Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007780.1 Hibiscus syriacus cultivar Beakdansim tig00110063_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: 764298
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:272981 original size:21 final size:21
Alignment explanation
Indices: 272956--273004 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
272946 ATGAATGGTG
272956 CTACAGTGTACCGATGCACTA
1 CTACAGTGTACCGATGCACTA
* *
272977 CTACAGTGTATCGATGCACTG
1 CTACAGTGTACCGATGCACTA
272998 CTACAGT
1 CTACAGT
273005 ACTTTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
CTACAGTGTACCGATGCACTA
Found at i:275403 original size:26 final size:26
Alignment explanation
Indices: 275367--275424 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
275357 TTCTCAGATA
*
275367 CTGTTCTAGACATTGATTGATCCTCT
1 CTGTTTTAGACATTGATTGATCCTCT
275393 CTGTTTTAGACATTGATTGATCCTCT
1 CTGTTTTAGACATTGATTGATCCTCT
275419 CTGTTT
1 CTGTTT
275425 GTCCATCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.47
Consensus pattern (26 bp):
CTGTTTTAGACATTGATTGATCCTCT
Found at i:276764 original size:2 final size:2
Alignment explanation
Indices: 276759--276799 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
276749 ATGTACATGC
276759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
276800 CTATCATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:277079 original size:18 final size:18
Alignment explanation
Indices: 277056--277102 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
277046 AGGGATTAAC
277056 AGTGGTCCTTCGAAACAT
1 AGTGGTCCTTCGAAACAT
* **
277074 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGAAACAT
*
277092 AATGGTCCTTC
1 AGTGGTCCTTC
277103 AGGACAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGAAACAT
Found at i:277107 original size:18 final size:18
Alignment explanation
Indices: 277070--277108 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
277060 GTCCTTCGAA
* *
277070 ACATAGTGGTCATTCGGG
1 ACATAATGGTCATTCAGG
*
277088 ACATAATGGTCCTTCAGG
1 ACATAATGGTCATTCAGG
277106 ACA
1 ACA
277109 AATATTCAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
ACATAATGGTCATTCAGG
Found at i:290590 original size:21 final size:19
Alignment explanation
Indices: 290552--290590 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
290542 ATTTGAATTC
*
290552 AAATATTTAATTATATTTT
1 AAATATTTAATTAAATTTT
290571 AAATATTTATTATTAAATTT
1 AAATATTTA--ATTAAATTT
290591 ATTTTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATATTTAATTAAATTTT
Found at i:296181 original size:21 final size:21
Alignment explanation
Indices: 296139--296181 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
296129 TTTTAAATAA
*
296139 AAATAAATATTTTACTTTTAT
1 AAATAAATATTTTACTTATAT
*
296160 AAATAAATCTATTT-CTTATAT
1 AAATAAATAT-TTTACTTATAT
296181 A
1 A
296182 TATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAAATATTTTACTTATAT
Found at i:296295 original size:23 final size:25
Alignment explanation
Indices: 296269--296314 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
296259 CTTTTTCTGA
296269 TATTTATAAATAA-ATAA-ATATCT
1 TATTTATAAATAATATAATATATCT
*
296292 TATTTATATATAATATAATATAT
1 TATTTATAAATAATATAATATAT
296315 TTTTCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTTATAAATAATATAATATATCT
Found at i:296824 original size:28 final size:27
Alignment explanation
Indices: 296793--296848 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
296783 TAATTCTTTC
296793 TTTTCAAAAT-TTCTATATATACTTATTT
1 TTTTCAAAATATT-TATATATA-TTATTT
*
296821 TTTTCATAATATTTATATATATTATTT
1 TTTTCAAAATATTTATATATATTATTT
296848 T
1 T
296849 ATTAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.27
28 17 0.65
29 2 0.08
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTT
Found at i:296854 original size:24 final size:20
Alignment explanation
Indices: 296827--296878 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
296817 ATTTTTTTCA
296827 TAATATTTATATATATTATTTTAT
1 TAATATTT-TAT-T-TTATTTT-T
*
296851 TAATGTTTTATTTTATTTTT
1 TAATATTTTATTTTATTTTT
296871 TAAGTATT
1 TAA-TATT
296879 AAATTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 10 0.40
22 1 0.04
23 3 0.12
24 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TAATATTTTATTTTATTTTT
Found at i:300179 original size:15 final size:15
Alignment explanation
Indices: 300159--300190 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
300149 ATCAATATCT
*
300159 TTTTGCATACATTCA
1 TTTTGCACACATTCA
300174 TTTTGCACACATTCA
1 TTTTGCACACATTCA
300189 TT
1 TT
300191 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:0.22, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCACACATTCA
Found at i:308719 original size:16 final size:17
Alignment explanation
Indices: 308693--308729 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
308683 AATATTATCT
*
308693 TTTTGAAATTCAATTTC
1 TTTTGAAATTCAATTTA
308710 TTTT-AAATTCAATTTA
1 TTTTGAAATTCAATTTA
308726 TTTT
1 TTTT
308730 TCACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTGAAATTCAATTTA
Found at i:310302 original size:113 final size:113
Alignment explanation
Indices: 310034--310345 Score: 441
Period size: 113 Copynumber: 2.8 Consensus size: 113
310024 ATCAACTTCT
*
310034 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * * * *
310099 GCTTGTTCAACCTTTTGCTTGAATTCATTATTTGATGTATCAGCATTG
66 ACTTGTTCAACCTTTTGCTTGAATTCATCACTAGATGGATCAGAATTG
*
310147 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
310212 ATTTTTTCAAACCTTTTGTTTGAATTCATCACTAGATGGATCA-AATTTT
66 ACTTGTTC-AACCTTTTGCTTGAATTCATCACTAGATGGATCAGAA-TTG
* * *
310261 CTAGAGAAAGTTCATAATTAGAAGAACTTATCTGAAG-AGGAATAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
*
310325 GCTTGTTCAACCTTTT-CTTGA
66 ACTTGTTCAACCTTTTGCTTGA
310346 CTCTATCACA
Statistics
Matches: 177, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
111 4 0.02
112 8 0.05
113 99 0.56
114 66 0.37
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACCTTTTGCTTGAATTCATCACTAGATGGATCAGAATTG
Found at i:310714 original size:9 final size:8
Alignment explanation
Indices: 310702--310752 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
310692 TTTCATTTGA
310702 ATATTATT
1 ATATTATT
310710 -TATATATT
1 ATAT-TATT
310718 ATTATTATT
1 A-TATTATT
310727 ATAATTATT
1 AT-ATTATT
*
310736 ATATTTTT
1 ATATTATT
*
310744 TTATTATT
1 ATATTATT
310752 A
1 A
310753 AATAATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.09
8 16 0.46
9 13 0.37
10 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATATTATT
Found at i:310763 original size:3 final size:3
Alignment explanation
Indices: 310703--310752 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
310693 TTCATTTGAA
* *
310703 TAT TATT TAT ATAT TAT TAT TAT TAT AAT TAT TA- TAT T-T TTT TAT
1 TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
310748 TAT TA
1 TAT TA
310753 AATAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:310768 original size:27 final size:28
Alignment explanation
Indices: 310716--310769 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
310706 TATTTATATA
* *
310716 TTATTATTATTATAATTATTATATTTTT
1 TTATTATTATAATAATTATTACATTTTT
310744 TTATTATTA-AATAATTATTACATTTT
1 TTATTATTATAATAATTATTACATTTT
310770 ACAAGCCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATTATTATAATAATTATTACATTTTT
Found at i:312409 original size:21 final size:21
Alignment explanation
Indices: 312384--312426 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
312374 TTTTAAATAA
312384 AAATAAATAT-TTTACTTTTAT
1 AAATAAATATATTT-CTTTTAT
*
312405 AAATAAATCTATTTCTTTTAT
1 AAATAAATATATTTCTTTTAT
312426 A
1 A
312427 TATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAAATATATTTCTTTTAT
Found at i:312545 original size:23 final size:25
Alignment explanation
Indices: 312515--312560 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
312505 CCTTTTCTAA
312515 TATTTATATATA-AATA-AATATTT
1 TATTTATATATATAATATAATATTT
312538 TATTTATATATATAATATAATAT
1 TATTTATATATATAATATAATAT
312561 AATATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTATATATATAATATAATATTT
Found at i:322231 original size:31 final size:31
Alignment explanation
Indices: 322135--322223 Score: 164
Period size: 31 Copynumber: 2.9 Consensus size: 31
322125 AATTTAAGGC
322135 AAATGGTTTTTGGACTTGAATTGAATTTACA
1 AAATGGTTTTTGGACTTGAATTGAATTTACA
322166 AAATGGTTTTTGGACTTGAATTGAATTTACA
1 AAATGGTTTTTGGACTTGAATTGAATTTACA
322197 AAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAATGGTTTTTGGACTTGAATTGAATTTA
322224 TTCAAAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.19
30 12 0.21
31 35 0.60
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.44
Consensus pattern (31 bp):
AAATGGTTTTTGGACTTGAATTGAATTTACA
Found at i:322315 original size:19 final size:19
Alignment explanation
Indices: 322288--322335 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
322278 AATGTTTTTA
* *
322288 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
322307 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
322326 TGAACAGTAA
1 TGAACAGTAA
322336 CCCGGCTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:322463 original size:20 final size:21
Alignment explanation
Indices: 322438--322478 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
322428 ATTTGAATAT
*
322438 TATGAA-GGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
322458 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
322479 CCCATTCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:322799 original size:34 final size:32
Alignment explanation
Indices: 322760--322829 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
322750 TTTTGTAAAG
*
322760 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
322794 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
322826 GGGA
1 GGGA
322830 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:328028 original size:21 final size:21
Alignment explanation
Indices: 328002--328041 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
327992 ACAGAAATGT
328002 TAAAAA-AATTAATATTTTAGA
1 TAAAAATAA-TAATATTTTAGA
328023 TAAAAATAATAATATTTTA
1 TAAAAATAATAATATTTTA
328042 AATATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:332221 original size:17 final size:17
Alignment explanation
Indices: 332188--332243 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
332178 CGAAGCATAG
*
332188 GTGCCCA-CTGAGGGGA
1 GTGCCCACCTGAGAGGA
332204 GTGCCCACCTGAGAGGA
1 GTGCCCACCTGAGAGGA
332221 GTGCCCACCTGAGAGGA
1 GTGCCCACCTGAGAGGA
332238 GTGCCC
1 GTGCCC
332244 TCAGATTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 7 0.18
17 31 0.82
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (17 bp):
GTGCCCACCTGAGAGGA
Found at i:332623 original size:78 final size:78
Alignment explanation
Indices: 332492--332712 Score: 282
Period size: 78 Copynumber: 2.8 Consensus size: 78
