Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 57 of 126
Found at i:16644209 original size:35 final size:35
Alignment explanation
Indices: 16644141--16644209 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
16644131 CTTTCTCTTG
* *
16644141 CTCTCTTTATTTTTTCTTCTTTTTTGTTGTTTTTT
1 CTCTCTTTATTTTTTCCTATTTTTTGTTGTTTTTT
16644176 CTCTCTTT-TTTTTTCCTATTTTGTTGTT-TTTTTT
1 CTCTCTTTATTTTTTCCTATTTT-TTGTTGTTTTTT
16644210 ATTGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (35 bp):
CTCTCTTTATTTTTTCCTATTTTTTGTTGTTTTTT
Found at i:16650966 original size:43 final size:42
Alignment explanation
Indices: 16650851--16651119 Score: 274
Period size: 43 Copynumber: 6.3 Consensus size: 42
16650841 CAAAGCCATA
* * * * * *
16650851 AGTCTTCCTTTAAACATAA-CTTGATGCTCATTCCGAGTCACG
1 AGTCTTCATTTATACATAATC-TCATGCTCATTCCAAGACATG
* * *
16650893 AGTCTTC-CTTAAACATAATCTCATGCTCATTCCAAGTCATG
1 AGTCTTCATTTATACATAATCTCATGCTCATTCCAAGACATG
* * * **
16650934 AGTCTTCAATTTATACATAATCTAATGCTCATTCCGAGTCACA
1 AGTCTTC-ATTTATACATAATCTCATGCTCATTCCAAGACATG
**
16650977 AGTCTTTCATTTATACATAATCTCATGCTCACCCCAAGACATG
1 AGTC-TTCATTTATACATAATCTCATGCTCATTCCAAGACATG
*
16651020 AGTCTTCCATTTATACATAATCTCATGCTCA-TCTCGAGACATG
1 AGTCTT-CATTTATACATAATCTCATGCTCATTC-CAAGACATG
* *
16651063 AGTCTTCTATTTATACATAATCTCATGTTCATCCCAGAGACATG
1 AGTCTTC-ATTTATACATAATCTCATGCTCATTCCA-AGACATG
16651107 AGTCTTCCATTTA
1 AGTCTT-CATTTA
16651120 CGCCAAGTGA
Statistics
Matches: 195, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
41 35 0.18
42 12 0.06
43 125 0.64
44 22 0.11
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (42 bp):
AGTCTTCATTTATACATAATCTCATGCTCATTCCAAGACATG
Found at i:16651023 original size:86 final size:85
Alignment explanation
Indices: 16650851--16651119 Score: 348
Period size: 86 Copynumber: 3.2 Consensus size: 85
16650841 CAAAGCCATA
* * * *
16650851 AGTCTTCC-TTTAAACATAA-CTTGATGCTCATTCCGAGTCACGAGTCTTC-CTTAAACATAATC
1 AGTCTTCCATTTATACATAATC-TAATGCTCATTCCGAGTCACGAGTCTTCATTTATACATAATC
* *
16650913 TCATGCTCATTCCAAGTCATG
65 TCATGCTCATCCCAAGACATG
* *
16650934 AGTCTTCAATTTATACATAATCTAATGCTCATTCCGAGTCACAAGTCTTTCATTTATACATAATC
1 AGTCTTCCATTTATACATAATCTAATGCTCATTCCGAGTCACGAGTC-TTCATTTATACATAATC
*
16650999 TCATGCTCACCCCAAGACATG
65 TCATGCTCATCCCAAGACATG
* * *
16651020 AGTCTTCCATTTATACATAATCTCATGCTCA-TCTCGAGACATGAGTCTTCTATTTATACATAAT
1 AGTCTTCCATTTATACATAATCTAATGCTCATTC-CGAGTCACGAGTCTTC-ATTTATACATAAT
*
16651084 CTCATGTTCATCCCAGAGACATG
64 CTCATGCTCATCCCA-AGACATG
16651107 AGTCTTCCATTTA
1 AGTCTTCCATTTA
16651120 CGCCAAGTGA
Statistics
Matches: 163, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
83 7 0.04
84 33 0.20
85 9 0.06
86 94 0.58
87 20 0.12
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (85 bp):
AGTCTTCCATTTATACATAATCTAATGCTCATTCCGAGTCACGAGTCTTCATTTATACATAATCT
CATGCTCATCCCAAGACATG
Found at i:16656360 original size:12 final size:12
Alignment explanation
Indices: 16656343--16656368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16656333 ACTTTACGAG
16656343 TTTTTATTTATT
1 TTTTTATTTATT
16656355 TTTTTATTTATT
1 TTTTTATTTATT
16656367 TT
1 TT
16656369 CTTACATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:16657961 original size:120 final size:120
Alignment explanation
Indices: 16657744--16657962 Score: 330
Period size: 120 Copynumber: 1.8 Consensus size: 120
16657734 TTCCACAAGT
* *
16657744 TATAATCCAAAATTTTATCCTCATGTCTATATCAACTCTGTTACCAGTATACCATGCTGCTCACA
1 TATAATCCAAAATTTCATCCTCATGTCTATATCAACTCTGTTACCAGTATACCATGCTACTCACA
* *
16657809 TGAGATGTCGAGGACTCGCAACATATGCGGTACCCCAACCATCGATATGGTATGC
66 CGAGATGTCGAGGACTCACAACATATGCGGTACCCCAACCATCGATATGGTATGC
* * * * * *
16657864 TATAATCCAGAATTTCATTCTCATGTCTGTATCAACTCTGTTGCCAGTATACGATGTTACTCACA
1 TATAATCCAAAATTTCATCCTCATGTCTATATCAACTCTGTTACCAGTATACCATGCTACTCACA
* *
16657929 CGAGCTGTCGAGGACTCACAACATATGTGGTACC
66 CGAGATGTCGAGGACTCACAACATATGCGGTACC
16657963 TTAGCCATCT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (120 bp):
TATAATCCAAAATTTCATCCTCATGTCTATATCAACTCTGTTACCAGTATACCATGCTACTCACA
CGAGATGTCGAGGACTCACAACATATGCGGTACCCCAACCATCGATATGGTATGC
Found at i:16660686 original size:153 final size:149
Alignment explanation
Indices: 16660518--16661085 Score: 677
Period size: 153 Copynumber: 3.8 Consensus size: 149
16660508 CGAAAATTTC
* * *
16660518 TTTTTTTTTTATTAAAATCAAAAGCTTTCTTTTAATTAAAT-AAAATCACTACTTTACTTCAAAG
1 TTTTTATTTT-TTAAAATCAAAA-CTTTCTTTT--TTAAATGAAAATCACTACTTTACTTAAAAA
* * * *
16660582 TCAAAACTTTTATTTCTAAATAATTAAAAAAAATCAAAACTTTGTTTTAACAATTTAAAGTTTTT
62 TCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTG-TTTAAAAATTTAAACTTTTT
*
16660647 CTTTAAAATCACTAAAAAAATAGA
126 CTTTAAAATAACTAAAAAAATAGA
**
16660671 TTTTTATTTTTTTAAAATCTAATTTTCTTTCTTTTTT-AATGAAAATCACTACTTTACTTAAAAA
1 TTTTTA-TTTTTTAAAATC-AA--AACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAA
* * *
16660735 TCCAAACTTTTATTTCGAAATTGTTAAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTCTTT
62 TCAAAACTTTTATTTCGAAATAGTT-AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTT
*
16660800 CTTTAAAATTACTAAAAAACAT--A
126 CTTTAAAATAACTAAAAAA-ATAGA
* * * * *
16660823 TTTTTATTTTTTAAAATCTAAATTTTCTTTCTTTTTAATGAAAATCATTACCTTACTTAAAAATC
1 TTTTTATTTTTTAAAATCAAAACTTTC-TT-TTTTAAATGAAAATCACTACTTTACTTAAAAATC
*
16660888 CAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTT
64 AAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTT
*
16660952 TAAAATAACT-AAAAAACAGA
129 TAAAATAACTAAAAAAATAGA
* * * *
16660972 TTTTTATTTTTAAAAAT-ATAAACTCTCTTTTTTAAA-GAAAATAACTATTTTACTTAAAAATCA
1 TTTTTATTTTTTAAAATCA-AAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCA
* * *
16661035 AAACTTTTATTTCGAAATTATTTAAAAAAAAACTAAAACTTT-TTTCAAAAT
65 AAACTTTTATTTCGAAA-TAGTTAAAAAAAATC-AAAACTTTGTTTAAAAAT
16661086 CAAGCTATTT
Statistics
Matches: 363, Mismatches: 36, Indels: 37
0.83 0.08 0.08
Matches are distributed among these distances:
146 39 0.11
147 11 0.03
148 27 0.07
149 82 0.23
150 5 0.01
151 61 0.17
152 10 0.03
153 92 0.25
154 27 0.07
155 9 0.02
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (149 bp):
TTTTTATTTTTTAAAATCAAAACTTTCTTTTTTAAATGAAAATCACTACTTTACTTAAAAATCAA
AACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTA
AAATAACTAAAAAAATAGA
Found at i:16660988 original size:149 final size:150
Alignment explanation
Indices: 16660559--16661085 Score: 715
Period size: 149 Copynumber: 3.5 Consensus size: 150
16660549 TTAATTAAAT
* * * *
16660559 AAAATCACTACTTTACTTCAAAGTCAAAACTTTTATTTCTAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* * * *
16660624 TGTTTTAACAATTTAAAGTTTTTCTTTAAAATCACTAAAAAAATAGATTTTTATTTTTTTAAAAT
66 TG-TTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACAGATTTTTA-TTTTTTAAAAT
16660689 CT-AATTTTCTTTCTTTTTTAATG
128 CTAAATTTTCTTTC-TTTTTAATG
* *
16660712 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATTGTTAAAAAAAAATCAAAACT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTT-AAAAAAAATCAAAACT
* * *
16660777 TTGTTTAAAAATTTAAACTCTTTCTTTAAAATTACTAAAAAACATATTTTTATTTTTTAAAATCT
65 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATCT
16660842 AAATTTTCTTTCTTTTTAATG
130 AAATTTTCTTTCTTTTTAATG
* * *
16660863 AAAATCATTACCTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* *
16660927 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATCTA
* * *
16660992 AA--CTCTCT-TTTTTAAAG
131 AATTTTCTTTCTTTTTAATG
* * * *
16661009 AAAATAACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATTATTTAAAAAAAAACTAAAAC
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAA-TAGTTAAAAAAAATC-AAAAC
*
16661074 TTT-TTTCAAAAT
64 TTTGTTTAAAAAT
16661086 CAAGCTATTT
Statistics
Matches: 338, Mismatches: 31, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
146 46 0.14
147 8 0.02
148 16 0.05
149 86 0.25
151 67 0.20
152 25 0.07
153 71 0.21
154 19 0.06
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (150 bp):
AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAATCTA
AATTTTCTTTCTTTTTAATG
Found at i:16661508 original size:3 final size:3
Alignment explanation
Indices: 16661502--16661539 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16661492 AATAATAATA
16661502 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
16661540 TTGGGCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16662909 original size:23 final size:23
Alignment explanation
Indices: 16662865--16662909 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16662855 AAGTCAAAAA
* **
16662865 AAATTTTTAAGGTAGTCGAAATT
1 AAATTTTTAAGATAGTAAAAATT
*
16662888 AAATTTTTACGATAGTAAAAAT
1 AAATTTTTAAGATAGTAAAAAT
16662910 GTAATTTCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (23 bp):
AAATTTTTAAGATAGTAAAAATT
Found at i:16663733 original size:17 final size:17
Alignment explanation
Indices: 16663695--16663772 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
16663685 AACTTTTAAT
*
16663695 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
16663712 TTTTTAAATTTAAATTCA
1 -TTTTAAATTTAAATTTA
* *
16663730 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
16663747 CTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
16663764 CTTTAAATT
1 TTTTAAATT
16663773 AAAAAATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
17 36 0.71
18 15 0.29
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:16665649 original size:28 final size:27
Alignment explanation
Indices: 16665617--16665716 Score: 69
Period size: 29 Copynumber: 3.5 Consensus size: 27
16665607 TGAACTTTCC
16665617 AAAAATTACATTTTACCCCCGGATTTT
1 AAAAATTACATTTTACCCCCGGATTTT
* *
16665644 AAAAAATT-CTATTTTTGA-CCCCGAACTTCT
1 -AAAAATTAC-A-TTTT-ACCCCCGGA-TTTT
* **
16665674 AAAAATTATCATTTTACCCTCGGATATCC
1 AAAAATTA-CATTTTACCCCCGGAT-TTT
*
16665703 AAAAATTCCATTTT
1 AAAAATTACATTTT
16665717 TGACCCCGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
27 1 0.02
28 16 0.28
29 35 0.60
30 5 0.09
31 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (27 bp):
AAAAATTACATTTTACCCCCGGATTTT
Found at i:16665665 original size:29 final size:28
Alignment explanation
Indices: 16665633--16665724 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
16665623 TACATTTTAC
16665633 CCCCGGATTTTAAAAAATTCTATTTTTGA
1 CCCCGGATTTT-AAAAATTCTATTTTTGA
* * *
16665662 CCCCGAACTTCTAAAAATTATCA-TTTT-A
1 CCCCGGA-TTTTAAAAATTCT-ATTTTTGA
** *
16665690 CCCTCGGATATCCAAAAATTCCATTTTTGA
1 CCC-CGGAT-TTTAAAAATTCTATTTTTGA
16665720 CCCCG
1 CCCCG
16665725 AACCTTCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
28 6 0.12
29 36 0.72
30 8 0.16
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (28 bp):
CCCCGGATTTTAAAAATTCTATTTTTGA
Found at i:16665687 original size:58 final size:56
Alignment explanation
Indices: 16665616--16665746 Score: 181
Period size: 58 Copynumber: 2.3 Consensus size: 56
16665606 CTGAACTTTC
* * *
16665616 CAAAAATTACATTTTACCCCCGGATTTTAAAAAATTCTATTTTTGACCCCGAACTT
