Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003053.1 Hibiscus syriacus cultivar Beakdansim tig00006365_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: 776842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:272955 original size:113 final size:113
Alignment explanation
Indices: 272757--273539 Score: 1155
Period size: 113 Copynumber: 7.0 Consensus size: 113
272747 GCAAAGATTT
* * * * *
272757 AAATCCATCATTTAATGGATCAACAGTGT-CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAA
1 AAATCCATCACTTGATGGATCAAC-TTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
272821 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
272870 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
272935 AAGGAAGAAGAAGTTCATAATGAGAAGATTTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
272983 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
273048 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
273096 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
273161 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
273209 AAATCCATCACTTGATGGATCAACTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
273274 AATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *** * *
273322 GAATTCATCATTTGATGGATTAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAATTCATCTGAAT
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
273387 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * **** *
273434 GAATTCATCACTTAATGGATCAACCTTTACAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
273499 AA-G-AG-A-AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
273540 AATGACTCTA
Statistics
Matches: 628, Mismatches: 40, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
108 26 0.04
109 7 0.01
110 2 0.00
111 1 0.00
112 67 0.11
113 525 0.84
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:278695 original size:29 final size:29
Alignment explanation
Indices: 278653--278711 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
278643 ATTTTCACCT
278653 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
278682 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
278711 A
1 A
278712 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:283379 original size:29 final size:29
Alignment explanation
Indices: 283337--283395 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
283327 ATTTTCACCT
283337 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
283366 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
283395 A
1 A
283396 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:293080 original size:18 final size:18
Alignment explanation
Indices: 293052--293094 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
293042 TCTTCTTATT
*
293052 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
*
293071 TTTATTTAATCGTTTTTA
1 TTTATTTAATCGCTTTTA
293089 -TTATTT
1 TTTATTT
293095 TAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:298384 original size:18 final size:18
Alignment explanation
Indices: 298338--298380 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
298328 TCTTCTTATT
*
298338 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
298357 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
298375 -TTATTT
1 TTTATTT
298381 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:298390 original size:18 final size:18
Alignment explanation
Indices: 298338--298391 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
298328 TCTTCTTATT
*
298338 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATAGCTTTTA
*
298357 TTTATTTAATCGCTTTTA
1 TTTATTTAATAGCTTTTA
*
298375 -TTATTTTAATATCTTTT
1 TTTA-TTTAATAGCTTTT
298392 TACCAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATTTAATAGCTTTTA
Found at i:300238 original size:20 final size:20
Alignment explanation
Indices: 300209--300256 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
300199 TTTCTGGAAG
*
300209 CCTTCTTCCTCTTGCTTTCT
1 CCTTCCTCCTCTTGCTTTCT
300229 CCTTCCTCCTCTTGCTTTCT
1 CCTTCCTCCTCTTGCTTTCT
300249 CCTTCCTC
1 CCTTCCTC
300257 TCGTAAGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50
Consensus pattern (20 bp):
CCTTCCTCCTCTTGCTTTCT
Found at i:301892 original size:31 final size:31
Alignment explanation
Indices: 301675--301877 Score: 334
Period size: 31 Copynumber: 6.5 Consensus size: 31
301665 AGGGTCGAGG
*
301675 GTTTACCTATGTTCTTCGGGGCATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
301706 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
301737 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
301768 GTTTACCTATGTTTTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
301799 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
301830 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
301861 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
301878 AAAATCTATG
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 160 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:302935 original size:54 final size:54
Alignment explanation
Indices: 302871--303030 Score: 221
Period size: 54 Copynumber: 3.0 Consensus size: 54
302861 TGTACTACAT
*
302871 GCACTATGTGTGCAACCCATAGAATTCATCATAAATTGATGAACAACCGTATAG
1 GCACTATGTGTGCAACCCATAGAATTCATCATGAATTGATGAACAACCGTATAG
* ** * * * *
302925 GCACTATGTGTGTAACCCGCAGAATTCATCATGAGTTGATGAACGACCGTACAT
1 GCACTATGTGTGCAACCCATAGAATTCATCATGAATTGATGAACAACCGTATAG
* * *
302979 GCACTATGTTTGCAACCCATGGAATTCATCATGAATTGATGAATAACCGTAT
1 GCACTATGTGTGCAACCCATAGAATTCATCATGAATTGATGAACAACCGTAT
303031 GAACGATCGT
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (54 bp):
GCACTATGTGTGCAACCCATAGAATTCATCATGAATTGATGAACAACCGTATAG
Found at i:317938 original size:24 final size:24
Alignment explanation
Indices: 317893--317938 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
317883 GTTTGAGATA
* * **
317893 CAACATCACCTCCATCTTCCATTT
1 CAACATCAACACCATCAACCATTT
317917 CAACATCAACACCATCAACCAT
1 CAACATCAACACCATCAACCAT
317939 CTTCCATCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (24 bp):
CAACATCAACACCATCAACCATTT
Found at i:321818 original size:2 final size:2
Alignment explanation
Indices: 321811--321860 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
321801 ATTAATATTA
* *
321811 AT AT AT AT AT AT AT GAG AT AT AT AT AT TT GAT 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
321855 AT AT AT
1 AT AT AT
321861 TAGTGTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321831 original size:15 final size:15
Alignment explanation
Indices: 321813--321854 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
321803 TAATATTAAT
321813 ATATATATATATGAG
1 ATATATATATATGAG
* *
321828 ATATATATATTTGAT
1 ATATATATATATGAG
321843 ATATATATATAT
1 ATATATATATAT
321855 ATATATTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
ATATATATATATGAG
Found at i:321833 original size:13 final size:12
Alignment explanation
Indices: 321815--321860 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
321805 ATATTAATAT
321815 ATATATATATGAG
1 ATATATATAT-AG
*
321828 ATATATATATTTG
1 ATATATATA-TAG
*
321841 ATATATATATAT
1 ATATATATATAG
321853 ATATATAT
1 ATATATAT
321861 TAGTGTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 9 0.31
13 19 0.66
14 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATATATATAG
Found at i:321880 original size:32 final size:36
Alignment explanation
Indices: 321807--321883 Score: 76
Period size: 34 Copynumber: 2.3 Consensus size: 36
321797 TATAATTAAT
*
321807 ATTA-ATATATAT-ATATATGAGATATATATATTTG
1 ATTATATATATATAATATATGAGATATATATATTTA
* *
321841 A-TATATATATATATATATATTAG-TGTA-AT-TTTA
1 ATTATATATATATA-ATATATGAGATATATATATTTA
321874 ATTATATATA
1 ATTATATATA
321884 AAAACGTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
33 6 0.17
34 19 0.53
35 3 0.08
36 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (36 bp):
ATTATATATATATAATATATGAGATATATATATTTA
Found at i:324146 original size:2 final size:2
Alignment explanation
Indices: 324139--324177 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
324129 ATTACACCCG
324139 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
324178 TAATATTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:326739 original size:11 final size:11
Alignment explanation
Indices: 326715--326759 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
326705 TTGGTGCTGG
326715 AAACAAGATAA
1 AAACAAGATAA
* *
326726 AAATAAGATTA
1 AAACAAGATAA
326737 AAACAAGATAA
1 AAACAAGATAA
326748 AGAA-AAGATAA
