Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 51
Found at i:347883 original size:78 final size:80
Alignment explanation
Indices: 347707--347881 Score: 218
Period size: 78 Copynumber: 2.2 Consensus size: 80
347697 ATATACTTTG
*
347707 TATTATATGCT-TATATACTTTAGTCTTTATAATTATACTTTATATATATATAATATACTTATAC
1 TATTATATACTATATATACTTTAGTCTTTATAATTATAC-TTATATATATATAATATACTTATAC
347771 TTTATATTATTATATA
65 TTTATATTATTATATA
* * *
347787 TACTTTATATACTA-ATATACTTTATTCTTTATAATTGTAC-T-T-TATATATAATATGCTTATA
1 TA--TTATATACTATATATACTTTAGTCTTTATAATTATACTTATATATATATAATATACTTATA
*
347848 CTTTATATTATTATATG
64 CTTTATATTATTATATA
* *
347865 TA-TATATGCTTTATATA
1 TATTATATACTATATATA
347882 TATATATATA
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
75 7 0.08
76 5 0.06
78 36 0.43
79 1 0.01
80 3 0.04
82 32 0.38
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (80 bp):
TATTATATACTATATATACTTTAGTCTTTATAATTATACTTATATATATATAATATACTTATACT
TTATATTATTATATA
Found at i:347902 original size:39 final size:38
Alignment explanation
Indices: 347851--347960 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 38
347841 GCTTATACTT
* ** *
347851 TATAT-TAT-TATATGTATATATGCTTTATATATATATA
1 TATATATATATATATATATATATAATTTATACATAT-TA
347888 TATATATATATATATATATATATAATTTATACATATTA
1 TATATATATATATATATATATATAATTTATACATATTA
* * *
347926 TATATA-ATATATA-ATTATACATAATATATAAATAT
1 TATATATATATATATA-TATATATAATTTATACATAT
347961 AAGCTGTACA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
36 1 0.02
37 29 0.46
38 11 0.17
39 22 0.35
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (38 bp):
TATATATATATATATATATATATAATTTATACATATTA
Found at i:347936 original size:37 final size:38
Alignment explanation
Indices: 347879--347961 Score: 64
Period size: 41 Copynumber: 2.1 Consensus size: 38
347869 TATGCTTTAT
* * *
347879 ATATATATATATATATATATATATATATATATAATTTATA
1 ATATATATATATATATA-ATTTATAAATATAT-ATATATA
*
347919 CATATTATATATAATATATAA-TTATACATA-ATATATA-A
1 -ATA-TATATAT-ATATATAATTTATAAATATATATATATA
347957 ATATA
1 ATATA
347962 AGCTGTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
36 2 0.05
37 3 0.08
38 1 0.03
39 4 0.11
40 2 0.05
41 10 0.27
42 8 0.22
43 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (38 bp):
ATATATATATATATATAATTTATAAATATATATATATA
Found at i:347970 original size:24 final size:24
Alignment explanation
Indices: 347876--347972 Score: 76
Period size: 24 Copynumber: 4.0 Consensus size: 24
347866 ATATATGCTT
*
347876 TATAT-ATATAT-A-TATATATATA
1 TATATAATATATAACTATACATA-A
*
347898 TATATATATATATAATTTATACATATTA
1 TATATA-ATATATAA-CTATACATA--A
*
347926 TATATAATATATAATTATACATAA
1 TATATAATATATAACTATACATAA
*
347950 TATATAA-ATATAAGCTGTACATA
1 TATATAATATATAA-CTATACATA
347973 GTTAAATATA
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
22 5 0.08
23 6 0.09
24 21 0.32
25 1 0.02
26 9 0.14
27 15 0.23
28 8 0.12
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
TATATAATATATAACTATACATAA
Found at i:348117 original size:14 final size:15
Alignment explanation
Indices: 348075--348125 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
348065 AATATATATA
* *
348075 TATATATATATA-TA
1 TATATATACATAGTT
*
348089 TATATATATATAGTT
1 TATATATACATAGTT
348104 TATATATACA-AGTT
1 TATATATACATAGTT
348118 TATATATA
1 TATATATA
348126 GTTTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (15 bp):
TATATATACATAGTT
Found at i:348125 original size:2 final size:2
Alignment explanation
Indices: 348066--348111 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
348056 TTTATACATA
*
348066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
348109 AT A
1 AT A
348112 CAAGTTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:348198 original size:20 final size:18
Alignment explanation
Indices: 348162--348209 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
348152 CTCTATCTAG
*
348162 TTTATATATAATATATATA
1 TTTATATA-AAAATATATA
348181 CTTTATATAAAAACTATATA
1 -TTTATATAAAAA-TATATA
*
348201 TATATATAA
1 TTTATATAA
348210 TTGTTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTATATAAAAATATATA
Found at i:348316 original size:13 final size:13
Alignment explanation
Indices: 348298--348323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348288 TGTTGTTGAA
348298 TTTATTTAAATTT
1 TTTATTTAAATTT
348311 TTTATTTAAATTT
1 TTTATTTAAATTT
348324 CATATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTAAATTT
Found at i:357459 original size:55 final size:55
Alignment explanation
Indices: 357384--357986 Score: 520
Period size: 55 Copynumber: 11.0 Consensus size: 55
357374 GGATAAGTGA
* *
357384 GACTTGAAAAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAGGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* ** * *
357439 GACTTGAACAATCTTTGGAAAACATGTCTGCTCCTTCTTCCTTCAAGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * * ** *
357494 GACTAGAATAATTTTTGGAAAACGTGT-TAACTCATTCTT-TTTAAAGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCT-GCTCCCTCTTCTTTCAAGGAGTATAG
* * * * *
357548 GACTTGAACAGTCTTCGGAAAATGGGT-TCGCTCACTCTTTTTTCAATGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCT-GCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * *
357603 GACTT-AAAAATCTTTGGAAAAACATGG-CCGCTCCTTATTCTTTCAAGGAGTATAG
1 GACTTGAACAATCTTCGG-AAAAC-GGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * *
357658 GACTTGAACAATCTTCAGAAAATGGGTCTGTTCCCTCTTCTATCAAGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * *
357713 GACTCGAACAATCTTC-GACAAACGTGTTTGTTCCCTCTTCTTTTAGGGAGTATAG
1 GACTTGAACAATCTTCGGA-AAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * * * *
357768 GACTCGAATAATCTTCAGAAAATGGGTTTGTTCCTTCTTATTTCAAGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
** * * ** *
357823 GACTCAAACAATCTAT-GGCAAACGTGTCCACTCCCTCTTCTTTCAGGGAGTATAG
1 GACTTGAACAATCT-TCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * *
357878 GACTCGAACAATCTTCAGAAAATGGGCCCGCTCCTTCTTCTTTCAAGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
* * * * * *
357933 GACTTGAACAATCTTCGAAAAATGGGTC-CCTCTCTCTTCTCTCAGGGAGTATAG
1 GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
357987 ACTAAATCTA
Statistics
Matches: 444, Mismatches: 93, Indels: 23
0.79 0.17 0.04
Matches are distributed among these distances:
54 78 0.18
55 352 0.79
56 14 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (55 bp):
GACTTGAACAATCTTCGGAAAACGGGTCTGCTCCCTCTTCTTTCAAGGAGTATAG
Found at i:362320 original size:2 final size:2
Alignment explanation
Indices: 362313--362376 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
362303 TAAAGAGAAG
362313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362355 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
362377 GGGAGAATCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:362869 original size:19 final size:19
Alignment explanation
Indices: 362841--362884 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
362831 CCCAGTTAAG
* *
362841 GTCTTCACCAGCTAATCTT
1 GTCTTTACCAGCCAATCTT
362860 GTCTTTACCAGCCAATCTT
1 GTCTTTACCAGCCAATCTT
362879 GTCTTT
1 GTCTTT
362885 CTCATTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.41
Consensus pattern (19 bp):
GTCTTTACCAGCCAATCTT
Found at i:367860 original size:54 final size:53
Alignment explanation
Indices: 367793--367913 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 53
367783 TACATCAGCT
* *
367793 GTGTATCGATACCCAACTTACATTCGATG-TAGGGGTGTATCGATACCTAAAAGA
1 GTGTATCG-TACCCAAATTACATTCGATGCTA-GGGTGTATCGATACATAAAAGA
*
367847 GTGTATCAGTACCCAAATTACATTCGATGCTAGGGTGTATCGATACATCAAAGA
1 GTGTATC-GTACCCAAATTACATTCGATGCTAGGGTGTATCGATACATAAAAGA
367901 GTGTATCGGTACC
1 GTGTATC-GTACC
367914 ACCCTTTGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
54 58 0.95
55 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (53 bp):
GTGTATCGTACCCAAATTACATTCGATGCTAGGGTGTATCGATACATAAAAGA
Found at i:368208 original size:12 final size:13
Alignment explanation
Indices: 368191--368222 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
368181 TAAGATTTTC
368191 TTTGAAAACC-AT
1 TTTGAAAACCAAT
368203 TTTG-AAACCAAT
1 TTTGAAAACCAAT
368215 TTTGAAAA
1 TTTGAAAA
368223 TTACTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 10 0.56
13 3 0.17
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (13 bp):
TTTGAAAACCAAT
Found at i:371698 original size:26 final size:26
Alignment explanation
Indices: 371669--371722 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
371659 CAAATATTAT
371669 ATCATCAACATAAATTTGAACTACTA
1 ATCATCAACATAAATTTGAACTACTA
371695 ATCATCAACATAAATTTGAACTACTA
1 ATCATCAACATAAATTTGAACTACTA
371721 AT
1 AT
371723 AAATCTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (26 bp):
ATCATCAACATAAATTTGAACTACTA
Found at i:376202 original size:23 final size:21
Alignment explanation
Indices: 376166--376220 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
376156 AGCATGGGTA
*
376166 TATCGGTACACTCTCTAGGTG
1 TATCGGTACACTCTCTAGGGG
*
376187 TATCGTTACACTCTCTAGGGG
1 TATCGGTACACTCTCTAGGGG
376208 TATCGGTACACTC
1 TATCGGTACACTC
376221 AGTGTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (21 bp):
TATCGGTACACTCTCTAGGGG
Found at i:376411 original size:54 final size:54
Alignment explanation
Indices: 376324--376463 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 54
376314 GGAGCCAGGT
* ** *
376324 GTGTATCGGTACATC-AACTGTGTATCGATACCCAAATTACATTCGATGTTGGG
1 GTGTATCGATACATCAAAGAGTGTATCGGTACCCAAATTACATTCGATGTTGGG
* *
376377 GTGTATTGATACATCAATGAGTGTATCGGTACCCAAATTACATTCGATGTTGGG
1 GTGTATCGATACATCAAAGAGTGTATCGGTACCCAAATTACATTCGATGTTGGG
376431 GTGTATCGATACATCAAAGAGTGTATCGGTACC
1 GTGTATCGATACATCAAAGAGTGTATCGGTACC
376464 TCCCTTTGTA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 13 0.17
54 65 0.83
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (54 bp):
GTGTATCGATACATCAAAGAGTGTATCGGTACCCAAATTACATTCGATGTTGGG
Found at i:377773 original size:20 final size:20
Alignment explanation
Indices: 377744--377795 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
377734 CAATGTTGGT
*
377744 AGTATCGATACTACCTACTG
1 AGTATTGATACTACCTACTG
*
377764 AGTATTGATACTACCTAGTG
1 AGTATTGATACTACCTACTG
377784 AGTATTGATACT
1 AGTATTGATACT
377796 TCTCTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
AGTATTGATACTACCTACTG
Found at i:382491 original size:18 final size:18
Alignment explanation
Indices: 382468--382503 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
382458 TATAGTAAAT
382468 ATAGTAGCCATTTTCTTA
1 ATAGTAGCCATTTTCTTA
382486 ATAGTAGCCATTTTCTTA
1 ATAGTAGCCATTTTCTTA
382504 GTTTTTGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
ATAGTAGCCATTTTCTTA
Found at i:383502 original size:10 final size:10
Alignment explanation
Indices: 383489--383527 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
383479 AACAAAAATG
*
383489 AACGAATATA
1 AACGAACATA
*
383499 AACGAGCATA
1 AACGAACATA
383509 AACGAACATA
1 AACGAACATA
383519 AACGAACAT
1 AACGAACAT
383528 TATTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:384165 original size:27 final size:31
Alignment explanation
Indices: 384130--384208 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
384120 TATTAATTTC
*
384130 ATAGAAATAATATTATTA-A-A-TTATTAATA
1 ATAG-AATAATATTATTATATATTTAATAATA
384159 AT-GAATAATATTATTTATATATTTAATAATA
