Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 44 of 171
Found at i:18828539 original size:15 final size:15
Alignment explanation
Indices: 18828519--18828547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18828509 TTTTTTATTT
18828519 TTAATTCATTTTTAA
1 TTAATTCATTTTTAA
18828534 TTAATTCATTTTTA
1 TTAATTCATTTTTA
18828548 TTTATATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTCATTTTTAA
Found at i:18852241 original size:28 final size:28
Alignment explanation
Indices: 18852201--18852271 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
18852191 AGAGACTGCC
* *
18852201 ATTTACTTCTGCTGCCCCTTGATCTAAT
1 ATTTATTTCTGCTGCCCCGTGATCTAAT
18852229 ATTTATTTCTGCTGCCCCGTGATCTAAT
1 ATTTATTTCTGCTGCCCCGTGATCTAAT
18852257 ATTTATTTCTGCTGC
1 ATTTATTTCTGCTGC
18852272 TCAGGGTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.13, T:0.45
Consensus pattern (28 bp):
ATTTATTTCTGCTGCCCCGTGATCTAAT
Found at i:18854159 original size:1 final size:1
Alignment explanation
Indices: 18854153--18854186 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
18854143 ATAAAAGCAG
*
18854153 CCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
18854187 ATTTATTGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:18859723 original size:7 final size:7
Alignment explanation
Indices: 18859711--18859744 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
18859701 AAATTCTCCT
18859711 CCATTGC
1 CCATTGC
18859718 CCATTGC
1 CCATTGC
18859725 CCATTGC
1 CCATTGC
18859732 CCATTGC
1 CCATTGC
18859739 CCATTG
1 CCATTG
18859745 GCTTTGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.29
Consensus pattern (7 bp):
CCATTGC
Found at i:18877697 original size:201 final size:201
Alignment explanation
Indices: 18877095--18877886 Score: 1005
Period size: 201 Copynumber: 4.0 Consensus size: 201
18877085 TAATCTTAAG
* * * * *
18877095 TGCTCCATTCCACTAATATCTTCCCTAATTGG-CAACTCGGCAGCTGGAGCAGTAAGAATCACAG
1 TGCTCCATTCTACCAATATCTT-CCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAG
*** * * ** * * *
18877159 TCTTGCGTCTATTCTTCCTCAAGGGGGATTGGTGTTGTGAAGT-GATGGCAGACTTGGCCCTCCC
65 TCTTGCGTCTGCCCTTCCTCGAGGGGGCTTCTTGTTGTGAAGTAGCT-GCATACTTGGCCCTCTC
* ** * * *
18877223 AACCTCACTCCTATCTTGTACAATTGCATCCAATTCTTCAGTTGTGCCTTTTCCTAGAACCGGTG
129 AACCTCACTACTATCTTCAACAATTGCATCCAATTCTTCAGTCGTGCCTTTCCCTACAACCGGTG
18877288 CCT-TCAAC
194 CCTCT-AAC
* * * * *
18877296 TGCTCCGTACTACCAATATCTTCCTTACTT-GCCAAATCTGCAGCTGGAGCAGTAAGAATCACTG
1 TGCTCCATTCTACCAATATCTTCCTTA-TTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAG
* * * **
18877360 TCTTGCGTCTGTTCC-TCCTCGAGGGGG---C---TTGTGAAGAAAG-GGCACCCTTGGCCCTCT
65 TCTTGCGTCTG-CCCTTCCTCGAGGGGGCTTCTTGTTGTGAAG-TAGCTGCATACTTGGCCCTCT
* * * * *
18877417 CAACCTCACTACTATCTTCCACAACTGCATCCAATTCTTCAGTCTTGCCTTTTCCTACAAGCGGT
128 CAACCTCACTACTATCTTCAACAATTGCATCCAATTCTTCAGTCGTGCCTTTCCCTACAACCGGT
*
18877482 GCCTCTAGC
193 GCCTCTAAC
18877491 TGCTCCATTCTACCAATATCTTCCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGT
1 TGCTCCATTCTACCAATATCTTCCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGT
*
18877556 CTTGCGTCTGCCCTTCCTCGAGGGGGCTTCTTGTTGTGAAGTAGCTGCATACTTGGCCCTCTCGA
66 CTTGCGTCTGCCCTTCCTCGAGGGGGCTTCTTGTTGTGAAGTAGCTGCATACTTGGCCCTCTCAA
*
18877621 CCTCACTACTATCTTCAACAATTGCATCTAATTCTTCAGTCGTGCCTTTCCCTACAACCGGTGCC
131 CCTCACTACTATCTTCAACAATTGCATCCAATTCTTCAGTCGTGCCTTTCCCTACAACCGGTGCC
18877686 TCTAAC
196 TCTAAC
*
18877692 TGCTCCGTTCTACCAATATCTTCCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGT
1 TGCTCCATTCTACCAATATCTTCCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGT
* *
18877757 CTTGCGTCTGCCCCTCCTCGAGGGGGCTTCTTGTTGTGAATTAGCTGCATACTTGGCCCTCTCAA
66 CTTGCGTCTGCCCTTCCTCGAGGGGGCTTCTTGTTGTGAAGTAGCTGCATACTTGGCCCTCTCAA
* * * * * * *
18877822 CCTCACTACTGTCTTCGACAATTGCATCCAATTCTTCAGCCGAGCCCTTCCCTCCAACCGATGCC
131 CCTCACTACTATCTTCAACAATTGCATCCAATTCTTCAGTCGTGCCTTTCCCTACAACCGGTGCC
18877887 AAATCGGCAG
Statistics
Matches: 520, Mismatches: 56, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
194 4 0.01
195 163 0.31
196 1 0.00
197 1 0.00
198 1 0.00
200 7 0.01
201 341 0.66
202 2 0.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.30
Consensus pattern (201 bp):
TGCTCCATTCTACCAATATCTTCCTTATTGGCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGT
CTTGCGTCTGCCCTTCCTCGAGGGGGCTTCTTGTTGTGAAGTAGCTGCATACTTGGCCCTCTCAA
CCTCACTACTATCTTCAACAATTGCATCCAATTCTTCAGTCGTGCCTTTCCCTACAACCGGTGCC
TCTAAC
Found at i:18877918 original size:162 final size:161
Alignment explanation
Indices: 18877722--18878178 Score: 682
Period size: 162 Copynumber: 2.8 Consensus size: 161
18877712 TTCCTTATTG
* * *
18877722 GCCAAATCGGCAGCTGGAGCAGTAAGAACCACAGTCTTGCGTCTGCCCCTCCTCGAGGGGGCTTC
1 GCCAAATCGGCAGCTGGAGCGGTAAGAGCCACAGTCTTGCGTCTGCTCCTCCTCGAGGGGGCTTC
* * *
18877787 TTGTTGTGAATTAGCTGCATACTTGGCCCTCTCAACCTCACTACTGTCTTCGACAATTGCATCCA
66 TTGTTGTGAAGTAGC-GCATACTTGGCCCTCTCAACCTCACTACTATCTTCAACAATTGCATCCA
*
18877852 ATTCTTCAGCCGAGCCCTTCCCTCCAACCGAT
130 ATTCTTCAGCCGAGCCCTTCCCTACAACCGAT
*
18877884 GCCAAATCGGCAGCTGGAGCGGTAAGAGCCACAGTATTGCGTCTGCTCCTCCTCGAGGGGGCTTC
1 GCCAAATCGGCAGCTGGAGCGGTAAGAGCCACAGTCTTGCGTCTGCTCCTCCTCGAGGGGGCTTC
* *
18877949 TTGTTGTGAAGTAGCCGCATACTTGGCCCTCTCAACCTTACTGCTATCTTCAACAATTGCATCCA
66 TTGTTGTGAAGTAG-CGCATACTTGGCCCTCTCAACCTCACTACTATCTTCAACAATTGCATCCA
* *
18878014 ATTCTTCAGTCGAGCCCTTCCCTACAACCGGT
130 ATTCTTCAGCCGAGCCCTTCCCTACAACCGAT
* * * *
18878046 GCCAAATCAGCAGCTGGAGCGGTATGAGCCACAGTCTTGCGTCTGCTCCTTCTCGA-GGGGCTTG
1 GCCAAATCGGCAGCTGGAGCGGTAAGAGCCACAGTCTTGCGTCTGCTCCTCCTCGAGGGGGCTTC
* * * * * *
18878110 TTGTTGTGAAGTAACGACACACTTGACCTTCTCAACCTCACTACTCTCTTCCACAATTGCATCCA
66 TTGTTGTGAAGTAGCG-CATACTTGGCCCTCTCAACCTCACTACTATCTTCAACAATTGCATCCA
18878175 ATTC
130 ATTC
18878179 AGCACTCCAG
Statistics
Matches: 268, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
160 2 0.01
161 65 0.24
162 200 0.75
163 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.27
Consensus pattern (161 bp):
GCCAAATCGGCAGCTGGAGCGGTAAGAGCCACAGTCTTGCGTCTGCTCCTCCTCGAGGGGGCTTC
TTGTTGTGAAGTAGCGCATACTTGGCCCTCTCAACCTCACTACTATCTTCAACAATTGCATCCAA
TTCTTCAGCCGAGCCCTTCCCTACAACCGAT
Found at i:18887295 original size:15 final size:14
Alignment explanation
Indices: 18887258--18887295 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
18887248 AAAATATATT
18887258 TATTTTAT-TTTAA
1 TATTTTATATTTAA
*
18887271 TATTTAATATTTAA
1 TATTTTATATTTAA
18887285 TAATTTTATAT
1 T-ATTTTATAT
18887296 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:18890220 original size:9 final size:9
