Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 64
Found at i:2898557 original size:24 final size:24
Alignment explanation
Indices: 2898525--2898572 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2898515 CCTAAGTAAG
2898525 GAGAATAAGTGATGCAAGAGCAAT
1 GAGAATAAGTGATGCAAGAGCAAT
*
2898549 GAGAATAAGTGATGCATGAGCAAT
1 GAGAATAAGTGATGCAAGAGCAAT
2898573 AAATATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.29, T:0.19
Consensus pattern (24 bp):
GAGAATAAGTGATGCAAGAGCAAT
Found at i:2900972 original size:116 final size:116
Alignment explanation
Indices: 2900636--2901067 Score: 421
Period size: 116 Copynumber: 3.7 Consensus size: 116
2900626 TCATTCAGGG
* * * *
2900636 AGGAAGAAGAAATTTATATAAGAGAGCTT-TTCAA-GTTCAGAATGACCTTTATGGAAGAACAAT
1 AGGAAGAAGAAATTCATATAAGAGAGCTTGTTCAACCTT-AGAATGACCTTTATGGAAAAATAAT
* * * *
2900699 GAGTTTATGTAGGAGAGCTCATCTAATCTTTTCAGAGAGGAGGAAGCGTCCCA
65 GAGTTCATATAGGAGAGCTCATCTAATCTTTTCAGAGAGGAGAAAGCG-ACCA
* * * ** * * *
2900752 AAGAAGAAGAAGTTCATAT-AGAAGTGCTTGTTTGATCTCAAAATGACCTTTATGGAAAAAATAA
1 AGGAAGAAGAAATTCATATAAG-AGAGCTTGTTCAACCTTAGAATGACCTTTATGG-AAAAATAA
* * *
2900816 TGAGTTTATATAGGAGAGCTCATCTAATCTTTCCATAGAGGAGAAAGCGACCA
64 TGAGTTCATATAGGAGAGCTCATCTAATCTTTTCAGAGAGGAGAAAGCGACCA
* * *
2900869 AGGAAGAACAAATTCATATAAGTGAGCTTGTTCAACCTTA-ATATAACCTTTATGGAAAAATAGA
1 AGGAAGAAGAAATTCATATAAGAGAGCTTGTTCAACCTTAGA-ATGACCTTTATGGAAAAATA-A
* ****
2900933 -GAGTTCATATAGGAGATCTC-TACTAATCTTTTCAGAGAGGAGAAATATTCCAA
64 TGAGTTCATATAGGAGAGCTCAT-CTAATCTTTTCAGAGAGGAGAAAGCGACC-A
* * * * * * *
2900986 ACTG-AGAAGAAGTTCATATAAGAGAGCTTTTTCAGCCTTAGAATCACC-TTATGGAAGAATAAA
1 A-GGAAGAAGAAATTCATATAAGAGAGCTTGTTCAACCTTAGAATGACCTTTATGGAAAAATAAT
2901049 GAGTTCATATAGGAGAGCT
65 GAGTTCATATAGGAGAGCT
2901068 TGTCTAGTAT
Statistics
Matches: 261, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
115 4 0.02
116 101 0.39
117 100 0.38
118 56 0.21
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (116 bp):
AGGAAGAAGAAATTCATATAAGAGAGCTTGTTCAACCTTAGAATGACCTTTATGGAAAAATAATG
AGTTCATATAGGAGAGCTCATCTAATCTTTTCAGAGAGGAGAAAGCGACCA
Found at i:2912020 original size:17 final size:17
Alignment explanation
Indices: 2911998--2912031 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2911988 CTGTTAACTC
2911998 CTGTTAATTCATTAACA
1 CTGTTAATTCATTAACA
2912015 CTGTTAATTCATTAACA
1 CTGTTAATTCATTAACA
2912032 GAAGTGTTAC
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:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
CTGTTAATTCATTAACA
Found at i:2912939 original size:2 final size:2
Alignment explanation
Indices: 2912932--2912959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2912922 CACTGATGAG
2912932 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2912960 TATTTGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2927901 original size:1 final size:1
Alignment explanation
Indices: 2927891--2927992 Score: 60
Period size: 1 Copynumber: 102.0 Consensus size: 1
2927881 AAATAAAAGG
* * * * * * * * *
2927891 AAAAAGAAAAAGAAAAAAGAAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
2927956 GAAAAGAAAAATAAGAAAAAGAAAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2927993 TGAGAGGTTC
Statistics
Matches: 69, Mismatches: 32, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (1 bp):
A
Found at i:2927901 original size:7 final size:7
Alignment explanation
Indices: 2927885--2927987 Score: 138
Period size: 7 Copynumber: 14.3 Consensus size: 7
2927875 CCTAAGAAAT
*
2927885 AAAAGGA
1 AAAAGAA
2927892 AAAAG-A
1 AAAAGAA
2927898 AAAAGAA
1 AAAAGAA
2927905 AAAAGAAA
1 AAAAG-AA
2927913 AAAAGAA
1 AAAAGAA
2927920 AAAAGAA
1 AAAAGAA
2927927 AAAAGAA
1 AAAAGAA
2927934 AAAAGAA
1 AAAAGAA
2927941 AAAAGAA
1 AAAAGAA
2927948 AAAAGAAA
1 AAAAG-AA
2927956 GAAAAGAA
1 -AAAAGAA
2927964 AAATA-AGA
1 AAA-AGA-A
2927972 AAAAGAA
1 AAAAGAA
2927979 AAAAGAA
1 AAAAGAA
2927986 AA
1 AA
2927988 GAAAATGAGA
Statistics
Matches: 89, Mismatches: 0, Indels: 14
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.07
7 61 0.69
8 17 0.19
9 5 0.06
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:2928859 original size:24 final size:24
Alignment explanation
Indices: 2928832--2928877 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2928822 CAGAGAGTCG
* * *
2928832 ACAAAGATTCATTTCACAACTTCA
1 ACAAAGAATCAGTCCACAACTTCA
2928856 ACAAAGAATCAGTCCACAACTT
1 ACAAAGAATCAGTCCACAACTT
2928878 TCATGGATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (24 bp):
ACAAAGAATCAGTCCACAACTTCA
Found at i:2929346 original size:135 final size:134
Alignment explanation
Indices: 2929018--2929489 Score: 570
Period size: 136 Copynumber: 3.5 Consensus size: 134
2929008 TCCAATGAAA
* *
2929018 AGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * * ** * *
2929083 ATCCTATTGCTCAATTCACGACACTTCGAATCAGCAACACCTCGCTTGAGAAATCGATATTTTCA
66 AACCTATTGCTCGATTCACGACACTTCAAATCAGCAACGCCTCACTTAAG-GATTAAAATTCT-A
*
2929148 ATGGAG
129 ATAGAG
* * ** *
2929154 AGTTCATAATGAA-AAGAATTCATTCGACAGAGGGAGAAAATTTTCATAATGAAAAGAACTTGTT
1 AGTTCATAAT-AAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTT
* * * *
2929218 CAACATATTGCTCGATTCAGGACACTTCAAATCAGAAACGCCTCACTTATAGGATTAACATTCTA
65 CAACCTATTGCTCGATTCACGACACTTCAAATCAGCAACGCCTCACTTA-AGGATTAAAATTCTA
*
2929283 ATTGAG
129 ATAGAG
* * *
2929289 AGTTCATAATAAGAAGAACTCATTCGA-ATGATGGAGAAAAAGTTCACAATGAGAAGAACTTGTT
1 AGTTCATAATAAGAAGAACTCATCCGACA-GAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTT
* * *
2929353 CAACCTATTGCTCGATTCACGACACTTCAAATCAGCAACGCCTCAATTGAGGGATTAAAATTTCC
65 CAACCTATTGCTCGATTCACGACACTTCAAATCAGCAACGCCTCACTT-AAGGATTAAAA-TTCT
2929418 AATAGAG
128 AATAGAG
* * *
2929425 AGTTCATAATCAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
2929490 GATATTATAA
Statistics
Matches: 287, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
134 3 0.01
135 111 0.39
136 169 0.59
137 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (134 bp):
AGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTATTGCTCGATTCACGACACTTCAAATCAGCAACGCCTCACTTAAGGATTAAAATTCTAAT
AGAG
Found at i:2930375 original size:81 final size:81
Alignment explanation
Indices: 2930277--2930453 Score: 257
Period size: 81 Copynumber: 2.2 Consensus size: 81
2930267 GCACCTTTAG
* * * *
2930277 GCATTAGTCTTTTATCCTAAATGCATTTAACCTTTATTTTAACTTGCATTATT-GACACGTTTCT
1 GCATTAGTCTTTTATCCTAAAGGCATTTAACCTTCATTCTAACTTGCATTATTAG-CACATTTCT
*
2930341 TCCAAATGCACAGTTAC
65 GCCAAATGCACAGTTAC
* * *
2930358 GCATTAATCTTTTATCCTAAAGGCATTTAACCTTCCTTCTAACTTGCATTATTAGCATATTTCTG
1 GCATTAGTCTTTTATCCTAAAGGCATTTAACCTTCATTCTAACTTGCATTATTAGCACATTTCTG
*
2930423 CCAAATGCACAGTTAG
66 CCAAATGCACAGTTAC
2930439 GCATTAGTCTTTTAT
1 GCATTAGTCTTTTAT
2930454 TTTAGAACAA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 84 0.99
82 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (81 bp):
GCATTAGTCTTTTATCCTAAAGGCATTTAACCTTCATTCTAACTTGCATTATTAGCACATTTCTG
CCAAATGCACAGTTAC
Found at i:2930656 original size:54 final size:54
Alignment explanation
Indices: 2930590--2931089 Score: 644
Period size: 54 Copynumber: 9.3 Consensus size: 54
2930580 TTTATTAAGA
* * * *
2930590 TGCACACGTAGTGCCTATACGGTTCTTCATCAAC-TCATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATGATGAATTCCGTGAAT
* * * **
2930644 TGCACACTTAGTGCCAAAACGGTTATACATCAACATATGATTAATTCAATGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
2930698 TGCACACCTAGTGCCGAAATGATTATTCATCAACATATGATGAATTCC-TGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * * * *
2930751 TGCACACTTAGTTCCAAAATGGTTATTCATCAACATATGATGAATTTCATGTAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*** ** * *
2930805 TGCACACTTAGTGTTAAAACAATTATTCATCAACATTTGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
2930859 TGCACACTTAGTGTCGAAACTGTTATTCATCAACATATGATGAATTCCGTAAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
2930913 TGCACACTAAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
2930967 TGCACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
2931021 TGCCCACTTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGCGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
2931075 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
2931090 TATTTGGTAA
Statistics
Matches: 391, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 48 0.12
54 342 0.87
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:2936204 original size:81 final size:81
Alignment explanation
Indices: 2936072--2936293 Score: 257
Period size: 81 Copynumber: 2.7 Consensus size: 81
2936062 CGGTTCTTCA
* * * * * * *
2936072 TCTAACTTGTATTAGTGGCACATTTCTGCCATATTGCACCATTATGCATTAGTCTTTTATCCCAA
1 TCTAACTTGCATTATTGACACATTTCTGCCA-AATGAACAATTACGCATTAGTCTTTTATCCCAA
* *
2936137 ATGCATTTAACCTTTCT
65 AGGCATTTAACCTTCCT
* * * * * *
2936154 TTTAACTTGCATTATTGACATC-TTTTTGCCAAATGCACAGTTACGCATTAGTCTTTTATCCTAG
1 TCTAACTTGCATTATTGACA-CATTTCTGCCAAATGAACAATTACGCATTAGTCTTTTATCCCAA
2936218 AGGCATTTAACCTTCCT
65 AGGCATTTAACCTTCCT
* * *
2936235 TCTAACTTGCATTATTGGCACATTTCTGCCAAATGAACAATTAGGCATTAGGCTTTTAT
1 TCTAACTTGCATTATTGACACATTTCTGCCAAATGAACAATTACGCATTAGTCTTTTAT
2936294 TTAAGAACAA
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 92 0.78
82 24 0.20
83 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.40
Consensus pattern (81 bp):
TCTAACTTGCATTATTGACACATTTCTGCCAAATGAACAATTACGCATTAGTCTTTTATCCCAAA
GGCATTTAACCTTCCT
Found at i:2936496 original size:54 final size:54
Alignment explanation
Indices: 2936430--2936743 Score: 441
Period size: 54 Copynumber: 5.8 Consensus size: 54
2936420 TTTATTAAGA
* * * *
2936430 TGCACACGTAGTGCCTATACGGTTGTTCATCAA-ATCATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACAT-ATGATGAATTCCGTGAAT
* ** * *
2936484 TACACACTTAGTGCTGAAACGGTTATTCATCAATATATGATGAATTCCATGAAT
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
2936538 TGCACACTTAGTACCGAAACGGTTATTCATGAACATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * * *
2936592 TGCAAACTTAGTGTCGAAACGGTTATTCATCAATATATGATGAATTCCATGAAT
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
2936646 TGCACACTTAGTTCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
2936700 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAA
1 TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAA
2936744 GAAATAACTA
Statistics
Matches: 231, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
54 229 0.99
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:2942061 original size:12 final size:12
Alignment explanation
Indices: 2942044--2942076 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2942034 TTCTTCGAGC
*
2942044 AAAAAAATA-AA
1 AAAAAAAAACAA
2942055 AAAAAAAAACAA
1 AAAAAAAAACAA
2942067 AAAAAAAAAC
1 AAAAAAAAAC
2942077 GTGACCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:2942062 original size:13 final size:13