332482 ATGTGGTAGT
* * *
332492 AGGAAATCAAAGTTTATACATATCAATT-ATGAAGAAACGATATCCAGAGATCATGAATCAGATA
1 AGGAAATCAAAGTTTAGACATATCAATTCA-GTAGAAACGATATCCAGAGATCATGAATCAGACA
*
332556 GGCAGAGTGATAGC
65 GGCAGAGTGATAGA
* * *
332570 AGGAAATCAAAGTTTAGACATATCAATTCAGTAGAAACAATATCCAGATATCATGAATCAGACAT
1 AGGAAATCAAAGTTTAGACATATCAATTCAGTAGAAACGATATCCAGAGATCATGAATCAGACAG
*
332635 GCAGAGTGGTAGA
66 GCAGAGTGATAGA
* * * * * * * *
332648 ATGAAATTAGAGTTCAGACATATCAATTCAATAGAAATGGTATCCAGAGATCATGAATCAAACAG
1 AGGAAATCAAAGTTTAGACATATCAATTCAGTAGAAACGATATCCAGAGATCATGAATCAGACAG
332713 ACATACTTAA
Statistics
Matches: 123, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
78 122 0.99
79 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (78 bp):
AGGAAATCAAAGTTTAGACATATCAATTCAGTAGAAACGATATCCAGAGATCATGAATCAGACAG
GCAGAGTGATAGA
Found at i:333680 original size:27 final size:27
Alignment explanation
Indices: 333623--333680 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
333613 TAATATAGCC
* * *
333623 ATTTTACACTTCAAGGGTATTTTGGTC
1 ATTTTACACTTCAAGGGAATTTTGATA
*
333650 ATTTTACACTTCAGGGGCAATTTT-ATA
1 ATTTTACACTTCAAGGG-AATTTTGATA
333677 ATTT
1 ATTT
333681 CATAATCAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGAATTTTGATA
Found at i:334266 original size:14 final size:14
Alignment explanation
Indices: 334244--334293 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
334234 AAGTCAATGG
*
334244 GTTGTCTCAGACGA
1 GTTGACTCAGACGA
334258 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
334272 GTTGAATCAGATGA
1 GTTGACTCAGACGA
334286 GTTGACTC
1 GTTGACTC
334294 GATCTGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:347527 original size:78 final size:78
Alignment explanation
Indices: 347398--347621 Score: 317
Period size: 78 Copynumber: 2.9 Consensus size: 78
347388 TATAGTAACC
* * * * *
347398 AGTGGTAGTAGGAAATCAGAGTTTAGATATATTAATTCTGTAGAAACGGTATCCAGAGATCATGA
1 AGTGGTAGCAGGAAATCAGAGTTCAGATATATCAATTCAGTAGAAATGGTATCCAGAGATCATGA
*
347463 ATCAAAC-ATGCAT
66 ATCAAACGA-ACAT
*
347476 AGTGGTAGCAGGAAATCAGAGTTCAGACATATCAATTCAGTAGAAATGGTATCCAGAGATCATGA
1 AGTGGTAGCAGGAAATCAGAGTTCAGATATATCAATTCAGTAGAAATGGTATCCAGAGATCATGA
*
347541 ATCAGACGAACAT
66 ATCAAACGAACAT
* * * *
347554 AGTGGTAGCTGGAAATTAGAGTTCAGATACATCAATT-AGTAGAAATGGTATCCAGATATCATGA
1 AGTGGTAGCAGGAAATCAGAGTTCAGATATATCAATTCAGTAGAAATGGTATCCAGAGATCATGA
347618 ATCA
66 ATCA
347622 GACAGGTAGA
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
77 30 0.23
78 101 0.77
79 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (78 bp):
AGTGGTAGCAGGAAATCAGAGTTCAGATATATCAATTCAGTAGAAATGGTATCCAGAGATCATGA
ATCAAACGAACAT
Found at i:359562 original size:22 final size:22
Alignment explanation
Indices: 359531--359583 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
359521 ACCGATACTC
*
359531 GGGGAAGTATCGATACTAAAAGA
1 GGGG-AGTATCGATACCAAAAGA
*
359554 GGGGAGTATCGATACCCAAAGA
1 GGGGAGTATCGATACCAAAAGA
359576 GGGG-GTAT
1 GGGGAGTAT
359584 TAGTACCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (22 bp):
GGGGAGTATCGATACCAAAAGA
Found at i:361364 original size:18 final size:18
Alignment explanation
Indices: 361341--361413 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 18
361331 ACTGAAAATT
*
361341 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
361359 TGTCCCAAAAGACTACTA
1 TGTCCCGAAGGACCACTA
* * * *
361377 TGTCCAGGAGGAACATTA
1 TGTCCCGAAGGACCACTA
361395 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
361413 T
1 T
361414 CCATATGTCC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:365410 original size:63 final size:63
Alignment explanation
Indices: 365337--365461 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
365327 TTTACCCGAC
*
365337 TTAATTAACTAACCTAA-AAGAGCTCTTACTTCCATGATTGACCTATGTAGATGAATTTGACTT
1 TTAATTAACTAACCTAAGAA-AGCTCTTACTTCCATGATTGACCTATGTAGATAAATTTGACTT
*
365400 TTAATTAACTAACCTAAGAAAGCTCTTACTTCCATGTTTGACCTATGTAGATAAATTTGACT
1 TTAATTAACTAACCTAAGAAAGCTCTTACTTCCATGATTGACCTATGTAGATAAATTTGACT
365462 GATTCACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 57 0.97
64 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (63 bp):
TTAATTAACTAACCTAAGAAAGCTCTTACTTCCATGATTGACCTATGTAGATAAATTTGACTT
Found at i:366805 original size:202 final size:205
Alignment explanation
Indices: 366457--366835 Score: 529
Period size: 202 Copynumber: 1.8 Consensus size: 205
366447 TCTGTTTGGA
* *
366457 TACAAAGCACATTAGTCCCCCTATCTACCATAGCTGATAAAGCATCTGAATGAAATACATGATCA
1 TACAAAGCACATTAATCCCCC--TCTACCATAGCTGACAAAGCATCTGAATGAAATA-ATGAT-A
*
366522 GATAAAAAAAAAAAGCCTGGGCCAAAATTTTTAACACAAGATAATTTTAAAAAAGAACACGAGCA
62 GATAAAAAAAAAAAGCCTGGGCCAAAATTTTTAACACAAAATAATTTTAAAAAAGAACACGAGCA
*
366587 CTTGAAACATGCAAATTCTAGCTTATAACATCAAAAAGTTTTAGGGTTGTATTAGTGAACTTTTC
127 CTTAAAACATGCAAATTCTAGCTTATAACATCAAAAAGTTTTAGGGTTGTATTAGTGAACTTTTC
366652 TGTTTATGGTACGG
192 TGTTTATGGTACGG
* * *
366666 TACAAAGCACATTAATCCCCC-CTACCATAGCTGACAATGCATCTGAGTGAAAT-AT-AT-GATC
1 TACAAAGCACATTAATCCCCCTCTACCATAGCTGACAAAGCATCTGAATGAAATAATGATAGATA
** *
366727 AAATCAAAAAGCCTGGGTCC-AAA-TTTTAATCACCAAAATAA-TTTAAAACAAGAACATGAGCA
66 AAAAAAAAAAGCCTGGG-CCAAAATTTTTAA-CA-CAAAATAATTTTAAAA-AAGAACACGAGCA
* *
366789 CTTAAAACATGCAAATTCTAGCTTATACCATCAAAGAGTTTTAGGGT
127 CTTAAAACATGCAAATTCTAGCTTATAACATCAAAAAGTTTTAGGGT
366836 ATGAAGTAAT
Statistics
Matches: 154, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
200 6 0.04
201 30 0.19
202 65 0.42
203 2 0.01
204 2 0.01
206 29 0.19
209 20 0.13
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (205 bp):
TACAAAGCACATTAATCCCCCTCTACCATAGCTGACAAAGCATCTGAATGAAATAATGATAGATA
AAAAAAAAAAGCCTGGGCCAAAATTTTTAACACAAAATAATTTTAAAAAAGAACACGAGCACTTA
AAACATGCAAATTCTAGCTTATAACATCAAAAAGTTTTAGGGTTGTATTAGTGAACTTTTCTGTT
TATGGTACGG
Found at i:371039 original size:18 final size:18
Alignment explanation
Indices: 371016--371053 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
371006 GTGAGTAATA
* *
371016 TTAAACAAGAATATATTT
1 TTAAACAAAAATACATTT
371034 TTAAACAAAAATACATTT
1 TTAAACAAAAATACATTT
371052 TT
1 TT
371054 CTTCAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (18 bp):
TTAAACAAAAATACATTT
Found at i:373323 original size:2 final size:2
Alignment explanation
Indices: 373316--373348 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
373306 TCCATACATT
373316 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 T
373349 TTGCAATCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:373403 original size:11 final size:11
Alignment explanation
Indices: 373387--373411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
373377 TAATATATAG
373387 TTTTGAAAACA
1 TTTTGAAAACA
373398 TTTTGAAAACA
1 TTTTGAAAACA
373409 TTT
1 TTT
373412 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:373403 original size:38 final size:37
Alignment explanation
Indices: 373361--373590 Score: 207
Period size: 38 Copynumber: 6.1 Consensus size: 37
373351 GCAATCGGTC
*
373361 TTTGAAAATACGTATATAATATATAG-TTTTGAAAACAT
1 TTTGAAAATA--TATATAATATATAGTTTTTAAAAACAT
* *
373399 TTTGAAAACATTTATATATTATATAGTTTTTAAAAAACAT
1 TTTG-AAA-ATATATATAATATATAGTTTTT-AAAAACAT
*
373439 TTTGAAAATATATATAATATAT-GTTTTT-TAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACA-T
* * *
373475 TTTGAAAATATATATATTATATAGTTTTTTAAAACGTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAAC-AT
*** * *
373513 TTTGAAAATGCGTATAAAATATAATTTTTAAAAAAACAT
1 TTTGAAAATATATATAATATATAGTTTTT--AAAAACAT
* * * *
373552 TTTGAAAATTTATATATTATAT-GTTTTTGAAAATAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAACAT
373588 TTT
1 TTT
373591 TATATATAAT
Statistics
Matches: 157, Mismatches: 25, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
35 5 0.03
36 31 0.20
37 12 0.08
38 63 0.40
39 28 0.18
40 18 0.11
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAAACAT
Found at i:373478 original size:76 final size:73
Alignment explanation
Indices: 373361--373584 Score: 238
Period size: 76 Copynumber: 2.9 Consensus size: 73
373351 GCAATCGGTC
*
373361 TTTGAAAATACGTATATAATATATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGT
1 TTTGAAAATA--TATATAATATAT-GTTTTAAAAACATTTTG-AAA-ATTTATATATTATATAGT
373426 TTTTAAAAAAC-AT
61 TTTT-AAAAACGAT
** *
373439 TTTGAAAATATATATAATATATGTTTTTTAAACATTTTTGAAAATATATATATTATATAGTTTTT
1 TTTGAAAATATATATAATATATGTTTTAAAAACA-TTTTGAAAATTTATATATTATATAGTTTTT
* *
373504 TAAAACGTT
65 AAAAACGAT
* *
373513 TTTGAAAATGCGTATAAAATATAAT-TTTTAAAAAAACATTTTGAAAATTTATATATTATAT-GT
1 TTTGAAAAT--ATATATAATAT-ATGTTTT--AAAAACATTTTGAAAATTTATATATTATATAGT
*
373576 TTTTGAAAA
61 TTTTAAAAA
373585 TATTTTTATA
Statistics
Matches: 128, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
73 5 0.04
74 31 0.24
75 13 0.10
76 40 0.31
77 24 0.19
78 15 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (73 bp):
TTTGAAAATATATATAATATATGTTTTAAAAACATTTTGAAAATTTATATATTATATAGTTTTTA
AAAACGAT
Found at i:373610 original size:3 final size:3
Alignment explanation
Indices: 373602--373642 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
373592 ATATATAATA
373602 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT CT-T TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT T
373643 TATTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:373630 original size:22 final size:22
Alignment explanation
Indices: 373602--373646 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
373592 ATATATAATA
373602 TATTATTAT-TATTATTATTTAT
1 TATTATTATCT-TTATTATTTAT
373624 TATTATTATCTTTATTATTTAT
1 TATTATTATCTTTATTATTTAT
373646 T
1 T
373647 TATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTATTATCTTTATTATTTAT
Found at i:374968 original size:45 final size:45
Alignment explanation
Indices: 374891--374995 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
374881 TTATTTTCTA
* * * * *
374891 TTTTATTTTATTTTTCTTCTTTTTTTCGTTTT-CTTTGATTTCTTT
1 TTTTATTTTATTTTTATTATCTTATTCGTTTTCCTTTGACTT-TTT
374936 TTTTATTTTATTTTTAATTATCTTATTC-TTTTCCTTTGACTTTTT
1 TTTTATTTTATTTTT-ATTATCTTATTCGTTTTCCTTTGACTTTTT
* *
374981 CTTTCTTTTATTTTT
1 TTTTATTTTATTTTT
374996 TCTTATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 35 0.69
46 16 0.31
ACGTcount: A:0.10, C:0.11, G:0.03, T:0.75
Consensus pattern (45 bp):
TTTTATTTTATTTTTATTATCTTATTCGTTTTCCTTTGACTTTTT
Found at i:375042 original size:19 final size:19
Alignment explanation
Indices: 375017--375073 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
375007 CCTTTATTTA
375017 ATTTATTATTTAATTTTTT
1 ATTTATTATTTAATTTTTT
*
375036 GTTTATT-TTT-ATTTTTT
1 ATTTATTATTTAATTTTTT
*
375053 ATATATATATTTATATTTTTT
1 ATTTAT-TATTTA-ATTTTTT
375074 CTCTTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 11 0.35
18 4 0.13
19 9 0.29
21 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTATTATTTAATTTTTT
Found at i:375096 original size:4 final size:4
Alignment explanation
Indices: 375087--375146 Score: 68
