Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014990.1 Kokia drynarioides strain JFW-HI SEQ_130034, 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: 743029
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 631 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:407913 original size:17 final size:16
Alignment explanation
Indices: 407891--407982 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 16
407881 ACTTTTATTC
407891 ATTTAAATTTAGAATAA
1 ATTTAAATTTA-AATAA
407908 ATTTAAATTTAAATTAA
1 ATTTAAATTTAAA-TAA
*
407925 ATTTAAATTTTAAAAAA
1 ATTTAAA-TTTAAATAA
*
407942 AATTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
* *
407959 AATT-ATTCTTAAAATAA
1 ATTTAAAT-TT-AAATAA
407976 ATTTAAA
1 ATTTAAA
407983 ATGGGTTTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.11
17 50 0.78
18 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:407934 original size:34 final size:33
Alignment explanation
Indices: 407891--407982 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 33
407881 ACTTTTATTC
*
407891 ATTTAAATTTAGAATAAATTTAAATTTAAATTAA
1 ATTTAAATTTA-AATAAATTTAAATTTAAAATAA
* *
407925 ATTTAAATTTTAAAAAAAATTAAATTTAAAATAA
1 ATTTAAA-TTTAAATAAATTTAAATTTAAAATAA
* *
407959 AATT-ATTCTTAAAATAAATTTAAA
1 ATTTAAAT-TT-AAATAAATTTAAA
407983 ATGGGTTTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
32 1 0.02
33 3 0.06
34 40 0.83
35 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTTAAATTTAAATAAATTTAAATTTAAAATAA
Found at i:407953 original size:6 final size:6
Alignment explanation
Indices: 407891--407934 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
407881 ACTTTTATTC
407891 ATTTAA ATTTAGA A--TAA ATTTAA ATTTAA A-TTAA ATTTAA ATTT
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
407935 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 2 0.06
5 7 0.21
6 23 0.68
7 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:415536 original size:2 final size:2
Alignment explanation
Indices: 415524--415560 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
415514 ATCATACCAT
*
415524 TA TA AA 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 T
415561 TTTAATTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:419625 original size:29 final size:31
Alignment explanation
Indices: 419555--419625 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
419545 TACCCAATTG
*
419555 AAATTAAAACA-TAAATATCCAAAATCCATGA
1 AAATTAAAA-ATTAAATATCCAAAATCCATAA
*
419586 AAATTAAAAATTAAATAT-CAAAA-CCTTAA
1 AAATTAAAAATTAAATATCCAAAATCCATAA
*
419615 AAATTCAAAAT
1 AAATTAAAAAT
419626 AATCAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 14 0.39
30 6 0.17
31 16 0.44
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.25
Consensus pattern (31 bp):
AAATTAAAAATTAAATATCCAAAATCCATAA
Found at i:421860 original size:19 final size:20
Alignment explanation
Indices: 421836--421875 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
421826 AATATTTAGC
421836 TCAAAA-AATAAAAAAAAAA
1 TCAAAATAATAAAAAAAAAA
*
421855 TCAAAATTATAAAAAAAAAA
1 TCAAAATAATAAAAAAAAAA
421875 T
1 T
421876 ATATCACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
TCAAAATAATAAAAAAAAAA
Found at i:427134 original size:27 final size:26
Alignment explanation
Indices: 427057--427135 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
427047 AAGTCAACAA
* *
427057 CAAAGTCAATGGGTCGGGTTAATAGGT
1 CAAAGTCAATGGGTTGGGTTAA-CGGT
*
427084 CAAAGTCAATGGGTTGTGTTAACGGAT
1 CAAAGTCAATGGGTTGGGTTAACGG-T
* *
427111 CAAAGTCAATAGGTTGGGTCAACGG
1 CAAAGTCAATGGGTTGGGTTAACGG
427136 GTCGAGTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.04
27 43 0.96
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (26 bp):
CAAAGTCAATGGGTTGGGTTAACGGT
Found at i:427485 original size:12 final size:13
Alignment explanation
Indices: 427468--427514 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
427458 TGTTATTTTC
427468 TTATTTTT-GTTT
1 TTATTTTTAGTTT
*
427480 TTATTTTTATTTT
1 TTATTTTTAGTTT
*
427493 TTATTTTATAAGTTG
1 TTATTTT-T-AGTTT
427508 TTATTTT
1 TTATTTT
427515 CTTTTGACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.28
13 10 0.34
14 1 0.03
15 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (13 bp):
TTATTTTTAGTTT
Found at i:427493 original size:13 final size:13
Alignment explanation
Indices: 427460--427499 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
427450 TAAAAAATTG
427460 TTATTTTCTTATTT
1 TTATTTT-TTATTT
*
427474 TT-GTTTTTATTT
1 TTATTTTTTATTT
427486 TTATTTTTTATTT
1 TTATTTTTTATTT
427499 T
1 T
427500 ATAAGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:428807 original size:11 final size:11
Alignment explanation
Indices: 428767--428809 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
428757 TGGGTTATTG
*
428767 GGTTGGGGTTT
1 GGTTTGGGTTT
* *
428778 AGTTTGGATTT
1 GGTTTGGGTTT
428789 GGTTTGGGTTT
1 GGTTTGGGTTT
428800 GGTTTGGGTT
1 GGTTTGGGTT
428810 CACCCTTAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (11 bp):
GGTTTGGGTTT
Found at i:437837 original size:53 final size:53
Alignment explanation
Indices: 437757--438105 Score: 558
Period size: 53 Copynumber: 6.6 Consensus size: 53
437747 GTAAATGCAA
*
437757 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* *
437810 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTAGTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
437863 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * * *
437916 AAAGGTACGATGACTATGTGTCATCGTGATTTATATGAATCCTA-TACGGACT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * *
437968 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAATCCTATTAAGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * *
438021 AAAGGTCCGATAAATCTGTTTCATCGTGAGTTATATGAATCCTA-TACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
*
438073 AAAGGTCCGATGACTCTGTGTCATCATGAGTTA
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTA
438106 CCAAATATGA
Statistics
Matches: 269, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
52 82 0.30
53 187 0.70
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:438020 original size:105 final size:105
Alignment explanation
Indices: 437757--438105 Score: 572
Period size: 105 Copynumber: 3.3 Consensus size: 105
437747 GTAAATGCAA
* *
437757 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATGGATTAAAGGTCCGATG
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTAAGGATTAAAGGTCCGATG
437822 ACTCTGTATCATCGTGAGTTATATGAATCCTAGTACGGATT
66 ACTCTGTATCATCGTGAGTTATATGAATCCTA-TACGGATT
* * *
437863 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTACGATG
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTAAGGATTAAAGGTCCGATG
* * * *
437928 ACTATGTGTCATCGTGATTTATATGAATCCTATACGGACT
66 ACTCTGTATCATCGTGAGTTATATGAATCCTATACGGATT
* *
437968 AAAGGTCCGATGACTCTATGTCATCATGAGTTATATGAATCCTATTAAGGATTAAAGGTCCGATA
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTAAGGATTAAAGGTCCGATG
* *
438033 AATCTGTTTCATCGTGAGTTATATGAATCCTATACGGATT
66 ACTCTGTATCATCGTGAGTTATATGAATCCTATACGGATT
438073 AAAGGTCCGATGACTCTGTGTCATCATGAGTTA
1 AAAGGTCCGATGACTCTGTGTCATCATGAGTTA
438106 CCAAATATGA
Statistics
Matches: 226, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 134 0.59
106 92 0.41
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (105 bp):
AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTAAGGATTAAAGGTCCGATG
ACTCTGTATCATCGTGAGTTATATGAATCCTATACGGATT
Found at i:440017 original size:7 final size:7
Alignment explanation
Indices: 440005--440059 Score: 101
Period size: 7 Copynumber: 7.9 Consensus size: 7
439995 TCAAACTTCT
440005 CCAACTC
1 CCAACTC
440012 CCAACTC
1 CCAACTC
440019 CCAACTC
1 CCAACTC
*
440026 CCAATTC
1 CCAACTC
440033 CCAACTC
1 CCAACTC
440040 CCAACTC
1 CCAACTC
440047 CCAACTC
1 CCAACTC
440054 CCAACT
1 CCAACT
440060 TATTTATTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.29, C:0.55, G:0.00, T:0.16
Consensus pattern (7 bp):
CCAACTC
Found at i:441465 original size:15 final size:16
Alignment explanation
Indices: 441435--441467 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
441425 GCGGCTCTTG
*
441435 TTATTTTAATTAACAT
1 TTATTTAAATTAACAT
441451 TTATTTAAATT-ACAT
1 TTATTTAAATTAACAT
441466 TT
1 TT
441468 CATCACCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTAAATTAACAT
Found at i:442128 original size:149 final size:149
Alignment explanation
Indices: 441959--442261 Score: 606
Period size: 149 Copynumber: 2.0 Consensus size: 149
441949 AAAAAAAAAA
441959 TTCATTTTTTACATTTTCATTTTTAACCATCTACAAATTTAAGGTTTAAAAAAATATTTCAAAAC
