Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 5 of 14
Found at i:457450 original size:20 final size:20
Alignment explanation
Indices: 457412--457465 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
457402 ACATAATAAA
457412 AAATAA-TTTTTATAGATTT
1 AAATAATTTTTTATAGATTT
*
457431 AATATAATTTTTTAT-TATTT
1 AA-ATAATTTTTTATAGATTT
457451 AAATTAATTTTTTAT
1 AAA-TAATTTTTTAT
457466 CAATTAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 21 0.68
21 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AAATAATTTTTTATAGATTT
Found at i:457472 original size:20 final size:20
Alignment explanation
Indices: 457435--457474 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
457425 AGATTTAATA
* *
457435 TAATTTTTTATTATTTAAAT
1 TAATTTTTTATCAATTAAAT
457455 TAATTTTTTATCAATTAAAT
1 TAATTTTTTATCAATTAAAT
457475 GGATCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTTTATCAATTAAAT
Found at i:457705 original size:20 final size:20
Alignment explanation
Indices: 457670--457712 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
457660 TTTATAAATT
457670 TTAAAAAATTAATAATTTATA
1 TTAAAAAATTAATAATTTA-A
*
457691 TTAAAAAATT-TTAATTTAA
1 TTAAAAAATTAATAATTTAA
457710 TTA
1 TTA
457713 TATATTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAAATTAATAATTTAA
Found at i:462208 original size:25 final size:25
Alignment explanation
Indices: 462180--462229 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
462170 GTTTTCAAAT
* * *
462180 TATAATATATTATTTTTATTATATA
1 TATAATATATAATTTATATCATATA
*
462205 TATATTATATAATTTATATCATATA
1 TATAATATATAATTTATATCATATA
462230 GAATTAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATAATATATAATTTATATCATATA
Found at i:462331 original size:15 final size:17
Alignment explanation
Indices: 462299--462340 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
462289 AGAAAACCTT
462299 ATAAAAAATATAAGATA
1 ATAAAAAATATAAGATA
462316 ATAAAAAAT-TAA-ATA
1 ATAAAAAATATAAGATA
*
462331 AAAAAAAATA
1 ATAAAAAATA
462341 CTTTTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
ATAAAAAATATAAGATA
Found at i:463490 original size:17 final size:17
Alignment explanation
Indices: 463468--463513 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
463458 ATATTAGATT
463468 TAAAAATTAAATTTAAA
1 TAAAAATTAAATTTAAA
* **
463485 TAAAAATAAAATTTATT
1 TAAAAATTAAATTTAAA
463502 TAAAAA-TAAATT
1 TAAAAATTAAATT
463514 ATGTCTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATTAAATTTAAA
Found at i:463613 original size:29 final size:30
Alignment explanation
Indices: 463581--463639 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
463571 ATATTATTTT
* *
463581 TATATTTAATA-TATTATATAAAAATTAAA
1 TATATATAATATTATAATATAAAAATTAAA
463610 TATATATAATATTATAATATAAAAATTAAA
1 TATATATAATATTATAATATAAAAATTAAA
463640 AATTATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATATATAATATTATAATATAAAAATTAAA
Found at i:463617 original size:17 final size:17
Alignment explanation
Indices: 463595--463639 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 17
463585 TTTAATATAT
463595 TATATAAAAATTAAATA
1 TATATAAAAATTAAATA
*
463612 TATAT-AATATT--ATA
1 TATATAAAAATTAAATA
463626 -ATATAAAAATTAAA
1 TATATAAAAATTAAA
463640 AATTATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
16 6 0.26
17 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATAAAAATTAAATA
Found at i:463876 original size:22 final size:22
Alignment explanation
Indices: 463851--463895 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
463841 ATATATATCT
*
463851 ATTATTATAAAATTCTTGACTG
1 ATTATTATAAAACTCTTGACTG
463873 ATTATTATAAAACTCTTGACTG
1 ATTATTATAAAACTCTTGACTG
463895 A
1 A
463896 ATTAATGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTATTATAAAACTCTTGACTG
Found at i:464053 original size:20 final size:20
Alignment explanation
Indices: 464012--464055 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
464002 CTATTCAATT
*
464012 TTTTTTATTAAAAATACCAA
1 TTTTTTATTAAAAATAACAA
*
464032 TTTTTTATTTAAAAA-AATAA
1 TTTTTTA-TTAAAAATAACAA
464052 TTTT
1 TTTT
464056 CACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTTATTAAAAATAACAA
Found at i:465214 original size:29 final size:29
Alignment explanation
Indices: 465158--465229 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 29
465148 TAAACTTGAA
465158 AATATTAAATATAAAAAATTACATAATACA-
1 AATA-TAAATATAAAAAATTACATAATA-AT
465188 AATAT-AATATAAAAAATTA-ATTAAATAAT
1 AATATAAATATAAAAAATTACA-T-AATAAT
465217 AATATAAATATAA
1 AATATAAATATAA
465230 TATAAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.03
28 16 0.42
29 10 0.26
30 11 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
AATATAAATATAAAAAATTACATAATAAT
Found at i:465219 original size:35 final size:34
Alignment explanation
Indices: 465180--465293 Score: 121
Period size: 35 Copynumber: 3.4 Consensus size: 34
465170 AAAAAATTAC
465180 ATAATACAAATATAATATAAAAAATTAATTAAATA
1 ATAATA-AAATATAATATAAAAAATTAATTAAATA
465215 ATAATATAAATATAATATAAAAAATT-A--AAATA
1 ATAATA-AAATATAATATAAAAAATTAATTAAATA
* *
465247 TATAATAAAAATATTAATATATAAAA--AATTATATA
1 -ATAAT-AAAATA-TAATATAAAAAATTAATTAAATA
*
465282 ATTATAAAATAT
1 ATAATAAAATAT
465294 TTAAATATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
32 6 0.09
33 17 0.25
34 17 0.25
35 29 0.42
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (34 bp):
ATAATAAAATATAATATAAAAAATTAATTAAATA
Found at i:465234 original size:19 final size:19
Alignment explanation
Indices: 465180--465335 Score: 74
Period size: 18 Copynumber: 8.2 Consensus size: 19
465170 AAAAAATTAC
*
465180 ATAATACAAATATAATATA
1 ATAATATAAATATAATATA
* *
465199 A-AAAATTAAT-TAA-ATA
1 ATAATATAAATATAATATA
465215 ATAATATAAATATAATATA
1 ATAATATAAATATAATATA
*
465234 A-AAAATTAAA-ATATATAATA
1 ATAATA-TAAATATA-AT-ATA
* *
465254 AAAATATTAATATATAA-AAA
1 ATAATA-TAA-ATATAATATA
* * *
465274 ATTATATAATTATAAAATA
1 ATAATATAAATATAATATA
* **
465293 TTTAAATATATTTATAATATA
1 -AT-AATATAAATATAATATA
* *
465314 ATAAAATAAATA-AATATG
1 ATAATATAAATATAATATA
465332 ATAA
1 ATAA
465336 AAATATACAA
Statistics
Matches: 104, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
16 4 0.04
17 10 0.10
18 29 0.28
19 23 0.22
20 12 0.12
21 21 0.20
22 2 0.02
23 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (19 bp):
ATAATATAAATATAATATA
Found at i:465262 original size:21 final size:22
Alignment explanation
Indices: 465224--465269 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
465214 AATAATATAA
465224 ATATAATATAAAAAATTAAAAT
1 ATATAATATAAAAAATTAAAAT
* *
465246 ATATAATA-AAAATATTAATAT
1 ATATAATATAAAAAATTAAAAT
465267 ATA
1 ATA
465270 AAAAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAATATAAAAAATTAAAAT
Found at i:465327 original size:9 final size:10
Alignment explanation
Indices: 465180--465342 Score: 61
Period size: 8 Copynumber: 17.3 Consensus size: 10
465170 AAAAAATTAC
465180 ATAATACAAAT
1 ATAATA-AAAT
465191 ATAATATAAA-
1 ATAATA-AAAT
* *
465201 A-AATTAATT
1 ATAATAAAAT
465210 A-AATAATAAT
1 ATAATAA-AAT
*
465220 ATAAATATAAT
1 AT-AATAAAAT
465231 ATAA-AAAAT
1 ATAATAAAAT
*
465240 -TAA-AATAT
1 ATAATAAAAT
465248 ATAATAAAA-
1 ATAATAAAAT
* *
465257 ATATTAATAT
1 ATAATAAAAT
465267 ATAA-AAAAT
1 ATAATAAAAT
*
465276 -T-ATATAAT
1 ATAATAAAAT
465284 -T-ATAAAAT
1 ATAATAAAAT
*
465292 AT--TTAAAT
1 ATAATAAAAT
* *
465300 ATATTTATAAT
1 ATA-ATAAAAT
465311 ATAATAAAAT
1 ATAATAAAAT
465321 A-AAT-AAAT
1 ATAATAAAAT
*
465329 ATGATAAAAAT
1 ATAAT-AAAAT
465340 ATA
1 ATA
465343 CAAAATTTTA
Statistics
Matches: 115, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.01