1 A-AACAAGATAA
326759 A
1 A
326760 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:326743 original size:22 final size:22
Alignment explanation
Indices: 326715--326756 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
326705 TTGGTGCTGG
326715 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
326737 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
326757 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:333518 original size:19 final size:18
Alignment explanation
Indices: 333494--333541 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 18
333484 TTTAAAAAAT
333494 AAATTA-TATAAATATTTAA
1 AAATTACTA-AAAT-TTTAA
333513 AAATTACTAAAATTTTAA
1 AAATTACTAAAATTTTAA
333531 ATTAATTACTA
1 A--AATTACTA
333542 TTTTTAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 10 0.38
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTACTAAAATTTTAA
Found at i:334697 original size:56 final size:56
Alignment explanation
Indices: 334625--334804 Score: 229
Period size: 56 Copynumber: 3.2 Consensus size: 56
334615 GTAGTGCTAA
*
334625 CCCGAGTATGACACATAAGGTCCTGCCCACCATATGCACTAATACTTTAGTACAAT
1 CCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTACAAT
* * *
334681 CCCGTGTATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTGCCAT
1 CCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTACAAT
** * *
334737 CCTAAGTATGACACATAAGGTTGTG-CCATCATATGCACTAGTTATACTTTAGTGA-AAT
1 CCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTA---ATACTTTAGT-ACAAT
*
334795 CCCGAATATG
1 CCCGAGTATG
334805 CAACATGCTG
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
55 14 0.13
56 73 0.69
58 19 0.18
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (56 bp):
CCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAATACTTTAGTACAAT
Found at i:339063 original size:29 final size:26
Alignment explanation
Indices: 339025--339079 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 26
339015 AGTTTTCTCT
339025 TTTTACTTTTCAAGTTCTTTTTATTTTTC
1 TTTTACTTTTCAAG--CTTTTT-TTTTTC
*
339054 TTTTATTTTTCAAGCTTTTTTTTTTC
1 TTTTACTTTTCAAGCTTTTTTTTTTC
339080 AAAATGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 6 0.24
29 13 0.52
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTACTTTTCAAGCTTTTTTTTTTC
Found at i:339642 original size:17 final size:17
Alignment explanation
Indices: 339613--339655 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
339603 ACTTTAATTG
339613 CTTTTACTTA-TTTAATCA
1 CTTTTA-TTATTTTAAT-A
339631 CTTTTATTATTTTAATA
1 CTTTTATTATTTTAATA
339648 -TTTTATTA
1 CTTTTATTA
339656 CCAAAATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 12 0.50
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTTATTATTTTAATA
Found at i:342522 original size:5 final size:6
Alignment explanation
Indices: 342506--342539 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
342496 TTTTCGTTAA
*
342506 ATTTTT ATTTTT ATTTTC ACTTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATT
342540 CGATCAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:346013 original size:17 final size:18
Alignment explanation
Indices: 345976--346015 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
345966 TTATTTTTAC
*
345976 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
345994 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
346011 TTTAA
1 TTTAA
346016 ATATTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:350131 original size:17 final size:17
Alignment explanation
Indices: 350109--350151 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
350099 AATTAAGAGT
350109 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
350126 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
350143 TAGTTTAAT
1 TAGTTTAAT
350152 TAATAAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:359085 original size:47 final size:45
Alignment explanation
Indices: 359014--359139 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
359004 TATAAAATCC
359014 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
359059 CTTACCATTTAAATTTCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
359106 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
359140 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:359339 original size:59 final size:59
Alignment explanation
Indices: 359247--359374 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
359237 CGTAGTGCTA
* * * **
359247 TCCCGAATATGATACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
359306 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
359365 TCCCGAATAT
1 TCCCGAATAT
359375 ACAGCCTGCT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:363336 original size:31 final size:29
Alignment explanation
Indices: 363270--363364 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
363260 AAGTGAAATA
* **
363270 TTTTTTTTTCATTTCTCATTTTTTCCCTTTC
1 TTTTCTTTTCATTT-TCATTTTTTTTC-TTC
363301 TTTTCTTTCTCATTTTCATTTTTTTTCTTC
1 TTTTCTTT-TCATTTTCATTTTTTTTCTTC
*
363331 GTTTTCATTTTCTTTTTCTATTTTTTTTCTTC
1 -TTTTC-TTTTCATTTTC-ATTTTTTTTCTTC
363363 TT
1 TT
363365 CTGTTTTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.05
31 31 0.55
32 22 0.39
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTTCTTTTCATTTTCATTTTTTTTCTTC
Found at i:363356 original size:15 final size:16
Alignment explanation
Indices: 363338--363381 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
363328 TTCGTTTTCA
*
363338 TTTTCTTTTTCTATTTT
1 TTTTCTTCTTCTA-TTT
*
363355 TTTTCTTCTTCT-GTT
1 TTTTCTTCTTCTATTT
363370 TTTTCTTCTTCT
1 TTTTCTTCTTCT
363382 TATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
17 11 0.44
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTCTTCTTCTATTT
Found at i:363358 original size:17 final size:17
Alignment explanation
Indices: 363338--363382 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
363328 TTCGTTTTCA
*
363338 TTTTCTTTTTCTATTTT
1 TTTTCTTCTTCTATTTT
*
363355 TTTTCTTCTTCTGTTTT
1 TTTTCTTCTTCTATTTT
363372 TTCTTCTTCTT
1 TT-TTCTTCTT
363383 ATAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTCTTCTTCTATTTT
Found at i:366262 original size:47 final size:45
Alignment explanation
Indices: 366191--366316 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
366181 TATAAAATCC
366191 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
366236 CTTACCATTTAAATTTCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
366283 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
366317 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:370471 original size:18 final size:17
Alignment explanation
Indices: 370450--370536 Score: 70
Period size: 17 Copynumber: 4.9 Consensus size: 17
370440 AGTGAAATAT
370450 TTTTTTTTTCATTTCTCA
1 TTTTTTTTTCATTT-TCA
**
370468 -TTTTTTTTCCCTTTC-
1 TTTTTTTTTCATTTTCA
*
370483 TTTTCTTTCTCATTTTCA
1 TTTT-TTTTTCATTTTCA
*
370501 TTTTTTTTCTTCGTTTTCA
1 -TTTTTTT-TTCATTTTCA
370520 TTTTCTTTTTCTATTTT
1 TTTT-TTTTTC-ATTTT
370537 TTTTCTTCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.09
17 20 0.37
18 10 0.19
19 19 0.35
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTCATTTTCA
Found at i:370503 original size:33 final size:31
Alignment explanation
Indices: 370450--370541 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 31
370440 AGTGAAATAT
*
370450 TTTTTTTTTCATTTCTCATTTTTTTTCCCTTTC-
1 TTTTCTTTTCATTT-TCATTTTTTTT-CC-TTCG
370483 TTTTCTTTCTCATTTTCATTTTTTTT-CTTCG
1 TTTTCTTT-TCATTTTCATTTTTTTTCCTTCG
*
370514 TTTTCATTTTCTTTTTCTATTTTTTTTC
1 TTTTC-TTTTCATTTTC-ATTTTTTTTC
370542 TTCTTCTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
30 3 0.06
31 13 0.25
32 12 0.23
33 18 0.35
34 6 0.12
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (31 bp):
TTTTCTTTTCATTTTCATTTTTTTTCCTTCG
Found at i:370536 original size:32 final size:31
Alignment explanation
Indices: 370461--370546 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 31
370451 TTTTTTTTCA
370461 TTTCTCATTTTTTTTCCCTTTCTTTTCTTTCTCAT
1 TTTCT-ATTTTTTTT--C-TTCTTTTCTTTCTCAT
*
370496 TTTC-ATTTTTTTTCTTCGTTTTCATTT-TCTT
1 TTTCTATTTTTTTTCTTC-TTTTC-TTTCTCAT
370527 TTTCTATTTTTTTTCTTCTT
1 TTTCTATTTTTTTTCTTCTT
370547 CTGTTTTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
30 3 0.06
31 15 0.32
32 16 0.34
33 9 0.19
35 4 0.09
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTCTATTTTTTTTCTTCTTTTCTTTCTCAT
Found at i:370538 original size:15 final size:16
Alignment explanation
Indices: 370520--370563 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