Alignment explanation
Indices: 2942044--2942075 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2942034 TTCTTCGAGC
*
2942044 AAAAAAATAAAAA
1 AAAAAAACAAAAA
2942057 AAAAAAACAAAAA
1 AAAAAAACAAAAA
2942070 AAAAAA
1 AAAAAA
2942076 CGTGACCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.94, C:0.03, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:2956846 original size:20 final size:20
Alignment explanation
Indices: 2956823--2956867 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2956813 ATTTTTGTCC
2956823 TTTAGTTTTAGTACTTTAAA
1 TTTAGTTTTAGTACTTTAAA
*
2956843 TTTATTTTTAGTACTTTAAA
1 TTTAGTTTTAGTACTTTAAA
2956863 TTTAG
1 TTTAG
2956868 CCCTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTAGTTTTAGTACTTTAAA
Found at i:2956874 original size:34 final size:33
Alignment explanation
Indices: 2956810--2956875 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
2956800 TGGTTAATTT
* ** *
2956810 TTTATTTTTGTCCTTTAGTTTTAGTACTTTAAA
1 TTTATTTTTGTACTTTAAATTTAGCACTTTAAA
*
2956843 TTTATTTTTAGTACTTTAAATTTAGCCCTTTAA
1 TTTATTTTT-GTACTTTAAATTTAGCACTTTAA
2956876 TTATTGCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (33 bp):
TTTATTTTTGTACTTTAAATTTAGCACTTTAAA
Found at i:2960782 original size:54 final size:55
Alignment explanation
Indices: 2960570--2960829 Score: 344
Period size: 55 Copynumber: 4.7 Consensus size: 55
2960560 GCATGTTGCT
* * * * * *
2960570 TAATAAGTTTATAAATTTTTGTTTGGGTATTGTTTGTGCAAAACTAAGAAATTCA
1 TAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* * * *
2960625 TAATAAGTTTATGAATTTCCGTATAGGCACTATGTGTGAAAAACTAAGAAATTCA
1 TAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
*
2960680 TAATAAGTTTATGAA-TTTCTGTATGGGCACTGTGTGTGCAAAACTAAGATATTCA
1 TAATAAGTTTATGAATTTTC-GTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* *
2960735 TAATAAGTTTATG-ATTTTCGTATGGGCTCTGTGTGTGGAAAACTAAGAAATTCA
1 TAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* * * *
2960789 TAATAAGTTTATGAATTTTTGTATTGGTAGTGTGTGTGCAA
1 TAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAA
2960830 CTCACGTAAA
Statistics
Matches: 178, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
54 49 0.28
55 129 0.72
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (55 bp):
TAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
Found at i:2960805 original size:109 final size:110
Alignment explanation
Indices: 2960570--2960829 Score: 387
Period size: 109 Copynumber: 2.4 Consensus size: 110
2960560 GCATGTTGCT
* * * *
2960570 TAATAAGTTTATAAATTTTTGTTTGGGTATTGTTTGTGCAAAACTAAGAAATTCATAATAAGTTT
1 TAATAAGTTTATGAATTTTTGTATGGGTACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTT
2960635 ATGAATTTCCGTATAGGCACTATGTGTGAAAAACTAAGAAATTCA
66 ATGAATTTCCGTATAGGCACTATGTGTGAAAAACTAAGAAATTCA
* * *
2960680 TAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGATATTCATAATAAGTTT
1 TAATAAGTTTATGAATTTTTGTATGGGTACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTT
* * * * *
2960745 ATG-ATTTTCGTATGGGCTCTGTGTGTGGAAAACTAAGAAATTCA
66 ATGAATTTCCGTATAGGCACTATGTGTGAAAAACTAAGAAATTCA
* *
2960789 TAATAAGTTTATGAATTTTTGTATTGGTAGTGTGTGTGCAA
1 TAATAAGTTTATGAATTTTTGTATGGGTACTGTGTGTGCAA
2960830 CTCACGTAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
109 73 0.54
110 61 0.46
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (110 bp):
TAATAAGTTTATGAATTTTTGTATGGGTACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTT
ATGAATTTCCGTATAGGCACTATGTGTGAAAAACTAAGAAATTCA
Found at i:2966902 original size:18 final size:18
Alignment explanation
Indices: 2966879--2966939 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
2966869 AATACAATTA
2966879 GTATCGATACTTAGTTGG
1 GTATCGATACTTAGTTGG
* *
2966897 GTATCGATAC--AATT-A
1 GTATCGATACTTAGTTGG
2966912 GTATCGATACTTAGTTGG
1 GTATCGATACTTAGTTGG
2966930 GTATCGATAC
1 GTATCGATAC
2966940 CATGAGGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.28
16 3 0.08
17 3 0.08
18 20 0.56
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (18 bp):
GTATCGATACTTAGTTGG
Found at i:2966912 original size:33 final size:33
Alignment explanation
Indices: 2966870--2966939 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
2966860 ATCGATACTA
2966870 ATACAATTAGTATCGATACTTAGTTGGGTATCG
1 ATACAATTAGTATCGATACTTAGTTGGGTATCG
2966903 ATACAATTAGTATCGATACTTAGTTGGGTATCG
1 ATACAATTAGTATCGATACTTAGTTGGGTATCG
2966936 ATAC
1 ATAC
2966940 CATGAGGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
ATACAATTAGTATCGATACTTAGTTGGGTATCG
Found at i:2966917 original size:15 final size:15
Alignment explanation
Indices: 2966870--2966921 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2966860 ATCGATACTA
2966870 ATACAATTAGTATCG
1 ATACAATTAGTATCG
* *
2966885 ATACTTAGTTGGGTATCG
1 ATAC--AATT-AGTATCG
2966903 ATACAATTAGTATCG
1 ATACAATTAGTATCG
2966918 ATAC
1 ATAC
2966922 TTAGTTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 14 0.47
16 3 0.10
17 3 0.10
18 10 0.33
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (15 bp):
ATACAATTAGTATCG
Found at i:2967031 original size:22 final size:19
Alignment explanation
Indices: 2966985--2967058 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
2966975 TGCATAAATG
2966985 GTATCGATACCATAATAGA
1 GTATCGATACCATAATAGA
*
2967004 GTATCGGTACCATAATATAGAA
1 GTATCGATACCAT-A-ATAG-A
* * * *
2967026 GTATCGATACTAAAAGACA
1 GTATCGATACCATAATAGA
2967045 GATATCGATACCAT
1 G-TATCGATACCAT
2967059 GGATTCAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 14 0.33
20 13 0.30
21 5 0.12
22 11 0.26
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
GTATCGATACCATAATAGA
Found at i:2967528 original size:55 final size:54
Alignment explanation
Indices: 2967444--2967687 Score: 371
Period size: 55 Copynumber: 4.4 Consensus size: 54
2967434 GCATGTTGCT
*
2967444 TAATAAGTTTATGAATTTTCGTTTGGGCACTGTGTGTGCAAAACTAAGAAATTCA
1 TAATAAGTTTATGAA-TTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* *
2967499 TAATAAGATTATGAAGTTTCGTATGGGCACTGTGTGTGTAAAACTAAGAAATTCA
1 TAATAAGTTTATGAA-TTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* *
2967554 TAATAAGTTTATGAATTTTCGTATGAGCACTGTGTGTGAAAAACTAAGAAATTCA
1 TAATAAGTTTATGAA-TTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
* * *
2967609 TAATATGTTTATGAATTTCTGTATGGGCATTGTGTGTGCAAAACTAAGAAATCCA
1 TAATAAGTTTATGAATTTC-GTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
2967664 TAATAAGTTTATGAATTTCCGTAT
1 TAATAAGTTTATGAATTT-CGTAT
2967688 TGTTAGTGGG
Statistics
Matches: 173, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
54 4 0.02
55 168 0.97
56 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (54 bp):
TAATAAGTTTATGAATTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCA
Found at i:2967899 original size:19 final size:18
Alignment explanation
Indices: 2967862--2967901 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2967852 CTCACTAAGA
2967862 AATTTCATAGCGTGTGTT
1 AATTTCATAGCGTGTGTT
2967880 AATTTCAT-GCGTAGGTGTT
1 AATTTCATAGCGT--GTGTT
2967899 AAT
1 AAT
2967902 ACAAGCGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (18 bp):
AATTTCATAGCGTGTGTT
Found at i:2968277 original size:15 final size:16
Alignment explanation
Indices: 2968252--2968285 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2968242 TGCACAGTAC
2968252 TTTTATTGCATGTGCA
1 TTTTATTGCATGTGCA
*
2968268 TTTT-TTGCATTTGCA
1 TTTTATTGCATGTGCA
2968283 TTT
1 TTT
2968286 ACCTTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTTATTGCATGTGCA
Found at i:2981631 original size:52 final size:52
Alignment explanation
Indices: 2981487--2981621 Score: 234
Period size: 52 Copynumber: 2.6 Consensus size: 52
2981477 AATATTCAGC
* *
2981487 CTTGACACTGTAAGAGCTTTGAGAGATTGTCTGGGGTCTAGGTGAAACACGT
1 CTTGACAATGTAAGAGCTTCGAGAGATTGTCTGGGGTCTAGGTGAAACACGT
* *
2981539 CTTGACATTGTAAGAGCTTCGAGAGATTGCCTGGGGTCTAGGTGAAACACGT
1 CTTGACAATGTAAGAGCTTCGAGAGATTGTCTGGGGTCTAGGTGAAACACGT
2981591 CTTGACAATGTAAGAGCTTCGAGAGATTGTC
1 CTTGACAATGTAAGAGCTTCGAGAGATTGTC
2981622 ATTTGTCTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (52 bp):
CTTGACAATGTAAGAGCTTCGAGAGATTGTCTGGGGTCTAGGTGAAACACGT
Found at i:2986069 original size:14 final size:14
Alignment explanation
Indices: 2986035--2986061 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2986025 TTTTGCCTCG
2986035 AATAAAATATGAAC
1 AATAAAATATGAAC
2986049 AATAAAATATGAA
1 AATAAAATATGAA
2986062 AGATAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AATAAAATATGAAC
Found at i:2987142 original size:43 final size:42
Alignment explanation
Indices: 2987036--2987142 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
2987026 ACAAATTTCT
* *****
2987036 TTGATTCTTCACAGAAGGAGTTGGATCAATATTTTTCATGAC
1 TTGATCCTTCACAGAAGGAGTTGGATCAATAACGACCATGAC
* * * * *
2987078 TCGATCCTTGACATAAAGAGTTGGATCAATAACGACCTTTGAC
1 TTGATCCTTCACAGAAGGAGTTGGATCAATAACGACC-ATGAC
2987121 TTGATCCTTCACAGAAGGAGTT
1 TTGATCCTTCACAGAAGGAGTT
2987143 CGACCAATGA
Statistics
Matches: 49, Mismatches: 15, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
42 27 0.55
43 22 0.45
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (42 bp):
TTGATCCTTCACAGAAGGAGTTGGATCAATAACGACCATGAC
Found at i:2988864 original size:2 final size:2
Alignment explanation
Indices: 2988857--2988914 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2988847 CTAAACGAGA
2988857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2988899 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2988915 TAGGTTTTGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2991299 original size:50 final size:50
Alignment explanation
Indices: 2991210--2991387 Score: 205
Period size: 50 Copynumber: 3.6 Consensus size: 50
2991200 GGAGTACTTA
* * * * *
2991210 TGTTTCGGATTTAGTTTATTAAATTTCCG-CAGTTAAACAGAAGTTAGTTC
1 TGTTTCGGGTTTAGTTTACTAAATTCCCGTC-GTTCAACAGAAGTTGGTTC
2991260 TGTTTCGGGTTTAGTTTACTAAATTCCCGTCGTTCAACAGAAGTTGGTTC
1 TGTTTCGGGTTTAGTTTACTAAATTCCCGTCGTTCAACAGAAGTTGGTTC
* * * * * * *
2991310 TATTTCAGGTTTAGTTTATTAAATTCCCGTTGTTCAACAAAAGGTGGTTA
1 TGTTTCGGGTTTAGTTTACTAAATTCCCGTCGTTCAACAGAAGTTGGTTC
* **
2991360 TGTTTCGAGTTTAAATTACTAAATTCCC
1 TGTTTCGGGTTTAGTTTACTAAATTCCC
2991388 TCCATTTAAC
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 108 0.99
51 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (50 bp):
TGTTTCGGGTTTAGTTTACTAAATTCCCGTCGTTCAACAGAAGTTGGTTC
Found at i:2992707 original size:18 final size:18
Alignment explanation
Indices: 2992684--2992718 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2992674 GAACCTCAAA
2992684 ATGGTATCGATACCATGC
1 ATGGTATCGATACCATGC
*
2992702 ATGGTATGGATACCATG
1 ATGGTATCGATACCATG
2992719 TAGTATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
ATGGTATCGATACCATGC
Found at i:2992751 original size:20 final size:20