8 33 0.29
9 32 0.28
10 18 0.16
11 27 0.23
12 4 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:465355 original size:99 final size:98
Alignment explanation
Indices: 465156--465339 Score: 232
Period size: 99 Copynumber: 1.9 Consensus size: 98
465146 ACTAAACTTG
*
465156 AAAATATTAAATATAAAAAATTACATAATACAAATATAATATAAAAAATTAATTAAATAATAATA
1 AAAATATTAAATATAAAAAATTACATAATACAAATATAATATAAAAAATTAATTAAATAATAAAA
465221 TAAATATAATATAAAAAATTAAAATATATAATA
66 TAAATATAATATAAAAAATTAAAATATATAATA
* * * * *
465254 AAAATATTAATATATAAAAAATTATATAATTATAAA-AT-ATTTAAATATATTTA-TAATATAAT
1 AAAATATTAA-ATATAAAAAATTACATAA-TACAAATATAATATAAA-AAATTAATTAA-ATAAT
465316 AAAATAAATA-AATATGATAAAAAT
62 AAAATAAATATAATAT-A-AAAAAT
465340 ATACAAAATT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
98 24 0.32
99 39 0.53
100 11 0.15
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (98 bp):
AAAATATTAAATATAAAAAATTACATAATACAAATATAATATAAAAAATTAATTAAATAATAAAA
TAAATATAATATAAAAAATTAAAATATATAATA
Found at i:465831 original size:37 final size:37
Alignment explanation
Indices: 465790--465868 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
465780 TATTTACATA
*
465790 ATAAAAAT-ATTATGTAAATTTAATTATAAATATTAAT
1 ATAAAAATAATT-TGTAAATTTAATTATAAATAATAAT
* * * * *
465827 ATAAAATTAATTTTTTAATTTTATTTTAAATAATAAT
1 ATAAAAATAATTTGTAAATTTAATTATAAATAATAAT
465864 ATAAA
1 ATAAA
465869 TTTTTAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 32 0.91
38 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (37 bp):
ATAAAAATAATTTGTAAATTTAATTATAAATAATAAT
Found at i:465836 original size:24 final size:23
Alignment explanation
Indices: 465794--465838 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
465784 TACATAATAA
* *
465794 AAATATTATGTAAATTTAATTAT
1 AAATATTATATAAAATTAATTAT
465817 AAATATTAATATAAAATTAATT
1 AAATATT-ATATAAAATTAATT
465839 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATATTATATAAAATTAATTAT
Found at i:466452 original size:56 final size:54
Alignment explanation
Indices: 466381--466487 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 54
466371 CAAATGCCAC
* *
466381 CCTTTGTATTTGTCAAATATGGT-AGTTTTTTTTGTATT-TATCAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTGA-TTATTTTTGT-TTGTA-CAAAT-TGGTGGTTT
466437 CCTTTATATTTGTCAAATATGGTGATTATTTTTGTTTGTACAAATTGGTGG
1 CCTTTATATTTGTCAAATATGGTGATTATTTTTGTTTGTACAAATTGGTGG
466488 CTTGTTGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
54 6 0.13
55 7 0.15
56 33 0.70
57 1 0.02
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51
Consensus pattern (54 bp):
CCTTTATATTTGTCAAATATGGTGATTATTTTTGTTTGTACAAATTGGTGGTTT
Found at i:466460 original size:28 final size:28
Alignment explanation
Indices: 466381--466460 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
466371 CAAATGCCAC
*
466381 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
** *
466409 TTTTTGTATTTATCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
466437 CCTTTATATTTGTCAAATATGGTG
1 CCTTTGTATTTGTCAAATATGGTG
466461 ATTATTTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:466505 original size:24 final size:24
Alignment explanation
Indices: 466468--466513 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
466458 GTGATTATTT
466468 TTGTTTGTACAAATTGGTGGCTTG
1 TTGTTTGTACAAATTGGTGGCTTG
466492 TTGTTTGT-CAAAATTGGTGGCT
1 TTGTTTGTAC-AAATTGGTGGCT
466514 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTACAAATTGGTGGCTTG
Found at i:466995 original size:17 final size:17
Alignment explanation
Indices: 466973--467010 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
466963 CTGTGGAGAT
466973 ATTTGATGGCAAGGGTC
1 ATTTGATGGCAAGGGTC
*
466990 ATTTGATGGCACGGGTC
1 ATTTGATGGCAAGGGTC
467007 ATTT
1 ATTT
467011 TGGCATGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (17 bp):
ATTTGATGGCAAGGGTC
Found at i:467237 original size:256 final size:255
Alignment explanation
Indices: 466783--467249 Score: 907
Period size: 256 Copynumber: 1.8 Consensus size: 255
466773 AAGTTACTCT
466783 GAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCCTCCACAACAGAAAAGATATCATTTGGCTATT
1 GAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCCTCCACAACAGAAAAGATATCATTTGGCTATT
466848 GTATTGGCAAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTGACATCAGCTGCATCAACATC
66 GTATTGGCAAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTGACATCAGCTGCATCAACATC
466913 TTCATCAGCACCCATTTGGGCTAGAACTGCTATGACAAATGGAAAATTGGCTGTGGAGATATTTG
131 TTCATCAGCACCCATTTGGGCTAGAACTGCTATGACAAATGGAAAATTGGCTGTGGAGATATTTG
466978 ATGGCAAGGGTCATTTGATGGCACGGGTCATTTTGGCATGTGGCATGGAAAATTGGCACA
196 ATGGCAAGGGTCATTTGATGGCACGGGTCATTTTGGCATGTGGCATGGAAAATTGGCACA
*
467038 GAGTATGCTCTGTGGTTGCAGCTTAGTCTGATCCTCCACAACAGAAAAGATATCATTTGGCTATT
1 GAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCCTCCACAACAGAAAAGATATCATTTGGCTATT
467103 GTATTGGCAAGCTATTGAAGAAATTTGTGATTCCAAAATGAGTTTGACATCAGCTGCATCAACAT
66 GTATTGGCAAGCTATTGAAG-AATTTGTGATTCCAAAATGAGTTTGACATCAGCTGCATCAACAT
467168 CTTCATCAGCACCCATTTGGGCTAGAACTGCTATGACAAATGGAAAATTGGCTGTGGAGATATTT
130 CTTCATCAGCACCCATTTGGGCTAGAACTGCTATGACAAATGGAAAATTGGCTGTGGAGATATTT
*
467233 GATGGCACGGGTCATTT
195 GATGGCAAGGGTCATTT
467250 TGGCATGTGG
Statistics
Matches: 209, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
255 84 0.40
256 125 0.60
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (255 bp):
GAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCCTCCACAACAGAAAAGATATCATTTGGCTATT
GTATTGGCAAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTGACATCAGCTGCATCAACATC
TTCATCAGCACCCATTTGGGCTAGAACTGCTATGACAAATGGAAAATTGGCTGTGGAGATATTTG
ATGGCAAGGGTCATTTGATGGCACGGGTCATTTTGGCATGTGGCATGGAAAATTGGCACA
Found at i:469344 original size:21 final size:22
Alignment explanation
Indices: 469315--469360 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
469305 TGTTCAGACA
** *
469315 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
469337 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
469358 AGT
1 AGT
469361 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:471235 original size:19 final size:19
Alignment explanation
Indices: 471211--471263 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
471201 TGGAGATTTG
*
471211 TGGTGGATGGCTATCCTTA
1 TGGTGGGTGGCTATCCTTA
471230 TGGTGGGTGGCTATCCTTA
1 TGGTGGGTGGCTATCCTTA
471249 TGGTGGGTGGCTATC
1 TGGTGGGTGGCTATC
471264 TCTAGTCAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.11, C:0.15, G:0.38, T:0.36
Consensus pattern (19 bp):
TGGTGGGTGGCTATCCTTA
Found at i:471362 original size:28 final size:28
Alignment explanation
Indices: 471283--471365 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
471273 CAAATGCCAC
*
471283 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
471311 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
471339 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
471366 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:471373 original size:56 final size:54
Alignment explanation
Indices: 471283--471389 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 54
471273 CAAATGCCAC
*
471283 CCTTTGTATTTGTCAAATATGGTAGTTTCCTTTGTATTTGT-CAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTAGTTTCCTTTG--TTTGTACAAAT-TGGTGGTTT
* *
471339 CCTTTATATTTGTCAAATATGGTGGTTAT-TTTTGTTTGTACAAATTGGTGG
1 CCTTTATATTTGTCAAATATGGTAGTT-TCCTTTGTTTGTACAAATTGGTGG
471390 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 11 0.24
55 5 0.11
56 29 0.63
57 1 0.02
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (54 bp):