370510 TTCGTTTTCA
*
370520 TTTTCTTTTTCTATTTT
1 TTTTCTTCTTCTA-TTT
*
370537 TTTTCTTCTTCT-GTT
1 TTTTCTTCTTCTATTT
370552 TTTTCTTCTTCT
1 TTTTCTTCTTCT
370564 TATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
17 11 0.44
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTCTTCTTCTATTT
Found at i:370556 original size:32 final size:32
Alignment explanation
Indices: 370452--370563 Score: 90
Period size: 32 Copynumber: 3.5 Consensus size: 32
370442 TGAAATATTT
* * *
370452 TTTTTTTC-ATTTCTCATTTTTTTTC-CCTTTC
1 TTTTTTTCTTTTTCT-ATTTTTTTTCTTCGTTC
370483 TTTTCTTTCTCATTTTC-ATTTTTTTTCTTCGTT-
1 TTTT-TTTCT--TTTTCTATTTTTTTTCTTCGTTC
*
370516 TTCATTTTCTTTTTCTATTTTTTTTCTTC-TTC
1 TT-TTTTTCTTTTTCTATTTTTTTTCTTCGTTC
*
370548 TGTTTTTTCTTCTTCT
1 T-TTTTTTCTTTTTCT
370564 TATAATATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
31 11 0.17
32 29 0.44
33 18 0.27
34 4 0.06
35 4 0.06
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (32 bp):
TTTTTTTCTTTTTCTATTTTTTTTCTTCGTTC
Found at i:373431 original size:47 final size:45
Alignment explanation
Indices: 373360--373485 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
373350 TATAAAATCC
373360 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
373405 CTTACCATTTAAATTTCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
373452 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
373486 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:373686 original size:59 final size:59
Alignment explanation
Indices: 373594--373722 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
373584 CGTAGTGCTA
* * * **
373594 TCCCGAATATGATACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
373653 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
373712 TCCCGAATATG
1 TCCCGAATATG
373723 CAGCCTACTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:376076 original size:46 final size:46
Alignment explanation
Indices: 376026--376139 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 46
376016 TATTCACAAA
* ** **
376026 AATCTTAACCGCATGATATCTTATTTGCATGCTTGTTCGAGAAAAT
1 AATCTTAACCGCATGATATCTAATTCACATAATTGTTCGAGAAAAT
* * *
376072 AATCTTAACTGCATGAAATCTAATTCATATAATTGTTCGAGAAAAT
1 AATCTTAACCGCATGATATCTAATTCACATAATTGTTCGAGAAAAT
* * *
376118 AAACCTAACCGCATGATTTCTA
1 AATCTTAACCGCATGATATCTA
376140 GTTCGCATGC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (46 bp):
AATCTTAACCGCATGATATCTAATTCACATAATTGTTCGAGAAAAT
Found at i:377978 original size:27 final size:27
Alignment explanation
Indices: 377938--377993 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
377928 CAGGGATTTT
*
377938 AGCCAATGAGCATCGAATATTGAATCA
1 AGCCAATGAACATCGAATATTGAATCA
377965 AGCCAATGAACATCGAATATTGAATCA
1 AGCCAATGAACATCGAATATTGAATCA
377992 AG
1 AG
377994 ATAGCTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (27 bp):
AGCCAATGAACATCGAATATTGAATCA
Found at i:379195 original size:26 final size:26
Alignment explanation
Indices: 379159--379215 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
379149 AATAAAGAAA
379159 GCATATAAAGCTTTAAGACCCTAATT
1 GCATATAAAGCTTTAAGACCCTAATT
379185 GCATATAAAGCTTTAAGACCCTAATT
1 GCATATAAAGCTTTAAGACCCTAATT
379211 GCATA
1 GCATA
379216 CATTCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (26 bp):
GCATATAAAGCTTTAAGACCCTAATT
Found at i:386475 original size:27 final size:27
Alignment explanation
Indices: 386437--386495 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
386427 GCTCTAAATT
*
386437 ATTCAGAACGTATTTATGTGTTGAATC
1 ATTCAGAACGTATTTATGTGCTGAATC
*
386464 ATTCAGAACGTATTTCTGTGCTGAATC
1 ATTCAGAACGTATTTATGTGCTGAATC
386491 ATTCA
1 ATTCA
386496 ACACTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTCAGAACGTATTTATGTGCTGAATC
Found at i:387296 original size:2 final size:2
Alignment explanation
Indices: 387289--387316 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
387279 TGTCACCAAA
387289 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
387317 TAAATTACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:391938 original size:24 final size:24
Alignment explanation
Indices: 391911--391964 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
391901 GAATAATGGG
*
391911 TTTTGGAGGACTAAA-AGATGTGAC
1 TTTTGGAGAAC-AAATAGATGTGAC
* *
391935 TTTTGAAGAACAAATAGTTGTGAC
1 TTTTGGAGAACAAATAGATGTGAC
391959 TTTTGG
1 TTTTGG
391965 TGATCCATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.35
Consensus pattern (24 bp):
TTTTGGAGAACAAATAGATGTGAC
Found at i:396755 original size:20 final size:20
Alignment explanation
Indices: 396726--396764 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
396716 AAAGCTCACA
*
396726 TATGATCATATAGATGCATT
1 TATGAGCATATAGATGCATT
*
396746 TATGAGCATATAGTTGCAT
1 TATGAGCATATAGATGCAT
396765 GTGGTGGAAT
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:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
TATGAGCATATAGATGCATT
Found at i:403478 original size:23 final size:23
Alignment explanation
Indices: 403419--403472 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
403409 CTCAATTTAC
403419 TTTTGCCAAGACATTTTTATCTA
1 TTTTGCCAAGACATTTTTATCTA
403442 TTTTGCCAAGACATTTTTATCTA
1 TTTTGCCAAGACATTTTTATCTA
403465 TTTTGCCA
1 TTTTGCCA
403473 CAACATCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTTGCCAAGACATTTTTATCTA
Found at i:408262 original size:19 final size:21
Alignment explanation
Indices: 408240--408285 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
408230 CAAAATCCTG
408240 AAAAG-AAATTG-AAGCACTC
1 AAAAGAAAATTGAAAGCACTC
408259 AAAAGAAAAAATTGAAAGCACTC
1 AAAAG--AAAATTGAAAGCACTC
408282 AAAA
1 AAAA
408286 AGAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (21 bp):
AAAAGAAAATTGAAAGCACTC
Found at i:408273 original size:22 final size:25
Alignment explanation
Indices: 408245--408294 Score: 79
Period size: 23 Copynumber: 2.1 Consensus size: 25
408235 TCCTGAAAAG
408245 AAATTG-AAGCACTC-AAAAGAA-A
1 AAATTGAAAGCACTCAAAAAGAAGA
408267 AAATTGAAAGCACTCAAAAAGAAGA
1 AAATTGAAAGCACTCAAAAAGAAGA
408292 AAA
1 AAA
408295 AAGAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 6 0.24
23 8 0.32
24 7 0.28
25 4 0.16
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (25 bp):
AAATTGAAAGCACTCAAAAAGAAGA
Found at i:408301 original size:16 final size:16
Alignment explanation
Indices: 408282--408317 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
408272 GAAAGCACTC
408282 AAAAAGAAGAAAAAAGA
1 AAAAAGAA-AAAAAAGA
*
408299 AAAAAGAAAAGAAAGA
1 AAAAAGAAAAAAAAGA
408315 AAA
1 AAA
408318 GTTGAAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:420174 original size:17 final size:17
Alignment explanation
Indices: 420152--420185 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
420142 TACCAACCTT
*
420152 TTTTTATCATTATTTTA
1 TTTTTATAATTATTTTA
*
420169 TTTTTATAATTCTTTTA
1 TTTTTATAATTATTTTA
420186 GAGTTTGTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATAATTATTTTA
Found at i:422426 original size:18 final size:16
Alignment explanation
Indices: 422395--422440 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
422385 TATTAAAAAA
*
422395 TTTAAAAATATTATTAT
1 TTTAAAAATCTTATT-T
422412 TTTAAACAATCTTATTT
1 TTTAAA-AATCTTATTT
422429 TTCTAAAAATCT
1 TT-TAAAAATCT
422441 CAAGAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAAATCTTATTT
Found at i:426389 original size:21 final size:21
Alignment explanation
Indices: 426348--426390 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
426338 TTCTGGGTTG
*
426348 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATACTCAA
*
426369 TGTGTATCGATGCACT-CTCAA
1 TGTGCATCGATGCA-TACTCAA
426390 T
1 T
426391 TAAATGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATACTCAA
Found at i:426541 original size:20 final size:21
Alignment explanation
Indices: 426497--426554 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
426487 TGCATGGTAG
426497 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
426521 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
* *
426541 TGCACCAATGCACT
1 TGCATCGATGCACT
426555 TCAATGGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:430530 original size:21 final size:21
Alignment explanation
Indices: 430489--430531 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
430479 TTCTGGGTTG
*
430489 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATACTCAA
*
430510 TGTGTATCGATGCACT-CTCAA
1 TGTGCATCGATGCA-TACTCAA
430531 T
1 T
430532 TAAAGGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATACTCAA
Found at i:430682 original size:20 final size:21
Alignment explanation
Indices: 430638--430695 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
430628 TGCATGGTAG
430638 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
430662 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
*
430682 TGCACCGATGCACT
1 TGCATCGATGCACT
430696 TCAATGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:431508 original size:28 final size:28
Alignment explanation
Indices: 431402--431500 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
431392 AGAGTCGAGG
* * *
431402 GTTCTACGTGGTCTTTCTGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
431430 GTTCTATGTGGTCCTTCGGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
431458 GTTCTATGTGGTCCTTCGGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
431486 GTTCTATGTGGTCCT
1 GTTCTATGTGGTCCT
431501 AAGGGACAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.41
Consensus pattern (28 bp):
GTTCTATGTGGTCCTTCGGGACATATGT
Found at i:438731 original size:20 final size:20
Alignment explanation
Indices: 438708--438757 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
438698 TTTGAGTTAA
438708 TTAAAATATGTTAAAAGTGT
1 TTAAAATATGTTAAAAGTGT
* * *
438728 TTAAAATGTGTTTAAAGTTT
1 TTAAAATATGTTAAAAGTGT
438748 TTAAAATATG
1 TTAAAATATG
438758 AAAACACTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (20 bp):
TTAAAATATGTTAAAAGTGT
Found at i:440821 original size:17 final size:17
Alignment explanation
Indices: 440780--440821 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
440770 TCAAATCCTT
*
440780 TCAAACCATCTCAAAGC
1 TCAAACCCTCTCAAAGC
* *
440797 CCAAACCCTCTTAAAGC
1 TCAAACCCTCTCAAAGC
440814 TCAAACCC
1 TCAAACCC
440822 GGTCAAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.40, G:0.05, T:0.17
Consensus pattern (17 bp):
TCAAACCCTCTCAAAGC
Found at i:443108 original size:16 final size:14
Alignment explanation
Indices: 443087--443122 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
443077 TAGATTCATA
443087 TATTTAATTATTTTT
1 TATTTAATT-TTTTT
443102 GTATTTAATTTTTTT
1 -TATTTAATTTTTTT
443117 TATTTA
1 TATTTA
443123 CAAACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 5 0.25
16 9 0.45
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TATTTAATTTTTTT
Found at i:443214 original size:38 final size:38
Alignment explanation
Indices: 443167--443248 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
443157 ATTACTTGAT
443167 TTATTTTGTTTATTACTTAATTCAAGC-AAATAATTTTA
1 TTATTTTGTTTATTACTTAATTCAAGCGAAA-AATTTTA
* **
443205 TTATTTTGTTTATTATTTAATTCAAGCGAAAGGTTTTA
1 TTATTTTGTTTATTACTTAATTCAAGCGAAAAATTTTA
443243 TTATTT
1 TTATTT
443249 AGTGATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 37 0.93
39 3 0.08
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (38 bp):
TTATTTTGTTTATTACTTAATTCAAGCGAAAAATTTTA
Found at i:443754 original size:2 final size:2
Alignment explanation
Indices: 443747--443797 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
443737 ACAGGATTTA
443747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
443789 AT AT AT AT A
1 AT AT AT AT A
443798 GGACTTTACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:443947 original size:13 final size:13
Alignment explanation
Indices: 443929--443955 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
443919 ACTGAGGTGC
443929 CCTATCGTTCTTA
1 CCTATCGTTCTTA
443942 CCTATCGTTCTTA
1 CCTATCGTTCTTA
443955 C
1 C
443956 ACAACTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (13 bp):
CCTATCGTTCTTA
Found at i:457035 original size:21 final size:18
Alignment explanation
Indices: 457011--457049 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
457001 TTTTTTTCAA
457011 ATAATCATATATAAAATAAAT
1 ATAAT-ATAT-TAAAA-AAAT
457032 ATAATATATTAAAAAAAT
1 ATAATATATTAAAAAAAT
457050 TACCTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATATTAAAAAAAT
Found at i:461343 original size:137 final size:138
Alignment explanation
Indices: 461179--461843 Score: 813
Period size: 137 Copynumber: 4.8 Consensus size: 138
461169 ATGTGAAGTA
* * * * *
461179 CTTCTTGTGGGATGCACATTTCCTTTTTTTTAGAAAATAGGTTATAATTGCCCTACTATGAGTGA
1 CTTCTTGTGGGACGCGCCTTTTCTTTTTTTTAGAAAATAGGTTATAATTGCCCTACTATGTGTGA
* * * *
461244 TGTCCCCCGGCGGGGCACTATTCACGTTAACAACTATTATGTTTGATGGGACGCAATAATGTGGT
66 TGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGACGCAACAATGTGGT
461309 GAAAGCT-
131 GAAAGCTG
* *
461316 CTTCTTGTGGGACGCGCCTTTTCTTTTTGTTAGAAAATAGGTTATAATTGCCCTATTATGTGTGA
1 CTTCTTGTGGGACGCGCCTTTTCTTTTTTTTAGAAAATAGGTTATAATTGCCCTACTATGTGTGA
* * * * * * * *
461381 TGTCCCCAGGCGGGGAACTGTTCACATCAATAACTATTATGTTTGATGGGACGTAACAATGTGGT
66 TGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGACGCAACAATGTGGT
*
461446 GAAA-ATG
131 GAAAGCTG
* * * * *
461453 CTTCTTGTGGGACGCGTC-TTTCTTTTTTGTCAGAAAATAGATTATAATTGCCTTATTATGTGTG
1 CTTCTTGTGGGACGCGCCTTTTCTTTTTT-TTAGAAAATAGGTTATAATTGCCCTACTATGTGTG
* * * * * *
461517 ATGTCCCCCAGTGAGGCACTATTCACGTCAACACCTATTATGGTTGAGGGGACACAACAATGTGA
65 ATGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGACGCAACAATGTGG
461582 TGAAAGC-G
130 TGAAAGCTG
* * * * * * * *
461590 CTTCTTGTGGGATGCACCTTTCCTTTTTGTAAGAGAATATGTTATAACTGCCCTACTATGTGTGA
1 CTTCTTGTGGGACGCGCCTTTTCTTTTTTTTAGAAAATAGGTTATAATTGCCCTACTATGTGTGA
* * * * *
461655 TGTCCCCCGGTGGGGCACTATTCACATCAACACCTATTATGTTTGAGGGGATGC-ACTAT-TCAC
66 TGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGACGCAACAATGT--G
461718 GTGAAAG-TG
129 GTGAAAGCTG
* *
461727 CTTCTTGTGGGACGTGCCTTTTCTTTTTTGTTAGAGAATAGGTTATAATTGCCCTACTATGTGTG
1 CTTCTTGTGGGACGCGCCTTTTCTTTTTT-TTAGAAAATAGGTTATAATTGCCCTACTATGTGTG
* *
461792 ATGTCCCCCGGTGGGGAACTATTCACGTCAACACCTATTATGTTTTATGGGA
65 ATGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGA
461844 TTAGAAGCTG
Statistics
Matches: 451, Mismatches: 69, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
135 1 0.00
136 14 0.03
137 348 0.77
138 88 0.20
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (138 bp):
CTTCTTGTGGGACGCGCCTTTTCTTTTTTTTAGAAAATAGGTTATAATTGCCCTACTATGTGTGA
TGTCCCCCGGTGGGGCACTATTCACGTCAACACCTATTATGTTTGATGGGACGCAACAATGTGGT
GAAAGCTG
Found at i:462187 original size:24 final size:24
Alignment explanation
Indices: 462110--462188 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 24
462100 CCATTCTTTG
* * *
462110 TGAACTTTAATTGGAATATGAAGT
1 TGAATTTTAATTGAAATATCAAGT
* * * *
462134 TGACTTTGAATTTCAAATA-CAAAT
1 TGAATTTTAA-TTGAAATATCAAGT
* *
462158 TAAATTTTAATTGAAATATTAAGT
1 TGAATTTTAATTGAAATATCAAGT
462182 TGAATTT
1 TGAATTT
462189 GGATTTGCAT
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
23 7 0.18
24 26 0.67
25 6 0.15
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.42
Consensus pattern (24 bp):
TGAATTTTAATTGAAATATCAAGT
Found at i:462244 original size:19 final size:20
Alignment explanation
Indices: 462205--462244 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
462195 GCATTTTAAA
* *
462205 AAACTTTTAACAAACACATT
1 AAACATTTAACAAAAACATT
462225 AAACATTTAA-AAAAACATT
1 AAACATTTAACAAAAACATT
462244 A
1 A
462245 CATAATCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
AAACATTTAACAAAAACATT
Found at i:462706 original size:17 final size:17
Alignment explanation
Indices: 462684--462716 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
462674 ACTGAAACAT
462684 AAATAT-ATAATTCTAAC
1 AAATATAAT-ATTCTAAC
462701 AAATATAATATTCTAA
1 AAATATAATATTCTAA
462717 TTATATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATATTCTAAC
Found at i:463958 original size:68 final size:68
Alignment explanation
Indices: 463844--464031 Score: 270
Period size: 68 Copynumber: 2.8 Consensus size: 68
463834 TATGTAAATG
* * * * * *
463844 TTCATCTAACTAGCGTAATTGACA-CATTCTTGCCAATTGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTAGCATAAATGACACCTTTC-TGTCAAATGCATAGTTAGGCCTCAAAGGCACTTA
463908 GCCT
65 GCCT
*
463912 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
463977 CCT
66 CCT
* * *
463980 TTAATCTAACTAGCATAAATGACACATTTCTATCAAATGCATAGTTAGGCCT
1 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCATAGTTAGGCCT
464032 ATTAATCTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 104 0.96
69 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:464337 original size:58 final size:59
Alignment explanation
Indices: 464253--464444 Score: 289
Period size: 59 Copynumber: 3.3 Consensus size: 59
464243 TCTCATATGA
* * *
464253 AAATTCATACACTTAGTAT-AAGTTTCTTATC-TTTTTGCACATAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAA-TTTCTTAACATTTTAGCACACAAAGTGCCCAATACGG