Alignment explanation
Indices: 2992726--2992800 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
2992716 ATGTAGTATA
*
2992726 GTAGTACTGATACTATGAAT
1 GTAGTACCGATACTATGAAT
2992746 GTAGTACCGATACTATGAAT
1 GTAGTACCGATACTATGAAT
2992766 GTAGTACCGATACTATGAAT
1 GTAGTACCGATACTATGAAT
2992786 GTAGTACCGATACTA
1 GTAGTACCGATACTA
2992801 CTCATTTGGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (20 bp):
GTAGTACCGATACTATGAAT
Found at i:2998643 original size:20 final size:22
Alignment explanation
Indices: 2998618--2998680 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 22
2998608 ATTTTGTGTA
2998618 CTTAGTATCGATATTGTTCAT-
1 CTTAGTATCGATATTGTTCATG
* *
2998639 C-TAGTATCGATACTGTTCTTG
1 CTTAGTATCGATATTGTTCATG
*
2998660 CTTAGTATTGATATTGTTCAT
1 CTTAGTATCGATATTGTTCAT
2998681 ACAGTGCCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 16 0.46
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (22 bp):
CTTAGTATCGATATTGTTCATG
Found at i:2998739 original size:35 final size:35
Alignment explanation
Indices: 2998688--2998768 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
2998678 CATACAGTGC
* *
2998688 CGATTCTACTTGATAGGGTATCAATACCATGGTAT
1 CGATACTACTCGATAGGGTATCAATACCATGGTAT
* *
2998723 CGATACTACTCGATAGGTTATCGATACCATGGTAT
1 CGATACTACTCGATAGGGTATCAATACCATGGTAT
2998758 CGATACTACTC
1 CGATACTACTC
2998769 TAAATTTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (35 bp):
CGATACTACTCGATAGGGTATCAATACCATGGTAT
Found at i:3000460 original size:19 final size:19
Alignment explanation
Indices: 3000436--3000515 Score: 115
Period size: 19 Copynumber: 4.2 Consensus size: 19
3000426 CAGTTATTCG
*
3000436 AGCTTCAACAGGATACTCA
1 AGCTTCAACGGGATACTCA
* *
3000455 AGCTTCAACGGGAGACTCG
1 AGCTTCAACGGGATACTCA
*
3000474 AGCTTCAACGGGATACTCG
1 AGCTTCAACGGGATACTCA
*
3000493 AGCTTTAACGGGATACTCA
1 AGCTTCAACGGGATACTCA
3000512 AGCT
1 AGCT
3000516 AGATTTGACG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (19 bp):
AGCTTCAACGGGATACTCA
Found at i:3002929 original size:35 final size:35
Alignment explanation
Indices: 3002889--3002956 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3002879 TTGATGTTAT
* *
3002889 TTATAATAAGTTATGTCACTTGGTGAATAGACTTA
1 TTATAATAAGTCATGTCACTTGGTAAATAGACTTA
*
3002924 TTATAATGAGTCATGTCACTTGGTAAATAGACT
1 TTATAATAAGTCATGTCACTTGGTAAATAGACT
3002957 GATTTTCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACTTGGTAAATAGACTTA
Found at i:3007060 original size:25 final size:26
Alignment explanation
Indices: 3007031--3007086 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3007021 CCCTAACTCA
3007031 TTTTATAA-ATAAATTTTTTTATTTT
1 TTTTATAATATAAATTTTTTTATTTT
* * *
3007056 TTTTATAATTTTAATTTTTTTCTTTT
1 TTTTATAATATAAATTTTTTTATTTT
3007082 TTTTA
1 TTTTA
3007087 AGGTTAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATAATATAAATTTTTTTATTTT
Found at i:3008353 original size:59 final size:59
Alignment explanation
Indices: 3008260--3008422 Score: 265
Period size: 59 Copynumber: 2.7 Consensus size: 59
3008250 ATTCAAAATG
*
3008260 TTGTGAATCGAGCAATAGGAAATGTTAATCCCTCAAGTGGGGCATTGTTGA-TCTGAAGTA
1 TTGTGAATCGAGCAA-AGGAAATGTTAATCCCTCAAGTGAGGCATTGTTGATTC-GAAGTA
* *
3008320 TTGTGAATCGAGCAAAGGAAATGTTGATCCCTCAAGTGAGGCATTGTTGATTCGAAGTG
1 TTGTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTGAGGCATTGTTGATTCGAAGTA
*
3008379 TTGTTAATCGAGCAAAGGAAATGTTAATCCCTCAAGTGAGGCAT
1 TTGTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTGAGGCAT
3008423 AGTTTCTTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 80 0.82
60 17 0.18
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (59 bp):
TTGTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTGAGGCATTGTTGATTCGAAGTA
Found at i:3008560 original size:74 final size:74
Alignment explanation
Indices: 3008435--3008632 Score: 305
Period size: 74 Copynumber: 2.7 Consensus size: 74
3008425 TTTCTTTTGT
*
3008435 GAAAAAAAATCTCAAGTGAGATGAAAT-TT-TGTTTCGAGTGAAACTATCTCAAGC-ATGACAAA
1 GAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA-GACAAA
*
3008497 ATTTGTTTTAA
64 ATTTATTTTAA
* *
3008508 GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAGAT
1 GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAT
*
3008573 TTATTTTAT
66 TTATTTTAA
3008582 GAAAAACAATCTCAAGTGAGAT-AATCTTCTGTTTCGAGTGAAACTATCTCA
1 GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCA
3008633 TACGAGATAA
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
72 4 0.03
73 52 0.44
74 60 0.51
75 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (74 bp):
GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAAAAT
TTATTTTAA
Found at i:3008603 original size:36 final size:35
Alignment explanation
Indices: 3008429--3009241 Score: 124
Period size: 36 Copynumber: 21.9 Consensus size: 35
3008419 GCATAGTTTC
* *
3008429 TTTTGTGAAAAAAAATCTCAAGTGAGATGAAATTT-
1 TTTTATGAAAAACAATCTCAAGTGAGAT-AAATTTA
* * *
3008464 TGTTTCGAGTG--AAACTATCTCAAGCATGACA-AAATTTG
1 T-TTT--A-TGAAAAACAATCTCAAG--TGAGATAAATTTA
* *
3008502 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* *
3008538 TGTTTCGAGTG--AAACTATCTCAAGCGAGATAAGATTTA
1 T-TTT--A-TGAAAAACAATCTCAAGTGAGATAA-ATTTA
*
3008576 TTTTATGAAAAACAATCTCAAGTGAGAT-AATCTTC
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* *
3008611 TGTTTCGAGTG--AAACTATCTCATA-CGAGATAAATTT-
1 T-TTT--A-TGAAAAACAATCTCA-AGTGAGATAAATTTA
** * * * * * *
3008647 TTTGCCTCGAGTGAAACTATCTGAAGCGAGATGAATCTTG
1 TTT-TAT-GA--AAAACAATCTCAAGTGAGATAAAT-TTA
* * * *
3008687 TTTTAAGACAAACAATATCAAGTGAGATAAATCTTC
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* * * * *
3008723 TGTTT-TGAGTGAAACTATCTCAAGCGAGATGAATCTTG
1 T-TTTATGA--AAAACAATCTCAAGTGAGATAAAT-TTA
* ** *
3008761 TTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTTA
1 TTTTATGAAAAACAATCTCAAGTGAGAT-AAA--T-TTA
* * *** * * * *
3008800 TTTCGA-GTTAAAATTGTCCCAAGCGAGACAAAGTTTG
1 TTT-TATG-AAAAACAATCTCAAGTGAGATAAA-TTTA
* *
3008837 TTTTAAGAAAAACAATCACAAGTGAGATAAAATTTA
1 TTTTATGAAAAACAATCTCAAGTGAGAT-AAATTTA
* * * *
3008873 TGTTTCGAGTG-AAAACTATCTCAAGCGAGATGAATCTTG
1 T-TTT--A-TGAAAAACAATCTCAAGTGAGATAAAT-TTA
* ** * *
3008912 TTTTAAGAAAAACAATCTTGAGTGAAATGAATCTTA
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* * *
3008948 TGTTTCGAGTG--AAACCATCTCAAGCGAGGAAAAATCTTA
1 T-TTT--A-TGAAAAACAATCTCAAGTGA-GATAAAT-TTA
* * * *
3008987 TTTTAAGAAAAGCACTCTCAAGTGAGATAAATATTC
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* * *
3009023 TGTTTCGAGTG--AAACTATCTCAAGCGAGATAAATCTTG
1 T-TTT--A-TGAAAAACAATCTCAAGTGAGATAAAT-TTA
* * * * *
3009061 TTTTAAGAAAAACAATCT-AGAGTTAAATGAATCTTC
1 TTTTATGAAAAACAATCTCA-AGTGAGATAAAT-TTA
* * * *
3009097 TGTTTCGAGTG--AAACCATCTCAAGCGAGGTAAAATCTTG
1 T-TTT--A-TGAAAAACAATCTCAAGTGAGAT-AAAT-TTA
*
3009136 TTTTAAGAAAAACAATCTCAAGTGAGATAAATATT-
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT-TTA
* * * * *
3009171 TTGTT-TCGAGTGAAACTATCTCAAGCGAGATGAATATTG
1 TT-TTAT-GA--AAAACAATCTCAAGTGAGATAAAT-TTA
* *
3009210 TTTTAAGAAAATCAATCTCAAGTGAGATAAAT
1 TTTTATGAAAAACAATCTCAAGTGAGATAAAT
3009242 CTTCGTATTA
Statistics
Matches: 564, Mismatches: 135, Indels: 157
0.66 0.16 0.18
Matches are distributed among these distances:
33 1 0.00
34 11 0.02
35 20 0.04
36 180 0.32
37 104 0.18
38 161 0.29
39 67 0.12
40 20 0.04
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (35 bp):
TTTTATGAAAAACAATCTCAAGTGAGATAAATTTA
Found at i:3008639 original size:73 final size:72
Alignment explanation
Indices: 3008429--3008646 Score: 300
Period size: 73 Copynumber: 3.0 Consensus size: 72
3008419 GCATAGTTTC
* *
3008429 TTTTGTGAAAAAAAATCTCAAGTGAGATGAAAT-TT-TGTTTCGAGTGAAACTATCTCAA-GCAT
1 TTTTATGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAACG-A-
* *
3008491 GACAAAATTTG
63 GA-TAAATTTA
*
3008502 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
1 TTTTATGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAA-CGAGA
3008567 TAAGATTTA
65 TAA-ATTTA
3008576 TTTTATGAAAAACAATCTCAAGTGAGAT-AATCTTCTGTTTCGAGTGAAACTATCTCATACGAGA
1 TTTTATGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCA-ACGAGA
3008640 TAAATTT
65 TAAATTT
3008647 TTTGCCTCGA
Statistics
Matches: 133, Mismatches: 6, Indels: 13
0.88 0.04 0.09
Matches are distributed among these distances:
72 8 0.06
73 66 0.50
74 57 0.43
75 1 0.01
76 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (72 bp):
TTTTATGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAACGAGAT
AAATTTA
Found at i:3008916 original size:75 final size:74
Alignment explanation
Indices: 3008653--3009245 Score: 717
Period size: 75 Copynumber: 7.9 Consensus size: 74
3008643 ATTTTTTGCC
* * * *
3008653 TCGAGTGAAACTATCTGAAGCGAGATGAATCTTGTTTTAAGACAAACAATATCAAGTGAGATAAA
1 TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
3008718 TCTTCTGTT
66 TCTTCTGTT
* * ** *
3008727 TTGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAA
1 TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AA
* *
3008792 AT-GTCTTATT
65 ATCTTC-TGTT
* * * * * *
3008802 TCGAGTTAAAATTGTCCCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCACAAGTGAGATA
1 TCGAG-TGAAACTATCTCAAGCGAGATAAA-TCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-
*
3008866 AAAT-TTATGTT
63 AAATCTTCTGTT
* ** * *
3008877 TCGAGTGAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGA
1 TCGAGTG-AAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
*
3008942 ATCTTATGTT
65 ATCTTCTGTT
* * * * *
3008952 TCGAGTGAAACCATCTCAAGCGAGGAAAAATCTTATTTTAAGAAAAGCACTCTCAAGTGAGATAA
1 TCGAGTGAAACTATCTCAAGCGA-GATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
*
3009017 ATATTCTGTT
65 ATCTTCTGTT
* * *
3009027 TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCT-AGAGTTAAATGA
1 TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCA-AGTGAGATAA
3009091 ATCTTCTGTT
65 ATCTTCTGTT
* *
3009101 TCGAGTGAAACCATCTCAAGCGAGGTAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
1 TCGAGTGAAACTATCTCAAGCGAGAT-AAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
* *
3009166 ATATTTTGTT
65 ATCTTCTGTT
* * *
3009176 TCGAGTGAAACTATCTCAAGCGAGATGAATATTGTTTTAAGAAAATCAATCTCAAGTGAGATAAA
1 TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
3009241 TCTTC
66 TCTTC
3009246 GTATTAAATG
Statistics
Matches: 438, Mismatches: 70, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.00
74 181 0.41
75 204 0.47
76 51 0.12
77 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (74 bp):
TCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
TCTTCTGTT
Found at i:3009090 original size:149 final size:148
Alignment explanation
Indices: 3008653--3009227 Score: 798
Period size: 149 Copynumber: 3.9 Consensus size: 148
3008643 ATTTTTTGCC
* * ** * *
3008653 TCGAGTGAAACTATCTGAAGCGAGATGAATCTTGTTTTAAGACAAACAATATCAAGTGAGATAAA
1 TCGAGTGAAACCATCTCAAGCGAGAAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
