Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003806.1 Hibiscus syriacus cultivar Beakdansim tig00008146_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1419252
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:812032 original size:31 final size:31
Alignment explanation
Indices: 811994--812057 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
811984 TTTTAGCATT
*
811994 TTATTATTATTA-TTTATTTTATATTTTTTAC
1 TTATTATTATTATTTTATTTTAT-TTTATTAC
*
812025 TTATTATTTTTATTTTATTTTATTTTATTAC
1 TTATTATTATTATTTTATTTTATTTTATTAC
812056 TT
1 TT
812058 TTAGAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (31 bp):
TTATTATTATTATTTTATTTTATTTTATTAC
Found at i:812042 original size:5 final size:5
Alignment explanation
Indices: 811991--812053 Score: 56
Period size: 5 Copynumber: 11.6 Consensus size: 5
811981 TATTTTTAGC
*
811991 ATTTT ATTATT ATTATTT ATTTT ATATT -TTTT ACTTATT ATTTTT ATTTT
1 ATTTT ATT-TT A-T-TTT ATTTT ATTTT ATTTT A-TT-TT A-TTTT ATTTT
812041 ATTTT ATTTT ATT
1 ATTTT ATTTT ATT
812054 ACTTTTAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 3 0.06
5 27 0.55
6 9 0.18
7 9 0.18
8 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:813046 original size:21 final size:22
Alignment explanation
Indices: 812996--813047 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
812986 GTCGAGGGTT
*
812996 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
813018 CCTATGTGGTCATTCGGGACAAA
1 -CTATGTGGTCATTCGGGACAAA
813041 -TATGTGG
1 CTATGTGG
813048 CACTTCAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 7 0.25
23 21 0.75
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:816238 original size:18 final size:18
Alignment explanation
Indices: 816215--816254 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
816205 GTTATCCGAA
816215 GTGGCATTTCTTGGACAT
1 GTGGCATTTCTTGGACAT
816233 GTGGCATTTCTTGGACAT
1 GTGGCATTTCTTGGACAT
816251 GTGG
1 GTGG
816255 TTTTTGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.38
Consensus pattern (18 bp):
GTGGCATTTCTTGGACAT
Found at i:819951 original size:21 final size:22
Alignment explanation
Indices: 819925--819973 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
819915 TCGAGGGTTC
819925 TATGTGGTC-CTTCGG-GACAAA-
1 TATGTGG-CACTTCGGTG-CAAAT
819946 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
819968 TATGTG
1 TATGTG
819974 AGCAGTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:820836 original size:2 final size:2
Alignment explanation
Indices: 820831--820863 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
820821 TCTCTCTCTC
820831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
820864 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:824103 original size:21 final size:20
Alignment explanation
Indices: 824066--824105 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
824056 AACGAAAATT
* *
824066 AAACTTTAATATTAAAATAC
1 AAACATTAATATAAAAATAC
824086 AAACATTATATATAAAAATA
1 AAACATTA-ATATAAAAATA
824106 AATACGACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
AAACATTAATATAAAAATAC
Found at i:824685 original size:28 final size:29
Alignment explanation
Indices: 824641--824696 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
824631 ATTGCCATTG
*
824641 TTTTCAAGCACTGGCTCGA-CGATATAATA
1 TTTTCAAGCACTAGCTCGATC-ATATAATA
824670 TTTT-AAGCACTAGCTCGATCATATAAT
1 TTTTCAAGCACTAGCTCGATCATATAAT
824697 GTAAACAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (29 bp):
TTTTCAAGCACTAGCTCGATCATATAATA
Found at i:826410 original size:2 final size:2
Alignment explanation
Indices: 826403--826433 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
826393 ATTGTCAGTC
826403 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
826434 GTGCTGCATT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:830133 original size:27 final size:28
Alignment explanation
Indices: 830101--830166 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
830091 ATTCAAAAAA
830101 TTTAATT-CGTAGTCACTTTTGTTTCGT
1 TTTAATTACGTAGTCACTTTTGTTTCGT
* *
830128 TTTAATTAAGATGTGGTCACTTTTGTTTCGT
1 TTTAATT---ACGTAGTCACTTTTGTTTCGT
830159 TTTAATTA
1 TTTAATTA
830167 AGATGTGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 7 0.21
28 1 0.03
31 25 0.76
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.55
Consensus pattern (28 bp):
TTTAATTACGTAGTCACTTTTGTTTCGT
Found at i:830149 original size:31 final size:31
Alignment explanation
Indices: 830112--830179 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
830102 TTAATTCGTA
830112 GTCACTTTTGTTTCGTTTTAATTAAGATGTG
1 GTCACTTTTGTTTCGTTTTAATTAAGATGTG
830143 GTCACTTTTGTTTCGTTTTAATTAAGATGTG
1 GTCACTTTTGTTTCGTTTTAATTAAGATGTG
830174 GTCACT
1 GTCACT
830180 GTGATGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (31 bp):
GTCACTTTTGTTTCGTTTTAATTAAGATGTG
Found at i:830219 original size:38 final size:38
Alignment explanation
Indices: 830168--830249 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
830158 TTTTAATTAA
* *
830168 GATGTGGTCACTGTGATGTTAACTTATGTTATTTTGAT
1 GATGTGATCACTGTGACGTTAACTTATGTTATTTTGAT
*
830206 GATGTGATCACTGTGACGTTAACTTTTGTTATTTTGAT
1 GATGTGATCACTGTGACGTTAACTTATGTTATTTTGAT
*
830244 AATGTG
1 GATGTG
830250 GCACGTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (38 bp):
GATGTGATCACTGTGACGTTAACTTATGTTATTTTGAT
Found at i:831025 original size:8 final size:8
Alignment explanation
Indices: 831007--831054 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
830997 TGGATTAAGA
831007 AAAAAATAT
1 AAAAAA-AT
831016 AAAAAAAT
1 AAAAAAAT
* *
831024 AATAAAGT
1 AAAAAAAT
831032 AAATAAAAT
1 AAA-AAAAT
831041 AAAAAAAT
1 AAAAAAAT
831049 AAAAAA
1 AAAAAA
831055 TGTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 21 0.62
9 13 0.38
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:831044 original size:22 final size:22
Alignment explanation
Indices: 831010--831051 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
831000 ATTAAGAAAA
*
831010 AAATATAAAAAAATAATAAAGT
1 AAATATAAAAAAAAAATAAAGT
831032 AAATA-AAATAAAAAAATAAA
1 AAATATAAA-AAAAAAATAAA
831052 AAATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATATAAAAAAAAAATAAAGT
Found at i:833830 original size:84 final size:84
Alignment explanation
Indices: 832562--833818 Score: 1524
Period size: 84 Copynumber: 15.0 Consensus size: 84
832552 TTATTGACAT
* * * * * * * *
832562 ATAACCCTTCTTGCCTTGAGCTATGTTGTAAATTTAATTTGCCTCTGAGTTGAATGTAATCGAAC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
832627 TCGACA---ATTTTGTTGACAG
64 TCGA-AGGTCTTTTGTTGGCAG
* * * * * * * *
832646 ATAACCCTTCTTTCTTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATCGAAC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * *
832711 TCGAAGGTC-TTTGATGACAA
64 TCGAAGGTCTTTTGTTGGCAG
** * ** * * * *
832731 ATAACCCTTCTCACCTTGAGTTATGCTATAAATTTGATTTGCCTCTGAGTTGAATGTAATCG-A-
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
832794 --GAAGGTC-TTTGATGACAG
64 TCGAAGGTCTTTTGTTGGCAG
** * * ** * *
832812 ATAACCCTTCTCACATTGAGTTATGCTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAAC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
832877 TCGAAGGTCTTTTGTTGGCAG
64 TCGAAGGTCTTTTGTTGGCAG
* * **
832898 ATAACCATTCTTGCCTTGAGATATGCTGCAAATAATGTTTCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
832963 GAAGGTCTTCTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * * *
832982 ATAGCCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGCGTAATAGAAATC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
833047 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * * *
833066 ATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTTCTTTTTAGCTGAGTATAATCAAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
833131 GAAGGACTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * *
833150 ATAACCTTTCTTGCCTTGAGATATGCTGTAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
833215 AAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * *
833234 ATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGTTGAATGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
833299 GAAGGTTTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
833318 ATAACCCTTCATGGCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
833383 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
833402 ATAACCCTTCTTGCCTTGAGATATACTGCAAATGATGTGCCTTTGACCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
833467 GAAGGTCATTTGTTGGAAG
66 GAAGGTCTTTTGTTGGCAG
*
833486 ATAACCCTTCTTGCCTTGTGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
833551 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * ** * * *
833570 ATAGCCCTTCTTTCCTTTTGATATGCTACAAATGATGTGCATTTGAGATGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
833635 GAAGGTCTTTTGTTGGCAA
66 GAAGGTCTTTTGTTGGCAG
* * *
833654 ATAACCCTTCTTACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
833719 GAAGGTCTTTTTTTGGAAG
66 GAAGGTCTTTTGTTGGCAG
* * * * *
833738 ATAGCCCTTCTTACCTTGAGCTATGCTGCAAATAATGTTCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
833803 GAAGGTGTTTTGTTGG
66 GAAGGTCTTTTGTTGG
833819 TAGGTAGCCC
Statistics
Matches: 1049, Mismatches: 116, Indels: 16
0.89 0.10 0.01
Matches are distributed among these distances:
81 75 0.07
82 1 0.00
83 1 0.00
84 865 0.82
85 73 0.07
86 34 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (84 bp):
ATAACCCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAG
Found at i:834788 original size:10 final size:12
Alignment explanation
Indices: 834764--834795 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
834754 TGTTGACCTC
834764 CTTTGACCAGAA
1 CTTTGACCAGAA
834776 CTTTGACC-G-A
1 CTTTGACCAGAA
834786 CTTTGACCAG
1 CTTTGACCAG
834796 CTATTAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (12 bp):
CTTTGACCAGAA
Found at i:841821 original size:13 final size:13
