGTGCTT
600465 TTCTACATCTAGCTTTGCTGAAGCAACAAGGAGT
66 TTCTACATCTAGCTTTGCTGAAGCAACAAGGAGT
600499 GGATCACTTACTAAGTTGCGAATCACACTATTATTTTTTGTGGTTGATATTGTTGAATGGTGCTT
1 GGATCACTTACTAAGTTGCGAATCACACTATTATTTTTTGTGGTTGATATTGTTGAATGGTGCTT
600564 TTCTACATCTAGCTTTGCTGAAGCAACAAGGAGT
66 TTCTACATCTAGCTTTGCTGAAGCAACAAGGAGT
600598 CGGTGTCGAG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (99 bp):
GGATCACTTACTAAGTTGCGAATCACACTATTATTTTTTGTGGTTGATATTGTTGAATGGTGCTT
TTCTACATCTAGCTTTGCTGAAGCAACAAGGAGT
Found at i:603073 original size:4 final size:4
Alignment explanation
Indices: 603064--603114 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
603054 TCTGAGATAG
* *
603064 TCTT TCTT TCTT TCTT TCTT TCTT TCTT ACTT TCTT TCTT TCTT TTTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
603112 TCT
1 TCT
603115 GGAAGTCGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:607801 original size:53 final size:53
Alignment explanation
Indices: 607721--607827 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
607711 TCTTATTCTA
607721 CGTTGATCTTACTTTTGATGATCTTTCCACTAGTAAATCCCTAACACTCAAGC
1 CGTTGATCTTACTTTTGATGATCTTTCCACTAGTAAATCCCTAACACTCAAGC
*
607774 CGTTGATCTTACTTTTGATGATCTTTCCACTAGTAAATTCCTAACACTCAAGC
1 CGTTGATCTTACTTTTGATGATCTTTCCACTAGTAAATCCCTAACACTCAAGC
607827 C
1 C
607828 AAAACATGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (53 bp):
CGTTGATCTTACTTTTGATGATCTTTCCACTAGTAAATCCCTAACACTCAAGC
Found at i:610851 original size:109 final size:115
Alignment explanation
Indices: 610736--610961 Score: 304
Period size: 109 Copynumber: 2.0 Consensus size: 115
610726 ACATATAAAA
* *
610736 ATATATAATAAAACATTAAAGCACAAAAAGTCTATTATACTTTAAACATATA-A-A-A-AGT-TA
1 ATATATAATAAAACATTAAAGCACAAAAAATCTATCATACTTTAAACATATATATATACA-TATA
* * *
610796 ACATGA-AAAACAAG-CAAAATATATCATATTATCCTTATAATATATACAT
65 AAAAGAGAAAACAAGCCAAAATATATCATATTATCCTTATAATACATACAT
* *
610845 ATATATAATAAAACATTGAAGCATAAAAAATCTATCATACTTTAAACATATATATATACATATAA
1 ATATATAATAAAACATTAAAGCACAAAAAATCTATCATACTTTAAACATATATATATACATATAA
* *
610910 AAAGATGAAAGCAAGCCAAAATATATCATATTCTCCTTATAATACATACAT
66 AAAGA-GAAAACAAGCCAAAATATATCATATTATCCTTATAATACATACAT
610961 A
1 A
610962 CATACATACA
Statistics
Matches: 100, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
109 48 0.48
110 1 0.01
111 1 0.01
112 2 0.02
113 7 0.07
115 7 0.07
116 34 0.34
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (115 bp):
ATATATAATAAAACATTAAAGCACAAAAAATCTATCATACTTTAAACATATATATATACATATAA
AAAGAGAAAACAAGCCAAAATATATCATATTATCCTTATAATACATACAT
Found at i:610960 original size:4 final size:4
Alignment explanation
Indices: 610951--611527 Score: 1140
Period size: 4 Copynumber: 144.8 Consensus size: 4
610941 TCTCCTTATA
610951 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
610999 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611047 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611094 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611142 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611190 ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611237 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611285 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611333 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611381 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611429 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611477 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