1 CAAAAATTACATTTTACCCCCGGATATCAAAAAATTCCATTTTTGACCCCGAACTT
* *
16665672 CTAAAAATTATCATTTTACCCTCGGATATCCAAAAATTCCATTTTTGACCCCGAACCTT
1 C-AAAAATTA-CATTTTACCCCCGGATATCAAAAAATTCCATTTTTGACCCCGAA-CTT
16665731 CAAAAATTACTATTTT
1 CAAAAATTAC-ATTTT
16665747 GCCCGGAAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
56 1 0.02
57 9 0.14
58 52 0.79
59 4 0.06
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (56 bp):
CAAAAATTACATTTTACCCCCGGATATCAAAAAATTCCATTTTTGACCCCGAACTT
Found at i:16665747 original size:29 final size:28
Alignment explanation
Indices: 16665645--16665746 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 28
16665635 CCGGATTTTA
16665645 AAAAATTCTATTTTTGACCCCGAACTTC
1 AAAAATTCTATTTTTGACCCCGAACTTC
* *
16665673 TAAAAATTATCA-TTTT-ACCCTCGGATA-TCC
1 -AAAAATTCT-ATTTTTGACCC-C-GA-ACTTC
*
16665703 AAAAATTCCATTTTTGACCCCGAACCTTC
1 AAAAATTCTATTTTTGACCCCGAA-CTTC
16665732 AAAAATTACTATTTT
1 AAAAATT-CTATTTT
16665747 GCCCGGAAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
27 1 0.02
28 7 0.12
29 34 0.59
30 15 0.26
31 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (28 bp):
AAAAATTCTATTTTTGACCCCGAACTTC
Found at i:16678255 original size:210 final size:210
Alignment explanation
Indices: 16677892--16678585 Score: 988
Period size: 209 Copynumber: 3.3 Consensus size: 210
16677882 TGCGATTACC
* * * * *
16677892 CAAAACAAGCGATGTGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-CA
1 CAAAACAAGTGATGCGATCATCTTCCTGAAGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
* * *
16677956 AAGCTCAATGTGAGCGAAA-CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAA
66 AGGCTCAAAGTGAGC-AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * * * *
16678020 GCAATAAA-ATAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
130 GCAATAAAGA-GGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGA
*
16678084 GATACAGAGAAGCGGGT
194 GATACAGAGAAGCGGAT
** * *
16678101 TGAAACAAGTGATGCGGTCATCTTCCTGAAGAAATACTGAGAAGTAGACCAAATCAATGAAACCA
1 CAAAACAAGTGATGCGATCATCTTCCTGAAGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
** * *
16678166 AGGCTCAAAGTGAGCAAATCTTCGAATACTAGCTTCCTGATGAGATACAGAGAAGCAGGTCGAAG
66 AGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
16678231 CAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCATCTTCCTGATGAGA
131 CAATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGA
* *
16678296 CACAAAGAAGTC-GAT
196 TACAGAGAAG-CGGAT
16678311 CAAAACAAGTGATGCGATCATCTTCCT-AATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
1 CAAAACAAGTGATGCGATCATCTTCCTGAA-GAGATACTGAGAAGTAGACCAAATCAATGAAACC
* *
16678375 -AGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGC-GCTTCGA
65 AAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAG-GTCGA
* *
16678438 AGAAATAAAGAGGTTACCTTCCTGATGAGATACAGAAAAGTGAACCAGATCCGTCTTCCTGATGA
129 AGCAATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGA
*
16678503 GATACAGAGAAGTGGAT
194 GATACAGAGAAGCGGAT
* * *
16678520 CAAAACAAGTGATGCGATCATCTACCTGATGAGATACTGAGAAGTAGACCAAATCAATGACACCA
1 CAAAACAAGTGATGCGATCATCTTCCTGAAGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
16678585 A
66 A
16678586 ACCACTGAAG
Statistics
Matches: 432, Mismatches: 44, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
208 1 0.00
209 248 0.57
210 182 0.42
211 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (210 bp):
CAAAACAAGTGATGCGATCATCTTCCTGAAGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
AGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
CAATAAAGAGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGA
TACAGAGAAGCGGAT
Found at i:16678900 original size:17 final size:17
Alignment explanation
Indices: 16678878--16678972 Score: 118
Period size: 17 Copynumber: 5.5 Consensus size: 17
16678868 AACTTTTAAT
*
16678878 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
16678895 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
16678912 TTTTTAAATTTAAATTCA
1 -TTTTAAATTTAAATTTA
* *
16678930 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
16678947 CTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
16678964 TTTTAAATT
1 TTTTAAATT
16678973 AAAAAAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
17 51 0.77
18 15 0.23
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:16678917 original size:35 final size:35
Alignment explanation
Indices: 16678876--16678972 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 35
16678866 CCAACTTTTA
* *
16678876 ATTTTTAAATTTTAATTTATTTTAAATTTGAATTT
1 ATTTTTAAATTTAAATTTATTTTAAATTTAAATTT
* * *
16678911 ATTTTTAAATTTAAATTCATTTTGAGTTTAAATTT
1 ATTTTTAAATTTAAATTTATTTTAAATTTAAATTT
* *
16678946 A-CTTTAAATTTGAATTTATTTTAAATT
1 ATTTTTAAATTTAAATTTATTTTAAATT
16678973 AAAAAAATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 21 0.40
35 31 0.60
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (35 bp):
ATTTTTAAATTTAAATTTATTTTAAATTTAAATTT
Found at i:16678925 original size:6 final size:6
Alignment explanation
Indices: 16678879--16678972 Score: 52
Period size: 6 Copynumber: 16.3 Consensus size: 6
16678869 ACTTTTAATT
* * * **
16678879 TTTAAA TTTTAA TTT-AT TTTAAA TTTGAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
16678926 -TTCAT TTTGAG TTTAAA TTT-AC TTTAAA TTTGAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
16678971 TT
1 TT
16678973 AAAAAAATTA
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
5 15 0.23
6 49 0.77
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:16680993 original size:28 final size:29
Alignment explanation
Indices: 16680887--16681004 Score: 120
Period size: 29 Copynumber: 4.1 Consensus size: 29
16680877 TGGACATCCG
* *
16680887 GGGT-AAAATGGTAATTTTTGAAAGTTTTA
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTGA
* * *
16680916 GGGTTAAAATGGAATTTTTAGAAGTTTTG-
1 GGGTAAAAATGTAATTTTTGGAAG-TTTGA
16680945 GGGTTAAAAATG-AATTTTTGGAAGTTTGA
1 GGG-TAAAAATGTAATTTTTGGAAGTTTGA
16680974 GGGTAAAAATGTAA-TTTTGGATAGTTT-A
1 GGGTAAAAATGTAATTTTTGGA-AGTTTGA
16681002 GGG
1 GGG
16681005 ACCTCTAGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
28 23 0.30
29 39 0.51
30 15 0.19
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTGA
Found at i:16682059 original size:16 final size:16
Alignment explanation
Indices: 16682038--16682075 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16682028 TTTCTTTTTT
16682038 TTAATA-TTATTAGATA
1 TTAATATTTATTAGA-A
*
16682054 TTAATATTTATTATAA
1 TTAATATTTATTAGAA
16682070 TTAATA
1 TTAATA
16682076 GGTTCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAATATTTATTAGAA
Found at i:16684207 original size:58 final size:58
Alignment explanation
Indices: 16684091--16684249 Score: 159
Period size: 58 Copynumber: 2.8 Consensus size: 58
16684081 CTGAACTTTT
* * *
16684091 CAAAAATTAT--TTTTACCCCCGAATTTCTAAAAATTCCATTTTTGAATCCGAACTTC
1 CAAAAATTATCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGAATCCGAACCTC
* *
16684147 CAAAAATTATCATTTTACCCCCGGATGTCCAAAAATTTCATTTTTG-A-CCTTGAACCTC
1 CAAAAATTATCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGAATCC--GAACCTC
* * *
16684205 CAAAGATTA-CTATTTTACCCTCGAA-GTGCCCAAAATTACCATTTT
1 CAAAAATTATC-ATTTTACCCCCGAATGT-CCAAAAATT-CCATTTT
16684250 ACCCCCCGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
56 12 0.14
57 4 0.05
58 64 0.74
59 6 0.07
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.35
Consensus pattern (58 bp):
CAAAAATTATCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGAATCCGAACCTC
Found at i:16685897 original size:21 final size:21
Alignment explanation
Indices: 16685858--16685899 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16685848 CATAAATATT
*
16685858 TTTAAAAAATATAATAATAAA
1 TTTAAAAAATATAAAAATAAA
16685879 TTTAAAAACATA-AAAAATAAA
1 TTTAAAAA-ATATAAAAATAAA
16685900 AAATATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TTTAAAAAATATAAAAATAAA
Found at i:16685960 original size:22 final size:23
Alignment explanation
Indices: 16685935--16685991 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
16685925 TATATAAATT
16685935 ATAAAATTTAAAAAAAT-TAAAA
1 ATAAAATTTAAAAAAATGTAAAA
* *
16685957 ATAAATATTTTCAAAAAATGTAATA
1 ATAAA-A-TTTAAAAAAATGTAAAA
16685982 AT-AAATTTAA
1 ATAAAATTTAA
16685992 TTTTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 9 0.31
23 2 0.07
24 12 0.41
25 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAATTTAAAAAAATGTAAAA
Found at i:16687109 original size:12 final size:12
Alignment explanation
Indices: 16687082--16687123 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
16687072 TAATATAGTT
*
16687082 ATATTTAT-TTA
1 ATATTTATATAA
16687093 ATATTTATATAA
1 ATATTTATATAA
*
16687105 ATATTAATATAAA
1 ATATTTATAT-AA
16687118 ATATTT
1 ATATTT
16687124 TGAAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 8 0.31
12 11 0.42
13 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTTATATAA
Found at i:16687136 original size:22 final size:22
Alignment explanation
Indices: 16687103--16687154 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
16687093 ATATTTATAT
16687103 AAATATTAATATAAAATATTTTG
1 AAATATTAATATAAAAT-TTTTG
* *
16687126 AAAT-TTAATATTATATTTTTG
1 AAATATTAATATAAAATTTTTG
16687147 AAAATATT
1 -AAATATT
16687155 TATGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 5 0.20
22 14 0.56
23 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATATTAATATAAAATTTTTG
Found at i:16687670 original size:24 final size:27
Alignment explanation
Indices: 16687634--16687686 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
16687624 AATTAGATAA
16687634 AAAATTTAATAAATA-AAAAAT-ATAT
1 AAAATTTAATAAATATAAAAATAATAT
* *
16687659 AAAA-TTATTAAATATTAAAATAATAT
1 AAAATTTAATAAATATAAAAATAATAT
16687685 AA
1 AA
16687687 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 9 0.38
26 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATTTAATAAATATAAAAATAATAT
Found at i:16687989 original size:1 final size:1
Alignment explanation
Indices: 16687943--16687982 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
16687933 TGTGGATAGT
*
16687943 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
16687983 TTGGGGGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:16695245 original size:16 final size:17
Alignment explanation
Indices: 16695212--16695246 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16695202 AGTAAAATTT
16695212 TAAACTTAAATCTAATC
1 TAAACTTAAATCTAATC
*
16695229 TAAACTT-AATCTGATC
1 TAAACTTAAATCTAATC
16695245 TA
1 TA
16695247 TGAGCACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAACTTAAATCTAATC
Found at i:16697943 original size:20 final size:20
Alignment explanation
Indices: 16697902--16697945 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
16697892 TCATTTTCTT
* *
16697902 AATTTTTTTAAAAATATATA
1 AATTTTTTAAAAAAAATATA
16697922 AATTGTTTTAAAAAAAAT-TA
1 AATT-TTTTAAAAAAAATATA
16697942 AATT
1 AATT