Alignment explanation
Indices: 841803--841839 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
841793 CGACCCATTT
* *
841803 ACCCGTTTACCTG
1 ACCCGTTGACCCG
841816 ACCCGTTGACCCG
1 ACCCGTTGACCCG
841829 ACCCGTTGACC
1 ACCCGTTGACC
841840 GTTGACCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.43, G:0.19, T:0.22
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:841908 original size:28 final size:28
Alignment explanation
Indices: 841847--841921 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
841837 ACCGTTGACC
*** *
841847 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCT-GGAATTAATTCGAAATG
*
841876 TGTGCTATTCTGGAATTAATTCGAAATG
1 GGTGCTATTCTGGAATTAATTCGAAATG
*
841904 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGG-AATT
841922 TTTTAAAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 24 0.63
29 14 0.37
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.44
Consensus pattern (28 bp):
GGTGCTATTCTGGAATTAATTCGAAATG
Found at i:843463 original size:84 final size:84
Alignment explanation
Indices: 843360--843679 Score: 426
Period size: 84 Copynumber: 3.8 Consensus size: 84
843350 TTACATTTTC
* * * *
843360 GCCTTGAGCTATGCTACAAATGATATGCCTTTAAGCTAAGTGTAATCGAACTCGAAGGTATTTTG
1 GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG
* *
843425 TTGGCAGATATCCCTTATT
66 TTGGCAGATAGCCCTTCTT
* *
843444 GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTTTTTTG
1 GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG
843509 TTGGCAGATAGCCCTTCTT
66 TTGGCAGATAGCCCTTCTT
* * * *
843528 GCCTTGAGCTAGGCTGCAAATGATGTGACTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG
** * *
843593 TTTCCAGGTAGCTCTTCTCT
66 TTGGCAGATAGCCCTTCT-T
** ** * *
843613 -TATTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAATGTCTTTTG
1 GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG
843677 TTG
66 TTG
843680 AAGGTGCTCT
Statistics
Matches: 211, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
84 210 1.00
85 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (84 bp):
GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG
TTGGCAGATAGCCCTTCTT
Found at i:847096 original size:265 final size:265
Alignment explanation
Indices: 846623--847158 Score: 1000
Period size: 265 Copynumber: 2.0 Consensus size: 265
846613 AATTCACACG
* *
846623 AAGACATAAGGTATATGAATCTCGAAGGTTACTTGCTAGGCATCTAGGCCCACACGGAGAATAAA
1 AAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAAGCATCTAGGCCCACACGGAGAATAAA
* *
846688 TTCTCACGAAGGCGTCGTTTTTACCCCCACTTAAAAGGGTTCAGAGCTCGGGTATAGAGCCTTAG
66 TTCTCACGAAGGCATCGTTTTTACCCCCACTTAAAAGAGTTCAGAGCTCGGGTATAGAGCCTTAG
* *
846753 ATGAAAATAGCTTAGTACGCTGAAACCATTGAAAGAAAACGTCAATACAACTATTTATTTGAAAA
131 ATGAAAAAAGCTTAGTACGCTGAAACCATTGAAAGAAAACGTCAATACAACTATTTATTTAAAAA
846818 AAATAATCAAAGATAAATAATTGGAATCGAATAAATAAATTAAAATTTAAACTTGCAATTTTCAC
196 AAATAATCAAAGATAAATAATTGGAATCGAATAAATAAATTAAAATTTAAACTTGCAATTTTCAC
846883 TCAAA
261 TCAAA
846888 AAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAAGCATCTAGGCCCACACGGAGAATAAA
1 AAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAAGCATCTAGGCCCACACGGAGAATAAA
846953 TTCTCACGAAGGCATCGTTTTTACCCCCACTTAAAAGAGTTCAGAGCTCGGGTATAGAGCCTTAG
66 TTCTCACGAAGGCATCGTTTTTACCCCCACTTAAAAGAGTTCAGAGCTCGGGTATAGAGCCTTAG
*
847018 ATGAAAAAAGCTTAGTACGCTGAAACCATTGAAAGAAAACGTCAGTACAACTATTTATTTAAAAA
131 ATGAAAAAAGCTTAGTACGCTGAAACCATTGAAAGAAAACGTCAATACAACTATTTATTTAAAAA
*
847083 AAATAATCAAAGATAAATAATTGGAATCGAATAAATAAATTAAAATTTAAACTTGCAATTTTCGC
196 AAATAATCAAAGATAAATAATTGGAATCGAATAAATAAATTAAAATTTAAACTTGCAATTTTCAC
847148 TCAAA
261 TCAAA
847153 AAGACA
1 AAGACA
847159 ACCGGAAATT
Statistics
Matches: 263, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
265 263 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (265 bp):
AAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAAGCATCTAGGCCCACACGGAGAATAAA
TTCTCACGAAGGCATCGTTTTTACCCCCACTTAAAAGAGTTCAGAGCTCGGGTATAGAGCCTTAG
ATGAAAAAAGCTTAGTACGCTGAAACCATTGAAAGAAAACGTCAATACAACTATTTATTTAAAAA
AAATAATCAAAGATAAATAATTGGAATCGAATAAATAAATTAAAATTTAAACTTGCAATTTTCAC
TCAAA
Found at i:847650 original size:15 final size:15
Alignment explanation
Indices: 847614--847664 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
847604 TGGATTAAGA
*
847614 ATAAAAAATA-AAGT
1 ATAAAAAATATAAAT
847628 A-AAGAAAATATAAAT
1 ATAA-AAAATATAAAT
847643 ATAAAAAATATAAAT
1 ATAAAAAATATAAAT
847658 ATAAAAA
1 ATAAAAA
847665 TATGTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 2 0.06
14 7 0.21
15 22 0.67
16 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
ATAAAAAATATAAAT
Found at i:848810 original size:42 final size:42
Alignment explanation
Indices: 848758--849015 Score: 401
Period size: 42 Copynumber: 6.2 Consensus size: 42
848748 TGATGTTGAT
* * *
848758 TTTA-TTTAGACTTATTGAGGCTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
* *
848799 TTTATTTTAGACTTATTGAGACTTAATTGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
848841 TTTATTTTAGACTTATTGACACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
* *
848883 TTTATTTTAGACTTATTGAGATTTAATAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
848925 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
* *
848967 TTTATTTTAGACTTCTTGAGATTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
*
849009 TGTATTT
1 TTTATTT
849016 ACTTGTTTAT
Statistics
Matches: 199, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
41 4 0.02
42 195 0.98
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
Found at i:863268 original size:8 final size:8
Alignment explanation
Indices: 863255--863305 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
863245 TGGTCCGGAC
863255 TTATATTA
1 TTATATTA
863263 TTATATTA
1 TTATATTA
*
863271 TTATATTCGT
1 TTATATT--A
*
863281 TTTTATTA
1 TTATATTA
863289 TTATATTA
1 TTATATTA
863297 TTATTATTA
1 TTA-TATTA
863306 CAAAACCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 25 0.69
9 5 0.14
10 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TTATATTA
Found at i:863326 original size:24 final size:23
Alignment explanation
Indices: 863299--863354 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
863289 TTATATTATT
863299 ATTATTACAAAACCCGAAGGCCC
1 ATTATTACAAAACCCGAAGGCCC
**
863322 AATTACAACAAAACCCGAAGGCCC
1 -ATTATTACAAAACCCGAAGGCCC
863346 ATT-TTACAA
1 ATTATTACAA
863355 GTCCAACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.14
23 3 0.11
24 21 0.75
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.18
Consensus pattern (23 bp):
ATTATTACAAAACCCGAAGGCCC
Found at i:865231 original size:20 final size:20
Alignment explanation
Indices: 865208--865263 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
865198 TTATGAATAT
865208 TGAACAGTACCCGTGAACAG
1 TGAACAGTACCCGTGAACAG
865228 TGAACA--A----T-AACAG
1 TGAACAGTACCCGTGAACAG
*
865241 TGGACAGTACCCGTGAACAG
1 TGAACAGTACCCGTGAACAG
865261 TGA
1 TGA
865264 GAGAATCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 14
0.63 0.05 0.33
Matches are distributed among these distances:
13 10 0.37
14 1 0.04
15 1 0.04
18 1 0.04
19 1 0.04
20 13 0.48
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (20 bp):
TGAACAGTACCCGTGAACAG
Found at i:865795 original size:24 final size:24
Alignment explanation
Indices: 865768--865837 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
865758 CCATTTATCT
865768 CATAAGCTCGTAAGCTTATTTTAC
1 CATAAGCTCGTAAGCTTATTTTAC
*
865792 CATATA-CT--T-A-C-CATTTATAC
1 CATA-AGCTCGTAAGCTTATTT-TAC
865812 CATAAGCTCGTAAGCTTATTTTAC
1 CATAAGCTCGTAAGCTTATTTTAC
865836 CA
1 CA
865838 ATATACTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
19 5 0.14
20 10 0.28
21 1 0.03
22 2 0.06
23 1 0.03
24 12 0.33
25 5 0.14
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (24 bp):
CATAAGCTCGTAAGCTTATTTTAC
Found at i:865816 original size:44 final size:45
Alignment explanation
Indices: 865708--865876 Score: 236
Period size: 44 Copynumber: 3.8 Consensus size: 45
865698 ATACAATATT
* * *
865708 TTACCATTTATTAACCGTAAGCTCGTAAGTTTATTTTACCAAAATAC
1 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAATATAC
865755 TTACCATTTAT-CTCATAAGCTCGTAAGCTTATTTTACC-ATATAC
1 TTACCATTTATAC-CATAAGCTCGTAAGCTTATTTTACCAATATAC
865799 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
865844 TTTCCA-TTATTCCATAAGCTCGTAAGCATATTT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTT
865877 GCATACTTAC
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
44 67 0.59
45 35 0.31
46 1 0.01
47 10 0.09
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:865819 original size:89 final size:90
Alignment explanation
Indices: 865708--865899 Score: 263
Period size: 89 Copynumber: 2.2 Consensus size: 90
865698 ATACAATATT
* *
865708 TTACCATTTATTAACCGTAAGCTCGTAAGTTTATTTTACCAAAATACTTACCATT-TATCTCATA
1 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTAT-TC-CATA
*
865772 AGCTCGTAAGCTTATTTTACCATATAC
64 AGCTCGTAAGCATATTTTACCATATAC
* *
865799 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTTCCATTATTCCATAAG
1 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCATAAG
*
865862 CTCGTAAGCATA-TTT-GC--ATAC
66 CTCGTAAGCATATTTTACCATATAC
865883 TTACCATTTATTAACCA
1 TTACCATTTATTAACCA
865900 ATAAACCATA
Statistics
Matches: 92, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
84 14 0.15
85 1 0.01
86 5 0.05
87 3 0.03
88 17 0.18
89 40 0.43
90 2 0.02
91 10 0.11
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (90 bp):
TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCATAAG
CTCGTAAGCATATTTTACCATATAC
Found at i:872587 original size:123 final size:123
Alignment explanation
Indices: 872368--872615 Score: 478
Period size: 123 Copynumber: 2.0 Consensus size: 123
872358 TTGACAGTGG
* *
872368 TGAATTTAGAAAGAAACCACCAATGAAAAAGAAGGAAAGTGAGGTAAATCATGAGAGGAAATATG