1 ATAGAATAATATTA-TTATATATTTAATAATA
*
384190 ATATAATAATATTATTATA
1 ATAGAATAATATTATTATA
384209 AAGATATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 10 0.23
28 4 0.09
29 3 0.07
30 1 0.02
31 15 0.35
32 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
ATAGAATAATATTATTATATATTTAATAATA
Found at i:384207 original size:54 final size:49
Alignment explanation
Indices: 384075--384207 Score: 121
Period size: 54 Copynumber: 2.6 Consensus size: 49
384065 TATTATGCTT
* *
384075 TTATTTAATAAT-ATATAATAA-ATTATTAATAAAATTTATATTATTTA
1 TTATTTAATAATAATATAATAATATTATTATTAAAATTAATATTATTTA
* * *
384122 TTAATTTCAT-AGAA-ATAATATTATTAAATTATTAATAATGAATAATATTATTTA
1 TT-ATTTAATAATAATATAATAATATT--ATTATTAA-AAT---TAATATTATTTA
384176 TATATTTAATAATAATATAATAATATTATTAT
1 T-TATTTAATAATAATATAATAATATTATTAT
384208 AAAGATATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
47 9 0.14
48 10 0.15
50 7 0.11
51 3 0.05
54 23 0.35
55 4 0.06
56 10 0.15
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (49 bp):
TTATTTAATAATAATATAATAATATTATTATTAAAATTAATATTATTTA
Found at i:384216 original size:35 final size:32
Alignment explanation
Indices: 384135--384241 Score: 86
Period size: 35 Copynumber: 3.4 Consensus size: 32
384125 ATTTCATAGA
* *
384135 AATAATATTA-TTA-A-A-TTATTAATAAT-G
1 AATAATATTATTTAGATATTTAATAATAATAT
*
384162 AATAATATTATTTATATATTTAATAATAATAT
1 AATAATATTATTTAGATATTTAATAATAATAT
384194 AATAATATTATTATAAAGATATTTAA-AAT-ATACT
1 AATAATATTATT-T--AGATATTTAATAATAATA-T
384228 AATTAATATT-TTTA
1 AA-TAATATTATTTA
384242 AAATATAATA
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
27 10 0.15
28 3 0.04
29 1 0.01
30 1 0.01
31 11 0.16
32 12 0.18
33 5 0.07
34 8 0.12
35 16 0.24
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (32 bp):
AATAATATTATTTAGATATTTAATAATAATAT
Found at i:384326 original size:33 final size:32
Alignment explanation
Indices: 384289--384352 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
384279 ATATAATTTA
*
384289 TAATATTTTTATTTCAATAAAA-TATACAAATAT
1 TAATATTTTTA-TT-AATAAAATTATAAAAATAT
384322 TAATATTTTTATTAATAAAATTATAAAAATA
1 TAATATTTTTATTAATAAAATTATAAAAATA
384353 ATAGTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 7 0.24
32 11 0.38
33 11 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATATTTTTATTAATAAAATTATAAAAATAT
Found at i:384382 original size:28 final size:27
Alignment explanation
Indices: 384351--384459 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 27
384341 ATTATAAAAA
*
384351 TAATAGTTTAATAATAAATAAATTATTT
1 TAATA-TTTAATAATAAATAAATAATTT
*
384379 TAATATTT--TAA-AAAT-AATAATAT
1 TAATATTTAATAATAAATAAATAATTT
*
384402 TAAGT-TTT-ATAATAAATAATATTATTT
1 TAA-TATTTAATAATAAATAA-ATAATTT
* *
384429 ATTATATTTAATATTTATAATAAATAATTT
1 -TAATATTTAATA-ATA-AATAAATAATTT
384459 T
1 T
384460 TAAAAAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
23 12 0.19
24 8 0.12
25 7 0.11
26 1 0.02
27 9 0.14
28 10 0.16
29 4 0.06
30 8 0.12
31 5 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAATATTTAATAATAAATAAATAATTT
Found at i:384388 original size:89 final size:89
Alignment explanation
Indices: 384217--384387 Score: 204
Period size: 91 Copynumber: 1.9 Consensus size: 89
384207 TAAAGATATT
* * * * * *
384217 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAACTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
384282 TAATTTATAATATTTTTATTTCAA
66 TAATTTATAATATTTTTATTTCAA
* *
384306 TAAAATATACAAATATTAATATTTTTATTAATAAAATTATAAAAATAATAGTTTAAT-AATAAAT
1 TAAAATATAC-AA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
384370 AA-ATTATTT-TAATATTTT
62 AATATAATTTATAATATTTT
384388 AAAAATAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
89 10 0.14
90 10 0.14
91 19 0.28
92 14 0.20
93 16 0.23
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (89 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
TAATTTATAATATTTTTATTTCAA
Found at i:384409 original size:22 final size:22
Alignment explanation
Indices: 384366--384425 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
384356 GTTTAATAAT
* * *
384366 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAA-GTTTTA
384389 AAA-ATAATAATATTAAGTTTTA
1 AAATA-AATAATATTAAGTTTTA
*
384411 TAATAAATAATATTA
1 AAATAAATAATATTA
384426 TTTATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATAAATAATATTAAGTTTTA
Found at i:384678 original size:32 final size:32
Alignment explanation
Indices: 384625--384690 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 32
384615 CAGGCTAAAA
384625 TTTTGCTCCATGGGATTACCCGACGTCTTTAGT
1 TTTTGCTCCAT-GGATTACCCGACGTCTTTAGT
*
384658 TTTTGCTCCTAT-GATTACCCGGCGTCTTTAGT
1 TTTTGCTCC-ATGGATTACCCGACGTCTTTAGT
384690 T
1 T
384691 AAAATCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 20 0.65
33 9 0.29
34 2 0.06
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
TTTTGCTCCATGGATTACCCGACGTCTTTAGT
Found at i:385754 original size:532 final size:539
Alignment explanation
Indices: 384908--385950 Score: 1715
Period size: 532 Copynumber: 1.9 Consensus size: 539
384898 TATTTGAAAA
*
384908 AAAATATTATAGTAATTAATTTCAATTAATTTTTGTGGCTGTAAAATTGGAAAGCGAGAGAATAC
1 AAAATATTATAGTAATTAATTTCAATTAATTTTTGTGGCTATAAAATTGGAAAGCGAGAGAATAC
*
384973 GTCGAAATATTTTTGTCGATACGGTAATAATATAAAATTATATTATTTAAATTATTTACGTTTAT
66 GTCGAAATATTTTTGCCGATACGG--ATAATAT--AA-TATATTA--TAAATTATTTACGTTTAT
* *
385038 ATGTAAGAATGAAGCGAATTTCAGCTATTGTTTATTATGATGGAGAAATTCAAGAAGATGTAACC
124 ATGTAAGAATGAAGCGAATTTCAACTATTGTTTATTATGATGGAGAAATTCAAGAAGATGAAACC
* *
385103 GACGTTGTTTTCGTATCAAATCATTATGTTAAAATATCCTTCAGGAGAAACATAACTCTTGAGGA
189 GACGTTGTTTTCGTATCAAATCATTATGTTAAAATATCATTAAGGAGAAACATAACTCTTGAGGA
* *
385168 TGTGATAATGAAGATTTCAAGGAAGGTTTATGTTAGAAGTACTAGAAGAAAGACGTCGCTTTAGT
254 GGTGATAATGAAGATTTCAAGGAAGGTTCATGTTAGAAGTACTAGAAGAAAGACGTCGCTTTAGT
*
385233 ACAGATTTTAACATAATGATTTAAGGAAAAAAATAAAATACTAAAAAAATTAAATAATACAAAGG
319 ACAAATTTTAACATAATGATTTAAGG-AAAAAATAAAATACTAAAAAAATTAAATAATACAAAGG
* * * *
385298 GTGTTAGACCGAGAATATTATTTCAAATGGTGTATGACACGTAAATATTTAAGGAAAATGTTATT
383 GTGTTAGACAGAGAATATTATTTCAAAGGGTGTATGACACGTAAATATTTAAGGAAAATGTGATA
* * *
385363 TTTCGGGAAAGTCTCTAAAAATGCACAGTAATCAG-AAAAATATTTAACTAAAGACGCCGAGATA
448 TTTAGGGAAAGTCTCCAAAAATGCACAGTAATCAGAAAAAAAATTTAACTAAAGACGCCGAGATA
385427 TCTTGGGGACTTTAAGAGGTACTGTAG
513 TCTTGGGGACTTTAAGAGGTACTGTAG
* * *
385454 AAAATATTATAGTAATTATTTTCAATTAATTTTTGTGGTTATAAAATTGGAAAGCGAGAGCATAC
1 AAAATATTATAGTAATTAATTTCAATTAATTTTTGTGGCTATAAAATTGGAAAGCGAGAGAATAC
* *
385519 GTTGAAATATTTTTGCCGATACGG-T-A-AT-A-ATA-TA-AAATTATTTACGTTTATGTGTAAG
66 GTCGAAATATTTTTGCCGATACGGATAATATAATATATTATAAATTATTTACGTTTATATGTAAG
*
385577 AATGAAGCGAATTTCAACTATTGTTTATTATGATGGAGAAATTCAGGAAGATGAAACCGACGTTG
131 AATGAAGCGAATTTCAACTATTGTTTATTATGATGGAGAAATTCAAGAAGATGAAACCGACGTTG
*
385642 TTTTCGTATCAAATCATTATGTTAAACTATCATTAAGGAGAAACATAACTCTTGAGGAGGTGATA
196 TTTTCGTATCAAATCATTATGTTAAAATATCATTAAGGAGAAACATAACTCTTGAGGAGGTGATA
* *
385707 ATGAAGATTTCAAGGAAGGTTCATGTTATAAGTACTTGAAGAAAGACGTCGCTTTAGTACAAATT
261 ATGAAGATTTCAAGGAAGGTTCATGTTAGAAGTACTAGAAGAAAGACGTCGCTTTAGTACAAATT
385772 TTAACATAATGATTTAAGGAAAAAATAAAATACTAAAAAAATTAAATAATACAAAGGGTGTTAGA
326 TTAACATAATGATTTAAGGAAAAAATAAAATACTAAAAAAATTAAATAATACAAAGGGTGTTAGA
* *
385837 TAGAGAATATTATTTCAAAGGGTGTCTGACACGTAAATATTTAAGGAAAATGTGATATTTAGGGA
391 CAGAGAATATTATTTCAAAGGGTGTATGACACGTAAATATTTAAGGAAAATGTGATATTTAGGGA
385902 AAGTCTCCAAAAATGCACAGTAATCAGAAAAAAAATTTAACTAAAGACG
456 AAGTCTCCAAAAATGCACAGTAATCAGAAAAAAAATTTAACTAAAGACG
385951 TCTGGTAATC
Statistics
Matches: 469, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
531 130 0.28
532 246 0.52
535 2 0.00
536 3 0.01
538 1 0.00
541 2 0.00
542 1 0.00
543 1 0.00
546 83 0.18
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (539 bp):
AAAATATTATAGTAATTAATTTCAATTAATTTTTGTGGCTATAAAATTGGAAAGCGAGAGAATAC
GTCGAAATATTTTTGCCGATACGGATAATATAATATATTATAAATTATTTACGTTTATATGTAAG
AATGAAGCGAATTTCAACTATTGTTTATTATGATGGAGAAATTCAAGAAGATGAAACCGACGTTG
TTTTCGTATCAAATCATTATGTTAAAATATCATTAAGGAGAAACATAACTCTTGAGGAGGTGATA
ATGAAGATTTCAAGGAAGGTTCATGTTAGAAGTACTAGAAGAAAGACGTCGCTTTAGTACAAATT
TTAACATAATGATTTAAGGAAAAAATAAAATACTAAAAAAATTAAATAATACAAAGGGTGTTAGA
CAGAGAATATTATTTCAAAGGGTGTATGACACGTAAATATTTAAGGAAAATGTGATATTTAGGGA
AAGTCTCCAAAAATGCACAGTAATCAGAAAAAAAATTTAACTAAAGACGCCGAGATATCTTGGGG
ACTTTAAGAGGTACTGTAG
Found at i:387538 original size:13 final size:14
Alignment explanation
Indices: 387503--387548 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
387493 ATGGTTTATG
387503 GTTTAGGGTTTA-A
1 GTTTAGGGTTTAGA
*
387516 GTTTA-TGTTTAGA
1 GTTTAGGGTTTAGA
387529 -TTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
387542 GTTTAGG
1 GTTTAGG
387549 ATTCATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 9 0.32
13 13 0.46
14 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:389520 original size:19 final size:19
Alignment explanation
Indices: 389482--389520 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
389472 TCTTACCCTT
*
389482 TAAATTCAGTTAGTTATGC
1 TAAATTCAGTTAGCTATGC
*
389501 TAAATTCAGTTAGCTCTGC
1 TAAATTCAGTTAGCTATGC
389520 T
1 T
389521 GTAGGAGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (19 bp):
TAAATTCAGTTAGCTATGC
Found at i:390164 original size:15 final size:15
Alignment explanation
Indices: 390144--390175 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
390134 AATAAAGATA
390144 TTTTTTAAAGGAATT
1 TTTTTTAAAGGAATT
*
390159 TTTTTTAAAGGCATT
1 TTTTTTAAAGGAATT
390174 TT
1 TT
390176 AGTCCAAAAC
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:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTTTTAAAGGAATT
Found at i:391049 original size:17 final size:17
Alignment explanation
Indices: 391027--391064 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
391017 CTTAAATCTC
* *
391027 TAATTTTAATTTAAAAT
1 TAATTTAAATTCAAAAT
391044 TAATTTAAATTCAAAAT
1 TAATTTAAATTCAAAAT
391061 TAAT
1 TAAT
391065 GTGAGCCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTAAATTCAAAAT
Found at i:392644 original size:31 final size:31
Alignment explanation
Indices: 392602--392670 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
392592 ACTTGAGTCA
* *
392602 AAAACTCTAAAATGAAGCTTGATTCTACTCG
1 AAAACTTTAAAATGAAGCTTGATTCGACTCG
392633 AAAACTTTAAAATGAAGCTTGATTCGACTCG
1 AAAACTTTAAAATGAAGCTTGATTCGACTCG
392664 AAAACTT
1 AAAACTT
392671 GTGAACCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (31 bp):
AAAACTTTAAAATGAAGCTTGATTCGACTCG
Found at i:392964 original size:16 final size:17
Alignment explanation
Indices: 392938--392971 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
392928 TGAGCTTAAA
392938 ATAAGTATTTAATATAT
1 ATAAGTATTTAATATAT
392955 ATAA-TATTTAATATAT
1 ATAAGTATTTAATATAT
392971 A
1 A
392972 ATTTCGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAAGTATTTAATATAT
Found at i:396046 original size:8 final size:8
Alignment explanation
Indices: 396032--396086 Score: 56
Period size: 8 Copynumber: 6.2 Consensus size: 8
396022 TACTACACTC
396032 AAAAAAAG
1 AAAAAAAG
*
396040 GAAAAAAG
1 AAAAAAAG
396048 AAAAAAAAG
1 -AAAAAAAG
396057 AAAAAAAG
1 AAAAAAAG
396065 AAAGAATAAG
1 AAA-AA-AAG
396075 TAAGAAAAAG
1 -AA-AAAAAG
396085 AA
1 AA
396087 TAAGGAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 18 0.45
9 11 0.28