16697946 AAGGTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTTTTTAAAAAAAATATA
Found at i:16702277 original size:72 final size:72
Alignment explanation
Indices: 16702160--16702310 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
16702150 TAACAAAAAT
* * *
16702160 ATCAAGAAGATCGAGACCTACAAAGATTGGCATAAGAAGTTATCATTTTCTCTCTATGCTTATTG
1 ATCAAGAAGATCAAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCTCTACGCTTATTG
16702225 AACATCA
66 AACATCA
*
16702232 ATCAAGAAGATCAAGACCTACAAAGATTGGCATGAGAAGTTATCATTTGCTCTCTACGCTTATTG
1 ATCAAGAAGATCAAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCTCTACGCTTATTG
16702297 AACATCA
66 AACATCA
16702304 ATCAAGA
1 ATCAAGA
16702311 TTTTGTTGGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (72 bp):
ATCAAGAAGATCAAGACCTACAAAGATTGGCATAAGAAGTTATCATTTGCTCTCTACGCTTATTG
AACATCA
Found at i:16702783 original size:19 final size:20
Alignment explanation
Indices: 16702761--16702812 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
16702751 AAAAGGGAAG
16702761 AGAAAAGAAAAGAAAAA-AA
1 AGAAAAGAAAAGAAAAAGAA
*
16702780 AGAAAAAAAAAGAAAAAGAA
1 AGAAAAGAAAAGAAAAAGAA
*
16702800 GGAAAAAGAAAAG
1 AG-AAAAGAAAAG
16702813 GAGAGGTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 3 0.11
21 9 0.32
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAGAAAAAGAA
Found at i:16702807 original size:10 final size:10
Alignment explanation
Indices: 16702758--16702810 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
16702748 AAAAAAAGGG
16702758 AAGAGAAAAGAA
1 AAGA-AAAAG-A
16702770 AAGAAAAA-A
1 AAGAAAAAGA
*
16702779 AAGAAAAAAA
1 AAGAAAAAGA
16702789 AAGAAAAAGA
1 AAGAAAAAGA
*
16702799 AGGAAAAAGA
1 AAGAAAAAGA
16702809 AA
1 AA
16702811 AGGAGAGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 9 0.24
10 20 0.54
11 4 0.11
12 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:16702812 original size:5 final size:5
Alignment explanation
Indices: 16702761--16702795 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
16702751 AAAAGGGAAG
*
16702761 AGAAA AGAAA AGAAA A-AAA AGAAA AAAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
16702796 AGAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:16703355 original size:112 final size:111
Alignment explanation
Indices: 16703124--16703442 Score: 425
Period size: 112 Copynumber: 2.9 Consensus size: 111
16703114 AATGTGGGTC
* *
16703124 ATTTTTAATCTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATTCACCTTACAA
1 ATTTTTAATCTTTTCATTAATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* *
16703189 ------CAAGCATTCTTACATCAAAATAACGGTTACTGGACCAATG
66 CCTGTTCAAGCATTTTTACATCAAAATAACGGTTAGTGGACCAATG
** * *
16703229 ATTCGTAATATTTTCATTAATACGAGCTTTGCCTCCAATAACATTCAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTTCATTAATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
16703294 CCTTGTTCAAGCATTTTTACATCAAAATAACGGTTAGTGGACCAATG
66 CC-TGTTCAAGCATTTTTACATCAAAATAACGGTTAGTGGACCAATG
* * * * *
16703341 ATTTTTATTCTTTTCATTTACACGAGCTTTGCCTCCAATAAAATTTAATTTTATCCACCTAACAA
1 ATTTTTAATCTTTTCATTAATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* ** *
16703406 CCCTGTTCAAACATTTTTACATTGAAATGACGGTTAG
66 -CCTGTTCAAGCATTTTTACATCAAAATAACGGTTAG
16703443 CGGTCTAACG
Statistics
Matches: 185, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
105 59 0.32
112 124 0.67
113 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.37
Consensus pattern (111 bp):
ATTTTTAATCTTTTCATTAATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
CCTGTTCAAGCATTTTTACATCAAAATAACGGTTAGTGGACCAATG
Found at i:16704186 original size:49 final size:49
Alignment explanation
Indices: 16703871--16704432 Score: 347
Period size: 49 Copynumber: 11.4 Consensus size: 49
16703861 GGAAACATTG
* * * * * *
16703871 AGATTTGAAGGGAAAGGTTGA-GTCACAACGACGAACCCGGTACCTTAGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCAT-GA
* * * *
16703920 AGATGTGATGGG-AAGGATTAAGGCCGCAACGATGAATCCAGTACCATGA
1 AGATATGATGGGAAAGG-TTGAGGCCGCAACGATGAACCCGGTACCATGA
* *
16703969 A-ATATAATGGGAAAGGTTTAGGCCGCAACGATGAACCCGGTACCATGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCATGA
* * * * * * * *
16704017 AGATTTTAAGGGAAAAGTTGAGGCCGTAACGACGAACCTGGTACCTTAGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCAT-GA
* * ***
16704067 AGACATGATGGG-AAGGATTGAGGCCAG-AACGGTGAATATGGTACCATGA
1 AGATATGATGGGAAAGG-TTGAGGCC-GCAACGATGAACCCGGTACCATGA
** * *
16704116 A-ATGCGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGGTACCATGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCATGA
* * * * * * *
16704164 AGATATGACGAGAAAGGTTGAGGTCGCAATGGTGAACCCGGTACCTTAAA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCAT-GA
* ** * * *
16704214 AGATGTGATGGGAAAGGTTGAGATCGCAACGGTAAACCCAGTACCATGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCATGA
* * * * * *
16704263 ATAGATGAAGGGAAAGGTTGAGGCCACAAC-AGTGAACTCGGTACC-TTA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGA-TGAACCCGGTACCATGA
* * * **
16704311 AAAAACGTGATGGG-AAGGATTGAGGCCGTAACGAT-AAGTTCGAG-ACCAATGA
1 AGATA--TGATGGGAAAGG-TTGAGGCCGCAACGATGAA-CCCG-GTACC-ATGA
* * * * * * * *
16704363 TGACATTAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAGA
1 AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCAT-GA
* *
16704413 A-ACATGATGGGAAAGATTGA
1 AGATATGATGGGAAAGGTTGA
16704433 AGACAAACAG
Statistics
Matches: 394, Mismatches: 95, Indels: 48
0.73 0.18 0.09
Matches are distributed among these distances:
47 1 0.00
48 79 0.20
49 159 0.40
50 142 0.36
51 9 0.02
52 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (49 bp):
AGATATGATGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCATGA
Found at i:16704235 original size:147 final size:147
Alignment explanation
Indices: 16703896--16704292 Score: 431
Period size: 147 Copynumber: 2.7 Consensus size: 147
16703886 GGTTGAGTCA
* *
16703896 CAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTAAGGCCGCAACGATGAATCCAG
1 CAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGATGAATACAG
* * * * *
16703961 TACCATGAAATATAATGGGAAAGGTTTAGGCCGCAACGATGAACCCGGTACCATGAAGATTTTAA
66 TACCATGAAATACAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGAAGATATGAA
*
16704026 GGGAAAAGTTGAGGCCG
131 GAGAAAAGTTGAGGCCG
* * ** * **
16704043 TAACGACGAACCTGGTACCTTAGAAGACATGATGGGAAGGATTGAGGCCAG-AACGGTGAATATG
1 CAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCC-GCAACGATGAATACA
* * *
16704107 GTACCATGAAATGCGATGGGAAAGGTTGAGGCTGCAACGACGAACCCGGTACCATGAAGATATGA
65 GTACCATGAAATACAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGAAGATATGA
* * *
16704172 CGAGAAAGGTTGAGGTCG
130 AGAGAAAAGTTGAGGCCG
* ** * ** * * **
16704190 CAATGGTGAACCCGGTACCTTAAAAGATGTGATGGGAAAGG-TTGAGATCGCAACGGTAAACCCA
1 CAACGACGAACCCGGTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCCGCAACGATGAATACA
* * *
16704254 GTACCATG-AATAGATGAAGGGAAAGGTTGAGGCCACAAC
65 GTACCATGAAATACA--ATGGGAAAGGTTGAGGCCGCAAC
16704293 AGTGAACTCG
Statistics
Matches: 203, Mismatches: 42, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
146 4 0.02
147 174 0.86
148 25 0.12
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (147 bp):
CAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGATGAATACAG
TACCATGAAATACAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGAAGATATGAA
GAGAAAAGTTGAGGCCG
Found at i:16704252 original size:99 final size:97
Alignment explanation
Indices: 16703876--16704432 Score: 317
Period size: 99 Copynumber: 5.7 Consensus size: 97
16703866 CATTGAGATT
* * * ** * * *
16703876 TGAAGGGAAAGGTTGA-GTCACAACGACGAACCCGGTACCTTAGAAGATGTGATGGG-AAGGATT
1 TGAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTA-AAAAAGTGATGGGAAAGG-TT
* * * * *
16703939 AAGGCCGCAACGATGAATCCAGTACCATGAA-ATA
64 GA-GCCGCAACGATAAACCCGGTACCATGAAGACA
* * * * * * * ** * * *
16703973 T-AATGGGAAAGGTTTAGGCCGCAACGATGAACCCGGTACCATGAAGATTTTAAGGGAAAAGTTG
1 TGAA-GGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAAAAAAGTGATGGGAAAGGTTG
* ** * *
16704037 AGGCCGTAACGACGAACCTGGTACCTTAGAAGACA
65 A-GCCGCAACGATAAACCCGGTACCAT-GAAGACA
* * * * * * *
16704072 TGATGGG-AAGGATTGAGGCCAG-AACGGTGAA-TATGGTACCAT-GAAATGCGATGGGAAAGGT
1 TGAAGGGAAAGG-TTGAGGCC-GCAATGGTGAACT-CGGTACCTTAAAAAAGTGATGGGAAAGGT
* ** *
16704133 TGAGGCTGCAACGACGAACCCGGTACCATGAAGATA
63 TGA-GCCGCAACGATAAACCCGGTACCATGAAGACA
* * * * *
16704169 TGACGAGAAAGGTTGAGGTCGCAATGGTGAACCCGGTACCTTAAAAGATGTGATGGGAAAGGTTG
1 TGAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAAAA-AAGTGATGGGAAAGGTTG
* * * * *
16704234 AGATCGCAACGGTAAACCCAGTACCATGAATAGA
65 AG-CCGCAACGATAAACCCGGTACCATGAAGACA
* **
16704268 TGAAGGGAAAGGTTGAGGCCACAACAGTGAACTCGGTACCTTAAAAAACGTGATGGG-AAGGATT
1 TGAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAAAAAA-GTGATGGGAAAGG-TT
* *** *
16704332 GAGGCCGTAACGATAAGTTCGAG-ACCAATGATGACA
64 GA-GCCGCAACGATAAACCCG-GTACC-ATGAAGACA
* * *
16704368 TTAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAGAAACA-TGATGGGAAAGATTG
1 TGAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTA-AAAAAGTGATGGGAAAGGTTG
16704432 A
65 A
16704433 AGACAAACAG
Statistics
Matches: 362, Mismatches: 76, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
96 3 0.01
97 78 0.22
98 80 0.22
99 145 0.40
100 52 0.14
101 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (97 bp):
TGAAGGGAAAGGTTGAGGCCGCAATGGTGAACTCGGTACCTTAAAAAAGTGATGGGAAAGGTTGA
GCCGCAACGATAAACCCGGTACCATGAAGACA
Found at i:16704711 original size:39 final size:39
Alignment explanation
Indices: 16704657--16705092 Score: 391
Period size: 39 Copynumber: 11.0 Consensus size: 39
16704647 AGTTACATTA
* *
16704657 CCATCCAATCTCTTACCTCGATCATGGGGCAGATTGCAG
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * * *
16704696 CCATCCAGTCTCTTACCCCGATCATGGGACAGATTAAAAA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATT-GAAG
* *
16704736 CCATCCAATCTCTTACCCCTG-TCATGGGGTAGATCGCAA-
1 CCATCCAATCTCTTACCCC-GATCATGGGGCAGATTG-AAG
* * *
16704775 CCATCCAATCTCTTACCCCGATCATAGGGCAAATTGAAAA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AAG
* * *
16704815 CCATTCAATCTCTTACCCTGATCATGGGGCAAATTGAAG
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* **
16704854 -CATCCAATCTTTTACCCTAATC-TGAGGGCAGATTGAAG
1 CCATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG
* *
16704892 ACACAT-CGATCTTTTACCCCGATCATGGGGCAGATTGAAG
1 -C-CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* *** * *
16704932 -CATCCAATTTCTTACCTTAATCA-GAAGGAAGATTGAAG
1 CCATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG
* * *
16704970 ACATCGCCAATCTCTTACCCCAATCATGGGGGCATATTGAAG
1 CCAT--CCAATCTCTTACCCCGATCAT-GGGGCAGATTGAAG
* * *
16705012 ACATCATCCAATCTCTTACCCCGATCATGGGACAAATTAAAG
1 -C--CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
* * *
16705054 CCGTCCAATCTCTTAACCTGATCATGGGGCAGATTGAAG
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
16705093 ACACACCTGT
Statistics