Alignment explanation
Indices: 18890191--18890242 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
18890181 TTGAAGTTAG
18890191 AATTAAATT
1 AATTAAATT
18890200 AATTGAGAAATT
1 AATT---AAATT
18890212 AACTT-AATT
1 AA-TTAAATT
18890221 AATTAAATT
1 AATTAAATT
18890230 AATTAAATT
1 AATTAAATT
18890239 AATT
1 AATT
18890243 GATTAAATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.05
9 27 0.71
12 7 0.18
13 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:18890226 original size:13 final size:14
Alignment explanation
Indices: 18890191--18890250 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 14
18890181 TTGAAGTTAG
18890191 AATTAAATTAATTGAGA
1 AATTAAATTAATT---A
*
18890208 AATTAACTTAATT-
1 AATTAAATTAATTA
18890221 AATTAAATTAATTA
1 AATTAAATTAATTA
*
18890235 AATT-AATTGATTA
1 AATTAAATTAATTA
18890248 AAT
1 AAT
18890251 AGATATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
13 23 0.59
14 4 0.10
17 12 0.31
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTAAATTAATTA
Found at i:18890247 original size:22 final size:22
Alignment explanation
Indices: 18890208--18890250 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18890198 TTAATTGAGA
*
18890208 AATTAACTTAATTAATTAAATT
1 AATTAAATTAATTAATTAAATT
*
18890230 AATTAAATTAATTGATTAAAT
1 AATTAAATTAATTAATTAAAT
18890251 AGATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAATTAATTAATTAAATT
Found at i:18892261 original size:6 final size:6
Alignment explanation
Indices: 18892250--18892291 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
18892240 GGGAGTGCGA
18892250 GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC
1 GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC GCAGCC
18892292 AGCAAGCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.33, T:0.00
Consensus pattern (6 bp):
GCAGCC
Found at i:18899558 original size:15 final size:15
Alignment explanation
Indices: 18899538--18899593 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 15
18899528 ATGATTTTTA
18899538 AAATTTTTAAAATAT
1 AAATTTTTAAAATAT
* *
18899553 AAATTTTTTAAAGAT
1 AAATTTTTAAAATAT
* *
18899568 -ATTTTTTAATATA-
1 AAATTTTTAAAATAT
*
18899581 AAATTATTAAAAT
1 AAATTTTTAAAAT
18899594 TATTAAATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AAATTTTTAAAATAT
Found at i:18899560 original size:16 final size:17
Alignment explanation
Indices: 18899536--18899569 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18899526 AAATGATTTT
18899536 TAAAATTTTTAAA-ATA
1 TAAAATTTTTAAAGATA
*
18899552 TAAATTTTTTAAAGATA
1 TAAAATTTTTAAAGATA
18899569 T
1 T
18899570 TTTTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAATTTTTAAAGATA
Found at i:18899572 original size:27 final size:25
Alignment explanation
Indices: 18899531--18899600 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 25
18899521 TCAGCAAATG
18899531 ATTTTTAAAATTTTTAAAATATAAA
1 ATTTTTAAAATTTTTAAAATATAAA
* **
18899556 TTTTTTAAAGATATTTTTTAATATAAA
1 ATTTTTAAA-AT-TTTTAAAATATAAA
* *
18899583 ATTATTAAAATTATTAAA
1 ATTTTTAAAATTTTTAAA
18899601 TAATTTTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
25 12 0.34
26 4 0.11
27 19 0.54
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (25 bp):
ATTTTTAAAATTTTTAAAATATAAA
Found at i:18899695 original size:34 final size:35
Alignment explanation
Indices: 18899656--18899733 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
18899646 CAATTTCATC
18899656 TTCTTCTCA-CCATTTTTCCATCTAACACCAATTA
1 TTCTTCTCACCCATTTTTCCATCTAACACCAATTA
* *
18899690 TTCTTCTCACCCATTTTTCCATCTAACACCACTTC
1 TTCTTCTCACCCATTTTTCCATCTAACACCAATTA
18899725 TTCTTCTCA
1 TTCTTCTCA
18899734 TCATCCAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 9 0.22
35 32 0.78
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (35 bp):
TTCTTCTCACCCATTTTTCCATCTAACACCAATTA
Found at i:18900592 original size:28 final size:30
Alignment explanation
Indices: 18900552--18900624 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
18900542 GATGATGATG
18900552 ATTTTAATAATTTTATA-TTT-AAAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAAATA
18900580 ATTTTAATAATTTTATATTTTAAAAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAAATA
18900610 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
18900625 AAATCATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 17 0.40
29 3 0.07
30 23 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTAATAATTTTATATTTTAAAAAAATA
Found at i:18900609 original size:21 final size:23
Alignment explanation
Indices: 18900585--18900627 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
18900575 AAATAATTTT
18900585 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
18900606 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
18900628 TCATTTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:18909011 original size:17 final size:17
Alignment explanation
Indices: 18908986--18909024 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
18908976 CGACACCCCT
*
18908986 TTTTGTCAGATAAAAAA
1 TTTTCTCAGATAAAAAA
18909003 TTTTCTCAGATAAAAAA
1 TTTTCTCAGATAAAAAA
18909020 TTTTC
1 TTTTC
18909025 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (17 bp):
TTTTCTCAGATAAAAAA
Found at i:18909158 original size:61 final size:60
Alignment explanation
Indices: 18909004--18909598 Score: 533
Period size: 64 Copynumber: 9.6 Consensus size: 60
18908994 GATAAAAAAT
* ** ** * **
18909004 TTTCTCAGATAAAAAATTTTCAATTTTTTTTTATGTTGGCCATGCAATGGTTGACACCCCACCCC
1 TTTCTCAGATAAAAAAATTT-AAAATTTTTTGGTGTTGTCCATGCAATGGCCGACA---C-CCCC
* * *
18909069 TTGTTCTCAGATAAAAAAATTCAAAATTTTTTGGTGTTGTCCATGCATTGGTCGACACTCCCC
1 -T-TTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACAC-CCCC
* *
18909132 TTTCTCAGATAAAAAAATTTGAAATTTTTTTGGTATTAG-CCATGCAATGGCCGACACCCCC
1 TTTCTCAGATAAAAAAATTT-AAAATTTTTTGGTGTT-GTCCATGCAATGGCCGACACCCCC
* * *
18909193 TGTTCTCAGATAAAAAAAATTCAAAATTTTTTTGTGTTAGT-CATGCCATGGTCGACACGACACC
1 T-TTCTCAGAT-AAAAAAATTTAAAATTTTTTGGTGTT-GTCCATGCAAT-G--G-C-CGACACC
18909257 CCC
58 CCC
* * * * * *
18909260 TTT-TCAGATAAAAAAATTTCAATTTTTTTTGTGTTGGCCATACAATGGTCGACACCCCC
1 TTTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCC
* * *
18909319 TTTTCTCAGAT-AAAAAATTT--ATTTTTTTGGCGTTG-GCATGCAATGGCCGACACCCCC
1 -TTTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCC
* * * * *
18909376 TGTTCTCAGATAAAAAAATTCAAAATTTTTTAGTGTTGGT-CATGCCATGGCCGACAGCCCT
1 T-TTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTT-GTCCATGCAATGGCCGACACCCCC