* * **
464311 AAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGG
*
464370 AAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGG
464429 AAATTCATACACTTAG
1 AAATTCATACACTTAG
464445 GTGGTGTTTG
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
58 26 0.21
59 95 0.79
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGG
Found at i:464664 original size:31 final size:31
Alignment explanation
Indices: 464628--464686 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
464618 AACTTAAAAG
* * *
464628 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAAAACTGAAATTTAAATAATTTT
464659 AGTTTTACAAAACTGAAATTTAAATAAT
1 AGTTTTACAAAACTGAAATTTAAATAAT
464687 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTTTACAAAACTGAAATTTAAATAATTTT
Found at i:464762 original size:22 final size:22
Alignment explanation
Indices: 464713--464761 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
464703 ATAAATTATT
* **
464713 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
464735 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
464758 TAAA
1 TAAA
464762 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:464765 original size:54 final size:54
Alignment explanation
Indices: 464701--464997 Score: 313
Period size: 54 Copynumber: 5.5 Consensus size: 54
464691 ACAACTACAA
464701 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
*** * * *
464755 TAATAAATTATTTAAAATAAATCAAT-TCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCT-ATA-TTTTAAAATAAATCAATCCATAC
* * * *
464808 -CAT--A-T-TTTAAAATAAATCAACCCATACTATTTAAAATAAATTAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCTATA-T-TTTAAAATAAATCAATCCATAC
*
464859 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * * **
464913 TAATAAATTATTTAAAATAAGTCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C-TA-TATTTTAA-AATAAATCAATCCATAC
*
464971 TAATAAACTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
464998 CATACAACTA
Statistics
Matches: 202, Mismatches: 26, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
48 19 0.09
49 6 0.03
50 10 0.05
51 1 0.00
52 4 0.02
53 2 0.01
54 85 0.42
55 8 0.04
56 21 0.10
57 5 0.02
58 41 0.20
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
Found at i:464771 original size:32 final size:31
Alignment explanation
Indices: 464733--465395 Score: 314
Period size: 32 Copynumber: 24.4 Consensus size: 31
464723 CAATCTATAT
464733 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
464765 TTTAAAATAAATCAATTCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
464795 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
464813 TTTAAAATAAATCAACCCATAC-------TA
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
464837 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
464869 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
464891 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
464923 TTTAAAATAAGTCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
464953 --T--AATAAATCAATCCATACTAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
464981 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
465011 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
* *
465029 TTTAAAATAAATCAATCGATACTAAAAAAATA
1 TTTAAAATAAATCAATCCATACT-AATAAATA
465061 TTTAAAATAAATC-A---AT-CT-AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
465083 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
465115 TTTATAATAATTCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
465137 TTTAAAATAAATCAATCGATACTAATAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATA
465168 TTTAAAATAAATC-A---AT-CT-AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
465190 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
465222 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
465244 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
465276 TTTAAAGTAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
**
465298 TTTAAAATAAATCAATTTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
465330 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
465352 TTTAAAATAAATCAATCCATACTAATAAATTT
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
465384 TTTAAAATAAAT
1 TTTAAAATAAAT
465396 TATTTTAAAA
Statistics
Matches: 495, Mismatches: 24, Indels: 224
0.67 0.03 0.30
Matches are distributed among these distances:
20 2 0.00
22 129 0.26
23 16 0.03
24 29 0.06
25 4 0.01
26 65 0.13
27 11 0.02
28 25 0.05
30 13 0.03
31 30 0.06
32 171 0.35
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:464894 original size:22 final size:22
Alignment explanation
Indices: 464869--464911 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
464859 TAATAAATTA
464869 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
464891 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
464912 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:464920 original size:22 final size:22
Alignment explanation
Indices: 464871--464919 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
464861 ATAAATTATT
**
464871 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
464893 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
464916 TAAA
1 TAAA
464920 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:464963 original size:26 final size:26
Alignment explanation
Indices: 464928--465027 Score: 112
Period size: 26 Copynumber: 3.6 Consensus size: 26
464918 AATTATTTAA
*
464928 AATAAGTCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
*
464954 AATAAATCAATCCATACTAA-TAAACTATTTAA
1 AATAAATCAATCCATAC-AACT--AC-A---AT
464986 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
465012 AATAAATCAATCCATA
1 AATAAATCAATCCATA
465028 TTTTAAAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
26 34 0.54
27 2 0.03
28 2 0.03
29 2 0.03
30 2 0.03
31 2 0.03
32 19 0.30
ACGTcount: A:0.53, C:0.20, G:0.01, T:0.26
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:464986 original size:58 final size:58
Alignment explanation
Indices: 464813--465027 Score: 298
Period size: 58 Copynumber: 3.8 Consensus size: 58
464803 CAATCCATAT
* * ** *
464813 TTTAAAATAAATCAACCCATACTA-TTTAA-AATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTA
* **
464869 TTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTA
* *
464923 TTTAAAATAAGTCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAACTA
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTA
464981 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA
465028 TTTTAAAATA
Statistics
Matches: 146, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
53 1 0.01
54 50 0.34
56 19 0.13
57 4 0.03
58 72 0.49
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.31
Consensus pattern (58 bp):
TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTA
Found at i:465057 original size:22 final size:22
Alignment explanation
Indices: 464984--465057 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
464974 TAAACTATTT
464984 AAAATAAATCAATCCATACAACTACA
1 AAAATAAATCAATCCAT---ACTA-A
* * **
465010 ATAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATACTAA
*
465032 AAAATAAATCAATCGATACTAA
1 AAAATAAATCAATCCATACTAA
465054 AAAA
1 AAAA
465058 ATATTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 21 0.54
23 2 0.05
26 16 0.41
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (22 bp):
AAAATAAATCAATCCATACTAA
Found at i:465076 original size:192 final size:189
Alignment explanation
Indices: 464818--465184 Score: 567
Period size: 192 Copynumber: 1.9 Consensus size: 189
464808 CATATTTTAA
* * *
464818 AATAAATCAACCCATACTATTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCA
1 AATAAATCAACCCATACTATTTAAAATAAATCAATCCATACTAAAAAAATATTTAAAATAAATCA
464883 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAGTCAATCCATACAAC
66 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAGTCAATCCAT---AC
464948 TACAATAATAAATCAATCCATACTAATAAACTATTTAAAATAAATCAATCCATACAACTACAAT
128 TACAA-AATAAATCAATCCATACTAATAAA-TATTTAAAATAAATCAATCCATACAACTACAAT
* *
465012 AATAAATCAATCCATA-T-TTTAAAATAAATCAATCGATACTAAAAAAATATTTAAAATAAATCA
1 AATAAATCAACCCATACTATTTAAAATAAATCAATCCATACTAAAAAAATATTTAAAATAAATCA
* * * * **
465075 ATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTATAATAATTCAATCCATATTTT
66 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAGTCAATCCATACTAC
*
465140 AAAATAAATCAATCGATACTAATAAATATTTAAAATAAATCAATC
131 AAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATC
465185 TATATTTTAA
Statistics
Matches: 161, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
187 19 0.12
188 23 0.14
189 4 0.02
192 99 0.61
193 1 0.01
194 15 0.09
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (189 bp):
AATAAATCAACCCATACTATTTAAAATAAATCAATCCATACTAAAAAAATATTTAAAATAAATCA
ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAGTCAATCCATACTAC
AAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:465094 original size:54 final size:54
Alignment explanation
Indices: 465012--465395 Score: 644
Period size: 54 Copynumber: 7.1 Consensus size: 54
465002 CAACTACAAT
* * *
465012 AATAAATCAATCCATATTTTAAAATAAATCAATCGATACTAAAAAAATATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
465066 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
465120 AATAATTCAATCCATATTTTAAAATAAATCAATCGATACTAATAAA-TATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
465173 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
465227 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* **
465281 AGTAAATCAATCCATATTTTAAAATAAATCAATTTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
465335 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTTTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
465389 AATAAAT
1 AATAAAT
465396 TATTTTAAAA
Statistics
Matches: 307, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
53 49 0.16
54 258 0.84
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:465112 original size:22 final size:22
Alignment explanation
Indices: 465063--465111 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
465053 AAAAAATATT
* **
465063 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
465085 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
465108 TAAA
1 TAAA
465112 TTATTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:465205 original size:161 final size:162
Alignment explanation
Indices: 465012--465395 Score: 655
Period size: 161 Copynumber: 2.4 Consensus size: 162
465002 CAACTACAAT
* * *
465012 AATAAATCAATCCATATTTTAAAATAAATCAATCGATACTAAAAAAATATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * *
465077 CTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTATAA-TAATTCAATCCATATTTTA
66 CCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTA-AAGTAAATCAATCCATATTTTA
465141 AAATAAATCAATCGATACTAATAAA-TATTTAA
130 AAATAAATCAATCGATACTAATAAATTATTTAA
*
465173 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
465238 CCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAGTAAATCAATCCATATTTTAA
66 CCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAGTAAATCAATCCATATTTTAA
**
465303 AATAAATCAATTTATACTAATAAATTATTTAA
131 AATAAATCAATCGATACTAATAAATTATTTAA
*
465335 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTTTTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
465396 TATTTTAAAA
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
160 2 0.01
161 142 0.68
162 66 0.31
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (162 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAGTAAATCAATCCATATTTTAA
AATAAATCAATCGATACTAATAAATTATTTAA
Found at i:465219 original size:22 final size:22
Alignment explanation
Indices: 465170--465218 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
465160 AATAAATATT
* **
465170 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
465192 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
465215 TAAA
1 TAAA
465219 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:465248 original size:22 final size:22
Alignment explanation
Indices: 465222--465264 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
465212 TAATAAATTA
465222 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
465244 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
465265 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:465273 original size:22 final size:22
Alignment explanation
Indices: 465224--465272 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
465214 ATAAATTATT
***
465224 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
465246 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
465269 TAAA
1 TAAA
465273 TTATTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:465338 original size:14 final size:15
Alignment explanation
Indices: 465298--465345 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
465288 CAATCCATAT
465298 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
*
465313 TTTATACTAATAAAT-TA
1 TTTA-A--AATAAATCAA
465330 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
465345 T
1 T
465346 CCATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 2 0.07
17 5 0.19
18 7 0.26
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAATAAATCAA
Found at i:465356 original size:22 final size:22
Alignment explanation
Indices: 465330--465372 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
465320 TAATAAATTA
465330 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
465352 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
465373 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:465381 original size:22 final size:22
Alignment explanation
Indices: 465332--465380 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
465322 ATAAATTATT
**
465332 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
465354 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
465377 TAAA
1 TAAA
465381 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:465403 original size:15 final size:15
Alignment explanation
Indices: 465375--465483 Score: 89
Period size: 15 Copynumber: 7.0 Consensus size: 15
465365 AATCCATACT
465375 AATAAATT-TTTTAA
1 AATAAATTATTTTAA
465389 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
465404 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
465426 AATAATTTATTTTAA
1 AATAAATTATTTTAA
465441 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* **
465456 AATAAATAACCTT-A
1 AATAAATTATTTTAA
465470 AAT-AATTATTTTAA
1 AATAAATTATTTTAA
465484 TAAATAACCA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
13 6 0.08
14 13 0.17
15 40 0.53
17 1 0.01
18 2 0.03
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:465453 original size:69 final size:67
Alignment explanation
Indices: 465295--465462 Score: 180
Period size: 69 Copynumber: 2.5 Consensus size: 67
465285 AATCAATCCA
* *
465295 TATTTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
1 TATTTTAAAATAAAT-AATTTTTA-AAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
465360 AAAT
64 AAAT
* ** * *
465364 CAATCCATACTAATAAAT--TTTTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATA
1 -TAT-TTTA-AAATAAATAATTTTTAAAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAA
*
465427 ATAATT
62 ATAAAT
*
465433 TATTTTAAAATAAATTA-TTTTAAAATAAAT
1 TATTTTAAAATAAATAATTTTTAAAATAAAT
465463 AACCTTAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
66 7 0.09
67 15 0.19
68 11 0.14
69 37 0.46
70 2 0.02
71 2 0.02
72 7 0.09
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (67 bp):
TATTTTAAAATAAATAATTTTTAAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
AT
Found at i:465458 original size:52 final size:47
Alignment explanation
Indices: 465134--465462 Score: 221
Period size: 54 Copynumber: 6.3 Consensus size: 47
465124 ATTCAATCCA
* * *
465134 TATTTTAAAATAAATCAATCGATACTAATAAA-TATTTAAAATAAATCAATCT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTTTTTAAAAT--A--AA--T
* *
465186 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 -TATTTTAAAATAAATCAATCCATAATAATAAATTTTTTAAAAT--A--AAT
* *
465238 CCATATTTTAAAATAAATCAATCCATACA-AATAAATTATTTAAAGTAAATCAAT
1 ---TATTTTAAAATAAATCAATCCATA-ATAATAAATT-TTT-TA--AAATAAAT
** * *
465292 CCATATTTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATCAAT
1 ---TATTTTAAAATAAATCAATCCATAATAATAAATTTTTTAAAAT--A--AAT
*
465346 CCATATTTTAAAATAAATCAATCCATACTAATAAATTTTTTAAAATAAAT
1 ---TATTTTAAAATAAATCAATCCATAATAATAAATTTTTTAAAATAAAT
*
465396 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAATT-TTTTAAAATAAAT
465448 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
465463 AACCTTAAAT
Statistics
Matches: 242, Mismatches: 16, Indels: 37
0.82 0.05 0.13
Matches are distributed among these distances:
47 24 0.10
50 7 0.03
51 8 0.03
52 31 0.13
53 33 0.14
54 132 0.55
55 2 0.01
56 1 0.00
58 4 0.02
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATCCATAATAATAAATTTTTTAAAATAAAT
Found at i:465492 original size:26 final size:28
Alignment explanation