Period size: 4 Copynumber: 15.0 Consensus size: 4
375077 TTGATTTAAC
* * *
375087 ATTT ATTT ATTTT ATTT -CTT ATCT ATCT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
*
375135 ATTT ATTC ATTT
1 ATTT ATTT ATTT
375147 TTTCTAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 2 0.04
4 42 0.88
5 4 0.08
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:375097 original size:28 final size:28
Alignment explanation
Indices: 375009--375130 Score: 76
Period size: 28 Copynumber: 4.4 Consensus size: 28
374999 TATTTTTTCC
* * * * * *
375009 TTTATTTAATTTATTATTTAATTTTTTG
1 TTTATTTTATTTCTTATCTAACTATTTA
* *
375037 TTTATTTTTATTTTTTATATATA-TATTTA
1 TTTA-TTTTATTTCTTATCTA-ACTATTTA
*
375066 --TATTTT-TTCTCTTGATTTAAC-ATTTA
1 TTTATTTTATT-TCTT-ATCTAACTATTTA
*
375092 TTTATTTTATTTCTTATCTATCTATTTA
1 TTTATTTTATTTCTTATCTAACTATTTA
375120 TTTA-TTTATTT
1 TTTATTTTATTT
375131 ATTTATTTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.03
26 13 0.17
27 18 0.24
28 23 0.30
29 19 0.25
30 1 0.01
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTATTTTATTTCTTATCTAACTATTTA
Found at i:375127 original size:8 final size:8
Alignment explanation
Indices: 375009--375146 Score: 74
Period size: 8 Copynumber: 17.4 Consensus size: 8
374999 TATTTTTTCC
375009 TTTATTTAA
1 TTTATTT-A
375018 TTTA-TTA
1 TTTATTTA
375025 TTTAATTT-
1 TTT-ATTTA
*
375033 TTTGTTTA
1 TTTATTTA
375041 -TT-TTTA
1 TTTATTTA
375047 TTT-TTTA
1 TTTATTTA
* *
375054 TATATATA
1 TTTATTTA
*
375062 TTTATATTT
1 TTTAT-TTA
*
375071 TTTCTCTTGA
1 TTTAT-TT-A
**
375081 TTTA-ACA
1 TTTATTTA
375088 TTTATTTA
1 TTTATTTA
375096 TTTTATTT-
1 -TTTATTTA
* *
375104 CTTATCTA
1 TTTATTTA
*
375112 TCTATTTA
1 TTTATTTA
375120 TTTATTTA
1 TTTATTTA
375128 TTTATTTA
1 TTTATTTA
*
375136 TTTATTCA
1 TTTATTTA
375144 TTT
1 TTT
375147 TTTCTAACAT
Statistics
Matches: 98, Mismatches: 21, Indels: 21
0.70 0.15 0.15
Matches are distributed among these distances:
6 4 0.04
7 27 0.28
8 44 0.45
9 20 0.20
10 3 0.03
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTATTTA
Found at i:375133 original size:12 final size:12
Alignment explanation
Indices: 375009--375146 Score: 74
Period size: 12 Copynumber: 11.6 Consensus size: 12
374999 TATTTTTTCC
375009 TTTATTTAATTTA
1 TTTATTT-ATTTA
375022 -TTATTTAATTT-
1 TTTATTT-ATTTA
*
375033 TTTGTTTA-TT-
1 TTTATTTATTTA
375043 TTTATTT-TTTA
1 TTTATTTATTTA
* *
375054 TATATATATTTA
1 TTTATTTATTTA
* *
375066 TATTTTTTCTCTTGA
1 T-TTATTTAT-TT-A
**
375081 TTTA-ACATTTA
1 TTTATTTATTTA
375092 TTTATTTTATTT-
1 TTTA-TTTATTTA
* * *
375104 CTTATCTATCTA
1 TTTATTTATTTA
375116 TTTATTTATTTA
1 TTTATTTATTTA
375128 TTTATTTATTTA
1 TTTATTTATTTA
*
375140 TTCATTT
1 TTTATTT
375147 TTTCTAACAT
Statistics
Matches: 94, Mismatches: 21, Indels: 21
0.69 0.15 0.15
Matches are distributed among these distances:
10 10 0.11
11 16 0.17
12 53 0.56
13 9 0.10
14 4 0.04
15 2 0.02
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:389420 original size:95 final size:94
Alignment explanation
Indices: 389250--389504 Score: 336
Period size: 95 Copynumber: 2.7 Consensus size: 94
389240 TTTTACGGAG
* * *
389250 TTATCATATATAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTATG
1 TTAT-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATG
389315 GATAAGATTCAGCTAGCCTGATAAAGGTGA
65 GATAAGATTCAGCTAGCCTGATAAAGGTGA
* ** *
389345 TTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGGCCCTGCTTTATG
1 TTAT-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATG
*
389410 GATAATATTCAGCTAGCCTGATAAAGGTGA
65 GATAAGATTCAGCTAGCCTGATAAAGGTGA
* * ** * *
389440 TTATAT-TACAATGATA--TTAAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCACGACTTTATG
1 TTATATATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATG
389502 GAT
65 GAT
389505 TCAGCTAGCC
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
92 42 0.30
93 6 0.04
94 4 0.03
95 90 0.63
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (94 bp):
TTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGA
Found at i:390490 original size:84 final size:84
Alignment explanation
Indices: 390337--391670 Score: 1534
Period size: 84 Copynumber: 15.9 Consensus size: 84
390327 TTGACTTGTT
* * **
390337 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAATATAGA-TCAAGGC
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATA-ACTCAAGGC
* * * *
390401 GAGAAGGGCTATTTTCCAAC
65 TAGAAGGGTTATCTGCCAAC
* * * * * *
390421 AAAAGACCTTCGAGTTCAACTATGCTCAGCTCCAAGGCATATCATTTGCAGCATACCTTAAGTCA
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
390486 AGAAGGGCTATCTGCCAAC
66 AGAAGGGTTATCTGCCAAC
* * *
390505 AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTGAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
390570 AGAAGGGTTATCTACCAAC
66 AGAAGGGTTATCTGCCAAC
* * * *
390589 AAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCGTTTTCAGCATAGCTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
* * *
390654 AGAAGGGCTATCTTCCACC
66 AGAAGGGTTATCTGCCAAC
* * ** **
390673 AAAAGACCTTTGAGTTCGACTACGCTCATCTCCAAGGCATATCATTTATAATATAACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
390738 AGTAGGGTTATCTGCCAAC
66 AGAAGGGTTATCTGCCAAC
* * * * * * * * * * * *
390757 CAAAGACCTTTGAGTTCGACTATGTTTAGCTCAAAGGCACATCATTTACAGCATAGCTTAAGTCG
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
* * *
390822 AGAAGGGCTATCTTCCAAT
66 AGAAGGGTTATCTGCCAAC
* * * * * * * * * *
390841 GAAAGACCTTCGAGTTCGACTATGCTCAGATCCAAGGCACATCATTTACAGAATAGCTTAAGTCG
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
390906 AGAAGGGTTATCTTCCAAC
66 AGAAGGGTTATCTGCCAAC
* *
390925 CAAAGTCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
390990 AGAAGGGTTATCTGCCAGC
66 AGAAGGGTTATCTGCCAAC
* * * * ** * *
391009 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCAATTGTGGTATGACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
391074 AGAAGGGCTATCT----AC
66 AGAAGGGTTATCTGCCAAC
* * * * * *
391089 CAAAGACCTTC-AGGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGG
1 AAAAGACCTTCGA-GTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTCAAGG
391153 CTAGAAGGGTTATCTGCCAAC
64 CTAGAAGGGTTATCTGCCAAC
* * * * * *
391174 -AAATACCTTCGAGTTCGACTATGCTAAGCTCAAAGGCATATCATTTGCAGTATAACTCAAGGAT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
391238 AGAAGGGTTATCTGCCAACC
66 AGAAGGGTTATCTGCCAA-C
* * * *
391258 AAAA-ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTTGCAACATAGCTCAAGGCA
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
* *
391322 AGAAGGGCTATTTGCCAAC
66 AGAAGGGTTATCTGCCAAC
* *
391341 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGTATATCATTTGCAGCATAACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
391406 AGAAGGGTTATCTGCCAAC
66 AGAAGGGTTATCTGCCAAC
* * * * * * * *
391425 CAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTAGCAGCATAGCTTAAGTC
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTCAAGGC
* *
391489 GAGAAGGGTTATCTGCTAAC
65 TAGAAGGGTTATCTGCCAAC
* ** * *
391509 AAAAGACCTTCGAGTTTGACTACGCTCAATTCCAAGGCATATCATTTGTAGCATAACTTAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
391574 AGAAGGGTTATCTGCCAAC
66 AGAAGGGTTATCTGCCAAC
* * * * * * *
391593 TAAAGACCTTCGAGTTCGACTACGCTGAGCTCCAAGGCACATCATTTACAACATAGCTCAAGGCA
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
*
391658 ATAAGGGTTATCT
66 AGAAGGGTTATCT
391671 ATCAATAAAA
Statistics
Matches: 1068, Mismatches: 169, Indels: 26
0.85 0.13 0.02
Matches are distributed among these distances:
79 1 0.00
80 26 0.02
81 40 0.04
83 55 0.05
84 937 0.88
85 9 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCT
AGAAGGGTTATCTGCCAAC
Found at i:392282 original size:37 final size:36
Alignment explanation
Indices: 392198--392544 Score: 316
Period size: 37 Copynumber: 9.4 Consensus size: 36
392188 GCAAACGGTC
* * *
392198 TTTGAAAATACGTACATAATATATGGTTTTTAAAAACTTT
1 TTTGAAAATA--TATATAATATATAGTTTTT-AAAAC-AT
*
392238 TTTGAAAATGTATATAATATATAGTTTTTAAAACAT
1 TTTGAAAATATATATAATATATAGTTTTTAAAACAT
*
392274 TTTAGAAAATATATATAATATATAGTTTTTCAAATCAT
1 TTT-GAAAATATATATAATATATAGTTTTT-AAAACAT
* *
392312 TTTGAAAACATATATAATATATAGTTTTGAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAACA-T
* * *
392349 TTTAAAAATTTATATAATATATAGTTTTGAAAACA-
1 TTTGAAAATATATATAATATATAGTTTTTAAAACAT
392384 -TT-----TATATAT--TATATAGTTTTTAAAAAACAT
1 TTTGAAAATATATATAATATATAGTTTTT--AAAACAT
* * *
392414 TTTGAAAATATATATAATATATGGGTTTTCAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAACA-T
* *
392451 TTTGAATATATATATATTATATAGTTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAG-TTTTTAAAACA-T
** *
392489 TTTGAAAATACGTATAATATATAATTTTTTAAGAAAACAT
1 TTTGAAAATATATATAATATAT-AGTTTTT---AAAACAT
*
392529 TTTGAAAATTTATATA
1 TTTGAAAATATATATA
392545 TTACATGTTT
Statistics
Matches: 257, Mismatches: 30, Indels: 40
0.79 0.09 0.12
Matches are distributed among these distances:
27 11 0.04
29 12 0.05
31 2 0.01
34 2 0.01
36 21 0.08
37 109 0.42
38 70 0.27
39 1 0.00
40 23 0.09
41 6 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAACAT
Found at i:392396 original size:27 final size:26
Alignment explanation
Indices: 392347--392409 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 26
392337 TTTGAAAACA
392347 TTTTTAAAAATTTATATAATATATAG
1 TTTTTAAAAATTTATATAATATATAG
* *
392373 TTTTGAAAACATTTATATATTATATAG
1 TTTTTAAAA-ATTTATATAATATATAG
392400 TTTTTAAAAA
1 TTTTTAAAAA
392410 ACATTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
TTTTTAAAAATTTATATAATATATAG
Found at i:392425 original size:29 final size:27
Alignment explanation
Indices: 392347--392427 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 27
392337 TTTGAAAACA
* *
392347 TTTTTAAAA-ATTTATATAATATATAG
1 TTTTAAAAACATTTATAAAATATATAG
* * *
392373 TTTTGAAAACATTTATATATTATATAG
1 TTTTAAAAACATTTATAAAATATATAG
392400 TTTTTAAAAAACATTT-TGAAAATATATA
1 -TTTT-AAAAACATTTAT-AAAATATATA
392428 TAATATATGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.17
27 16 0.35
28 5 0.11
29 17 0.37
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTTAAAAACATTTATAAAATATATAG
Found at i:392429 original size:102 final size:102
Alignment explanation
Indices: 392285--392489 Score: 279
Period size: 102 Copynumber: 2.0 Consensus size: 102
392275 TTAGAAAATA
* *
392285 TATATAATATATAGTTTTTCAAATCATTTTGAAAACATATATAATATAT-AGTTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATATGAGTTTT-AAAACATT
*
392349 TTTAAAAATTTATATAATATATAG-TTTTGAAAACATT
65 TTTAAAAATATATATAATATATAGTTTTTGAAAACATT
* * * *
392386 TATATATTATATAGTTTTTAAAAAACATTTTGAAAATATATATAATATATGGGTTTTCAAACATT
1 TATATAATATATAGTTTTT-AAAAACATTTTGAAAACATATATAATATATGAGTTTTAAAACATT
* * * *
392451 TTTGAATATATATATATTATATAGTTTTTTAAAACATT
65 TTTAAAAATATATATAATATATAGTTTTTGAAAACATT
392489 T
1 T
392490 TTGAAAATAC
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 18 0.20
102 54 0.60
103 18 0.20