CCTTTATATTTGTCAAATATGGTAGTTTCCTTTGTTTGTACAAATTGGTGGTTT
Found at i:471407 original size:24 final size:24
Alignment explanation
Indices: 471370--471415 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
471360 GTGGTTATTT
471370 TTGTTTGTACAAATTGGTGGCTTG
1 TTGTTTGTACAAATTGGTGGCTTG
471394 TTGTTTGT-CAAAATTGGTGGCT
1 TTGTTTGTAC-AAATTGGTGGCT
471416 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTACAAATTGGTGGCTTG
Found at i:471839 original size:16 final size:16
Alignment explanation
Indices: 471818--471850 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
471808 CCCTCCTTGT
471818 TTCTC-TTCTTCTGAGC
1 TTCTCTTTCTT-TGAGC
471834 TTCTCTTTCTTTGAGC
1 TTCTCTTTCTTTGAGC
471850 T
1 T
471851 GTCAATGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.06, C:0.27, G:0.12, T:0.55
Consensus pattern (16 bp):
TTCTCTTTCTTTGAGC
Found at i:475010 original size:20 final size:20
Alignment explanation
Indices: 474968--475015 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
474958 ACTTATTTTT
** *
474968 TAATTATATAATATATTATA
1 TAATTATATAATATAAAAAA
*
474988 TAATTATATTATATAAAAAA
1 TAATTATATAATATAAAAAA
*
475008 TAAATATA
1 TAATTATA
475016 AAAATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTATATAATATAAAAAA
Found at i:475020 original size:12 final size:13
Alignment explanation
Indices: 474998--475087 Score: 53
Period size: 14 Copynumber: 6.8 Consensus size: 13
474988 TAATTATATT
474998 ATATAAAAAATAA
1 ATATAAAAAATAA
475011 ATAT-AAAAAT-A
1 ATATAAAAAATAA
* * *
475022 TTATAATATA-AA
1 ATATAAAAAATAA
475034 AT-TAATAAAATTAA
1 ATATAA-AAAA-TAA
* *
475048 ATTATTAAAATTAA
1 A-TATAAAAAATAA
*
475062 ATTTAAAAAATATA
1 ATATAAAAAATA-A
475076 ATATAAATAAAT
1 ATATAAA-AAAT
475088 TTAAATAAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
11 7 0.12
12 13 0.23
13 12 0.21
14 14 0.25
15 8 0.14
16 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATAAAAAATAA
Found at i:475049 original size:14 final size:14
Alignment explanation
Indices: 475032--475093 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
475022 TTATAATATA
475032 AAATTAATAAAATT
1 AAATTAATAAAATT
*
475046 AAATTATTAAAATT
1 AAATTAATAAAATT
475060 AAATTTAA-AAAATAT
1 AAA-TTAATAAAAT-T
* *
475075 AATATAAATAAATTT
1 AA-ATTAATAAAATT
475090 AAAT
1 AAAT
475094 AAACTTAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 23 0.57
15 12 0.30
16 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTAATAAAATT
Found at i:475049 original size:29 final size:28
Alignment explanation
Indices: 474993--475079 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 28
474983 TTATATAATT
* * *
474993 ATATTAT-ATAAAAAATAAATATAA-AA
1 ATATTATAATATAAAATTAATAAAATAA
475019 ATATTATAATATAAAATTAATAAAATTAA
1 ATATTATAATATAAAATTAATAAAA-TAA
* *
475048 ATTATTAAAAT-TAAATTTAA-AAAATATA
1 A-TATTATAATATAAAATTAATAAAATA-A
475076 ATAT
1 ATAT
475080 AAATAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 7 0.14
27 19 0.37
28 6 0.12
29 11 0.22
30 8 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATTATAATATAAAATTAATAAAATAA
Found at i:475648 original size:2 final size:2
Alignment explanation
Indices: 475643--475681 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
475633 TTTTTAGGTC
475643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
475682 AGATTAAGAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:476238 original size:11 final size:12
Alignment explanation
Indices: 476201--476251 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
476191 ATATTATACG
*
476201 ATATAATATAATT
1 ATATAATATAA-A
* *
476214 ACATAATAAAAAA
1 ATATAAT-ATAAA
476227 ATATAAT-TAAA
1 ATATAATATAAA
476238 ATATAATATAAA
1 ATATAATATAAA
476250 AT
1 AT
476252 TTGATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 12 0.39
14 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:476402 original size:13 final size:13
Alignment explanation
Indices: 476370--476413 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
476360 TATTTTAAGC
*
476370 ATAATATAAATACG
1 ATAATATAAATA-T
476384 ATAATATATAA-AT
1 ATAATATA-AATAT
476397 ATAATATAAATAT
1 ATAATATAAATAT
476410 ATAA
1 ATAA
476414 ATTACCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 14 0.52
14 9 0.33
15 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
ATAATATAAATAT
Found at i:476423 original size:18 final size:18
Alignment explanation
Indices: 476373--476430 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
476363 TTTAAGCATA
*
476373 ATATAAA-TACGAT-AAT
1 ATATAAATTACCATAAAT
**
476389 ATATAAATATAATATAAAT
1 ATATAAAT-TACCATAAAT
*
476408 ATATAAATTACCATAATT
1 ATATAAATTACCATAAAT
476426 ATATA
1 ATATA
476431 TCTGATCGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 7 0.21
18 16 0.47
19 11 0.32
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (18 bp):
ATATAAATTACCATAAAT
Found at i:477290 original size:2 final size:2
Alignment explanation
Indices: 477283--477324 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
477273 GAATTGCTTT
477283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
477325 AAGAAAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:477827 original size:21 final size:21
Alignment explanation
Indices: 477801--477840 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
477791 ATTTAAAAAT
477801 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
477822 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
477841 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:486618 original size:22 final size:22
Alignment explanation
Indices: 486570--486621 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
486560 TTATGATCAA
*
486570 ATTTTAAATATATTTTATTATT
1 ATTTTAAATATATTTTATTAAT
486592 ATTTTAAAT-TAATTTTATTTAAT
1 ATTTTAAATAT-ATTTTA-TTAAT
*
486615 TTTTTAA
1 ATTTTAA
486622 TAAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.58
23 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTAAATATATTTTATTAAT
Found at i:486703 original size:33 final size:34
Alignment explanation
Indices: 486665--486731 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
486655 TTTACTTATT
*
486665 AATTTTATTATAAATA-TATAAATATT-AATATAA
1 AATTTTAAT-TAAATATTATAAATATTAAATATAA
*
486698 AATTTTAATTAACTATTATAAATATTAAATATAA
1 AATTTTAATTAAATATTATAAATATTAAATATAA
486732 TTAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 5 0.17
33 18 0.60
34 7 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
AATTTTAATTAAATATTATAAATATTAAATATAA
Found at i:486725 original size:20 final size:19
Alignment explanation
Indices: 486670--486728 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
486660 TTATTAATTT
*
486670 TATTATAAATATATAAATAT
1 TATTATAAATAT-TAAATAC
* * *
486690 TAATATAAAATTTTAATTAAC
1 TATTAT-AAATATTAAAT-AC
486711 TATTATAAATATTAAATA
1 TATTATAAATATTAAATA
486729 TAATTAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.03
20 18 0.60
21 11 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTATAAATATTAAATAC
Found at i:487263 original size:17 final size:18
Alignment explanation
Indices: 487224--487257 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
487214 TGAATCAATT
487224 TTAATTTTTAATTTTTAA
1 TTAATTTTTAATTTTTAA
487242 TTAATTTTT-ATTTTTA
1 TTAATTTTTAATTTTTA
487258 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTAATTTTTAATTTTTAA
Found at i:491948 original size:16 final size:16
Alignment explanation
Indices: 491929--492027 Score: 57
Period size: 15 Copynumber: 6.1 Consensus size: 16
491919 ATATTTATAG
491929 ATATATATAATT-TTTA
1 ATATAT-TAATTATTTA
491945 ATATATTAATTATTT-