* * * * *
18909437 TTTTTCAGATAAAAAAATTTCAAATTTTTTGATGTTGGCAATGCAATGGCCGACACCCCC
1 TTTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCC
* *
18909497 TTTTCTCAGATAAAAAAATTTCAAATTTTTTTTTGGTGTTGGT-CATGCAATGGCCGACATCCCC
1 -TTTCTCAGATAAAAAAATTT-AAA--ATTTTTTGGTGTT-GTCCATGCAATGGCCGACACCCCC
*
18909561 TGTTCTCAGATAAAAAAATTTCAAAATTTTTTTGTGTT
1 T-TTCTCAGATAAAAAAATTT-AAAATTTTTTGGTGTT
18909599 AGCCATGTAA
Statistics
Matches: 444, Mismatches: 58, Indels: 58
0.79 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 28 0.06
58 21 0.05
59 11 0.02
60 70 0.16
61 69 0.16
62 75 0.17
63 19 0.04
64 82 0.18
65 8 0.02
66 32 0.07
67 28 0.06
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (60 bp):
TTTCTCAGATAAAAAAATTTAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCC
Found at i:18909187 original size:62 final size:61
Alignment explanation
Indices: 18909004--18909619 Score: 635
Period size: 62 Copynumber: 10.0 Consensus size: 61
18908994 GATAAAAAAT
* * ** **
18909004 TTTCTCAGATAAAAAATTTTCAATTTTTTTTTATGTTGGCCATGCAATGGTTGACACCCCACCCC
1 TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACA---C-CCCC
* * * *
18909069 TTGTTCTCAGATAAAAAAA-TTCAAAATTTTTTGGTGTTGTCCATGCATTGGTCGACACTCCCC
1 -T-TTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCC
* * *
18909132 TTTCTCAGATAAAAAAATTTGAAATTTTTTTGGTATTAGCCATGCAATGGCCGACACCCCC
1 TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* * * *
18909193 TGTTCTCAGATAAAAAAAATTCAAAATTTTTTT-GTGTTAGTCATGCCATGGTCGACACGACACC
1 T-TTCTCAGATAAAAAAATTTC-AAATTTTTTTGGTGTTGGCCATGCAAT-G--G-C-CGACACC
18909257 CCC
59 CCC
* * *
18909260 TTT-TCAGATAAAAAAATTTC-AATTTTTTTTGTGTTGGCCATACAATGGTCGACACCCCC
1 TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
*
18909319 TTTTCTCAGAT-AAAAAATTT---ATTTTTTTGGCGTTGG-CATGCAATGGCCGACACCCCC
1 -TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* * * * * *
18909376 TGTTCTCAGATAAAAAAA-TTCAAAATTTTTTAGTGTTGGTCATGCCATGGCCGACAGCCCT
1 T-TTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* * *
18909437 TTTTTCAGATAAAAAAATTTCAAA-TTTTTTGATGTTGGCAATGCAATGGCCGACACCCCC
1 TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* *
18909497 TTTTCTCAGATAAAAAAATTTCAAATTTTTTTTTGGTGTTGGTCATGCAATGGCCGACATCCCC
1 -TTTCTCAGATAAAAAAATTTCAAA--TTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
* * * *
18909561 TGTTCTCAGATAAAAAAATTTCAAAATTTTTTT-GTGTTAGCCATGTAATAGCCAACACC
1 T-TTCTCAGATAAAAAAATTTC-AAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC
18909620 AATTTCCCCT
Statistics
Matches: 469, Mismatches: 56, Indels: 54
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.00
57 30 0.06
58 20 0.04
59 10 0.02
60 69 0.15
61 76 0.16
62 84 0.18
63 34 0.07
64 64 0.14
65 20 0.04
66 35 0.07
67 26 0.06
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (61 bp):
TTTCTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCC
Found at i:18909823 original size:31 final size:31
Alignment explanation
Indices: 18909781--18909840 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
18909771 TACAATCAAA
* * *
18909781 TTTCGGGGTTGAGCTATATACTTTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
*
18909812 TTTCGGAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
18909841 GAAGCGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:18913585 original size:86 final size:86
Alignment explanation
Indices: 18913476--18913957 Score: 736
Period size: 86 Copynumber: 5.6 Consensus size: 86
18913466 CATTAAAATT
* * *
18913476 AATTTAACATTATTTAAATAAAAAA-ATTATTATTATATTACAATTTATATCAAATATTGTGTTC
1 AATTTAA-A-TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
* *
18913540 ATTTGACAAGACATTATTTAATCA
64 ATTTGACAATACATTATTTACT-A
** * * *
18913564 AATTTTCACATTTAAATAAAAAATATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
18913629 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
*
18913650 AATTTAAATATTTAAAT-AAAAA-ATTATTACTATATTACAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
* *
18913713 TTGATAATATATTATTTACTA
66 TTGACAATACATTATTTACTA
* *
18913734 AATTTAAATTTTTAAATAAAAAAGATTATTATTATATTATAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
*
18913799 TTGCCAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
*
18913820 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTATAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
18913885 TTGACAATACATTATTTACTA
66 TTGACAATACATTATTTACTA
18913906 AATTTAAATATTTAAATAAAAAAGATTATTATTATTATATTACAATTTTTAT
1 AATTTAAATATTTAAATAAAAAAG---ATTATTATTATATTACAATTTTTAT
18913958 TAGATTTTAA
Statistics
Matches: 363, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
84 74 0.20
85 10 0.03
86 194 0.53
87 56 0.15
88 5 0.01
89 24 0.07
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (86 bp):
AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
TTGACAATACATTATTTACTA
Found at i:18913850 original size:256 final size:261
Alignment explanation
Indices: 18913476--18913957 Score: 778
Period size: 256 Copynumber: 1.9 Consensus size: 261
18913466 CATTAAAATT
*
18913476 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTCA
1 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATGTGTTCA
** *
18913541 TTTGACAAGACATTATTTAATCAAATTTTCACATTTAAATAAAAAATATTATTATTATATTAAAA
66 TTTGACAAGACATTATTTAATCAAATTTAAACATTTAAATAAAAAAGATTATTATTATATTAAAA
18913606 TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAAT-AAA
131 TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAA
18913670 A-A-ATTATTACTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTTACT
196 AGATATTATTACTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTTACT
18913733 A
261 A
* * *
18913734 AATTTAA-ATT-TTTAAATAAAAAAGATTATTATTATATTATAATTTTTATCAAATAATGTGTTG
1 AATTTAACATTATTTAAATAAAAAA-ATTATTATTATATTACAATTTATATCAAATAATGTGTTC
* * * * *
18913797 ATTTGCCAATACATTATTTACT-AAATTTAAATATTTAAATAAAAAAGATTATTATTATATTATA
65 ATTTGACAAGACATTATTTAATCAAATTTAAACATTTAAATAAAAAAGATTATTATTATATTAAA
18913861 ATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAA
130 ATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAAT-AA
*
18913926 AAAGATTATTATTATTATATTACAATTTTTAT
194 AAAGA-TATTATTACTATATTACAATTTTTAT
18913958 TAGATTTTAA
Statistics
Matches: 205, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
256 112 0.55
257 57 0.28
258 11 0.05
259 1 0.00
261 24 0.12
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (261 bp):
AATTTAACATTATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATGTGTTCA
TTTGACAAGACATTATTTAATCAAATTTAAACATTTAAATAAAAAAGATTATTATTATATTAAAA
TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAA
AGATATTATTACTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTTACT
A
Found at i:18914124 original size:22 final size:23
Alignment explanation
Indices: 18914054--18914124 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 23
18914044 TGGACCTCCC
*
18914054 AAATTCTAGCTCACCTAAC-CCG
1 AAATTCTAGCTCACCTAACACCT
* *
18914076 AAATTCCAGCTCACCTAA-ATCT
1 AAATTCTAGCTCACCTAACACCT
18914098 AAATTCTAGCTCACC-AACACCT
1 AAATTCTAGCTCACCTAACACCT
*
18914120 CAATT
1 AAATT
18914125 TCGCCGTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.35, C:0.34, G:0.06, T:0.25
Consensus pattern (23 bp):
AAATTCTAGCTCACCTAACACCT
Found at i:18915166 original size:20 final size:20
Alignment explanation
Indices: 18915143--18915185 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
18915133 AATTTTTTAT
*
18915143 AATA-ATTTTTCTATTTTCGA
1 AATATATTTTTATATTTTC-A
*
18915163 AATATTTTTTTATATTTTCA
1 AATATATTTTTATATTTTCA
18915183 AAT
1 AAT
18915186 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (20 bp):
AATATATTTTTATATTTTCA
Found at i:18915934 original size:25 final size:24
Alignment explanation
Indices: 18915884--18915940 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
18915874 GAGCCCAATG
*
18915884 ACGAGCCCGCAGACGTGCCTGCGA
1 ACGAGCCCGCAGACGTGCCCGCGA
* *
18915908 ACGAGCCCGCGGGACGTGCCCGTGA
1 ACGAGCCCGC-AGACGTGCCCGCGA
18915933 ACGAGCCC
1 ACGAGCCC
18915941 TCGGACAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.19, C:0.39, G:0.35, T:0.07
Consensus pattern (24 bp):
ACGAGCCCGCAGACGTGCCCGCGA
Found at i:18916564 original size:34 final size:28
Alignment explanation
Indices: 18916493--18916546 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
18916483 TTAAATTTAA
*
18916493 TTTCCAATTTCCTGTATATTTTAATTTT
1 TTTCTAATTTCCTGTATATTTTAATTTT
18916521 TTTCTAATTTCCTGTATATTTTAATT
1 TTTCTAATTTCCTGTATATTTTAATT
18916547 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTCTAATTTCCTGTATATTTTAATTTT
Found at i:18917505 original size:70 final size:70
Alignment explanation
Indices: 18917424--18917683 Score: 229
Period size: 61 Copynumber: 4.0 Consensus size: 70
18917414 GAGGGTGTCG
* * *
18917424 ACCATTGCATGGTCAACA-CAAAAAAAATT-AAATTTTTTTTAATCTGAGAACAGGGGGTGTCGG
1 ACCATTGCATGGCCAACACCAAAAAAAATTGAAA-TTTTTTT-ATCTGAGAAAAGGAGGTGTCGG
18917487 CCATGCA
64 CCATGCA
*
18917494 ACCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGAGGTGT----C
1 ACCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCTGAGAAAAGGAGGTGTCGGCC
18917555 A-G--
66 ATGCA
** * ** *
18917557 -TTATGGCATGGCCAACACCAAAAAATTTTG-AATTTTTTTATCTGA-AAACAGGGGGTGTC-G-
1 ACCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCTGAGAAA-AGGAGGTGTCGGC
18917617 ---G--
65 CATGCA
* *
18917618 -CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAGG-GATGTCGGC
1 ACCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCTGAG-AAAAGGAGGTGTCGGC
18917681 CAT
65 CAT
18917684 TGCATAGCCA
Statistics
Matches: 163, Mismatches: 14, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
60 3 0.02
61 50 0.31
62 46 0.28
63 4 0.02
64 3 0.02
65 1 0.01
66 2 0.01
70 34 0.21
71 17 0.10
72 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (70 bp):
ACCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCTGAGAAAAGGAGGTGTCGGCC
ATGCA
Found at i:18917614 original size:61 final size:62
Alignment explanation
Indices: 18917495--18917704 Score: 280
Period size: 62 Copynumber: 3.4 Consensus size: 62
18917485 GGCCATGCAA
* *
18917495 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGAGGTGTCAG
1 CCATGGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGGTGTCAG
** * *
18917557 TTATGGCATGGCCAACACCAAAAAATTTTG-AATTTTTTTATCTGA-AAACAGGGGGTGTCGG
1 CCATGGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAA-AGGGGGTGTCAG
* * * *
18917618 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAGGGATGTCGG
1 CCATGGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGGTGTCAG
* * *
18917680 CCATTGCATAGCCAACACCCAAAAA
1 CCATGGCATGGCCAACACCAAAAAA
18917705 TTGGATTTTT
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
60 3 0.02
61 51 0.39
62 74 0.56
63 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (62 bp):
CCATGGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAGGGGGTGTCAG
Found at i:18917694 original size:123 final size:121
Alignment explanation
Indices: 18917358--18917721 Score: 380
Period size: 123 Copynumber: 2.9 Consensus size: 121
18917348 AGGGGAAGTT
* * * ** *
18917358 GGTGTCGGCCATTACATAGCCAACACC-AAAAAATTT--AA-TTTTTTACCAAATAAAAAGAGGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAG-GGG
* * * * *
18917419 TGTCGACCATTGCATGGTCAACACAAAAAAAATTAAATTTTTTTTAATCTGAGAACAGGG
65 TGTCGGCCATTGCATGGCCAACAC-CAAAAAATTGAA-TTTTTTT-ATCTGAAAACAGGG
18917479 GGTGTCGGCCATGCAACCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAG-A
1 GGTGTC-G----G---CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAA
* ** *
18917543 AAAGGAGGTGTCAGTTATGGCATGGCCAACACCAAAAAATTTTGAATTTTTTTATCTGAAAACAG
58 AAAGG-GGTGTCGGCCATTGCATGGCCAACACCAAAAAA--TTGAATTTTTTTATCTGAAAACAG
18917608 GG
120 GG
*
18917610 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAGGGAT
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAGGGGT
* * *
18917675 GTCGGCCATTGCATAGCCAACACCCAAAAATTGGA-TTTTTTATCTGA
66 GTCGGCCATTGCATGGCCAACACCAAAAAATTGAATTTTTTTATCTGA
18917722 CAAAAAAGGG
Statistics
Matches: 204, Mismatches: 23, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
120 12 0.06
121 10 0.05
122 1 0.00
123 73 0.36
124 6 0.03
126 2 0.01
129 17 0.08
130 10 0.05
131 26 0.13
132 34 0.17
133 13 0.06
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (121 bp):
GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAAAGGGGT
GTCGGCCATTGCATGGCCAACACCAAAAAATTGAATTTTTTTATCTGAAAACAGGG
Found at i:18918182 original size:18 final size:19
Alignment explanation
Indices: 18918136--18918185 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
18918126 GTATAAAATG
18918136 ATAA-AAATA-TATTTATA
1 ATAATAAATATTATTTATA
* *
18918153 ATAATATA-ATTATTTGTA
1 ATAATAAATATTATTTATA
18918171 A-AATAAATATTATTT
1 ATAATAAATATTATTT
18918186 TTATCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAATAAATATTATTTATA
Found at i:18923018 original size:7 final size:8
Alignment explanation
Indices: 18923001--18923027 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
18922991 GTAATTCACC
18923001 AAAAAGAA
1 AAAAAGAA
18923009 AAAAAGAA
1 AAAAAGAA
18923017 AAAAAGAA