10 6 0.15
11 4 0.10
12 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:396054 original size:17 final size:17
Alignment explanation
Indices: 396032--396086 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
396022 TACTACACTC
*
396032 AAAAAAAGGAAAAAAGA
1 AAAAAAAGAAAAAAAGA
396049 AAAAAAAGAAAAAAAGA
1 AAAAAAAGAAAAAAAGA
*
396066 AAGAATAAGTAAGAAAAAGA
1 AA-AAAAAG-AA-AAAAAGA
396086 A
1 A
396087 TAAGGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 18 0.55
18 5 0.15
19 2 0.06
20 8 0.24
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGA
Found at i:397938 original size:134 final size:134
Alignment explanation
Indices: 397750--398700 Score: 1110
Period size: 134 Copynumber: 7.1 Consensus size: 134
397740 TAATTTGCAT
* * *
397750 ATCTGATATTCCCTTCAGAAGAAGC-AGAACATGTCC-TTTTTTCCAAGATTTGATATTCCCTTA
1 ATCTGATATTCCCTTCAAAAGAAGCGA-AACATGTCCATCTTTTCCAAGATTTGATATTCCCTGA
* * *
397813 GTGACAGCGGAACAAGTTTGCCTCGATTCAATCTTCCCCGAGTGACAGCGAAATGGATCAACTCC
65 GTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCC
*
397878 TCTAG
130 CCTAG
* * * * * * * *
397883 ATATGATATTACTTTTAGAAGAAGTGAAACA-GATCCATCTTTTCTAAGATTTGATATTCCCTAA
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATG-TCCATCTTTTCCAAGATTTGATATTCCCTGA
* ** * * * *
397947 GTGATAGCTAAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGAAAACGGAATGGATTAACTCC
65 GTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCC
*
398012 TCC-AT
130 -CCTAG
* * * * *
398017 ATATGATTTTCCCTTTAAAAGAAGCGGAACATGTCCATCTTTTCCAAGATTTGATATTCCATGAG
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCATCTTTTCCAAGATTTGATATTCCCTGAG
* * *
398082 TGACAGCGGAATAAGTCTACCCCGATTCAATCTTCTCTGAGTGACAGC-AGAATGGATCAACTCC
66 TGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGA-AATGGATCAACTCC
*
398146 TCTAG
130 CCTAG
* * * * *
398151 ATCTGGTATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTAATATTCCCTGAG
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCATCTTTTCCAAGATTTGATATTCCCTGAG
* * * *
398216 TGACAGCGGAATAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCC
66 TGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCCC
398281 CTAG
131 CTAG
*
398285 ATCTGATATTCCCTTCAGAAGAAGCGAAACATGTCTC-TCTTTTCCAAGATTTGATATTCCCTGA
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTC-CATCTTTTCCAAGATTTGATATTCCCTGA
* * * * * *
398349 GTGACAGCGGAATAAGTCTGCCCCGATTCAATCTTCCATGAGTGACAGTGGAATGAATCAATTCC
65 GTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCC
398414 CCTAG
130 CCTAG
* * * * * * * *
398419 ATATGATATTCCCTTCAAAAGATGTGGAACATGCCCCTCTTTTCAAATATTTGATATTCCCTGAG
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCATCTTTTCCAAGATTTGATATTCCCTGAG
* * * * *
398484 TGACAACGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGC-AGAATGAATCAATTCC
66 TGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGA-AATGGATCAACTCC
* *
398548 CCCAT
130 CCTAG
* * ** * * *
398553 ATCTGAAATTCCCTTCAAAAGAAGCGAAATAAATCCCTCTTCTCCAAGATTTGATATTCCCTTAG
1 ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCATCTTTTCCAAGATTTGATATTCCCTGAG
* * *
398618 TGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGATTGACAG-TAGAATGGATCAACAT-
66 TGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGA-AATGGATCAAC-TC
398681 CCCTAG
129 CCCTAG
398687 ATCTGATATTCCCT
1 ATCTGATATTCCCT
398701 GAATGACAGC
Statistics
Matches: 701, Mismatches: 104, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
132 1 0.00
133 29 0.04
134 667 0.95
135 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (134 bp):
ATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCATCTTTTCCAAGATTTGATATTCCCTGAG
TGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACTCCC
CTAG
Found at i:398267 original size:268 final size:266
Alignment explanation
Indices: 397747--398700 Score: 1232
Period size: 268 Copynumber: 3.6 Consensus size: 266
397737 GTTTAATTTG
* *
397747 CATATCTGATATTCCCTTCAGAAGAAGC-AGAACATGTCCTTTTTTCCAAGATTTGATATTCCCT
1 CATATCTGATATTCCCTTCAAAAGAAGCGA-AACATGTCCTCTTTTCCAAGATTTGATATTCCCT
* * * * *
397811 TAGTGACAGCGGAACAAGTTTGCCTCGATTCAATCTTCCCCGAGTGACAGC-GAAATGGATCAAC
65 GAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAG-AATGGATCAAC
* * * * *
397875 TCCTCTAGATATGATATTACTTTTAGAAGAAGTGAAACA-GATCCATCTTTTCTAAGATTTGATA
129 TCCTCTAGATATGATATTCCCTTCAGAAGAAGTGGAACATG-TCCATCTTTTCAAAGATTTGATA
* * * * *
397939 TTCCCTAAGTGATAGCTAAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGAAAACGGAATGGA
193 TTCCCTGAGTGACAGCGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGA
*
398004 TTAACTCCTC
258 TCAACTCC-C
* * * * *
398014 CATATATGATTTTCCCTTTAAAAGAAGCGGAACATGTCCATCTTTTCCAAGATTTGATATTCCAT
1 CATATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCC-TCTTTTCCAAGATTTGATATTCCCT
* *
398079 GAGTGACAGCGGAATAAGTCTACCCCGATTCAATCTTCTCTGAGTGACAGCAGAATGGATCAACT
65 GAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAACT
* * * * * *
398144 CCTCTAGATCTGGTATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTAATATT
130 CCTCTAGATATGATATTCCCTTCAGAAGAAGTGGAACATGTCCATCTTTTCAAAGATTTGATATT
* *
398209 CCCTGAGTGACAGCGGAATAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGATC
195 CCCTGAGTGACAGCGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGATC
398274 AACTCCC
260 AACTCCC
* *
398281 CTAGATCTGATATTCCCTTCAGAAGAAGCGAAACATGTCTCTCTTTTCCAAGATTTGATATTCCC
1 C-ATATCTGATATTCCCTTCAAAAGAAGCGAAACATGTC-CTCTTTTCCAAGATTTGATATTCCC
* * * ** * *
398346 TGAGTGACAGCGGAATAAGTCTGCCCCGATTCAATCTTCCATGAGTGACAGTGGAATGAATCAAT
64 TGAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAAC
* * * * * *
398411 TCCCCTAGATATGATATTCCCTTCAAAAGATGTGGAACATGCCCCTCTTTTCAAATATTTGATAT
129 TCCTCTAGATATGATATTCCCTTCAGAAGAAGTGGAACATGTCCATCTTTTCAAAGATTTGATAT
* * * *
398476 TCCCTGAGTGACAACGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCAGAATGAAT
194 TCCCTGAGTGACAGCGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGAT
*
398541 CAATTCCCC
259 CAACT-CCC
* * ** *
398550 CATATCTGAAATTCCCTTCAAAAGAAGCGAAATAAATCCCTCTTCTCCAAGATTTGATATTCCCT
1 CATATCTGATATTCCCTTCAAAAGAAGCGAAACATGT-CCTCTTTTCCAAGATTTGATATTCCCT
* * *
398615 TAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGATTGACAGTAGAATGGATCAACA
65 GAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAAC-
*
398680 TCC-CTAGATCTGATATTCCCT
129 TCCTCTAGATATGATATTCCCT
398701 GAATGACAGC
Statistics
Matches: 598, Mismatches: 80, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
267 35 0.06
268 552 0.92
269 11 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (266 bp):
CATATCTGATATTCCCTTCAAAAGAAGCGAAACATGTCCTCTTTTCCAAGATTTGATATTCCCTG
AGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAACTC
CTCTAGATATGATATTCCCTTCAGAAGAAGTGGAACATGTCCATCTTTTCAAAGATTTGATATTC
CCTGAGTGACAGCGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGATCA
ACTCCC
Found at i:398532 original size:402 final size:402
Alignment explanation
Indices: 397750--398700 Score: 1257
Period size: 402 Copynumber: 2.4 Consensus size: 402
397740 TAATTTGCAT
*
397750 ATCTGATATTCCCTTCAGAAGAAGCAGAACATGTCCTT-TTTTCCAAGATTTGATATTCCCTTAG
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTGATATTCCCTTAG
* * *
397814 TGACAGCGGAACAAGTTTG-CCTCGATTCAATCTTCCCCGAGTGACAGCGAAATGGATCAACTCC
66 TGACAGCGGAACAAGTCTGCCCT-GATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCC
* * * * * * *
397878 TCTAGATATGATATTACTTTTAGAAGAAGTGAAACAGATCCATCTTTTCTAAGATTTGATATTCC
130 CCTAGATCTGATATTCCCTTCAGAAGAAGCGAAACAGATCCATCTTTTCCAAGATTTGATATTCC
* * * * *
397943 CTAAGTGATAGCTAAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGAAAACGGAATGGATTAA
195 CTAAGTGACAGCGAAACAAGTCTGCCCCGATTCAATCTTCCATGAGTGAAAACGGAATGAATCAA
* * * * *
398008 CTCCTCCATATATGATTTTCCCTTTAAAAGAAGCGGAACATGTCCATCTTTTCCAAGATTTGATA
260 CTCCTCCAGATATGATATTCCCTTCAAAAGAAGCGGAACATGCCCATCTTTTCAAAGATTTGATA
* * * * *
398073 TTCCATGAGTGACAGCGGAATAAGTCTACCCCGATTCAATCTTCTCTGAGTGACAGCAGAATGGA
325 TTCCATGAGTGACAACGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGAA
* *
398138 TCAACTCCTCTAG
390 TCAACTCCCCCAG
* * *
398151 ATCTGGTATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTAATATTCCCTGAG
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTGATATTCCCTTAG
* *
398216 TGACAGCGGAATAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCC
66 TGACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCC
398281 CTAGATCTGATATTCCCTTCAGAAGAAGCGAAACATG-TCTC-TCTTTTCCAAGATTTGATATTC
131 CTAGATCTGATATTCCCTTCAGAAGAAGCGAAACA-GATC-CATCTTTTCCAAGATTTGATATTC
* * * * **
398344 CCTGAGTGACAGCGGAATAAGTCTGCCCCGATTCAATCTTCCATGAGTGACAGTGGAATGAATCA
194 CCTAAGTGACAGCGAAACAAGTCTGCCCCGATTCAATCTTCCATGAGTGAAAACGGAATGAATCA
* * * * *
398409 ATTCC-CCTAGATATGATATTCCCTTCAAAAGATGTGGAACATGCCCCTCTTTTCAAATATTTGA
259 ACTCCTCC-AGATATGATATTCCCTTCAAAAGAAGCGGAACATGCCCATCTTTTCAAAGATTTGA
* * *
398473 TATTCCCTGAGTGACAACGAAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCAGAATG
323 TATTCCATGAGTGACAACGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATG
* *
398538 AATCAATTCCCCCAT
388 AATCAACTCCCCCAG
* * * * ** * *
398553 ATCTGAAATTCCCTTCAAAAGAAGCGAAATAAATCCCTCTTCTCCAAGATTTGATATTCCCTTAG
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTGATATTCCCTTAG
* * * **
398618 TGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGATTGACAGTAGAATGGATCAACAT-C
66 TGACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAAC-TCC
398682 CCTAGATCTGATATTCCCT
130 CCTAGATCTGATATTCCCT
398701 GAATGACAGC
Statistics
Matches: 477, Mismatches: 67, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
401 38 0.08
402 433 0.91
403 6 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (402 bp):
ATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCTTCTTTTCCAAGATTTGATATTCCCTTAG
TGACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCC
CTAGATCTGATATTCCCTTCAGAAGAAGCGAAACAGATCCATCTTTTCCAAGATTTGATATTCCC
TAAGTGACAGCGAAACAAGTCTGCCCCGATTCAATCTTCCATGAGTGAAAACGGAATGAATCAAC
TCCTCCAGATATGATATTCCCTTCAAAAGAAGCGGAACATGCCCATCTTTTCAAAGATTTGATAT
TCCATGAGTGACAACGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCAGAATGAAT
CAACTCCCCCAG
Found at i:398789 original size:3 final size:3
Alignment explanation
Indices: 398781--398830 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
398771 CAAAATTTTA
* * *
398781 ATT ATT ATT ATT ATT A-T ATT ATT ATT ACT ATT ATT AAT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
398828 ATT
1 ATT
398831 CCATTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:410026 original size:5 final size:5
Alignment explanation
Indices: 410016--410053 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
410006 AATTAATGTT
* *
410016 AAATA AAATA AAATA AAATA AAATC AAATC AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
410054 AGATCAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:411294 original size:11 final size:12
Alignment explanation
Indices: 411281--411330 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
411271 ATAAAATCAA
411281 AATAATAAATA-
1 AATAATAAATAT
*
411292 AATAA-ATATAT
1 AATAATAAATAT
411303 AAT-ATAAATAT
1 AATAATAAATAT
*
411314 AATAATATACTAT
1 AATAATA-AATAT
411327 AATA
1 AATA
411331 TATATATGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.16
11 16 0.50
12 3 0.09
13 8 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:411294 original size:22 final size:21