1 TTCATTTTTTACATTTTCATTTTTAACCATCTACAAATTTAAGGTTTAAAAAAATATTTCAAAAC
442024 ATATCTAAATTCGTATTATGATATTTAGGTAGATGATAAATTATTTACTGAAAAGAAATTATTTT
66 ATATCTAAATTCGTATTATGATATTTAGGTAGATGATAAATTATTTACTGAAAAGAAATTATTTT
442089 TAAAAAATAGTTTTAAGTT
131 TAAAAAATAGTTTTAAGTT
442108 TTCATTTTTTACATTTTCATTTTTAACCATCTACAAATTTAAGGTTTAAAAAAATATTTCAAAAC
1 TTCATTTTTTACATTTTCATTTTTAACCATCTACAAATTTAAGGTTTAAAAAAATATTTCAAAAC
442173 ATATCTAAATTCGTATTATGATATTTAGGTAGATGATAAATTATTTACTGAAAAGAAATTATTTT
66 ATATCTAAATTCGTATTATGATATTTAGGTAGATGATAAATTATTTACTGAAAAGAAATTATTTT
442238 TAAAAAATAGTTTTAAGTT
131 TAAAAAATAGTTTTAAGTT
442257 TTCAT
1 TTCAT
442262 CATTAATATT
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (149 bp):
TTCATTTTTTACATTTTCATTTTTAACCATCTACAAATTTAAGGTTTAAAAAAATATTTCAAAAC
ATATCTAAATTCGTATTATGATATTTAGGTAGATGATAAATTATTTACTGAAAAGAAATTATTTT
TAAAAAATAGTTTTAAGTT
Found at i:447741 original size:29 final size:31
Alignment explanation
Indices: 447684--447743 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
447674 TATTTGATTG
447684 GATTTGATATTTCTAGATCTTTTTATAATTT
1 GATTTGATATTTCTAGATCTTTTTATAATTT
*
447715 GATTTGAT-TTT-TA-ATTTTTTTAGTAATTT
1 GATTTGATATTTCTAGATCTTTTTA-TAATTT
447744 TGAGTTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 8 0.30
30 3 0.11
31 8 0.30
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (31 bp):
GATTTGATATTTCTAGATCTTTTTATAATTT
Found at i:450201 original size:17 final size:17
Alignment explanation
Indices: 450179--450222 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
450169 TATGAAACAT
*
450179 AATCTTCGAAGATATGC
1 AATCTTAGAAGATATGC
* *
450196 AATCTTAGAAGATTTGT
1 AATCTTAGAAGATATGC
450213 AATCTTAGAA
1 AATCTTAGAA
450223 TAGTTGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (17 bp):
AATCTTAGAAGATATGC
Found at i:457518 original size:58 final size:58
Alignment explanation
Indices: 457454--457563 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
457444 ATTGAATCTG
* * * * *
457454 AAAAAAACTTAGGTACCAAATTA-GAAAATATTGTCAAGTTCAGGTACCAAATTGGATC
1 AAAAAAACTTAAGTACCAAATTAGGAAAA-AGTATCAAGCTCAAGTACCAAATTGGATC
*
457512 AAAAAAATTTAAGTACCAAATTAGGAAAAAGTATCAAGCTCAAGTACCAAAT
1 AAAAAAACTTAAGTACCAAATTAGGAAAAAGTATCAAGCTCAAGTACCAAAT
457564 ATTATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 40 0.89
59 5 0.11
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (58 bp):
AAAAAAACTTAAGTACCAAATTAGGAAAAAGTATCAAGCTCAAGTACCAAATTGGATC
Found at i:459434 original size:22 final size:21
Alignment explanation
Indices: 459394--459434 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
459384 CATCAACCAA
*
459394 GAAAAAAAAATCTCAAATACC
1 GAAAAAAAAATATCAAATACC
*
459415 GAAAAAATAAATATCGAATA
1 GAAAAAA-AAATATCAAATA
459435 TCCAAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.17
Consensus pattern (21 bp):
GAAAAAAAAATATCAAATACC
Found at i:461229 original size:2 final size:2
Alignment explanation
Indices: 461222--461247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
461212 AAAGAATGAT
461222 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
461248 TCTATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:464642 original size:60 final size:59
Alignment explanation
Indices: 464563--464816 Score: 191
Period size: 57 Copynumber: 4.3 Consensus size: 59
464553 TGAGTGTCTA
* * *
464563 CCAAGCCATGGTCAACACCCCATTTTTTACATTAAAAAAATAAATTTTTTTGGGTGTTTG
1 CCAAGCCATGGTCCACACCCC-TTTTTTACAATAAAAAAATAAATATTTTTGGGTGTTTG
* ****** * *
464623 CCAAGCCAGGGTCCACACCCAAAAAATACGAATAAAAAACT--AT-TTTTCGGGTGTTTG
1 CCAAGCCATGGTCCACACCCCTTTTTTAC-AATAAAAAAATAAATATTTTTGGGTGTTTG
* * * * * * *
464680 CCAAGACATGG-CCGACACCTCCTTTTCTA-TATACAAAAAAAAAATATTTTTGGATGTCTA
1 CCAAGCCATGGTCC-ACACC-CCTTTTTTACAATA-AAAAAATAAATATTTTTGGGTGTTTG
* *
464740 CCAAGCCATGGTCGACACTCCCTTTTTCA-AAT-AAAAAA-AAATATTTTTGGGTGTTTG
1 CCAAGCCATGGTCCACAC-CCCTTTTTTACAATAAAAAAATAAATATTTTTGGGTGTTTG
* *
464797 CCAAGCCATGATCGACACCC
1 CCAAGCCATGGTCCACACCC
464817 AAAAAAAAGT
Statistics
Matches: 150, Mismatches: 35, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
56 7 0.05
57 65 0.43
58 11 0.07
59 5 0.03
60 60 0.40
61 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (59 bp):
CCAAGCCATGGTCCACACCCCTTTTTTACAATAAAAAAATAAATATTTTTGGGTGTTTG
Found at i:465755 original size:24 final size:24
Alignment explanation
Indices: 465728--465798 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
465718 TGACTCAAAT
* *
465728 AAATAGACATAATTTAATTGAAAC
1 AAATAAACAGAATTTAATTGAAAC
* *
465752 AAATAAACAGAGTTTATTTGAAAC
1 AAATAAACAGAATTTAATTGAAAC
* * *
465776 AATTAAACAGAGTTTAACTGAAA
1 AAATAAACAGAATTTAATTGAAA
465799 GATTATTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATAAACAGAATTTAATTGAAAC
Found at i:466508 original size:56 final size:58
Alignment explanation
Indices: 466357--466509 Score: 143
Period size: 60 Copynumber: 2.6 Consensus size: 58
466347 TAATACGAAT
* * *
466357 AAAAATATTTTTTTGGTGTCTGCCAA-ACCATGGTCGACACCCCCTTTTCCAGATACCAA
1 AAAAATA-TTTTTTGGTGTTTGCCAACA-CATGATCGACACCCACTTTTCCAGATACCAA
** * * * * *
466416 AAAATATATTTTTTGGGTGTTTATCATCCCATGATCGACACCCACTTTTTCTGAT-CC-G
1 AAAA-ATATTTTTT-GGTGTTTGCCAACACATGATCGACACCCACTTTTCCAGATACCAA
466474 AAAAATA-TTTTTGAGTGTTTGCCAACACATGATCGA
1 AAAAATATTTTTTG-GTGTTTGCCAACACATGATCGA
466510 GATCACCTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
55 1 0.01
56 23 0.30
57 3 0.04
58 4 0.05
59 12 0.16
60 33 0.43
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (58 bp):
AAAAATATTTTTTGGTGTTTGCCAACACATGATCGACACCCACTTTTCCAGATACCAA
Found at i:469853 original size:17 final size:17
Alignment explanation
Indices: 469827--469960 Score: 82
Period size: 17 Copynumber: 7.7 Consensus size: 17
469817 TTACAAAGTA
469827 AAATGAAATTAAAGTTG
1 AAATGAAATTAAAGTTG
* *
469844 AAATGGAATTAAATTTG
1 AAATGAAATTAAAGTTG
*
469861 AAATGAAATTAACA-TACG
1 AAATGAAATTAA-AGT-TG
* *
469879 -AAGGCAAAGTT-TAGTTG
1 AAATG-AAA-TTAAAGTTG
469896 AAATTGAAAATTAAA--TG
1 AAA-TG-AAATTAAAGTTG
469913 AAATTGAAATTAAAGTTG
1 AAA-TGAAATTAAAGTTG
*
469931 AAATGAAAATTGAA-TTCG
1 AAATG-AAATTAAAGTT-G
*
469949 AAATTAAATTAA
1 AAATGAAATTAA
469961 TAAAAATTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
16 8 0.09
17 50 0.54
18 27 0.29
19 7 0.08
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (17 bp):
AAATGAAATTAAAGTTG
Found at i:469904 original size:6 final size:6
Alignment explanation
Indices: 469893--469958 Score: 54
Period size: 5 Copynumber: 11.3 Consensus size: 6
469883 CAAAGTTTAG
469893 TTGAAA TTGAAAA TT-AAA -TGAAA TTGAAA TT-AAA GTTGAAA -TGAAAA
1 TTGAAA TTG-AAA TTGAAA TTGAAA TTGAAA TTGAAA -TTGAAA TTG-AAA
469940 TTG-AA TTCGAAA TT-AAA TT
1 TTGAAA TT-GAAA TTGAAA TT
469959 AATAAAAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
4 1 0.02
5 20 0.39
6 16 0.31
7 14 0.27
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.33
Consensus pattern (6 bp):
TTGAAA
Found at i:469923 original size:23 final size:24
Alignment explanation
Indices: 469893--469957 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
469883 CAAAGTTTAG
469893 TTGAAATTGAAAATTAAATG-AAA
1 TTGAAATTGAAAATTAAATGAAAA
*
469916 TTGAAATT-AAAGTTGAAATGAAAA
1 TTGAAATTGAAAATT-AAATGAAAA
469940 TTG-AATTCG-AAATTAAAT
1 TTGAAATT-GAAAATTAAAT
469958 TAATAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 5 0.14
23 21 0.58
24 10 0.28
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (24 bp):
TTGAAATTGAAAATTAAATGAAAA
Found at i:469933 original size:12 final size:12
Alignment explanation
Indices: 469893--469944 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
469883 CAAAGTTTAG
469893 TTGAAATTGAAAA
1 TTGAAA-TGAAAA
469906 TT-AAATG-AAA
1 TTGAAATGAAAA
* *
469916 TTGAAATTAAAG
1 TTGAAATGAAAA
469928 TTGAAATGAAAA
1 TTGAAATGAAAA
469940 TTGAA
1 TTGAA
469945 TTCGAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 5 0.15
11 6 0.18
12 20 0.61
13 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
TTGAAATGAAAA
Found at i:470172 original size:19 final size:19
Alignment explanation
Indices: 470148--470187 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
470138 TTAGATTTTA
*
470148 AATTGTAAGAATTTAACTT
1 AATTGTAAAAATTTAACTT
*
470167 AATTGTAAAAATTTAATTT
1 AATTGTAAAAATTTAACTT
470186 AA
1 AA
470188 ACATTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (19 bp):
AATTGTAAAAATTTAACTT
Found at i:471297 original size:31 final size:31
Alignment explanation
Indices: 471259--471338 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
471249 TGCTTCACAT
471259 GACAGTATATAATTCAACT-TCGACAATATAA