1 TGAATTTAGAAAGAAACCACCAATAAAAAAGAAGGAAAGTGACGTAAATCATGAGAGGAAATATG
872433 AATCCAATAATATCATGGTCTCTCGACCTCAGGATATAGGATCCTCTACACAAAACCC
66 AATCCAATAATATCATGGTCTCTCGACCTCAGGATATAGGATCCTCTACACAAAACCC
872491 TGAATTTAGAAAGAAACCACCAATAAAAAAGAAGGAAAGTGACGTAAATCATGAGAGGAAATATG
1 TGAATTTAGAAAGAAACCACCAATAAAAAAGAAGGAAAGTGACGTAAATCATGAGAGGAAATATG
872556 AATCCAATAATATCATGGTCTCTCGACCTCAGGATATAGGATCCTCTACACAAAACCC
66 AATCCAATAATATCATGGTCTCTCGACCTCAGGATATAGGATCCTCTACACAAAACCC
872614 TG
1 TG
872616 CCAAGCAAGG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (123 bp):
TGAATTTAGAAAGAAACCACCAATAAAAAAGAAGGAAAGTGACGTAAATCATGAGAGGAAATATG
AATCCAATAATATCATGGTCTCTCGACCTCAGGATATAGGATCCTCTACACAAAACCC
Found at i:886530 original size:43 final size:43
Alignment explanation
Indices: 886446--886549 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
886436 GGCCATTCAT
* * **
886446 GATTTCAAATCCACGACGGAGGATATCATATCCACGGATCCAC
1 GATTTCAACTCCACGACGGAGGATATCATACCCACACATCCAC
* * * *
886489 GATTTCAACTCCACGATGGAGGATATCGTGCCCACACATCCAT
1 GATTTCAACTCCACGACGGAGGATATCATACCCACACATCCAC
* *
886532 GGTTTCAACTTCACGACG
1 GATTTCAACTCCACGACG
886550 AAGGGAATCG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
GATTTCAACTCCACGACGGAGGATATCATACCCACACATCCAC
Found at i:886807 original size:335 final size:335
Alignment explanation
Indices: 886190--886807 Score: 1029
Period size: 335 Copynumber: 1.8 Consensus size: 335
886180 ACGAATGGGT
* *
886190 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTATAAACAAGCAGCATTCATCTCTAGATTG
1 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACAAACAAGCAGCATCCATCTCTAGATTG
* * *
886255 GATTTCAACTTCACGACGAAGGATATTCAACTTAAAGAAGGAGTGGTTGTCAATAAACTTTCCAG
66 GATTTCAACTTCACGACAAAGGATATTCAACTCAAAGAAGGAGTGGATGTCAATAAACTTTCCAG
* * * *
886320 TTTCAGAGTCAATTTTAACTTTACAGTGAAGGATATTGGACTCAAAACAGCGCAAGCTTGGATTT
131 TTTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAAACAACACAAGCTTGGATTT
* * * *
886385 CAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAAATTCATGATGAAGGGGCCATTCATGATT
196 CAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAAATTCACGACGAAGGGGCCATCCATGATT
886450 TCAAATCCACGACGGAGGATATCATATCCACGGATCCACGATTTCAACTCCACGATGGAGGATAT
261 TCAAATCCACGACGGAGGATATCATATCCACGGATCCACGATTTCAACTCCACGATGGAGGATAT
886515 CGTGCCCACA
326 CGTGCCCACA
* * *
886525 CATCCATGGTTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAGCATCCATTTCTAGATTG
1 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACAAACAAGCAGCATCCATCTCTAGATTG
* * *
886590 GATTTCAACTTCACTACAAAGGATATTCAACTCAAAGAAGGAGTGGATGTCAATAAATTTTCTAG
66 GATTTCAACTTCACGACAAAGGATATTCAACTCAAAGAAGGAGTGGATGTCAATAAACTTTCCAG
886655 TTTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAAACAACACAAGCTTGGATTT
131 TTTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAAACAACACAAGCTTGGATTT
* *
886720 TAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCATGATT
196 CAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAAATTCACGACGAAGGGGCCATCCATGATT
* *
886785 TCAACTCCACGATGGAGGATATC
261 TCAAATCCACGACGGAGGATATC
886808 GTGCCCACAC
Statistics
Matches: 260, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
335 260 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (335 bp):
CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACAAACAAGCAGCATCCATCTCTAGATTG
GATTTCAACTTCACGACAAAGGATATTCAACTCAAAGAAGGAGTGGATGTCAATAAACTTTCCAG
TTTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAAACAACACAAGCTTGGATTT
CAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAAATTCACGACGAAGGGGCCATCCATGATT
TCAAATCCACGACGGAGGATATCATATCCACGGATCCACGATTTCAACTCCACGATGGAGGATAT
CGTGCCCACA
Found at i:887394 original size:24 final size:24
Alignment explanation
Indices: 887362--887411 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
887352 GCTCTGCCGC
*
887362 CCGACCACTAATCCATGTTTCAAG
1 CCGACCACTAATCCATGTTCCAAG
*
887386 CCGACCACTAATCCCTGTTCCAAG
1 CCGACCACTAATCCATGTTCCAAG
887410 CC
1 CC
887412 ACTCAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (24 bp):
CCGACCACTAATCCATGTTCCAAG
Found at i:891063 original size:45 final size:45
Alignment explanation
Indices: 890848--891065 Score: 255
Period size: 45 Copynumber: 4.9 Consensus size: 45
890838 AACATAACAT
890848 CTTTTCTGTTGATAATGCACCCATATGCATTTCAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* * * * *
890893 CTTTTATGTT-AAAATGTACCCATATACATCTCAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* ** * *
890937 CTTTTCTGTTGATAATGTAATCATATACATTTCTACTCTA-TCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGT-ATA
* *
890982 CTTTTCTGTTGATAATGCACTCATAAGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* *
891027 CTTTTCTATTGATAATGCACCCCTATGCATTTCAACTCT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
891066 GGCATTAGTT
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
44 40 0.27
45 107 0.72
46 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:891632 original size:22 final size:22
Alignment explanation
Indices: 891606--891647 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
891596 GAATTGATAC
891606 CCCTACTATGGTATCGATACTA
1 CCCTACTATGGTATCGATACTA
891628 CCCTACTATGGTATCGATAC
1 CCCTACTATGGTATCGATAC
891648 CCCTTACCAG
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:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (22 bp):
CCCTACTATGGTATCGATACTA
Found at i:891742 original size:22 final size:21
Alignment explanation
Indices: 891691--891763 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 21
891681 ATGTGGCCCA
891691 GTATCGATACCCATATCACAG
1 GTATCGATACCCATATCACAG
*
891712 GTATTGATA-CCACTAT-ACTATG
1 GTATCGATACCCA-TATCAC-A-G
*
891734 GTATCGATACTCC-TAT-A-GG
1 GTATCGATAC-CCATATCACAG
891753 GTATCGATACC
1 GTATCGATACC
891764 AAAATTAGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 1 0.02
19 11 0.25
20 5 0.11
21 12 0.27
22 13 0.30
24 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCATATCACAG
Found at i:893955 original size:35 final size:35
Alignment explanation
Indices: 893895--894234 Score: 369
Period size: 35 Copynumber: 10.0 Consensus size: 35
893885 GAGTAATAAA
* *
893895 GCAATTCAGCCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* *
893930 GCAATCCAACCTTTACAGCAA-AGTAGT--A--AA-
1 GCAATCCAACCTTCACA-AAAGAGTAGTGAAGCAAT
** *
893960 GCAATTTAGCCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* * *
893995 GCAATCCAATCTTTATAAAAGAGTAGTGAAGCAAT
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* *
894030 GCAATCCAACCTTCACAAAAGAGTAGTGAAACAAC
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* *
894065 GCAATCCAATCTTCACAAAAGAGTAGTGAAACAAT
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
*
894100 GCAATCCAACCTTCACAAAAGAGTATTGAAGCAAT
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* * * *
894135 GCAATCCAACCTTTATAGAATAGTAGT--A--AA-
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* * *
894165 GTAATACAACCTTCACAAAAGAGTAGTGAAGCAAA
1 GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
* *
894200 GCAATCAAAGCCTTCACATAAGAGTAGTGAAGCAA
1 GCAATCCAA-CCTTCACAAAAGAGTAGTGAAGCAA
894235 ATCAATCTCA
Statistics
Matches: 252, Mismatches: 40, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.01
30 40 0.16
31 4 0.02
32 2 0.01
33 2 0.01
34 4 0.02
35 172 0.68
36 26 0.10
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (35 bp):
GCAATCCAACCTTCACAAAAGAGTAGTGAAGCAAT
Found at i:893985 original size:30 final size:30
Alignment explanation
Indices: 893856--893994 Score: 100
Period size: 30 Copynumber: 4.5 Consensus size: 30
893846 TTTACAGAAA
* * * ***
893856 AGTAGTAAAGCAATTCATCATTTACGGTAG
1 AGTAGTAAAGCAATTCAGCCTTCACAAAAG
*
893886 AGTAATAAAGCAATTCAGCCTTCACAAAAG
1 AGTAGTAAAGCAATTCAGCCTTCACAAAAG
* * * *
893916 AGTAGTGAAGCAATGCAATCCAACCTTTACAGCAA-
1 AGTAGT--A--AA-GCAATTCAGCCTTCACA-AAAG
*
893951 AGTAGTAAAGCAATTTAGCCTTCACAAAAG
1 AGTAGTAAAGCAATTCAGCCTTCACAAAAG
*
893981 AGTAGTGAAGCAAT
1 AGTAGTAAAGCAAT
893995 GCAATCCAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
29 2 0.02
30 54 0.64
31 2 0.02
32 1 0.01
33 1 0.01
34 2 0.02
35 20 0.24
36 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (30 bp):
AGTAGTAAAGCAATTCAGCCTTCACAAAAG
Found at i:894411 original size:3 final size:3
Alignment explanation
Indices: 894403--894453 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
894393 TCTGGACTTA
*
894403 TAT TAT TA- TAT TAT TA- TAT TCAT TTT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
894446 TAT TAT TA
1 TAT TAT TA
894454 CAAAACTCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:894451 original size:20 final size:19
Alignment explanation
Indices: 894403--894451 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
894393 TCTGGACTTA
894403 TATTATTATATTATTATAT
1 TATTATTATATTATTATAT
*
894422 TCATTTTTATATTATTATTAT
1 T-ATTATTATATTATTA-TAT
894443 TATTATTAT
1 TATTATTAT
894452 TACAAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.81
21 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATTATATTATTATAT
Found at i:894549 original size:24 final size:24
Alignment explanation
Indices: 894453--894534 Score: 146
Period size: 24 Copynumber: 3.4 Consensus size: 24
894443 TATTATTATT
*
894453 ACAAAACTCGAAGGCCTAGTTACA
1 ACAAAACTCGAAGGCCCAGTTACA
*
894477 ACAAAACCCGAAGGCCCAGTTACA
1 ACAAAACTCGAAGGCCCAGTTACA
894501 ACAAAACTCGAAGGCCCAGTTACA
1 ACAAAACTCGAAGGCCCAGTTACA
894525 ACAAAACTCG
1 ACAAAACTCG
894535 GAGCCCATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.12
Consensus pattern (24 bp):
ACAAAACTCGAAGGCCCAGTTACA
Found at i:903516 original size:28 final size:28
Alignment explanation
Indices: 903485--903569 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
903475 AACTCTGTTT
*
903485 ATATTATGTCGTCGATCTAGTGCTTTAA
1 ATATTATGTCGTCGATCTAGTGCTTGAA
*
903513 ATATTATGTCGTTGAGT-TAGTGCTTGAA
1 ATATTATGTCGTCGA-TCTAGTGCTTGAA