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (102 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATATGAGTTTTAAAACATTT
TTAAAAATATATATAATATATAGTTTTTGAAAACATT
Found at i:392510 original size:38 final size:37
Alignment explanation
Indices: 392386--392544 Score: 158
Period size: 38 Copynumber: 4.2 Consensus size: 37
392376 TGAAAACATT
* *
392386 TATATATTATATAGTTTTTAAAAAACATTTTGAAAATA
1 TATATAATATATAGTTTTT-TAAAACATTTTGAAAATA
** * *
392424 TATATAATATAT-GGGTTTTCAAACATTTTTGAATATA
1 TATATAATATATAGTTTTTTAAAACA-TTTTGAAAATA
*
392461 TATATATTATATAGTTTTTTAAAACATTTTTGAAAATA
1 TATATAATATATAGTTTTTTAAAACA-TTTTGAAAATA
** * *
392499 CGTATAATATATAATTTTTTAAGAAAACATTTTGAAAATT
1 TATATAATATATAGTTTTTT---AAAACATTTTGAAAATA
392539 TATATA
1 TATATA
392545 TTACATGTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
36 5 0.05
37 25 0.26
38 48 0.49
40 14 0.14
41 6 0.06
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTTTAAAACATTTTGAAAATA
Found at i:393981 original size:27 final size:27
Alignment explanation
Indices: 393921--394013 Score: 82
Period size: 27 Copynumber: 3.3 Consensus size: 27
393911 TTCTTTGATT
* *
393921 TTTTTATTTATTTTATTCTTTTCCTTTGA
1 TTTTTATTTATTTAATT-TTTTGCTTT-A
* *
393950 CTTTTTATTTCTTTCATTTTTT-C-TTA
1 -TTTTTATTTATTTAATTTTTTGCTTTA
*
393976 TTTTTTGCTTTATTTAATTTTTTGCTTTA
1 -TTTTT-ATTTATTTAATTTTTTGCTTTA
394005 TTTTTATTT
1 TTTTTATTT
394014 TCATTTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 6 0.11
27 18 0.34
28 7 0.13
29 7 0.13
30 15 0.28
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (27 bp):
TTTTTATTTATTTAATTTTTTGCTTTA
Found at i:394011 original size:23 final size:22
Alignment explanation
Indices: 393984--394036 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
393974 TATTTTTTGC
*
393984 TTTATTTAATTTTTTGCTTTATT
1 TTTATTTAA-TTTTTGATTTATT
*
394007 TTTATTTTCATTTTTGATTTATT
1 TTTA-TTTAATTTTTGATTTATT
*
394030 TTCATTT
1 TTTATTT
394037 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 19 0.73
24 4 0.15
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTATTTAATTTTTGATTTATT
Found at i:394014 original size:17 final size:17
Alignment explanation
Indices: 393975--394007 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
393965 ATTTTTTCTT
393975 ATTTTTTGCTTTATTTA
1 ATTTTTTGCTTTATTTA
393992 ATTTTTTGCTTTATTT
1 ATTTTTTGCTTTATTT
394008 TTATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
ATTTTTTGCTTTATTTA
Found at i:394037 original size:23 final size:23
Alignment explanation
Indices: 393994--394037 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
393984 TTTATTTAAT
* *
393994 TTTTTGCTTTATTTTTATTTTCA
1 TTTTTGATTTATTTTCATTTTCA
394017 TTTTTGATTTATTTTCATTTT
1 TTTTTGATTTATTTTCATTTT
394038 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTTTGATTTATTTTCATTTTCA
Found at i:395850 original size:17 final size:19
Alignment explanation
Indices: 395828--395869 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
395818 GAATATAATT
395828 TATATA-ATTTT-AAAATA
1 TATATAGATTTTGAAAATA
* *
395845 TATATAGCTTTTGAATATA
1 TATATAGATTTTGAAAATA
395864 TATATA
1 TATATA
395870 TATATATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 4 0.19
19 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
TATATAGATTTTGAAAATA
Found at i:395913 original size:63 final size:61
Alignment explanation
Indices: 395844--395966 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 61
395834 ATTTTAAAAT
* * *
395844 ATATATAGCTTTTGAATATATATATATATATATGTATAGTTTTTAGAAAATAAATAATATATA
1 ATATATAGCTTTTAAAAATATATATATATATAT-AATAGTTTTTA-AAAATAAATAATATATA
* ** *
395907 ATATATAGTTTTTAAAAATATATATATATATATAATTTTTTTTAAAAATATATAATATAT
1 ATATATAGCTTTTAAAAATATATATATATATATAATAGTTTTTAAAAATAAATAATATAT
395967 TATAATTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 15 0.28
62 8 0.15
63 30 0.57
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (61 bp):
ATATATAGCTTTTAAAAATATATATATATATATAATAGTTTTTAAAAATAAATAATATATA
Found at i:395936 original size:30 final size:29
Alignment explanation
Indices: 395842--395990 Score: 142
Period size: 30 Copynumber: 5.0 Consensus size: 29
395832 TAATTTTAAA
* *
395842 ATATATATAGCTTTTGAATATATATATATAT
1 ATATATATAG-TTTTTAA-AAATATATATAT
* *
395873 ATATGTATAGTTTTTAGAAAATAAATAATAT
1 ATATATATAGTTTTTA-AAAATATAT-ATAT
395904 ATAATATATAGTTTTTAAAAATATATATAT
1 AT-ATATATAGTTTTTAAAAATATATATAT
**
395934 ATATATAATTTTTTTTAAAAATATATA-AT
1 ATATAT-ATAGTTTTTAAAAATATATATAT
* * *
395963 ATAT-TATA-ATTTTATATATATATATAT
1 ATATATATAGTTTTTAAAAATATATATAT
395990 A
1 A
395991 GTTTTTAAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.13
27 5 0.05
28 1 0.01
29 10 0.10
30 35 0.35
31 24 0.24
32 13 0.13
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (29 bp):
ATATATATAGTTTTTAAAAATATATATAT
Found at i:395987 original size:21 final size:21
Alignment explanation
Indices: 395954--396010 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
395944 TTTTTTAAAA
395954 ATATATAATATATTATAATTTT
1 ATATAT-ATATATTATAATTTT
*
395976 ATATATATATA-TATAGTTTT
1 ATATATATATATTATAATTTT
* *
395996 -TAAATATATGTTATA
1 ATATATATATATTATA
396011 TGGTTTTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 8 0.26
20 12 0.39
21 5 0.16
22 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
ATATATATATATTATAATTTT
Found at i:396016 original size:22 final size:21
Alignment explanation
Indices: 395972--396040 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
395962 TATATTATAA
*
395972 TTTTATATATATATATATAGT
1 TTTTAAATATATATATATAGT
* *
395993 TTTTAAATATATGTTATATGGT
1 TTTTAAATATAT-ATATATAGT
*
396015 TTTCTAGAAAATATATATTATA-T
1 TTT-TA-AATATATATA-TATAGT
396038 TTT
1 TTT
396041 ATATTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.29
22 10 0.26
23 8 0.21
24 9 0.24
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTAAATATATATATATAGT
Found at i:405004 original size:30 final size:30
Alignment explanation
Indices: 404941--405006 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
404931 AGAACCGAAA
* * *
404941 GAACCGGCTGAAAATCGGGAAAATCGGGGT
1 GAACCGGCTGAAAACCGGCAAAATCAGGGT
**
404971 GAACCGGCTGAAAACCGGCAAAATCAGTTT
1 GAACCGGCTGAAAACCGGCAAAATCAGGGT
405001 GAACCG
1 GAACCG
405007 CCGGTTCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.30, T:0.14
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAATCAGGGT
Found at i:405260 original size:24 final size:24
Alignment explanation
Indices: 405230--405309 Score: 151
Period size: 24 Copynumber: 3.3 Consensus size: 24
405220 TAGAAGTTCG
405230 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
405254 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
405278 ATTGAAGCCTAAATTTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
405302 ATTGAAGC
1 ATTGAAGC
405310 GAAAGAATAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:408507 original size:25 final size:28
Alignment explanation
Indices: 408456--408509 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 28
408446 TACATGTAAC
*
408456 ACAAAAACTATACATCACTATTATATTT
1 ACAAAAACTATACATCAATATTATATTT
408484 ACAAAAACT-TAC-T-AATATTATATTT
1 ACAAAAACTATACATCAATATTATATTT
408509 A
1 A
408510 AAAGCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 12 0.48
26 1 0.04
27 3 0.12
28 9 0.36
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (28 bp):
ACAAAAACTATACATCAATATTATATTT
Found at i:409706 original size:44 final size:42
Alignment explanation
Indices: 409647--409730 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 42
409637 CACGATGGGG
*
409647 TGTTAATCTACCTCATACTATGATAGAATCAAGA-AAAATGTCCA
1 TGTTAATCCACCTCATACTATGAT-GAA-CAA-ACAAAATGTCCA
* *
409691 TGTTGATCCACCTCATACTGTGATGAACAAACAAAATGTC
1 TGTTAATCCACCTCATACTATGATGAACAAACAAAATGTC
409731 AACACTGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.03
42 11 0.31
43 3 0.08
44 21 0.58
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (42 bp):
TGTTAATCCACCTCATACTATGATGAACAAACAAAATGTCCA
Found at i:410622 original size:5 final size:6
Alignment explanation
Indices: 410596--410642 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
410586 TTATTTTTTA
*
410596 TTTTCT CTTTTC- TATTCT TTTTCT TTTTCT TTTTCTT TTTTCT TTTT
1 TTTTCT -TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTT
410643 TTCAACAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 4 0.11
6 21 0.58
7 11 0.31
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:434945 original size:16 final size:18
Alignment explanation
Indices: 434924--434960 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
434914 GTTCTCCCCC
434924 ATATTTT-AAAATAC-TT
1 ATATTTTGAAAATACATT
*
434940 ATATTTTGTAAATACATT
1 ATATTTTGAAAATACATT
434958 ATA
1 ATA
434961 CATTGGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATTTTGAAAATACATT
Found at i:435471 original size:30 final size:30
Alignment explanation
Indices: 435435--435495 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
435425 TCAACATGCA
435435 TATTTTCATTCAAATCAACACAATTATCAT
1 TATTTTCATTCAAATCAACACAATTATCAT
* *
435465 TATTTTCATTCAAATTAACACAATTTTCAT
1 TATTTTCATTCAAATCAACACAATTATCAT
435495 T
1 T
435496 CGAAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (30 bp):
TATTTTCATTCAAATCAACACAATTATCAT
Found at i:436876 original size:23 final size:23
Alignment explanation
Indices: 436846--436897 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
436836 CCAAATAAGA
436846 GAAAATATCA-CTTTCACACATT
1 GAAAATATCAGCTTTCACACATT
* *
436868 GAAAGATATCAGTTTTCACACTTT
1 GAAA-ATATCAGCTTTCACACATT
436892 GAAAAT
1 GAAAAT
436898 GTGTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 4 0.15
23 8 0.31
24 14 0.54
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (23 bp):
GAAAATATCAGCTTTCACACATT
Found at i:441170 original size:36 final size:36
Alignment explanation
Indices: 441010--441278 Score: 216
Period size: 36 Copynumber: 7.5 Consensus size: 36
441000 TGGGCAAAAG
* * ** *
441010 ATCATGCTTATAATCATTATTTGCAAGAACATGAAT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
** ** ** **
441046 ATCATGCATATAATCAACAGCAAAAAGCGTGTGTAT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
* * * * * *
441082 ATCATGCATGTAATCATCAGTAGCAAGCTCAAGCAT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
* * * * * *
441118 ATAATGAATATGATCATTATTAGCATGTGCATATAT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
* * * **
441154 ATCATGCATATAATCATTATTACCAAGAGTATGCGT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
* * *
441190 ATCATGCATGTAATCATTAATAGC-AGACACATGTAT
1 ATCATGCATATAATCATTATTAGCAAG-CGCATGTAT
*
441226 ATCATCCATATAATCATTATTAGCAAGCGCATGTAT
1 ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
441262 ATCATGCATATAATCAT
1 ATCATGCATATAATCAT
441279 CAACAATAAG
Statistics
Matches: 173, Mismatches: 58, Indels: 4
0.74 0.25 0.02
Matches are distributed among these distances:
35 2 0.01
36 169 0.98
37 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (36 bp):