1 GACAGTATATAATTCAACTCT-GACAATATAA
*
471290 GACAGTATATAATTCAACTCTGACAATATAT
1 GACAGTATATAATTCAACTCTGACAATATAA
*
471321 GACATTATATAATTCAAC
1 GACAGTATATAATTCAAC
471339 CCAGAAATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 45 0.98
32 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
GACAGTATATAATTCAACTCTGACAATATAA
Found at i:471622 original size:59 final size:58
Alignment explanation
Indices: 471525--471667 Score: 169
Period size: 59 Copynumber: 2.4 Consensus size: 58
471515 CGTTACCAAG
* * * * * *
471525 CACCAAAAAAAATATTTTTTAATTCTTATTTTTATGGGTTTTGATCATTAGTTGTCAAA
1 CACCAAAAAAAATATTTTTT-ATTCGTATTTTTATGGGTGTCGACCATTAGATGACAAA
* *
471584 CACGAAAAAAAATATTTTTTATTCGTATTATTTGTGGGTGTCGACCATTAGATGACAAA
1 CACCAAAAAAAATATTTTTTATTCGTATT-TTTATGGGTGTCGACCATTAGATGACAAA
*
471643 CACCAAAATATAAATTTTTTTTATT
1 CACCAAAA-A-AAATATTTTTTATT
471668 TTTGGGTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
58 8 0.11
59 49 0.69
60 1 0.01
61 13 0.18
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (58 bp):
CACCAAAAAAAATATTTTTTATTCGTATTTTTATGGGTGTCGACCATTAGATGACAAA
Found at i:476187 original size:21 final size:20
Alignment explanation
Indices: 476151--476200 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
476141 CAATTAAGCT
476151 TTAATT-AATCATTTTAAATC
1 TTAATTAAATCATTTTAAA-C
*
476171 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCAT-TTTAAAC
476191 TTAATATAAA
1 TTAAT-TAAA
476201 CCATGCCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAAATCATTTTAAAC
Found at i:491717 original size:23 final size:23
Alignment explanation
Indices: 491691--491748 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
491681 CTGACGTGGC
*
491691 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCCAGAAG
* *
491714 ATCCAATCAACAGCTTCCAGAAG
1 ATCCAGTCAGCAGCTTCCAGAAG
* *
491737 GTCTAGTCAGCA
1 ATCCAGTCAGCA
491749 AGGATGGACT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCCAGAAG
Found at i:510651 original size:22 final size:24
Alignment explanation
Indices: 510626--510676 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
510616 ACACTTAAAC
*
510626 TTAAATTTTAAAATAA-A-AAAAA
1 TTAAATTTTAAAAAAACACAAAAA
510648 TTAAA--TTAAAAAAACACAAAAA
1 TTAAATTTTAAAAAAACACAAAAA
510670 TTAAATT
1 TTAAATT
510677 CGAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAATTTTAAAAAAACACAAAAA
Found at i:514358 original size:18 final size:17
Alignment explanation
Indices: 514334--514379 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
514324 CACTTTTTTC
*
514334 TTTTTTAAATAATTTTA
1 TTTTTTAAATAATTGTA
*
514351 TTTATTTATATAATTGTA
1 TTT-TTTAAATAATTGTA
514369 TTTTTTAAATA
1 TTTTTTAAATA
514380 CATGTGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTTAAATAATTGTA
Found at i:517846 original size:29 final size:28
Alignment explanation
Indices: 517770--517848 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
517760 ATTTATAAGT
* * *
517770 TGGTACTTAAATTATCATTTTTCATATAT
1 TGGTACTTAAATTA-CTTTTTTCATAAAG
* * * *
517799 TGATATTTAAATT-TTTTTTTTACTAAAG
1 TGGTACTTAAATTACTTTTTTCA-TAAAG
517827 TGGTACTTAAATTACTTTTTTC
1 TGGTACTTAAATTACTTTTTTC
517849 TCAAGTTGAT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
27 6 0.16
28 14 0.38
29 17 0.46
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (28 bp):
TGGTACTTAAATTACTTTTTTCATAAAG
Found at i:523252 original size:90 final size:90
Alignment explanation
Indices: 523099--523271 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 90
523089 ATTTCAATGC
* * *
523099 TCCAATTTTGCCTTCTGTGTTATTGTCATTGCAACTCCTTCCTCTGGCTCTTCTACTCCAGATTC
1 TCCAATTCTACCTTCTGTGTTACTGTCATTGCAACTCCTTCCTCTGGCTCTTCTACTCCAGATTC
523164 AACAACATGCCAATACTCCAATACT
66 AACAACATGCCAATACTCCAATACT
523189 TCCAATTCTACCTTCTGTGTTACTGTCATTGCAACTCCTTCCTCTGGCTCTTCTACTCCAGATTC
1 TCCAATTCTACCTTCTGTGTTACTGTCATTGCAACTCCTTCCTCTGGCTCTTCTACTCCAGATTC
*
523254 AACAACATGGCAATACTC
66 AACAACATGCCAATACTC
523272 TTTAGACCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (90 bp):
TCCAATTCTACCTTCTGTGTTACTGTCATTGCAACTCCTTCCTCTGGCTCTTCTACTCCAGATTC
AACAACATGCCAATACTCCAATACT
Found at i:531343 original size:6 final size:6
Alignment explanation
Indices: 531332--531381 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
531322 AAAAATATTC
531332 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAGTCT ATAAAT A-AAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA---T ATAAAT ATAAAT ATAAAT
531381 A
1 A
531382 ACATATCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.24
6 25 0.61
9 6 0.15
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:531512 original size:16 final size:17
Alignment explanation
Indices: 531493--531525 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
531483 CCCCAAAATC
531493 AAAATA-ATAATAAGTT
1 AAAATATATAATAAGTT
*
531509 AAAATATATACTAAGTT
1 AAAATATATAATAAGTT
531526 TATGAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
AAAATATATAATAAGTT
Found at i:531642 original size:2 final size:2
Alignment explanation
Indices: 531635--531670 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
531625 ATTCAACCTA
531635 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
531671 TAACCTAGCA
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:532611 original size:22 final size:22
Alignment explanation
Indices: 532583--532628 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
532573 AAAAAGTCAA
532583 CGATCAACAATCGGTCAACGCT
1 CGATCAACAATCGGTCAACGCT
* *
532605 CGATCAACACTTGGTCAACGCT
1 CGATCAACAATCGGTCAACGCT
532627 CG
1 CG
532629 GTTAATGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (22 bp):
CGATCAACAATCGGTCAACGCT
Found at i:533774 original size:46 final size:46
Alignment explanation
Indices: 533654--533877 Score: 261
Period size: 46 Copynumber: 4.8 Consensus size: 46
533644 CATGTGAAAG
* * * *
533654 TAATAGTGCTTGATTACCCGTTTGGGTTAAACCTACATGAATAAGAAA
1 TAATAGTGCTTGGTTACCCGTTAGGGTTAAACCTACACGAAT-A-ACA
* * * *
533702 TCATAGTGCCTGGTTACCCGCTAGGGTTAAACCTACATGAATAACA
1 TAATAGTGCTTGGTTACCCGTTAGGGTTAAACCTACACGAATAACA
* * * * * *
533748 TAATAGTGCTTGGTCACTCATTAGGGTTGAACCTATACGAAAAACA
1 TAATAGTGCTTGGTTACCCGTTAGGGTTAAACCTACACGAATAACA
* *
533794 TAATAGTGCTTGGTCACCCGTTAGGGTTAAACCTATACGAATAACA
1 TAATAGTGCTTGGTTACCCGTTAGGGTTAAACCTACACGAATAACA
*
533840 TAATAGTG-TCTGGTTACCCGTTAGGGTTGAACCTACAC
1 TAATAGTGCT-TGGTTACCCGTTAGGGTTAAACCTACAC
533878 AACAATTAGC
Statistics
Matches: 152, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
45 1 0.01
46 113 0.74
47 1 0.01
48 37 0.24
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (46 bp):
TAATAGTGCTTGGTTACCCGTTAGGGTTAAACCTACACGAATAACA
Found at i:534833 original size:20 final size:20
Alignment explanation
Indices: 534809--534856 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
534799 AATTAGTTTA
*
534809 TTAATTAATTAATCCTTAACC
1 TTAATTAATTAA-CATTAACC
*
534830 -TAATTTATTAACATTAACC
1 TTAATTAATTAACATTAACC
534849 TTAATTAA
1 TTAATTAA
534857 CCATTTTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAATTAACATTAACC
Found at i:536622 original size:20 final size:20
Alignment explanation
Indices: 536557--536622 Score: 114
Period size: 20 Copynumber: 3.2 Consensus size: 20
536547 CAACAAATAA
536557 TTTTAAAATTATTAAAATTATT
1 TTTTAAAA-TA-TAAAATTATT
536579 TTTTAAAATATAAAATTATT
1 TTTTAAAATATAAAATTATT
536599 TTTTAAAATATAAAATTATT
1 TTTTAAAATATAAAATTATT
536619 TTTT
1 TTTT
536623 TGAAATAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 34 0.77
21 2 0.05
22 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAATATAAAATTATT
Found at i:536623 original size:22 final size:21
Alignment explanation
Indices: 536577--536640 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
536567 ATTAAAATTA
536577 TTTTTTAAAATATAAAATTA-T
1 TTTTT-AAAATATAAAATTATT
536598 TTTTTAAAATATAAAATTATT
1 TTTTTAAAATATAAAATTATT
* *
536619 TTTTTGAAATAATAAAACTATT
1 TTTTTAAAAT-ATAAAATTATT
536641 AAATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 14 0.36
21 15 0.38
22 10 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTTAAAATATAAAATTATT
Found at i:537791 original size:22 final size:22
Alignment explanation
Indices: 537763--537826 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
537753 AAAATTATTT
537763 AATAATTTTATTATTTTAAAAA
1 AATAATTTTATTATTTTAAAAA
537785 AATAATTTTA-TATTTT-AAAA
1 AATAATTTTATTATTTTAAAAA
*
537805 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATTATTTTAAAA
537827 GCATTTACTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
20 13 0.34
21 7 0.18