* * *
903541 ATATTATATCGTCGAGCCAGTGCTTGAA
1 ATATTATGTCGTCGATCTAGTGCTTGAA
903569 A
1 A
903570 ATAACGACGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 48 0.98
29 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (28 bp):
ATATTATGTCGTCGATCTAGTGCTTGAA
Found at i:908364 original size:19 final size:19
Alignment explanation
Indices: 908340--908378 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
908330 TATAGTACTA
*
908340 TCGTTTTCTTTCTTCCTTG
1 TCGTTTTCATTCTTCCTTG
908359 TCGTTTTCATTCTTCCTTG
1 TCGTTTTCATTCTTCCTTG
908378 T
1 T
908379 TCTGCTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.03, C:0.26, G:0.10, T:0.62
Consensus pattern (19 bp):
TCGTTTTCATTCTTCCTTG
Found at i:914289 original size:23 final size:22
Alignment explanation
Indices: 914263--914305 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
914253 ATATAAAATT
914263 TATCCCGAAGGACCTCATGTATA
1 TATCCCGAAGGACCT-ATGTATA
914286 TATCCCGAAGGACCTATGTA
1 TATCCCGAAGGACCTATGTA
914306 ACCCTCGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
TATCCCGAAGGACCTATGTATA
Found at i:916755 original size:11 final size:10
Alignment explanation
Indices: 916738--916762 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
916728 TTTCGAACAG
916738 CTTTTTTTTT
1 CTTTTTTTTT
916748 CTTTTTTTTT
1 CTTTTTTTTT
916758 CTTTT
1 CTTTT
916763 CGAATTGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:916763 original size:32 final size:35
Alignment explanation
Indices: 916713--916780 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 35
916703 TTCTTTCATG
916713 TCTTTTTTTCTTCTTTTTCGAACAGCT-TTTTTTT
1 TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTTTTT
**
916747 TCTTTTTTT-TTC-TTTTCGAATTGCTGTTTTTTT
1 TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTTTTT
916780 T
1 T
916781 TCTCGATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 11 0.35
33 11 0.35
34 9 0.29
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.71
Consensus pattern (35 bp):
TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTTTTT
Found at i:925048 original size:23 final size:22
Alignment explanation
Indices: 925017--925059 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
925007 ATATAAAATT
*
925017 TGTCTCGAAGGACCTCATGTATA
1 TGTCCCGAAGGACCT-ATGTATA
925040 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
925060 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:925962 original size:20 final size:20
Alignment explanation
Indices: 925937--925976 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
925927 CAGTATCGGT
925937 ACTGGATGAAGAAGTACCGA
1 ACTGGATGAAGAAGTACCGA
925957 ACTGGATGAAGAAGTACCGA
1 ACTGGATGAAGAAGTACCGA
925977 CACTCATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (20 bp):
ACTGGATGAAGAAGTACCGA
Found at i:937588 original size:26 final size:26
Alignment explanation
Indices: 937552--937629 Score: 122
Period size: 26 Copynumber: 3.0 Consensus size: 26
937542 CAAAACTGAT
937552 GCCCCTATATGTTGTCCTGGGCCGTC
1 GCCCCTATATGTTGTCCTGGGCCGTC
937578 GCCCCTATATGTTGTCCTGGGCCGTC
1 GCCCCTATATGTTGTCCTGGGCCGTC
* *
937604 GCCCCTACATGCTT-CCCTGGGCCGTC
1 GCCCCTATATG-TTGTCCTGGGCCGTC
937630 ACCCATCTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 47 0.96
27 2 0.04
ACGTcount: A:0.08, C:0.38, G:0.26, T:0.28
Consensus pattern (26 bp):
GCCCCTATATGTTGTCCTGGGCCGTC
Found at i:951326 original size:42 final size:42
Alignment explanation
Indices: 951174--951327 Score: 107
Period size: 42 Copynumber: 3.5 Consensus size: 42
951164 ATCTCACTAC
* **
951174 ATCTTCAAGGAAGGTTGAATCTAGATCAATTTGCTTCACTTAA
1 ATCTTCAAGGAA-GTTAAATCTAGATTGATTTGCTTCACTTAA
* ** * **
951217 ATCTTC-AGGAAGTTTTCAAATCTAAAATTCTGATTTAATCCA-TTGT
1 ATCTTCAAGGAAG--TT-AAATCT-AGA-T-TGATTTGCTTCACTTAA
* *
951263 ATCTTCAAGGAGGGTTGAATCTAGATTGATTTGCTTCACTTAA
1 ATCTTCAAGGA-AGTTAAATCTAGATTGATTTGCTTCACTTAA
951306 ATCTTC-AGGAAGTTCAAATCTA
1 ATCTTCAAGGAAGTT-AAATCTA
951328 AAATTTTGAT
Statistics
Matches: 82, Mismatches: 19, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
41 4 0.05
42 24 0.29
43 17 0.21
44 7 0.09
45 7 0.09
46 11 0.13
47 11 0.13
48 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (42 bp):
ATCTTCAAGGAAGTTAAATCTAGATTGATTTGCTTCACTTAA
Found at i:951364 original size:87 final size:88
Alignment explanation
Indices: 951168--951374 Score: 335
Period size: 89 Copynumber: 2.4 Consensus size: 88
951158 ATATTCATCT
* *
951168 CACTACATCTTCAAGGAAGGTTGAATCTAGATCAATTTGCTTCACTTAAATCTTCAGGAAGTTTT
1 CACTATATCTTCAAGGAGGGTTGAATCTAGATCAATTTGCTTCACTTAAATCTTCAGGAAG-TTT
951233 CAAATCTAAAATTCTGATTTAATC
65 CAAATCTAAAATTCTGATTTAATC
* * **
951257 CATTGTATCTTCAAGGAGGGTTGAATCTAGATTGATTTGCTTCACTTAAATCTTCAGGAAG-TTC
1 CACTATATCTTCAAGGAGGGTTGAATCTAGATCAATTTGCTTCACTTAAATCTTCAGGAAGTTTC
*
951321 AAATCTAAAATTTTGATTTAATC
66 AAATCTAAAATTCTGATTTAATC
951344 CACTATATCTTCAAGGAGGGTTGAATCTAGA
1 CACTATATCTTCAAGGAGGGTTGAATCTAGA
951375 AATCAATCTA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
87 54 0.50
89 55 0.50
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (88 bp):
CACTATATCTTCAAGGAGGGTTGAATCTAGATCAATTTGCTTCACTTAAATCTTCAGGAAGTTTC
AAATCTAAAATTCTGATTTAATC
Found at i:951371 original size:45 final size:45
Alignment explanation
Indices: 951235--951377 Score: 134
Period size: 45 Copynumber: 3.2 Consensus size: 45
951225 GAAGTTTTCA
* * *
951235 AATCTAAAATTCTGATTTAATCCATTGTATCTTCAAGGAGGGTTG
1 AATCTAAAATTTTGATTTAATCCACTATATCTTCAAGGAGGGTTG
* ** * * * *
951280 AATCT-AGA--TTGATTTGCTTCACTTAAATCTTC-AGGA-AGTTCA
1 AATCTAAAATTTTGATTTAATCCAC-TATATCTTCAAGGAGGGTT-G
951322 AATCTAAAATTTTGATTTAATCCACTATATCTTCAAGGAGGGTTG
1 AATCTAAAATTTTGATTTAATCCACTATATCTTCAAGGAGGGTTG
951367 AATCTAGAAAT
1 AATCTA-AAAT
951378 CAATCTACTC
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
41 3 0.04
42 18 0.25
43 9 0.12
44 10 0.14
45 26 0.36
46 7 0.10
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (45 bp):
AATCTAAAATTTTGATTTAATCCACTATATCTTCAAGGAGGGTTG
Found at i:952363 original size:18 final size:18
Alignment explanation
Indices: 952340--952381 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
952330 GTCATAACCT
*
952340 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
*
952358 GACCCGACCGGTTGACCC
1 GACCCGACCCGTTGACCC
952376 GACCCG
1 GACCCG
952382 TTGACCTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:952374 original size:13 final size:13
Alignment explanation
Indices: 952358--952387 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
952348 CCGTTTACCC
*
952358 GACCCGACCGGTT
1 GACCCGACCCGTT
952371 GACCCGACCCGTT
1 GACCCGACCCGTT
952384 GACC
1 GACC
952388 TGTTGACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:952387 original size:8 final size:8
Alignment explanation
Indices: 952376--952427 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
952366 CGGTTGACCC
952376 GACCCGTT
1 GACCCGTT
*
952384 GACCTGTT
1 GACCCGTT
952392 GA-CCGTT
1 GACCCGTT
952399 GACCCGTT
1 GACCCGTT
*
952407 GA-TCGTT
1 GACCCGTT
952414 GACCGGCGTT
1 GACC--CGTT
952424 GACC
1 GACC
952428 AACCAAAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 12 0.33
8 16 0.44
10 8 0.22
ACGTcount: A:0.13, C:0.31, G:0.29, T:0.27
Consensus pattern (8 bp):
GACCCGTT
Found at i:952399 original size:15 final size:15
Alignment explanation
Indices: 952379--952427 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
952369 TTGACCCGAC
*
952379 CCGTTGACCTGTTGA
1 CCGTTGACCCGTTGA
952394 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
*
952409 TCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
952426 CC
1 CC
952428 AACCAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 22 0.76
17 7 0.24
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.29
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:952401 original size:7 final size:7
Alignment explanation
Indices: 952379--952418 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
952369 TTGACCCGAC
952379 CCGTTGA
1 CCGTTGA
952386 CCTGTTGA
1 CC-GTTGA
952394 CCGTTGA
1 CCGTTGA
952401 CCCGTTGA
1 -CCGTTGA
*
952409 TCGTTGA
1 CCGTTGA
952416 CCG
1 CCG
952419 GCGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.12, C:0.30, G:0.28, T:0.30
Consensus pattern (7 bp):
CCGTTGA
Found at i:953737 original size:18 final size:18
Alignment explanation
Indices: 953711--953745 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
953701 TCGAAAGGAC
*
953711 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
953729 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
953746 CCGGATGGCA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:955039 original size:24 final size:24
Alignment explanation
Indices: 954941--955035 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
954931 TTCGATTTGA
*
954941 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
954965 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACCTGG
954989 ATTCTGATCT-ATTACTTGACCT-G
1 ATTCTGATCTGA-TACTTGACCTGG
* *
955012 ATTTCTGATATGATACTTAACCTG
1 A-TTCTGATCTGATACTTGACCTG
955036 ATTTATGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
23 3 0.05
24 59 0.94
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:956064 original size:41 final size:41
Alignment explanation
Indices: 956019--956116 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
956009 TTGGTAATCG
* * * *
956019 CCTGAAGGATTTAACATCATGTTTGAGAGGTTTACTGATGA
1 CCTGAAGGATTTAACATCATGCTTGAAAGATTTAATGATGA
* *
956060 CCTGAAGGATTTAATATCATGCTTGAAAGATTTAATGATGG
1 CCTGAAGGATTTAACATCATGCTTGAAAGATTTAATGATGA
*
956101 TCTGAA-GATCTTAACA
1 CCTGAAGGAT-TTAACA
956117 ATTGAGAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.06
41 45 0.94
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (41 bp):
CCTGAAGGATTTAACATCATGCTTGAAAGATTTAATGATGA
Found at i:961428 original size:14 final size:14