ATCATGCATATAATCATTATTAGCAAGCGCATGTAT
Found at i:441214 original size:108 final size:108
Alignment explanation
Indices: 441081--441278 Score: 272
Period size: 108 Copynumber: 1.8 Consensus size: 108
441071 AGCGTGTGTA
* * * * *
441081 TATCATGCATGTAATCATCAGTAGCA-AGCTCAAGCATATAATGAATATGATCATTATTAGCATG
1 TATCATGCATGTAATCATCAATAGCAGA-CACAAGCATATAATCAATATAATCATTATTAGCAAG
*
441145 TGCATATATATCATGCATATAATCATTATTACCAAGAGTATGCG
65 CGCATATATATCATGCATATAATCATTATTACCAAGAGTATGCG
* * * * *
441189 TATCATGCATGTAATCATTAATAGCAGACACATGTATATCATCCATATAATCATTATTAGCAAGC
1 TATCATGCATGTAATCATCAATAGCAGACACAAGCATATAATCAATATAATCATTATTAGCAAGC
*
441254 GCATGTATATCATGCATATAATCAT
66 GCATATATATCATGCATATAATCAT
441279 CAACAATAAG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
108 76 0.99
109 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (108 bp):
TATCATGCATGTAATCATCAATAGCAGACACAAGCATATAATCAATATAATCATTATTAGCAAGC
GCATATATATCATGCATATAATCATTATTACCAAGAGTATGCG
Found at i:442138 original size:19 final size:19
Alignment explanation
Indices: 442102--442271 Score: 137
Period size: 19 Copynumber: 8.9 Consensus size: 19
442092 GACTTACCCT
* *
442102 TAAAGATCTGGTTCCCAACC
1 TAAA-ATCTGATTTCCAACC
442122 TAAAATCTGATTTCCAACC
1 TAAAATCTGATTTCCAACC
*
442141 TGAAATCT-AGTTTCCAACC
1 TAAAATCTGA-TTTCCAACC
* *
442160 TAAAATTTGGTTTCCAACC
1 TAAAATCTGATTTCCAACC
* * *
442179 TAAAATCTGGTTTGCAACT
1 TAAAATCTGATTTCCAACC
* * * *
442198 TGAAATATGTTTTCCAACA
1 TAAAATCTGATTTCCAACC
* *
442217 TGAAATCTGATTTTCAACC
1 TAAAATCTGATTTCCAACC
* * *
442236 TGAAATATGTTTTCCAACC
1 TAAAATCTGATTTCCAACC
*
442255 TTAAATCT-AGTTTCCAA
1 TAAAATCTGA-TTTCCAA
442272 TAGTGTGATC
Statistics
Matches: 123, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
18 1 0.01
19 118 0.96
20 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (19 bp):
TAAAATCTGATTTCCAACC
Found at i:442174 original size:38 final size:38
Alignment explanation
Indices: 442107--442271 Score: 179
Period size: 38 Copynumber: 4.3 Consensus size: 38
442097 ACCCTTAAAG
* * * *
442107 ATCTGGTTCCCAACCTAAAATCTGATTTCCAACCTGAA
1 ATCTAGTTTCCAACCTAAAATATGTTTTCCAACCTGAA
* * *
442145 ATCTAGTTTCCAACCTAAAATTTGGTTTCCAACCTAAA
1 ATCTAGTTTCCAACCTAAAATATGTTTTCCAACCTGAA
* * * * *
442183 ATCTGGTTTGCAACTTGAAATATGTTTTCCAACATGAA
1 ATCTAGTTTCCAACCTAAAATATGTTTTCCAACCTGAA
* * *
442221 ATCT-GATTTTCAACCTGAAATATGTTTTCCAACCTTAA
1 ATCTAG-TTTCCAACCTAAAATATGTTTTCCAACCTGAA
442259 ATCTAGTTTCCAA
1 ATCTAGTTTCCAA
442272 TAGTGTGATC
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 105 0.98
39 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (38 bp):
ATCTAGTTTCCAACCTAAAATATGTTTTCCAACCTGAA
Found at i:442202 original size:57 final size:57
Alignment explanation
Indices: 442102--442271 Score: 182
Period size: 57 Copynumber: 3.0 Consensus size: 57
442092 GACTTACCCT
* * *
442102 TAAAGATCTGGTTCCCAACCTAAAATCTGATTTCCAACCTGAAATCTAGTTTCCAACC
1 TAAA-ATCTGGTTTCCAACCTAAAATCTGATTTCCAACTTGAAATCTAGTTTCCAACA
* * * *
442160 TAAAATTTGGTTTCCAACCTAAAATCTGGTTTGCAACTTGAAATAT-GTTTTCCAACA
1 TAAAATCTGGTTTCCAACCTAAAATCTGATTTCCAACTTGAAATCTAG-TTTCCAACA
* * * * * *
442217 TGAAATCTGATTTTCAACCTGAAATATGTTTTCCAACCTT-AAATCTAGTTTCCAA
1 TAAAATCTGGTTTCCAACCTAAAATCTGATTTCCAA-CTTGAAATCTAGTTTCCAA
442272 TAGTGTGATC
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
56 1 0.01
57 84 0.90
58 8 0.09
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (57 bp):
TAAAATCTGGTTTCCAACCTAAAATCTGATTTCCAACTTGAAATCTAGTTTCCAACA
Found at i:445904 original size:3 final size:3
Alignment explanation
Indices: 445891--445952 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
445881 CCATTTTGAT
* *
445891 TTA TT- TTA TTA TTA TTA TTA TTA TTC TTA TTA -TA TTA TTA TTA -AA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
445936 TATA TTA TTA TTA TTA T
1 T-TA TTA TTA TTA TTA T
445953 ATATATTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 5 0.10
3 44 0.86
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:445972 original size:15 final size:15
Alignment explanation
Indices: 445929--445972 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
445919 ATTATATTAT
445929 TATTAAATATAT-TA
1 TATTAAATATATATA
445943 TTATT--AT-TATATA
1 -TATTAAATATATATA
445956 TATTAAATATATATA
1 TATTAAATATATATA
445971 TA
1 TA
445973 AATAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.28
13 4 0.16
14 2 0.08
15 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAAATATATATA
Found at i:447803 original size:150 final size:153
Alignment explanation
Indices: 447547--447851 Score: 573
Period size: 151 Copynumber: 2.0 Consensus size: 153
447537 TTTGGTTATA
447547 AACGCAGATCGTTCATTTTTTAATTGATGTTTTCTTAAAACTCTTTTAAAAAAAATAATTTTTAG
1 AACGCAGATCGTTCATTTTTTAATTGATGTTTTCTTAAAACTCTTTTAAAAAAAATAATTTTTAG
447612 GTATTCGAACCTACCTGACCCAAAAGGCCGATGGCGACTCCCAATTATTTT-CAAAAACCATTTA
66 GTATTCGAACCTACCTGACCCAAAAGGCCGATGGCGACTCCCAATTATTTTCCAAAAACCATTTA
447676 TTCACATCAATTTCCCGCCAAAT
131 TTCACATCAATTTCCCGCCAAAT
447699 AACGCAGATCAGTTCATTTTTTAATTGATGTTTTCTTAAAACTCTTTT-AAAAAAAT-ATTTTTA
1 AACGCAGATC-GTTCATTTTTTAATTGATGTTTTCTTAAAACTCTTTTAAAAAAAATAATTTTTA
447762 GGTATTCG-ACCTACCTGACCCAAAAGGCCGATGGCGACTCCCAATTATTTTCCAAAAACCATTT
65 GGTATTCGAACCTACCTGACCCAAAAGGCCGATGGCGACTCCCAATTATTTTCCAAAAACCATTT
447826 ATTCACATCAATTTCCCGCCAAAT
130 ATTCACATCAATTTCCCGCCAAAT
447850 AA
1 AA
447852 ATATTTCGTA
Statistics
Matches: 151, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
150 43 0.28
151 53 0.35
152 18 0.12
153 37 0.25
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (153 bp):
AACGCAGATCGTTCATTTTTTAATTGATGTTTTCTTAAAACTCTTTTAAAAAAAATAATTTTTAG
GTATTCGAACCTACCTGACCCAAAAGGCCGATGGCGACTCCCAATTATTTTCCAAAAACCATTTA
TTCACATCAATTTCCCGCCAAAT
Found at i:451243 original size:15 final size:15
Alignment explanation
Indices: 451223--451254 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
451213 ATCAATATCT
451223 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
451238 TTTTGCATACATTCA
1 TTTTGCATACATGCA
451253 TT
1 TT
451255 ATTCATTTCA
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:458662 original size:15 final size:16
Alignment explanation
Indices: 458642--458675 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
458632 TTCTATCTAT
458642 TTTAAG-TTCAATTTA
1 TTTAAGATTCAATTTA
458657 TTTAAGATTCAATTTA
1 TTTAAGATTCAATTTA
458673 TTT
1 TTT
458676 TCAAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAGATTCAATTTA
Found at i:459991 original size:92 final size:83
Alignment explanation
Indices: 459686--459993 Score: 442
Period size: 92 Copynumber: 3.6 Consensus size: 83
459676 AACAAATGCC
* * *
459686 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
459750 ATT-AATTT-GAAGAGGA
66 ATTGAATTTGGAAGAGGA
459766 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
459831 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
459849 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-AA--A-A
* *
459914 TAACCATTTATTGAATTTGGAAGAGGA
60 T---CAATCATTGAATTTGGAAGAGGA
* * *
459941 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
459994 ATATAAAACC
Statistics
Matches: 208, Mismatches: 8, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
80 49 0.24
81 15 0.07
82 5 0.02
83 62 0.30
85 1 0.00
86 2 0.01
88 1 0.00
89 2 0.01
92 71 0.34
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGA
Found at i:460478 original size:94 final size:95
Alignment explanation
Indices: 460316--460514 Score: 382
Period size: 94 Copynumber: 2.1 Consensus size: 95
460306 TATTCTCCTC
*
460316 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
460381 AAAGGTCACTTCATAATCAGATGAGTTGTT
66 AAAGGTCACTTCATAATCAGATGAGTTGTT
460411 ATCAGAATCAGAAATCAAGATTTCTCGGT-TTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
460475 AAAGGTCACTTCATAATCAGATGAGTTGTT
66 AAAGGTCACTTCATAATCAGATGAGTTGTT
460505 ATCAGAATCA
1 ATCAGAATCA
460515 ACATGTTGCA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 75 0.73
95 28 0.27
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
AAAGGTCACTTCATAATCAGATGAGTTGTT
Found at i:461098 original size:124 final size:123
Alignment explanation
Indices: 460954--461355 Score: 474
Period size: 123 Copynumber: 3.3 Consensus size: 123
460944 CATTTGCCAG
* * *
460954 AAGTGTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGT-TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTAT
* * * * * *
461019 TTAATCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAGAGA
65 TCAACCTTTTGCT-GACTCTATCACAGAAGGAGATAGATAGGCAACAACATTTCCAGAGA
* * *
461079 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTCTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATT
* * * * *
461143 CAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTA-GCATCAACCTTTCCAGAGA
66 CAACCTTTTGC-TGACTCTATCACAGAAGGAGATAGA-TAGGCAACAACATTTCCAGAGA
* *
461202 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAAAATAAGAAGAGCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATT
* * * ** *
461267 CAACCTTTGGAATGACTCTATCACAGAA-GA-A-A-ATAGGTCAACATCATCCCCAGCGGA
66 CAACCTTTTG-CTGACTCTATCACAGAAGGAGATAGATAGG-CAACAACATTTCCAG-AGA
461324 AAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAA
461356 AGAGAAAAAT
Statistics
Matches: 241, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
119 2 0.01
120 2 0.01
121 11 0.05
122 35 0.15
123 107 0.44
124 80 0.33
125 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (123 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATT
CAACCTTTTGCTGACTCTATCACAGAAGGAGATAGATAGGCAACAACATTTCCAGAGA
Found at i:461516 original size:3 final size:3
Alignment explanation
Indices: 461508--461566 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
461498 TTAAATTTAT
* * *
461508 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TTA -TA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
461555 TTA TTA TTA TTA
1 TTA TTA TTA TTA
461567 ATATATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:466945 original size:15 final size:15
Alignment explanation
Indices: 466925--466956 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
466915 ATCAATACAT
466925 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
466940 TTTTGCATACATTCA
1 TTTTGCATACATGCA
466955 TT
1 TT
466957 ATTCATTTCA
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:473796 original size:83 final size:82
Alignment explanation
Indices: 473650--473914 Score: 316
Period size: 92 Copynumber: 3.1 Consensus size: 82
473640 GATGACCGAA
* * * *
473650 CTGGTTTGGTAGAACCAGTCATT-AATTTTGAAGAGGAATGTGCTCATAGCATTTTCTGGAAGTG
1 CTGGTTTGGTA-AAACAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTG
473714 TTCTTTGAGTTATCTGAT
65 TTCTTTGAGTTATCTGAT
**
473732 CTGGTTTGGTAAAATCAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTATAAGTG
1 CTGGTTTGGTAAAA-CAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTG
473797 TTCTTTGAGTTATCTGAT