1 ATATATTAATTATTTA
*
491960 ATA-ATTAATAAATATTA
1 ATATATTAAT-TAT-TTA
*
491977 ATATATTTTTATTATTT-
1 ATATA--TTAATTATTTA
*
491994 TTATATT--TTATTATA
1 ATATATTAATTATT-TA
*
492009 ATATATATAATTTTTTA
1 ATATAT-TAATTATTTA
492026 AT
1 AT
492028 TTTTTATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
13 5 0.08
14 7 0.11
15 17 0.26
16 12 0.18
17 11 0.17
18 7 0.11
19 2 0.03
20 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTAATTATTTA
Found at i:491964 original size:25 final size:25
Alignment explanation
Indices: 491929--491984 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
491919 ATATTTATAG
* **
491929 ATATATATAATTTTTAATATATTAAT
1 ATATTTATAATTAATAA-ATATTAAT
491955 -TATTTATAATTAATAAATATTAAT
1 ATATTTATAATTAATAAATATTAAT
491979 ATATTT
1 ATATTT
491985 TTATTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATTTATAATTAATAAATATTAAT
Found at i:491992 original size:17 final size:17
Alignment explanation
Indices: 491972--492014 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
491962 AATTAATAAA
491972 TATTAATATATTTTTAT
1 TATTAATATATTTTTAT
**
491989 TATTTTTATA-TTTTAT
1 TATTAATATATTTTTAT
492005 TA-TAATATAT
1 TATTAATATAT
492015 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTAATATATTTTTAT
Found at i:492022 original size:27 final size:27
Alignment explanation
Indices: 491992--492043 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
491982 TTTTTATTAT
491992 TTTTAT-ATTTTATTATAATATATATAA
1 TTTTATAATTTT-TTATAATATATATAA
* *
492019 TTTTTTAATTTTTTATATTATATAT
1 TTTTATAATTTTTTATAATATATAT
492044 TTATATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTATAATTTTTTATAATATATATAA
Found at i:492740 original size:18 final size:18
Alignment explanation
Indices: 492720--492755 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
492710 AAATATTTTA
492720 TTTTTAATATAAATATAAT
1 TTTTTAA-ATAAATATAAT
*
492739 TTTTTAAATATATATAA
1 TTTTTAAATAAATATAA
492756 ATTAATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTAAATAAATATAAT
Found at i:494384 original size:19 final size:19
Alignment explanation
Indices: 494362--494400 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
494352 ATTAATATGT
**
494362 AAATAATTTTTTAATTTAA
1 AAATAATTTTAAAATTTAA
*
494381 AAATTATTTTAAAATTTAA
1 AAATAATTTTAAAATTTAA
494400 A
1 A
494401 TACTTTTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATTTTAAAATTTAA
Found at i:494484 original size:21 final size:21
Alignment explanation
Indices: 494460--494522 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 21
494450 ATATCTAACA
* *
494460 TATATTTTATCATATAATATT
1 TATATTTTATAATATAATAAT
* *
494481 TATATATTTTTAATTAAAATAAT
1 TATAT-TTTATAA-TATAATAAT
* *
494504 TATATTTTATTATCTAATA
1 TATATTTTATAATATAATA
494523 CTTAATTCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 10 0.31
22 10 0.31
23 12 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTTATAATATAATAAT
Found at i:495764 original size:40 final size:39
Alignment explanation
Indices: 495711--495799 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
495701 ATATAATATA
*
495711 AAAAATAATTAATA-AAAGATATAAATATATAAATATTTT
1 AAAAATAATTAATATAAA-ATATAAATATATAAAAATTTT
* * *
495750 AAAATTAATATAATATAAATTATTAATATATAAAAATTTAT
1 AAAAATAAT-TAATATAAAATATAAATATATAAAAATTT-T
495791 ATAAAATAA
1 A-AAAATAA
495800 AAAATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 8 0.20
40 22 0.54
41 5 0.12
42 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAAATAATTAATATAAAATATAAATATATAAAAATTTT
Found at i:495786 original size:32 final size:33
Alignment explanation
Indices: 495729--495800 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
495719 TTAATAAAAG
* *
495729 ATATAAATATATAAATATTTTAAAATTAATATA
1 ATATAAATATATAAATATATAAAAATTAATATA
* *
495762 ATATAAAT-TATTAATATATAAAAATTTATATA
1 ATATAAATATATAAATATATAAAAATTAATATA
*
495794 AAATAAA
1 ATATAAA
495801 AAATAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 26 0.76
33 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
ATATAAATATATAAATATATAAAAATTAATATA
Found at i:495790 original size:18 final size:18
Alignment explanation
Indices: 495753--495804 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
495743 ATATTTTAAA
*
495753 ATTAATATAATATAAA-TT
1 ATTAATAT-ATAAAAATTT
495771 ATTAATATATAAAAATTT
1 ATTAATATATAAAAATTT
*
495789 ATATAAAATA-AAAAAT
1 AT-TAATATATAAAAAT
495805 AATTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 6 0.20
18 18 0.60
19 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAATATATAAAAATTT
Found at i:501391 original size:21 final size:22
Alignment explanation
Indices: 501367--501422 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
501357 CATTTTACTA
*
501367 TTATATAATATA-TATTTAATT
1 TTATATAATATATTATGTAATT
*
501388 TTATATTTTATATATTATGTAATT
1 TTATA--TAATATATTATGTAATT
501412 TT-TATAATATA
1 TTATATAATATA
501423 AAAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 11 0.38
23 8 0.28
24 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATATAATATATTATGTAATT
Found at i:508428 original size:34 final size:32
Alignment explanation
Indices: 508360--508442 Score: 100
Period size: 34 Copynumber: 2.6 Consensus size: 32
508350 AAATATTTTA
*
508360 TATATT-TAT-AAATTTAATAAATTAGTAATT
1 TATATTATATAAAATTTAAAAAATTAGTAATT
508390 TATATTATATAAAATTTAAAAATATTTA-TATATT
1 TATATTATATAAAATTTAAAAA-A-TTAGTA-ATT
*
508424 TATATTATATAATATTTAA
1 TATATTATATAAAATTTAA
508443 TTATTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
30 6 0.13
31 3 0.07
32 10 0.22
33 3 0.07
34 24 0.52
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TATATTATATAAAATTTAAAAAATTAGTAATT
Found at i:509161 original size:16 final size:16
Alignment explanation
Indices: 509140--509172 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
509130 TATTAATATT
509140 ATTTATATTT-ATTTAA
1 ATTTAT-TTTGATTTAA
509156 ATTTATTTTGATTTAA
1 ATTTATTTTGATTTAA
509172 A
1 A
509173 ATATAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTATTTTGATTTAA
Found at i:509193 original size:41 final size:42
Alignment explanation
Indices: 509141--509244 Score: 108
Period size: 41 Copynumber: 2.5 Consensus size: 42
509131 ATTAATATTA
* *
509141 TTTATATTTATTTAAATTTATTTT-GATTTA-AAATATA-AG
1 TTTAAATTTATTTAAATTTATTTTAGATTTATAAATAAATAG
* *
509180 TTTTAAATTTTATTTAAGTTT-TTTTATATTTATAAATAAATAG
1 -TTTAAA-TTTATTTAAATTTATTTTAGATTTATAAATAAATAG
* *
509223 TTTAAACTCATTTAAATTTATT
1 TTTAAATTTATTTAAATTTATT
509245 CATATTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
40 9 0.17
41 27 0.52
42 14 0.27
43 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (42 bp):
TTTAAATTTATTTAAATTTATTTTAGATTTATAAATAAATAG
Found at i:511940 original size:34 final size:34
Alignment explanation
Indices: 511892--511962 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
511882 CTTGTCCCGA
*
511892 GAAGGAATTCAGGACCGCGGGTCGCTGAATTATG
1 GAAGGAATTCAGGACCGCGGCTCGCTGAATTATG
*
511926 GAAGTAATTCAGGACCGCGGCTCGCTGAATTATG
1 GAAGGAATTCAGGACCGCGGCTCGCTGAATTATG
511960 GAA
1 GAA
511963 AAACTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.21
Consensus pattern (34 bp):
GAAGGAATTCAGGACCGCGGCTCGCTGAATTATG
Found at i:514740 original size:74 final size:74
Alignment explanation
Indices: 514619--514766 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
514609 ATCTTTGATT
* *
514619 GCTTGAAGCACTCTTTATGGCTGTGGCACACCCTACGATGCAAGTGGTTAAATGCTTGGCAATGT
1 GCTTGAAGCAATCTTTATGGCTGTGGCACACCCTACGATGCAAGTGGTTAAATGCATGGCAATGT
514684 ATATTTGTA
66 ATATTTGTA
* **
514693 GCTTGAAGTAATCTTTATGGCTGTGGCACACCCTACGATGGTAGTGGTTAAATGCATGGCAATGT