* *
3008718 TCTTCTGTTTTGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGAG
66 TATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGAG
3008783 TGAAATGAAATGTCTTA--TT
131 TGAAATG-AA--TCTTATGTT
* *** * * *
3008802 TCGAGTTAAAATTGTCCCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCACAAGTGAGATA
1 TCGAG-TGAAACCATCTCAAGCGAGA-AAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
*
3008866 AA-ATTTATGTTTCGAGTGAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
64 AATA-TTCTGTTTCGAGTG-AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
3008930 TGAGTGAAATGAATCTTATGTT
127 TGAGTGAAATGAATCTTATGTT
* * *
3008952 TCGAGTGAAACCATCTCAAGCGAGGAAAAATCTTATTTTAAGAAAAGCACTCTCAAGTGAGATAA
1 TCGAGTGAAACCATCTCAAGCGA-GAAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
* *
3009017 ATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTAGA
65 ATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGA
* *
3009082 GTTAAATGAATCTTCTGTT
130 GTGAAATGAATCTTATGTT
*
3009101 TCGAGTGAAACCATCTCAAGCGAGGTAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
1 TCGAGTGAAACCATCTCAAGCGA-GAAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
* * *
3009166 ATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATATTGTTTTAAGAAAATCAATCT
65 ATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
3009228 CAAGTGAGAT
Statistics
Matches: 380, Mismatches: 37, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
148 5 0.01
149 204 0.54
150 112 0.29
151 59 0.16
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (148 bp):
TCGAGTGAAACCATCTCAAGCGAGAAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
TATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTTGAG
TGAAATGAATCTTATGTT
Found at i:3012076 original size:29 final size:29
Alignment explanation
Indices: 3012036--3012370 Score: 449
Period size: 29 Copynumber: 11.6 Consensus size: 29
3012026 TAGAAATTAA
* *
3012036 TTACAAAACTAGCACCCTGTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * *
3012065 TAATGAAACTAGCACCCTGTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
*
3012094 TTACGAAACTACCACCCTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
*
3012123 TTACGAAACTAGCACCGTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* *
3012152 TAACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
3012181 TTACGAAACTAGCA-CCTTTTCAAAAATAT
1 TTACGAAACTAGCACCCTTTT-AAAAATAT
* *
3012210 TTACGAAACTAACACCGTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * *
3012239 TTACAAAACTAACACCCTTTTAAATATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* *
3012268 TTACAAAACTAGCACCCTTTCAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * * *
3012297 TTACGAAACTAACAGCCTTTTACAATTAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
*
3012326 TTAAGAAACTAGCACCCTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
3012355 TTACAGAAA-TAGCACC
1 TTAC-GAAACTAGCACC
3012371 TAACATAAAT
Statistics
Matches: 269, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
28 6 0.02
29 254 0.94
30 9 0.03
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (29 bp):
TTACGAAACTAGCACCCTTTTAAAAATAT
Found at i:3013001 original size:32 final size:32
Alignment explanation
Indices: 3012965--3013025 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3012955 TTGTTTTAAC
*
3012965 TAAAACAA-ATAGCAACATGGCTTAGTGGTATA
1 TAAAAAAATATAGCAACAT-GCTTAGTGGTATA
*
3012997 TAAAAAAATATAGCATCATGCTTAGTGGT
1 TAAAAAAATATAGCAACATGCTTAGTGGT
3013026 TAGCTATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (32 bp):
TAAAAAAATATAGCAACATGCTTAGTGGTATA
Found at i:3019660 original size:29 final size:29
Alignment explanation
Indices: 3019616--3019950 Score: 404
Period size: 29 Copynumber: 11.6 Consensus size: 29
3019606 TAGAAATTAA
* *
3019616 TTACAAAACTAGCACCCTGTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * * *
3019645 TAATGAAACTATCACCCTGTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
3019674 TTACGAAACTAGCACCCTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* *
3019703 CTACGAAACTAGCACCGTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * *
3019732 TAATGAAACTTA-TACCCTTTTAAAAATAT
1 TTACGAAAC-TAGCACCCTTTTAAAAATAT
*
3019761 TTACGAAACTAGCACCCTTTCAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
** * *
3019790 TTTTGAAACTAACACCGTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * *
3019819 TTACAAAACTAACACCCTTTTAAATATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* *
3019848 TTACAAAACTAGCACCCTTTCAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
* * * *
3019877 TTACGAAACTAACAGCCTTTTACAATTAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
*
3019906 TTAAGAAACTAGCACCCTTTTAAAAATAT
1 TTACGAAACTAGCACCCTTTTAAAAATAT
3019935 TTACAGAAA-TAGCACC
1 TTAC-GAAACTAGCACC
3019951 TAACATAAAT
Statistics
Matches: 259, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
28 2 0.01
29 251 0.97
30 6 0.02
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (29 bp):
TTACGAAACTAGCACCCTTTTAAAAATAT
Found at i:3019983 original size:87 final size:87
Alignment explanation
Indices: 3019585--3020009 Score: 369
Period size: 87 Copynumber: 4.9 Consensus size: 87
3019575 ACATTCAACT
* * * * *
3019585 TTTACAAAAATAGCA-CCTAA-ATAGAAATTAATTACAAAACTAGCACCCTGTTAAAAATATTAA
1 TTTACAAAACTAGCACCCTAACA-A-AAA-TAATTACGAAACTAACACCCTTTTAAAAATATTTA
** * *
3019648 TGAAACTATCACCCTGTTAAAAATA
63 CAAAACTAACACCCTTTTAAAAATA
* *** * * * **
3019673 TTTACGAAACTAGCACCCTTTTAAAAAT-ATCTACGAAACTAGCACCGTTTTAAAAATATTAATG
1 TTTACAAAACTAGCACCCTAACAAAAATAAT-TACGAAACTAACACCCTTTTAAAAATATTTACA
* *
3019737 AAACTTATACCCTTTTAAAAATA
65 AAACTAACACCCTTTTAAAAATA
* ** * ** *
3019760 TTTACGAAACTAGCACCCTTTCAAAAATATTTTTGAAACTAACACCGTTTTAAAAATATTTACAA
1 TTTACAAAACTAGCACCCTAACAAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACAA
*
3019825 AACTAACACCCTTTTAAATATA
66 AACTAACACCCTTTTAAAAATA
** * * * *
3019847 TTTACAAAACTAGCACCCTTTCAAAAATATTTACGAAACTAACAGCCTTTTACAATTATTTA-AG
1 TTTACAAAACTAGCACCCTAACAAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACA-
*
3019911 AAACTAGCACCCTTTTAAAAATA
65 AAACTAACACCCTTTTAAAAATA
* ***
3019934 TTTACAGAAA-TAGCA-CCTAACATAAATTAATTACG-TGTTAGACACCCTTTTAAAAATATTTA
1 TTTACA-AAACTAGCACCCTAACA-AAAATAATTACGAAACTA-ACACCCTTTTAAAAATATTTA
*
3019996 CAAAAATAACACCC
63 CAAAACTAACACCC
3020010 GAGGCTTTCA
Statistics
Matches: 285, Mismatches: 43, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
86 10 0.04
87 249 0.87
88 21 0.07
89 4 0.01
90 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (87 bp):
TTTACAAAACTAGCACCCTAACAAAAATAATTACGAAACTAACACCCTTTTAAAAATATTTACAA
AACTAACACCCTTTTAAAAATA
Found at i:3020591 original size:33 final size:32
Alignment explanation
Indices: 3020544--3020606 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
3020534 ATTGTTTTAA
*
3020544 ATAAAACAAATAGCAACATGGCTTAGTGGTAT
1 ATAAAAAAAATAGCAACATGGCTTAGTGGTAT
*
3020576 ATAAAAAAATATAGCATCATGGCTTAGTGGT
1 ATAAAAAAA-ATAGCAACATGGCTTAGTGGT
3020607 TAGCTATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (32 bp):
ATAAAAAAAATAGCAACATGGCTTAGTGGTAT
Found at i:3027262 original size:29 final size:29
Alignment explanation
Indices: 3027229--3027661 Score: 534
Period size: 29 Copynumber: 15.1 Consensus size: 29
3027219 ATTAATTTCA
* *
3027229 AAACTAGCACCCTATTAAAAATATTTATG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* *
3027258 AAACTAGCA-CCTGTTAAAAATATTTACA
1 AAACTAGCACCCTTTTAAAAATATTTACG
*
3027286 AAACTAGCACCCTTTTAAAAATATTTACA
1 AAACTAGCACCCTTTTAAAAATATTTACG
3027315 AAACTAGCA-CCTTTTAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* * *
3027343 AAACTAACA-TCTTTTTAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* * *
3027371 AAACTAACACGCTTTTAAAAATATTTATG
1 AAACTAGCACCCTTTTAAAAATATTTACG
*
3027400 AAACTAGCACCCTTTCAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* *
3027429 AAACTAACACCGTTTTAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* *** *
3027458 AAACTAACATTGTTTTAAATATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
*
3027487 AAACTAGCACCCTTTCAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* ***
3027516 AAACTAACAGAGTTTTAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* * *
3027545 ACACTAACACCCTTTTAAATATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* **
3027574 AAACTAGTACATTTTTAAAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
* * *
3027603 AAACTAACACCCTTTTACAATTATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
3027632 AAACTAGCA-CCTTTT-AAAATATTTACG
1 AAACTAGCACCCTTTTAAAAATATTTACG
3027659 AAA
1 AAA
3027662 AATAACACCT
Statistics
Matches: 350, Mismatches: 52, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
27 13 0.04
28 83 0.24
29 254 0.73
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (29 bp):
AAACTAGCACCCTTTTAAAAATATTTACG
Found at i:3032157 original size:16 final size:16
Alignment explanation
Indices: 3032136--3032166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3032126 AAATGAATGG
3032136 TAAAAATAAAATAAAT
1 TAAAAATAAAATAAAT
*
3032152 TAAAAATAAATTAAA
1 TAAAAATAAAATAAA
3032167 GGGCTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATAAAT
Found at i:3032616 original size:16 final size:16
Alignment explanation
Indices: 3032580--3032616 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3032570 TAAATACAAC
3032580 TTTTTCATTTTTTATA
1 TTTTTCATTTTTTATA
* *
3032596 ATTTTCATTTTTTCTA
1 TTTTTCATTTTTTATA
3032612 TTTTT
1 TTTTT
3032617 TTAAAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTTTTATA
Found at i:3034463 original size:16 final size:16
Alignment explanation
Indices: 3034442--3034472 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3034432 AAATGAATGG
3034442 TAAAAATAAATTAAAT
1 TAAAAATAAATTAAAT
3034458 TAAAAATAAATTAAA
1 TAAAAATAAATTAAA
3034473 GGGCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATAAATTAAAT
Found at i:3034924 original size:17 final size:17
Alignment explanation
Indices: 3034886--3034924 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3034876 TAAATACAAC
3034886 TTTTTCATTTTTTTATA
1 TTTTTCATTTTTTTATA
*
3034903 ATTTTCATTTTTTCTAT-
1 TTTTTCATTTTTT-TATA
3034920 TTTTT
1 TTTTT
3034925 TAAAAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCATTTTTTTATA
Found at i:3037214 original size:17 final size:17
Alignment explanation
Indices: 3037176--3037214 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3037166 TAAATACAAC
3037176 TTTTTCATTTTTTTATA
1 TTTTTCATTTTTTTATA
*
3037193 ATTTTCATTTTTTCTAT-
1 TTTTTCATTTTTT-TATA
3037210 TTTTT
1 TTTTT
3037215 TAAAAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCATTTTTTTATA
Found at i:3039060 original size:16 final size:16
Alignment explanation
Indices: 3039039--3039069 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3039029 AAATGAATGG