Alignment explanation
Indices: 411269--411332 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
411259 TTGATCCTAA
411269 AAATAAA-ATCAAAATAATAAAT
1 AAATAAATAT-AAAAT-ATAAAT
*
411291 AAATAAATATATAATATAAAT
1 AAATAAATATAAAATATAAAT
*
411312 ATAATAATATACTATAATATA
1 A-AATAA-ATA-TAAAATATA
411333 TATATGCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 7 0.19
22 16 0.43
23 5 0.14
24 9 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATATAAAATATAAAT
Found at i:411306 original size:19 final size:22
Alignment explanation
Indices: 411282--411612 Score: 67
Period size: 21 Copynumber: 14.8 Consensus size: 22
411272 TAAAATCAAA
411282 ATAATAAATA-AATAA-ATA-T
1 ATAATAAATATAATAATATACT
411301 ATAATATAAATATAATAATATACT
1 AT-A-ATAAATATAATAATATACT
* ** *
411325 ATAATATATAT-ATGCTATAAT
1 ATAATAAATATAATAATATACT
**
411346 AT-ATACCGTATATATAATATA-T
1 ATAATA-AATATA-ATAATATACT
* *
411368 AT-ATAACACCATGATAATATACT
1 ATAATAA-A-TATAATAATATACT
*
411391 -TAAT--ATAT-ATAATATAAT
1 ATAATAAATATAATAATATACT
* * *
411409 ATAATATATATTAT-ATATA-A
1 ATAATAAATATAATAATATACT
* *
411429 AAATATAAACTATACTAATATA-T
1 ATA-ATAAA-TATAATAATATACT
411452 ATATATATATATATATATATATATA-T
1 ATA-ATA-A-ATATA-ATA-ATATACT
411478 AATATGATATAAATATAAT-ATATACT
1 -A--T-A-ATAAATATAATAATATACT
*
411504 ATAATATATACT-ATAATATA-T
1 ATAATAAATA-TAATAATATACT
* * *
411525 AT-ATCATAATATATTATTTTTA-T
1 ATAAT-A-AATATAATA-ATATACT
* * *
411548 ATATATATACATAAT-ATATACC
1 ATA-ATAAATATAATAATATACT
*
411570 AT-ATAATATATAATATATTATAAT
1 ATAATAA-ATATAATA-A-TATACT
411594 ATAATATAATATAATAATA
1 ATAATA-AATATAATAATA
411613 ATAATAATAC
Statistics
Matches: 232, Mismatches: 37, Indels: 82
0.66 0.11 0.23
Matches are distributed among these distances:
18 9 0.04
19 8 0.03
20 12 0.05
21 54 0.23
22 47 0.20
23 41 0.18
24 16 0.07
25 22 0.09
26 8 0.03
27 3 0.01
28 5 0.02
29 2 0.01
30 5 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (22 bp):
ATAATAAATATAATAATATACT
Found at i:411330 original size:10 final size:9
Alignment explanation
Indices: 411282--411700 Score: 214
Period size: 9 Copynumber: 46.9 Consensus size: 9
411272 TAAAATCAAA
*
411282 ATAATAAAT
1 ATAATATAT
*
411291 A-AATAAAT
1 ATAATATAT
411299 AT-ATA-AT
1 ATAATATAT
411306 ATAA-ATAT
1 ATAATATAT
411314 AATAATATACT
1 -ATAATATA-T
411325 ATAATATAT
1 ATAATATAT
**
411334 AT-AT-GCT
1 ATAATATAT
411341 ATAATATAT
1 ATAATATAT
***
411350 ACCGTATAT
1 ATAATATAT
411359 ATAATATATAT
1 AT-A-ATATAT
* *
411370 ATAACACCAT
1 ATAATA-TAT
411380 GATAATATACT
1 -ATAATATA-T
411391 -TAATATAT
1 ATAATATAT
411399 ATAATATAAT
1 ATAATAT-AT
411409 ATAATATAT
1 ATAATATAT
411418 AT--TATAT
1 ATAATATAT
*
411425 ATAA-AAAT
1 ATAATATAT
411433 ATAA-ACTAT
1 ATAATA-TAT
411442 ACTAATATAT
1 A-TAATATAT
411452 AT-ATATAT
1 ATAATATAT
411460 AT-ATATAT
1 ATAATATAT
411468 AT-ATATAT
1 ATAATATAT
411476 ATAATATGAT
1 ATAATAT-AT
411486 ATAA-ATAT
1 ATAATATAT
411494 A-ATATATACT
1 ATA-ATATA-T
411504 ATAATATAT
1 ATAATATAT
411513 ACT-ATA-AT
1 A-TAATATAT
411521 AT-ATATAT
1 ATAATATAT
411529 CATAATATAT
1 -ATAATATAT
* *
411539 -TATTTTTAT
1 ATA-ATATAT
*
411548 ATATATATAC
1 ATA-ATATAT
411558 ATAATATAT
1 ATAATATAT
*
411567 ACCATATAATAT
1 A-TA-AT-ATAT
411579 ATAATATATT
1 ATAATATA-T
411589 ATAATATAAT
1 ATAATAT-AT
411599 ATAATATA-
1 ATAATATAT
411607 ATAATA-AT
1 ATAATATAT
411615 AATAATACTACT
1 -ATAATA-TA-T
411627 AT-ATA-ATT
1 ATAATATA-T
*
411635 ATAACATAT
1 ATAATATAT
*
411644 AT-A-CTAT
1 ATAATATAT
*
411651 ATACTATAT
1 ATAATATAT
*
411660 ATAATACCAT
1 ATAATA-TAT
411670 AT-AT-TAT
1 ATAATATAT
411677 ATAA-A-AT
1 ATAATATAT
*
411684 ATACTATAT
1 ATAATATAT
411693 ATAATATA
1 ATAATATA
411701 AATATAAATA
Statistics
Matches: 325, Mismatches: 34, Indels: 102
0.70 0.07 0.22
Matches are distributed among these distances:
7 35 0.11
8 75 0.23
9 99 0.30
10 87 0.27
11 23 0.07
12 6 0.02
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (9 bp):
ATAATATAT
Found at i:411335 original size:2 final size:2
Alignment explanation
Indices: 411297--411706 Score: 207
Period size: 2 Copynumber: 215.5 Consensus size: 2
411287 AAATAAATAA
*
411297 AT AT AT A- AT AT AA AT AT A- AT A- AT AT ACT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * *
411336 AT GCT AT A- AT AT AT ACC GT AT AT AT A- AT AT AT AT AT A- AC ACC
1 AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T
411378 AT GAT A- AT AT ACT -T A- AT AT AT AT A- AT AT A- AT AT A- AT AT
1 AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
411416 AT AT -T AT AT AT AA AA AT AT AA ACT AT ACT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT
*
411458 AT AT AT AT AT AT AT AT AT AT A- AT AT GAT AT AA AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
411499 AT ACT AT A- AT AT AT ACT AT A- AT AT AT AT AT CAT A- AT AT AT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT -AT AT AT AT AT
* * * *
411539 -T AT TT TT AT AT AT AT AT AC AT A- AT AT AT ACC AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
411579 AT A- AT AT AT -T AT A- AT AT A- AT AT A- AT AT A- AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
411613 AT A- AT A- AT ACT ACT AT AT A- AT -T AT A- AC AT AT AT ACT AT
1 AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
411651 AT ACT AT AT AT A- AT ACC AT AT AT -T AT AT A- AA AT AT ACT AT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
*
411691 AT AT A- AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT A
411707 AATAAAAGTC
Statistics
Matches: 323, Mismatches: 27, Indels: 116
0.69 0.06 0.25
Matches are distributed among these distances:
1 40 0.12
2 251 0.78
3 32 0.10
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:411499 original size:100 final size:97
Alignment explanation
Indices: 411395--411711 Score: 267
Period size: 100 Copynumber: 3.2 Consensus size: 97
411385 TATACTTAAT
411395 ATATATAATATAATATAATATATATTATATATAAAAATATAAACTATACTAATATATATATATAT
1 ATATATAATATAATATAATATATATTATATATAAAAATAT-AACTATA-TAATATATATATATAT
411460 ATATATATATATATATATAATATGATATAAATATA
64 ATATATATATATATATATAATAT-ATATAAATATA
* * * * * * *
411495 ATATATACTATAATAT-ATACTATAATATATATATCATAATAT-ATTATTTTTATATATATATAC
1 ATATATAATATAATATAATA-TAT-AT-TATATATAAAAATATAACTA-TATAATATATATATAT
*
411558 ATAATATATACCATATAATATATAATATAT-TATAATAT-
62 AT-ATATATA-TATAT-ATATATAATATATATA-AATATA
* * * *
411596 A-ATATAATATAATAATAATA-ATAATACTACTATATAATTATAACATATATACTATATACTATA
1 ATATATAATATAAT-ATAATATATATTA-TA-TATAAAAATATAAC-TATATAATATATA-TATA
* * *
411659 TATA-ATACCATATAT-TATATAAAATATACTATATATA
61 TATATATA-TATATATATATATAATATATA-TAAATATA
411696 ATATA-AATATAA-ATAA
1 ATATATAATATAATATAA
411712 AAGTCCCGGA
Statistics
Matches: 174, Mismatches: 23, Indels: 42
0.73 0.10 0.18
Matches are distributed among these distances:
98 17 0.10
99 10 0.06
100 72 0.41
101 29 0.17
102 35 0.20
103 11 0.06
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (97 bp):
ATATATAATATAATATAATATATATTATATATAAAAATATAACTATATAATATATATATATATAT
ATATATATATATATATAATATATATAAATATA
Found at i:411612 original size:3 final size:3
Alignment explanation
Indices: 411572--411621 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
411562 TATATACCAT
*
411572 ATA ATA TATA ATA TATT ATA AT- ATA AT- ATA AT- ATA ATA ATA ATA
1 ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
411616 ATA ATA
1 ATA ATA
411622 CTACTATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 29 0.73
4 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:411632 original size:19 final size:18
Alignment explanation
Indices: 411381--411698 Score: 111
Period size: 17 Copynumber: 18.2 Consensus size: 18
411371 TAACACCATG
411381 ATAATATACT-TA-ATATA
1 ATAATATACTATATA-ATA
411398 TATAATATA--ATATAAT-
1 -ATAATATACTATATAATA
*
411414 AT-ATATTA-TATATAAAA
1 ATAATA-TACTATATAATA
*
411431 AT-ATAAACTATACTAAT-
1 ATAATATACTATA-TAATA
411448 ATATATATA-TATATATATA
1 ATA-ATATACTATATA-ATA
*
411467 TATATATATA-TAATATGAT-
1 -ATA-ATATACT-ATATAATA
* *
411486 ATAAATATAATATATACT-
1 AT-AATATACTATATAATA
411504 ATAATATA-TACTATAATA
1 ATAATATACTA-TATAATA
* * *
411522 TATATATCATAATATATTATT
1 -ATA-AT-ATACTATATAATA
* *
411543 TTTATATA-TATATACATA
1 ATAATATACTATATA-ATA
*
411561 AT-ATATACCATATAATA
1 ATAATATACTATATAATA
411578 TATAATATA-T-TATAAT-
1 -ATAATATACTATATAATA
*
411594 ATAATATAATATAATAATA
1 ATAATATACTAT-ATAATA
411613 ATAATAATACTACTAT-ATA
1 ATAAT-ATACTA-TATAATA
*
411632 ATTATA-AC-ATAT-ATA
1 ATAATATACTATATAATA
*
411647 CT-ATATACTATAT-ATA
1 ATAATATACTATATAATA
411663 ATACCATATA-T-TAT-ATA
1 ATA--ATATACTATATAATA
411680 A-AATATACTATAT-ATA
1 ATAATATACTATATAATA
411696 ATA
1 ATA
411699 TAAATATAAA
Statistics
Matches: 240, Mismatches: 21, Indels: 79
0.71 0.06 0.23
Matches are distributed among these distances:
14 11 0.05
15 22 0.09
16 27 0.11
17 58 0.24
18 52 0.22
19 33 0.14
20 22 0.09
21 13 0.05
22 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATACTATATAATA
Found at i:412247 original size:47 final size:47
Alignment explanation
Indices: 412193--412289 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
412183 TGTTGACCCA
* ***
412193 TTCGTCGTGAAGTTGAGTTAATCTTGAATGATTTAAGCACGATATCC
1 TTCGTCGTGAAGTTAAACCAATCTTGAATGATTTAAGCACGATATCC
*
412240 TTCGTCGTGAAGTTAAACCAATCTTGAATGATTTGAGCACGATATCC
1 TTCGTCGTGAAGTTAAACCAATCTTGAATGATTTAAGCACGATATCC
412287 TTC
1 TTC
412290 ATCATGAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (47 bp):
TTCGTCGTGAAGTTAAACCAATCTTGAATGATTTAAGCACGATATCC
Found at i:433845 original size:90 final size:88
Alignment explanation
Indices: 433694--433859 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 88
433684 CCTTTCATAG
* * *
433694 CCAAGTTATCCTAATCATATTAGGGTTTTATTATTCAAATTAATTAAATCTATATTTAATTAATT
1 CCAAGTTACCCTAATCATATTAGGATTTTATTATTCAAATTAATTAAATCTATAATTAATTAATT
* *
433759 GGAATTTAATAATCCTCTTATAT
66 GAAATTAAATAATCCTCTTATAT
433782 CCAAGTTACCCTAATCATATTGAGGATTTTATTATTTCAAATTAATTAAATCTATAATTAATTAA
1 CCAAGTTACCCTAATCATATT-AGGATTTTATTA-TTCAAATTAATTAAATCTATAATTAATTAA
433847 TTGAAATTAAATA
64 TTGAAATTAAATA
433860 TTTGGGATTA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
88 20 0.28
89 11 0.15
90 40 0.56
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (88 bp):
CCAAGTTACCCTAATCATATTAGGATTTTATTATTCAAATTAATTAAATCTATAATTAATTAATT
GAAATTAAATAATCCTCTTATAT
Found at i:437662 original size:2 final size:2
Alignment explanation
Indices: 437657--437917 Score: 165
Period size: 2 Copynumber: 129.5 Consensus size: 2
437647 TAAAAAATAA
*
437657 AT AT AT A- AT AT ACT AT ACT AT A- AT AT AT ACC AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * *
437698 A- AT AT AT AT AT AT AT AT A- AC ACC AT GAT A- AT AT ACT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT A-T AT AT
* *
437738 A- AT AT AT AT AT AT AT A- AT GCT AT AT GAT AT AA AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT
*
437779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
437819 AT ACT AT AT A- AGT AT A- AT AT AT AT ACT AT AT ACT AT AT ACT AT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT
* * *
437862 AT ACT AT AT AT A- AT ACC AT AT ACT AT GT A- AA AT AT ACT AT AT
1 AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT A-T AT AT
*
437904 AT A- AT AT AA AT AT A
1 AT AT AT AT AT AT AT A
437918 AATAAAAGTC
Statistics
Matches: 209, Mismatches: 18, Indels: 64