1 AAAAAGAA
18923025 AAA
1 AAA
18923028 GTTGATGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:18925060 original size:7 final size:7
Alignment explanation
Indices: 18925048--18925082 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
18925038 TAGTAGAAAT
18925048 AATAATA
1 AATAATA
18925055 AATAATA
1 AATAATA
18925062 AATAATA
1 AATAATA
18925069 AATAATA
1 AATAATA
18925076 AATAATA
1 AATAATA
18925083 TTAACTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:18926735 original size:17 final size:16
Alignment explanation
Indices: 18926694--18926743 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
18926684 AGTTAAACTC
18926694 ATATTTTGT-ATTTAAT
1 ATATTTT-TAATTTAAT
*
18926710 -TATTCTTAATTTCAAT
1 ATATTTTTAATTT-AAT
18926726 ATATTTTTAAATTTAAT
1 ATATTTTT-AATTTAAT
18926743 A
1 A
18926744 AATAATCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 9 0.32
16 3 0.11
17 10 0.36
18 5 0.18
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATTTTTAATTTAAT
Found at i:18928094 original size:93 final size:93
Alignment explanation
Indices: 18927935--18928120 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
18927925 TTTGGCATGA
* * * *
18927935 TGAAAGCGAGATTAGAAGTGCATCAATATTAGTCTGTTCAATAGATTAATCGATCAGCTAATCGA
1 TGAAAGCGAGATTAAAAGTGCATCAATACTAGCCTGTTCAATAGATTAATCAATCAGCTAATCGA
18928000 TTTGAATTATTATTAATCGAATTAATCG
66 TTTGAATTATTATTAATCGAATTAATCG
* * *
18928028 TGAAAGTGAGATTAAAAGTGCATCAGTACTAGCCTGTTCAATAGATTAATCAATCAGTTAATCGA
1 TGAAAGCGAGATTAAAAGTGCATCAATACTAGCCTGTTCAATAGATTAATCAATCAGCTAATCGA
18928093 TTTGAATTATTATTAATCGAATTAATCG
66 TTTGAATTATTATTAATCGAATTAATCG
18928121 ATTTTTTAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (93 bp):
TGAAAGCGAGATTAAAAGTGCATCAATACTAGCCTGTTCAATAGATTAATCAATCAGCTAATCGA
TTTGAATTATTATTAATCGAATTAATCG
Found at i:18928652 original size:22 final size:22
Alignment explanation
Indices: 18928615--18928679 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
18928605 GTATAATGAT
18928615 TTATTTAGTTTTAAATTATTTTAG
1 TTATTTA--TTTAAATTATTTTAG
18928639 TTATTTATTTAAATT-TTTTAG
1 TTATTTATTTAAATTATTTTAG
*
18928660 TT-TTTAAATTTATATTATTT
1 TTATTT--ATTTAAATTATTT
18928680 GTTAAATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 3 0.08
21 8 0.22
22 16 0.43
23 3 0.08
24 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTATTTATTTAAATTATTTTAG
Found at i:18929797 original size:20 final size:20
Alignment explanation
Indices: 18929772--18929810 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
18929762 ATATTAAGAT
18929772 ATATTTAA-ATTTATAAAATA
1 ATATTTAATATTTA-AAAATA
18929792 ATATTTAATATTTAAAAAT
1 ATATTTAATATTTAAAAAT
18929811 TTTCAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTAATATTTAAAAATA
Found at i:18932312 original size:29 final size:28
Alignment explanation
Indices: 18932264--18932338 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
18932254 TTTTTCATAT
18932264 AATTATAAAAA-TA-AA-AAATATGGAAAA
1 AATTATAAAAATTATAAGAAATAT--AAAA
*
18932291 TATT-T-AAAATTATTAAGAAATATAAAA
1 AATTATAAAAATTA-TAAGAAATATAAAA
18932318 AATTATAAAAATTATAAGAAA
1 AATTATAAAAATTATAAGAAA
18932339 CACCTCATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
25 4 0.10
26 3 0.08
27 10 0.25
28 10 0.25
29 13 0.32
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (28 bp):
AATTATAAAAATTATAAGAAATATAAAA
Found at i:18933612 original size:23 final size:24
Alignment explanation
Indices: 18933576--18933622 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
18933566 CAAATCATCA
*
18933576 AAGAATATGATGGGAAAGATGGGG
1 AAGAATATAATGGGAAAGATGGGG
*
18933600 AAGAA-ATAATGGGGAAGATGGGG
1 AAGAATATAATGGGAAAGATGGGG
18933623 GATGAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.15
Consensus pattern (24 bp):
AAGAATATAATGGGAAAGATGGGG
Found at i:18933709 original size:30 final size:30
Alignment explanation
Indices: 18933655--18933727 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 30
18933645 ATCAAAATTA
18933655 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAAT-AT
18933686 TTTAATAATTTTA-TA-TTCTAAAAAAATAT
1 TTTAATAATTTTATTATTTC-AAAAAAATAT
18933715 TTTAATAATTTTA
1 TTTAATAATTTTA
18933728 AAATCATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 18 0.44
30 10 0.24
31 13 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTCAAAAAAATAT
Found at i:18937739 original size:29 final size:31
Alignment explanation
Indices: 18937696--18937757 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
18937686 TTTAATTTAA
**
18937696 TGTACAATTTGATAT-TTAAAT-TTTGATTT
1 TGTACAATTTGATATACAAAATATTTGATTT
18937725 TGTACAATTAT-ATATACAAAATATTTGATTT
1 TGTACAATT-TGATATACAAAATATTTGATTT
18937756 TG
1 TG
18937758 GTGCAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 13 0.46
30 5 0.18
31 10 0.36
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (31 bp):
TGTACAATTTGATATACAAAATATTTGATTT
Found at i:18937755 original size:31 final size:31
Alignment explanation
Indices: 18937713--18937777 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
18937703 TTTGATATTT
*
18937713 AAATTTTGATTTT-GTACAATTATATATACA
1 AAATTTTGATTTTGGTACAAATATATATACA
* *
18937743 AAATATTTGATTTTGGTGCAAATGTATATACA
1 AAAT-TTTGATTTTGGTACAAATATATATACA
18937775 AAA
1 AAA
18937778 ACTTTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.13
31 9 0.30
32 17 0.57
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (31 bp):
AAATTTTGATTTTGGTACAAATATATATACA
Found at i:18941202 original size:28 final size:28
Alignment explanation
Indices: 18941089--18941202 Score: 111
Period size: 28 Copynumber: 4.1 Consensus size: 28
18941079 GTTAGCTTTT
* ** *
18941089 ATATATGGTCGGCTTTATTGCCTGAATG
1 ATATATGGTCGGCTCTGCTGCCTGAATA
* * *
18941117 ATATATGGTCAGCTATGCTGCCTGAATG
1 ATATATGGTCGGCTCTGCTGCCTGAATA
* **
18941145 ATATATGGTCGACTCTGCTGCCCAAATA
1 ATATATGGTCGGCTCTGCTGCCTGAATA
* * *
18941173 ATATATGGTCGGCTCCGCTGCTTGAGTA
1 ATATATGGTCGGCTCTGCTGCCTGAATA
18941201 AT
1 AT
18941203 TGTATTATGT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (28 bp):
ATATATGGTCGGCTCTGCTGCCTGAATA
Found at i:18941340 original size:28 final size:28
Alignment explanation
Indices: 18941299--18941353 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
18941289 GGTTGATCGA
* *
18941299 CTCTACCGCTTGAATAATATATGGTTGG
1 CTCTAACGCCTGAATAATATATGGTTGG
18941327 CTCTAACGCCTGAATAATATATGGTTG
1 CTCTAACGCCTGAATAATATATGGTTG
18941354 ATCCTGCCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (28 bp):
CTCTAACGCCTGAATAATATATGGTTGG
Found at i:18942912 original size:566 final size:565