611525 ATA
1 ATA
611528 ATAAAACATT
Statistics
Matches: 571, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
3 6 0.01
4 565 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:613426 original size:12 final size:12
Alignment explanation
Indices: 613409--613482 Score: 78
Period size: 12 Copynumber: 6.2 Consensus size: 12
613399 CATTTTAGAA
613409 AAATTTAAATAT
1 AAATTTAAATAT
*
613421 AAATTTTAAT-T
1 AAATTTAAATAT
** *
613432 AAAAATAAATAC
1 AAATTTAAATAT
*
613444 AAATTCAAATAT
1 AAATTTAAATAT
*
613456 GAATTTTAAATAT
1 -AAATTTAAATAT
613469 AAATTTAAATAT
1 AAATTTAAATAT
613481 AA
1 AA
613483 GTACCACAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.17
12 30 0.62
13 10 0.21
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (12 bp):
AAATTTAAATAT
Found at i:627634 original size:30 final size:30
Alignment explanation
Indices: 627587--627663 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
627577 TGTTAAGAAT
627587 TAAGACTTAACTA-TTTTTT-TAGCTAAGA
1 TAAGACTTAACTATTTTTTTCTAGCTAAGA
*
627615 TAAGACTTAACTATTTTTTTCTGGCTAAGA
1 TAAGACTTAACTATTTTTTTCTAGCTAAGA
627645 TAAGACTTAACTATTTTTT
1 TAAGACTTAACTATTTTTT
627664 AATTACACTA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 13 0.28
29 6 0.13
30 27 0.59
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (30 bp):
TAAGACTTAACTATTTTTTTCTAGCTAAGA
Found at i:628230 original size:36 final size:36
Alignment explanation
Indices: 628183--628251 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
628173 ACAATGCAAG
* *
628183 AGCCGAGGGTGTGTACTGTAGAATTCAGCAGTCGAT
1 AGCCGAGGGTGTGTACTGTAGAATACAACAGTCGAT
628219 AGCCGAGGGTGTGTACTGTAGAATACAACAGTC
1 AGCCGAGGGTGTGTACTGTAGAATACAACAGTC
628252 AAGTAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (36 bp):
AGCCGAGGGTGTGTACTGTAGAATACAACAGTCGAT
Found at i:628996 original size:159 final size:160
Alignment explanation
Indices: 628803--629120 Score: 464
Period size: 164 Copynumber: 2.0 Consensus size: 160
628793 CAATCTATTT
* * * * *
628803 TCATTCATCAACGGTCCTAAATCTGTGTAAAACTAAAATAGTTTTACATTGTGTAACAGGATTC-
1 TCATTCATCAACAGTCCTAAATATGTGTAAAACTAAAAAAGTTTTACATTATATAACAGGA-TCA
* *
628867 TATCCC-ATATATATAT-TACACAGATTTAGGATCGTTGGATGAGTGAAAGTGGATGGATGAGAT
65 TATCCCAATATATATATATACACAGAGTTAGGATCGTTGGATGAGTGAAAGTGGATGGATAAGAT
* *
628930 TACAAGTATTA-AATGAGAAGATATTCAATGG
130 TACAAGTA-GAGAATGAAAAGATATTCAATGG
*
628961 TCATTCATCTAATAGTCCTAAATATGTGTAAAACTAAAAAAGTTTTACATTATATAACAGGATCA
1 TCATTCATC-AACAGTCCTAAATATGTGTAAAACTAAAAAAGTTTTACATTATATAACAGGATCA
629026 TATCCCATATATATATATACATACACAGAGTTAGGATCGTTGGATGAGTGAAAGTGGATGGATAA
65 TATCCCA-ATATATATAT--ATACACAGAGTTAGGATCGTTGGATGAGTGAAAGTGGATGGATAA
629091 GATTACAAGTAGAGAATGAAAAGATATTCA
127 GATTACAAGTAGAGAATGAAAAGATATTCA
629121 CTGGAAAAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
158 11 0.08
159 52 0.37
161 10 0.07
163 1 0.01
164 68 0.48
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (160 bp):
TCATTCATCAACAGTCCTAAATATGTGTAAAACTAAAAAAGTTTTACATTATATAACAGGATCAT
ATCCCAATATATATATATACACAGAGTTAGGATCGTTGGATGAGTGAAAGTGGATGGATAAGATT