65 TTCTTTGAGTTATCTGAT
* * *
473815 CTGGATTGGTATGAACCACAGAACCATTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTT
1 CTGGTTTGGTA--AA--AC---A--A-TCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTT
*
473880 CTGGAAGTGTTCTTTGAGTTCTCTGAT
56 CTGGAAGTGTTCTTTGAGTTATCTGAT
*
473907 TTGGTTTG
1 CTGGTTTG
473915 ATATAAAACC
Statistics
Matches: 157, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
81 2 0.01
82 18 0.11
83 65 0.41
85 2 0.01
86 1 0.01
87 1 0.01
89 1 0.01
91 1 0.01
92 66 0.42
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (82 bp):
CTGGTTTGGTAAAACAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGT
TCTTTGAGTTATCTGAT
Found at i:474403 original size:94 final size:95
Alignment explanation
Indices: 474241--474439 Score: 364
Period size: 94 Copynumber: 2.1 Consensus size: 95
474231 TATTCTCCTC
*
474241 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
* *
474306 AAAGGTCACTTTATAATCAGATGAGTTGTT
66 AAAGGTCACTTCATAATCAGATAAGTTGTT
474336 ATCAGAATCAGAAATCAAGATTTCTCGGT-TTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
474400 AAAGGTCACTTCATAATCAGATAAGTTGTT
66 AAAGGTCACTTCATAATCAGATAAGTTGTT
474430 ATCAGAATCA
1 ATCAGAATCA
474440 ACATGTTGCA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 73 0.72
95 28 0.28
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (95 bp):
ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
AAAGGTCACTTCATAATCAGATAAGTTGTT
Found at i:474948 original size:113 final size:113
Alignment explanation
Indices: 474750--474963 Score: 360
Period size: 113 Copynumber: 1.9 Consensus size: 113
474740 CCATCATTCA
*
474750 ATGGATCAACATTGCTAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
474815 TCATAATGAGAAGAACTTGTTCAA-CTTTTTGCTCGAATTCATCTCTTG
66 TCATAATGAGAAGAACTTGTTCAATC-TTTTGCTCGAATTCATCTCTTG
*
474863 ATGGATCAACATTTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACA-TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
474927 TTCATAATGAGAATAACTTGTTTAATCTTTTGCTCGA
65 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGA
474964 CGCTATCACA
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 87 0.92
114 8 0.08
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (113 bp):
ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGAATTCATCTCTTG
Found at i:475097 original size:123 final size:124
Alignment explanation
Indices: 474869--475293 Score: 472
Period size: 123 Copynumber: 3.5 Consensus size: 124
474859 CTTGATGGAT
** *
474869 CAACATTTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 CAACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAA
* * * * * * * *
474933 ATGAGAATAACTTGTTTAATCTTTTGC-TCGACGCTATCACAGAAGGAGATAGATCGGCAC
65 ATGAGAAGAGCTTATTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATAGGCAA
* * *
474993 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCACAA
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
* * * * *
475057 TGAGAAGAGCTTCTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTA-GCAT
66 TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGA-TAGGCAA
* * *
475116 CAACCTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAAAA
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
* * *
475181 TAAGAAGAGCTTATTCAACCTTTGGAATGACTCTATCACAGAA-GA-A-A-ATAGGTCAA
66 TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATAGG-CAA
* ** * *
475237 CATCATCCCCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 CAACATTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
475294 TTTATTCAAC
Statistics
Matches: 257, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
119 2 0.01
120 2 0.01
121 17 0.07
122 35 0.14
123 110 0.43
124 91 0.35
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (124 bp):
CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATAGGCAA
Found at i:475448 original size:3 final size:3
Alignment explanation
Indices: 475440--475526 Score: 120
Period size: 3 Copynumber: 29.0 Consensus size: 3
475430 TTAAATTTAT
* * * *
475440 TTA TTA TTA TTA ATA CTA TAA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
475488 TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
475527 AATATATATA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:478501 original size:15 final size:16
Alignment explanation
Indices: 478476--478510 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
478466 GGTAAAACTC
*
478476 TCTTCTTTGTTTTGTT
1 TCTTCTTTGTTTTGGT
478492 TCTT-TTTGTTTTGGT
1 TCTTCTTTGTTTTGGT
478507 TCTT
1 TCTT
478511 AGGTCCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (16 bp):
TCTTCTTTGTTTTGGT
Found at i:479945 original size:54 final size:54
Alignment explanation
Indices: 479882--480526 Score: 835
Period size: 54 Copynumber: 11.9 Consensus size: 54
479872 TTACCAAATA
* * *
479882 GGCACTAAGTGTGCATTTCATGGAATTCATCATATGTTGATGAATGACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
479936 GGCACTAAGTGTGCATTTAACAGAATTCAGCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
*** **
479990 GGCACTAAGTGTGCATTTCATAAAATTCATCATATGTTGATGAATGACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
480044 GGTACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
480098 GACACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
480152 GGCACTAAGTGTGTC-TTTCACGGAACTCATCATATGTTGATGAATGACCGTTTT
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* ** **
480206 GGCACTAAGTGTGTC-TTTCATGGAATTCATCATAAATTGATGAATGACCAATTC
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * *
480260 AGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * * **
480314 GGCAGTCAGTGTTCATTTCACGGAATTCATTATATATTGATGAATGACCAATTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* ** *
480368 GGCACTAAGTTTGCATTTCACATAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * *
480422 GGCACTAAGTGTGAATTTCAAGGAATTCATCATATGTTGATGAATGACCCTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * *
480476 GGCACTAAGTGTTCATTTCACGGAATTCATAATATGTTTATGAATAACCGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGT
480527 ATGGGTACTA
Statistics
Matches: 505, Mismatches: 84, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
54 504 1.00
55 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
Found at i:484442 original size:54 final size:54
Alignment explanation
Indices: 484365--484705 Score: 504
Period size: 54 Copynumber: 6.3 Consensus size: 54
484355 TTACCAAATA
484365 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
484419 GGCACTAAATGTGAATTTAACGGAATTCATCATATATTGATGAATGACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
484473 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
484527 GGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATGACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
** * *
484581 GATACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGCCCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
484635 GGCACTAAGTGTGCATTTCACGGAA-TCTGTAATATGTTTATGAATGACCGTATG
1 GGCACTAAGTGTGCATTTCACGGAATTC-ATCATATGTTGATGAATGACCGTTTC
* *
484689 GGCACTATGGGTGCATT
1 GGCACTAAGTGTGCATT
484706 ATAAAGAAAT
Statistics
Matches: 257, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.01
54 255 0.99
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
Found at i:485468 original size:24 final size:24
Alignment explanation
Indices: 485439--485492 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
485429 GGACCTACAA
**
485439 AATAAAATAAAATG-TTTTAATAAT
1 AATAAAAT-AAATGATAATAATAAT
485463 AATAAAATAAATGATAATAATAAT
1 AATAAAATAAATGATAATAATAAT
485487 AATAAA
1 AATAAA
485493 TAGACTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AATAAAATAAATGATAATAATAAT
Found at i:488951 original size:21 final size:21
Alignment explanation
Indices: 488895--488951 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
488885 TTTTCGTAAG
*
488895 AGTACTTTGTGTAATTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
488916 AGTACTTTGTATACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
488937 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
488952 ATGGCACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:489529 original size:4 final size:4
Alignment explanation
Indices: 489520--491245 Score: 3292
Period size: 4 Copynumber: 435.5 Consensus size: 4
489510 TTTAACATTA
489520 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489568 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489616 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489664 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489709 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489757 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489805 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489853 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489901 TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489948 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
489996 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490044 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490092 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490140 TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490187 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490235 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490283 TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490329 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490376 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490424 TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490471 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490519 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490565 TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490611 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490657 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490705 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490752 TATG TATG TATG TATG TATG TATG TAGTG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TA-TG TATG TATG TATG TATG TATG
490801 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490849 TATG TATG TATG TATG TATG -ATG TATGG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TAT-G TATG TATG TATG TATG TATG
490897 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490945 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
490993 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
491041 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
491089 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
491137 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
491183 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TTATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG -TATG
491232 TATG TATG TATG TA
1 TATG TATG TATG TA
491246 ATGACATCAC
Statistics
Matches: 1700, Mismatches: 0, Indels: 44
0.97 0.00 0.03
Matches are distributed among these distances:
2 12 0.01
3 21 0.01
4 1655 0.97
5 12 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:492498 original size:16 final size:15
Alignment explanation
Indices: 492472--492501 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
492462 TCTATCTATT
492472 TTAAGTTCAATTTAA
1 TTAAGTTCAATTTAA
492487 TTAAGATTCAATTTA
1 TTAAG-TTCAATTTA
492502 TTTTCGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TTAAGTTCAATTTAA
Found at i:493614 original size:82 final size:83
Alignment explanation
Indices: 493515--493824 Score: 451
Period size: 83 Copynumber: 3.6 Consensus size: 83
493505 AACAAATGCC
493515 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
*
493580 ATT-AATTTTGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* * *
493597 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
493662 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
493680 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAA-C-CA
*
493745 GAACCATTTATTGAATTTGGAAGAGGA
63 G------TCATTGAATTTGGAAGAGGA
* * *
493772 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
493825 ATATAAAACC
Statistics
Matches: 205, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
82 65 0.32
83 68 0.33
84 2 0.01
86 2 0.01
92 68 0.33
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
ATTGAATTTGGAAGAGGA
Found at i:493822 original size:92 final size:90
Alignment explanation
Indices: 493515--493854 Score: 426
Period size: 92 Copynumber: 3.9 Consensus size: 90
493505 AACAAATGCC
*
493515 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAA-C-CAG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAACCACAG
*
493578 -----TCATT-AATTTTGAAGAGGA
66 AACCATCATTGAATTTGGAAGAGGA
493597 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AA--ATC-
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAACCA-CA
493658 --A--ATCATTGAATTTGGAAGAGGA
65 GAACCATCATTGAATTTGGAAGAGGA
*
493680 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AACCACA
*
493745 GAACCATTTATTGAATTTGGAAGAGGA
65 GAACCA-TCATTGAATTTGGAAGAGGA
* * * *
493772 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTGATATAAAACC-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT--AACCAC
493836 AGAACCAATCATTGGAATT
64 AGAACC-ATCATT-GAATT
493855 AAAAGATGAA
Statistics
Matches: 230, Mismatches: 10, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
81 2 0.01
82 62 0.27
83 68 0.30
85 2 0.01
86 1 0.00
87 1 0.00
89 1 0.00
91 1 0.00
92 82 0.36
93 10 0.04
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (90 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAACCACAG
AACCATCATTGAATTTGGAAGAGGA
Found at i:494313 original size:94 final size:95
Alignment explanation
Indices: 494151--494349 Score: 382
Period size: 94 Copynumber: 2.1 Consensus size: 95
494141 TATTCTCCTC
*
494151 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
494216 AAAGGTCACTTCATAATCAGATGAGTTGTT
66 AAAGGTCACTTCATAATCAGATGAGTTGTT
494246 ATCAGAATCAGAAATCAAGATTTCTCGGT-TTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
494310 AAAGGTCACTTCATAATCAGATGAGTTGTT
66 AAAGGTCACTTCATAATCAGATGAGTTGTT
494340 ATCAGAATCA
1 ATCAGAATCA
494350 ACATGTTGCA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 75 0.73
95 28 0.27
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCAGAATCAGAAATCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
AAAGGTCACTTCATAATCAGATGAGTTGTT
Found at i:494857 original size:112 final size:113
Alignment explanation
Indices: 494660--494872 Score: 358
Period size: 112 Copynumber: 1.9 Consensus size: 113
494650 CCATCATTCA
* *
494660 ATGGATCAGCATTGCTAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
494725 TCATAATGAGAAGAACTTGTTCAA-CTTTTGCTCGAATTCATCTCTTG
66 TCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGAATTCATCTCTTG
*
494772 ATGGATCAACATTTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACA-TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
494836 TTCATAATGAGAATAACTTGTTTAATCTTTTGCTCGA
65 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGA
494873 CGCTATCACA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 76 0.81
113 18 0.19
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (113 bp):
ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGAATTCATCTCTTG
Found at i:495006 original size:123 final size:124
Alignment explanation
Indices: 494795--495202 Score: 486
Period size: 123 Copynumber: 3.3 Consensus size: 124
494785 TGCCAGAAGT
* * * * *
494795 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATTCA
* * * * *
494860 ATCTTTTGC-TCGACGCTATCACAGAAGGAGATAGATCGGCACCAACTTTTCCAGAGAAA
66 ACCTTTTGCAT-GACTCTATCACAGAAGCAGATAGATCAGCACCAACCTTTCCAGAGAAA
* * *
494919 GTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTCTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATTCA
* * * *
494983 ACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATCAACCTTTCCAGAGAAA
66 ACCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACCAACCTTTCCAGAGAAA
* *
495042 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAAAATAAGAAGAGCTTATTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATTCA
* * * * * * * * *
495107 ACCTTTGGAATGACTCTATCACAGAAGAAAATAGGTCAACATCATCC---CCAGCGGAAA
66 ACCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACCAACCTTTCCAG-AGAAA
* *
495164 GTTCATATTGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
495203 TTTATTCAAC
Statistics
Matches: 247, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
121 11 0.04
122 33 0.13
123 106 0.43
124 97 0.39
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (124 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTATTCA
ACCTTTTGCATGACTCTATCACAGAAGCAGATAGATCAGCACCAACCTTTCCAGAGAAA
Found at i:495358 original size:3 final size:3
Alignment explanation
Indices: 495350--495436 Score: 120
Period size: 3 Copynumber: 29.0 Consensus size: 3
495340 TTAAATTTAT
* * *
495350 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
495398 TAA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
495437 AATATATATA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:498404 original size:15 final size:16
Alignment explanation
Indices: 498379--498413 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
498369 GGTAAAACTC
*
498379 TCTTCTTTGTTTTGTT
1 TCTTCTTTGTTTTGGT
498395 TCTT-TTTGTTTTGGT
1 TCTTCTTTGTTTTGGT
498410 TCTT
1 TCTT
498414 AGGTCCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (16 bp):
TCTTCTTTGTTTTGGT
Found at i:499846 original size:54 final size:54
Alignment explanation
Indices: 499783--500427 Score: 817
Period size: 54 Copynumber: 11.9 Consensus size: 54
499773 TTACCAAATA
* * *
499783 GGCACTAAGTGTGCATTTCATGGAATTCATCATATGTTGATGAATGACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
499837 GGCACTAAGTGTGCATTTAACAGAATTCAGCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
*** **
499891 GGCACTAAGTGTGCATTTCATAAAATTCATCATATGTTGATGAATGACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
499945 GGTACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
499999 GACACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
500053 GGCACTAAGTGTGTC-TTTCACGGAACTCATCATATGTTGATGAATGACCGTTTT
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* ** **
500107 GGCACTAAGTGTGTC-TTTCATGGAATTCATCATAAATTGATGAATGACCAATTC
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * *
500161 AGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * * **
500215 GGCAGTCAGTGTTCATTTCACGGAATTCATTATATATTGATGAATGACCAATTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* ** * *
500269 GGCACTAAGTTTGCATTTCACATAATTCATCATATGTTGATGAATGATCGTTAC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
500323 GGCACTAAGTGTGAATTTCAAGGAATTCAACATATGTTGATGAATGACCCTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * *
500377 GGCACTAAGTGTTCATTTCACGGAATTCATAATATGTTTATGAATAACCGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGT
500428 ATGGGTACTA
Statistics
Matches: 501, Mismatches: 88, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
54 500 1.00
55 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
Found at i:507098 original size:54 final size:54
Alignment explanation
Indices: 507021--507361 Score: 511
Period size: 54 Copynumber: 6.3 Consensus size: 54
507011 TTACCAAATA
507021 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
507075 GGCACTAAATGTGAATTTAACGGAATTCATCATATATTGATGAATGACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
507129 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
*
507183 GGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
** * *
507237 GATACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGCCCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * * * *
507291 GGCACTAAGTGTGCATTTCACGGAATCCGTAATATGTTTATGAATGATCGTATG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
507345 GGCACTATGGGTGCATT
1 GGCACTAAGTGTGCATT
507362 ATAAAGAAAT
Statistics
Matches: 258, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 258 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
Found at i:508124 original size:24 final size:24
Alignment explanation
Indices: 508095--508148 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
508085 GGACCTGCAA
**
508095 AATAAAATAAAATG-TTTTAATAAT
1 AATAAAAT-AAATGATAATAATAAT
508119 AATAAAATAAATGATAATAATAAT
1 AATAAAATAAATGATAATAATAAT
508143 AATAAA
1 AATAAA
508149 TAGACTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AATAAAATAAATGATAATAATAAT
Found at i:511605 original size:21 final size:21
Alignment explanation
Indices: 511549--511605 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
511539 TTTTCGTAAG
*
511549 AGTACTTTGTGTAATTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
511570 AGTACTTTGTATACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
511591 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
511606 ATGGCACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:512183 original size:4 final size:4
Alignment explanation
Indices: 512174--514971 Score: 5449
Period size: 4 Copynumber: 704.8 Consensus size: 4
512164 TTTAACATTA
512174 TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512220 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512266 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512314 TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512360 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512408 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512456 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512504 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512552 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512600 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512648 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512696 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512744 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512792 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512840 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512888 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512936 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