0.72 0.06 0.22
Matches are distributed among these distances:
1 15 0.07
2 164 0.78
3 30 0.14
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:437803 original size:60 final size:58
Alignment explanation
Indices: 437651--437917 Score: 205
Period size: 60 Copynumber: 4.5 Consensus size: 58
437641 ATAAAATAAA
*
437651 AAATA-AATATATA-ATATACTATACTATAATATATACCATATATATATAA-TATATATAT
1 AAATATAATATATATATATA-TATA-TAT-ATATATACTATATATATATAATTATATATAT
* * * * *
437709 ATATATAACACCATGATA-ATATA-CTATGTA-ATA-TATATATATATAATGCTATATGATAT
1 AAATATAATA-TAT-ATATATATATATATATATATACTATATATATATAAT--TATAT-ATAT
437768 AAATATAATATATATATATATATATATATATATA-TATATATATATAAATTAATACTATAT
1 AAATATAATATATATATATATATATATATATATACTATATATATAT-AATT-ATA-TATAT
* *
437828 AAGTATAATATATATACTATATACTATATACTATATACTATATATA-ATACCA-TATACTATGT
1 AAATATAATATATATA-TATATA-TATATA-TATATACTATATATATATA--ATTATA-TATAT
* *
437890 AAAATATACTATATATA-ATATAAATATA
1 -AAATATAATATATATATATATATATATA
437918 AATAAAAGTC
Statistics
Matches: 172, Mismatches: 16, Indels: 40
0.75 0.07 0.18
Matches are distributed among these distances:
55 12 0.07
56 3 0.02
57 5 0.03
58 19 0.11
59 21 0.12
60 45 0.26
61 19 0.11
62 16 0.09
63 23 0.13
64 9 0.05
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (58 bp):
AAATATAATATATATATATATATATATATATATACTATATATATATAATTATATATAT
Found at i:441517 original size:15 final size:14
Alignment explanation
Indices: 441499--441553 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 14
441489 AATTCATGTT
441499 TTAATTTGTGAATTA
1 TTAATTTGT-AATTA
*
441514 TTAATTTTTTAATTTA
1 TTAA-TTTGTAA-TTA
441530 TT-ATTTGT-ATTA
1 TTAATTTGTAATTA
441542 TTAATTT-TAATT
1 TTAATTTGTAATT
441554 TATTCTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
12 6 0.18
13 8 0.24
14 4 0.12
15 7 0.21
16 9 0.26
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (14 bp):
TTAATTTGTAATTA
Found at i:441990 original size:141 final size:141
Alignment explanation
Indices: 441736--442269 Score: 773
Period size: 141 Copynumber: 3.9 Consensus size: 141
441726 GGATTTCTCA
* *
441736 CACTTTAGTCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCAAGGGACC
1 CACTTTAATCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCGAGGGACC
*
441801 ATATCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTT
66 ATTTCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTT
441866 AGGTTTAATAT
131 AGGTTTAATAT
* * * * * *
441877 CACTTTAATTCTTTAATTTAGGGAGTAATTTAAATTGGTTCTCGCATTAACATGCACGAGGGATC
1 CACTTTAATCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCGAGGGACC
* * * *
441942 ATTTCGATTATTCGACTCAATAATTGATTAAAATAAATTATGATTAATATTAGATCCTCCAATTT
66 ATTTCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTT
442007 AGGTTTAATAT
131 AGGTTTAATAT
* * * *
442018 CACTTTAGTCCTTTAATTTAGGGAGTAGTTTGAATTGGCTCCCACATTAACATGCCTGAGGGACC
1 CACTTTAATCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCGAGGGACC
*
442083 ATTTCGATTATTCGACTCAATAATTGGTTAACATAAATTAGGATTAATATTAGAGCCTCCACTTT
66 ATTTCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTT
*
442148 AGGTTTAATTT
131 AGGTTTAATAT
* **
442159 CACTTTAATCATTTAATTTAGGGAG----TTG-A----CTCTTGCATTAACATGCCCGAGGGACC
1 CACTTTAATCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCGAGGGACC
* *
442215 ATTTCGATTATTTGACTCAATAATTGGTTAAAATAAATTA-GAGTCAATATTAGAG
66 ATTTCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGA-TTAATATTAGAG
442270 TCTTTATTTT
Statistics
Matches: 354, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
131 2 0.01
132 72 0.20
136 1 0.00
137 3 0.01
141 276 0.78
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (141 bp):
CACTTTAATCCTTTAATTTAGGGAGTAATTTGAATTGGCTCTCACATTAACATGCCCGAGGGACC
ATTTCGATTATTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTT
AGGTTTAATAT
Found at i:451297 original size:45 final size:45
Alignment explanation
Indices: 451232--451504 Score: 336
Period size: 45 Copynumber: 6.1 Consensus size: 45
451222 TATCCTTTAT
* * *
451232 TTTCATTTATAGG-ATTCTTTCATG-CTTATAATGCACCGTTATACA
1 TTTCATTTAT-GGCATCCTTTCATGTCGT-TAATGCACCGTTATGCA
*
451277 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGATATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
* * *
451322 TTTCATTTATGGCATCCTTTCATGCCCTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
* * * *
451367 TTTCATTTATGGTATCATTTCATGTCGTTAGTGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
* *
451412 TTTCATTTATGGCATCCTTTCATGTCGTTAGTGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
* * * **
451457 TTTCATTTATGGCATCATTTTAT-TCCATTAATGCACTATTATGCA
1 TTTCATTTATGGCATCCTTTCATGT-CGTTAATGCACCGTTATGCA
451502 TTT
1 TTT
451505 TATTCATTCA
Statistics
Matches: 201, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
44 3 0.01
45 196 0.98
46 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
Found at i:468022 original size:19 final size:19
Alignment explanation
Indices: 467998--468036 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
467988 AGTTCTCACC
467998 TTTGGTACTTCCGTTGTCA
1 TTTGGTACTTCCGTTGTCA
468017 TTTGGTACTTCCGTTGTCA
1 TTTGGTACTTCCGTTGTCA
468036 T
1 T
468037 CACCTCACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (19 bp):
TTTGGTACTTCCGTTGTCA
Found at i:472584 original size:11 final size:11
Alignment explanation
Indices: 472563--472605 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
472553 TCAAGGTGAA
472563 AAGAA-AAAAG
1 AAGAAGAAAAG
472573 AAGAAGAAAAG
1 AAGAAGAAAAG
472584 AAGAAGAAAA-
1 AAGAAGAAAAG
*
472594 AAG-GGAAAAG
1 AAGAAGAAAAG
472604 AA
1 AA
472606 ATAAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 5 0.17
10 10 0.33
11 15 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAG
Found at i:475423 original size:66 final size:65
Alignment explanation
Indices: 475290--475438 Score: 183
Period size: 66 Copynumber: 2.3 Consensus size: 65
475280 CATTGAGATA
* * *
475290 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTCCGGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCCCTCGAAACATAAA-CTTCCGAAT
475355 T
65 T
* * * **
475356 GTTTCTCTCGAAACAAATTTTGTCTCGCTTGAGAGAGTTTTCCCTCGAAACATAAA-TTTTGAAA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA-ATTTCCCTCGAAACATAAACTTCCG-AA
475420 TT
64 TT
*
475422 GTTTCACTTGAAACAAA
1 GTTTCTCTTGAAACAAA
475439 ATTGATCTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
65 3 0.04
66 52 0.73
67 16 0.23
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (65 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCCCTCGAAACATAAACTTCCGAATT
Found at i:475483 original size:102 final size:103
Alignment explanation
Indices: 475366--475556 Score: 242
Period size: 102 Copynumber: 1.9 Consensus size: 103
475356 GTTTCTCTCG
* ** * * *
475366 AAACAAATTTTGTCTCGCTTGAGAGAGTTTTCCCTCGAAACATAAATTTTGAAATTGTTTCACTT
1 AAACAAATTTTGTCTCACTTGAGAGAGTTTAACCTCGAAACACAAATTTGGAAATTGTTTCACTC
475431 GAAACAAAATT-GATCTCACTTGATATTATTTTACTAA
66 GAAACAAAATTAGATCTCACTTGATATTATTTTACTAA
* * **
475468 AAAC-AATTTTCGTCTCACTTGAGATAGTTTAACCTTGAAATGCAAATTTGGAAATTGTTTCACT
1 AAACAAATTTT-GTCTCACTTGAGAGAGTTTAACCTCGAAACACAAATTTGGAAATTGTTTCACT
* * *
475532 CGATATAAAATTATATCTCACTTGA
65 CGAAACAAAATTAGATCTCACTTGA
475557 GATAGTTTCT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
101 6 0.08
102 57 0.77
103 11 0.15
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (103 bp):
AAACAAATTTTGTCTCACTTGAGAGAGTTTAACCTCGAAACACAAATTTGGAAATTGTTTCACTC
GAAACAAAATTAGATCTCACTTGATATTATTTTACTAA
Found at i:481730 original size:32 final size:32
Alignment explanation
Indices: 481614--481730 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
481604 GTAACTGTTA
*
481614 TGCATTATCTGAATACAAC-CTTGACATTGA-TG
1 TGCATTATCTGAATGCAACAC-TGACATT-ATTG
* * * * *
481646 TTCATTATTTGAATGCAACATTGACACTGTTG
1 TGCATTATCTGAATGCAACACTGACATTATTG
* * * *
481678 TACATTATCTAAATGCAACACTAATATTATTG
1 TGCATTATCTGAATGCAACACTGACATTATTG
481710 TGCATTATCTGAATGCAACAC
1 TGCATTATCTGAATGCAACAC
481731 ACTGCTAGTA
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTGACATTATTG
Found at i:486376 original size:31 final size:33
Alignment explanation
Indices: 486306--486389 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 33
486296 CCTGACTTTG
* *
486306 TTGTGCATTATCTAAATGCAATATTAACACTAC
1 TTGTGTATTATCTAAATGCAATATTAACAATAC
**
486339 TT-TGTATTATCTAAATGTTA-ATTAACAATA-
1 TTGTGTATTATCTAAATGCAATATTAACAATAC
*
486369 TTGTGTATTATCTGAATGCAA
1 TTGTGTATTATCTAAATGCAA
486390 CACACTACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 24 0.56
32 15 0.35
33 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (33 bp):
TTGTGTATTATCTAAATGCAATATTAACAATAC
Found at i:492382 original size:32 final size:32
Alignment explanation
Indices: 492346--492413 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
492336 ATCTGGATGC
*
492346 AACATTTACACTATTGTACATTATATGAATAT
1 AACATTAACACTATTGTACATTATATGAATAT
* * * *
492378 AACATTAATACTATTGTGCATTATTTGAATGT
1 AACATTAACACTATTGTACATTATATGAATAT
492410 AACA
1 AACA
492414 AATTGCTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (32 bp):
AACATTAACACTATTGTACATTATATGAATAT
Found at i:493652 original size:25 final size:25
Alignment explanation
Indices: 493613--493703 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
493603 TTTGGTGTCG
493613 GATTTGGTA-CTCTTTTCAAGAGTTA
1 GATTTGGTATC-CTTTTCAAGAGTTA
* *
493638 GATTTGGTATCCTTTTTCAA-CG-TC
1 GATTTGGTATCC-TTTTCAAGAGTTA
* * * *
493662 GAATTTGTTATCCTTTTCCAGTGTTG
1 G-ATTTGGTATCCTTTTCAAGAGTTA
493688 GATTTGGTATCCTTTT
1 GATTTGGTATCCTTTT
493704 TCAGCATTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 8 0.15
25 36 0.67
26 10 0.19
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.48
Consensus pattern (25 bp):
GATTTGGTATCCTTTTCAAGAGTTA
Found at i:494927 original size:13 final size:13
Alignment explanation
Indices: 494911--494941 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
494901 TTTATGAAAC
*
494911 ACATTTATGACTT
1 ACATTTACGACTT
494924 ACATTTACGACTT
1 ACATTTACGACTT
494937 ACATT
1 ACATT
494942 GCGTGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (13 bp):
ACATTTACGACTT
Found at i:496034 original size:12 final size:12
Alignment explanation
Indices: 496017--496047 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
496007 ATATATTGAT
496017 AATCAAATGAAA
1 AATCAAATGAAA
496029 AATCAAATGAAA
1 AATCAAATGAAA
*
496041 AAACAAA
1 AATCAAA
496048 CTCGGGACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:498172 original size:65 final size:65
Alignment explanation
Indices: 498039--498173 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
498029 GGTGGAGCTA
* ** *
498039 TTGTTCATAATATTTTATAGTAATTGATGACATGATGAAGACGTTTTATGATTTTCTCTTTTTCT
1 TTGTTCATAATACTTTATAGTAATTGATGACATGATGAAGACGTTTTATGATTGACTATTTTTCT
*
498104 TTGTTCATAATACTTTATAGTAATTGATGGCATGATGAAGAC-TTATT-TGTAGTTGACTATTTT
1 TTGTTCATAATACTTTATAGTAATTGATGACATGATGAAGACGTT-TTATG-A-TTGACTATTTT
498167 T-T
63 TCT
498169 TTGTT
1 TTGTT
498174 GTTACAGCTA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
64 4 0.06
65 49 0.79
66 9 0.15
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (65 bp):
TTGTTCATAATACTTTATAGTAATTGATGACATGATGAAGACGTTTTATGATTGACTATTTTTCT
Found at i:500891 original size:20 final size:20
Alignment explanation
Indices: 500863--500902 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