Alignment explanation
Indices: 961411--961462 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
961401 GTTAATTTGG
961411 CTGAGTCAACTCAT
1 CTGAGTCAACTCAT
*
961425 CTGAGTCAAAC-CAGA
1 CTGAGTC-AACTCA-T
*
961440 GTGAGTCAACTCAT
1 CTGAGTCAACTCAT
*
961454 CCGAGTCAA
1 CTGAGTCAA
961463 ATTGTTGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (14 bp):
CTGAGTCAACTCAT
Found at i:962797 original size:25 final size:25
Alignment explanation
Indices: 962769--962829 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
962759 CTCTAATGTT
962769 TAAATGACCAAAATACCCTAAACCC
1 TAAATGACCAAAATACCCTAAACCC
* * *
962794 TAAAAGAACCAAAATATCTTAAACCC
1 TAAATG-ACCAAAATACCCTAAACCC
962820 TAAGATGACC
1 TAA-ATGACC
962830 GAAGTAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 23 0.77
27 2 0.07
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.18
Consensus pattern (25 bp):
TAAATGACCAAAATACCCTAAACCC
Found at i:964147 original size:25 final size:25
Alignment explanation
Indices: 964110--964168 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
964100 ACGATACTCC
* *
964110 CTTAGAGTGGCATCTTTGTTGTGTG
1 CTTAGGGTAGCATCTTTGTTGTGTG
964135 CTTAGGGTAGCATCTTTGTTGTGTG
1 CTTAGGGTAGCATCTTTGTTGTGTG
964160 CTTAGGGTA
1 CTTAGGGTA
964169 AGTCCTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.14, C:0.12, G:0.32, T:0.42
Consensus pattern (25 bp):
CTTAGGGTAGCATCTTTGTTGTGTG
Found at i:967250 original size:18 final size:19
Alignment explanation
Indices: 967227--967266 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
967217 CTTAAATCTG
967227 ATTTGA-AGTATC-TAATAA
1 ATTTGAGAGTATCAT-ATAA
967245 ATTTGAGAGTATCATATAA
1 ATTTGAGAGTATCATATAA
967264 ATT
1 ATT
967267 ACTAATGCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 13 0.65
20 1 0.05
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
ATTTGAGAGTATCATATAA
Found at i:970990 original size:20 final size:20
Alignment explanation
Indices: 970967--971015 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
970957 AGGAATGCAT
970967 CGATGCACTGTAGAATGTAC
1 CGATGCACTGTAGAATGTAC
970987 CGATGCACTGTAGAATGTAC
1 CGATGCACTGTAGAATGTAC
971007 CGATGCACT
1 CGATGCACT
971016 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (20 bp):
CGATGCACTGTAGAATGTAC
Found at i:972471 original size:23 final size:23
Alignment explanation
Indices: 972441--972498 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
972431 TTTTATATGA
972441 CACTTCGGTGCAATTCTAAGAGG
1 CACTTCGGTGCAATTCTAAGAGG
* *
972464 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTAAGAGG
*
972487 CACTTTGGTGCA
1 CACTTCGGTGCA
972499 TTTATACGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTAAGAGG
Found at i:972506 original size:23 final size:23
Alignment explanation
Indices: 972441--972506 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
972431 TTTTATATGA
* * *
972441 CACTTCGGTGCAATTCTAAGAGG
1 CACTTCGGTGCAATTATACGTGG
*
972464 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTATACGTGG
* *
972487 CACTTTGGTGCATTTATACG
1 CACTTCGGTGCAATTATACG
972507 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCAATTATACGTGG
Found at i:977526 original size:23 final size:23
Alignment explanation
Indices: 977458--977518 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
977448 ACATTTTATA
977458 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
977481 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
977504 TGGCACTTTGGTGCA
1 TGGCACTTCGGTGCA
977519 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:979569 original size:12 final size:12
Alignment explanation
Indices: 979552--979582 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
979542 TACCTGTCGA
*
979552 CGGCGATCACTC
1 CGGCGAGCACTC
979564 CGGCGAGCACTC
1 CGGCGAGCACTC
979576 CGGCGAG
1 CGGCGAG
979583 GGCGGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.39, G:0.35, T:0.10
Consensus pattern (12 bp):
CGGCGAGCACTC
Found at i:983091 original size:23 final size:23
Alignment explanation
Indices: 983045--983136 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 23
983035 TTTAATGAAA
*
983045 TAATAATTATTAA-AATTTATTAT
1 TAATAATT-TTAATAATATATTAT
*
983068 TAATAATTTTAATAATATAATAT
1 TAATAATTTTAATAATATATTAT
* * *
983091 T--TTATTTTAATATTATCATTTT
1 TAATAATTTTAATAATAT-ATTAT
*
983113 TAAT-ATTATAATAATAT-TT-T
1 TAATAATTTTAATAATATATTAT
983133 TAAT
1 TAAT
983137 TTAATAAGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.09
21 15 0.26
22 8 0.14
23 28 0.49
24 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATAATTTTAATAATATATTAT
Found at i:983098 original size:21 final size:21
Alignment explanation
Indices: 983071--983143 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
983061 TTATTATTAA
983071 TAATTTTAATAATATAATATTT
1 TAATTTTAATAATATAAT-TTT
* *
983093 T-ATTTTAATATTATCATTTT
1 TAATTTTAATAATATAATTTT
*
983113 TAATATT-ATAATA-ATATTTT
1 TAATTTTAATAATATA-ATTTT
983133 TAA-TTTAATAA
1 TAATTTTAATAA
983144 GTAATTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
20 21 0.50
21 18 0.43
22 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTTAATAATATAATTTT
Found at i:983148 original size:21 final size:20
Alignment explanation
Indices: 983058--983148 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
983048 TAATTATTAA
* * *
983058 AATTTATTATTAATAATTTT
1 AATTTAATAATAATATTTTT
983078 AA--TAAT-ATAATA-TTTT
1 AATTTAATAATAATATTTTT
* *
983094 ATTTTAAT-ATTATCATTTTT
1 AATTTAATAATAAT-ATTTTT
983114 AATATT-ATAATAATATTTTT
1 AAT-TTAATAATAATATTTTT
983134 AATTTAATAAGTAAT
1 AATTTAATAA-TAAT
983149 TAATATAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 5 0.09
17 5 0.09
18 11 0.19
19 3 0.05
20 23 0.40
21 10 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
AATTTAATAATAATATTTTT
Found at i:983218 original size:15 final size:16
Alignment explanation
Indices: 983175--983218 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
983165 GTAATATTCA
983175 TATTTTAATAAAAAAT
1 TATTTTAATAAAAAAT
* *
983191 TACTAT-ATAAAAAAT
1 TATTTTAATAAAAAAT
983206 TATTTTAATAAAA
1 TATTTTAATAAAA
983219 TATAATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTTTAATAAAAAAT
Found at i:983941 original size:16 final size:16
Alignment explanation
Indices: 983922--983955 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
983912 CAATATACGA
983922 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
983938 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
983954 AT
1 AT
983956 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:984030 original size:16 final size:18
Alignment explanation
Indices: 983998--984031 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
983988 TATTAATGTA
983998 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
984016 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
984032 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:984702 original size:130 final size:130
Alignment explanation
Indices: 984498--984745 Score: 370
Period size: 130 Copynumber: 1.9 Consensus size: 130
984488 AATTTTCTTC
* * * ***
984498 TAATTAGGTGGTGACATGTGTCACCAATAACATATATTATGATCATGTGTTGACACATGTCAGAT
1 TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGATCATGTGCCAACACATGTCAGAT
* ** *
984563 TCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
984628 TAATTAGGTGGTGACAAGTGTCACCAATGACACGTGTCATGATCATGTGCCAACACATGTCAGAT
1 TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGATCATGTGCCAACACATGTCAGAT
*
984693 CCTAATTAAATGATTAATTTATTGAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
984746 TATATAAATA
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
130 104 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACAAGTGTCACCAATAACACATATCATGATCATGTGCCAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:985182 original size:35 final size:35
Alignment explanation
Indices: 985143--985216 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
985133 AATTTAATTT
* * *
985143 AATTAAATTATTTTAGAATTTAGGATTTAGAATGA
1 AATTAAATTACTTTAGAAATTAGGATTTAGAATAA
* * *
985178 AATTAAATTACTTTGGAAATTGGGGTTTAGAATAA
1 AATTAAATTACTTTAGAAATTAGGATTTAGAATAA
985213 AATT
1 AATT
985217 GAAGACTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.41
Consensus pattern (35 bp):
AATTAAATTACTTTAGAAATTAGGATTTAGAATAA
Found at i:993003 original size:65 final size:64
Alignment explanation
Indices: 992894--993031 Score: 179
Period size: 65 Copynumber: 2.1 Consensus size: 64
992884 ACACCCTATT
* * * * * *
992894 TCGAATGCATTTTGTGTACCGATGCACAACCATACATCGATGCACTC-TTGATTTTATTGAAACA
1 TCGAATGTATTTTATGCACCGATACACAACCATACATCGATGCACTCATGGATCTT-TTGAAACA
* *
992958 TTGAATGTATTTTATGCACCGATACACATACCATGCATCGATGCACTCATGGATCTTTTGAAACA
1 TCGAATGTATTTTATGCACCGATACACA-ACCATACATCGATGCACTCATGGATCTTTTGAAACA
993023 TCGAATGTA
1 TCGAATGTA
993032 ATTAGTGTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 23 0.37
65 34 0.54
66 6 0.10
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (64 bp):
TCGAATGTATTTTATGCACCGATACACAACCATACATCGATGCACTCATGGATCTTTTGAAACA
Found at i:995009 original size:21 final size:21
Alignment explanation
Indices: 994983--995022 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
994973 GAGAAATTAT
994983 TTTTAAAATACAAAAATGATA
1 TTTTAAAATACAAAAATGATA
**
995004 TTTTAAAATTGAAAAATGA
1 TTTTAAAATACAAAAATGA
995023 AAATAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
TTTTAAAATACAAAAATGATA
Found at i:998898 original size:21 final size:21
Alignment explanation
Indices: 998830--998903 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 21
998820 TTGTGTTCTA
*
998830 TGCATCGATACACTATAAAAG
1 TGCATCGATACACTATGAAAG
* *
998851 TGTATCGATGCATCCCT-TGAATA-
1 TGCATCGAT--A-CACTATGAA-AG
*
998874 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAAG
*
998895 TGCACCGAT
1 TGCATCGAT
998904 GCATTCTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 3 0.08