22 15 0.39
23 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTATTATTTTAAAAA
Found at i:538445 original size:2 final size:2
Alignment explanation
Indices: 538438--538466 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
538428 CACTCATTAT
538438 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 T
538467 TTAGCTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:538937 original size:19 final size:19
Alignment explanation
Indices: 538915--538951 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
538905 AATATTATAA
538915 AATAAAATAATTATTTTTT
1 AATAAAATAATTATTTTTT
* *
538934 AATATAATTATTATTTTT
1 AATAAAATAATTATTTTT
538952 GTGTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAAAATAATTATTTTTT
Found at i:539128 original size:18 final size:18
Alignment explanation
Indices: 539102--539136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
539092 AAAATATTTA
*
539102 TTAATTAAAAATATAAAT
1 TTAAATAAAAATATAAAT
*
539120 TTAAATAAAAATTTAAA
1 TTAAATAAAAATATAAA
539137 ACAATATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAATAAAAATATAAAT
Found at i:539390 original size:142 final size:141
Alignment explanation
Indices: 539128--539435 Score: 476
Period size: 142 Copynumber: 2.2 Consensus size: 141
539118 ATTTAAATAA
* *
539128 AAATTTAAAACAATATGAAATAAAAATTACAAATATGTTTAGAAAAGGGGAATTGAACTTGGGTC
1 AAATTTAAAACAACATGAAATAAAAATTACAAATATGTTTAGAAAAGGGGAATTGAACATGGGTC
* * * * * * *
539193 TCAATGATGAAATCATTATTATTTAGTTATTTAACTAAGGAAGCTGATATGTTAAAAACATTTAT
66 TCAAAGATAAAATCATTATTATTTAATCATTTAACTAAGGAAGCTAATATATTAAAAACATTCAT
539258 TAAAGAAAAGAAG
131 TAAA-AAAAG-AG
*
539271 AAATTTAAAACAACATGAAATAAAAATTACAAATGTGTTTAGAAAA-GGGAATTGAACATGGGTC
1 AAATTTAAAACAACATGAAATAAAAATTACAAATATGTTTAGAAAAGGGGAATTGAACATGGGTC
*
539335 TCAAAGATAAAATCATTTTTATTTAATCATTTAACTAAGGAAGCTAATATATTAAAAACATTCAT
66 TCAAAGATAAAATCATTATTATTTAATCATTTAACTAAGGAAGCTAATATATTAAAAACATTCAT
539400 TAAAAAAAGAG
131 TAAAAAAAGAG
*
539411 -AGTTTAAAACAACATGAAATAAAAA
1 AAATTTAAAACAACATGAAATAAAAA
539436 ATATAAAAAT
Statistics
Matches: 153, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
139 24 0.16
140 2 0.01
141 5 0.03
142 78 0.51
143 44 0.29
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (141 bp):
AAATTTAAAACAACATGAAATAAAAATTACAAATATGTTTAGAAAAGGGGAATTGAACATGGGTC
TCAAAGATAAAATCATTATTATTTAATCATTTAACTAAGGAAGCTAATATATTAAAAACATTCAT
TAAAAAAAGAG
Found at i:541209 original size:21 final size:21
Alignment explanation
Indices: 541159--541209 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
541149 GGATTATGTA
541159 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * * * *
541180 GTATAGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
541201 ATTTGGATT
1 ATTTGGATT
541210 ATGCTATTAT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:541965 original size:30 final size:32
Alignment explanation
Indices: 541907--541967 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
541897 TTGTTGGTGT
541907 TTTTTCTTTTTACAAGTTTATGAAAATTTTAA
1 TTTTTCTTTTTACAAGTTTATGAAAATTTTAA
* * *
541939 TTTTT-TTTTTATAA-TTTTTGAGAATTTTA
1 TTTTTCTTTTTACAAGTTTATGAAAATTTTA
541968 GGTTTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 8 0.31
32 5 0.19
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (32 bp):
TTTTTCTTTTTACAAGTTTATGAAAATTTTAA
Found at i:543321 original size:14 final size:15
Alignment explanation
Indices: 543302--543334 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
543292 ACAATTTTTC
*
543302 TTTTTCTCT-CGAAA
1 TTTTTCTCTGCAAAA
543316 TTTTTCTCTGCAAAA
1 TTTTTCTCTGCAAAA
543331 TTTT
1 TTTT
543335 CATACGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (15 bp):
TTTTTCTCTGCAAAA
Found at i:554428 original size:26 final size:24
Alignment explanation
Indices: 554371--554421 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
554361 TTTTTTGGTG
554371 AATATTAAAAATATATTATTAATT
1 AATATTAAAAATATATTATTAATT
* *
554395 GATATTAAAAATATATTTTATAATT
1 AATATTAAAAATATATTAT-TAATT
554420 AA
1 AA
554422 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATATTAAAAATATATTATTAATT
Found at i:554439 original size:32 final size:31
Alignment explanation
Indices: 554401--554461 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
554391 AATTGATATT
554401 AAAAATATATTTTA-TAATTAAATTTTAATTTA
1 AAAAATAT-TTTTATTAATTAAA-TTTAATTTA
*
554433 AAAAATATTTTTATTATTTAAATTTAATT
1 AAAAATATTTTTATTAATTAAATTTAATT
554462 CGAATCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAAATATTTTTATTAATTAAATTTAATTTA
Found at i:555911 original size:3 final size:3
Alignment explanation
Indices: 555898--555932 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
555888 GTTTACAATC
*
555898 TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
555933 ACTGTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:560861 original size:16 final size:16
Alignment explanation
Indices: 560840--560884 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
560830 ACTGGGATGA
560840 AAATAAAATTTTAATT
1 AAATAAAATTTTAATT
560856 AAAT-AAA-TTTAATT
1 AAATAAAATTTTAATT
*
560870 AATTAAAAATTTTAA
1 AAAT-AAAATTTTAA
560885 ACTAATTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAAAATTTTAATT
Found at i:562168 original size:43 final size:43
Alignment explanation
Indices: 562099--562186 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
562089 TTGGAAGGCT
562099 TGCTACTTGTTTGTTTGGGGTAAAGGCTTTAGAAAAATTGAAG
1 TGCTACTTGTTTGTTTGGGGTAAAGGCTTTAGAAAAATTGAAG
* * *
562142 TGCTGCTTGTTTGTTTGGGGTGAAGGCTTTGGAAAAATTGAAG
1 TGCTACTTGTTTGTTTGGGGTAAAGGCTTTAGAAAAATTGAAG
562185 TG
1 TG
562187 GAAAGTGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.38
Consensus pattern (43 bp):
TGCTACTTGTTTGTTTGGGGTAAAGGCTTTAGAAAAATTGAAG
Found at i:562511 original size:21 final size:22
Alignment explanation
Indices: 562468--562512 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
562458 ATCTCTTCAT
*
562468 TTTTGTAAAATATTTTATCAAA
1 TTTTGTAAAATATTTTATAAAA
* *
562490 TTTT-TAAGATATTTTTTAAAA
1 TTTTGTAAAATATTTTATAAAA
562511 TT
1 TT
562513 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTGTAAAATATTTTATAAAA
Found at i:565449 original size:28 final size:27
Alignment explanation
Indices: 565398--565454 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
565388 GTTGGAATTG
565398 ATCTCTCTTTTATTTCTTTATAAAAAA
1 ATCTCTCTTTTATTTCTTTATAAAAAA
* * * *
565425 ATCTCTTTTATTATTTTTTTCTAAATAA
1 ATCTCTCTT-TTATTTCTTTATAAAAAA
565453 AT
1 AT
565455 ATTGTGGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (27 bp):
ATCTCTCTTTTATTTCTTTATAAAAAA
Found at i:567460 original size:15 final size:14
Alignment explanation
Indices: 567432--567479 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
567422 AAATTTGTGA
567432 TTTAATTTTTATAT
1 TTTAATTTTTATAT
567446 TTTAATTTTTAATAT
1 TTTAATTTTT-ATAT
* *
567461 AATTTGAGTTTTATAT
1 --TTTAATTTTTATAT
567477 TTT
1 TTT
567480 CATAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.45
15 4 0.14
16 4 0.14
17 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:573662 original size:50 final size:50
Alignment explanation
Indices: 573603--573704 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
573593 TCATTACTGA
573603 GATAAAATCACAATTCAATAAGGGCAAAAATGTCATTTTCACGATTTTTG
1 GATAAAATCACAATTCAATAAGGGCAAAAATGTCATTTTCACGATTTTTG
573653 GATAAAATCACAATTCAATAAGGGCAAAAATGTCATTTTCACGATTTTTG
1 GATAAAATCACAATTCAATAAGGGCAAAAATGTCATTTTCACGATTTTTG
573703 GA
1 GA
573705 GACTTCTATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (50 bp):
GATAAAATCACAATTCAATAAGGGCAAAAATGTCATTTTCACGATTTTTG
Found at i:580312 original size:21 final size:21
Alignment explanation
Indices: 580267--580351 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
580257 CAGTGTAGTT
** **
580267 TTCTACCGATACAAGTAACAG
1 TTCTACCGATACAAAAAACTC
580288 TTCTACCGATACAAAAAACTC
1 TTCTACCGATACAAAAAACTC
* * **
580309 TTCTACCAAAACAAATCA-TGC
1 TTCTACCGATACAAAAAACT-C
* *
580330 TTTTACCGATACTAAAAACTC
1 TTCTACCGATACAAAAAACTC
580351 T
1 T
580352 AGAGAGCTAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.27
Consensus pattern (21 bp):
TTCTACCGATACAAAAAACTC
Found at i:587363 original size:14 final size:13
Alignment explanation
Indices: 587330--587363 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
587320 AAATATGTAA
587330 TATTTTATTTTTT
1 TATTTTATTTTTT
*
587343 TAGTTTATTTTTTT
1 TATTTTA-TTTTTT
587357 TATTTTA
1 TATTTTA
587364 CAAGCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:594959 original size:17 final size:17
Alignment explanation