500853 CTTGAAATAA
500863 GTTAATTACTTTC-GGTGGTT
1 GTTAATTAC-TTCAGGTGGTT
*
500883 GTTAGTTACTTCAGGTGGTT
1 GTTAATTACTTCAGGTGGTT
500903 TACCTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.15, C:0.10, G:0.28, T:0.47
Consensus pattern (20 bp):
GTTAATTACTTCAGGTGGTT
Found at i:500951 original size:24 final size:25
Alignment explanation
Indices: 500924--500990 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
500914 AACACACACC
500924 TCATATTATAAAAACTCACA-CATT
1 TCATATTATAAAAACTCACACCATT
* * *
500948 TCATATTA-ACAACACACACACCCTT
1 TCATATTATA-AAAACTCACACCATT
500973 T-ATATTATAAAAACTCAC
1 TCATATTATAAAAACTCAC
500991 TCACACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 29 0.83
25 5 0.14
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (25 bp):
TCATATTATAAAAACTCACACCATT
Found at i:501020 original size:54 final size:52
Alignment explanation
Indices: 500926--501057 Score: 175
Period size: 54 Copynumber: 2.6 Consensus size: 52
500916 CACACACCTC
500926 ATATTATAAAAACT----CACACATTTCATATTAACAACACACACACCCTTT
1 ATATTATAAAAACTCACACACACATTTCATATTAACAACACACACACCCTTT
*
500974 ATATTATAAAAACTCACTCACACACATTTCATATTAA-AAGAGCACACACCCTTT
1 ATATTATAAAAACTCA--CACACACATTTCATATTAACAACA-CACACACCCTTT
* *
501028 ATATTATAATAATTCACACACACATTTCAT
1 ATATTATAAAAACTCACACACACATTTCAT
501058 GTATACATTA
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
48 14 0.19
52 14 0.19
53 3 0.04
54 43 0.58
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (52 bp):
ATATTATAAAAACTCACACACACATTTCATATTAACAACACACACACCCTTT
Found at i:501045 original size:26 final size:24
Alignment explanation
Indices: 500962--501048 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 24
500952 ATTAACAACA
500962 CACACACCCTTTATATTATAAAAACT
1 CACACACCCTTTATATTAT-AAAA-T
* *
500988 CACTCACACACATTTCATATTA-AAAGAG
1 CA--CACAC-CCTTT-ATATTATAAA-AT
501016 CACACACCCTTTATATTATAATAATT
1 CACACACCCTTTATATTATAA-AA-T
501042 CACACAC
1 CACACAC
501049 ACATTTCATG
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
24 6 0.12
25 7 0.14
26 15 0.31
28 10 0.20
29 5 0.10
30 6 0.12
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.29
Consensus pattern (24 bp):
CACACACCCTTTATATTATAAAAT
Found at i:501124 original size:52 final size:53
Alignment explanation
Indices: 501059--501216 Score: 165
Period size: 56 Copynumber: 2.9 Consensus size: 53
501049 ACATTTCATG
* *** * *
501059 TATACATTAAACACACACGTGTATTACATAAT-AAAAAGCACACACACATACA
1 TATATATTAAACACACACACATATTACATAATAAAAAAGAACACACACATAAA
* *
501111 TATATATTAAACACACACACATATTGCATAATAAAAAAAGAATACACACATAAA
1 TATATATTAAACACACACACATATTACATAAT-AAAAAAGAACACACACATAAA
* * * *
501165 TATATATTAAATACACACACACTTACTGCATAATAAAAAAAATACACACACA
1 TATATATT-AA-ACACACACACATATTACATAATAAAAAAGA-ACACACACA
501217 CTTACTGCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 27 0.30
54 25 0.28
55 9 0.10
56 28 0.31
ACGTcount: A:0.54, C:0.20, G:0.04, T:0.22
Consensus pattern (53 bp):
TATATATTAAACACACACACATATTACATAATAAAAAAGAACACACACATAAA
Found at i:501170 original size:56 final size:53
Alignment explanation
Indices: 501059--501214 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 53
501049 ACATTTCATG
* *** * * *
501059 TATACATTAAACACACACGTGTATTACATAAT-AAAAAGCACACACACATACA
1 TATATATTAAACACACACACATATTGCATAATAAAAAAGAATACACACATACA
*
501111 TATATATTAAACACACACACATATTGCATAATAAAAAAAGAATACACACATAAA
1 TATATATTAAACACACACACATATTGCATAAT-AAAAAAGAATACACACATACA
* *
501165 TATATATTAAATACACACACACTTACTGCATAATAAAAAA-AATACACACA
1 TATATATT-AA-ACACACACACATATTGCATAATAAAAAAGAATACACACA
501215 CACTTACTGC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 27 0.30
54 35 0.39
55 8 0.09
56 20 0.22
ACGTcount: A:0.54, C:0.20, G:0.04, T:0.22
Consensus pattern (53 bp):
TATATATTAAACACACACACATATTGCATAATAAAAAAGAATACACACATACA
Found at i:501215 original size:56 final size:54
Alignment explanation
Indices: 501086--501216 Score: 174
Period size: 56 Copynumber: 2.4 Consensus size: 54
501076 CGTGTATTAC
* * *
501086 ATAATAAAAAGCACACACACATACATATATATTAAACACACACACATATTGCATA
1 ATAA-AAAAAGAACACACACATAAATATATATTAAACACACACACATACTGCATA
* *
501141 ATAAAAAAAGAATACACACATAAATATATATTAAATACACACACACTTACTGCATA
1 ATAAAAAAAGAACACACACATAAATATATATT-AA-ACACACACACATACTGCATA
501197 ATAAAAAAA-ATACACACACA
1 ATAAAAAAAGA-ACACACACA
501217 CTTACTGCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
54 25 0.37
55 7 0.10
56 35 0.52
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.21
Consensus pattern (54 bp):
ATAAAAAAAGAACACACACATAAATATATATTAAACACACACACATACTGCATA
Found at i:501242 original size:30 final size:30
Alignment explanation
Indices: 501173--501315 Score: 183
Period size: 30 Copynumber: 5.0 Consensus size: 30
501163 AATATATATT
501173 AAATACACACACACTTACTGCATAATAAAAA
1 AAATACACACACACTTACTGCATAAT-AAAA
501204 AAATACACACACACTTACTGCATAAT-AAA
1 AAATACACACACACTTACTGCATAATAAAA
* * * **
501233 AAA-GCACACACA-TGAAT--AT-AT-ATT
1 AAATACACACACACTTACTGCATAATAAAA
501257 AAATACACACACACTTACTGCATAATAAAA
1 AAATACACACACACTTACTGCATAATAAAA
501287 AAATACACACACACTTACTGCATAATAAA
1 AAATACACACACACTTACTGCATAATAAA
501316 CAATCTTTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.06
25 10 0.10
26 3 0.03
27 3 0.03
28 10 0.10
29 8 0.08
30 30 0.31
31 26 0.27
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.21
Consensus pattern (30 bp):
AAATACACACACACTTACTGCATAATAAAA
Found at i:501262 original size:84 final size:84
Alignment explanation
Indices: 501121--501315 Score: 320
Period size: 84 Copynumber: 2.3 Consensus size: 84
501111 TATATATTAA
* * *
501121 ACACACACACATATTGCATAATAAAAAAAGAATACACACATAAATATATATTAAATACACACACA
1 ACACACACACTTACTGCATAAT-AAAAAAG-ACACACACATAAATATATATTAAATACACACACA
501186 CTTACTGCATAATAAAAAAAAT
64 CTTACTGCATAAT-AAAAAAAT
*
501208 ACACACACACTTACTGCATAATAAAAAAG-CACACACATGAATATATATTAAATACACACACACT
1 ACACACACACTTACTGCATAATAAAAAAGACACACACATAAATATATATTAAATACACACACACT
501272 TACTGCATAATAAAAAAAT
66 TACTGCATAATAAAAAAAT
501291 ACACACACACTTACTGCATAATAAA
1 ACACACACACTTACTGCATAATAAA
501316 CAATCTTTTA
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
83 33 0.32
84 44 0.42
86 7 0.07
87 20 0.19
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.22
Consensus pattern (84 bp):
ACACACACACTTACTGCATAATAAAAAAGACACACACATAAATATATATTAAATACACACACACT
TACTGCATAATAAAAAAAT
Found at i:505191 original size:21 final size:21
Alignment explanation
Indices: 505161--505218 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
505151 TAGCCTATAG
*
505161 AGTATCGATATCTTTTCTTCA
1 AGTATTGATATCTTTTCTTCA
* * *
505182 AGTATTGATA-CCTTCCATCA
1 AGTATTGATATCTTTTCTTCA
505202 AGTATTGATAT-TTTTCT
1 AGTATTGATATCTTTTCT
505219 ATTAAATATC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
AGTATTGATATCTTTTCTTCA
Found at i:508636 original size:50 final size:49
Alignment explanation
Indices: 508492--508645 Score: 182
Period size: 49 Copynumber: 3.1 Consensus size: 49
508482 AATTGCTCTA
* * * * *
508492 TAATGCAAGTTAAATGCATAAAGGCGCATTTTTGGCAGAAATGTGCCAC
1 TAATACAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGTCAT
* ** * ** *
508541 TAATGCAAGTTAAATTTAGAATTGTGCATTTTTGGCAAAAAGGTGTCAT
1 TAATACAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGTCAT
*
508590 TAATACAAGTTAAATGCATAAAGGTACATTTTTTGGCAGAAAGGTGTCAT
1 TAATACAAGTTAAATGCATAAAGGTGCA-TTTTTGGCAGAAAGGTGTCAT
508640 TAATAC
1 TAATAC
508646 CGTTGGAATA
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 60 0.70
50 26 0.30
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (49 bp):
TAATACAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGTCAT
Found at i:512681 original size:85 final size:85
Alignment explanation
Indices: 512538--512707 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
512528 GTTGGCAGCA
*
512538 GTTTGCTTTAAAGATTTGATGCCATTATCTGTATGGTAAGCGATGTTATAGTTATGCAAATTATA
1 GTTTGCTTTAAAGATTTGACGCCATTATCTGTATGGTAAGCGATGTTATAGTTATGCAAATTATA
512603 AAAGCCTAAAGTACTTGTGG
66 AAAGCCTAAAGTACTTGTGG
*
512623 GTTTGCTTTAAAGATTTGACGCCATTATCTGTATGGTAAGCGGTGTTATAGTTATGCAAATTATA
1 GTTTGCTTTAAAGATTTGACGCCATTATCTGTATGGTAAGCGATGTTATAGTTATGCAAATTATA
512688 AAAGCCTAAAGTACTTGTGG
66 AAAGCCTAAAGTACTTGTGG
512708 ACATAAAAAG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (85 bp):
GTTTGCTTTAAAGATTTGACGCCATTATCTGTATGGTAAGCGATGTTATAGTTATGCAAATTATA
AAAGCCTAAAGTACTTGTGG
Found at i:516055 original size:137 final size:137
Alignment explanation
Indices: 515878--516155 Score: 344
Period size: 137 Copynumber: 2.0 Consensus size: 137
515868 TCATAGGTGT
* ** * ** * * *
515878 ATTTCGACATAAATTGTATGTAATGGTTATCGATGGATTTTGAGTAATGCATAATGGTGCATTTT
1 ATTTCGACATAAAATGTATGTAAAAGTTATCGATCGATTTTGAGTAACCCAAAACGATGCATTTT
* * * *
515943 TGTATCAGTACTATTTGTACTTTCGGCACTA-GATTGCAACCATGGTATTCATAATGAGTTTGTG
66 CGTATCAGTACTATATGTACTTTCGGCACTATGAGTGCAACCATGGAATTCATAATGAGTTTGTG
516007 AATTACC
131 AATTACC
**
516014 ATTTCGACATAAAAT-TATGTATAAAAGTTATCGATCGATTTTGTTTAACCCAAAACGATGCATT
1 ATTTCGACATAAAATGTATG--TAAAAGTTATCGATCGATTTTGAGTAACCCAAAACGATGCATT
* * **
516078 TTCGTATCAGTACTATATGTACTTTCGGCACTATGGGTGTATTCATGGAATTCATAATGAGTTTG
64 TTCGTATCAGTACTATATGTACTTTCGGCACTATGAGTGCAACCATGGAATTCATAATGAGTTTG
*
516143 TGAATTTCC
129 TGAATTACC
516152 ATTT
1 ATTT
516156 AGGCCTTAGG
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
135 4 0.03
136 14 0.12
137 64 0.54
138 37 0.31
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (137 bp):
ATTTCGACATAAAATGTATGTAAAAGTTATCGATCGATTTTGAGTAACCCAAAACGATGCATTTT
CGTATCAGTACTATATGTACTTTCGGCACTATGAGTGCAACCATGGAATTCATAATGAGTTTGTG
AATTACC
Found at i:516223 original size:20 final size:20
Alignment explanation
Indices: 516198--516236 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
516188 CTCATTTGAC
**
516198 ATAAATTGGGCAAATAATGG
1 ATAAATTGGAAAAATAATGG
516218 ATAAATTGGAAAAATAATG
1 ATAAATTGGAAAAATAATG
516237 ATTGATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.26
Consensus pattern (20 bp):
ATAAATTGGAAAAATAATGG
Found at i:516781 original size:81 final size:81
Alignment explanation
Indices: 516688--516839 Score: 295
Period size: 81 Copynumber: 1.9 Consensus size: 81
516678 TTGAGTAGAC
*
516688 GTGTGTAATTGAAGAATGTTTTATAAACTATATTATTAAATTGTTTTATCTAAAGAAACAAAATA
1 GTGTGTAATTGAAGAATGTTTTATAAACTATATTATTAAATTATTTTATCTAAAGAAACAAAATA
516753 ATTTGTGTGTTTGTGT
66 ATTTGTGTGTTTGTGT
516769 GTGTGTAATTGAAGAATGTTTTATAAACTATATTATTAAATTATTTTATCTAAAGAAACAAAATA
1 GTGTGTAATTGAAGAATGTTTTATAAACTATATTATTAAATTATTTTATCTAAAGAAACAAAATA
516834 ATTTGT
66 ATTTGT
516840 TGGTTTTCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (81 bp):
GTGTGTAATTGAAGAATGTTTTATAAACTATATTATTAAATTATTTTATCTAAAGAAACAAAATA
ATTTGTGTGTTTGTGT
Found at i:528324 original size:40 final size:40
Alignment explanation
Indices: 528252--528333 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
528242 ATAGGAGTCC
* * * *
528252 AATATTGCACAATAGTGCTGAGGTCAATCTTTGCTCACCT
1 AATAATGCACAATAGTGCTAAGGTCAAGCTTTGCGCACCT
**
528292 AATAATGCACAATAGTGCTAAGGTCGGGCTTTGCGCACCT
1 AATAATGCACAATAGTGCTAAGGTCAAGCTTTGCGCACCT
528332 AA
1 AA
528334 CTTGTACTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (40 bp):
AATAATGCACAATAGTGCTAAGGTCAAGCTTTGCGCACCT
Found at i:529174 original size:30 final size:30
Alignment explanation