Matches: 325, Mismatches: 52, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
37 6 0.02
38 56 0.17
39 101 0.31
40 93 0.29
41 24 0.07
42 21 0.06
43 21 0.06
45 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (39 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG
Found at i:16704889 original size:78 final size:79
Alignment explanation
Indices: 16704656--16705092 Score: 408
Period size: 79 Copynumber: 5.5 Consensus size: 79
16704646 AAGTTACATT
* *
16704656 ACCATCCAATCTCTTA-CCTCGATCATGGGGCAGATTGCAGCCATCCAGTCTCTTACCCCGATCA
1 ACCATCCAATCTCTTACCCT-GATCATGGGGCAGATTGAAG-CATCCAATCTCTTACCCCGATCA
* *
16704720 TG-GGACAGATTAAAA
64 TGAGGGCAGATTGAAA
* * *
16704735 ACCATCCAATCTCTTACCCCTG-TCATGGGGTAGATCGCAACCATCCAATCTCTTACCCCGATCA
1 ACCATCCAATCTCTTA-CCCTGATCATGGGGCAGATTG-AAGCATCCAATCTCTTACCCCGATCA
*
16704799 T-AGGGCAAATTGAAA
64 TGAGGGCAGATTGAAA
* * * **
16704814 ACCATTCAATCTCTTACCCTGATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAATC-TG
1 ACCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCCCGATCATG
*
16704878 AGGGCAGATTGAAG
66 AGGGCAGATTGAAA
* * * * ***
16704892 ACACAT-CGATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCCAATTTCTTACCTTAATCA-
1 AC-CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCCCGATCAT
* * *
16704955 GAAGGAAGATTGAAG
65 GAGGGCAGATTGAAA
** *
16704970 A-CATCGCCAATCTCTTACCCCAATCATGGGGGCATATTGAAGACATCATCCAATCTCTTACCCC
1 ACCAT--CCAATCTCTTACCCTGATCAT-GGGGCAGATTGAAG----CATCCAATCTCTTACCCC
* *
16705034 GATCATG-GGACAAATT-AAA
59 GATCATGAGGGCAGATTGAAA
* * *
16705053 GCCGTCCAATCTCTTAACCTGATCATGGGGCAGATTGAAG
1 ACCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAG
16705093 ACACACCTGT
Statistics
Matches: 294, Mismatches: 46, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
76 3 0.01
77 1 0.00
78 103 0.35
79 109 0.37
80 15 0.05
81 16 0.05
82 18 0.06
83 2 0.01
84 26 0.09
85 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (79 bp):
ACCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCCCGATCATG
AGGGCAGATTGAAA
Found at i:16704986 original size:41 final size:41
Alignment explanation
Indices: 16704661--16705040 Score: 154
Period size: 40 Copynumber: 9.5 Consensus size: 41
16704651 ACATTACCAT
* * * * * *
16704661 CCAATCTCTTACCTCGATCATG-GGGCAGATTGCAGCCAT-
1 CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
* * * *
16704700 CCAGTCTCTTACCCCGATCATG--GGACAGATTAAAAACCAT-
1 CCAATCTCTTACCCCAATCATGAAGGA-AGATTGAAGA-CATC
** * * * *
16704740 CCAATCTCTTACCCCTGTCATG-GGGTAGATCGCAA-CCAT-
1 CCAATCTCTTACCCCAATCATGAAGGAAGATTG-AAGACATC
* * *
16704779 CCAATCTCTTACCCCGATCAT-AGGGCAA-ATTGAAAACCAT-
1 CCAATCTCTTACCCCAATCATGAAGG-AAGATTGAAGA-CATC
* ** *
16704819 TCAATCTCTTACCCTGATCATG-GGGCAA-ATTGAAG-CAT-
1 CCAATCTCTTACCCCAATCATGAAGG-AAGATTGAAGACATC
* * * *
16704857 CCAATCTTTTACCCTAATC-TGAGGGCAGATTGAAGACA-C
1 CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
* * * * * *
16704896 ATCGATCTTTTACCCCGATCATG-GGGCAGATTGAAG-CAT-
1 -CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
* **
16704935 CCAATTTCTTACCTTAATCA-GAAGGAAGATTGAAGACATC
1 CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
** * *
16704975 GCCAATCTCTTACCCCAATCATGGGGGCATATTGAAGACATC
1 -CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
*
16705017 ATCCAATCTCTTACCCCGATCATG
1 --CCAATCTCTTACCCCAATCATG
16705041 GGACAAATTA
Statistics
Matches: 271, Mismatches: 48, Indels: 40
0.75 0.13 0.11
Matches are distributed among these distances:
37 4 0.01
38 57 0.21
39 61 0.23
40 89 0.33
41 23 0.08
42 16 0.06
43 21 0.08
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (41 bp):
CCAATCTCTTACCCCAATCATGAAGGAAGATTGAAGACATC
Found at i:16705778 original size:16 final size:16
Alignment explanation
Indices: 16705759--16705801 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
16705749 AACACAAAGC
*
16705759 ATGAATAATTATACGA
1 ATGAATAAATATACGA
16705775 ATGAATAAATATACGA
1 ATGAATAAATATACGA
16705791 A--AATAAATATA
1 ATGAATAAATATA
16705802 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 10 0.38
16 16 0.62
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (16 bp):
ATGAATAAATATACGA
Found at i:16705797 original size:14 final size:14
Alignment explanation
Indices: 16705762--16705807 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
16705752 ACAAAGCATG
*
16705762 AATAATTATACGAA
1 AATAAATATACGAA
16705776 TGAATAAATATACGAA
1 --AATAAATATACGAA
*
16705792 AATAAATATAAGAA
1 AATAAATATACGAA
16705806 AA
1 AA
16705808 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
16 13 0.46
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:16706029 original size:59 final size:59
Alignment explanation
Indices: 16705927--16706294 Score: 358
Period size: 59 Copynumber: 6.3 Consensus size: 59
16705917 AGTTTCAAAG
* * * * *
16705927 AGTTCGA-GGTTAAAATGTAATTTTGGA-AAGTT-TAGGGGTAAAAATGTAATTTTAGGA
1 AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGA-GGGTAAAAATGTGATTTTTGGA
** * * *
16705984 AGTTCGAGAATAAAAATGTTATTTTTGAGAAGTTTGAGGATAAAAATGTGATTTTTGGA
1 AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGA
* * *
16706043 AGTTTG-GGAGCAAAAATGTAATTTTT-AAAAGTTCGAGGGT-AAAATGTGATTTTTGAGA
1 AGTTCGAGG-GTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTG-GA
* * * *
16706101 AGTTCGAGGATAAAAATGTGATTTTTG-GAAATTCGAGGGGTAAAAATGTGATTTTTGAA
1 AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGA-GGGTAAAAATGTGATTTTTGGA
* * * *
16706160 AGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTCGGGGGCAACAATGTGATTTTTGGA
1 AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGA
* * * * * * *
16706219 AATTCG-GGGCAAAAATGTAAATTTTGAGAAGTTTG-GGGTTAAAATGTAATTTTAGAGA
1 AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTG-GA
* *
16706277 AGTTTGAGGGTCAAAATG
1 AGTTCGAGGGTAAAAATG
16706295 GGATTTTTAA
Statistics
Matches: 253, Mismatches: 46, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
57 37 0.15
58 87 0.34
59 106 0.42
60 23 0.09
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
AGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGA
Found at i:16706084 original size:117 final size:116
Alignment explanation
Indices: 16705938--16706305 Score: 361
Period size: 117 Copynumber: 3.1 Consensus size: 116
16705928 GTTCGAGGTT
** * * * *
16705938 AAAATGTAATTTTGGAAAGTT-TAGGGGTAAAAATGTAATTTTAGGAAGTTCGAGAATAAAAATG
1 AAAATGTAATTTTTAAAAGTTCGA-GGGTAAAAATGTGATTTTTGGAAGTTCGAGGATAAAAATG
* *
16706002 TTATTTTTGAGAAGTTTGAGGATAAAAATGTGATTTTTGGAAGTTTGGGAGCA
65 TAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTGGG-GCA
16706055 AAAATGTAATTTTTAAAAGTTCGAGGGT-AAAATGTGATTTTTGAGAAGTTCGAGGATAAAAATG
1 AAAATGTAATTTTTAAAAGTTCGAGGGTAAAAATGTGATTTTTG-GAAGTTCGAGGATAAAAATG
* * * * ** *
16706119 TGATTTTTG-GAAATTCGAGGGGTAAAAATGTGATTTTTGAAAGTTCAAGGGTA
65 TAATTTTTGAGAAGTTTGA-GGGTAAAAATGTGATTTTTGGAAGTT-TGGGGCA
* * * * * **
16706172 AAAATGTAATTTTTGAGAAGTTCGGGGGCAACAATGTGATTTTTGGAAATTCG-GGGCAAAAATG
1 AAAATGTAATTTTT-AAAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTCGAGGATAAAAATG
* * * *
16706236 TAAATTTTGAGAAGTTTG-GGGTTAAAATGTAATTTTAGAGAAGTTTGAGGGTC-
65 TAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTG-GAAGTTTG-GGG-CA
**
16706289 AAAATGGGATTTTTAAA
1 AAAATGTAATTTTTAAA
16706306 GGAAACATGG
Statistics
Matches: 206, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
116 39 0.19
117 126 0.61
118 27 0.13
119 14 0.07
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (116 bp):
AAAATGTAATTTTTAAAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTCGAGGATAAAAATGT
AATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTGGGGCA
Found at i:16706301 original size:30 final size:30
Alignment explanation
Indices: 16705927--16706302 Score: 337
Period size: 29 Copynumber: 12.9 Consensus size: 30
16705917 AGTTTCAAAG
* * *
16705927 AGTTCGA-GGTTAAAATGTAATTTTGGA-A
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * *
16705955 AGTT-TAGGGGTAAAAATGTAATTTTAG-GA
1 AGTTCGA-GGGTAAAAATGTGATTTTTGAGA
** *
16705984 AGTTCGAGAATAAAAATGTTATTTTTGAGA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* *
16706014 AGTTTGAGGATAAAAATGTGATTTTTG-GA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * * *
16706043 AGTTTG-GGAGCAAAAATGTAATTTTT-AAA
1 AGTTCGAGG-GTAAAAATGTGATTTTTGAGA
16706072 AGTTCGAGGGT-AAAATGTGATTTTTGAGA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
*
16706101 AGTTCGAGGATAAAAATGTGATTTTTG-GA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
*
16706130 AATTCGAGGGGTAAAAATGTGATTTTTGA-A
1 AGTTCGA-GGGTAAAAATGTGATTTTTGAGA
* *
16706160 AGTTCAAGGGTAAAAATGTAATTTTTGAGA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * *
16706190 AGTTCGGGGGCAACAATGTGATTTTTG-GA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * * *
16706219 AATTCG-GGGCAAAAATGTAAATTTTGAGA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * * *
16706248 AGTTTG-GGGTTAAAATGTAATTTTAGAGA
1 AGTTCGAGGGTAAAAATGTGATTTTTGAGA
* * *
16706277 AGTTTGAGGGTCAAAATGGGATTTTT
1 AGTTCGAGGGTAAAAATGTGATTTTT
16706303 AAAGGAAACA
Statistics
Matches: 289, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.00
28 36 0.12
29 145 0.50
30 107 0.37
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
AGTTCGAGGGTAAAAATGTGATTTTTGAGA
Found at i:16708507 original size:39 final size:39
Alignment explanation
Indices: 16708456--16708945 Score: 309
Period size: 39 Copynumber: 12.6 Consensus size: 39
16708446 GGTTACGATT
* *
16708456 TGCCCCTGGCTCGAGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
** *
16708495 TGCCTTAGGCTCGGGGTAAGAGA-T--CGGATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG--ATC
16708534 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* ** ** * *
16708573 TGCCCCAGGCTC-GGATAAGAGAGCGAATTACT-GTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATC
* * *
16708611 TGCTCCAGGCTTGGGGTAAGAGATTGACTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* * * *
16708650 TGCCCTAAGCTCGGGGTAAAAGA-T--CGGATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG--ATC
** * * *
16708689 TGCCCTTGACTTGGGGTAAGAGATTGGCTGATAGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
** * * ** *
16708728 TGCCTTAGGCTCGGGGTAAAAGATCGAATGACT-GTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATC
* * * *
16708767 TGCCCCAAGCTCGGGGTAAGGGATTGGCTAATGGTGGTC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* * * * ** *
16708806 TGCCCCAAGCTTGGGGTAAAAGATCGAATGACT-GTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATC
* * *
16708845 TG-CCCAAGCTTGGGGTAAGAGATTGGCTAATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* ** * * * ** * **
16708883 TACCTTAGGCTTGGGGTAAAAGATCGAATGATTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
*
16708922 TGCCCCAAGCTCGGGGTAAGAGAT
1 TGCCCCAGGCTCGGGGTAAGAGAT
16708946 CATAATCTTC
Statistics
Matches: 342, Mismatches: 89, Indels: 40
0.73 0.19 0.08
Matches are distributed among these distances:
36 12 0.04
37 5 0.01
38 60 0.18
39 246 0.72
40 4 0.01
41 4 0.01