1 GCTTGAAGCAATCTTTATGGCTGTGGCACACCCTACGATGCAAGTGGTTAAATGCATGGCAATGT
514758 ATATTTGTA
66 ATATTTGTA
514767 AACTAATGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (74 bp):
GCTTGAAGCAATCTTTATGGCTGTGGCACACCCTACGATGCAAGTGGTTAAATGCATGGCAATGT
ATATTTGTA
Found at i:515798 original size:20 final size:21
Alignment explanation
Indices: 515770--515808 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
515760 TAATTATATT
*
515770 ATTATAATATAA-ATAAAATA
1 ATTAAAATATAATATAAAATA
515790 ATTAAAATATAATATAAAA
1 ATTAAAATATAATATAAAA
515809 ATATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAATATAATATAAAATA
Found at i:515821 original size:13 final size:13
Alignment explanation
Indices: 515772--515813 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
515762 ATTATATTAT
515772 TATAATATAAATAA
1 TATAATATAAA-AA
*
515786 AATAAT-T-AAAA
1 TATAATATAAAAA
515797 TATAATATAAAAA
1 TATAATATAAAAA
515810 TATA
1 TATA
515814 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 7 0.29
12 3 0.12
13 9 0.38
14 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATAATATAAAAA
Found at i:515827 original size:27 final size:26
Alignment explanation
Indices: 515770--515841 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
515760 TAATTATATT
* *
515770 ATTATAATATAAATAAAATA-ATTAAA
1 ATTATAATATAAA-AATATATTTTAAA
515796 A-TATAATATAAAAATATATTTTAAA
1 ATTATAATATAAAAATATATTTTAAA
* *
515821 ATTTATAAAATATAAAT-TATT
1 A-TTATAATATAAAAATATATT
515842 AATATGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 5 0.13
25 17 0.44
26 5 0.13
27 12 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTATAATATAAAAATATATTTTAAA
Found at i:515846 original size:34 final size:33
Alignment explanation
Indices: 515796--515874 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
515786 AATAATTAAA
*
515796 ATAT-AATATAAAA-A-T-ATATTTTAAAATTT
1 ATATAAATATAAAATATTAATATGTTAAAATTT
*
515825 ATA-AAATATAAATTATTAATATGTTAAAATTT
1 ATATAAATATAAAATATTAATATGTTAAAATTT
*
515857 TTATAAATATAAAATATT
1 ATATAAATATAAAATATT
515875 TTTAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.27
30 1 0.02
31 1 0.02
32 15 0.37
33 13 0.32
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATAAATATAAAATATTAATATGTTAAAATTT
Found at i:519071 original size:20 final size:21
Alignment explanation
Indices: 519020--519069 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
519010 TACAAATTAA
*
519020 TTATAAATTTGTTATAATATT
1 TTATTAATTTGTTATAATATT
*
519041 TTTTTAATTTG-TATAA-ATT
1 TTATTAATTTGTTATAATATT
519060 TTATTAATTT
1 TTATTAATTT
519070 TGATGATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 12 0.46
20 5 0.19
21 9 0.35
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTATTAATTTGTTATAATATT
Found at i:519238 original size:30 final size:30
Alignment explanation
Indices: 519180--519239 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
519170 GTTGGTCAAG
** *
519180 ATTTTTGAAAAAAAAGGGTAAAGTAAATTT
1 ATTTTTGAAAAAAAAAAGTAAAGAAAATTT
519210 ATTTTTGAAGAAAAAAAAG-AAAGAAAATTT
1 ATTTTTGAA-AAAAAAAAGTAAAGAAAATTT
519240 TAAATGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (30 bp):
ATTTTTGAAAAAAAAAAGTAAAGAAAATTT
Found at i:519351 original size:16 final size:16
Alignment explanation
Indices: 519332--519397 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
519322 AAGTTTTGAA
519332 TTTGATTTATTTTAAT
1 TTTGATTTATTTTAAT
519348 TTTGATTTATTTTAATT
1 TTTGATTTATTTTAA-T
*
519365 TTTGA-TTATTTTAAA
1 TTTGATTTATTTTAAT
* *
519380 TTT-AATTATTTTTAT
1 TTTGATTTATTTTAAT
519395 TTT
1 TTT
519398 AAATTAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.02
15 14 0.31
16 24 0.53
17 6 0.13
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTGATTTATTTTAAT
Found at i:519376 original size:32 final size:32
Alignment explanation
Indices: 519332--519397 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
519322 AAGTTTTGAA
* *
519332 TTTGATTTATTTTAATTTTGATTTATTTTAATT
1 TTTGATTTATTTTAAATTT-AATTATTTTAATT
*
519365 TTTGA-TTATTTTAAATTTAATTATTTTTATT
1 TTTGATTTATTTTAAATTTAATTATTTTAATT
519396 TT
1 TT
519398 AAATTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 13 0.43
32 12 0.40
33 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (32 bp):
TTTGATTTATTTTAAATTTAATTATTTTAATT
Found at i:519439 original size:21 final size:21
Alignment explanation
Indices: 519396--519435 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
519386 TATTTTTATT
519396 TTAAATTAATTAAATTAATTA
1 TTAAATTAATTAAATTAATTA
519417 TTAAATT-ATTAAATTAATT
1 TTAAATTAATTAAATTAATT
519436 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATTAATTAAATTAATTA
Found at i:519453 original size:21 final size:19
Alignment explanation
Indices: 519370--519446 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 19
519360 TAATTTTTGA
*
519370 TTATTTTAAATTTAATTATTT
1 TTATTTTAAA-TTAATTA-AT
519391 TTATTTTAAATTAATTAAAT
1 TTATTTTAAATTAATT-AAT
*
519411 TAATTATTAAATTATTAAATTAAT
1 TTATT-TT-AA--ATT-AATTAAT
519435 TTATTTTAAATT
1 TTATTTTAAATT
519447 CATATTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
20 14 0.30
21 13 0.28
22 4 0.09
23 2 0.04
24 10 0.21
25 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTTAAATTAATTAAT
Found at i:520874 original size:33 final size:33
Alignment explanation
Indices: 520837--520907 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
520827 ATTTATGTAT
*
520837 TTTTAAATTTA-TAATTATATTTAT-TTATATAAA
1 TTTTAAATTAATTAA-TA-ATTTATATTATATAAA
*
520870 TTTT-AATTAATTAATAATTTATATTATGTAAA
1 TTTTAAATTAATTAATAATTTATATTATATAAA
520902 TTTTAA
1 TTTTAA
520908 TATATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
31 6 0.18
32 19 0.58
33 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TTTTAAATTAATTAATAATTTATATTATATAAA
Found at i:520903 original size:32 final size:29
Alignment explanation
Indices: 520848--520918 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 29
520838 TTTAAATTTA
520848 TAATTATATTTATTTATATAAATTTTAAT
1 TAATTATATTTATTTATATAAATTTTAAT
*
520877 TAATTAATAATTTATATTATGTAAATTTTAAT
1 TAATT-AT-ATTTAT-TTATATAAATTTTAAT
*
520909 ATATTTATAT
1 -TAATTATAT
520919 ATTTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 5 0.14
30 2 0.06
31 8 0.22
32 17 0.47
33 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TAATTATATTTATTTATATAAATTTTAAT
Found at i:521458 original size:16 final size:15
Alignment explanation
Indices: 521437--521466 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
521427 TTAATATTCA
521437 ATTTAAATTATAATTT
1 ATTTAAATT-TAATTT
521453 ATTTAAATTTAATT
1 ATTTAAATTTAATT
521467 ATAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:521471 original size:12 final size:12
Alignment explanation
Indices: 521436--521483 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
521426 ATTAATATTC
521436 AATTTAAATTAT-
1 AATTT-AATTATA
521448 AATTT-ATT-TA
1 AATTTAATTATA
521458 AATTTAATTATA
1 AATTTAATTATA
521470 AATATTAA-TATA
1 AAT-TTAATTATA
521482 AA
1 AA
521484 AATACTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
11 3 0.09
12 16 0.50
13 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTTAATTATA
Found at i:523905 original size:18 final size:18
Alignment explanation
Indices: 523882--523931 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
523872 TATGTCAATG
523882 CTCTTCATTGTAATCTGT
1 CTCTTCATTGTAATCTGT
** *
523900 CTCTTC--TCAAAACT-T
1 CTCTTCATTGTAATCTGT
523915 CTCTTCATTGTAATCTG
1 CTCTTCATTGTAATCTG
523932 CAATATCCTT
Statistics
Matches: 23, Mismatches: 6, Indels: 6
0.66 0.17 0.17
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.20, C:0.26, G:0.08, T:0.46