Indices: 529140--529208 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
529130 TAACCATTCA
** *
529140 CAACTTTTTC-AAAATTGTTAAATTGGTCCC
1 CAACTTTTTCAAAAATT-ACAAAATGGTCCC
529170 CAAC-TTTTCAAAAATTACAAAATGGTCCC
1 CAACTTTTTCAAAAATTACAAAATGGTCCC
*
529199 CAAATTTTTC
1 CAACTTTTTC
529209 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (30 bp):
CAACTTTTTCAAAAATTACAAAATGGTCCC
Found at i:532670 original size:15 final size:14
Alignment explanation
Indices: 532635--532688 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
532625 ACTTACTATT
* *
532635 TTTAGGATTTAGGG
1 TTTAGGGTTTATGG
532649 TTTAGGGTTTATAGG
1 TTTAGGGTTTAT-GG
* * *
532664 TTAAGGGATTATGA
1 TTTAGGGTTTATGG
532678 TTTAGGGTTTA
1 TTTAGGGTTTA
532689 GAATTTAGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:532928 original size:38 final size:41
Alignment explanation
Indices: 532886--532975 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 41
532876 TCAAATATTC
*
532886 AAAAAATTAAAATAATA-ATACTAAAAA-ATTAAA-T-TAAT
1 AAAAAATTAAAAT-ATACATACTAAAAATACTAAACTATAAT
* *
532924 AAAAAATT-AAATATACATATTAAAAATACTAAACTATTAT
1 AAAAAATTAAAATATACATACTAAAAATACTAAACTATAAT
532964 AAAAAATTAAAA
1 AAAAAATTAAAA
532976 ATTTTGAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 3 0.07
37 13 0.30
38 13 0.30
39 1 0.02
40 11 0.25
41 3 0.07
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (41 bp):
AAAAAATTAAAATATACATACTAAAAATACTAAACTATAAT
Found at i:533150 original size:25 final size:25
Alignment explanation
Indices: 533122--533173 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
533112 TGGATTAATA
533122 GAGAATTACAAAATTTAAATTAGTC
1 GAGAATTACAAAATTTAAATTAGTC
* * **
533147 GAGACTTATAATTTTTAAATTAGTC
1 GAGAATTACAAAATTTAAATTAGTC
533172 GA
1 GA
533174 AACTTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (25 bp):
GAGAATTACAAAATTTAAATTAGTC
Found at i:533491 original size:27 final size:26
Alignment explanation
Indices: 533461--533512 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
533451 TTAATATATA
533461 TTCA-AATTTTTAGTAGTTTAATTTTTT
1 TTCATAATTTTTA-TA-TTTAATTTTTT
*
533488 TTCATATTTTTTATATTTAATTTTT
1 TTCATAATTTTTATATTTAATTTTT
533513 GAATATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 6 0.26
28 7 0.30
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (26 bp):
TTCATAATTTTTATATTTAATTTTTT
Found at i:534412 original size:44 final size:46
Alignment explanation
Indices: 534292--534417 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 46
534282 TATAAAATCT
* * *
534292 CTTACAATTT-ATCCCATATGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
534337 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
534384 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
534418 ACATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 23 0.33
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:538277 original size:17 final size:18
Alignment explanation
Indices: 538257--538365 Score: 70
Period size: 17 Copynumber: 6.1 Consensus size: 18
538247 TCTCTCATTT
538257 TTTC-TCTTTTTTTTTTC
1 TTTCTTCTTTTTTTTTTC
538274 TTTC-TCGTTTTTATTTTT-
1 TTTCTTC-TTTTT-TTTTTC
** *
538292 TCTTCTTCGTTTTCATTTTA
1 T-TTCTTC-TTTTTTTTTTC
538312 TTT-TT-TTATTTTTTTT-
1 TTTCTTCTT-TTTTTTTTC
*
538328 TTTCTTCTGTTTTTTTTC
1 TTTCTTCTTTTTTTTTTC
*
538346 -TTCTTCTGTTTTTTCTTC
1 TTTCTTCT-TTTTTTTTTC
538364 TT
1 TT
538366 CTTATAATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
16 5 0.07
17 29 0.39
18 17 0.23
19 15 0.20
20 8 0.11
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTCTTCTTTTTTTTTTC
Found at i:538292 original size:20 final size:17
Alignment explanation
Indices: 538263--538359 Score: 88
Period size: 17 Copynumber: 5.3 Consensus size: 17
538253 ATTTTTTCTC
538263 TTTTTTTTTTCTTTCTCGT
1 TTTTTTTTTTC-TTCT-GT
538282 TTTTATTTTTTCTTCTTCGT
1 TTTT-TTTTTTCTTC-T-GT
* *
538302 TTTCATTTTATTT-TTTTAT
1 TTT--TTTT-TTTCTTCTGT
538321 TTTTTTTTTTCTTCTGT
1 TTTTTTTTTTCTTCTGT
*
538338 TTTTTTTCTTCTTCTGT
1 TTTTTTTTTTCTTCTGT
538355 TTTTT
1 TTTTT
538360 CTTCTTCTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
16 3 0.04
17 29 0.43
19 11 0.16
20 15 0.22
21 5 0.07
22 4 0.06
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTCTTCTGT
Found at i:541264 original size:47 final size:45
Alignment explanation
Indices: 541194--541319 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
541184 TATAAAATCT
*
541194 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
541239 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
541286 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
541320 GCATGGTAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:545573 original size:51 final size:49
Alignment explanation
Indices: 545518--545619 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 49
545508 CACGTAGGGT
* *
545518 TATAGCGCGGGGCAGGGGCCGCTCCTTACCTTTAATTCTGACATAATTATA
1 TATAGCGCGGGGCAGGGGCCGCGCCATACCTTTAA--CTGACATAATTATA
*
545569 TATAGCGCGGGGCAGGGGCCGCGCCATACCTTTAACTGATATAATTATA
1 TATAGCGCGGGGCAGGGGCCGCGCCATACCTTTAACTGACATAATTATA
545618 TA
1 TA
545620 AGGCACGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 15 0.31
51 33 0.69
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (49 bp):
TATAGCGCGGGGCAGGGGCCGCGCCATACCTTTAACTGACATAATTATA
Found at i:545857 original size:16 final size:16
Alignment explanation
Indices: 545833--545881 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
545823 AAGTAGGTAA
* *
545833 TTTTGTTATAATTTTT
1 TTTTATTATAATTATT
*
545849 TTTTATTATACTTATT
1 TTTTATTATAATTATT
* *
545865 GTTTATTATGATTATT
1 TTTTATTATAATTATT
545881 T
1 T
545882 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:549329 original size:35 final size:34
Alignment explanation
Indices: 549244--549330 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
549234 AAAATAATTT
*
549244 TAAATATAACAAACTTACAATAAGTATTAAATGG
1 TAAATATAACAAAATTACAATAAGTATTAAATGG
*
549278 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ATAACAAAATTACAATAA--G-TATTAAATGG
549316 T-AATA-AACAAAATTA
1 TAAATATAACAAAATTA
549331 ACTGGAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 5 0.11
35 25 0.54
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATATAACAAAATTACAATAAGTATTAAATGG
Found at i:551683 original size:17 final size:18
Alignment explanation
Indices: 551642--551680 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
551632 ATTATATAAG
551642 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
551659 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
551677 TAAA
1 TAAA
551681 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:551742 original size:10 final size:10
Alignment explanation
Indices: 551719--551768 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
551709 CACCTTAAAC
* *
551719 AGAGAATATA
1 AGAGAATTTG
*
551729 AGAGTATTTG
1 AGAGAATTTG
*
551739 AGAGAAGTTG
1 AGAGAATTTG
*
551749 AGAGAAATTG
1 AGAGAATTTG
551759 AGAGAATTTG
1 AGAGAATTTG
551769 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:555398 original size:2 final size:2
Alignment explanation
Indices: 555391--555429 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
555381 TATTATTATT
555391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
555430 TGATTTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:555564 original size:11 final size:12
Alignment explanation
Indices: 555542--555570 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
555532 CTATTTATAA
555542 ATTTTATAAATT
1 ATTTTATAAATT
555554 ATTTT-TAAATT
1 ATTTTATAAATT
555565 ATTTTA
1 ATTTTA
555571 ATTATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTATAAATT
Found at i:555811 original size:127 final size:128
Alignment explanation
Indices: 555567--555805 Score: 299
Period size: 127 Copynumber: 1.9 Consensus size: 128
555557 TTTAAATTAT
* * * *
555567 TTTAATTATGTTTTTAAATATTAAGAAAGGGCAGTCTTAAAATAACTGGATGTCCATTTTCTGAT
1 TTTAATTATGTTTTTAAATATTAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
* *
555632 ATTTTAAATAATTAAATATATTACTTTTATAAATTATATCTATTTTAAATAAATGCTTTAATA
66 ATTTTAAATAAATAAATATATTACTTTTATAAATTATATATATTTTAAATAAATGCTTTAATA
* * * *
555695 TTTATTTAT-TTTTT-AATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCC-TTTTCTGA
1 TTTAATTATGTTTTTAAATATTAAG-AAAGAGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGA
*
555757 TATTTCTAAATAAATAAATATCTTA-TTTATATTTAAATTA-ATATATTTT
65 TATTT-TAAATAAATAAATATATTACTTT-TA--TAAATTATATATATTTT
555806 CATAAAATCA
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
126 25 0.26
127 47 0.49
128 16 0.17
129 7 0.07
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (128 bp):
TTTAATTATGTTTTTAAATATTAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTTTCTGAT
ATTTTAAATAAATAAATATATTACTTTTATAAATTATATATATTTTAAATAAATGCTTTAATA
Found at i:557814 original size:43 final size:44
Alignment explanation
Indices: 557747--557831 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 44
557737 TGGCTTTAGA
* *
557747 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGCT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTGCT
* *
557790 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAAGTTTTG
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTG
557832 TTTGATGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 28 0.76
44 9 0.24
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAAGTTTTGCT
Found at i:564293 original size:45 final size:46
Alignment explanation
Indices: 564216--564303 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
564206 CTGACCAGAA
* * *
564216 ATCTGTGCATAAGTCACATGAAATGATGAATGTGTTGTCAAATAGC
1 ATCTGTGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATAGC
*
564262 ATCTGTGCAGAAGCCACA-GGAAGGATGAATGTGTTGTCAAAT
1 ATCTGTGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAAT
564304 GTTTTACTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 22 0.58
46 16 0.42
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (46 bp):
ATCTGTGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATAGC
Found at i:564315 original size:53 final size:54
Alignment explanation
Indices: 564258--564364 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
564248 TGTTGTCAAA
* * * *
564258 TAGCATCTGTGCAGAAGCCACAGGA-AGGATGAATGTGTTGTCAAATGTTTTAC
1 TAGCATCTGAGCAGAAACCACAGGAGAGGATGAATGTATTGACAAATGTTTTAC
* * *
564311 TAGCATCTGAGCATAAACCACATGAGATGATGAATGTATTGACAAATGTTTTAC
1 TAGCATCTGAGCAGAAACCACAGGAGAGGATGAATGTATTGACAAATGTTTTAC
564365 GAACCAGTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 21 0.46
54 25 0.54
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (54 bp):
TAGCATCTGAGCAGAAACCACAGGAGAGGATGAATGTATTGACAAATGTTTTAC
Found at i:565596 original size:223 final size:223
Alignment explanation
Indices: 565176--565805 Score: 996
Period size: 223 Copynumber: 2.8 Consensus size: 223
565166 GATTCAAATC
* * * **
565176 CATCATTCAATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-
565240 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCA
65 --AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCA
**
565305 ACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATG
128 ACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATG
*
565370 AGAAGAATCCGTTCAACCTTTTTCTCGAATT
193 AGAAGAATCCATTCAACCTTTTTCTCGAATT
565401 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