42 11 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
Found at i:16708571 original size:78 final size:78
Alignment explanation
Indices: 16708456--16708945 Score: 597
Period size: 78 Copynumber: 6.3 Consensus size: 78
16708446 GGTTACGATT
* * * *
16708456 TGCCCCTGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTCGGGGTAAGAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
* *
16708521 GATGGCTGCAATC
66 AATGACTGCAATC
* * * *
16708534 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC-GGATAAGAGAGCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
* *
16708598 AATTACTGTAATC
66 AATGACTGCAATC
* * * *
16708611 TGCTCCAGGCTTGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
* *
16708676 GATGGCTGCAATC
66 AATGACTGCAATC
** * * * *
16708689 TGCCCTTGACTTGGGGTAAGAGATTGGCTGATAGTGATCTGCCTTAGGCTCGGGGTAAAAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
*
16708754 AATGACTGTAATC
66 AATGACTGCAATC
* * * * * * *
16708767 TGCCCCAAGCTCGGGGTAAGGGATTGGCTAATGGTGGTCTGCCCCAAGCTTGGGGTAAAAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
*
16708832 AATGACTGTAATC
66 AATGACTGCAATC
* * * * * *
16708845 TG-CCCAAGCTTGGGGTAAGAGATTGGCTAATGGTGATCTACCTTAGGCTTGGGGTAAAAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
*
16708909 AATGATTGCAATC
66 AATGACTGCAATC
*
16708922 TGCCCCAAGCTCGGGGTAAGAGAT
1 TGCCCCAGGCTCGGGGTAAGAGAT
16708946 CATAATCTTC
Statistics
Matches: 354, Mismatches: 56, Indels: 4
0.86 0.14 0.01
Matches are distributed among these distances:
77 134 0.38
78 220 0.62
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (78 bp):
TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCG
AATGACTGCAATC
Found at i:16708925 original size:155 final size:155
Alignment explanation
Indices: 16708464--16708945 Score: 642
Period size: 155 Copynumber: 3.1 Consensus size: 155
16708454 TTTGCCCCTG
* * * *
16708464 GCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTCGGGGTAAGAGATCGGATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
* * ** * * *
16708529 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC-TCGGATAAGA
66 CAATCTG-CCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTTGGGGTAAAA
* * * *
16708593 GAGCGAATTACTGTAATCTGCTCCAG
130 GATCGAATGACTGTAATCTGCCCCAA
* *
16708619 GCTTGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
** * *
16708684 CAATCTGCCCTTGACTTGGGGTAAGAGATTGGCTGATAGTGATCTGCCTTAGGCTCGGGGTAAAA
66 CAATCTGCCCAAG-CTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTTGGGGTAAAA
16708749 GATCGAATGACTGTAATCTGCCCCAA
130 GATCGAATGACTGTAATCTGCCCCAA
* * * * * * *
16708775 GCTCGGGGTAAGGGATTGGCTAATGGTGGTCTGCCCCAAGCTTGGGGTAAAAGATCGAATGACTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
* * *
16708840 TAATCTGCCCAAGCTTGGGGTAAGAGATTGGCTAATGGTGATCTACCTTAGGCTTGGGGTAAAAG
66 CAATCTGCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTTGGGGTAAAAG
* *
16708905 ATCGAATGATTGCAATCTGCCCCAA
131 ATCGAATGACTGTAATCTGCCCCAA
16708930 GCTCGGGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
16708946 CATAATCTTC
Statistics
Matches: 286, Mismatches: 39, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
154 4 0.01
155 188 0.66
156 94 0.33
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (155 bp):
GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
CAATCTGCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTTGGGGTAAAAG
ATCGAATGACTGTAATCTGCCCCAA
Found at i:16711181 original size:29 final size:29
Alignment explanation
Indices: 16711124--16711405 Score: 239
Period size: 29 Copynumber: 9.7 Consensus size: 29
16711114 GAAGTATACC
* *
16711124 TTGGAAGTTCAGGGG-AAAAATGTAGTTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
*
16711152 TTGGAAGTTTGGGGGCAAAAATGTAATTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
* ** * *
16711181 TTAGAAGTTTAGGGGTAAAAATGTGATTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
* * *
16711210 TTGAGAAGTTCGAGGGTAAAAATGTGATTT
1 TTG-GAAGTTCGGGGGCAAAAATGTAATTT
* *
16711240 TTTGAAGTTCGGGGGTAAAAATGTAATTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
* * * *
16711269 TTGAGAAATTTGGGGG-TAAAATGTGATTT
1 TTG-GAAGTTCGGGGGCAAAAATGTAATTT
* *** *
16711298 TTGGAAGTTTGGGGGGGGAAATGTGATTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
***
16711327 TTGGAAGTTCAAAGGC-AAAATGTAATTT
1 TTGGAAGTTCGGGGGCAAAAATGTAATTT
* *
16711355 TTGAGAAGTTCGGGGTC-AAAATATAATTT
1 TTG-GAAGTTCGGGGGCAAAAATGTAATTT
*
16711384 TTGAGAAGTTTGGGGGTCAAAA
1 TTG-GAAGTTCGGGGG-CAAAA
16711406 TGAGATTTTT
Statistics
Matches: 211, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
28 37 0.18
29 135 0.64
30 36 0.17
31 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
TTGGAAGTTCGGGGGCAAAAATGTAATTT
Found at i:16711320 original size:58 final size:58
Alignment explanation
Indices: 16711124--16711415 Score: 277
Period size: 59 Copynumber: 5.0 Consensus size: 58
16711114 GAAGTATACC
** * * *
16711124 TTGGAAGTTCAGGGG-AAAAATGTAGTTTTTG-GAAGTTTGGGGGCAAAAATGTAATTT
1 TTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGG-TAAAATGTGATTT
* * * * *
16711181 TTAGAAGTTTAGGGGTAAAAATGTGATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTT
1 TTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGGT-AAAATGTGATTT
* * *
16711240 TTTGAAGTTCGGGGGTAAAAATGTAATTTTTGAGAAATTTGGGGGTAAAATGTGATTT
1 TTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGGTAAAATGTGATTT
*** * **** * *
16711298 TTGGAAGTTTGGGGGGGGAAATGTGATTTTTG-GAAGTTCAAAGGCAAAATGTAATTT
1 TTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGGTAAAATGTGATTT
* * * *
16711355 TTGAGAAG-TTCGGGGTCAAAATATAATTTTTGAGAAGTTTGGGGGTCAAAATGAGATTT
1 TTG-GAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGGT-AAAATGTGATTT
16711414 TT
1 TT
16711416 AAAGAAAATA
Statistics
Matches: 188, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
57 52 0.28
58 64 0.34
59 72 0.38
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
TTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAGAAGTTTGGGGGTAAAATGTGATTT
Found at i:16712264 original size:17 final size:19
Alignment explanation
Indices: 16712244--16712278 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
16712234 TTGATTGTTT
16712244 TTTTCT-TTTTCA-ATCTC
1 TTTTCTCTTTTCAGATCTC
16712261 TTTTCTCTTTTCAGATCT
1 TTTTCTCTTTTCAGATCT
16712279 GTTCTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.11, C:0.23, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTCTCTTTTCAGATCTC
Found at i:16713257 original size:42 final size:40
Alignment explanation
Indices: 16713155--16713292 Score: 161
Period size: 42 Copynumber: 3.4 Consensus size: 40
16713145 CTACTACAAC
* *
16713155 ACCAATCTTTTACCCAGATCATGGGGCAGATTGAAGC-CA
1 ACCAATCTCTTACCCAGATCATGGGGCAAATTGAAGCACA
* * * *
16713194 TCCGATCTCTTACCCCGATCATGGGGCATATTGAAGACATCA
1 ACCAATCTCTTACCCAGATCATGGGGCAAATTGAAG-CA-CA
*
16713236 ACCAATCTCTTACCCTGATCATGGGGCAAATTGAAGCCACA
1 ACCAATCTCTTACCCAGATCATGGGGCAAATTGAAG-CACA
*
16713277 ATCCAATCTTTTACCC
1 A-CCAATCTCTTACCC
16713293 CTAAATCAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 31 0.37
40 1 0.01
41 3 0.04
42 49 0.58
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (40 bp):
ACCAATCTCTTACCCAGATCATGGGGCAAATTGAAGCACA
Found at i:16719291 original size:43 final size:44
Alignment explanation
Indices: 16719219--16719366 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
16719209 AACGTATATG
* * ** **
16719219 TGGATGGAGTCACCAAATTTTGCAAACAAGTTGTTATGTAGGTTA
1 TGGATGAAGCCACCAAA-TTTGCGGACAAGTTGACATGTAGGTTA
* * * *
16719264 TGGAT-AAACCACCAAATTTGCGGACAAGCTGACATATAGGTTG
1 TGGATGAAGCCACCAAATTTGCGGACAAGTTGACATGTAGGTTA
* * * *
16719307 GGGATGAAGTCACC-AATATTGCGGACAAGTTGCCATGTAGGTTT
1 TGGATGAAGCCACCAAAT-TTGCGGACAAGTTGACATGTAGGTTA
16719351 TGGATGAAGCCACCAA
1 TGGATGAAGCCACCAA
16719367 TTCTTCCTCC
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
43 27 0.33
44 48 0.59
45 6 0.07
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (44 bp):
TGGATGAAGCCACCAAATTTGCGGACAAGTTGACATGTAGGTTA
Found at i:16719430 original size:2 final size:2
Alignment explanation
Indices: 16719418--16719457 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
16719408 ACCACAATGA
*
16719418 AC AC A- AC AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
16719458 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16725026 original size:6 final size:6
Alignment explanation
Indices: 16725015--16725091 Score: 154
Period size: 6 Copynumber: 12.8 Consensus size: 6
16725005 GGCATACTGT
16725015 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
16725063 TACATA TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACATA TACAT
16725092 TTATATTCTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:16729577 original size:14 final size:14
Alignment explanation
Indices: 16729558--16729592 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
16729548 GTGTGTAGAC
16729558 CTGACATAATTGCA
1 CTGACATAATTGCA
16729572 CTGACATAATTGCA
1 CTGACATAATTGCA
16729586 CTGACAT
1 CTGACAT
16729593 TCTTACTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (14 bp):
CTGACATAATTGCA
Found at i:16730611 original size:16 final size:16
Alignment explanation
Indices: 16730590--16730620 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16730580 AGAATGTGAA
16730590 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
16730606 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
16730621 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:16731482 original size:26 final size:27
Alignment explanation
Indices: 16731422--16731482 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
16731412 ATACTGGGCT
16731422 CAATTC-TGGACACGTTCATGCAGCGA
1 CAATTCTTGGACACGTTCATGCAGCGA
*
16731448 CAATT-TTGGACATGTTCATGCAGCGA
1 CAATTCTTGGACACGTTCATGCAGCGA
16731474 C-ATTCTTGG
1 CAATTCTTGG
16731483 GTGCAATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (27 bp):
CAATTCTTGGACACGTTCATGCAGCGA
Found at i:16731510 original size:37 final size:38
Alignment explanation
Indices: 16731469--16731559 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
16731459 ATGTTCATGC
*
16731469 AGCGACATTCTTGGGTGCAA-TTGAAGAATAGATATGT
1 AGCGACATTCTTGGGTGCAATTTAAAGAATAGATATGT
* * **
16731506 AGCGATAGTTC-TGGATGCAATTTAAAGAATATTTATGT
1 AGCGACA-TTCTTGGGTGCAATTTAAAGAATAGATATGT
*
16731544 AGCGACAGTCTTGGGT
1 AGCGACATTCTTGGGT
16731560 ACATTCCGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
37 16 0.37
38 27 0.63
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (38 bp):
AGCGACATTCTTGGGTGCAATTTAAAGAATAGATATGT
Found at i:16731628 original size:37 final size:37
Alignment explanation
Indices: 16731587--16731661 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
16731577 TTGCGGCAAT
*
16731587 AGTTTTGGGTGCAATCTAGAAGTGCTCATGCAGCGAC
1 AGTTTTGGGCGCAATCTAGAAGTGCTCATGCAGCGAC
16731624 AGTTTTGGGCGCAATCTAGAAGTGCTCATGCAGCGAC
1 AGTTTTGGGCGCAATCTAGAAGTGCTCATGCAGCGAC