Indices: 465440--465492 Score: 83
Period size: 26 Copynumber: 1.9 Consensus size: 28
465430 ATTTATTTTA
465440 AAATAAATTATTTTAAAATAAATAACCTT
1 AAATAAATTATTTT-AAATAAATAACCTT
465469 AAAT-AATTATTTT-AATAAATAACC
1 AAATAAATTATTTTAAATAAATAACC
465493 ATATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
28 9 0.38
29 4 0.17
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATAAATTATTTTAAATAAATAACCTT
Found at i:465775 original size:59 final size:59
Alignment explanation
Indices: 465696--465851 Score: 249
Period size: 59 Copynumber: 2.6 Consensus size: 59
465686 CAAACACAGG
* * * *
465696 CTTAGTATGGACTTCTTAACATTTTAGCACACATAGTTCCCAATACGAAAATTCATACA
1 CTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCAATACGAAAATTCATACA
* *
465755 CTTAGTATGAATTTTTTAACATTTTAGCACACATAGTGCCCAATACGGAAATTCATACA
1 CTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCAATACGAAAATTCATACA
*
465814 CTTAGTATGAATTTATTAACATTTTAGCACACTTAGTG
1 CTTAGTATGAATTTATTAACATTTTAGCACACATAGTG
465852 TCATTTGGTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 90 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (59 bp):
CTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCAATACGAAAATTCATACA
Found at i:467084 original size:15 final size:15
Alignment explanation
Indices: 467064--467096 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
467054 GGGGTATTAC
*
467064 ATTATTTAATTAAAA
1 ATTATTTAAATAAAA
467079 ATTATTTAAATAAAA
1 ATTATTTAAATAAAA
467094 ATT
1 ATT
467097 TAGTTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATTTAAATAAAA
Found at i:467899 original size:24 final size:27
Alignment explanation
Indices: 467843--467899 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
467833 CATTCCAAAA
467843 ATTTAAAATTAATACAAATTCATGAAAC
1 ATTT-AAATTAATACAAATTCATGAAAC
* *
467871 CTTTAAATTAA-A-AAATT-ATTAAAC
1 ATTTAAATTAATACAAATTCATGAAAC
467895 ATTTA
1 ATTTA
467900 CATAAGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 10 0.38
25 5 0.19
26 1 0.04
27 7 0.27
28 3 0.12
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTTAAATTAATACAAATTCATGAAAC
Found at i:468131 original size:22 final size:21
Alignment explanation
Indices: 468092--468138 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
468082 ACATTATTTT
468092 TATAAAACTATTTATAAAAAA
1 TATAAAACTATTTATAAAAAA
* * *
468113 TATAACAACTTTTTTTAAAATA
1 TATAA-AACTATTTATAAAAAA
468135 TATA
1 TATA
468139 CTAATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAACTATTTATAAAAAA
Found at i:469854 original size:47 final size:47
Alignment explanation
Indices: 469800--469894 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
469790 TGTAATTGGG
469800 TTCTTTTTAATAAAAACCCTCTTTTGTTTGCTTTTACATTGTTTTTC
1 TTCTTTTTAATAAAAACCCTCTTTTGTTTGCTTTTACATTGTTTTTC
** * *
469847 TTCTTTTTAATAAAAGTCCTCTTTTGTTTGCTTTTTCCTTGTTTTTC
1 TTCTTTTTAATAAAAACCCTCTTTTGTTTGCTTTTACATTGTTTTTC
469894 T
1 T
469895 CCTACTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.16, C:0.17, G:0.07, T:0.60
Consensus pattern (47 bp):
TTCTTTTTAATAAAAACCCTCTTTTGTTTGCTTTTACATTGTTTTTC
Found at i:479846 original size:42 final size:40
Alignment explanation
Indices: 479776--479853 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 40
479766 ATTCTACAAG
479776 GAAGAAAAAAAAACATGAAGCATATTTGCAAGAATGTAAT
1 GAAGAAAAAAAAACATGAAGCATATTTGCAAGAATGTAAT
* *
479816 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATG
1 GAAGAAAAA-A-AAACATGAAGCATATTTGCAAGAATG
479854 CACCGGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 9 0.26
41 1 0.03
42 24 0.71
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.19
Consensus pattern (40 bp):
GAAGAAAAAAAAACATGAAGCATATTTGCAAGAATGTAAT
Found at i:479876 original size:41 final size:42
Alignment explanation
Indices: 479776--479885 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 42
479766 ATTCTACAAG
* * * *
479776 GAAG-AAAAAA-AAACATGAAGCATATTTGCAAGAATGTAAT
1 GAAGAAAAAAAGAAACTTGAAGCATCTTTGCAAGAATGCAAC
* *
479816 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGCACC
1 GAAGAAAAAAAGAAACTTGAAGCATCTTTGCAAGAATGCAAC
* * *
479858 G-GGAAAAAAAGAAACTTGAGGCGTCTTT
1 GAAGAAAAAAAGAAACTTGAAGCATCTTT
479886 TAAAAAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.07
41 28 0.48
42 26 0.45
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (42 bp):
GAAGAAAAAAAGAAACTTGAAGCATCTTTGCAAGAATGCAAC
Found at i:482475 original size:145 final size:145
Alignment explanation
Indices: 482212--482507 Score: 556
Period size: 145 Copynumber: 2.0 Consensus size: 145
482202 ATGTGACAGA
*
482212 AGCATTTCAATCTCCTGAGTGGAAAAAGGCTGTGGAAGAGGAGATAAAAGCGTTGCAAAAGAATA
1 AGCATTTCAATCTCCTGAGTGGAAAAAGGCTGTGGAAGAGAAGATAAAAGCGTTGCAAAAGAATA
*
482277 AGACATGGAGTTTGACAGATTTTCCAGAAGGGAAGTTGATCTACCTTTCACTGACCAGGCCTGAT
66 AGACATGGAGTTTGACAGATTTGCCAGAAGGGAAGTTGATCTACCTTTCACTGACCAGGCCTGAT
482342 ATTGCATACTCAGTG
131 ATTGCATACTCAGTG
482357 AGCATTTCAATCTCCTGAGTGGAAAAAGGCTGTGGAAGAGAAGATAAAAGCGTTGCAAAAGAATA
1 AGCATTTCAATCTCCTGAGTGGAAAAAGGCTGTGGAAGAGAAGATAAAAGCGTTGCAAAAGAATA
* *
482422 AGACATGGAGTTTGACAGATTTGCTAGAAGGGAAGTTGATCTACCTTTCACTGACCAGGCCTGGT
66 AGACATGGAGTTTGACAGATTTGCCAGAAGGGAAGTTGATCTACCTTTCACTGACCAGGCCTGAT
482487 ATTGCATACTCAGTG
131 ATTGCATACTCAGTG
482502 AGCATT
1 AGCATT
482508 GTCAGCCAAC
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (145 bp):
AGCATTTCAATCTCCTGAGTGGAAAAAGGCTGTGGAAGAGAAGATAAAAGCGTTGCAAAAGAATA
AGACATGGAGTTTGACAGATTTGCCAGAAGGGAAGTTGATCTACCTTTCACTGACCAGGCCTGAT
ATTGCATACTCAGTG
Found at i:486141 original size:58 final size:59
Alignment explanation
Indices: 486075--486230 Score: 183
Period size: 58 Copynumber: 2.7 Consensus size: 59
486065 ATAGTCAATT
* * * * * * * *
486075 GATCATTTTGTAACATTTAATAATTGGAGGACTCAACAAAGCAATA-TCTTATAGTC-AGG
1 GATCATTTTATAACTTTTAATAGTTGGAGGACTTAACAAA--AAAAGCCCTATAATCAAGG
* *
486134 GAT-ATTTTTTAACTTTTAATAGTTGAAGGACTTAACAAAAAAAGCCCTATAATCAAGG
1 GATCATTTTATAACTTTTAATAGTTGGAGGACTTAACAAAAAAAGCCCTATAATCAAGG
486192 GATCATTTTATAACTTTTAATAGTTGGAGGACTTAACAA
1 GATCATTTTATAACTTTTAATAGTTGGAGGACTTAACAA
486231 GAATAATACT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.04
57 7 0.08
58 37 0.45
59 36 0.43
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (59 bp):
GATCATTTTATAACTTTTAATAGTTGGAGGACTTAACAAAAAAAGCCCTATAATCAAGG
Found at i:488644 original size:12 final size:12
Alignment explanation
Indices: 488627--488660 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
488617 GAAAAATAAC
*
488627 AAGAAGAGAAGA
1 AAGAAGAAAAGA
488639 AAGAAGAAAAGA
1 AAGAAGAAAAGA
488651 AAGAA-AAAAG
1 AAGAAGAAAAG
488661 TGTCGCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGA
Found at i:493572 original size:17 final size:19
Alignment explanation
Indices: 493540--493576 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
493530 TTTCTTTGTC
493540 CTCTATCTTCTTTCTTCTT
1 CTCTATCTTCTTTCTTCTT
493559 CTCTATC-T-TTTCTTCTT
1 CTCTATCTTCTTTCTTCTT
493576 C
1 C
493577 AAGAAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.62
Consensus pattern (19 bp):
CTCTATCTTCTTTCTTCTT
Found at i:496808 original size:11 final size:11
Alignment explanation
Indices: 496792--496820 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
496782 AGATTGAAGT
496792 GAAGAAGAAAA
1 GAAGAAGAAAA
496803 GAAGAAGAAAA
1 GAAGAAGAAAA
496814 GAAGAAG
1 GAAGAAG
496821 TTCCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAA
Found at i:501383 original size:18 final size:19
Alignment explanation
Indices: 501344--501383 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
501334 TGCAAATTTG
*
501344 TTTAATATTTTTATGATAAA
1 TTTAATACTTTTAT-ATAAA
501364 TTTAATACTTTTAT-TAAA
1 TTTAATACTTTTATATAAA
501382 TT
1 TT
501384 ATTATCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAATACTTTTATATAAA
Found at i:504299 original size:28 final size:28
Alignment explanation
Indices: 504229--504292 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
504219 TCTTAAGGAA
504229 TGGTCCTTTGGGACATATGTATTATATG
1 TGGTCCTTTGGGACATATGTATTATATG
* *
504257 TGGTCTTTTGGGACATATGTGTTATATG
1 TGGTCCTTTGGGACATATGTATTATATG
504285 TGGTCCTT
1 TGGTCCTT
504293 CAGGACAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (28 bp):
TGGTCCTTTGGGACATATGTATTATATG
Found at i:507877 original size:8 final size:8
Alignment explanation
Indices: 507864--507892 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
507854 TCCTATAGTA
507864 GAATACAT
1 GAATACAT
507872 GAATACAT
1 GAATACAT
507880 GAATACAT
1 GAATACAT
507888 GAATA
1 GAATA