3039039 TAAAAATAAAATAAAT
1 TAAAAATAAAATAAAT
*
3039055 TAAAAATAAATTAAA
1 TAAAAATAAAATAAA
3039070 GGGCTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATAAAT
Found at i:3041364 original size:16 final size:16
Alignment explanation
Indices: 3041343--3041373 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3041333 AAATGAATGG
3041343 TAAAAATAAAATAAAT
1 TAAAAATAAAATAAAT
*
3041359 TAAAAATAAATTAAA
1 TAAAAATAAAATAAA
3041374 GGGCTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATAAAT
Found at i:3041821 original size:17 final size:17
Alignment explanation
Indices: 3041783--3041821 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3041773 TAAATACAAC
3041783 TTTTTCATTTTTTTATA
1 TTTTTCATTTTTTTATA
* *
3041800 ATTTTCATTTTTTTCTA
1 TTTTTCATTTTTTTATA
3041817 TTTTT
1 TTTTT
3041822 TTAAAAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCATTTTTTTATA
Found at i:3044075 original size:18 final size:18
Alignment explanation
Indices: 3044049--3044109 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
3044039 GAAAATCGTC
* *
3044049 CCCTAGCTGGCAATAGGG
1 CCCTCGCTGTCAATAGGG
3044067 CCCTCGCTGTCAATAGGG
1 CCCTCGCTGTCAATAGGG
3044085 CCCTCGCTGTCAATAGGG
1 CCCTCGCTGTCAATAGGG
3044103 CCCTCGC
1 CCCTCGC
3044110 CGGCTACTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.16, C:0.36, G:0.28, T:0.20
Consensus pattern (18 bp):
CCCTCGCTGTCAATAGGG
Found at i:3046892 original size:38 final size:38
Alignment explanation
Indices: 3046841--3046920 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
3046831 GAAGGCGTCA
3046841 CAAAAATATTGAGATCAAATATAGGTTAATAAAAAGGG
1 CAAAAATATTGAGATCAAATATAGGTTAATAAAAAGGG
*
3046879 CAAAAATATTGAGATCGAATATAGGTTAATAAAAAGGG
1 CAAAAATATTGAGATCAAATATAGGTTAATAAAAAGGG
3046917 -AAAA
1 CAAAA
3046921 TTTGATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 4 0.10
38 37 0.90
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.23
Consensus pattern (38 bp):
CAAAAATATTGAGATCAAATATAGGTTAATAAAAAGGG
Found at i:3047351 original size:23 final size:23
Alignment explanation
Indices: 3047326--3047416 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
3047316 TACAGTAACG
*
3047326 TTCACAAACATGTTCATTTAA-C
1 TTCACAAACATTTTCATTTAATC
***
3047348 GTTCGTGAACATTTTCATTTAATC
1 -TTCACAAACATTTTCATTTAATC
3047372 TTCACAAACATTTTCATTTAATC
1 TTCACAAACATTTTCATTTAATC
3047395 TTCACAAACATTTTCATTTAAT
1 TTCACAAACATTTTCATTTAAT
3047417 GTTTGATAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 59 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (23 bp):
TTCACAAACATTTTCATTTAATC
Found at i:3050386 original size:19 final size:19
Alignment explanation
Indices: 3050342--3050391 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
3050332 GTATATTATA
*
3050342 AATGATA-TTATTGTAATT
1 AATGATATTTATGGTAATT
*
3050360 AATAATATTTATGGTAAATT
1 AATGATATTTATGGT-AATT
3050380 -ATGATATATTAT
1 AATGATAT-TTAT
3050392 AGTATATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (19 bp):
AATGATATTTATGGTAATT
Found at i:3052401 original size:157 final size:157
Alignment explanation
Indices: 3052115--3052429 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
3052105 ATAAGACTAG
3052115 GAAGACTGGTGGTGCTAGTTATTCAGTAAGAGGTATTGTTTCTTCCCTTTCCTAATGGTTGTATT
1 GAAGACTGGTGGTGCTAGTTATTCAGTAAGAGGTATTGTTTCTTCCCTTTCCTAATGGTTGTATT
3052180 TTTTGGAATGTTAGGGGATTTAATCATCCAAAAAAACAAGCTAAATTTCTGTACAGGGTGGAAAA
66 TTTTGGAATGTTAGGGGATTTAATCATCCAAAAAAACAAGCTAAATTTCTGTACAGGGTGGAAAA
3052245 GTTGCATGTTGAAATGTTTTGCATTTT
131 GTTGCATGTTGAAATGTTTTGCATTTT
3052272 GAAGACTGGTGGTGCTAGTTATTCAGTAAGAGGTATTGTTTCTTCCCTTTCCTAATGGTTGTATT
1 GAAGACTGGTGGTGCTAGTTATTCAGTAAGAGGTATTGTTTCTTCCCTTTCCTAATGGTTGTATT
3052337 TTTTGGAATGTTAGGGGATTTAATCATCCAAAAAAACAAGCTAAATTTCTGTACAGGGTGGAAAA
66 TTTTGGAATGTTAGGGGATTTAATCATCCAAAAAAACAAGCTAAATTTCTGTACAGGGTGGAAAA
3052402 GTTGCATGTTGAAATGTTTTGCATTTT
131 GTTGCATGTTGAAATGTTTTGCATTTT
3052429 G
1 G
3052430 GAAAATAGAG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (157 bp):
GAAGACTGGTGGTGCTAGTTATTCAGTAAGAGGTATTGTTTCTTCCCTTTCCTAATGGTTGTATT
TTTTGGAATGTTAGGGGATTTAATCATCCAAAAAAACAAGCTAAATTTCTGTACAGGGTGGAAAA
GTTGCATGTTGAAATGTTTTGCATTTT
Found at i:3062421 original size:48 final size:48
Alignment explanation
Indices: 3062301--3062483 Score: 174
Period size: 48 Copynumber: 3.8 Consensus size: 48
3062291 GTGGAGCAAT
* * *
3062301 TAGCATGTCTGACATCTTTGTGATGGTGGTGCTACTATTAATACTGAT-T
1 TAGCACGTCTGACATCTTTGTGACGGTGGTGCTACTATT-A-ACTGATAA
* *
3062350 TAGCACGTCTGGCGTCTTTGTGACGGTGGTGCTACTATTAAC-GATAAA
1 TAGCACGTCTGACATCTTTGTGACGGTGGTGCTACTATTAACTGAT-AA
* * * * * * *
3062398 TAGCACATCTGACGTCTATGTGACAGTGGTGCTATTATGAACTG-TACC
1 TAGCACGTCTGACATCTTTGTGACGGTGGTGCTACTATTAACTGATA-A
* * *
3062446 TAGCACGTCTAACATCTGTGTGACGTTGGTGCTACTAT
1 TAGCACGTCTGACATCTTTGTGACGGTGGTGCTACTAT
3062484 CGATGGTACC
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
46 3 0.03
47 3 0.03
48 69 0.62
49 36 0.32
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (48 bp):
TAGCACGTCTGACATCTTTGTGACGGTGGTGCTACTATTAACTGATAA
Found at i:3062700 original size:30 final size:28
Alignment explanation
Indices: 3062595--3062739 Score: 159
Period size: 28 Copynumber: 5.0 Consensus size: 28
3062585 TATAAAACGA
*
3062595 AAAAGTGAAT-AGTATATGCTATGAAATG
1 AAAAGTGAATGA-TACATGCTATGAAATG
3062623 AAAAGTGAATGATACATGCTATGAAATG
1 AAAAGTGAATGATACATGCTATGAAATG
*
3062651 AAAAGTGAATGATACATGCTATGTAATG
1 AAAAGTGAATGATACATGCTATGAAATG
* * * *
3062679 AATTAAATGAATTATATATGCTATGAAATA
1 AA--AAGTGAATGATACATGCTATGAAATG
*
3062709 AATGAAGTGAATTGA-ACATGCTATGATATG
1 AA--AAGTGAA-TGATACATGCTATGAAATG
3062739 A
1 A
3062740 TATGTTATGA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 54 0.54
29 1 0.01
30 43 0.43
31 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.30
Consensus pattern (28 bp):
AAAAGTGAATGATACATGCTATGAAATG
Found at i:3066964 original size:13 final size:13
Alignment explanation
Indices: 3066946--3066972 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3066936 GATACCTGGC
3066946 ATATTAACTATAT
1 ATATTAACTATAT
3066959 ATATTAACTATAT
1 ATATTAACTATAT
3066972 A
1 A
3066973 AGAGTATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTAACTATAT
Found at i:3073370 original size:26 final size:25
Alignment explanation
Indices: 3073340--3073401 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
3073330 AGTTTTCTTA
3073340 GCAGTCAATAACTCTATAAAGCACAG
1 GCAGTCAATAACT-TATAAAGCACAG
*
3073366 GCAGTCAATAA-TTCTAAAGCACAG
1 GCAGTCAATAACTTATAAAGCACAG
3073390 GCAGTCAATAAC
1 GCAGTCAATAAC
3073402 CCTAAAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 22 0.65
25 1 0.03
26 11 0.32
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (25 bp):
GCAGTCAATAACTTATAAAGCACAG
Found at i:3073388 original size:24 final size:24
Alignment explanation
Indices: 3073340--3073415 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
3073330 AGTTTTCTTA
*
3073340 GCAGTCAATAACTCTATAAAGCACAG
1 GCAGTCAATAA-T-TCTAAAGCACAG
3073366 GCAGTCAATAATTCTAAAGCACAG
1 GCAGTCAATAATTCTAAAGCACAG
** *
3073390 GCAGTCAATAACCCTAAAGAACAG
1 GCAGTCAATAATTCTAAAGCACAG
3073414 GC
1 GC
3073416 GGAACACGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 34 0.74
25 1 0.02
26 11 0.24
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (24 bp):
GCAGTCAATAATTCTAAAGCACAG
Found at i:3073701 original size:31 final size:31
Alignment explanation
Indices: 3073655--3073771 Score: 137
Period size: 31 Copynumber: 3.8 Consensus size: 31
3073645 ATTTTCTTGA
* * *
3073655 AAAATTATAAATTAAACCTTCAAAAATTTTG
1 AAAATTTTAATTTAAACCTTCAAATATTTTG
* * *
3073686 AAAATTTTGATTTAAATCTTTAAATA-TTTG
1 AAAATTTTAATTTAAACCTTCAAATATTTTG
* *
3073716 AAAATTTTAATCTAAACCTTCAAATATTTTT
1 AAAATTTTAATTTAAACCTTCAAATATTTTG
* *
3073747 AAAATTTTAAGTTAACCCTTCAAAT
1 AAAATTTTAATTTAAACCTTCAAAT
3073772 CTATCACCAA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
30 26 0.37
31 45 0.63
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTTTAATTTAAACCTTCAAATATTTTG
Found at i:3076937 original size:29 final size:27
Alignment explanation
Indices: 3076893--3076960 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
3076883 TTTAAAAGTG
*
3076893 TATTTTATTTTTTATTAT-AAAAATGAA
1 TATTTTATTTTATATTATGAAAAAT-AA
*
3076920 TATGTTTATCTTTATATTTTGAAAAATAA
1 TAT-TTTAT-TTTATATTATGAAAAATAA
*
3076949 TATTTTAATTTA
1 TATTTTATTTTA
3076961 GAATATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 7 0.20
28 9 0.26
29 13 0.37
30 6 0.17
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (27 bp):
TATTTTATTTTATATTATGAAAAATAA
Found at i:3077001 original size:18 final size:20
Alignment explanation
Indices: 3076967--3077003 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3076957 TTTAGAATAT
3076967 TAAAATTATTGTTAATTTAC
1 TAAAATTATTGTTAATTTAC
3076987 TAAAA-TATT-TTAATTTA
1 TAAAATTATTGTTAATTTA
3077004 AGTATTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TAAAATTATTGTTAATTTAC
Found at i:3078321 original size:29 final size:29
Alignment explanation
Indices: 3078289--3078346 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3078279 AAAGTGAAGG
3078289 ACAAAAG-GTTTTATAAATTATAATAAAGT
1 ACAAAAGTG-TTTATAAATTATAATAAAGT
*
3078318 ACAAAATTGTTTATAAATTATAATAAAGT
1 ACAAAAGTGTTTATAAATTATAATAAAGT
3078347 GTTAAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (29 bp):
ACAAAAGTGTTTATAAATTATAATAAAGT
Found at i:3078425 original size:28 final size:28
Alignment explanation
Indices: 3078377--3078432 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3078367 AAGTATACTT
* **
3078377 TTTTTTTATAAATTATGATAAAGGACAA
1 TTTTTTTATAAAATACAATAAAGGACAA
3078405 TTTTTTTATAAAATACAATAAAGGACAA
1 TTTTTTTATAAAATACAATAAAGGACAA
3078433 CTTCTCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (28 bp):
TTTTTTTATAAAATACAATAAAGGACAA
Found at i:3078450 original size:27 final size:28
Alignment explanation
Indices: 3078384--3078452 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
3078374 CTTTTTTTTT
** * * *
3078384 ATAAATTATGATAAAGGACAATTTTTTT
1 ATAAATTACAATAAAGGACAATCTTCTC
*
3078412 ATAAAATACAATAAAGGACAA-CTTCTC
1 ATAAATTACAATAAAGGACAATCTTCTC
3078439 ATAAATTACAATAA
1 ATAAATTACAATAA
3078453 CACTATCATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (28 bp):
ATAAATTACAATAAAGGACAATCTTCTC
Found at i:3078632 original size:22 final size:22
Alignment explanation
Indices: 3078604--3078663 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
3078594 ATACGGATGG
*
3078604 TGGAAGAAGGTTGCACGAATGC
1 TGGAAGAAGGCTGCACGAATGC
3078626 TGGAAGAAGGCTGCACGAATGC
1 TGGAAGAAGGCTGCACGAATGC
**
3078648 TGGAAGCGGGCTGCAC
1 TGGAAGAAGGCTGCAC
3078664 AGGCGCTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.38, T:0.15
Consensus pattern (22 bp):
TGGAAGAAGGCTGCACGAATGC