Consensus pattern (18 bp):
CTCTTCATTGTAATCTGT
Found at i:524089 original size:2 final size:2
Alignment explanation
Indices: 524082--524126 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
524072 CGATACACAT
524082 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
524124 TA T
1 TA T
524127 GTACACACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:524880 original size:14 final size:15
Alignment explanation
Indices: 524863--524891 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
524853 GGATATATTT
524863 TTTATTAT-ATTATA
1 TTTATTATGATTATA
524877 TTTATTATGATTATA
1 TTTATTATGATTATA
524892 AATATAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTATTATGATTATA
Found at i:524971 original size:15 final size:16
Alignment explanation
Indices: 524945--524977 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
524935 TACGTAATTT
524945 ATTATAAAATATAATA
1 ATTATAAAATATAATA
524961 ATTAT-AAATATAATA
1 ATTATAAAATATAATA
524976 AT
1 AT
524978 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATAAAATATAATA
Found at i:527801 original size:20 final size:20
Alignment explanation
Indices: 527767--527842 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
527757 ACGGATTAAA
527767 TATTTA-TAATTTTTAAATT
1 TATTTATTAATTTTTAAATT
* *
527786 TATTTATTATTTTTTAAA-A
1 TATTTATTAATTTTTAAATT
* *
527805 TATTTGTTAAATATTT-AATT
1 TATTTATT-AATTTTTAAATT
*
527825 TATTAATTAATTTTTAAA
1 TATTTATTAATTTTTAAA
527843 ATTAAATATA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 21 0.48
20 23 0.52
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTTATTAATTTTTAAATT
Found at i:527867 original size:26 final size:27
Alignment explanation
Indices: 527811--527868 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
527801 AAAATATTTG
* * * * *
527811 TTAAATATTTAATTTATTAATTAATTT
1 TTAAATATTAAATATATTAAATAAATA
527838 TTAAA-ATTAAATATATTAAATAAATA
1 TTAAATATTAAATATATTAAATAAATA
527864 TTAAA
1 TTAAA
527869 CTTTGATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAATATTAAATATATTAAATAAATA
Found at i:528282 original size:32 final size:33
Alignment explanation
Indices: 528227--528307 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 33
528217 ATACGAATAC
*
528227 TATATAAATAT-ACATA--AATATATTAAAATT
1 TATATAAATATAAAATATTAATATATTAAAATT
*
528257 TATAT-AATATAAATTATTAATATATTAAAATT
1 TATATAAATATAAAATATTAATATATTAAAATT
528289 TATATAAATATAAAATATT
1 TATATAAATATAAAATATT
528308 TTAAATATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 5 0.11
30 8 0.18
32 19 0.43
33 12 0.27
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TATATAAATATAAAATATTAATATATTAAAATT
Found at i:528285 original size:16 final size:14
Alignment explanation
Indices: 528243--528294 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
528233 AATATACATA
528243 AATATATTAAAATT
1 AATATATTAAAATT
*
528257 TATATAATATAAATTATT
1 AATAT-AT-TAAA--ATT
528275 AATATATTAAAATT
1 AATATATTAAAATT
*
528289 TATATA
1 AATATA
528295 AATATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 8 0.26
17 2 0.06
18 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATATTAAAATT
Found at i:528302 original size:17 final size:17
Alignment explanation
Indices: 528250--528304 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
528240 ATAAATATAT
528250 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
528266 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
528281 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
528299 TAAAAT
1 TAAAAT
528305 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:529469 original size:16 final size:17
Alignment explanation
Indices: 529450--529530 Score: 66
Period size: 16 Copynumber: 5.0 Consensus size: 17
529440 ATATATTTTT
529450 TAAAAT-TTATATAATA
1 TAAAATATTATATAATA
*
529466 TAAATTATTA-AT-ATA
1 TAAAATATTATATAATA
529481 TTAAAAT-TTATATAAATA
1 -TAAAATATTATAT-AATA
*
529499 TAAAATATTTTA-AATA
1 TAAAATATTATATAATA
* *
529515 T-AATTATAATATAATA
1 TAAAATATTATATAATA
529531 AAATAAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
15 13 0.25
16 23 0.44
17 9 0.17
18 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATATTATATAATA
Found at i:535897 original size:2 final size:2
Alignment explanation
Indices: 535885--535937 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
535875 AGGCCCATAC
* * * *
535885 AT AT AT TT AT AT A- AT AC AT AT AC AT AT AC 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
*
535926 AT AT AC AT AT AT
1 AT AT AT AT AT AT
535938 TTCTAAGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:535907 original size:6 final size:6
Alignment explanation
Indices: 535898--535936 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
535888 TATTTATATA
* *
535898 ATACAT ATACAT ATACAT ATATAT ATATAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
535937 TTTCTAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (6 bp):
ATACAT
Found at i:536968 original size:23 final size:23
Alignment explanation
Indices: 536941--536999 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
536931 AAAATAATTT
536941 ATATAAATATAAAATAT-ATAAA
1 ATATAAATATAAAATATAATAAA
*
536963 ATTATATTAAAATAAAATATCAAATAAA
1 A-TATA--AATATAAAATAT--AATAAA
536991 ATATAAATA
1 ATATAAATA
537000 CATAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 1 0.03
23 4 0.14
25 14 0.48
27 4 0.14
28 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATATAAATATAAAATATAATAAA
Found at i:537374 original size:18 final size:17
Alignment explanation
Indices: 537351--537392 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
537341 GGTAATGAGC
537351 TTAAATCAATTTAATTTA
1 TTAAATCAA-TTAATTTA
*
537369 TTAAATTTAATTAATTTA
1 TTAAA-TCAATTAATTTA
537387 TTAAAT
1 TTAAAT
537393 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATCAATTAATTTA
Found at i:537422 original size:17 final size:18
Alignment explanation
Indices: 537358--537436 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
537348 AGCTTAAATC
*
537358 AATTTAATTTATTAAATTT
1 AATTT-ATTTAATAAATTT
* *
537377 AATTAATTTATTAAATGTT
1 AATTTATTTAATAAAT-TT
*
537396 AAAATAATTTTTTAATAAATTT
1 --AAT--TTATTTAATAAATTT
* *
537418 AATTTATTTTATAAGTTT
1 AATTTATTTAATAAATTT
537436 A
1 A
537437 TTCGATCTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
18 24 0.50
19 6 0.12
20 3 0.06
21 3 0.06
22 2 0.04
23 10 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTATTTAATAAATTT
Found at i:538635 original size:24 final size:23
Alignment explanation
Indices: 538590--538651 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
538580 ATTATACGAA
538590 TATAATATAAATAATATATTTAT
1 TATAATATAAATAATATATTTAT
538613 TATACATATAAAT-ATAT-TTT-T
1 TATA-ATATAAATAATATATTTAT
* * *
538634 TAAAATTTATATAATATA
1 TATAATATAAATAATATA
538652 AATTATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 3 0.09
23 8 0.24
24 8 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAATATAAATAATATATTTAT
Found at i:539291 original size:23 final size:24
Alignment explanation
Indices: 539246--539296 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
539236 TTTTTTATTC
539246 ATATTTTTATTTAATAAATATAAA
1 ATATTTTTATTTAATAAATATAAA
539270 ATATTTTTATTT-A-AAATCATAAA
1 ATATTTTTATTTAATAAAT-ATAAA
539293 ATAT
1 ATAT
539297 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.15
23 10 0.38
24 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTTTATTTAATAAATATAAA
Found at i:540301 original size:2 final size:2
Alignment explanation
Indices: 540294--540324 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