Indices: 594937--594970 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
594927 ACTACCTTGA
594937 AAAGCTTTATTGAAAAG
1 AAAGCTTTATTGAAAAG
594954 AAAGCTTTATTGAAAAG
1 AAAGCTTTATTGAAAAG
594971 GATAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (17 bp):
AAAGCTTTATTGAAAAG
Found at i:601065 original size:28 final size:28
Alignment explanation
Indices: 601016--601077 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
601006 AAATGAGACT
601016 TTTTGGATACTCGAGGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
* *
601044 TTTTGGATTCTTCGA-GGTAAAATGGTAA
1 TTTTGGATAC-TCGAGGGCAAAATGGTAA
601072 TTTTGG
1 TTTTGG
601078 GAAATTTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:601123 original size:58 final size:57
Alignment explanation
Indices: 601034--601457 Score: 200
Period size: 59 Copynumber: 7.2 Consensus size: 57
601024 ACTCGAGGGC
* **
601034 AAAATGGTAATTTTGGATTCTTCGA-GGTAAAATGGTAATTTTGGGAAATTTTGGGGTTT
1 AAAATGG-AATTTTGGA-TATTCGAGGGTAAAATGGTAATTTT-GGAAATTTTGGGGTCA
* * * ** **** * *
601093 AAAATGGAATTTTAGATATTCGAGGGTAAAACGATAAATTTAAGAAAAAGCGGGATAA
1 AAAATGGAATTTTGGATATTCGAGGGTAAAATGGT-AATTTTGGAAATTTTGGGGTCA
** * * * * *
601151 AAAATAAAAAATTTTGGATATTCGTGAGTAAAATGGTAATTTTTGAGAGTTTTGGGGT-T
1 AAAAT--GGAATTTTGGATATTCGAGGGTAAAATGGTAATTTTGGA-AATTTTGGGGTCA
* * * * *
601210 AAAATGGAGTTTTTTG-TCATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCA
1 AAAATGGA-ATTTTGGAT-ATTCGAGGGTAAAATGGTAATTTTGGAAA-TTTTGGGGTCA
* ** * * * *
601269 AAAATGGAATTTTCGA-AGGGCTGGGGGTAAAAAT-GCAATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAATTTTGGATA-TTC-GAGGGT-AAAATGGTAA-TTTTGGAAATTTTGGGGTCA
* ** * * *
601328 AAAATGGAATTTTGGA-AGTTCGAGGATAAAAATGG-AATTTTCAAAAGCTTCGAGGTCA
1 AAAATGGAATTTTGGATA-TTCGAGGGT-AAAATGGTAATTTTGGAAA-TTTTGGGGTCA
* * ***
601386 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-ATAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGGAA-TTTTGGATA-TTCGAGGGT-AAAATGGTAATTTTGGAAA-TTTTGGGGTCA
601445 AAAATGGAATTTT
1 AAAATGGAATTTT
601458 TGGACAGTTT
Statistics
Matches: 282, Mismatches: 65, Indels: 37
0.73 0.17 0.10
Matches are distributed among these distances:
57 16 0.06
58 106 0.38
59 120 0.43
60 40 0.14
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAATGGAATTTTGGATATTCGAGGGTAAAATGGTAATTTTGGAAATTTTGGGGTCA
Found at i:601214 original size:30 final size:29
Alignment explanation
Indices: 601179--601340 Score: 98
Period size: 30 Copynumber: 5.5 Consensus size: 29
601169 TATTCGTGAG
601179 TAAAATGGTAATTTTTGAGAGTTTTGGGGT
1 TAAAATGG-AATTTTTGAGAGTTTTGGGGT
* ** * *
601209 TAAAATGGAGTTTTTTGTCA--TTCGGGGG
1 TAAAATGGA-ATTTTTGAGAGTTTTGGGGT
* *
601237 TAAAATGGTAATTTTTGAAAGTTTTGAGGT
1 TAAAATGG-AATTTTTGAGAGTTTTGGGGT
* * ** *
601267 CAAAAATGGAATTTTCGA-AGGGCTGGGGGT
1 -TAAAATGGAATTTTTGAGA-GTTTTGGGGT
* *
601297 AAAAATGCAATTTTTG-GAAGTTTTGGGGT
1 TAAAATGGAATTTTTGAG-AGTTTTGGGGT
*
601326 CGAAAATGGAATTTT
1 -TAAAATGGAATTTT
601341 GGAAGTTCGA
Statistics
Matches: 99, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
28 21 0.21
29 24 0.24
30 47 0.47
31 7 0.07
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (29 bp):
TAAAATGGAATTTTTGAGAGTTTTGGGGT
Found at i:601251 original size:28 final size:29
Alignment explanation
Indices: 601178--601259 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
601168 ATATTCGTGA
* *
601178 GTAAAATGGTAATTTTTGAGAGTTTTGGGG
1 GTAAAATGGTAATTTTTGACAG-TTCGGGG
* * *
601208 TTAAAATGG-AGTTTTTTGTCA-TTCGGGG
1 GTAAAATGGTA-ATTTTTGACAGTTCGGGG
*
601236 GTAAAATGGTAATTTTTGAAAGTT
1 GTAAAATGGTAATTTTTGACAGTT
601260 TTGAGGTCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
28 21 0.52
29 4 0.10
30 15 0.38
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGACAGTTCGGGG
Found at i:601309 original size:59 final size:58
Alignment explanation
Indices: 601229--601466 Score: 262
Period size: 59 Copynumber: 4.0 Consensus size: 58
601219 TTTTTTGTCA
* * *
601229 TTCGGGGGT-AAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTCGAAG
1 TTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAG
** * * * * * *
601287 GGCTGGGGGTAAAAATGCAATTTTTGGAAGTTTTGGGGTCGAAAATGGAATTTTGGAAG
1 TTC-GAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAG
* * ** *
601346 TTCGAGGATAAAAATGGAATTTTCAAAAGCTTCGAGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAA-TTTTGGAAG
* *
601405 TTCGAGGGTAAAAATATAATTTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTTGGACAG
1 TTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAA-TTTTGGA-AG
601465 TT
1 TT
601467 TAGGAACCTC
Statistics
Matches: 150, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
58 37 0.25
59 104 0.69
60 9 0.06
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.32
Consensus pattern (58 bp):
TTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAG
Found at i:601324 original size:29 final size:30
Alignment explanation
Indices: 601238--601467 Score: 177
Period size: 29 Copynumber: 7.7 Consensus size: 30
601228 ATTCGGGGGT
* * *
601238 AAAATGGTAATTTTTGAAAGTTTTGAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCA
* ** *
601269 AAAATGGAA-TTTTCGAAGGGCTGGGGGT-A
1 AAAATGGAATTTTTGGAA-GTTTCGGGGTCA
* * *
601298 AAAATGCAATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
*
601328 AAAATGGAA-TTTTGGAAG-TTCGAGGAT-A
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
*** * *
601356 AAAATGGAATTTTCAAAAGCTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
601386 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
** * **
601415 AAAATATAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
601445 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
601468 AGGAACCTCT
Statistics
Matches: 155, Mismatches: 33, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
28 12 0.08
29 66 0.43
30 65 0.42
31 12 0.08
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCA
Found at i:601382 original size:30 final size:29
Alignment explanation
Indices: 601238--601459 Score: 182
Period size: 30 Copynumber: 7.5 Consensus size: 29
601228 ATTCGGGGGT
*
601238 AAAATGGTAATTTTTGAAAGTTTTGAGGTCA
1 AAAATGG-AATTTTTGAAAG-TTCGAGGTCA
* * * * *
601269 AAAATGGAATTTTCGAAGGGCTGGGGGT-A
1 AAAATGGAATTTTTGAA-AGTTCGAGGTCA
* * * * *
601298 AAAATGCAATTTTTGGAAGTTTTGGGGTCG
1 AAAATGGAATTTTTGAAAG-TTCGAGGTCA
*
601328 AAAATGGAA-TTTTGGAAGTTCGAGGAT-A
1 AAAATGGAATTTTTGAAAGTTCGAGG-TCA
**
601356 AAAATGGAATTTTCAAAAGCTTCGAGGTCA
1 AAAATGGAATTTTTGAAAG-TTCGAGGTCA
*
601386 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
1 AAAATGGAATTTTTGAAAGTTCGA-GGTCA
** *
601415 AAAATATAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGAAAG-TTCGAGGTCA
601445 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
601460 GACAGTTTAG
Statistics
Matches: 153, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.10
29 63 0.41
30 67 0.44
31 8 0.05
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTCGAGGTCA
Found at i:602899 original size:24 final size:23
Alignment explanation
Indices: 602872--602929 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
602862 TGCAACTGAA
602872 GCTGGTGGTGGCAC-TGCTGGTGGT
1 GCTGGTGGTGGCACATGCTGGT--T
* *
602896 GCT-GTCGTGGCACATTCTGGTT
1 GCTGGTGGTGGCACATGCTGGTT
602918 GACTGGTGGTGG
1 G-CTGGTGGTGG
602930 AGGTGGCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 11 0.39
24 15 0.54
ACGTcount: A:0.07, C:0.17, G:0.45, T:0.31
Consensus pattern (23 bp):
GCTGGTGGTGGCACATGCTGGTT
Found at i:603155 original size:17 final size:17
Alignment explanation
Indices: 603127--603253 Score: 103
Period size: 17 Copynumber: 7.4 Consensus size: 17
603117 ATTTTAAAGT
* *
603127 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
603143 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
603161 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
* ** *
603178 TTTCAATTTCAATTTCAA
1 TTTAAATTT-AAAATAAA
* * **
603196 TTTAAAATGAATTTAAA
1 TTTAAATTTAAAATAAA
*
603213 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAATAAA
603230 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
603248 TTTAAA
1 TTTAAA
603254 AATTAATCTA
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
16 3 0.03
17 58 0.66
18 27 0.31
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:603168 original size:6 final size:6
Alignment explanation
Indices: 603142--603253 Score: 88
Period size: 6 Copynumber: 19.2 Consensus size: 6
603132 GTTTAAAATT
* ** * *
603142 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTCA ATTTCA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