Found at i:3080130 original size:131 final size:131
Alignment explanation
Indices: 3079887--3080195 Score: 485
Period size: 131 Copynumber: 2.4 Consensus size: 131
3079877 ATAATTCTAA
* * * *
3079887 GAGAGAAAACGGTAATATCTAATAATTTCCATTCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * *
3079952 GTCATTTATTACTCCGATCGAAATGAAGAGATATCACTATTTTGTCTTAAAATTCAATATTGGTT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
3080017 C
131 C
3080018 GAGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
3080083 ATCATTTATTACTCTAATTGAAATGAAGAGATATCAAC-ATTTCGTCTTAAAAATCAATATTGAT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATC-ACTATTTCGTCTTAAAAATCAATATTGAT
3080147 TC
130 TC
* *
3080149 GAGAGAAAATGATAAAATCTAATTATTTCCAATCGAGAATAAATGAC
1 GAGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGAC
3080196 GTTGTAACAC
Statistics
Matches: 164, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 162 0.99
132 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (131 bp):
GAGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
C
Found at i:3084423 original size:20 final size:21
Alignment explanation
Indices: 3084384--3084423 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3084374 GAAAAACTGG
3084384 TTTATTTTGAATACTAATAACT
1 TTTATTTTG-ATACTAATAACT
*
3084406 TTTATTTTG-TACTCATAA
1 TTTATTTTGATACTAATAA
3084424 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTATTTTGATACTAATAACT
Found at i:3085128 original size:2 final size:2
Alignment explanation
Indices: 3085123--3085154 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3085113 AAATAACATA
3085123 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
3085155 TATTTATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3086325 original size:17 final size:17
Alignment explanation
Indices: 3086303--3086344 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3086293 GTCACAGGAT
3086303 AGATCTTCTCATTGCAC
1 AGATCTTCTCATTGCAC
3086320 AGATCTTCTCATTGCAC
1 AGATCTTCTCATTGCAC
3086337 AGATCTTC
1 AGATCTTC
3086345 GGTTTGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (17 bp):
AGATCTTCTCATTGCAC
Found at i:3086937 original size:3 final size:3
Alignment explanation
Indices: 3086929--3086958 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3086919 AAACAAAACA
3086929 AAT AAT AAT AAT AAT AAT ACAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA
3086959 CCCGGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3092273 original size:92 final size:93
Alignment explanation
Indices: 3092116--3092301 Score: 365
Period size: 92 Copynumber: 2.0 Consensus size: 93
3092106 AACGGCGGCA
3092116 GCAACAGTAATGCTAGGGTTTAGAAACCCTAGCTGAAACCCCAAATTAGTTTAGGGTTTCCATTT
1 GCAACAGTAATGCTAGGGTTTAGAAACCCTAGCTGAAACCCCAAATTAGTTTAGGGTTTCCATTT
3092181 AGG-TTGGGTTGGGTCTGGGATTTGAAT
66 AGGTTTGGGTTGGGTCTGGGATTTGAAT
3092208 GCAACAGTAATGCTAGGGTTTAGAAACCCTAGCTGAAACCCCAAATTAGTTTAGGGTTTCCATTT
1 GCAACAGTAATGCTAGGGTTTAGAAACCCTAGCTGAAACCCCAAATTAGTTTAGGGTTTCCATTT
3092273 AGGTTTGGGTTGGGTCTGGGATTTGAAT
66 AGGTTTGGGTTGGGTCTGGGATTTGAAT
3092301 G
1 G
3092302 TAATTGGGCT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 68 0.73
93 25 0.27
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (93 bp):
GCAACAGTAATGCTAGGGTTTAGAAACCCTAGCTGAAACCCCAAATTAGTTTAGGGTTTCCATTT
AGGTTTGGGTTGGGTCTGGGATTTGAAT
Found at i:3092352 original size:3 final size:3
Alignment explanation
Indices: 3092334--3092411 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
3092324 TTGTAATATT
* * * *
3092334 TAA TAAA TAA TAAA TAA TAT TAC TAT TAA TAA TTA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
3092381 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3092412 TTAAAATGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3092694 original size:76 final size:76
Alignment explanation
Indices: 3092568--3093101 Score: 921
Period size: 76 Copynumber: 7.0 Consensus size: 76
3092558 GGTCTTATGA
*
3092568 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
3092632 CAGGACTTACAG
65 AAGGACTTACAG
* * *
3092644 ATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3092709 AGGACTTACAG
66 AGGACTTACAG
3092720 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3092785 AGGACTTACAG
66 AGGACTTACAG
* *
3092796 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTTGGAAACATCATGCACTG
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTG
*
3092861 AAGGGCTTACAG
65 AAGGACTTACAG
*
3092873 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
3092938 ATGACTTACAG
66 AGGACTTACAG
*
3092949 ATGACCCGAAGGTTTTGAAAAC-TC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3093012 AGGACTTACAG
66 AGGACTTACAG
*
3093023 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3093088 AGGACTTACAG
66 AGGACTTACAG
3093099 ATG
1 ATG
3093102 TAGGAAATAG
Statistics
Matches: 438, Mismatches: 16, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
74 70 0.16
75 4 0.01
76 290 0.66
77 74 0.17
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:3092935 original size:153 final size:152
Alignment explanation
Indices: 3092568--3093101 Score: 930
Period size: 153 Copynumber: 3.5 Consensus size: 152
3092558 GGTCTTATGA
*
3092568 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* * * *
3092632 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAAC
65 AAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
3092697 ATCATGCACTGTAGGACTTACAG
130 ATCATGCACTGAAGGACTTACAG
3092720 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
3092785 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTTGGAAAC
66 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAAC
*
3092850 ATCATGCACTGAAGGGCTTACAG
130 ATCATGCACTGAAGGACTTACAG
*
3092873 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
3092938 ATGACTTACAGATGACCCGAAGGTTTTGAAAAC-TC-AAAAGCTCCCGAAGGCTTTTTGGAAACA
66 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
3093001 TCATGCACTGAAGGACTTACAG
131 TCATGCACTGAAGGACTTACAG
*
3093023 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3093088 AGGACTTACAGATG
66 AGGACTTACAGATG
3093102 TAGGAAATAG
Statistics
Matches: 365, Mismatches: 15, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
150 109 0.30
151 16 0.04
152 112 0.31
153 128 0.35
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (152 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
TCATGCACTGAAGGACTTACAG
Found at i:3092968 original size:229 final size:226
Alignment explanation
Indices: 3092568--3093101 Score: 935
Period size: 229 Copynumber: 2.3 Consensus size: 226
3092558 GGTCTTATGA
*
3092568 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
3092632 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAAC
65 AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAAC
*
3092697 ATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
130 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC-TC-AAAAGCTCCCGAAGGC
3092762 TTTTTGGAAACATCATGCACTGAAGGACTTACAG
193 TTTTTGGAAACATCATGCACTGAAGGACTTACAG
*
3092796 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTTGGAAACATCATGCACTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTG
* * *
3092861 AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGACGGCTTTTTGGAAAC
65 AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAAC
* *
3092926 ATCATGCACTGAATGACTTACAGATGACCCGAAGGTTTTGAAAACTCAAAAGCTCCCGAAGGCTT
130 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACTCAAAAGCTCCCGAAGGCTT
3092991 TTTGGAAACATCATGCACTGAAGGACTTACAG
195 TTTGGAAACATCATGCACTGAAGGACTTACAG
3093023 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
3093088 AGGACTTACAGATG
66 AGGACTTACAGATG
3093102 TAGGAAATAG
Statistics
Matches: 292, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
226 36 0.12
227 92 0.32
228 40 0.14
229 124 0.42
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (226 bp):
ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACA
TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACTCAAAAGCTCCCGAAGGCTTT
TTGGAAACATCATGCACTGAAGGACTTACAG
Found at i:3093790 original size:22 final size:22
Alignment explanation
Indices: 3093760--3093807 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3093750 TTTGTTTGAA
* *
3093760 CTTTGAAAAGAGAATCTGTCAT
1 CTTTAAAAAGAGAATCTATCAT
3093782 CTTTAAAAAGAGAATCTATCAT
1 CTTTAAAAAGAGAATCTATCAT
3093804 CTTT
1 CTTT
3093808 GAAGAGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
CTTTAAAAAGAGAATCTATCAT
Found at i:3094225 original size:51 final size:52
Alignment explanation
Indices: 3094170--3094319 Score: 189
Period size: 51 Copynumber: 2.9 Consensus size: 52
3094160 AGAATAGCAG
* ***
3094170 GTTCGTAAAACATTTGATAGTGCATTCATCCTTCCTGTGGCTTCTGCTC-AT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTCCTGTGGCTTCTGCTCAAT
* * *
3094221 GTTCGTAAAACATTTGACAACACATTC-T-TTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTCCTGTGGCTTCTGCTCA-AT
*
3094272 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCC-TTCCTGTGGCTTCTGC
3094320 CAAGATTTCT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
49 16 0.19
50 1 0.01
51 52 0.63
52 1 0.01
54 13 0.16
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTCCTGTGGCTTCTGCTCAAT
Found at i:3096616 original size:93 final size:91
Alignment explanation
Indices: 3096441--3096725 Score: 399
Period size: 94 Copynumber: 3.1 Consensus size: 91
3096431 TCCTTATTTC
* * * * *
3096441 TACTATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCA
1 TACTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGG-TTTCATACCAAACCAGATCA
*
3096506 GATAATTCAAAGAACACTTCCAGAAGA
65 GATAACTCAAAGAACACTTCCAGAAGA
* * * *
3096533 TGCTATGAGTACATTCATCTTCCAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGACC
1 TACTATGAGCACATTCATCTTCCAAATTCAATGATTGGTT-T-TGGTTTCATACCAAACCAGATC
*
3096598 AGATAACTCAAAGAACACTTCCCAAAAGA
64 AGATAACTCAAAGAACACTT-CCAGAAGA
* *
3096627 TTCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTATGGTTTCATACCAAACCAGGTC
1 TACTATGAGCACATTCATCTTCCAAATTCAATGATTGGTT-T-TGGTTTCATACCAAACCAGATC
3096692 AGATAACTCAAAGAACACTTCCAGAAGA
64 AGATAACTCAAAGAACACTTCCAGAAGA
3096720 TACTAT
1 TACTAT
3096726 TGGGTCTTCT
Statistics
Matches: 170, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
92 34 0.20
93 48 0.28
94 88 0.52
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (91 bp):
TACTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGA
Found at i:3098892 original size:2 final size:2
Alignment explanation
Indices: 3098885--3098928 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3098875 ACAACAAATG
3098885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3098927 AT
1 AT
3098929 TAAAGGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3103204 original size:22 final size:18
Alignment explanation