540284 TTCGAGGTCC
540294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540325 GATTGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546539 original size:70 final size:70
Alignment explanation
Indices: 546426--546637 Score: 415
Period size: 70 Copynumber: 3.0 Consensus size: 70
546416 CCAACCACAA
546426 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
1 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
546491 AAAAG
66 AAAAG
546496 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
1 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
546561 AAAAG
66 AAAAG
*
546566 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCTAAATTAGCAGGCAGAAT
1 AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
546631 AAAAG
66 AAAAG
546636 AA
1 AA
546638 AGAAAAAAAG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 141 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (70 bp):
AACCTACTGAACAATAAACCGTATTCACTTCCATCAGTATGAAAAGCCAAATTAGCAGGCAGAAT
AAAAG
Found at i:548120 original size:60 final size:60
Alignment explanation
Indices: 548027--548148 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
548017 ATTATAGAAT
* * *
548027 CAAGTCCACATTCAATTTTATCTTCAGACTGTGGATGATGACGAAGAAGCTTCTCTACCA
1 CAAGTCCACATCCAATTTTATCTGCAGAATGTGGATGATGACGAAGAAGCTTCTCTACCA
548087 CAAGTCCACATCCAATTTTATCTGCAGAATGTGGATGATGACGAAGAAGCTTCTCTACCA
1 CAAGTCCACATCCAATTTTATCTGCAGAATGTGGATGATGACGAAGAAGCTTCTCTACCA
548147 CA
1 CA
548149 GCTTCCTCGT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (60 bp):
CAAGTCCACATCCAATTTTATCTGCAGAATGTGGATGATGACGAAGAAGCTTCTCTACCA
Found at i:548889 original size:35 final size:36
Alignment explanation
Indices: 548826--548913 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 36
548816 TATATGTATA
* * * *
548826 AAAT-ATAATAATTA-ATCAAAATTTTATTTCTATT
1 AAATAATAACAATTATATTAAAATTGTATTTATATT
*
548860 AAATAATAA-AATTTTATTAAAATTGTATTTATATT
1 AAATAATAACAATTATATTAAAATTGTATTTATATT
548895 AAATAATAACAATTATATT
1 AAATAATAACAATTATATT
548914 TGTATTTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 8 0.17
35 30 0.65
36 8 0.17
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
AAATAATAACAATTATATTAAAATTGTATTTATATT
Found at i:548938 original size:29 final size:31
Alignment explanation
Indices: 548882--548939 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
548872 TTTATTAAAA
* *
548882 TTGTATTTATATTAAATAATAACAATTATAT
1 TTGTATTTATATAAAATAATAAAAATTATAT
*
548913 TTGTATTTA-ATAAAAT-TTAAAAATTAT
1 TTGTATTTATATAAAATAATAAAAATTAT
548940 TATAAATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 6 0.25
31 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
TTGTATTTATATAAAATAATAAAAATTATAT
Found at i:549143 original size:2 final size:2
Alignment explanation
Indices: 549138--549173 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
549128 TTGTGTGTGC
549138 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
549174 GTATTCCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549980 original size:3 final size:3
Alignment explanation
Indices: 549972--549999 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
549962 TTAATACAAA
549972 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
550000 AATTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:553947 original size:2 final size:2
Alignment explanation
Indices: 553940--553966 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
553930 AATCCACCAA
553940 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
553967 AAAGAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:554909 original size:20 final size:20
Alignment explanation
Indices: 554884--554942 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
554874 TCTAAAATTT
554884 TAAATATTAAATAATTAAAA
1 TAAATATTAAATAATTAAAA
* *
554904 TAAATATGAAATATATT-TAA
1 TAAATATTAAATA-ATTAAAA
*
554924 TAAATTATT-ATTAATTAAA
1 TAAA-TATTAAATAATTAAA
554943 TTTAATAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.10
20 22 0.71
21 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATATTAAATAATTAAAA
Found at i:555913 original size:21 final size:19
Alignment explanation
Indices: 555876--555920 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
555866 ATATAATCTT
*
555876 TTAAAAAAATTTTAAATAC
1 TTAAAAAAATTTAAAATAC
*
555895 TTAAAAAAACCTTTAAAATAT
1 TTAAAAAAA--TTTAAAATAC
555916 TTAAA
1 TTAAA
555921 TATACTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAAAATTTAAAATAC
Found at i:556458 original size:4 final size:4
Alignment explanation
Indices: 556451--556475 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
556441 ATATATATAT
556451 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
556476 CACACACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:565076 original size:23 final size:22
Alignment explanation
Indices: 565044--565086 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
565034 ATATTATAAA
*
565044 TAATAATTAAATAATCAATTTT
1 TAATAATTAAATAATAAATTTT
*
565066 TAATAAATTAATTAATAAATT
1 TAAT-AATTAAATAATAAATT
565087 AATAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATTAAATAATAAATTTT
Found at i:565080 original size:12 final size:12
Alignment explanation
Indices: 565044--565089 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
565034 ATATTATAAA
*
565044 TAAT-AATTAAA
1 TAATAAATTAAT
* *
565055 TAATCAATT-TT
1 TAATAAATTAAT
565066 TAATAAATTAAT
1 TAATAAATTAAT
565078 TAATAAATTAAT
1 TAATAAATTAAT
565090 AAATCAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 12 0.41
12 17 0.59
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAAATTAAT
Found at i:565634 original size:15 final size:16
Alignment explanation
Indices: 565616--565722 Score: 55
Period size: 15 Copynumber: 6.6 Consensus size: 16
565606 CTTTTTTTTT
565616 TATTTTT-TATTTATA
1 TATTTTTATATTTATA
565631 TATTTATTTTATATTTATA
1 TA--T-TTTTATATTTATA
565650 TATTTTTA-ATATTATA
1 TATTTTTATAT-TTATA
* * *
565666 -ATTATATTAAAAATAATA
1 TATT-T-TT-ATATTTATA
*
565684 TATTTTAATATATTAT-
1 TATTTTTATAT-TTATA
*
565700 T-TATTTATATTT-TA
1 TATTTTTATATTTATA
565714 TATTTTTAT
1 TATTTTTAT
565723 GTAATTTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 26
0.67 0.09 0.25
Matches are distributed among these distances:
13 1 0.01
14 3 0.04
15 20 0.29
16 14 0.20
17 8 0.11
18 10 0.14
19 14 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTTATATTTATA
Found at i:565638 original size:19 final size:19
Alignment explanation
Indices: 565614--565654 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
565604 GGCTTTTTTT
*
565614 TTTATTTTTTATTTATATA
1 TTTATTTTATATTTATATA
565633 TTTATTTTATATTTATATA
1 TTTATTTTATATTTATATA
565652 TTT
1 TTT
565655 TTAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTTATATTTATATA
Found at i:566503 original size:8 final size:8
Alignment explanation
Indices: 566479--566518 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
566469 ATTAAATTAA
566479 TTAAAATT
1 TTAAAATT
*
566487 TAATAAATT
1 TTA-AAATT
*
566496 TTTAAATT
1 TTAAAATT
566504 TTAAAATT
1 TTAAAATT
566512 TTAAAAT
1 TTAAAAT
566519 AAATACACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:569060 original size:16 final size:17
Alignment explanation
Indices: 569024--569061 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
569014 AAAAATAGTA
*
569024 ATTTTTATTAAACAATG
1 ATTTTTATTAAAAAATG
*
569041 ATTTTTTTTAAAAAAT-
1 ATTTTTATTAAAAAATG
569057 ATTTT
1 ATTTT
569062 ATAAGACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTTATTAAAAAATG
Found at i:569144 original size:14 final size:13