603189 ATTTCA ATTTAA A-ATGA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
603235 ATTTAA AAATAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
603254 AATTAATCTA
Statistics
Matches: 83, Mismatches: 18, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
5 14 0.17
6 65 0.78
7 4 0.05
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:603197 original size:29 final size:29
Alignment explanation
Indices: 603146--603224 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
603136 AAAATTATTT
*
603146 CAAATTTAAA-CTAAATTTAAATTTAAAA
1 CAAATTTAAATTTAAATTTAAATTTAAAA
* * *
603174 CAAATTTCAATTTCAATTTCAATTTAAAA
1 CAAATTTAAATTTAAATTTAAATTTAAAA
**
603203 TGAATTTAAATTTAAATTTAAA
1 CAAATTTAAATTTAAATTTAAA
603225 GTAAATTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.41
Consensus pattern (29 bp):
CAAATTTAAATTTAAATTTAAATTTAAAA
Found at i:603208 original size:23 final size:23
Alignment explanation
Indices: 603182--603241 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
603172 AACAAATTTC
* * *
603182 AATTTCAATTTCAATTTAAAATG
1 AATTTAAATTTAAATTTAAAATA
*
603205 AATTTAAATTTAAATTTAAAGTA
1 AATTTAAATTTAAATTTAAAATA
603228 AATTTAAATTTAAA
1 AATTTAAATTTAAA
603242 AATAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
AATTTAAATTTAAATTTAAAATA
Found at i:603237 original size:29 final size:27
Alignment explanation
Indices: 603147--603255 Score: 84
Period size: 29 Copynumber: 4.1 Consensus size: 27
603137 AAATTATTTC
*
603147 AAATTTAAA-CTAAATTTAAATTTAAAA
1 AAATTTAAATTTAAATTTAAATTT-AAA
* * *
603174 CAAATTTCAATTTCAATTTCAATTT--A
1 -AAATTTAAATTTAAATTTAAATTTAAA
*
603200 AAA--TGAATTTAAATTTAAATTTAAA
1 AAATTTAAATTTAAATTTAAATTTAAA
**
603225 GTAAATTTAAATTTAAAAATAAATTTAAA
1 --AAATTTAAATTTAAATTTAAATTTAAA
603254 AA
1 AA
603256 TTAATCTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
23 16 0.25
25 4 0.06
26 1 0.02
27 5 0.08
28 8 0.12
29 30 0.47
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
AAATTTAAATTTAAATTTAAATTTAAA
Found at i:603247 original size:23 final size:23
Alignment explanation
Indices: 603152--603247 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
603142 ATTTCAAATT
*
603152 TAAACTAAATTTAAATTTAAAACA
1 TAAAATAAATTTAAATTTAAAA-A
** * * * **
603176 -AATTTCAATTTCAATTTCAATT
1 TAAAATAAATTTAAATTTAAAAA
* **
603198 TAAAATGAATTTAAATTTAAATT
1 TAAAATAAATTTAAATTTAAAAA
*
603221 TAAAGTAAATTTAAATTTAAAAA
1 TAAAATAAATTTAAATTTAAAAA
603244 TAAA
1 TAAA
603248 TTTAAAAATT
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAATAAATTTAAATTTAAAAA
Found at i:603254 original size:12 final size:12
Alignment explanation
Indices: 603232--603256 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
603222 AAAGTAAATT
603232 TAAATTTAAAAA
1 TAAATTTAAAAA
603244 TAAATTTAAAAA
1 TAAATTTAAAAA
603256 T
1 T
603257 TAATCTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:604866 original size:15 final size:15
Alignment explanation
Indices: 604842--604876 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
604832 TGGCCCTCGA
*
604842 AATTTTAATTTTTTC
1 AATTTAAATTTTTTC
*
604857 AATTTAAATTTTTTT
1 AATTTAAATTTTTTC
604872 AATTT
1 AATTT
604877 TAAACTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTAAATTTTTTC
Found at i:605511 original size:31 final size:31
Alignment explanation
Indices: 605476--605574 Score: 139
Period size: 31 Copynumber: 3.2 Consensus size: 31
605466 ACTAAATAGT
605476 TAAACCCTACACCCAACATCATTCTAAACCA
1 TAAACCCTACACCCAACATCATTCTAAACCA
* *
605507 TAAACCTTGCACCCAACATCATTCTAAATCC-
1 TAAACCCTACACCCAACATCATTCTAAA-CCA
*
605538 TAACCCCTACACCCAACATCA-TCTTAAACCA
1 TAAACCCTACACCCAACATCATTC-TAAACCA
605569 TAAACC
1 TAAACC
605575 GTAAACCATA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.07
31 53 0.90
32 2 0.03
ACGTcount: A:0.39, C:0.38, G:0.01, T:0.21
Consensus pattern (31 bp):
TAAACCCTACACCCAACATCATTCTAAACCA
Found at i:605581 original size:14 final size:14
Alignment explanation
Indices: 605562--605595 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
605552 AACATCATCT
605562 TAAACCATAAA-CC
1 TAAACCATAAATCC
605575 GTAAACCATAAATCC
1 -TAAACCATAAATCC
605590 TAAACC
1 TAAACC
605596 CGTCAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAACCATAAATCC
Found at i:609039 original size:21 final size:21
Alignment explanation
Indices: 609015--609056 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
609005 TAAGTCACTT
609015 GTGAATTAAGTTAAGGAAATG
1 GTGAATTAAGTTAAGGAAATG
609036 GTGAATTAAGTTAAGGAAATG
1 GTGAATTAAGTTAAGGAAATG
609057 AAAAACTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (21 bp):
GTGAATTAAGTTAAGGAAATG
Found at i:613367 original size:6 final size:6
Alignment explanation
Indices: 613356--613400 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
613346 TGATCAAAAT
* * *
613356 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
613401 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:614952 original size:50 final size:50
Alignment explanation
Indices: 614920--615081 Score: 225
Period size: 50 Copynumber: 3.2 Consensus size: 50
614910 CCTTTTCCAA
* * * *
614920 CTTTAGGAGTATAAGATTCGCCCTTGCGGCTTCAATCTGCCCCTCTACAG
1 CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATTTGCCCCTCTACAG
* *
614970 CTTTAGGTGTATGAGATTCACCATTGTGGCTTCAATTTGCCCCTCTACAG
1 CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATTTGCCCCTCTACAG
** **
615020 CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCCGTTCCTCTACAG
1 CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATTTGCCCCTCTACAG
*
615070 CTTTAGGGGTAT
1 CTTTAGGTGTAT
615082 AGGATTTGAT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (50 bp):
CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATTTGCCCCTCTACAG
Found at i:615048 original size:100 final size:100
Alignment explanation
Indices: 614893--615081 Score: 261
Period size: 100 Copynumber: 1.9 Consensus size: 100
614883 TAATTTGCTC
* * * * *
614893 TTGTAGCTTCAATTTACCCTTTTCCAACTTTAGGAGTATAAGATTCGCCCTTGCGGCTTCAATCT
1 TTGTAGCTTCAATTTACCCCTCTACAACTTTAGGAGTATAAGATTCGCCATTGCGGCTTCAATCC
*
614958 GCCCCTCTACAGCTTTAGGTGTATGAGATTCACCA
66 GCCCCTCTACAGCTTTAGGGGTATGAGATTCACCA
* * * * *
614993 TTGTGGCTTCAATTTGCCCCTCTACAGCTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCC
1 TTGTAGCTTCAATTTACCCCTCTACAACTTTAGGAGTATAAGATTCGCCATTGCGGCTTCAATCC
**
615058 GTTCCTCTACAGCTTTAGGGGTAT
66 GCCCCTCTACAGCTTTAGGGGTAT
615082 AGGATTTGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (100 bp):
TTGTAGCTTCAATTTACCCCTCTACAACTTTAGGAGTATAAGATTCGCCATTGCGGCTTCAATCC
GCCCCTCTACAGCTTTAGGGGTATGAGATTCACCA
Found at i:627678 original size:20 final size:18
Alignment explanation
Indices: 627649--627693 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
627639 TTAGTTTCGA
627649 AATA-AAAATAAATACATAT
1 AATATAAAATAAAT-CA-AT
627668 AATATAAAATAAATCAAT
1 AATATAAAATAAATCAAT
627686 ATATATAA
1 A-ATATAA
627694 GTATAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAAATAAATCAAT
Found at i:627686 original size:24 final size:26
Alignment explanation
Indices: 627654--627704 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
627644 TTCGAAATAA
627654 AAATAAATACATATAA-TATAA-AAT
1 AAATAAATACATATAAGTATAACAAT
* *
627678 AAATCAATATATATAAGTATAACAAT
1 AAATAAATACATATAAGTATAACAAT
627704 A
1 A
627705 TACCTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 5 0.22
26 4 0.17
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAAATACATATAAGTATAACAAT
Found at i:631591 original size:60 final size:59
Alignment explanation
Indices: 631521--631695 Score: 214
Period size: 59 Copynumber: 3.0 Consensus size: 59
631511 TTTTTAAACA
* * *
631521 TTCGAGGGTAAAAGGGTAATTTTTGAG-AGTTTCGGGATCAAAAAATGAAAGTTTTGGAAG
1 TTCGAGGGTAAAAAGGTAATTTTTGAGAAGTTTTGGGGTC-AAAAATGAAA-TTTTGGAAG
* * *
631581 TTTGAGGGTAAAATGGTAATTTTT-AGAAGTTTTGGGGTC-AAAATCGAGATTTTTGGAAG
1 TTCGAGGGTAAAAAGGTAATTTTTGAGAAGTTTTGGGGTCAAAAAT-GA-AATTTTGGAAG
* *
631640 TTCGAGGGTAAAAATGTAATTTTTG-GAAGTTTTGGGGTCAAAAATGGAATTTTGGA
1 TTCGAGGGTAAAAAGGTAATTTTTGAGAAGTTTTGGGGTCAAAAATGAAATTTTGGA
631696 GAAGTTTAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
58 13 0.13
59 49 0.49
60 38 0.38
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
TTCGAGGGTAAAAAGGTAATTTTTGAGAAGTTTTGGGGTCAAAAATGAAATTTTGGAAG
Found at i:631609 original size:29 final size:29
Alignment explanation
Indices: 631562--631732 Score: 154
Period size: 30 Copynumber: 5.8 Consensus size: 29
631552 TCGGGATCAA
* *
631562 AAAATGAAAGTTTTGGAAGTTTGAGGGT-
1 AAAATGTAATTTTTGGAAGTTTGAGGGTC
*
631590 AAAATGGTAATTTTTAGAAGTTTTG-GGGTC