512982 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513030 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513078 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513126 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513174 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513222 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513270 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513318 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513364 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513412 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513460 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513508 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513556 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513604 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513652 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513700 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513748 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513796 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513844 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513892 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513940 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
513988 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514034 TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514079 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514127 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514173 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514219 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514267 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514315 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514363 TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514409 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514457 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514505 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514553 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514601 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514649 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514697 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514745 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514793 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514841 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514889 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
514937 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
514972 TTGAAGAATG
Statistics
Matches: 2773, Mismatches: 0, Indels: 42
0.99 0.00 0.01
Matches are distributed among these distances:
2 20 0.01
3 3 0.00
4 2750 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:515165 original size:30 final size:30
Alignment explanation
Indices: 515129--515199 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
515119 CCTTACTTCT
515129 TGTACTATTTAACATTGGTGGCCAAGTCCC
1 TGTACTATTTAACATTGGTGGCCAAGTCCC
* *
515159 TGTACTATTTAACCTTGGTGGTCAAGTCCC
1 TGTACTATTTAACATTGGTGGCCAAGTCCC
*
515189 TATACTATTTA
1 TGTACTATTTA
515200 GTTCTTAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (30 bp):
TGTACTATTTAACATTGGTGGCCAAGTCCC
Found at i:515587 original size:25 final size:25
Alignment explanation
Indices: 515534--515598 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
515524 TTTCGAAAGG
*
515534 TGAAAATGTTTGA-GAAATAAGTTT
1 TGAAAATGTTTGATGAAAGAAGTTT
*
515558 TGAAAATGTTTTATGAAAGAA-TTT
1 TGAAAATGTTTGATGAAAGAAGTTT
*
515582 TGGAAAATATTTGATGA
1 T-GAAAATGTTTGATGA
515599 TGTTTTGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (25 bp):
TGAAAATGTTTGATGAAAGAAGTTT
Found at i:516098 original size:5 final size:5
Alignment explanation
Indices: 516082--516143 Score: 108
Period size: 5 Copynumber: 12.6 Consensus size: 5
516072 ACTGAAACTC
*
516082 TTTAA TTT-A TTTAA TTTAA TTTAA TTTAA ATTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
516131 TTTAA TTTAA TTT
1 TTTAA TTTAA TTT
516144 TCCTTTGTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
4 4 0.07
5 50 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:522851 original size:13 final size:13
Alignment explanation
Indices: 522830--522894 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
522820 AATGACGCTC
522830 AATGCGCGTCATA
1 AATGCGCGTCATA
*
522843 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
522856 AATGTGTGTCATA
1 AATGCGCGTCATA
*
522869 AATGCGTGTCATA
1 AATGCGCGTCATA
522882 AATGCGCGTCATA
1 AATGCGCGTCATA
522895 GATTTATGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:525593 original size:3 final size:3
Alignment explanation
Indices: 525578--525625 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
525568 TAAAATGTAT
*
525578 TAA TAA TAT TAA TAA TAA TAA -AA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
525623 TAA
1 TAA
525626 AGAGACCTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:525608 original size:27 final size:28
Alignment explanation
Indices: 525561--525626 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
525551 AGGCCTACAA
* * *
525561 AATAA-AATAAAATGTATTAATAATATT
1 AATAATAATAAAATGAAATAATAATAAT
525588 AATAATAATAAAAT-AAATAATAATAAT
1 AATAATAATAAAATGAAATAATAATAAT
525615 AATAATAATAAA
1 AATAATAATAAA
525627 GAGACCTGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 27 0.77
28 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
AATAATAATAAAATGAAATAATAATAAT
Found at i:526996 original size:36 final size:36
Alignment explanation
Indices: 526899--527194 Score: 296
Period size: 36 Copynumber: 8.2 Consensus size: 36
526889 AGATCATTCC
** * * * * *
526899 TATAATCATTATTCTCAATCATATGAATACCATCCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
** *
526935 TATAATCATTAGCAACAAGCACATGTATATCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
* * * * *
526971 TGTAACCATCAGTAGCAAGCGCATGTATATCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
* *
527007 TAT-ATCATTATTAG-AAGGCGCGTGTATATCATGCA
1 TATAATCATTATTAGCAA-GCACATGTATATCATGCA
* * *
527042 TATAATGATTATTAGCAAGCACAAGTATACCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
*
527078 TATAATCATTATTAGC-AGACACATGTATATCATACA
1 TATAATCATTATTAGCAAG-CACATGTATATCATGCA
* *
527114 TATGATCATTATTAG-AAGGCACATGTATATCAAGCA
1 TATAATCATTATTAGCAA-GCACATGTATATCATGCA
* *
527150 TATAATCATTATTAGAAAGCGA-ATATATATCATGCA
1 TATAATCATTATTAGCAAGC-ACATGTATATCATGCA
527186 TATAATCAT
1 TATAATCAT
527195 CAACAACTAG
Statistics
Matches: 217, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
34 2 0.01
35 30 0.14
36 179 0.82
37 6 0.03
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (36 bp):
TATAATCATTATTAGCAAGCACATGTATATCATGCA
Found at i:528087 original size:38 final size:38
Alignment explanation
Indices: 528027--528290 Score: 242
Period size: 38 Copynumber: 6.9 Consensus size: 38
528017 AAAGATATGG
* * * *
528027 TTTCCAACCTAAAATATCGTTTCCAACCTGAAATTTGA
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATCTGA
* * * *
528065 TTTCCAACCTGAAATCTGGTTTCCAACTTGAAATCTAA
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATCTGA
* * * ** * *
528103 TTTCCAACTTGAAATCTAATTTCCAACTTGAAAT-TCAA
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATCT-GA
**
528141 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATAGGGA
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAAT-CTGA
* ** * *
528180 TTTCTAACCTGAAATCATCATATCCAATCTGAAATCTGA
1 TTTCTAACCTAAAATC-TGGTTTCCAACCTGAAATCTGA
* *
528219 TTTCTAACCTAAAATCTGGTTTTCAACCTAAAATCTGA
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATCTGA
* * * *
528257 TTTTTAACCTAAAATATGATTTCCAACCAGAAAT
1 TTTCTAACCTAAAATCTGGTTTCCAACCTGAAAT
528291 ATGTTTTCAT
Statistics
Matches: 185, Mismatches: 37, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
37 1 0.01
38 137 0.74
39 33 0.18
40 14 0.08
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (38 bp):
TTTCTAACCTAAAATCTGGTTTCCAACCTGAAATCTGA
Found at i:528293 original size:19 final size:19
Alignment explanation
Indices: 528027--528290 Score: 217
Period size: 19 Copynumber: 13.8 Consensus size: 19
528017 AAAGATATGG
* *
528027 TTTCCAACCTAAAATATCG-
1 TTTCCAACCTGAAATCT-GA
*
528046 TTTCCAACCTGAAATTTGA
1 TTTCCAACCTGAAATCTGA
*
528065 TTTCCAACCTGAAATCTGG
1 TTTCCAACCTGAAATCTGA
* *
528084 TTTCCAACTTGAAATCTAA
1 TTTCCAACCTGAAATCTGA
* *
528103 TTTCCAACTTGAAATCTAA
1 TTTCCAACCTGAAATCTGA
* *
528122 TTTCCAACTTGAAAT-TCAA
1 TTTCCAACCTGAAATCT-GA
* * *
528141 TTTCTAACCTAAAATCTGG
1 TTTCCAACCTGAAATCTGA
**
528160 TTTCCAACCTGAAATAGGGA
1 TTTCCAACCTGAAAT-CTGA
* *
528180 TTTCTAACCTGAAATCATCA
1 TTTCCAACCTGAAATC-TGA
* *
528200 TATCCAATCTGAAATCTGA
1 TTTCCAACCTGAAATCTGA
* * *
528219 TTTCTAACCTAAAATCTGG
1 TTTCCAACCTGAAATCTGA
* *
528238 TTTTCAACCTAAAATCTGA
1 TTTCCAACCTGAAATCTGA
** * *
528257 TTTTTAACCTAAAATATGA
1 TTTCCAACCTGAAATCTGA
*
528276 TTTCCAACCAGAAAT
1 TTTCCAACCTGAAAT
528291 ATGTTTTCAT
Statistics
Matches: 201, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
18 2 0.01
19 169 0.84
20 30 0.15
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (19 bp):
TTTCCAACCTGAAATCTGA
Found at i:529824 original size:56 final size:56
Alignment explanation
Indices: 529738--529849 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
529728 TCTTTTGTTC
*
529738 TTAGAAGATAAACCTTTGTATATCTATGTGAACATATACAAAGGTGATATAATAGT
1 TTAGAAGATAAACCTTTGTATATATATGTGAACATATACAAAGGTGATATAATAGT
* *
529794 TTAGAAGATAAACCTTTGTATATATGTGTGATCATATACAAAGGTGATATAATAGT
1 TTAGAAGATAAACCTTTGTATATATATGTGAACATATACAAAGGTGATATAATAGT
529850 GTTTTCCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (56 bp):
TTAGAAGATAAACCTTTGTATATATATGTGAACATATACAAAGGTGATATAATAGT
Found at i:539861 original size:21 final size:21
Alignment explanation
Indices: 539837--539877 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
539827 CAATTATGGG
* *
539837 TATTTAATGTTGAATTTTAAT
1 TATTGAATGTTGAAGTTTAAT
539858 TATTGAATGTTGAAGTTTAA
1 TATTGAATGTTGAAGTTTAA
539878 GTTGGAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
TATTGAATGTTGAAGTTTAAT
Found at i:542063 original size:21 final size:22
Alignment explanation
Indices: 542039--542080 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
542029 TTGAAGAATT
542039 TTTGTAGA-AAGAG-AGAAATGC
1 TTTG-AGAGAAGAGAAGAAATGC
*
542060 TTTGAGAGCAGAGAAGAAATG
1 TTTGAGAGAAGAGAAGAAATG
542081 TTTTCTACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 7 0.39
ACGTcount: A:0.43, C:0.05, G:0.31, T:0.21
Consensus pattern (22 bp):
TTTGAGAGAAGAGAAGAAATGC
Done.