Alignment explanation
Indices: 569125--569163 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
569115 TTTAATTTTT
569125 TAATTTAAATTAA
1 TAATTTAAATTAA
*
569138 TATATTTAATTTAA
1 TA-ATTTAAATTAA
569152 TAATATTAAATT
1 TAAT-TTAAATT
569164 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATTTAAATTAA
Found at i:569163 original size:15 final size:15
Alignment explanation
Indices: 569125--569167 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
569115 TTTAATTTTT
569125 TAAT-TTAAA-TTAA
1 TAATATTAAATTTAA
*
569138 T-ATATTTAATTTAA
1 TAATATTAAATTTAA
569152 TAATATTAAATTTAA
1 TAATATTAAATTTAA
569167 T
1 T
569168 TAAAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.08
13 5 0.20
14 5 0.20
15 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATATTAAATTTAA
Found at i:569654 original size:19 final size:19
Alignment explanation
Indices: 569630--569682 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
569620 TTTAATAAAA
*
569630 ATAAAATATTATAAATAAT
1 ATAAAATATTATAAATAAG
*
569649 ATAAAATATTATTTAATAAG
1 ATAAAATATTA-TAAATAAG
*
569669 ATTAAA-ATTATAAA
1 ATAAAATATTATAAA
569683 ATTAATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.10
19 15 0.52
20 11 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATATTATAAATAAG
Found at i:569811 original size:15 final size:15
Alignment explanation
Indices: 569767--569804 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
569757 AATATATCAA
* *
569767 ATAAATTTTATA-AT
1 ATAAATTTAATATTT
569781 ATAAATTTAATATTT
1 ATAAATTTAATATTT
569796 ATAAATTTA
1 ATAAATTTA
569805 GTGTTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATTTAATATTT
Found at i:570896 original size:64 final size:64
Alignment explanation
Indices: 570822--570951 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
570812 TAAGAAACAA
570822 TAACCAATAATTATGGACATAAAAATATTTCAATTAATTGTCAATAAAAAATTATTGCAAAATC
1 TAACCAATAATTATGGACATAAAAATATTTCAATTAATTGTCAATAAAAAATTATTGCAAAATC
570886 TAACCAATAATTATGGACATAAAAATATTTCAATTAATTGTCAATAAAAAATTATTGCAAAATC
1 TAACCAATAATTATGGACATAAAAATATTTCAATTAATTGTCAATAAAAAATTATTGCAAAATC
570950 TA
1 TA
570952 TATCACAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (64 bp):
TAACCAATAATTATGGACATAAAAATATTTCAATTAATTGTCAATAAAAAATTATTGCAAAATC
Found at i:571877 original size:13 final size:13
Alignment explanation
Indices: 571859--571884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
571849 CATTTTTCTG
571859 TGTATCGATACAT
1 TGTATCGATACAT
571872 TGTATCGATACAT
1 TGTATCGATACAT
571885 CTATTTTTTG
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:574408 original size:28 final size:27
Alignment explanation
Indices: 574341--574414 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
574331 ATTTTTCATA
* *
574341 ATCGCGGATACTCAAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
574368 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
574394 TTCGAGGGGATACTCCAACCC
1 ATC--GGGGATACTCCAACCC
574415 TTGCTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 4 0.10
27 21 0.51
28 16 0.39
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:574462 original size:51 final size:52
Alignment explanation
Indices: 574399--574621 Score: 148
Period size: 52 Copynumber: 4.3 Consensus size: 52
574389 TTATTTTCGA
** * * * *
574399 GGGGATACTCCAACCCTTGCTTTATT-CTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCCGGCTTTATTGC-TAAAACACTAATTTCTCCACAATC
* *
574450 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTGCTAAAACACTAATTTCTCCACAATC
** * * **
574502 GGGGATACTCCAACCCCGATTTTATT-TTCAAAACACCAATTT-TCCTTTAATC
1 GGGGATACTCCAACCCCGGCTTTATTGCT-AAAACACTAATTTCTCC-ACAATC
* * ** ** * * * * *
574554 AGGGATACTCCAGCTTCGATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGGCTTTA-TTGCTAAAACACTAATTTCTCCACAATC
*
574607 GAGGATACTCCAACC
1 GGGGATACTCCAACC
574622 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
51 39 0.28
52 68 0.49
53 30 0.22
54 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGCTTTATTGCTAAAACACTAATTTCTCCACAATC
Found at i:574516 original size:52 final size:51
Alignment explanation
Indices: 574446--574621 Score: 192
Period size: 52 Copynumber: 3.4 Consensus size: 51
574436 GATTTCTCAT
* *
574446 AATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACCAATTTTTCCAC
* **
574498 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTTCC-AC
* * ** * *
574550 AATCAGGGATACTCCAGCTTCGATTTTATTTCCAAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTTCCAC
*
574603 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
574622 TCGTTATTTC
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
51 7 0.07
52 62 0.61
53 27 0.27
54 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTTCCAC
Found at i:574632 original size:31 final size:28
Alignment explanation
Indices: 574604--574680 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
574594 TTTTTTCACA
*
574604 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
574632 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
574660 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
574681 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:574703 original size:264 final size:262
Alignment explanation
Indices: 574235--574731 Score: 719
Period size: 264 Copynumber: 1.9 Consensus size: 262
574225 TAATTCTCCG
* * * * * *
574235 CAATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAATTTTCTAAAATCGGGGATACC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTAAAATCAGGGATACC
* * *
574300 CCAATTCCGATTTTATTTCTAAAAAACTCCAATTTTTCATAATCGCGGATACTCAAACCCCGTTA
66 CCAATTCCGATTTTATTTCTAAAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCCGTTA
** * ** **
574365 ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTTGCTTTATTCTTAA
131 ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
574430 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
574495 CA
261 CA
**
574497 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTAAAATCAGGGATAC
* * * * *
574562 TCCAGCTT-CGATTTTATTTC-CAAAAACACCAATTTTTTCACAATCGAGGATACTCCAACCTCG
65 CCCA-ATTCCGATTTTATTTCTAAAAAACACCAA-TTTTTCACAATCGAGGATACTCAAACCCCG
*
574625 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTC
128 TTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTC
*
574690 CCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
192 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
574732 TTATTTCTGA
Statistics
Matches: 206, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
262 53 0.26
263 57 0.28
264 96 0.47
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (262 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTAAAATCAGGGATACC
CCAATTCCGATTTTATTTCTAAAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTC
CA
Found at i:576972 original size:29 final size:29
Alignment explanation
Indices: 576914--576973 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
576904 TTCCAATATT
** *
576914 AATATATAAATATCAAATTTATTAATAAA
1 AATATATAAATATCAAATTTAAGAAGAAA
576943 AATATAT-AATATCAAATTTAAAGAAGAAA
1 AATATATAAATATCAAATTT-AAGAAGAAA
576972 AA
1 AA
576974 GGAAAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
AATATATAAATATCAAATTTAAGAAGAAA
Found at i:577241 original size:15 final size:15
Alignment explanation
Indices: 577201--577243 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
577191 GTTTTGTATG
* *
577201 ATTTA-ATAATTTTA
1 ATTTATATAAATTAA
577215 ATTTATATTAAATTAA
1 ATTTATA-TAAATTAA
577231 ATTTATATAAATT
1 ATTTATATAAATT
577244 TTTATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATATAAATTAA
Done.