1 AAAAT-GTAATTTTTGGAAG-TTTGAGGGTC
* *
631620 AAAATCG-AGATTTTTGGAAGTTCGAGGGTA
1 AAAAT-GTA-ATTTTTGGAAGTTTGAGGGTC
631650 AAAATGTAATTTTTGGAAGTTTTG-GGGTC
1 AAAATGTAATTTTTGGAAG-TTTGAGGGTC
* *
631679 AAAAATGGAATTTTGGAGAAGTTT-AGGGGTC
1 -AAAATGTAATTTTTG-GAAGTTTGA-GGGTC
*
631710 AAAATATAATTTTTGGACAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
631733 AAGGACCTCC
Statistics
Matches: 117, Mismatches: 14, Indels: 22
0.76 0.09 0.14
Matches are distributed among these distances:
28 5 0.04
29 37 0.32
30 66 0.56
31 9 0.08
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTC
Found at i:631714 original size:60 final size:58
Alignment explanation
Indices: 631524--631732 Score: 203
Period size: 60 Copynumber: 3.5 Consensus size: 58
631514 TTAAACATTC
* * * * *
631524 GAGGGTAAAAGGGTAATTTTT-GAGAGTTTCGGGATCAAAAAATGAAAGTTTTGGAAGTTT
1 GAGGGTAAAA-TGTAATTTTTGGACAGTTTTGGGGTC-AAAAATGGAA-TTTTGGAAGTTT
* * *
631584 GAGGGTAAAATGGTAATTTTTAGA-AGTTTTGGGGTC-AAAATCGAGATTTTTGGAAGTTC
1 GAGGGTAAAAT-GTAATTTTTGGACAGTTTTGGGGTCAAAAAT-G-GAATTTTGGAAGTTT
631643 GAGGGTAAAAATGTAATTTTTGGA-AGTTTTGGGGTCAAAAATGGAATTTTGGAGAAGTTT
1 GAGGGT-AAAATGTAATTTTTGGACAGTTTTGGGGTCAAAAATGGAATTTT-G-GAAGTTT
*
631703 -AGGGGTCAAAATATAATTTTTGGACAGTTT
1 GA-GGGT-AAAATGTAATTTTTGGACAGTTT
631733 AAGGACCTCC
Statistics
Matches: 128, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
58 11 0.09
59 44 0.34
60 66 0.52
61 7 0.05
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (58 bp):
GAGGGTAAAATGTAATTTTTGGACAGTTTTGGGGTCAAAAATGGAATTTTGGAAGTTT
Found at i:631733 original size:30 final size:29
Alignment explanation
Indices: 631537--631733 Score: 134
Period size: 30 Copynumber: 6.6 Consensus size: 29
631527 GGTAAAAGGG
* * *
631537 TAATTTTT-GAGAGTTTCGGGATCAAAAAA
1 TAATTTTTGGA-AGTTTAGGGGTCAAAATA
* *
631566 TGAAAGTTTTGGAAGTTT-GAGGGT-AAAATGG
1 T--AATTTTTGGAAGTTTAG-GGGTCAAAAT-A
* * *
631597 TAATTTTTAGAAGTTTTGGGGTCAAAATC
1 TAATTTTTGGAAGTTTAGGGGTCAAAATA
* * * *
631626 GAGATTTTTGGAAG-TTCGAGGGTAAAAATG
1 TA-ATTTTTGGAAGTTTAG-GGGTCAAAATA
*
631656 TAATTTTTGGAAGTTTTGGGGTCAAAA-A
1 TAATTTTTGGAAGTTTAGGGGTCAAAATA
*
631684 TGGAATTTTGGAGAAGTTTAGGGGTCAAAATA
1 T--AATTTTTG-GAAGTTTAGGGGTCAAAATA
631716 TAATTTTTGGACAGTTTA
1 TAATTTTTGGA-AGTTTA
631734 AGGACCTCCA
Statistics
Matches: 134, Mismatches: 19, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
28 1 0.01
29 43 0.32
30 54 0.40
31 32 0.24
32 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTAGGGGTCAAAATA
Found at i:633484 original size:6 final size:6
Alignment explanation
Indices: 633475--633570 Score: 94
Period size: 6 Copynumber: 16.7 Consensus size: 6
633465 TTTGGACATT
* *
633475 AATTTA AATTTA AATTTA AACTTA AATTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * *
633521 ACTTAA AATTTA AATTT- -ATTATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
633567 AATT
1 AATT
633571 GTGTTGGGCC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
4 3 0.04
5 12 0.17
6 54 0.75
7 3 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:633509 original size:17 final size:17
Alignment explanation
Indices: 633475--633570 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
633465 TTTGGACATT
*
633475 AATTTAAATTTAAATTTA
1 AATTTAAATTT-ATTTTA
*
633493 AACTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
633510 AATTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
633527 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
* ***
633544 AATTTAATTTTAAAATA
1 AATTTAAATTTATTTTA
633561 AATTTAAATT
1 AATTTAAATT
633571 GTGTTGGGCC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
17 56 0.85
18 10 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:633532 original size:23 final size:24
Alignment explanation
Indices: 633475--633538 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 24
633465 TTTGGACATT
633475 AATTTAAATTTAAATTTAAACTTAA
1 AATTTAAATTTAAATTT-AACTTAA
633500 ATTTATTTTAAATTTAAATTT-ACTTAA
1 A---A-TTTAAATTTAAATTTAACTTAA
633527 AATTTAAATTTA
1 AATTTAAATTTA
633539 TTATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
23 10 0.29
24 1 0.03
25 1 0.03
27 7 0.20
28 1 0.03
29 15 0.43
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTTAAATTTAAATTTAACTTAA
Found at i:633564 original size:34 final size:34
Alignment explanation
Indices: 633475--633570 Score: 122
Period size: 34 Copynumber: 2.8 Consensus size: 34
633465 TTTGGACATT
* *
633475 AATTTAAATTTAAATTTAAACTTAAATTTATTTTA
1 AATTTAAATTTAAA-TTAAATTTAAATTTATTATA
*
633510 AATTTAAATTT-ACTTAAAATTTAAATTTATTATA
1 AATTTAAATTTAAATT-AAATTTAAATTTATTATA
* *
633544 AATTTAATTTTAAAATAAATTTAAATT
1 AATTTAAATTTAAATTAAATTTAAATT
633571 GTGTTGGGCC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
33 2 0.04
34 38 0.72
35 13 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (34 bp):
AATTTAAATTTAAATTAAATTTAAATTTATTATA
Found at i:633795 original size:21 final size:21
Alignment explanation
Indices: 633771--633853 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
633761 TTTAACTTTC
633771 TTTAT-ATATTTTTTAAAAATT
1 TTTATAAT-TTTTTTAAAAATT
*
633792 TTTATAATTTTTTTAAAAAAT
1 TTTATAATTTTTTTAAAAATT
633813 TTTATAATTTTTTTAAAAATT
1 TTTATAATTTTTTTAAAAATT
633834 TTTATAATTTTTTTAAAAAT
1 TTTATAATTTTTTTAAAAAT
633854 ATAAATTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
21 57 0.97
22 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATAATTTTTTTAAAAATT
Found at i:633888 original size:21 final size:22
Alignment explanation
Indices: 633771--633882 Score: 135
Period size: 21 Copynumber: 5.1 Consensus size: 22
633761 TTTAACTTTC
633771 TTTAT-ATATTTTTTAAAAAT-T
1 TTTATAAT-TTTTTTAAAAATAT
633792 TTTATAATTTTTTTAAAAA-AT
1 TTTATAATTTTTTTAAAAATAT
633813 TTTATAATTTTTTTAAAAAT-T
1 TTTATAATTTTTTTAAAAATAT
633834 TTTATAATTTTTTTAAAAATAT
1 TTTATAATTTTTTTAAAAATAT
* *
633856 AAATTT-TGATTTTTTTATAAATAT
1 ---TTTATAATTTTTTTAAAAATAT
633880 TTT
1 TTT
633883 GAATTTTAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
21 60 0.73
22 3 0.04
24 16 0.20
25 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
TTTATAATTTTTTTAAAAATAT
Found at i:633889 original size:18 final size:18
Alignment explanation
Indices: 633868--633916 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
633858 ATTTTGATTT
*
633868 TTTTATAAATATTTTGAA
1 TTTTATAAATATTTTCAA
*
633886 TTTTAAAAATTATTTTCAA
1 TTTTATAAA-TATTTTCAA
633905 TTTT-TAAA-ATTT
1 TTTTATAAATATTT
633917 ATTTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
18 11 0.41
19 12 0.44
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATAAATATTTTCAA
Found at i:633899 original size:19 final size:19
Alignment explanation
Indices: 633868--633926 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
633858 ATTTTGATTT
* *
633868 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTAAA
*
633886 TTTTAAAAATTATTTTCAAT
1 TTTTAAAAATTATTTT-AAA
*
633906 TTTTAAAATTTATTTTAAA
1 TTTTAAAAATTATTTTAAA
633925 TT
1 TT
633927 CTTCTTGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 10 0.29
20 16 0.47
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:633911 original size:20 final size:20
Alignment explanation
Indices: 633780--633926 Score: 81
Period size: 21 Copynumber: 7.1 Consensus size: 20
633770 CTTTATATAT
*
633780 TTTTTAAAAATT-TTTATAATT
1 TTTTTAAAAATTATTT-TAA-A
633801 TTTTTAAAAA--ATTTTATAA
1 TTTTTAAAAATTATTTTA-AA
*
633820 TTTTTTTAAAAATT-TTTATAATT
1 --TTTTTAAAAATTATTT-TAA-A
**
633843 TTTTTAAAAATATAAATTTTGATT
1 TTTTTAAAAAT-T--ATTTT-AAA
* *
633867 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTAAA
*
633886 -TTTTAAAAATTATTTTCAA
1 TTTTTAAAAATTATTTTAAA
*
633905 TTTTTAAAATTTATTTTAAA
1 TTTTTAAAAATTATTTTAAA
633925 TT
1 TT
633927 CTTCTTGTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
18 8 0.08
19 10 0.10
20 28 0.28
21 31 0.31
22 6 0.06
23 2 0.02
24 11 0.11
25 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTAAA
Found at i:634722 original size:31 final size:30
Alignment explanation
Indices: 634679--634745 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
634669 TAAACTATTT
*
634679 TTTTGTCCAATTTGGTATTC-AAACTTGACAC
1 TTTT-TCCAATTTGGTA-CCAAAACTTGACAC
*
634710 TTTTTCCTAATTTGGTACCAAAATTTGACAC
1 TTTTTCC-AATTTGGTACCAAAACTTGACAC
634741 TTTTT
1 TTTTT
634746 TTAAGTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (30 bp):
TTTTTCCAATTTGGTACCAAAACTTGACAC
Found at i:635128 original size:3 final size:3
Alignment explanation
Indices: 635120--635160 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
635110 TTAAGCCATT
*