16731661 A
1 A
16731662 TTAGTAGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (37 bp):
AGTTTTGGGCGCAATCTAGAAGTGCTCATGCAGCGAC
Found at i:16751343 original size:34 final size:34
Alignment explanation
Indices: 16751300--16751367 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
16751290 AGTCCGAAAG
16751300 ACAATTTCCTGCTACCTCATATCGACACCTTGGT
1 ACAATTTCCTGCTACCTCATATCGACACCTTGGT
16751334 ACAATTTCCTGCTACCTCATATCGACACCTTGGT
1 ACAATTTCCTGCTACCTCATATCGACACCTTGGT
16751368 GGACAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (34 bp):
ACAATTTCCTGCTACCTCATATCGACACCTTGGT
Found at i:16754147 original size:20 final size:20
Alignment explanation
Indices: 16754124--16754166 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
16754114 GAGGAGGTAG
16754124 ATCTACTCTTGACGAGGAGC
1 ATCTACTCTTGACGAGGAGC
*
16754144 ATCTGCTCTTGACGAGGAGC
1 ATCTACTCTTGACGAGGAGC
16754164 ATC
1 ATC
16754167 CTAAGCGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (20 bp):
ATCTACTCTTGACGAGGAGC
Found at i:16755813 original size:20 final size:21
Alignment explanation
Indices: 16755788--16755832 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16755778 CAATGTGTGC
*
16755788 TATTTTT-GACCAACATTTGT
1 TATTTTTGGACCAACATTTGA
*
16755808 TATTTTTGGACCAATATTTGA
1 TATTTTTGGACCAACATTTGA
16755829 TATT
1 TATT
16755833 GATTTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (21 bp):
TATTTTTGGACCAACATTTGA
Found at i:16756695 original size:101 final size:100
Alignment explanation
Indices: 16756580--16756826 Score: 273
Period size: 101 Copynumber: 2.5 Consensus size: 100
16756570 TGGAATAGAG
* * * *
16756580 TGAAGTTACAAAACCAAATCCTATATCCCTGAAGTTGCAATGGATCAGATTGAAGGTAC-GAAGG
1 TGAAGCTACAAAACCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT-AAAGT-CTGAAAG
** * *
16756644 GGAATCCTTATCT-CTCTAAAGTTGCAGCAGAGCAGGA
64 CAAATCCTTATCTCCT-TAAAGATGCAGCAGAGCAAGA
* * * *
16756681 TGAATCTACAAAACCAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAAGTCTTGAAAGC
1 TGAAGCTACAAAACCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTAAAGTC-TGAAAGC
* * **
16756746 AAATCTTTATCTCCTTGAAGATGCAGTGGAGCAAGA
65 AAATCCTTATCTCCTTAAAGATGCAGCAGAGCAAGA
* * *
16756782 TGAAGCTACAACATCAAATCCTATATCCCTGAAGTTACAGTGGAT
1 TGAAGCTACAAAACCAAATCCTATATCCCTGAAGTTGCAGTGGAT
16756827 TGGATTAAGG
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
99 1 0.01
100 4 0.03
101 114 0.94
102 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (100 bp):
TGAAGCTACAAAACCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTAAAGTCTGAAAGCA
AATCCTTATCTCCTTAAAGATGCAGCAGAGCAAGA
Found at i:16758851 original size:22 final size:21
Alignment explanation
Indices: 16758810--16758854 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
16758800 GTATTATTTA
16758810 TTTATTTTATATTCTATTGTC
1 TTTATTTTATATTCTATTGTC
*
16758831 TTTATTATTGTATT-TACTTGTC
1 TTTATT-TTATATTCTA-TTGTC
16758853 TT
1 TT
16758855 CCATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTATTTTATATTCTATTGTC
Found at i:16759978 original size:25 final size:25
Alignment explanation
Indices: 16759926--16759979 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
16759916 TTTTGTTAGT
* * *
16759926 TTTTATTTATTTTATTATTTGTTTA
1 TTTTATTAATTTTATAATGTGTTTA
16759951 TTTTATTAATTTTA-AATGTGTTTAA
1 TTTTATTAATTTTATAATGTGTTT-A
16759976 TTTT
1 TTTT
16759980 TCTTTTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTATTAATTTTATAATGTGTTTA
Found at i:16766219 original size:16 final size:18
Alignment explanation
Indices: 16766180--16766213 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16766170 GCAATATGCA
16766180 ATCACATATTATCTTGTT
1 ATCACATATTATCTTGTT
16766198 ATCACAT-TTA-CTTGTT
1 ATCACATATTATCTTGTT
16766214 TGCACAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (18 bp):
ATCACATATTATCTTGTT
Found at i:16773110 original size:13 final size:13
Alignment explanation
Indices: 16773092--16773121 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16773082 ATGCGATGAC
*
16773092 ATCTATCGGTGGT
1 ATCTATCGATGGT
16773105 ATCTATCGATGGT
1 ATCTATCGATGGT
16773118 ATCT
1 ATCT
16773122 TAGCTGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (13 bp):
ATCTATCGATGGT
Found at i:16791816 original size:24 final size:23
Alignment explanation
Indices: 16791776--16791820 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16791766 TCCCACTCCA
16791776 TCTCACCCCCTTATTTCTCCTTC
1 TCTCACCCCCTTATTTCTCCTTC
* *
16791799 TCTCACCATCCTTTTTTCTCCT
1 TCTCACC-CCCTTATTTCTCCT
16791821 CCTTAGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCACCCCCTTATTTCTCCTTC
Found at i:16810482 original size:23 final size:23
Alignment explanation
Indices: 16810456--16810502 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
16810446 AAAAAAAGAA
*
16810456 GAAAAAGAAAGCAAAGAAAAAGG
1 GAAAAAAAAAGCAAAGAAAAAGG
*
16810479 GAAAAAAAAAGCAAAGAATAAGG
1 GAAAAAAAAAGCAAAGAAAAAGG
16810502 G
1 G
16810503 TAAGTAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (23 bp):
GAAAAAAAAAGCAAAGAAAAAGG
Found at i:16813099 original size:36 final size:36
Alignment explanation
Indices: 16813059--16813131 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
16813049 AACACTCTCT
*
16813059 TGTATACCAAACATGTCCCGTTGAATGGAGCTTAGC
1 TGTATACCAAACATGTCCCATTGAATGGAGCTTAGC
* *
16813095 TGTATATCAAACATGTTCCATTGAATGGAGCTTAGC
1 TGTATACCAAACATGTCCCATTGAATGGAGCTTAGC
16813131 T
1 T
16813132 CACATTCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (36 bp):
TGTATACCAAACATGTCCCATTGAATGGAGCTTAGC
Found at i:16814150 original size:24 final size:25
Alignment explanation
Indices: 16814109--16814159 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
16814099 AACTTCTCCA
*
16814109 TTCATATATATATCACAT-AATCAT
1 TTCATATAGATATCACATAAATCAT
* *
16814133 TTCATATAGCTATTACATGAAATCAT
1 TTCATATAGATATCACAT-AAATCAT
16814159 T
1 T
16814160 CCCAGTAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCATATAGATATCACATAAATCAT
Found at i:16820400 original size:51 final size:51
Alignment explanation
Indices: 16820319--16820546 Score: 285
Period size: 51 Copynumber: 4.6 Consensus size: 51
16820309 GCTATAAACG
16820319 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16820371 AAAGGTCCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16820422 AAAGGTCCGGTGACTAAGTGTCATCGTGAG----T-AA---TTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * * *
16820465 AAAAGTCTGATGACTAAATGTCATTGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16820516 AAAGGTCCGATGAC-AATATGTCATCGTGAGT
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGT
16820547 GTTAAATGAA
Statistics
Matches: 155, Mismatches: 12, Indels: 19
0.83 0.06 0.10
Matches are distributed among these distances:
43 35 0.23
46 2 0.01
47 2 0.01
48 2 0.01
50 2 0.01
51 108 0.70
52 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:16820479 original size:43 final size:43
Alignment explanation
Indices: 16820412--16820497 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
16820402 AAATGAATCC
* * *
16820412 TTTACGGATTAAAGGTCCGGTGACTAAGTGTCATCGTGAGTAA
1 TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAA
* *
16820455 TTTACGGATTAAAAGTCTGATGACTAAATGTCATTGTGAGTAA
1 TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAA
16820498 ATGAATCCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (43 bp):
TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAA
Found at i:16820522 original size:94 final size:94
Alignment explanation
Indices: 16820361--16820546 Score: 266
Period size: 94 Copynumber: 2.0 Consensus size: 94
16820351 AAATGAATCC
* * * * * *
16820361 TTTACGGATTAAAGGTCCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
1 TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCATGACGAATTAAAG
* *
16820426 GTCCGGTGACTAA-GTGTCATCGTGAGTAA
66 GTCCGATGAC-AATATGTCATCGTGAGTAA
* *
16820455 TTTACGGATTAAAAGTCTGATGACTAAATGTCATTGTGAGTAAATGAATCCATGACGAATTAAAG
1 TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCATGACGAATTAAAG
16820520 GTCCGATGACAATATGTCATCGTGAGT
66 GTCCGATGACAATATGTCATCGTGAGT
16820547 GTTAAATGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 2 0.02
94 79 0.98
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (94 bp):
TTTACGGATTAAAAGTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCATGACGAATTAAAG
GTCCGATGACAATATGTCATCGTGAGTAA
Found at i:16830590 original size:16 final size:16
Alignment explanation
Indices: 16830569--16830628 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
16830559 GCACAAATTC
16830569 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
*
16830585 AGGCTTTATGCC-AGTGTTTT
1 AGGCTTTGTGCCTA--G---T
16830605 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
16830622 AGGCTTT
1 AGGCTTT
16830629 ATGCTAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 1 0.03
16 18 0.51
17 2 0.06
20 2 0.06
21 11 0.31
22 1 0.03
ACGTcount: A:0.13, C:0.18, G:0.28, T:0.40
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:16830609 original size:37 final size:37
Alignment explanation
Indices: 16830566--16830659 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
16830556 TTTGCACAAA
16830566 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCAGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCAGTGTT
*
16830603 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCTAGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCAGTGTT
16830640 TTCAGGCTTTGTGCCTAGTA
1 TTCAGGCTTTGTGCCTAGTA
16830660 AGCCTTGTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCAGTGTT
Found at i:16830611 original size:21 final size:21
Alignment explanation
Indices: 16830585--16830654 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
16830575 TGTGCCTAGT
16830585 AGGCTTTATGCCAGTGTTTTC
1 AGGCTTTATGCCAGTGTTTTC
*
16830606 AGGCTTTGTGCC--TAG---T-
1 AGGCTTTATGCCAGT-GTTTTC
*
16830622 AGGCTTTATGCTAGTGTTTTC
1 AGGCTTTATGCCAGTGTTTTC
*
16830643 AGGCTTTGTGCC
1 AGGCTTTATGCC
16830655 TAGTAAGCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
16 10 0.27
17 2 0.05
18 1 0.03
19 1 0.03
20 2 0.05
21 21 0.57
ACGTcount: A:0.13, C:0.19, G:0.27, T:0.41
Consensus pattern (21 bp):
AGGCTTTATGCCAGTGTTTTC
Found at i:16831521 original size:22 final size:22
Alignment explanation
Indices: 16831495--16831554 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
16831485 TTACTGTAGT
* *
16831495 TTTGGATATCGGTAGAAGTTTG
1 TTTGGGTATCGATAGAAGTTTG
16831517 TTTGGGTATCGATAGAAGTTTG
1 TTTGGGTATCGATAGAAGTTTG
16831539 TTTGGGTATCGATAGA
1 TTTGGGTATCGATAGA
16831555 TCTAGACCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.05, G:0.32, T:0.40
Consensus pattern (22 bp):
TTTGGGTATCGATAGAAGTTTG
Found at i:16833662 original size:21 final size:20
Alignment explanation
Indices: 16833638--16833689 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
16833628 TCTAATTAGG
*
16833638 TTTTAAATTTTTAAGTTTTAC
1 TTTTAAATTTTTAA-TTTTAA
**
16833659 TTTTATTGTTTTTAATTTTAA