21 21 0.52
23 12 0.30
24 4 0.10
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:998921 original size:23 final size:23
Alignment explanation
Indices: 998889--998934 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
998879 CGATACACTA
998889 TGAAGGTGCACCGATGCATTCTT
1 TGAAGGTGCACCGATGCATTCTT
* *
998912 TGAAGTTGCACCGTTGCATTCTT
1 TGAAGGTGCACCGATGCATTCTT
998935 CGGGTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (23 bp):
TGAAGGTGCACCGATGCATTCTT
Found at i:1010862 original size:12 final size:12
Alignment explanation
Indices: 1010845--1010879 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1010835 CCATTCTGGA
1010845 TTTGAATTTCTT
1 TTTGAATTTCTT
1010857 TTTGAATTTCTT
1 TTTGAATTTCTT
1010869 TTTGAATTTCT
1 TTTGAATTTCT
1010880 CCCTCTGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (12 bp):
TTTGAATTTCTT
Found at i:1012552 original size:5 final size:5
Alignment explanation
Indices: 1012528--1012623 Score: 60
Period size: 5 Copynumber: 18.8 Consensus size: 5
1012518 CATATCTAAG
* *
1012528 AAAAA AAAAT ATAAAT -AAAT AAAAT --ACT AAAAT AATAAAT CAAAGAGT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT -A-AAAT -AAA-A-T
1012576 AAAAAT A-AAT A-AAT CAAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAAA
1 AAA-AT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1012624 AAGAAAAAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 22
0.74 0.05 0.22
Matches are distributed among these distances:
3 2 0.03
4 14 0.19
5 36 0.48
6 12 0.16
7 10 0.13
8 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1012564 original size:20 final size:19
Alignment explanation
Indices: 1012541--1012611 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 19
1012531 AAAAAATATA
1012541 AATAAATAAAATACTAAAAT
1 AATAAATAAAATA-TAAAAT
1012561 AATAAATCAAAGAGTA-AAAAT
1 AATAAAT-AAA-A-TATAAAAT
*
1012582 AAATAAATCAAA-ATAAAAT
1 -AATAAATAAAATATAAAAT
1012601 -A-AAATAAAATA
1 AATAAATAAAATA
1012612 AAATAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
16 7 0.16
17 2 0.05
18 1 0.02
19 5 0.12
20 8 0.19
21 10 0.23
22 8 0.19
23 2 0.05
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (19 bp):
AATAAATAAAATATAAAAT
Found at i:1012624 original size:15 final size:15
Alignment explanation
Indices: 1012532--1012624 Score: 72
Period size: 15 Copynumber: 6.3 Consensus size: 15
1012522 TCTAAGAAAA
1012532 AAAAATATAAATAAAT
1 AAAAATA-AAATAAAT
1012548 AAAATACTAAAAT-AAT
1 AAAA-A-TAAAATAAAT
* * *
1012564 --AAATCAAA-GAGT
1 AAAAATAAAATAAAT
1012576 AAAAAT-AAATAAAT
1 AAAAATAAAATAAAT
*
1012590 CAAAATAAAATAAA-
1 AAAAATAAAATAAAT
1012604 ATAAAATAAAATAAAT
1 A-AAAATAAAATAAAT
1012620 AAAAA
1 AAAAA
1012625 AGAAAAAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
12 6 0.10
13 4 0.06
14 13 0.21
15 24 0.39
16 8 0.13
17 5 0.08
18 2 0.03
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:1012828 original size:29 final size:29
Alignment explanation
Indices: 1012764--1012829 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1012754 ATAAAGATAC
* * * *
1012764 ATAAAATTTAATAAAAAATAGTAATAATA
1 ATAAAATTAAATAAAAAACAGAAATAAGA
1012793 ATGAAAATTAAATAAAAAACCA-AAATAAGA
1 AT-AAAATTAAATAAAAAA-CAGAAATAAGA
1012823 ATAAAAT
1 ATAAAAT
1012830 AAAAAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 7 0.23
30 23 0.74
31 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (29 bp):
ATAAAATTAAATAAAAAACAGAAATAAGA
Found at i:1014250 original size:80 final size:80
Alignment explanation
Indices: 1014047--1014966 Score: 1173
Period size: 80 Copynumber: 11.3 Consensus size: 80
1014037 TTGTTGACAT
* * * * **
1014047 ATAGCCCTTCATGCCTTGAGCTATGCTGTAAATATGATTTGCCTCTGATTTGAGTGTAATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTG-CAA-ATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
1014112 TTGAAGGTCTTTGATGACAT
64 TCGAAGGTCTTTG--G-CAG
* * *
1014132 ATAACCCTTCTCT-CCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCT-TGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
*
1014196 CAAAGGTCTTTGGCAG
65 CGAAGGTCTTTGGCAG
*
1014212 ATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1014277 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* *
1014292 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTCCTTTGAGATGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1014357 GAAGGTATTTGGCAG
66 GAAGGTCTTTGGCAG
* * *
1014372 ATAACCCTTCTTGGCTTGAGC---GCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1014434 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
1014449 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1014514 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * *
1014529 ATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATATGCCTTTGAACTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1014594 GAAAGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * * * * * *
1014609 ATATCCCTTCTTGTCTTGAGCTATGCTGCAAATGATATGTCTTTGAGATTAGTGTAATTGAATTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
1014674 GAATGTCTTTTATTGGCAA
66 GAAGGTC---T-TTGGCAG
* ** * * * *
1014693 ATAACCCTTCTTGAATTGAGCTATGCAGCAAATGATGTGCCTTTGAGTTGAGTGTAGTCGAACTT
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
1014758 GAAGGTCTTTAGTAG
66 GAAGGTCTTTGGCAG
* * * *
1014773 ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1014838 GAAGGTCTTTTGTTGGCAA
66 GAAGGTC---T-TTGGCAG
* * *
1014857 ATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1014922 AAAGGTCTTTTGTTGGCAG
66 GAAGGTC---T-TTGGCAG
* *
1014941 ATATCCCTTCTCGCCTTGAGCTATGC
1 ATAGCCCTTCTTGCCTTGAGCTATGC
1014967 CTCAAATAGA
Statistics
Matches: 744, Mismatches: 78, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
77 71 0.10
79 1 0.00
80 434 0.58
81 2 0.00
83 41 0.06
84 171 0.23
85 23 0.03
86 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (80 bp):
ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTGGCAG
Found at i:1014476 original size:237 final size:240
Alignment explanation
Indices: 1014047--1014966 Score: 1134
Period size: 237 Copynumber: 3.8 Consensus size: 240
1014037 TTGTTGACAT
* * * * **
1014047 ATAGCCCTTCATGCCTTGAGCTATGCTGTAAATATGATTTGCCTCTGATTTGAGTGTAATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTG-CAA-ATGATGTGCCTTTGAGATGAGTGTAATCGAAC
* * * *
1014112 TTGAAGGTCTTTGATGACATATAACCCTTCTCT-CCTTGAGTTATGCTGTAAATGATGTGCCTTT
64 TCGAAGGTCTTTG--G-CAGATAACCCTTCT-TGCCTTGAG--CTGCTGCAAATGATGTGCCTTT
*
1014176 GAGCTGAGTGTAATCGAACTCAAAGGTC-T-TTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCT
123 GAGCTGAGTGTAATCGAACTCAAAGGTCTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCT
1014239 GCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
188 GCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
*
1014292 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTCCTTTGAGATGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTC
* * *
1014357 GAAGGTATTTGGCAGATAACCCTTCTTGGCTTGAGC-GCTACAAATGATGTGCCTTTGAGCTGAG
66 GAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTGCTGCAAATGATGTGCCTTTGAGCTGAG
*
1014421 TGTAATCGAACTCGAAGGTC-T-TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGA
131 TGTAATCGAACTCAAAGGTCTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGA
1014484 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
196 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* *
1014529 ATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATATGCCTTTGA-ACTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGA-TGAGTGTAATCGAACT
* * * * * *
1014593 CGAAAGTCTTTGGCAGATATCCCTTCTTGTCTTGAGCTATGCTGCAAATGATATGTCTTTGAGAT
65 CGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGC--TGCTGCAAATGATGTGCCTTTGAGCT
* * * * * * * ** *
1014658 TAGTGTAATTGAATTCGAATGTCTTTTATTGGCAAATAACCCTTCTTGAATTGAGCTATGCAGCA
128 GAGTGTAATCGAACTCAAAGGTC--TTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCA
* * * * *
1014723 AATGATGTGCCTTTGAGTTGAGTGTAGTCGAACTTGAAGGTCTTTAGTAG
191 AATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* * * * *
1014773 ATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTC
* * * * *
1014838 GAAGGTCTTTTGTTGGCAAATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGA
66 GAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGC--TGCTGCAAATGATGTGCCTTTGA
* * *
1014903 GCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATGC
125 GCTGAGTGTAATCGAACTCAAAGGTC--TTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGC
1014967 CTCAAATAGA
Statistics
Matches: 592, Mismatches: 69, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
236 1 0.00
237 224 0.38
239 1 0.00
240 59 0.10
241 1 0.00
243 39 0.07
244 142 0.24
245 27 0.05
247 1 0.00
248 97 0.16
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (240 bp):
ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTC
GAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTGCTGCAAATGATGTGCCTTTGAGCTGAG
TGTAATCGAACTCAAAGGTCTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGA
TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
Found at i:1016287 original size:95 final size:95
Alignment explanation
Indices: 1016100--1016362 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 95
1016090 GGCTAGCTGG
* * * * * * * *
1016100 ATCCATAAGGCCAGGCCGTTTAACCATTTACTCTAGAGGGACAAATCAATATCATTT-TATAGAT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAAATC-A-AGC-TTTAT-TATAT
1016164 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
1016198 ATCCATAAATCCGGGGCATTTAACCAATTGCTCTAGAGGGACAATTCAAGCTTTATTATATATTG
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAAATCAAGCTTTATTATATATTA
*
1016263 TAATCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * * *
1016293 ATCTATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAAATCAAGCTTTATTATATAT-T
1016358 ATAAT
65 ATAAT
1016363 ATTATAATCA