Alignment explanation
Indices: 18941637--18943254 Score: 2627
Period size: 566 Copynumber: 2.9 Consensus size: 565
18941627 TAAAGGCATG
*
18941637 AGCAACAGAATCAAGAAGCTCAATAACCACAACTATGGCTATTGATAGACTTGCATAGAGTCCTA
1 AGCAACAGAATCAAGAAGCTCAAAAACCACAACTATGGCTATTGATAGACTTGCATAGAGTCCTA
* * * * *
18941702 CCTATAAGGTCAAAATTTGTGG-AAA-A-T-ACTGGCACTAACACAACTTCTCCACTGAAGGAAA
66 CCTACAAGGTCAAGATTTGTGGAAAATAGTCACCGACACTAACACAACTCCTCCACTGAAGGAAA
* * * *
18941763 ATGCTGAAGCCTTGAGAAAATGAAATATCAAGGCTGGAAAAGCCTTATTTTTATTGAATACCACA
131 ATGCTGAAGCCTTGAGAAAATGGAATATCAAGGCTGGAAAAGCTTTATTTGTATTGAAGACCACA
*
18941828 ATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACTAGGAAATTACT
196 ATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACCAGGAAATTACT
* *
18941893 TTGGCGTAATTATTTTCAAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCATG
261 TTGGCGAAATTATTTTCGAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCATG
*
18941958 TATCTCACAAGGGAACTTAACTATTTCTATGTATTTCATTAAGGTGAAATCTATTTGTCGCAAGT
326 TATCTCACAAGGGAACTTAACTATTTCTATGTATTTCACTAAGGTGAAATCTATTTGTCGCAAGT
*
18942023 TAGAAAATAAAAAGGTTAACCGACTTCATAGAGATGGTGTAACATTATTTGTAGGTCCTAGGTCT
391 TAGAAAATAAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTATTTGTAGGTCCTAGGTCT
*
18942088 TCTATAGTGGGTGCGTTGGG-TCATCGAGTTTTTAACAATTGGTATCGAAGCGAGCAACTCGGGG
456 TCTATAGTGGGTGCGTTGGGCTCATCGAGTTTTCAACAATTGGTATCGAAGCGAGCAACTCGGGG
* *
18942152 CGATCACTAATTGAGGAAGCTTCGATAAGCACTGGGTGCTTACAT
521 CGATCACTAATTGAGGAAGCTTCGATAAGCACTAGGCGCTTACAT
* * * *
18942197 AGCAACGGAATCAAGAAGCTCAAAAACCATAACTATGGCTATTGACAGACTTGCATAGAGTTCTA
1 AGCAACAGAATCAAGAAGCTCAAAAACCACAACTATGGCTATTGATAGACTTGCATAGAGTCCTA
* *
18942262 CCTACAAGGTCAAGATTTGTGGAAAATAGTCATC-AGCACTAACACAACTCCTTCACTGAAGGAA
66 CCTACAAGGTCAAGATTTGTGGAAAATAGTCACCGA-CACTAACACAACTCCTCCACTGAAGGAA
* ** *
18942326 AATACTGAAGCCTTGAGAAAATGGAATATCAACACTGGAAAAGCTTTATTTGTATTGAAGCCCAC
130 AATGCTGAAGCCTTGAGAAAATGGAATATCAAGGCTGGAAAAGCTTTATTTGTATTGAAGACCAC
18942391 AATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACCAGGAAATTAC
195 AATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACCAGGAAATTAC
*
18942456 TTTGGCGCAATTATTTTCGAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCAT
260 TTTGGCGAAATTATTTTCGAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCAT
18942521 GTATCTCACAAGGGAACTTAACTATTTCTATGTATTTACACTAAGGTGAAATCTATTTGTCGCAA
325 GTATCTCACAAGGGAACTTAACTATTTCTATGTATTT-CACTAAGGTGAAATCTATTTGTCGCAA
* *
18942586 GTTAAAAAATTAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTATTTGTAGGTCCTAGGT
389 GTTAGAAAATAAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTATTTGTAGGTCCTAGGT
* * * * * *
18942651 CTTTTGTAGCGGGTACGTTGGGCTCATCGAGTTTTCAACAATTGGTATTGAAGCGAGCGACTCGG
454 CTTCTATAGTGGGTGCGTTGGGCTCATCGAGTTTTCAACAATTGGTATCGAAGCGAGCAACTCGG
* * *
18942716 GGCGGTCACTTATTGAGGAAGCTTTGATAAGCACTAGGCGCTTACAT
519 GGCGATCACTAATTGAGGAAGCTTCGATAAGCACTAGGCGCTTACAT
*
18942763 AGCAACAGAATCAAGAAGCTCAAAAACCACAACTATGGCTATTGATAGACTTGCATAAAGTCCTA
1 AGCAACAGAATCAAGAAGCTCAAAAACCACAACTATGGCTATTGATAGACTTGCATAGAGTCCTA
* *
18942828 CCTACAAGGTTAGGATTTGTGGAAAATAGTCACCGACACTAACACAACTCCTCCACTGAAGGAAA
66 CCTACAAGGTCAAGATTTGTGGAAAATAGTCACCGACACTAACACAACTCCTCCACTGAAGGAAA
*
18942893 ATGCTGAAGCCTTGAGAAAATGGAATATCAAGGTTGGAAAAGCTTTATTTGTATTGAAGACCACA
131 ATGCTGAAGCCTTGAGAAAATGGAATATCAAGGCTGGAAAAGCTTTATTTGTATTGAAGACCACA
* * *
18942958 ATCGAGGAGGACCTATTGGATCATATTCGTGACGATAAGACACCAAAGGCAACCTGGGAAATTAC
196 ATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACC-AGGAAATTAC
* * *
18943023 TTTGGCGAAATTATTTTCGAAGAAGAATGAAGCTCGCCTCCAACTCCTGGAAAATGAACTTGCAT
260 TTTGGCGAAATTATTTTCGAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCAT
* * * *
18943088 GTATCTCACAAGGGAACTTAACTATTTCTCTGTATTTCACTAAGGCGAAATCTATTTTTTGCAAG
325 GTATCTCACAAGGGAACTTAACTATTTCTATGTATTTCACTAAGGTGAAATCTATTTGTCGCAAG
* * * *
18943153 TTAGAAAATAAAAAGGTTAACCGACTTCATAGAGTTGGTGCAACATTACTTGCAAGTCCTAGGTC
390 TTAGAAAATAAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTATTTGTAGGTCCTAGGTC
* *
18943218 TTCTATAGTGGGTGTGTTGGGCTCATCGAATTTTCAA
455 TTCTATAGTGGGTGCGTTGGGCTCATCGAGTTTTCAA
18943255 TAGCCTTTAT
Statistics
Matches: 973, Mismatches: 76, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
560 80 0.08
561 3 0.00
562 1 0.00
563 1 0.00
564 248 0.25
565 106 0.11
566 427 0.44
567 107 0.11
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (565 bp):
AGCAACAGAATCAAGAAGCTCAAAAACCACAACTATGGCTATTGATAGACTTGCATAGAGTCCTA
CCTACAAGGTCAAGATTTGTGGAAAATAGTCACCGACACTAACACAACTCCTCCACTGAAGGAAA
ATGCTGAAGCCTTGAGAAAATGGAATATCAAGGCTGGAAAAGCTTTATTTGTATTGAAGACCACA
ATCGAGGAGGACCTATTGGAGCATATTCGTGACGATAAGACACCGAAGGCAACCAGGAAATTACT
TTGGCGAAATTATTTTCGAAGAAGAATGAAGCACGCCTCTAATTCCTGGAAAATGAACTTGCATG
TATCTCACAAGGGAACTTAACTATTTCTATGTATTTCACTAAGGTGAAATCTATTTGTCGCAAGT
TAGAAAATAAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTATTTGTAGGTCCTAGGTCT
TCTATAGTGGGTGCGTTGGGCTCATCGAGTTTTCAACAATTGGTATCGAAGCGAGCAACTCGGGG
CGATCACTAATTGAGGAAGCTTCGATAAGCACTAGGCGCTTACAT
Found at i:18945650 original size:21 final size:21
Alignment explanation
Indices: 18945625--18945674 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
18945615 GAATTTTAGC
*
18945625 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* *
18945646 AGCAAACTATGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
18945667 AGAAAACT
1 AGCAAACT
18945675 GAGGCATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:18950753 original size:103 final size:103
Alignment explanation
Indices: 18950565--18950756 Score: 253
Period size: 103 Copynumber: 1.9 Consensus size: 103
18950555 ATGTGTTAGA
* * *
18950565 CTGAGTAACCGGGGTGAAGTGCTTAGTTGTCATTTCACTTCGTGTCAAAAGGACTAATGCATTCT
1 CTGAGTAACCGGGATGAAGTGCTTAGGTGTCATTTCACTTCGTGTCAAAAGGACCAATGCATTCT
*
18950630 ACAAAAAAAGAGAAGAAAAAAATTGAGAGCATGTTGGG
66 ACAAAAAAAGAAAAGAAAAAAATTGAGAGCATGTTGGG
* * * * * *
18950668 CTGAGTAATCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGTGTCAAAAGGTCCAATGTATTCT
1 CTGAGTAACCGGGATGAAGTGCTTAGGTGTCATTTCACTTCGTGTCAAAAGGACCAATGCATTC-
*
18950733 TA-AAGAAAAA-AAAAGGAAAAAATT
65 TACAA-AAAAAGAAAAGAAAAAAATT
18950757 CACAAAATAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 69 0.91
104 7 0.09
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (103 bp):
CTGAGTAACCGGGATGAAGTGCTTAGGTGTCATTTCACTTCGTGTCAAAAGGACCAATGCATTCT
ACAAAAAAAGAAAAGAAAAAAATTGAGAGCATGTTGGG
Found at i:18951338 original size:19 final size:19
Alignment explanation