1 TTTTA-AATTTTTAATTTTAA
16833680 TTTT-AATTTT
1 TTTTAAATTTT
16833690 ATTTTGCTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.16
21 14 0.56
22 7 0.28
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTAAATTTTTAATTTTAA
Found at i:16833700 original size:27 final size:28
Alignment explanation
Indices: 16833646--16833701 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
16833636 GGTTTTAAAT
* *
16833646 TTTTAAGTTTTACTTTTATTGTTTTTAA
1 TTTTAAGTTTTAATTTTATTGTTCTTAA
16833674 TTTTAA-TTTTAATTTTATT-TTGCTTAA
1 TTTTAAGTTTTAATTTTATTGTT-CTTAA
16833701 T
1 T
16833702 AAAGGGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 17 0.68
28 6 0.24
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.68
Consensus pattern (28 bp):
TTTTAAGTTTTAATTTTATTGTTCTTAA
Found at i:16835352 original size:25 final size:24
Alignment explanation
Indices: 16835324--16835374 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
16835314 TAAATAATAA
16835324 AATATGAAAT-TATATTTAATAATTT
1 AATAT-AAATATATA-TTAATAATTT
*
16835349 AATATAAATATTTCATTAATAATTT
1 AATATAAATATAT-ATTAATAATTT
16835374 A
1 A
16835375 GGTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 18 0.78
26 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATAAATATATATTAATAATTT
Found at i:16854040 original size:15 final size:15
Alignment explanation
Indices: 16854017--16854057 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16854007 GAGAAGGATC
*
16854017 AAGATGAAGAAAAGA
1 AAGAAGAAGAAAAGA
16854032 AAGAAGAAGAGAAAGA
1 AAGAAGAAGA-AAAGA
16854048 AA-AAGAAGAA
1 AAGAAGAAGAA
16854058 GAACCTGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 16 0.67
16 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AAGAAGAAGAAAAGA
Found at i:16858855 original size:12 final size:12
Alignment explanation
Indices: 16858838--16858864 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16858828 AATTCAAGGA
16858838 ATATCAATATAC
1 ATATCAATATAC
16858850 ATATCAATATAC
1 ATATCAATATAC
16858862 ATA
1 ATA
16858865 CCTTCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATCAATATAC
Found at i:16859085 original size:22 final size:22
Alignment explanation
Indices: 16859060--16859102 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16859050 CTAATGAACA
16859060 GAGAGCAC-CAAGCTGCTAAATG
1 GAGAGCACTCAAG-TGCTAAATG
*
16859082 GAGAGCACTCACGTGCTAAAT
1 GAGAGCACTCAAGTGCTAAAT
16859103 AATGCAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (22 bp):
GAGAGCACTCAAGTGCTAAATG
Found at i:16871216 original size:20 final size:20
Alignment explanation
Indices: 16871193--16871235 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16871183 TCATAAAAGC
16871193 AATT-ATATAATCAAACATAA
1 AATTGATATAATCAAA-ATAA
* *
16871213 AATTGATTTAATGAAAATAA
1 AATTGATATAATCAAAATAA
16871233 AAT
1 AAT
16871236 AAACTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTGATATAATCAAAATAA
Found at i:16873541 original size:20 final size:19
Alignment explanation
Indices: 16873518--16873563 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
16873508 GAAAGGAGAG
16873518 AAGAAAAAG-AGAAATACAAA
1 AAGAAAAAGAAGAAA-A-AAA
16873538 AAGAAAAAAGAAGAAAAAAA
1 AAG-AAAAAGAAGAAAAAAA
16873558 AAGAAA
1 AAGAAA
16873564 CAAAGAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 3 0.12
20 9 0.38
21 7 0.29
22 5 0.21
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
AAGAAAAAGAAGAAAAAAA
Found at i:16873547 original size:21 final size:19
Alignment explanation
Indices: 16873521--16873569 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
16873511 AGGAGAGAAG
16873521 AAAAAGAGAAATACAAAAAGA
1 AAAAAGAGAAA-A-AAAAAGA
16873542 AAAAAGAAGAAAAAAAAAGA
1 AAAAAG-AGAAAAAAAAAGA
16873562 AACAAAGA
1 AA-AAAGA
16873570 ACATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.38
21 11 0.42
22 5 0.19
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAGAGAAAAAAAAAGA
Found at i:16878181 original size:129 final size:129
Alignment explanation
Indices: 16877950--16878206 Score: 390
Period size: 129 Copynumber: 2.0 Consensus size: 129
16877940 TCTACTGTCT
* * * *
16877950 GGTGAATGCCCAAACAATGCCTGGTATTCCGAAGCAACGCCTCCATTGACATCCTGTTTTTTATC
1 GGTGAATGCCCAAACAATGCCTGCTATTCCAAAGCAACGCCTCCATCGACATCCTCTTTTTTATC
* *
16878015 AATTCCTTTAACCTGACACTCAGAGAAGCCATCTTGAATGCAGACTGAAGAATCTCTCCCATCA
66 AATTCCCTTAACCTGACACTCAGAGAAACCATCTTGAATGCAGACTGAAGAATCTCTCCCATCA
*
16878079 GGTGAATGTCCAAACAATGCCTCGCT-TTCCAAAGCAACGCCTCCATCGACATCCTCTTTTTTAT
1 GGTGAATGCCCAAACAATGCCT-GCTATTCCAAAGCAACGCCTCCATCGACATCCTCTTTTTTAT
* * * * *
16878143 CAATTCCCTTCACCTGACACTCGGAGAAACCATTTTGAATGCAGATTGAAGTATCTCTCCCATC
65 CAATTCCCTTAACCTGACACTCAGAGAAACCATCTTGAATGCAGACTGAAGAATCTCTCCCATC
16878207 TGATCGTTGA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
129 113 0.98
130 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (129 bp):
GGTGAATGCCCAAACAATGCCTGCTATTCCAAAGCAACGCCTCCATCGACATCCTCTTTTTTATC
AATTCCCTTAACCTGACACTCAGAGAAACCATCTTGAATGCAGACTGAAGAATCTCTCCCATCA
Found at i:16879552 original size:22 final size:22
Alignment explanation
Indices: 16879527--16879573 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
16879517 TTCTCCTGAG
* *
16879527 CTTTTTCTCTCGTTCT-TTTGTT
1 CTTTTCCTCTCCTTCTGTTT-TT
16879549 CTTTTCCTCTCCTTCTGTTTTT
1 CTTTTCCTCTCCTTCTGTTTTT
16879571 CTT
1 CTT
16879574 CTTCACGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.00, C:0.28, G:0.06, T:0.66
Consensus pattern (22 bp):
CTTTTCCTCTCCTTCTGTTTTT
Found at i:16885553 original size:16 final size:17
Alignment explanation
Indices: 16885512--16885557 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
16885502 ATATTTATGA
*
16885512 TGAAATTTAATATTATT
1 TGAAATTAAATATTATT
*
16885529 TTAATATTAAATATT-TT
1 TGAA-ATTAAATATTATT
16885546 TGAAATTAAATA
1 TGAAATTAAATA
16885558 AGATTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TGAAATTAAATATTATT
Found at i:16886370 original size:23 final size:23
Alignment explanation
Indices: 16886344--16886390 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16886334 TGTTCACATA
16886344 TTATTATACCCTAATAGGAAATG
1 TTATTATACCCTAATAGGAAATG
16886367 TTATTATACCCTAATAGGAAATG
1 TTATTATACCCTAATAGGAAATG
16886390 T
1 T
16886391 ATGCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (23 bp):
TTATTATACCCTAATAGGAAATG
Found at i:16887041 original size:61 final size:61
Alignment explanation
Indices: 16886893--16887039 Score: 235
Period size: 59 Copynumber: 2.4 Consensus size: 61
16886883 TCAAGGACCT
* * *
16886893 TGTGAAATAATGAGGACATAAATTTTTAATAAATTATTATTACTATAAAAATATGATACGA
1 TGTGAAATAATGACGACATAAATTTTTAATAAATTATTATTACTATAAAAATAGGATACAA
* *
16886954 TGTGAAATAATGACGACATAAATTTTTAATAAA-TATTATTACTATCAAAA-AGGATGCAA
1 TGTGAAATAATGACGACATAAATTTTTAATAAATTATTATTACTATAAAAATAGGATACAA
16887013 TGTGAAATAATGACGACATAAATTTTT
1 TGTGAAATAATGACGACATAAATTTTT
16887040 TTTTAAAATT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 33 0.41
60 16 0.20
61 32 0.40
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (61 bp):
TGTGAAATAATGACGACATAAATTTTTAATAAATTATTATTACTATAAAAATAGGATACAA
Found at i:16892672 original size:27 final size:27
Alignment explanation
Indices: 16892639--16892705 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
16892629 ATAGAGTATA
*
16892639 GCTCATTCGAGCCCAGAAGAGTTTGTT
1 GCTCATTCGAGCCCAAAAGAGTTTGTT
*
16892666 GCTCATTCGAGCCCAAAATAGTTTGTT
1 GCTCATTCGAGCCCAAAAGAGTTTGTT
*
16892693 GCTCATTTGAGCC
1 GCTCATTCGAGCC
16892706 AGATTCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (27 bp):
GCTCATTCGAGCCCAAAAGAGTTTGTT
Found at i:16893291 original size:126 final size:126
Alignment explanation
Indices: 16893066--16893305 Score: 408
Period size: 126 Copynumber: 1.9 Consensus size: 126
16893056 AAAATACCCA
* * * *
16893066 TTTTTAATAAAACTCGTCATTAGCCACACCTTTACATATATCATATCAATCTCTACATGCAATTA
1 TTTTTAATAAAACCCATCATTAGCCACACCTTTAAATATATCATATCAATCCCTACATGCAATTA
16893131 TTTCACATCAAATACATTTACTTTTATCATTTTAACAATCTAGTCCTTACATATAATCATT
66 TTTCACATCAAATACATTTACTTTTATCATTTTAACAATCTAGTCCTTACATATAATCATT
** * *
16893192 TTTTTAATAAAACCCATCATTAGCTGCACCTTTAAATATATCATATTAGTCCCTACATGCAATTA
1 TTTTTAATAAAACCCATCATTAGCCACACCTTTAAATATATCATATCAATCCCTACATGCAATTA
16893257 TTTCACATCAAATACATTTACTTTTATCATTTTAACAATCTAGTCCTTA
66 TTTCACATCAAATACATTTACTTTTATCATTTTAACAATCTAGTCCTTA
16893306 AACGTTAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 106 1.00
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (126 bp):
TTTTTAATAAAACCCATCATTAGCCACACCTTTAAATATATCATATCAATCCCTACATGCAATTA
TTTCACATCAAATACATTTACTTTTATCATTTTAACAATCTAGTCCTTACATATAATCATT
Found at i:16897301 original size:8 final size:9
Alignment explanation
Indices: 16897278--16897302 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16897268 TTAAGTAATG
16897278 ATAAAAATA
1 ATAAAAATA
16897287 ATAAAAATA
1 ATAAAAATA
16897296 ATAAAAA
1 ATAAAAA
16897303 CAAAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
ATAAAAATA
Found at i:16898696 original size:47 final size:47
Alignment explanation
Indices: 16898642--16898897 Score: 251
Period size: 47 Copynumber: 5.4 Consensus size: 47
16898632 TAATGACACA
* *
16898642 GGCCTTGTACCTAACAGGCTTTAATGCTGGTGTATTGTACCGTATCG
1 GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
* * * *
16898689 GGCCTTGTGCCTAGCAGGCTTTAATGCCAGTGTTTTGTACCATATCG
1 GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
* * * * * * * * *
16898736 GGCCTTGTGCCTAGCAAGCTTTAATGCCAGTTTACTGTATCTTATCA
1 GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
* * * * * *
16898783 GACCTTGTACCTAACAGGCTTTAATGATGGTGTACTGTACCGTATTG
1 GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
* * * * *
16898830 GGCCTTGTACCTAGCAAGCTTTAATGCTAATGTATTGTACCATAACA
1 GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
* * *
16898877 GGTCTTGTGCCTAACATGCTT
1 GGCCTTGTACCTAACAGGCTT
16898898 CATTCCAATG
Statistics
Matches: 169, Mismatches: 40, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 169 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (47 bp):
GGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACCATATCG
Found at i:16898884 original size:94 final size:94
Alignment explanation
Indices: 16898642--16898897 Score: 287
Period size: 94 Copynumber: 2.7 Consensus size: 94
16898632 TAATGACACA
* * * * * *
16898642 GGCCTTGTACCTAACAGGCTTTAATGCTGGTGTATTGTACCGTATCGGGCCTTGTGCCTAGCAGG
1 GGCCTTGTACCTAGCAAGCTTTAATGCTAGTGTATTGTACCATATCAGGCCTTGTGCCTAACAGG
* **
16898707 CTTTAATGCCAGTGTTTTGTACCATATCG
66 CTTTAATGACAGTGTACTGTACCATATCG
* * * * * * * *
16898736 GGCCTTGTGCCTAGCAAGCTTTAATGCCAGTTTACTGTATCTTATCAGACCTTGTACCTAACAGG
1 GGCCTTGTACCTAGCAAGCTTTAATGCTAGTGTATTGTACCATATCAGGCCTTGTGCCTAACAGG
** * *
16898801 CTTTAATGATGGTGTACTGTACCGTATTG
66 CTTTAATGACAGTGTACTGTACCATATCG
* * * *
16898830 GGCCTTGTACCTAGCAAGCTTTAATGCTAATGTATTGTACCATAACAGGTCTTGTGCCTAACATG
1 GGCCTTGTACCTAGCAAGCTTTAATGCTAGTGTATTGTACCATATCAGGCCTTGTGCCTAACAGG