635120 TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T
635161 TTAATCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:635840 original size:23 final size:23
Alignment explanation
Indices: 635796--635840 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
635786 ATTTTTGAGC
635796 ACTTTCTTGAATTAACATTTTTT
1 ACTTTCTTGAATTAACATTTTTT
635819 ACTTCTCTTGAATTAACATTTT
1 ACTT-TCTTGAATTAACATTTT
635841 AGAGGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (23 bp):
ACTTTCTTGAATTAACATTTTTT
Found at i:641526 original size:39 final size:39
Alignment explanation
Indices: 641481--641558 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
641471 CCAAACACGA
641481 ATCTTAAGGAGAATTCTTGGAATCTCCTACGCCAACTAG
1 ATCTTAAGGAGAATTCTTGGAATCTCCTACGCCAACTAG
*
641520 ATCTTAAGGAGAATTCTTGGAATCTCTTACGCCAACTAG
1 ATCTTAAGGAGAATTCTTGGAATCTCCTACGCCAACTAG
641559 GATCAAATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (39 bp):
ATCTTAAGGAGAATTCTTGGAATCTCCTACGCCAACTAG
Found at i:644530 original size:9 final size:10
Alignment explanation
Indices: 644501--644530 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
644491 CAGAAGAAGT
644501 ATGGAGATTA
1 ATGGAGATTA
644511 ATGGAGATTA
1 ATGGAGATTA
644521 ATGG-GATTA
1 ATGGAGATTA
644530 A
1 A
644531 ATTTTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (10 bp):
ATGGAGATTA
Found at i:649413 original size:25 final size:27
Alignment explanation
Indices: 649385--649435 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
649375 TTTAATAGAT
*
649385 AATATTAA-T-AAATTATTTAAAATTA
1 AATATTAATTAAAATTATTAAAAATTA
649410 AATATTAATTAAAATTATTAAAAATT
1 AATATTAATTAAAATTATTAAAAATT
649436 CTCTTACTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 1 0.04
27 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATTAATTAAAATTATTAAAAATTA
Found at i:649956 original size:22 final size:22
Alignment explanation
Indices: 649930--649971 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
649920 AATTGAAACA
649930 TTGAATTTATTCATTAAATCTC
1 TTGAATTTATTCATTAAATCTC
649952 TTGAATTTATTCATTAAATC
1 TTGAATTTATTCATTAAATC
649972 GGTTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (22 bp):
TTGAATTTATTCATTAAATCTC
Found at i:653183 original size:15 final size:16
Alignment explanation
Indices: 653165--653213 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
653155 CTTTTAAAAA
653165 ATTTAAAAATA-TTTT
1 ATTTAAAAATACTTTT
* *
653180 ATTTAATAATATTTTT
1 ATTTAAAAATACTTTT
*
653196 ATCTCAAAAATACTTTT
1 AT-TTAAAAATACTTTT
653213 A
1 A
653214 AAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 10 0.36
16 6 0.21
17 12 0.43
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAAAAATACTTTT
Found at i:654504 original size:118 final size:119
Alignment explanation
Indices: 654292--654565 Score: 444
Period size: 118 Copynumber: 2.3 Consensus size: 119
654282 GAATCTTAGC
*
654292 GGTAGTTAAAATACTAATTAAC-AGAAGGTGCAATTTACGAGTGATAAATATAGTCAAGAACATA
1 GGTAGTTAAAGTACTAATTAACGA-AAGGTGCAATTTACGAGTGATAAATATAGTCAAGAACATA
* * * *
654356 GATCAAGCTTTAGATGGTATGCTATTTATCCGTAGAATCTTAGCTGTAGCTTGAT
65 GATCAAGCTTTAAATGGTATGCTATGTATCCGTAAAATCTTAGCTGCAGCTTGAT
* *
654411 GGTAGTTAAAGTACTAATTAACGAAAGGTGCAATTTACTAGTGAT-AATGTAGTCAAGAACATAG
1 GGTAGTTAAAGTACTAATTAACGAAAGGTGCAATTTACGAGTGATAAATATAGTCAAGAACATAG
654475 ATCAAGCTTTAAATGGTATGCTATGTATCCGTAAAATCTTAGCTGCAGCTTGAT
66 ATCAAGCTTTAAATGGTATGCTATGTATCCGTAAAATCTTAGCTGCAGCTTGAT
* *
654529 GGTAGTTAAAGTACTAATTAACGGAAGGTGTAATTTA
1 GGTAGTTAAAGTACTAATTAACGAAAGGTGCAATTTA
654566 TACTATAGTC
Statistics
Matches: 145, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
118 103 0.71
119 41 0.28
120 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (119 bp):
GGTAGTTAAAGTACTAATTAACGAAAGGTGCAATTTACGAGTGATAAATATAGTCAAGAACATAG
ATCAAGCTTTAAATGGTATGCTATGTATCCGTAAAATCTTAGCTGCAGCTTGAT
Found at i:664183 original size:40 final size:40
Alignment explanation
Indices: 664128--664207 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
664118 TATAATTGTA
664128 CGCATTGTTCTTACCAGCTCTCTTCAATCGTAAACTAACT
1 CGCATTGTTCTTACCAGCTCTCTTCAATCGTAAACTAACT
664168 CGCATTGTTCTTACCAGCTCTCTTCAATCGTAAACTAACT
1 CGCATTGTTCTTACCAGCTCTCTTCAATCGTAAACTAACT
664208 TTTCCAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (40 bp):
CGCATTGTTCTTACCAGCTCTCTTCAATCGTAAACTAACT
Found at i:667372 original size:29 final size:28
Alignment explanation
Indices: 667340--667442 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 28
667330 ACTTTTTCTT
*
667340 AATTTGGTACCTAAACTTTTTTTGGACTC
1 AATTTGGTACCTAAACTTTTTTT-AACTC
* * **
667369 AATTTAGTACCCAAACTTGGTATTTTTTCT-
1 AATTTGGTACCTAAACTT--T-TTTTAACTC
* *
667399 AATTTGGTACCTAAGCTTTTTTTAAATTC
1 AATTTGGTACCTAAACTTTTTTT-AACTC
667428 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
667443 TTTATTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
27 4 0.07
28 2 0.03
29 30 0.52
30 15 0.26
31 3 0.05
32 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTAACTC
Found at i:667686 original size:30 final size:31
Alignment explanation
Indices: 667650--667783 Score: 96
Period size: 31 Copynumber: 4.4 Consensus size: 31
667640 GGACCCCAAA
* *
667650 AAGTTTAAGTACCAACTTA-AAAAAAGTGTT
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
* * * *
667680 AAGTTTAGGTATCAAATTAGGAAACAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
* * ***
667711 AAGTTTGAGTACCAAATTGGACCAAAAA--AAA
1 AAGTTTAAGTACCAAATTAGA--AAAAAGTGTC
*
667742 AAGTTT-AGATACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAG-TACCAAATTAGAAAAAAGTGTC
*
667773 AAGTTCAAGTA
1 AAGTTTAAGTA
667784 TTAAATGTTA
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
29 5 0.07
30 18 0.24
31 47 0.62
32 2 0.03
33 4 0.05
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:679172 original size:22 final size:23
Alignment explanation
Indices: 679131--679178 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
679121 GAAAAAACTT
679131 TTAATTTTTAAAAATATTTT-TA
1 TTAATTTTTAAAAATATTTTATA
* * *
679153 TTAATTTTTAATATTTTTTTATA
1 TTAATTTTTAAAAATATTTTATA
679176 TTA
1 TTA
679179 TGACATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAATTTTTAAAAATATTTTATA
Found at i:683119 original size:2 final size:2
Alignment explanation
Indices: 683112--683136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
683102 TAAGTTGGTT
683112 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
683137 GTGTGTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:683879 original size:31 final size:31
Alignment explanation
Indices: 683830--683895 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
683820 CTTTTCAGTC
*
683830 CAATAACTTTAATAAAAACATTT-GAATAGTT
1 CAATAACTTAAATAAAAAC-TTTCGAATAGTT
* *
683861 CAATTACTTAAATGAAAACTTTCGAATAGTT
1 CAATAACTTAAATAAAAACTTTCGAATAGTT
683892 CAAT
1 CAAT
683896 GATCGAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTCGAATAGTT
Found at i:685766 original size:45 final size:45
Alignment explanation
Indices: 685714--685806 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
685704 ACCCGCTACT
685714 ACTCCTGTGAGTAAACCTAAGTCACCGGCTCCCACTGCTGCTCCA
1 ACTCCTGTGAGTAAACCTAAGTCACCGGCTCCCACTGCTGCTCCA
685759 ACTCCTGTGAGTAAACCTAAGTCACCGGCTCCCACTGCTGCTCCA
1 ACTCCTGTGAGTAAACCTAAGTCACCGGCTCCCACTGCTGCTCCA
685804 ACT
1 ACT
685807 GCTTCACCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (45 bp):
ACTCCTGTGAGTAAACCTAAGTCACCGGCTCCCACTGCTGCTCCA
Found at i:685821 original size:15 final size:15
Alignment explanation
Indices: 685801--685847 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
685791 CACTGCTGCT
*
685801 CCAACTGCTTCACCA
1 CCAACTTCTTCACCA
685816 CCAACTTCTTCACCA
1 CCAACTTCTTCACCA
685831 CCAACTTCTTCACCA
1 CCAACTTCTTCACCA
685846 CC
1 CC
685848 GGCTGCGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.26, C:0.49, G:0.02, T:0.23
Consensus pattern (15 bp):
CCAACTTCTTCACCA
Found at i:686091 original size:6 final size:6
Alignment explanation
Indices: 686080--686104 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
686070 ACCAGCTCCA
686080 AGCAAG AGCAAG AGCAAG AGCAAG A
1 AGCAAG AGCAAG AGCAAG AGCAAG A
686105 AGAAGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGCAAG
Found at i:689428 original size:18 final size:18
Alignment explanation
Indices: 689407--689442 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
689397 ATTATATAAT
689407 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
689425 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
689443 TTTTTGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Done.