Indices: 18951316--18951360 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
18951306 TTATATTAGG
18951316 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
18951335 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
18951354 ATTTAAT
1 ATTTAAT
18951361 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:18952198 original size:22 final size:22
Alignment explanation
Indices: 18952154--18952213 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
18952144 TTCGACTTTC
* *
18952154 CTATTTTCTATT-TTTTTAGTT
1 CTATTTTCTTTTATTTTTAATT
18952175 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
18952197 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
18952214 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:18953914 original size:26 final size:26
Alignment explanation
Indices: 18953884--18953959 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
18953874 TTGAATCTTT
*
18953884 GGTAACGGCTAGTTTGAGGAGTGTTC
1 GGTAACGGCTAGTTTGAGGAGCGTTC
*
18953910 GGTAACGGCTAGTTTGAGGAGCGTTT
1 GGTAACGGCTAGTTTGAGGAGCGTTC
*
18953936 GGTAACTGCTAGTTTGAGGAGCGT
1 GGTAACGGCTAGTTTGAGGAGCGT
18953960 GTTTGTGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (26 bp):
GGTAACGGCTAGTTTGAGGAGCGTTC
Found at i:18966441 original size:23 final size:22
Alignment explanation
Indices: 18966415--18966470 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
18966405 AATTTATAAT
*
18966415 AAAATAAATTAACTAAACTTCCA
1 AAAATAAATTAACTAAA-GTCCA
* * *
18966438 AAAATAAAATATCTAAAGTCCC
1 AAAATAAATTAACTAAAGTCCA
18966460 AAAATAAATTA
1 AAAATAAATTA
18966471 TATTTACAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATAAATTAACTAAAGTCCA
Found at i:18966530 original size:3 final size:3
Alignment explanation
Indices: 18966522--18966567 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
18966512 AAAATTCCAA
*
18966522 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AA
18966568 CCAAAATGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:18967659 original size:7 final size:7
Alignment explanation
Indices: 18967635--18967762 Score: 118
Period size: 7 Copynumber: 18.7 Consensus size: 7
18967625 TTCAAAAAAA
*
18967635 GTCAATG
1 GTCAACG
*
18967642 GTCAA-A
1 GTCAACG
18967648 GTCAACG
1 GTCAACG
*
18967655 ATCAACG
1 GTCAACG
18967662 GTCAACG
1 GTCAACG
*
18967669 GTCAA-A
1 GTCAACG
*
18967675 GTCAACA
1 GTCAACG
*
18967682 GTTAACG
1 GTCAACG
*
18967689 GTCAA-A
1 GTCAACG
*
18967695 GTCAATG
1 GTCAACG
18967702 GTCAACG
1 GTCAACG
* **
18967709 ATCAATT
1 GTCAACG
*
18967716 GTCAATG
1 GTCAACG
18967723 GTCAACG
1 GTCAACG
18967730 GTCAACG
1 GTCAACG
18967737 GTCAACG
1 GTCAACG
18967744 GTCAACG
1 GTCAACG
*
18967751 GTCAATG
1 GTCAACG
18967758 GTCAA
1 GTCAA
18967763 ATGTCAATGG
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
6 15 0.15
7 85 0.85
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:18967768 original size:14 final size:14
Alignment explanation
Indices: 18967688--18967774 Score: 86
Period size: 14 Copynumber: 6.3 Consensus size: 14
18967678 AACAGTTAAC
18967688 GGTCAAA-GTCAAT
1 GGTCAAAGGTCAAT
* *
18967701 GGTCAACGATCAAT
1 GGTCAAAGGTCAAT
* * *
18967715 TGTCAATGGTCAAC
1 GGTCAAAGGTCAAT
* *
18967729 GGTCAACGGTCAAC
1 GGTCAAAGGTCAAT
*
18967743 GGTCAACGGTCAAT
1 GGTCAAAGGTCAAT
*
18967757 GGTCAAATGTCAAT
1 GGTCAAAGGTCAAT
18967771 GGTC
1 GGTC
18967775 GATCAACGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
13 6 0.10
14 56 0.90
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (14 bp):
GGTCAAAGGTCAAT
Found at i:18967768 original size:21 final size:20
Alignment explanation
Indices: 18967662--18967774 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 20
18967652 ACGATCAACG
18967662 GTCAACGGTCAAAGTCAACA-
1 GTCAACGGTCAAAGTCAA-AT
*
18967682 GTTAACGGTCAAAGTC-AAT
1 GTCAACGGTCAAAGTCAAAT
* *
18967701 GGTCAACGATCAATTGTC-AAT
1 -GTCAACGGTCAA-AGTCAAAT
* **
18967722 GGTCAACGGTCAACGGTCAACG
1 -GTCAACGGTCAA-AGTCAAAT
*
18967744 GTCAACGGTCAATGGTCAAAT
1 GTCAACGGTCAA-AGTCAAAT
*
18967765 GTCAATGGTC
1 GTCAACGGTC
18967775 GATCAACGGC
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 25 0.33
21 48 0.63
22 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAAAT
Found at i:18973834 original size:3 final size:3
Alignment explanation
Indices: 18973826--18973867 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
18973816 AAAATTCTAA
* *
18973826 AAT AAT AAT AAT AAT AGT AGT AAT AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
18973868 CCAAAATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18974954 original size:7 final size:7
Alignment explanation
Indices: 18974930--18975002 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
18974920 TTTTTAAAAA
18974930 GTCAACG
1 GTCAACG
*
18974937 GTCAA-A
1 GTCAACG
*
18974943 ATCAACG
1 GTCAACG
18974950 GTCAACG
1 GTCAACG
*
18974957 GTCAATG
1 GTCAACG
18974964 GTCAACG
1 GTCAACG
* *
18974971 ATCAACA
1 GTCAACG
* *
18974978 ATCAA-T
1 GTCAACG
*
18974984 GTCAACT
1 GTCAACG
18974991 GTCAACG
1 GTCAACG
18974998 GTCAA
1 GTCAA
18975003 AGTCAATGGC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
6 8 0.15
7 45 0.85
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:18974955 original size:20 final size:20
Alignment explanation
Indices: 18974930--18975008 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
18974920 TTTTTAAAAA
*
18974930 GTCAACGGTCAAAATCAACG
1 GTCAACGGTCAAAGTCAACG
*
18974950 GTCAACGGTCAATGGTCAACG
1 GTCAACGGTCAA-AGTCAACG
* ** * *
18974971 ATCAACAATCAATGTCAACT
1 GTCAACGGTCAAAGTCAACG
18974991 GTCAACGGTCAAAGTCAA
1 GTCAACGGTCAAAGTCAA
18975009 TGGCCGATCA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
20 32 0.68
21 15 0.32
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAACG
Found at i:18974968 original size:34 final size:34
Alignment explanation
Indices: 18974930--18975002 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
18974920 TTTTTAAAAA
* *
18974930 GTCAACGGTCAA-AATCAACGGTCAACGGTCAATG
1 GTCAACGATCAACAATCAA-GGTCAACGGTCAACG
* *
18974964 GTCAACGATCAACAATCAATGTCAACTGTCAACG
1 GTCAACGATCAACAATCAAGGTCAACGGTCAACG
18974998 GTCAA
1 GTCAA
18975003 AGTCAATGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 28 0.82
35 6 0.18
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (34 bp):
GTCAACGATCAACAATCAAGGTCAACGGTCAACG
Found at i:18994037 original size:469 final size:469
Alignment explanation
Indices: 18993159--18994569 Score: 2542
Period size: 469 Copynumber: 3.0 Consensus size: 469
18993149 ACTAACTAGC
* * *