Indices: 3103161--3103232 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 18
3103151 ACAGAAAAAT
* *
3103161 AAATAATAAAATACT-TGC
1 AAATAAT-AAATATTATGA
3103179 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAATATT-AT--GA
*
3103201 AAATATATAAATACTATGA
1 AAATA-ATAAATATTATGA
3103220 AAATAATAAATAT
1 AAATAATAAATAT
3103233 ATAAAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 20 0.45
19 7 0.16
20 1 0.02
21 2 0.05
22 12 0.27
23 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATAATAAATATTATGA
Found at i:3103231 original size:18 final size:19
Alignment explanation
Indices: 3103161--3103229 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
3103151 ACAGAAAAAT
*
3103161 AAATAATAAAATACT-TGC
1 AAATAATAAAATACTATGA
* *
3103179 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAA-A-TACTATGA
3103201 AAAT-ATATAAATACTATGA
1 AAATAATA-AAATACTATGA
3103220 AAATAATAAA
1 AAATAATAAA
3103230 TATATAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
18 7 0.17
19 15 0.38
20 6 0.15
21 7 0.17
22 5 0.12
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
AAATAATAAAATACTATGA
Found at i:3103240 original size:18 final size:19
Alignment explanation
Indices: 3103179--3103241 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 19
3103169 AAATACTTGC
*
3103179 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAATACT-ATAA-A
*
3103201 AAATATATAAATACTAT-GA
1 AAATA-ATAAATACTATAAA
3103220 AAATAATAAATA-TATAAA
1 AAATAATAAATACTATAAA
3103238 AAAT
1 AAAT
3103242 TTGAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 3 0.08
18 12 0.33
19 6 0.17
21 2 0.06
22 11 0.31
23 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATAATAAATACTATAAA
Found at i:3105496 original size:3 final size:3
Alignment explanation
Indices: 3105478--3105543 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
3105468 TTGTAATATT
* * * *
3105478 TAA TAAA TAA TAAA TAA TAT TAC TAT TAA TAA TAA TAA TAA TTA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
3105525 TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
3105544 TTAAAATGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3106971 original size:15 final size:15
Alignment explanation
Indices: 3106951--3106979 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3106941 TTACACATTT
3106951 TCTTAAATTTTGATA
1 TCTTAAATTTTGATA
3106966 TCTTAAATTTTGAT
1 TCTTAAATTTTGAT
3106980 TCCATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
TCTTAAATTTTGATA
Found at i:3110699 original size:39 final size:39
Alignment explanation
Indices: 3110637--3110712 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
3110627 CACCTGGCAG
* *
3110637 TGCTGGAAGCTGTTGCAACTGATGCGTGGAGGGGCTGCT
1 TGCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
* *
3110676 TGCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTG
1 TGCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTG
3110713 TTGGATGGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.43, T:0.25
Consensus pattern (39 bp):
TGCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
Found at i:3111274 original size:139 final size:139
Alignment explanation
Indices: 3110963--3111308 Score: 464
Period size: 139 Copynumber: 2.5 Consensus size: 139
3110953 CTAGCAAAAA
* *
3110963 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
3111028 C-TCCTTCTGGAAATGCTGATCTTCAAAAGAGGGATTTGTTGATTCAACTCCATATGTGATGAAT
66 CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAAT
* *
3111092 TAAGGTAAG
131 CAAGGCAAG
* *
3111101 GTTGAACAAATTCTGCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
3111166 CTTCC-TCTGAAAATATTGATCCTCAAATGA-GGTTCTTCTTTCATTCAATTCCATAGGAGATGA
66 CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGAT-TT-GTTCATTCAACTCCATAGGAGATGA
*
3111229 ATCAATGCAAG
129 ATCAAGGCAAG
* * *
3111240 GTTGAACAAGTTCTTCTCGTTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
3111305 CTTC
66 CTTC
3111309 ACCTGGAAAT
Statistics
Matches: 182, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
137 3 0.02
138 84 0.46
139 95 0.52
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (139 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAAT
CAAGGCAAG
Found at i:3111505 original size:118 final size:123
Alignment explanation
Indices: 3111237--3111556 Score: 415
Period size: 118 Copynumber: 2.6 Consensus size: 123
3111227 GAATCAATGC
* * *
3111237 AAGGTTGAACAAGTTCTTCTCGTTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
3111302 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCGAGCAA
66 GAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCTTTGTGG-AATAGAGTCGAGCAA
* *
3111361 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCATCTT-CTCTTCAGATAAGCTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
3111425 GAACTTTCTCTGGAAA-AG-T-TGGTTGATCTATC-CTTCTGT-G-ATAGATTC-ATGCAA
66 GAACTTTCTCTGGAAATAGCTCT-GCTGATCTATCTCTT-TGTGGAATAGAGTCGA-GCAA
* *
3111479 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
3111544 GAACTTTCTCTGG
66 GAACTTTCTCTGG
3111557 CAACACTGAT
Statistics
Matches: 176, Mismatches: 15, Indels: 15
0.85 0.07 0.07
Matches are distributed among these distances:
117 1 0.01
118 46 0.26
119 37 0.21
120 5 0.03
121 12 0.07
122 2 0.01
123 35 0.20
124 38 0.22
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCTTTGTGGAATAGAGTCGAGCAA
Found at i:3112275 original size:76 final size:76
Alignment explanation
Indices: 3111721--3112274 Score: 805
Period size: 76 Copynumber: 7.4 Consensus size: 76
3111711 GAGGTCTTAT
* * * * *
3111721 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTT-AAGA--TCAAAAAGCTCCCGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
*
3111783 CTTTTTGAAAA
66 CTTTTTGGAAA
* * ** * * * * *
3111794 CATTATGCACTGTAGGTGTTACAGATGACCCTGAGGCTAT-AAGA--TCAAAAAGCTTCTGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
*
3111856 CTTTTTGAAAA
66 CTTTTTGGAAA
* * * *
3111867 CATCATGCATTGTAGGTCTTACAGATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGG-TTTGAAAACGTCAAAAAGCTCCCGAAG
3111932 GCTTTTTGGAAA
65 GCTTTTTGGAAA
* * * *
3111944 CATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
3112009 CTTTTTGGAAA
66 CTTTTTGGAAA
*
3112020 TATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
3112085 CTTTTTGGAAA
66 CTTTTTGGAAA
*
3112096 CATCATGCACTGCAGGACTTACAGATGTCCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
3112161 CTTTTTGGAAA
66 CTTTTTGGAAA
* *
3112172 CATCATGCACTGCAGGAGTTACAGATGTCCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
1 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
3112237 CTTTTTGGAAA
66 CTTTTTGGAAA
3112248 CATCATGCACTGCAGGACTTACAGATG
1 CATCATGCACTGCAGGACTTACAGATG
3112275 TGGGAAATAG
Statistics
Matches: 447, Mismatches: 30, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
73 99 0.22
74 2 0.00
75 3 0.01
76 285 0.64
77 58 0.13
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (76 bp):
CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACGTCAAAAAGCTCCCGAAGG
CTTTTTGGAAA
Found at i:3112547 original size:163 final size:164
Alignment explanation
Indices: 3112277--3112649 Score: 599
Period size: 163 Copynumber: 2.3 Consensus size: 164
3112267 TACAGATGTG
3112277 GGAAATAGTTTACTAAGT-AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
** * *
3112341 TAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAATATGTTGA
66 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAACATGTTAA
3112406 TTGGGTAACATGCCCCAATCTCAAGATAAGGGTT
131 TTGGGTAACATGCCCCAATCTCAAGATAAGGGTT
3112440 GGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
* **
3112504 TAGAAAAGATAAAATGAGAAAACTATGGAAATCG-TTTCTCATTATTTTTTGAAATAACATGTTA
66 TAGAAAAGATAAAATGAG-AAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAACATGTTA
3112568 ATTGGGTAACATGCCCCAATCTCAAGATAAGGGTT
130 ATTGGGTAACATGCCCCAATCTCAAGATAAGGGTT
* *
3112603 AGAAATAGTTTACTAAGTTAAATGAGAAACTATGGAAATCGTTTTCT
1 GGAAATAGTTTACTAAG-TAAA--A-AAACTAAGGAAATCGTTTTCT
3112650 CATTATTTTT
Statistics
Matches: 195, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
163 113 0.58
164 61 0.31
166 1 0.01
167 20 0.10
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (164 bp):
GGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAACATGTTAA
TTGGGTAACATGCCCCAATCTCAAGATAAGGGTT
Found at i:3115851 original size:93 final size:94
Alignment explanation
Indices: 3115749--3115920 Score: 319
Period size: 93 Copynumber: 1.8 Consensus size: 94
3115739 TTCATCTTTT
3115749 AATTCCAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCCAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAACACTTCCAG
3115814 AAGATGCTATTGGGCATATTCATCTTCCA
66 AAGATGCTATTGGGCATATTCATCTTCCA
3115843 AATT-CAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCCAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAACACTTCCAG
**
3115907 AAGATTTTATTGGG
66 AAGATGCTATTGGG
3115921 TCTCTTTATT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 72 0.95
94 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (94 bp):
AATTCCAATGATTGGTTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATTGGGCATATTCATCTTCCA
Found at i:3115998 original size:114 final size:114
Alignment explanation
Indices: 3115831--3116149 Score: 496
Period size: 114 Copynumber: 2.8 Consensus size: 114
3115821 TATTGGGCAT
* * * * * * * *
3115831 ATTCATCTTCCAAATTCAATGATTGGTTCTGTG-GTTCCTATCGAACCAGATCAGATAACTCAAA
1 ATTCATCTTTCAAATCCAATGATTGATTTTG-GAGTTCATACCAAATCAGATCAGATAACTCAAA
** * * *
3115895 GAACACTTCCAGAAGATTTTATTGGGTCTCTTTATTTGTACTATGAGCAA
65 GAACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACCATGAGCAA
3115945 ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAG
3116010 AACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACCATGAGCAA
66 AACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACCATGAGCAA
*
3116059 ATTCATCTTTCAAATCCAATGATTGATTTTGTAGTTCATACCAAATCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAG
3116124 AACACTTCCAGAAGATGCTATTGGGC
66 AACACTTCCAGAAGATGCTATTGGGC
3116150 ACATTCATCT
Statistics
Matches: 190, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 1 0.01
114 189 0.99
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (114 bp):
ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTACCATGAGCAA
Found at i:3116219 original size:94 final size:93
Alignment explanation
Indices: 3116059--3116242 Score: 305
Period size: 94 Copynumber: 2.0 Consensus size: 93
3116049 CCATGAGCAA
* * *
3116059 ATTCATCTTTCAAATCCAATGATTGATTTTGTAGTTCATACCAAATCAGATCAGATAACTCAAAG
1 ATTCATCTTCCAAATCCAATGATTGATTCTGTAGTTCATACCAAACCAGATCAGATAACTCAAAG
3116124 AACACTTCCAGAAGATGCTATTGGGCAC
66 AACACTTCCAGAAGATGCTATTGGGCAC
* * *
3116152 ATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCCAAATCCAATGATTGATTCTGTAG-TTCATACCAAACCAGATCAGATAACTCAAA
3116217 GAACACTTCCAGAAGATGCTATTGGG