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
95 96 0.67
96 8 0.06
97 1 0.01
98 39 0.27
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAAATCAAGCTTTATTATATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:1020141 original size:13 final size:13
Alignment explanation
Indices: 1020125--1020154 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1020115 TTTAATTGCA
1020125 AAAATTAAAAATT
1 AAAATTAAAAATT
*
1020138 AAAATTAAAATTT
1 AAAATTAAAAATT
1020151 AAAA
1 AAAA
1020155 CATTCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:1020180 original size:20 final size:20
Alignment explanation
Indices: 1020157--1020203 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1020147 ATTTAAAACA
1020157 TTCGATTCGAATTACTTACC
1 TTCGATTCGAATTACTTACC
1020177 TTCGATTCGAATTACTTACC
1 TTCGATTCGAATTACTTACC
1020197 TTCGATT
1 TTCGATT
1020204 GGTTGGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (20 bp):
TTCGATTCGAATTACTTACC
Found at i:1020288 original size:3 final size:3
Alignment explanation
Indices: 1020280--1020314 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1020270 AGATCCAAGA
1020280 AAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
1020315 ATCAGAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1020311 original size:5 final size:5
Alignment explanation
Indices: 1020279--1020370 Score: 55
Period size: 5 Copynumber: 17.6 Consensus size: 5
1020269 CAGATCCAAG
**
1020279 AAATA ATAATA ATAATA ATAAT- AAATA AAATAA TAAATCA GAAAGG AAA-A
1 AAATA A-AATA A-AATA A-AATA AAATA AAAT-A -AAAT-A -AAATA AAATA
* * *
1020329 AAAGA AAATA AATTA AATTA AAATA AAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
1020371 AAGTCAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
4 10 0.14
5 39 0.53
6 16 0.22
7 8 0.11
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:1020315 original size:12 final size:13
Alignment explanation
Indices: 1020280--1020316 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1020270 AGATCCAAGA
1020280 AATAATAAT-AAT
1 AATAATAATAAAT
1020292 AATAATAATAAAT
1 AATAATAATAAAT
1020305 AA-AATAATAAAT
1 AATAATAATAAAT
1020317 CAGAAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:1020555 original size:30 final size:27
Alignment explanation
Indices: 1020488--1020560 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 27
1020478 AAAATATCAT
1020488 AATAAAATAAATAAATAGAGATACATAA
1 AATAAAATAAA-AAATAGAGATACATAA
**
1020516 AATTTAATAAAAAATAGTAATGATA-ATGAA
1 AATAAAATAAAAAATAG--A-GATACAT-AA
1020546 AATAAAATAACAAAA
1 AATAAAATAA-AAAA
1020561 CAAAACAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 6 0.17
28 9 0.25
29 3 0.08
30 14 0.39
31 4 0.11
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (27 bp):
AATAAAATAAAAAATAGAGATACATAA
Found at i:1021462 original size:2 final size:2
Alignment explanation
Indices: 1021455--1021488 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1021445 TAAACATACG
*
1021455 CA CA CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1021489 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1026728 original size:2 final size:2
Alignment explanation
Indices: 1026721--1026747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1026711 CATACGATAA
1026721 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1026748 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1026752 original size:2 final size:2
Alignment explanation
Indices: 1026747--1026773 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1026737 ACACACACAC
1026747 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
1026774 AATTTGACAC
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:1027243 original size:272 final size:272
Alignment explanation
Indices: 1026757--1027317 Score: 969
Period size: 272 Copynumber: 2.1 Consensus size: 272
1026747 ATATATATAT
*
1026757 ATATATATATATATATAAATTTGACACGATTTTTTGAAATTATATAAAATATCTTGAAAATCCAG
1 ATATATATATATATATAAATTTGACACGATTTTTTGAAAATATATAAAATATCTTGAAAATCCAG
* *
1026822 ATTTTTAGACTCATCTACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAACT
66 ATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAACT
* * * * *
1026887 CCCTAGTCCCGGTTTGGACGTTATGACCAAATCTAGGTGGTTACATGTCGTATTCAGAAATTATT
131 CCCTAGTCCCGGCTTAGACGTTATAACCAAATCTACGTGGTTACATATCGTATTCAGAAATTATT
**
1026952 TTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAGTCATAAGAAAGATT
196 TTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
*
1027017 AATATGATAAAC
261 AATACGATAAAC
* * *
1027029 ATATATATATAAATATAAATTTGACCCGATTTTTTGAAAATATCTAAAATATCTTGAAAATCCAG
1 ATATATATATATATATAAATTTGACACGATTTTTTGAAAATATATAAAATATCTTGAAAATCCAG
1027094 ATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAACT
66 ATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAACT
* *
1027159 CCCTAGTCTCGGCTTAGACGTTATAACCAAATCTACGTGGTTACATATCGTATTCAGAAATTCTT
131 CCCTAGTCCCGGCTTAGACGTTATAACCAAATCTACGTGGTTACATATCGTATTCAGAAATTATT
1027224 TTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
196 TTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
*
1027289 CATACGATAAAC
261 AATACGATAAAC
1027301 ATATATATATATATATA
1 ATATATATATATATATA
1027318 TATATCATAA
Statistics
Matches: 271, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
272 271 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (272 bp):
ATATATATATATATATAAATTTGACACGATTTTTTGAAAATATATAAAATATCTTGAAAATCCAG
ATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAACT
CCCTAGTCCCGGCTTAGACGTTATAACCAAATCTACGTGGTTACATATCGTATTCAGAAATTATT
TTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
AATACGATAAAC
Found at i:1028814 original size:33 final size:33
Alignment explanation
Indices: 1028770--1028833 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1028760 CTTTACAAAC
1028770 TCCCTAACTTTTCA-CAGGCTAAACTAGAACCTT
1 TCCCTAACTTTT-AGCAGGCTAAACTAGAACCTT
* * *
1028803 TCCCTAGCTTTTAGCAGGCTCAGCTAGAACC
1 TCCCTAACTTTTAGCAGGCTAAACTAGAACC
1028834 AAAACCCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (33 bp):
TCCCTAACTTTTAGCAGGCTAAACTAGAACCTT
Found at i:1030051 original size:24 final size:20
Alignment explanation
Indices: 1030001--1030054 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 20
1029991 TGCAAAATGG
1030001 GTACCGATA-CTATGCAAGA
1 GTACCGATACCTATGCAAGA
*
1030020 GTATCGATACCATAATGCAAAGTA
1 GTACCGATACC-T-ATGC-AAG-A
1030044 GTACCGATACC
1 GTACCGATACC
1030055 CCTTATGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.29
20 1 0.04
21 1 0.04
22 4 0.14
23 3 0.11
24 11 0.39
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
GTACCGATACCTATGCAAGA
Found at i:1042065 original size:17 final size:19
Alignment explanation
Indices: 1042028--1042066 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1042018 CTCATCCAAA
*
1042028 ATAAATATATAATTAGGAC
1 ATAAATATATAATTAGAAC
1042047 ATAAATATA-AATTA-AAC
1 ATAAATATATAATTAGAAC
1042064 ATA
1 ATA
1042067 TAATTAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
ATAAATATATAATTAGAAC
Found at i:1043264 original size:19 final size:19
Alignment explanation
Indices: 1043227--1043267 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1043217 AATTAATTAA
* **
1043227 AAACCCTAAATTATCCCCT
1 AAACCCAAAATTAGACCCT
1043246 AAACCCAAAATTAGACCCT
1 AAACCCAAAATTAGACCCT
1043265 AAA
1 AAA
1043268 ATCATATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (19 bp):
AAACCCAAAATTAGACCCT
Found at i:1048783 original size:41 final size:41
Alignment explanation
Indices: 1048726--1048807 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1048716 ATCAAATCAG
1048726 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1048767 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1048808 CTGAATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (41 bp):
ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
Found at i:1049799 original size:13 final size:12
Alignment explanation
Indices: 1049768--1049810 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
1049758 TAAATTTTAA
1049768 TTTTATATATTAT
1 TTTTA-ATATTAT
*
1049781 TTTTAATATTTT
1 TTTTAATATTAT
1049793 TTATTAATATTAAT
1 TT-TTAATATT-AT
1049807 TTTT
1 TTTT
1049811 TATAATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 8 0.31
13 15 0.58
14 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTAATATTAT
Found at i:1049811 original size:19 final size:19
Alignment explanation
Indices: 1049764--1049814 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1049754 TAATTAAATT
* * *
1049764 TTAATTTTATATATTATTT
1 TTAATTTTTTATATTAATA
1049783 TTAATATTTTT-TATTAATA
1 TTAAT-TTTTTATATTAATA
1049802 TTAATTTTTTATA
1 TTAATTTTTTATA
1049815 ATGTAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATTTTTTATATTAATA
Found at i:1051638 original size:26 final size:26
Alignment explanation
Indices: 1051581--1051631 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1051571 ATGTTAGAAA
* *
1051581 ACAAATTTTTAAAGTTTTAATAAGAG
1 ACAAATTTATAAAATTTTAATAAGAG
1051607 ACAAATTTATAAAATTTTAATAAGA
1 ACAAATTTATAAAATTTTAATAAGA
1051632 TGAAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (26 bp):
ACAAATTTATAAAATTTTAATAAGAG
Found at i:1052640 original size:26 final size:22
Alignment explanation
Indices: 1052587--1052631 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1052577 ATTAAGAAAA
1052587 AGTCCTCCAATCATATCAATAT
1 AGTCCTCCAATCATATCAATAT
*
1052609 AGTCCTTCAATCATATCAATAT
1 AGTCCTCCAATCATATCAATAT
1052631 A
1 A
1052632 CTTAGTCCTC
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:0.24, G:0.04, T:0.33
Consensus pattern (22 bp):
AGTCCTCCAATCATATCAATAT
Found at i:1053616 original size:61 final size:60
Alignment explanation
Indices: 1053450--1053617 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
1053440 ATTATGACCC
* * ** * * **
1053450 TCATTTTAAATTAGTCCCTGAACTTTTAAGTATTCCAATTTTATCCTTAAACTATGACTA