ACAAGTAGAGAATGAAAAGATATTCAATGG
Found at i:629560 original size:60 final size:60
Alignment explanation
Indices: 629487--629606 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
629477 AATAAAAAAA
629487 AATATATGTTTAAAATAGACTGTATCCAGGCATTCCAGCCTTAAATCCCCACGTCCACGT
1 AATATATGTTTAAAATAGACTGTATCCAGGCATTCCAGCCTTAAATCCCCACGTCCACGT
*
629547 AATATATGTTTAAAATAGACTGTATCCAGGCATTCCAGCCTTAAATCCCTACGTCCACGT
1 AATATATGTTTAAAATAGACTGTATCCAGGCATTCCAGCCTTAAATCCCCACGTCCACGT
629607 CTGATAATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (60 bp):
AATATATGTTTAAAATAGACTGTATCCAGGCATTCCAGCCTTAAATCCCCACGTCCACGT
Found at i:630965 original size:25 final size:25
Alignment explanation
Indices: 630931--630992 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
630921 AAGTGGCAAA
630931 CGGGTCATTTCGATCGGGATCGGGT
1 CGGGTCATTTCGATCGGGATCGGGT
630956 CGGGTCATTTCGATCGGGATCGGGT
1 CGGGTCATTTCGATCGGGATCGGGT
*
630981 CGGGTTATTTCG
1 CGGGTCATTTCG
630993 GTTTGAGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.11, C:0.19, G:0.39, T:0.31
Consensus pattern (25 bp):
CGGGTCATTTCGATCGGGATCGGGT
Found at i:631152 original size:32 final size:31
Alignment explanation
Indices: 631095--631236 Score: 113
Period size: 32 Copynumber: 4.5 Consensus size: 31
631085 GATCAGGTTG
* * * * *
631095 GGTCAAAATCAAATCGATTGATTTTTGGGTC
1 GGTCAATATCAGATCGGTTGGTTTTCGGGTC
* * *
631126 GAGTCAATATCAGATTGGTTGGTTTTTGGGTT
1 G-GTCAATATCAGATCGGTTGGTTTTCGGGTC
* *
631158 GGATCAATACCAGATCGGTTGGTTTTCGAGTC
1 GG-TCAATATCAGATCGGTTGGTTTTCGGGTC
* * *
631190 TGGTCAATATCGGATCGGTCGATTTTCGGGTC
1 -GGTCAATATCAGATCGGTTGGTTTTCGGGTC
**
631222 ATATCAATATCAGAT
1 -GGTCAATATCAGAT
631237 TGGCCAATTT
Statistics
Matches: 88, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
31 2 0.02
32 84 0.95
33 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (31 bp):
GGTCAATATCAGATCGGTTGGTTTTCGGGTC
Found at i:633364 original size:24 final size:25
Alignment explanation
Indices: 633345--633412 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 25
633335 ATAAATTGCA
633345 CCGAAGTG-CCGCGTAGAAATTTGTC
1 CCGAAG-GACCGCGTAGAAATTTGTC
633370 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
* * *
633394 CCGAATGACCACATAGAAA
1 CCGAAGGACCGCGTAGAAA
633413 AATTCCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTGTC
Found at i:634665 original size:22 final size:23
Alignment explanation
Indices: 634629--634688 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
634619 ATATCCCATG
* *
634629 TTCATATAGCTCATATAA-CATT
1 TTCATATAACACATATAATCATT
* *
634651 TTCCTATAATACATA-AATCATT
1 TTCATATAACACATATAATCATT
634673 TTCATATAACACATAT
1 TTCATATAACACATAT
634689 CATAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (23 bp):
TTCATATAACACATATAATCATT
Found at i:635152 original size:21 final size:21
Alignment explanation
Indices: 635114--635172 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
635104 CGGTTGAGGG
635114 GGGTATCGATTCCCCCTTGAAT
1 GGGTATCGATT-CCCCTTGAAT
*
635136 GGGTACCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
635157 GGGTATCGATTCCCCT
1 GGGTATCGATTCCCCT
635173 AGCCCAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.31
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Done.