65 GAACACTTCCAGAAGATGCTATTGGG
3116243 TCTTCTTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 29 0.35
94 55 0.65
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (93 bp):
ATTCATCTTCCAAATCCAATGATTGATTCTGTAGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGCAC
Found at i:3120346 original size:27 final size:27
Alignment explanation
Indices: 3120316--3120371 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3120306 GTAATTATGT
3120316 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
3120343 AAAAATGTAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
3120370 AA
1 AA
3120372 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:3120466 original size:15 final size:15
Alignment explanation
Indices: 3120431--3120470 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3120421 ATAAAAGTAT
3120431 AAATGCAAAAAATGAA
1 AAATGC-AAAAATGAA
* *
3120447 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
3120462 AAATGCAAA
1 AAATGCAAA
3120471 TGTATGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.12
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:3123305 original size:2 final size:2
Alignment explanation
Indices: 3123298--3123343 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3123288 ATTTTAATAA
*
3123298 AT AT AT AT AT AT -T AT TT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3123338 AT AT AT
1 AT AT AT
3123344 TTATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3123315 original size:22 final size:22
Alignment explanation
Indices: 3123290--3123331 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3123280 AATATAGGAT
3123290 TTTAATAAATATATATATATTA
1 TTTAATAAATATATATATATTA
* *
3123312 TTTATTATATATATATATAT
1 TTTAATAAATATATATATAT
3123332 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATAAATATATATATATTA
Found at i:3123322 original size:14 final size:15
Alignment explanation
Indices: 3123301--3123348 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3123291 TTAATAAATA
3123301 TATATATATTATTTAT
1 TATATATA-TATTTAT
*
3123317 TATATATATATATAT
1 TATATATATATTTAT
3123332 ATATATATATATTTAT
1 -TATATATATATTTAT
3123348 T
1 T
3123349 TATTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATATATATTTAT
Found at i:3123322 original size:18 final size:18
Alignment explanation
Indices: 3123299--3123352 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
3123289 TTTTAATAAA
3123299 TATATATATATTATTTAT
1 TATATATATATTATTTAT
*
3123317 TATATATATA-TATATA-
1 TATATATATATTATTTAT
3123333 TATATATATATTTATTTAT
1 TATATATATA-TTATTTAT
3123352 T
1 T
3123353 TTTATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 15 0.48
19 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATATATATTATTTAT
Found at i:3123378 original size:14 final size:14
Alignment explanation
Indices: 3123359--3123387 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3123349 TATTTTTATA
3123359 AATAATAAAATAAT
1 AATAATAAAATAAT
3123373 AATAATAAAATAAT
1 AATAATAAAATAAT
3123387 A
1 A
3123388 TTGCAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:3124478 original size:39 final size:39
Alignment explanation
Indices: 3124417--3124493 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
3124407 ACCTGGCAGT
* *
3124417 GCTGGAAGCTGTTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
3124456 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
3124494 GGATGGAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:3125331 original size:24 final size:24
Alignment explanation
Indices: 3125286--3125331 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3125276 CCTCAATAGT
*
3125286 AGCTTCAACTTCTTCATCAGCAGC
1 AGCTTCAACTTCTCCATCAGCAGC
*
3125310 AGCTTCAA-TATCTCCATTAGCA
1 AGCTTCAACT-TCTCCATCAGCA
3125332 CCAGGGGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (24 bp):
AGCTTCAACTTCTCCATCAGCAGC
Found at i:3128076 original size:23 final size:23
Alignment explanation
Indices: 3128046--3128152 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
3128036 AGTCGAGGGT
*
3128046 TCTATGTGATCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
*
3128069 TCTATGTGGTCCTTCAGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* * *
3128092 TCTATATGGTCTTTTGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* * * *
3128115 CCTATGTGGTCATTTGGGATAAA
1 TCTATGTGGTCCTTCGGGACAAA
*
3128138 --TATGTGGTGCTTCGG
1 TCTATGTGGTCCTTCGG
3128153 TGTAAATTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
21 12 0.17
23 59 0.83
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:3128264 original size:18 final size:19
Alignment explanation
Indices: 3128241--3128276 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3128231 ATATTGGGCT
*
3128241 AATTAAATAAATT-ATATA
1 AATTAAACAAATTGATATA
3128259 AATTAAACAAATTGATAT
1 AATTAAACAAATTGATAT
3128277 GGAATGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTAAACAAATTGATATA
Found at i:3133426 original size:19 final size:19
Alignment explanation
Indices: 3133372--3133426 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3133362 AACCAATAAT
3133372 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
3133391 GATGAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
3133410 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
3133427 GAAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:3133536 original size:26 final size:26
Alignment explanation
Indices: 3133507--3133655 Score: 78
Period size: 26 Copynumber: 5.7 Consensus size: 26
3133497 GCAAAGAAAC
*
3133507 TAAAAATATAAT-GAAAATAAATAGTA
1 TAAAAATATAATAAAAAATAAATA-TA
*
3133533 TAAATAA-ATAATAAAAAATATATATA
1 TAAA-AATATAATAAAAAATAAATATA
** **
3133559 TAAAAATATAA-AAATGTATGTATAATA
1 TAAAAATATAATAAA-AAATAAAT-ATA
* *
3133586 TAATAAA-ATACTAAATAAT-AATA-A
1 TAA-AAATATAATAAAAAATAAATATA
* *
3133610 TAATAATA-AATGAAAAATAAATATA
1 TAAAAATATAATAAAAAATAAATATA
*
3133635 TATATAATATTAACTAAAAAA
1 TA-AAAATA-TAA-TAAAAAA
3133656 ATAGTAATCA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
23 9 0.09
24 9 0.09
25 9 0.09
26 32 0.34
27 22 0.23
28 8 0.08
29 6 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
TAAAAATATAATAAAAAATAAATATA
Found at i:3133539 original size:13 final size:12
Alignment explanation
Indices: 3133521--3133570 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
3133511 AATATAATGA
3133521 AAATAAATAGTAT
1 AAATAAATA-TAT
3133534 AAATAAATA-AT
1 AAATAAATATAT
3133545 AAA-AAATATAT
1 AAATAAATATAT
* *
3133556 ATATAAAAATAT
1 AAATAAATATAT
3133568 AAA
1 AAA
3133571 AATGTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 5 0.16
11 9 0.28
12 9 0.28
13 9 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:3133563 original size:14 final size:14
Alignment explanation
Indices: 3133508--3133568 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 14
3133498 CAAAGAAACT
*
3133508 AAAA-ATATA-ATG
1 AAAATATATATATA
*
3133520 AAAATAAATAGTATA
1 AAAATATATA-TATA
3133535 AATAA-ATA-ATA-A
1 AA-AATATATATATA
3133547 AAAATATATATATA
1 AAAATATATATATA
3133561 AAAATATA
1 AAAATATA
3133569 AAAATGTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
11 2 0.05
12 10 0.26
13 9 0.23
14 10 0.26
15 6 0.15
16 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:3133582 original size:24 final size:24
Alignment explanation
Indices: 3133525--3133588 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
3133515 TAATGAAAAT
3133525 AAATA-GTATAAATAAATAATAAA
1 AAATATGTATAAATAAATAATAAA
*
3133548 AAATATATATATAA-AAAT-ATAAA
1 AAATATGTATA-AATAAATAATAAA
*
3133571 AATGTATGTATAATATAA
1 AA-ATATGTATAA-ATAA
3133589 TAAAATACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 13 0.39
24 16 0.48
25 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATATGTATAAATAAATAATAAA
Found at i:3133590 original size:24 final size:22
Alignment explanation
Indices: 3133525--3133593 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
3133515 TAATGAAAAT
*
3133525 AAATAGTATAAATAAATAATAAA
1 AAATA-TATATATAAATAATAAA
3133548 AAATATATATATAAA-AATATAA
1 AAATATATATATAAATAATA-AA
* *
3133570 AAATGTATGTATAATATAATAAA
1 AAATATATATATAA-ATAATAAA
3133593 A
1 A
3133594 TACTAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.10
22 23 0.57
23 9 0.22
24 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATATATATATAAATAATAAA
Found at i:3134376 original size:37 final size:37
Alignment explanation
Indices: 3134283--3134384 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
3134273 ATACTTGTGG
* * ** * *
3134283 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
3134320 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
3134357 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3134385 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:3135320 original size:106 final size:106
Alignment explanation
Indices: 3135137--3136412 Score: 1931
Period size: 106 Copynumber: 12.0 Consensus size: 106
3135127 GCATTGTTTC
* * * * * *
3135137 GAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
3135202 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * *
3135243 GAGTCCAATATCCTTTGTTGTGAATTTGAAATTGGCTCAAAAAATGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3135308 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3135349 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3135414 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135455 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3135520 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
3135561 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
3135626 CCAGTGATCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3135667 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3135732 CCAGCGGTCCCTTCCTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135773 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
3135838 CCAGCGGTCCCTTCTTTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3135879 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
3135944 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3135985 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
3136050 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTTTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3136091 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3136156 CCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3136197 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3136262 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3136303 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
3136368 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3136409 GAGT
1 GAGT
3136413 GGCACGATAT
Statistics
Matches: 1072, Mismatches: 98, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 1072 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Done.