1 TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACTA
* * * * * *
1053510 TCATTCTAAATTAGTTCTTAAAATTTTGAACATTTCAGTTTCATCCCCAAAGTATGATCT-
1 TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGA-CTA
*
1053570 TCATTCTAAATTGGTCCCTAAACTTTTTAAACATTTCAATTTCATCCC
1 TCATTCTAAATTAGTCCCTAAAC-TTTTAAACATTTCAATTTCATCCC
1053618 AAATTATACG
Statistics
Matches: 86, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
60 62 0.72
61 24 0.28
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACTA
Found at i:1053968 original size:2 final size:2
Alignment explanation
Indices: 1053961--1053987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1053951 TAAATAAAAT
1053961 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 T
1053988 GTTGGGTGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1057492 original size:235 final size:235
Alignment explanation
Indices: 1057067--1057500 Score: 789
Period size: 235 Copynumber: 1.8 Consensus size: 235
1057057 TTGGATTGCG
*
1057067 GAAAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGT
1 GAAAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGC
* * *
1057132 ACCTTCAATTCAAAAAGATCTTGTCAATTGTTGTGCAGAAGAAACTACTAAGGAAATTATGAAAG
66 ACCTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAGAAGAAACTACAAAGGAAATTATGAAAG
1057197 ATCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAA
131 ATCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAA
1057262 ATGAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTT
196 ATGAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTT
1057302 GAAAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGC
1 GAAAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGC
*
1057367 ACCTTCAATTCAAAAAGAGCTTATCAATTGTTGTG-AGAAAGAAACTACAAAGGAAATTGTGAAA
66 ACCTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAG-AAGAAACTACAAAGGAAATTATGAAA
* *
1057431 GATCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGATGTGTCTTAAAAAGAACA
130 GATCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACA
1057496 AATGA
195 AATGA
1057501 CTTTTTGTGT
Statistics
Matches: 191, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
234 2 0.01
235 189 0.99
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (235 bp):
GAAAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGC
ACCTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAGAAGAAACTACAAAGGAAATTATGAAAG
ATCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAA
ATGAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTT
Found at i:1058069 original size:18 final size:18
Alignment explanation
Indices: 1058043--1058078 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1058033 TTGATTTGAT
1058043 TGATAATGATACTCGAAA
1 TGATAATGATACTCGAAA
* *
1058061 TGATGATGATGCTCGAAA
1 TGATAATGATACTCGAAA
1058079 AGCCGATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TGATAATGATACTCGAAA
Found at i:1073363 original size:46 final size:48
Alignment explanation
Indices: 1073272--1073365 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
1073262 TTAGTGTAAT
* *
1073272 TTTAATTTCTTGAATAAATGTATGCGAACTAAAGATCATACGGTTAGG
1 TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCATACGGTTAGG
* *
1073320 TTTAATTTCTTGAAT-AA-GCATGCGAACTAGATAGCATGA-GGTTAGG
1 TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCAT-ACGGTTAGG
1073366 ATGCTCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 23 0.56
47 3 0.07
48 15 0.37
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (48 bp):
TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCATACGGTTAGG
Found at i:1074133 original size:16 final size:18
Alignment explanation
Indices: 1074112--1074144 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1074102 ATTAGCTTAT
1074112 CAATTTG-TT-TATTCTG
1 CAATTTGCTTCTATTCTG
1074128 CAATTTGCTTCTATTCT
1 CAATTTGCTTCTATTCT
1074145 TATCATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (18 bp):
CAATTTGCTTCTATTCTG
Found at i:1079975 original size:22 final size:22
Alignment explanation
Indices: 1079950--1080061 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
1079940 TCCAAAATTT
1079950 ATAAGTCTTTCGAGCATGATGC
1 ATAAGTCTTTCGAGCATGATGC
* * * *
1079972 ATAAATCCTTCG-G-GTCAT-C
1 ATAAGTCTTTCGAGCATGATGC
*
1079991 AGTAAGTCTTTTGAGCATGATGC
1 A-TAAGTCTTTCGAGCATGATGC
* * * *
1080014 ATAAATCCTTCGGGTCAT-CTG-
1 ATAAGTCTTTCGAG-CATGATGC
*
1080035 -TAAGTCTTTCGAGCAAGATG-
1 ATAAGTCTTTCGAGCATGATGC
1080055 ATAAGTC
1 ATAAGTC
1080062 CTTTGGGCTA
Statistics
Matches: 64, Mismatches: 19, Indels: 15
0.65 0.19 0.15
Matches are distributed among these distances:
19 4 0.06
20 23 0.36
21 8 0.12
22 24 0.38
23 5 0.08
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (22 bp):
ATAAGTCTTTCGAGCATGATGC
Found at i:1080010 original size:42 final size:42
Alignment explanation
Indices: 1079951--1080064 Score: 185
Period size: 42 Copynumber: 2.7 Consensus size: 42
1079941 CCAAAATTTA
1079951 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
1 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
* *
1079993 TAAGTCTTTTGAGCATGATGCATAAATCCTTCGGGTCATCTG
1 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
* *
1080035 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTT
1 TAAGTCTTTCGAGCATGATGCATAAATCCTT
1080065 TGGGCTATCC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 9 0.13
42 58 0.87
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
Found at i:1080266 original size:42 final size:42
Alignment explanation
Indices: 1080203--1080313 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
1080193 TCCAAAATTT
* *
1080203 ATAAGTCTTCTGAG-AATGATGCATAAATCATTTGGGTCATCA
1 ATAAGTCTTCTGAGCAA-GATGCATAAATCATTCGAGTCATCA
* * *
1080245 ATAAGTCTTCTGAGCACGATGCATAAATCCTTCGAGTCATCT
1 ATAAGTCTTCTGAGCAAGATGCATAAATCATTCGAGTCATCA
*
1080287 GTAAGTCTT-TCGAGCAAGATG-ATAAAT
1 ATAAGTCTTCT-GAGCAAGATGCATAAAT
1080314 TCTTTGGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 7 0.12
42 52 0.87
43 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (42 bp):
ATAAGTCTTCTGAGCAAGATGCATAAATCATTCGAGTCATCA
Found at i:1080306 original size:253 final size:253
Alignment explanation
Indices: 1079858--1080529 Score: 1184
Period size: 253 Copynumber: 2.7 Consensus size: 253
1079848 ATGTAAAAAA
*
1079858 ATGAAATGCGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
1079923 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
* * *
1079988 ATCAGTAAGTCTTTTGAGCATGATGCATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
131 ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGA
* * *
1080053 TGATAAGTCCTTTGGGCTATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
196 TGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
*
1080111 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAAAAAGGTTTC
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
* * *
1080176 TTACCTAGTAAACTATTTCCAAAATTTATAAGTC-TTCTGAGAATGATGCATAAATCATTTGGGT
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTC-GAGCATGATGCATAAATCCTTCGGGT
*
1080240 CATCAATAAGTCTTCTGAGCACGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAG
130 CATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAG
*
1080305 ATGATAAATTCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
195 ATGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
*
1080364 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTT
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
*
1080429 TTACCTAGTAAAATATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
*
1080494 ATCAATAAGTCTTCAGAGCATGATGCATAAATCCTT
131 ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTT
1080530 TAGATCTGAT
Statistics
Matches: 396, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
252 3 0.01
253 390 0.98
254 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (253 bp):
ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGA
TGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
Found at i:1080481 original size:22 final size:21
Alignment explanation
Indices: 1080456--1080523 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
1080446 TCCAAAATTT
1080456 ATAAGTCTTTCGAGCATGATGC
1 ATAAGTC-TTCGAGCATGATGC
* * *
1080478 ATAAATCCTTCG-G-GTCAT-C
1 ATAAGT-CTTCGAGCATGATGC
1080497 AATAAGTCTTCAGAGCATGATGC
1 -ATAAGTCTTC-GAGCATGATGC
1080520 ATAA
1 ATAA
1080524 ATCCTTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 5 0.15
20 9 0.26
21 2 0.06
22 16 0.47
23 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
ATAAGTCTTCGAGCATGATGC
Found at i:1080958 original size:11 final size:11
Alignment explanation
Indices: 1080933--1080966 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1080923 TCATTTTTTG
1080933 ATATTATTGATA
1 ATATTATT-ATA
*
1080945 ATATTGTTATA
1 ATATTATTATA
1080956 ATATTATTATA
1 ATATTATTATA
1080967 TTTAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (11 bp):
ATATTATTATA
Found at i:1083452 original size:98 final size:100
Alignment explanation
Indices: 1083320--1083503 Score: 291
Period size: 98 Copynumber: 1.9 Consensus size: 100
1083310 TAATATTATG
* * *
1083320 TATACAATAAAGCTTGAGCTGTCCTTCTAGAGCAATTGGTTAAACGTCCCGGC-TTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCATCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
1083384 ATTCAACTAGCCTGAT-AAAGGTGATTATAATATA
66 ATTCAACTAGCCTGATCAAAGGTGATTATAATATA
* *
1083418 TATACAATAAAGCTTGAGTTGTCCATCTATAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCATCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
* *
1083483 ATTCATCTAGCTTGATCAAAG
66 ATTCAACTAGCCTGATCAAAG
1083504 AAAATTACAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 48 0.62
99 25 0.32
100 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (100 bp):
TATACAATAAAGCTTGAGCTGTCCATCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAACTAGCCTGATCAAAGGTGATTATAATATA
Done.