565466 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCAATGGATCAGCA
66 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACA
*
565531 TTGCCAGGAAGAGTTCATAATGAGAAGAACCCATCTAAAGAAGGAAGAAGAAATTCATAATGAGA
131 TTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGA
*
565596 AGAATTCATTCAACCTTTTTCTCGAATT
196 AGAATCCATTCAACCTTTTTCTCGAATT
565624 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-
* *
565689 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATTACTT-GATGGATC
64 -GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCGATGGATC
* * *
565753 AACTTTTCTA-GAGAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
127 AACATTGCCAGGA-AGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
565806 CTTGTTCAAT
Statistics
Matches: 375, Mismatches: 24, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
223 212 0.57
224 1 0.00
225 25 0.07
226 135 0.36
227 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (223 bp):
CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACA
TTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGA
AGAATCCATTCAACCTTTTTCTCGAATT
Found at i:565813 original size:113 final size:113
Alignment explanation
Indices: 565176--565805 Score: 884
Period size: 113 Copynumber: 5.6 Consensus size: 113
565166 GATTCAAATC
* * * *
565176 CATCATTCAATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
* *
565240 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
*
565288 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
* *
565353 AGAAGAAATTCATAATGAGAAGAA-TCCGTTCAACCTTTTT-CTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACT-TGTTCAA-CTTTTTGCTCGAATT
* * *
565401 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
* **
565464 -GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
* * * *
565511 CATCATTCAATGGATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACCCATCTAAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
* *
565576 AGAAGAAATTCATAATGAGAAGAA-TTCATTCAACCTTTTT-CTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTT-GTTCAA-CTTTTTGCTCGAATT
* * *
565624 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
565689 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
* * * *
565737 CATTACTT-GATGGATCAACTTTTCTAGAG-AGAGTTCATAATGAGAAGAACTCATCTAAAGAAG
1 CATCA-TTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAG
565800 GAAGAA
64 GAAGAA
565806 CTTGTTCAAT
Statistics
Matches: 464, Mismatches: 40, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
109 5 0.01
110 91 0.20
111 2 0.00
112 34 0.07
113 316 0.68
114 16 0.03
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
Found at i:567299 original size:32 final size:36
Alignment explanation
Indices: 567262--567335 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 36
567252 TGGCCATTTA
*
567262 ATATATTTAT-TTAATTATAAG-TATTA-TTATTTTT
1 ATATATATATATTAATT-TAAGTTATTATTTATTTTT
* *
567296 ATATATATATATTGATTTTAGTTATTATTTATTTTT
1 ATATATATATATTAATTTAAGTTATTATTTATTTTT
567332 ATAT
1 ATAT
567336 GTTCTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 12 0.35
35 10 0.29
36 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (36 bp):
ATATATATATATTAATTTAAGTTATTATTTATTTTT
Found at i:570228 original size:90 final size:88
Alignment explanation
Indices: 570114--570287 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 88
570104 TCTCGAATAT
*
570114 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
570179 GGTAACTTGGA-TATAAAAGGATTA
65 GGTAACTT-GACTATAAAAGGATTA
*
570203 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTTAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
570268 GGTAACTTGACTATAAAAGG
65 GGTAACTTGACTATAAAAGG
570288 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
88 2 0.02
89 39 0.48
90 40 0.49
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGACTATAAAAGGATTA
Found at i:570671 original size:16 final size:17
Alignment explanation
Indices: 570644--570680 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
570634 AGGGTTACAT
570644 TATAATAAATTAATAAC
1 TATAATAAATTAATAAC
*
570661 TATAA-AAATTAATAAT
1 TATAATAAATTAATAAC
570677 TATA
1 TATA
570681 TGTTTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATAAATTAATAAC
Found at i:571017 original size:21 final size:24
Alignment explanation
Indices: 570985--571029 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
570975 TTCTAATTAT
570985 AAAAATTCATT-A-TAATTATAAA
1 AAAAATTCATTAAGTAATTATAAA
571007 AAAAATT-ATTAAGTAATTATAAA
1 AAAAATTCATTAAGTAATTATAAA
571030 TATAGTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 8 0.38
23 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATTCATTAAGTAATTATAAA
Found at i:571531 original size:21 final size:21
Alignment explanation
Indices: 571502--571554 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
571492 TTGATTGTTT
*
571502 TTTTATTTA-TTTTATTATATTA
1 TTTT-TTTATTTTTAATA-ATTA
571524 TTTTTTTAATTTTTAATAATTA
1 TTTTTTT-ATTTTTAATAATTA
*
571546 TGTTTTTAT
1 TTTTTTTAT
571555 GATATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 15 0.56
23 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTTATTTTTAATAATTA
Found at i:571535 original size:22 final size:22
Alignment explanation
Indices: 571511--571553 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
571501 TTTTTATTTA
*
571511 TTTTATTATATTATTTTTTTAAT
1 TTTTAATA-ATTATTTTTTTAAT
*
571534 TTTTAATAATTATGTTTTTA
1 TTTTAATAATTATTTTTTTA
571554 TGATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTAATAATTATTTTTTTAAT
Found at i:572085 original size:72 final size:71
Alignment explanation
Indices: 572004--572218 Score: 322
Period size: 72 Copynumber: 3.0 Consensus size: 71
571994 GAGCATTTGA
* *
572004 ATAAGAAAAAAAGAAACATTTATAGTAAAGAAACGAAATAGACTTCTAGTTTGAGAATGTTTATG
1 ATAAGAAAAAAAGCAACATTTGTAGTAAAGAAACGAAATAGACTTCTAGTTTGAGAATGTTTATG
572069 AAAATG
66 AAAATG
* * *
572075 ATAAGAAAAAAAGCAATATTTGTAGTAAAAAAAATGAAATAGACTTCTAGTTTGAGAATGTTTAT
1 ATAAGAAAAAAAGCAACATTTGTAGT-AAAGAAACGAAATAGACTTCTAGTTTGAGAATGTTTAT
*
572140 GAAATTG
65 GAAAATG
* * *
572147 ATAACAAAAAAAAGCAACATTTGTAATAAAGAAACGAAATAGACTTCTAGTTTGAGAATATTTAT
1 ATAA-GAAAAAAAGCAACATTTGTAGTAAAGAAACGAAATAGACTTCTAGTTTGAGAATGTTTAT
*
572212 GATAATG
65 GAAAATG
572219 GAAAAGTGAT
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
71 23 0.18
72 86 0.67
73 19 0.15
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (71 bp):
ATAAGAAAAAAAGCAACATTTGTAGTAAAGAAACGAAATAGACTTCTAGTTTGAGAATGTTTATG
AAAATG
Found at i:572628 original size:14 final size:15
Alignment explanation
Indices: 572609--572638 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
572599 ATTAAATTTT
572609 TTTTTAAAAA-AATA
1 TTTTTAAAAATAATA
572623 TTTTTAAAAATAATA
1 TTTTTAAAAATAATA
572638 T
1 T
572639 AAACATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTTAAAAATAATA
Found at i:583092 original size:20 final size:20
Alignment explanation
Indices: 583067--583120 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
583057 AATCCCTTTA
583067 AAAATACATGATTTTTAATG
1 AAAATACATGATTTTTAATG
*
583087 AAAATACATGA-TTTCAATG
1 AAAATACATGATTTTTAATG
*
583106 AAAGTACATG-TTTTT
1 AAAATACATGATTTTT
583121 GGCCGAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:584059 original size:20 final size:21
Alignment explanation
Indices: 584029--584078 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
584019 TGCTACCATG
*
584029 ATATGTAAATGATAT-GAAAAC
1 ATATATAAATGA-ATCGAAAAC
*
584050 ATA-ATAAATGAATCTAAAAC
1 ATATATAAATGAATCGAAAAC
584070 ATATATAAA
1 ATATATAAA
584079 ACATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (21 bp):
ATATATAAATGAATCGAAAAC
Found at i:592620 original size:11 final size:12
Alignment explanation
Indices: 592608--592649 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
592598 ATGATTAAAA
592608 TAAAATAATAA-
1 TAAAATAATAAT
592619 TAAAATAATAAT
1 TAAAATAATAAT
**
592631 TAAAGCAATAAT
1 TAAAATAATAAT
592643 TAAAATA
1 TAAAATA
592650 TAAAAGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
TAAAATAATAAT
Found at i:594073 original size:3 final size:3
Alignment explanation
Indices: 594059--594103 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
594049 ATTTATTTAT
* * *
594059 ATA ATT ATA ATA ATA TATA TTA ATA ATA ATA ATA AAA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
594104 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:594912 original size:76 final size:76
Alignment explanation
Indices: 594248--594884 Score: 1123
Period size: 76 Copynumber: 8.4 Consensus size: 76
594238 GAAATGTTGA
* * * *
594248 AAACATCATGCACTAAAGGGCTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594313 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
594324 AAACATCATGCACTGCAGAACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594389 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
594400 AAACATCATGTACTACAGGACTTACAGATGACCCTAAGGGTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
594465 AGGATTTTTGG
66 AGGCTTTTTGG
*
594476 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594541 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
594552 AAACATCATGCACTACAGGACTTACAGATAACCCTAAGGTTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594617 AGGCTTTTTGG
66 AGGCTTTTTGG
594628 AAACATCATGCACTGA-AGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACT-ACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
594692 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
594704 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAGCATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594769 AGGCTTTTTGG
66 AGGCTTTTTGG
*
594780 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
594845 AGGCTTTTTGG
66 AGGCTTTTTGG
594856 AAACATCATGCACTACAGGACTTACAGAT
1 AAACATCATGCACTACAGGACTTACAGAT
594885 ATAGGAAAGA
Statistics
Matches: 533, Mismatches: 26, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
75 1 0.00
76 531 1.00
77 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:596253 original size:54 final size:54
Alignment explanation
Indices: 596123--596280 Score: 209
Period size: 54 Copynumber: 3.0 Consensus size: 54
596113 AGAATAACTG
* * * * *
596123 GTTCATAAAACATTTGACAACACATGCAT-CATCTCATGTGGTTTCTGCTCAGA-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGAT
*
596176 --T-GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
*
596227 GTTCGTAAAGCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
596281 TTCTCAATCA
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
50 38 0.41
51 5 0.05
53 1 0.01
54 48 0.52
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
Found at i:598693 original size:114 final size:114
Alignment explanation
Indices: 598493--598720 Score: 411
Period size: 114 Copynumber: 2.0 Consensus size: 114
598483 AGACTATCAT
* *
598493 CAAATTCATCTTTCAAATCCAATTATTGGTTTTGGGGTTCATACCGAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
598558 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
*
598607 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
* *
598672 AAGAACACTTCTAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
598721 AACGTGGAAC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (114 bp):
CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
Done.