507893 TAAGCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (8 bp):
GAATACAT
Found at i:514031 original size:3 final size:3
Alignment explanation
Indices: 514023--514069 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
514013 TTTCGTCCCA
514023 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
514070 AATAATAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:520653 original size:22 final size:22
Alignment explanation
Indices: 520626--520668 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
520616 TCCATTTCAA
520626 CATCAACACCATCAACATCTTT
1 CATCAACACCATCAACATCTTT
**
520648 CATCAAGGCCATCAACATCTT
1 CATCAACACCATCAACATCTT
520669 CATAATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.26
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTT
Found at i:524550 original size:50 final size:50
Alignment explanation
Indices: 524488--524585 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
524478 CACATGAGAG
* * *
524488 CTTTGGTGCCAAGTTG-AGGAGACACAACACCATTCGGCCAAGGGAGATAT
1 CTTTGGTACCAAGATGAAGAAG-CACAACACCATTCGGCCAAGGGAGATAT
* * **
524538 CTTTGGTACCAAGATGAATAAGTATGACACCATTCGGCCAAGGGAGAT
1 CTTTGGTACCAAGATGAAGAAGCACAACACCATTCGGCCAAGGGAGAT
524586 GTACCTTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 37 0.93
51 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (50 bp):
CTTTGGTACCAAGATGAAGAAGCACAACACCATTCGGCCAAGGGAGATAT
Found at i:533147 original size:11 final size:11
Alignment explanation
Indices: 533131--533160 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
533121 TCACCTATGG
533131 CCAGCTCACTT
1 CCAGCTCACTT
533142 CCAGCTCACTT
1 CCAGCTCACTT
533153 CCAGCTCA
1 CCAGCTCA
533161 ATTACCTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.47, G:0.10, T:0.23
Consensus pattern (11 bp):
CCAGCTCACTT
Found at i:533410 original size:50 final size:50
Alignment explanation
Indices: 533348--533445 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
533338 CACATGAGAG
* * *
533348 CTTTGGTGCCAAGTTG-AGGAGACACAACACCATTCGGCCAAGGGAGATAT
1 CTTTGGTACCAAGATGAAGAAG-CACAACACCATTCGGCCAAGGGAGATAT
* * **
533398 CTTTGGTACCAAGATGAATAAGTATGACACCATTCGGCCAAGGGAGAT
1 CTTTGGTACCAAGATGAAGAAGCACAACACCATTCGGCCAAGGGAGAT
533446 GTACCTTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 37 0.93
51 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (50 bp):
CTTTGGTACCAAGATGAAGAAGCACAACACCATTCGGCCAAGGGAGATAT
Found at i:546840 original size:22 final size:22
Alignment explanation
Indices: 546813--546856 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
546803 TCCATTTCAA
546813 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
546835 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
546857 ATAATTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.23
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:551364 original size:22 final size:22
Alignment explanation
Indices: 551337--551380 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
551327 TCTATTTCAA
551337 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
551359 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
551381 ATAATTTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.23
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:555888 original size:22 final size:22
Alignment explanation
Indices: 555861--555904 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
555851 TCCATTTCAA
555861 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
555883 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
555905 ATAATTTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.23
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:564611 original size:22 final size:22
Alignment explanation
Indices: 564584--564627 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
564574 TCCATTTCAA
564584 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
**
564606 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
564628 ATAATTTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.23
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:569051 original size:22 final size:22
Alignment explanation
Indices: 569024--569067 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
569014 TTCATTTCAA
569024 CATCAACA-CCACCAACATCTTC
1 CATCAA-AGCCACCAACATCTTC
*
569046 CATCAAAGCCATCAACATCTTC
1 CATCAAAGCCACCAACATCTTC
569068 ATAATTCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.36, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
CATCAAAGCCACCAACATCTTC
Found at i:575196 original size:90 final size:90
Alignment explanation
Indices: 575043--575653 Score: 799
Period size: 90 Copynumber: 6.9 Consensus size: 90
575033 GAAATTAATC
575043 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
* *
575108 AGAGAATTGGAGCAGATTCTTCTTA
66 AGAGTAGTGGAGCAGATTCTTCTTA
*
575133 TTTTAGATTTGGTCTTCCTGAAGAAGCAGTGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
* * *
575198 GGAGTATTGGAGCAGATTCTTATTA
66 AGAGTAGTGGAGCAGATTCTTCTTA
* * * * *
575223 TTTTATATTTGGTATTCCTGAAGAAGCAACAAAGCAAATCAATCCTTGAGTTTGATATCCCCTGA
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
* * *
575288 AGAGTAATGGAGAAGATTATTCTTA
66 AGAGTAGTGGAGCAGATTCTTCTTA
** * * *
575313 TTCCAGATTTGGTATTCCTAAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATATCCCCT-A
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
*
575377 AGGAGTAGTGGAGTAGATTCTTCTTA
66 A-GAGTAGTGGAGCAGATTCTTCTTA
* * *
575403 TTTCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTTCCTTGA
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
*
575468 AGAGTAGTGGAGCATATTCTTCTTA
66 AGAGTAGTGGAGCAGATTCTTCTTA
* * * * * *
575493 TTTCAGATTTGGTCTTCCTTAAGAAGCAGTGTAGTAAATTAATCCTTGAGTTTGATCTCCCCT-A
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
* *
575557 AAAGTAGTGAAGCA-A--CTTC-T-
66 AGAGTAGTGGAGCAGATTCTTCTTA
* * * * * * *
575577 TCTT--ATTTGGTCTTCCTGAAGAAGTAGTGAAGCAAATCAATCATTGAGTCTGATCTCTCCTAA
1 TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
575640 AGAGTAGTGGAGCA
66 AGAGTAGTGGAGCA
575654 TACCTGTCTT
Statistics
Matches: 465, Mismatches: 53, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
82 49 0.11
83 13 0.03
84 2 0.00
85 1 0.00
86 4 0.01
88 1 0.00
89 15 0.03
90 378 0.81
91 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (90 bp):
TTTTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCCTTGAGTTTGATCTCCCCTGA
AGAGTAGTGGAGCAGATTCTTCTTA
Found at i:575599 original size:82 final size:83
Alignment explanation
Indices: 575499--575653 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 83
575489 CTTATTTCAG
* * * * * *
575499 ATTTGGTCTTCCTTAAGAAGCAGTGTAGTAAATTAATCCTTGAGTTTGATCTCCCCTAAA-AGTA
1 ATTTGGTCTTCCTGAAGAAGCAGTGAAGCAAATCAATCATTGAGTCTGATCTCCCCTAAAGAGTA
575563 GTGAAGCAACTTCTTCTT
66 GTGAAGCAACTTCTTCTT
* *
575581 ATTTGGTCTTCCTGAAGAAGTAGTGAAGCAAATCAATCATTGAGTCTGATCTCTCCTAAAGAGTA
1 ATTTGGTCTTCCTGAAGAAGCAGTGAAGCAAATCAATCATTGAGTCTGATCTCCCCTAAAGAGTA
*
575646 GTGGAGCA
66 GTGAAGCA
575654 TACCTGTCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
82 52 0.83
83 11 0.17
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (83 bp):
ATTTGGTCTTCCTGAAGAAGCAGTGAAGCAAATCAATCATTGAGTCTGATCTCCCCTAAAGAGTA
GTGAAGCAACTTCTTCTT
Found at i:575678 original size:47 final size:47
Alignment explanation
Indices: 575620--575806 Score: 275
Period size: 47 Copynumber: 4.0 Consensus size: 47
575610 AAATCAATCA
* * * *
575620 TTGAGTCTGATCTCTCCTAAAGAGTAGTGGAGCATACCTGTCTTCCCT
1 TTGA-TCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCGTCTTCCCT
* * *
575668 TTAATCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCATCTTCTCT
1 TTGATCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCGTCTTCCCT
*
575715 TTGATCTGATCTCCCCTAAAGAGTAGTAGAACAAACCCGTCTTCCCT
1 TTGATCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCGTCTTCCCT
* *
575762 TTGATCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCGTCTTCC
1 TTGATCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCGTCTTCC
575807 ATCAGATTTG
Statistics
Matches: 125, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 122 0.98
48 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (47 bp):
TTGATCTGATCTCCCCTAAAGAGTAGTGGAACAAACCCGTCTTCCCT
Found at i:575995 original size:3 final size:3
Alignment explanation
Indices: 575989--576031 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
575979 AATAATAATA
*
575989 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
576032 AATAATTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Done.