16898895 CTT
66 CTT
16898898 CATTCCAATG
Statistics
Matches: 130, Mismatches: 32, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
94 130 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (94 bp):
GGCCTTGTACCTAGCAAGCTTTAATGCTAGTGTATTGTACCATATCAGGCCTTGTGCCTAACAGG
CTTTAATGACAGTGTACTGTACCATATCG
Found at i:16906419 original size:19 final size:22
Alignment explanation
Indices: 16906374--16906419 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 22
16906364 TATGATGAAT
16906374 TGATGTTGAATTTAGAATGATG
1 TGATGTTGAATTTAGAATGATG
* *
16906396 GGATG-TGAA-TT-GAATTATG
1 TGATGTTGAATTTAGAATGATG
16906415 TGATG
1 TGATG
16906420 AAATTGGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.52
20 2 0.10
21 4 0.19
22 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (22 bp):
TGATGTTGAATTTAGAATGATG
Found at i:16908095 original size:5 final size:5
Alignment explanation
Indices: 16908087--16908111 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16908077 ATCCTCGCCT
16908087 CACCC CACCC CACCC CACCC CACCC
1 CACCC CACCC CACCC CACCC CACCC
16908112 GCTCCACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCC
Found at i:16925171 original size:14 final size:14
Alignment explanation
Indices: 16925152--16925192 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
16925142 TTTTCAATTA
16925152 AATTTGAAAGTGTT
1 AATTTGAAAGTGTT
16925166 AATTTGAAAGTGTT
1 AATTTGAAAGTGTT
16925180 AATTTGAATAGTG
1 AATTTGAA-AGTG
16925193 CTCATGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
AATTTGAAAGTGTT
Found at i:16925732 original size:39 final size:39
Alignment explanation
Indices: 16925639--16925750 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 39
16925629 TAATGACCTG
16925639 GTAGTGTTTACAGTGTCACTACCAACTCAGTATAACATT
1 GTAGTGTTTACAGTGTCACTACCAACTCAGTATAACATT
** * * * **
16925678 ACAATGTCTATAGTGTCACTACCAGTTCAGTATAACATT
1 GTAGTGTTTACAGTGTCACTACCAACTCAGTATAACATT
* * *
16925717 GTAGTATTTACAGTGTTACTGCCAACTCAGTATA
1 GTAGTGTTTACAGTGTCACTACCAACTCAGTATA
16925751 TTTTCGACGT
Statistics
Matches: 56, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (39 bp):
GTAGTGTTTACAGTGTCACTACCAACTCAGTATAACATT
Found at i:16939844 original size:3 final size:3
Alignment explanation
Indices: 16939838--16939880 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
16939828 ATTAACCTAA
*
16939838 AAG AAG AAG AAA AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
16939881 AAAGTTGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16939864 original size:20 final size:20
Alignment explanation
Indices: 16939839--16939879 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
16939829 TTAACCTAAA
16939839 AGAAGAAGAAAAAGAAGAAG
1 AGAAGAAGAAAAAGAAGAAG
*
16939859 AGAAGAAGAAGAAGAAGAAG
1 AGAAGAAGAAAAAGAAGAAG
16939879 A
1 A
16939880 AAAAGTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAAAAAGAAGAAG
Found at i:16942750 original size:17 final size:16
Alignment explanation
Indices: 16942715--16942756 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16942705 TTTCATAATT
* *
16942715 TTCTCTCATTTTTCTC
1 TTCTCTCTTTTTTATC
16942731 TTCTCTCTTTTTTATGC
1 TTCTCTCTTTTTTAT-C
16942748 TTCTCTCTT
1 TTCTCTCTT
16942757 CAACAACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.05, C:0.29, G:0.02, T:0.64
Consensus pattern (16 bp):
TTCTCTCTTTTTTATC
Found at i:16943500 original size:12 final size:12
Alignment explanation
Indices: 16943483--16943509 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16943473 ACAGTTGAAT
16943483 AAGGTAACGATG
1 AAGGTAACGATG
16943495 AAGGTAACGATG
1 AAGGTAACGATG
16943507 AAG
1 AAG
16943510 AACAATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.33, T:0.15
Consensus pattern (12 bp):
AAGGTAACGATG
Found at i:16944198 original size:16 final size:16
Alignment explanation
Indices: 16944177--16944232 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
16944167 CCGCCAATAG
*
16944177 GAGTTCTCCAGATGAA
1 GAGTTCGCCAGATGAA
16944193 GAGTTCGCCA-AT--A
1 GAGTTCGCCAGATGAA
*
16944206 GAGGTTCGCTAGATGAA
1 GA-GTTCGCCAGATGAA
*
16944223 GAGTTTGCCA
1 GAGTTCGCCA
16944233 ATAGGGGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.09
14 7 0.22
15 4 0.12
16 15 0.47
17 3 0.09
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (16 bp):
GAGTTCGCCAGATGAA
Found at i:16944204 original size:30 final size:31
Alignment explanation
Indices: 16944168--16944241 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
16944158 TACATTAGTC
*
16944168 CGCCAATAGGA-GTTCTCCAGATGAAGAGTT
1 CGCCAATAGGAGGTTCGCCAGATGAAGAGTT
*
16944198 CGCCAATA-GAGGTTCGCTAGATGAAGAGTT
1 CGCCAATAGGAGGTTCGCCAGATGAAGAGTT
*
16944228 TGCCAATAGG-GGTT
1 CGCCAATAGGAGGTT
16944242 TGTCAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 36 0.92
31 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (31 bp):
CGCCAATAGGAGGTTCGCCAGATGAAGAGTT
Found at i:16944252 original size:30 final size:30
Alignment explanation
Indices: 16944188--16944259 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
16944178 AGTTCTCCAG
* *
16944188 ATGAAGAGTTCGCCAATAGAGGTTCGCTAG
1 ATGAAGAGTTTGCCAATAGAGGTTCGCTAA
* *
16944218 ATGAAGAGTTTGCCAATAGGGGTTTG-TCAA
1 ATGAAGAGTTTGCCAATAGAGGTTCGCT-AA
*
16944248 ATGAAAAGTTTG
1 ATGAAGAGTTTG
16944260 GCTCTCCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (30 bp):
ATGAAGAGTTTGCCAATAGAGGTTCGCTAA
Found at i:16945528 original size:18 final size:17
Alignment explanation
Indices: 16945480--16945529 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
16945470 CAAATGATAT
16945480 TTTTATTAATAATAATA
1 TTTTATTAATAATAATA
* *
16945497 TTATAATAAGTAATAATA
1 TTTTATTAA-TAATAATA
16945515 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
16945530 TTATAAAGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTTATTAATAATAATA
Found at i:16947420 original size:16 final size:16
Alignment explanation
Indices: 16947399--16947429 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16947389 CTATGAGTAG
16947399 TTATATTAATTTTATT
1 TTATATTAATTTTATT
*
16947415 TTATATTATTTTTAT
1 TTATATTAATTTTAT
16947430 GAGTTTTGAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:16965410 original size:12 final size:12
Alignment explanation
Indices: 16965393--16965435 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
16965383 CAGGTTCTTT
16965393 TTCTTCTTTCTC
1 TTCTTCTTTCTC
16965405 TTCTTCCTTTCT-
1 TTCTT-CTTTCTC
16965417 TTCTTC-TTCTC
1 TTCTTCTTTCTC
16965428 TTCTTCTT
1 TTCTTCTT
16965436 GATCCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.14
11 7 0.25
12 11 0.39
13 6 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:16965421 original size:15 final size:15
Alignment explanation
Indices: 16965387--16965425 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
16965377 CCTCAACAGG
16965387 TTCTTT-TTCTT-CT
1 TTCTTTCTTCTTCCT
16965400 TTC--TCTTCTTCCT
1 TTCTTTCTTCTTCCT
16965413 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
16965426 TCTTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.05
12 5 0.23
13 8 0.36
15 8 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTCTTCTTCCT
Found at i:16965429 original size:8 final size:8
Alignment explanation
Indices: 16965394--16965434 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
16965384 AGGTTCTTTT
16965394 TCTTCTTTC
1 TCTTC-TTC
16965403 TCTTCTTC
1 TCTTCTTC
16965411 -CTTTCTT-
1 TC-TTCTTC
16965418 TCTTCTTC
1 TCTTCTTC
16965426 TCTTCTTC
1 TCTTCTTC
16965434 T
1 T
16965435 TGATCCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.21
8 18 0.62
9 5 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TCTTCTTC
Found at i:16973673 original size:66 final size:66
Alignment explanation
Indices: 16973567--16973707 Score: 237
Period size: 66 Copynumber: 2.1 Consensus size: 66
16973557 ATAATCACTC
*
16973567 CACCTCTCGGTGCGAGCAACGATGTGTATTCAAGAACAAGTAACTAGAGTTTGTCCCAATCCCAA
1 CACCTCTCGGTGCGAGCAACGATGTGTATTAAAGAACAAGTAACTAGAGTTTGTCCCAATCCCAA
16973632 G
66 G
* * *
16973633 CACCTCTTGGTGCGATCAACGATGTGTATTAAAGAACAAGTAACTAGAGTTTGTCCCAGTCCCAA
1 CACCTCTCGGTGCGAGCAACGATGTGTATTAAAGAACAAGTAACTAGAGTTTGTCCCAATCCCAA
16973698 G
66 G
*
16973699 CAGCTCTCG
1 CACCTCTCG
16973708 CCTAACTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (66 bp):
CACCTCTCGGTGCGAGCAACGATGTGTATTAAAGAACAAGTAACTAGAGTTTGTCCCAATCCCAA
G
Found at i:16976764 original size:16 final size:16
Alignment explanation
Indices: 16976732--16976765 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16976722 TACTTCGAAG
* *
16976732 GTATATATATTTTTGT
1 GTATATATATGTGTGT
16976748 GTATATATATGTGTGT
1 GTATATATATGTGTGT
16976764 GT
1 GT
16976766 GTGTATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (16 bp):
GTATATATATGTGTGT
Found at i:16977841 original size:30 final size:30
Alignment explanation
Indices: 16977801--16977874 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
16977791 TTTATTCTGA
*
16977801 TTTTTTAAAATTAAATCCT-TTATTTTATT
1 TTTTTTAAAATTAAACCCTCTTATTTTATT
*
16977830 TTTTGTTAAAATTCAACCCTCTTATTTT-TGT
1 TTTT-TTAAAATTAAACCCTCTTATTTTAT-T
*
16977861 TCCTTTTAAAATTA
1 T-TTTTTAAAATTA
16977875 CCCTTTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 14 0.38
31 17 0.46
32 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTTTTAAAATTAAACCCTCTTATTTTATT
Found at i:16977887 original size:29 final size:30
Alignment explanation
Indices: 16977835--16977895 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 30
16977825 TTATTTTTTG
16977835 TTAAAATTCAACCCTCTTATTTTTGTTCCTT
1 TTAAAATT-AACCCTCTTATTTTTGTTCCTT
*
16977866 TTAAAATT-ACCCT-TTCATTTTTGTTTCTT
1 TTAAAATTAACCCTCTT-ATTTTTGTTCCTT
16977895 T
1 T
16977896 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 18 0.64
31 8 0.29
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (30 bp):
TTAAAATTAACCCTCTTATTTTTGTTCCTT
Found at i:16982678 original size:7 final size:7
Alignment explanation
Indices: 16982661--16982710 Score: 50
Period size: 6 Copynumber: 6.9 Consensus size: 7
16982651 ATAAAAAAGG
16982661 GAAAGAAA
1 GAAA-AAA
16982669 GAAAAAA
1 GAAAAAA
16982676 G-AAAAA
1 GAAAAAA
16982682 G-AAAAA
1 GAAAAAA
16982688 GAAAAGAGAA
1 G-AAA-A-AA
16982698 GAAAAAA
1 GAAAAAA
16982705 GAAAAA
1 GAAAAA
16982711 GGAGAGGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 12 0.32
7 12 0.32
8 7 0.18
9 4 0.11
10 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:16982682 original size:17 final size:18
Alignment explanation
Indices: 16982653--16982715 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
16982643 CTAAACAAAT
*
16982653 AAAAAAG-GGAAAGAAAG
1 AAAAAAGAGAAAAGAAAG
16982670 AAAAAAGA-AAAAGAAA-
1 AAAAAAGAGAAAAGAAAG
*
16982686 AAGAAAAGAGAAGAAAAAAG
1 AA-AAAAGAGAA-AAGAAAG
*
16982706 AAAAAGGAGA
1 AAAAAAGAGA
16982716 GGTCAAGGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.05
17 20 0.53
18 2 0.05
19 12 0.32
20 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAGAAAG
Done.