18993159 TTGTCTTTTGGGTACAATCTCTTATTTCTTTGAAAACTAAGAAATAACATACTATTTCTCGTTCT
1 TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
* *
18993224 TTCGCTGGGGCTAAGTATAGGTCTATGGATTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
66 TTCGCTGAGGCTGAGTATAGGTCTATGGATTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
18993289 GCTATTGAGCTTAGATGTTCATCATCCTAAAGCTATTCATTTTTTTGTGATAGTCAATCTACGTT
131 GCTATTGAGCTTAGATGTTCATCATCCTAAAGCTATTCATTTTTTTGTGATAGTCAATCTACGTT
18993354 GCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACTTTG
196 GCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACTTTG
18993419 TTCGAGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATTGGCT
261 TTCGAGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATTGGCT
*
18993484 GACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTATCAACTTGGGCATTTA
326 GACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTAACAACTTGGGCATTTA
18993549 TGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTAAAAA
391 TGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTAAAAA
18993614 TATATTGTATATTA
456 TATATTGTATATTA
18993628 TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
1 TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
* * *
18993693 TTCACTGAGGCTGAGTATAGGTCTATGGGTTGCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
66 TTCGCTGAGGCTGAGTATAGGTCTATGGATTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
*
18993758 GCTATTGAGCTTAGATGTTCATCATCCTAAAGCGATTCATTTTTTTGTGATAGTCAATCTACGTT
131 GCTATTGAGCTTAGATGTTCATCATCCTAAAGCTATTCATTTTTTTGTGATAGTCAATCTACGTT
18993823 GCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACTTTG
196 GCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACTTTG
18993888 TTCGAGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATTGGCT
261 TTCGAGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATTGGCT
18993953 GACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTAACAACTTGGGCATTTA
326 GACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTAACAACTTGGGCATTTA
18994018 TGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTAAAAA
391 TGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTAAAAA
18994083 TATATTGTATATTA
456 TATATTGTATATTA
18994097 TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
1 TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
*
18994162 TTCGCTGAGGCTGAGTATAGGTCTATGGCTTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
66 TTCGCTGAGGCTGAGTATAGGTCTATGGATTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
* * *
18994227 GCTATTGAGCTTA-AGTTTTCATCATCCAAAAGCTATTCATTTTTTTTTGTGATAGTCAATCTGC
131 GCTATTGAGCTTAGA-TGTTCATCATCCTAAAGCTATTCA--TTTTTTTGTGATAGTCAATCTAC
*
18994291 -TTGCATATTGCACAAAACCCTATATTTCACGAGCTTACTAAACATATTGAAGTGCATTGTCACT
193 GTTGCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACT
* *
18994355 TTG-TCCAGGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATTTTCGTTCAATT
258 TTGTTCGA-GATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATT
* * *
18994419 GGCTGACATTTTTACAAAGGCATTTGGCAAACCGCAATTTGAATACCTTATTAACAA-GTGGGCA
322 GGCTGACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTAACAACTTGGGCA
* * *
18994483 TTTATGATTTGCATGCTCCAACTTGAGAGGCGTGTTAGGATATTGATATGGGATATTATCTTTTA
387 TTTATGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTA
*
18994548 AAAACATATTGTATATTA
452 AAAATATATTGTATATTA
18994566 TTGT
1 TTGT
18994570 ATATCTTTTA
Statistics
Matches: 911, Mismatches: 27, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
468 1 0.00
469 712 0.78
470 176 0.19
471 22 0.02
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (469 bp):
TTGTCTTTTGGGTACAATCTCCTGTTTCTTGGAAAACTAAGAAATAACATACTATTTCTCGTTCT
TTCGCTGAGGCTGAGTATAGGTCTATGGATTCCGTCACTTGTGAGCTCAAGTCGCTGAAGGTCTT
GCTATTGAGCTTAGATGTTCATCATCCTAAAGCTATTCATTTTTTTGTGATAGTCAATCTACGTT
GCATATTGCACAAAACCCTATATTTCACAAGCTTACTAAACATATTGAAGTGCATTGTCACTTTG
TTCGAGATGCAATTCAGGATGGGTTGATTGCACCTTCTTATGTTCCGATCTTCGTTCAATTGGCT
GACATTTTTACAAAGGCGTTTGGCAAACCCCAATTTGAATACCTTATTAACAACTTGGGCATTTA
TGATTTGCATGCTCCAAATTGAGAGGGGTGTTAGGATATTGTTATGGGATATTATCTTTTAAAAA
TATATTGTATATTA
Found at i:19019753 original size:6 final size:6
Alignment explanation
Indices: 19019737--19019812 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
19019727 AAATAATAAA
* ** * **
19019737 TAAATTT TAAATT TAAATT T-ACTT TAAATTT TAAATGT CCAATT CATTTT
1 TAAA-TT TAAATT TAAATT TAAATT TAAA-TT TAAAT-T TAAATT TAAATT
19019787 TAAATT TAAATT T--ATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
19019813 AAATCCATGC
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 32 0.59
7 14 0.26
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:19019772 original size:42 final size:41
Alignment explanation
Indices: 19019726--19019809 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 41
19019716 GAACCAAAAA
19019726 TAAATAAT-AAATAAATTTTAAATTTAAATTTACTTTAAATTT
1 TAAAT-ATCAAATAAATTTTAAATTTAAATTTA-TTTAAATTT
* * * *
19019768 TAAATGTCCAATTCATTTTTAAATTTAAATTTATTTAAATTT
1 TAAATAT-CAAATAAATTTTAAATTTAAATTTATTTAAATTT
19019810 AAAAAATCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.03
42 14 0.39
43 21 0.58
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (41 bp):
TAAATATCAAATAAATTTTAAATTTAAATTTATTTAAATTT
Found at i:19020338 original size:4 final size:4
Alignment explanation
Indices: 19020331--19020361 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
19020321 AAATATATAA
19020331 ATTT ATTT ATTT ATTT ATTT ATTT ATGTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT AT
19020362 AACTGCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:19021542 original size:118 final size:119
Alignment explanation
Indices: 19021323--19021638 Score: 336
Period size: 118 Copynumber: 2.7 Consensus size: 119
19021313 TTTTTCTTTA
* * *
19021323 AAAATCATATTTTAACCCCTAAACTTTCCCAAAATTGTATTTGACCCTCAAACCTTTCCAAAATC
1 AAAATCACATTTTAACCCCTAAACTTTCCCAAAATTATATTTAACCCTCAAACCTTTCCAAAATC
* * * * * *
19021388 ACATTTTAGCCTCAAAACTTCTCTAAAATTATATTTTAATCCTCAAACTTCTCT
66 ACATTTTAACCCCAAAACTTCTCCAAAATTACATTTTAAACCTCAAACTTCTCC
* * * *
19021442 AAAATTACA-TTTAACCCC-AAACTTTTCCAAAATTATATTTTAACCCTCAAACTTTTCTAAAAT
1 AAAATCACATTTTAACCCCTAAACTTTCCCAAAATTATA-TTTAACCCTCAAACCTTTCCAAAAT
** * *
19021505 TGCATTTTAACCCCTAAAACTT-TCCAAAATTACATTTTAAACCTTAAACTTGTCC
65 CACATTTTAACCCC-AAAACTTCTCCAAAATTACATTTTAAACCTCAAACTTCTCC
* ** * * *
19021560 AAAATCACATTTTAACCCTTAAACCTTTCTAAAAATCACATTTCAACCC-CAAA-CTTCCCTAAA
1 AAAATCACATTTTAACCCCTAAA-CTTTCCCAAAATTATATTT-AACCCTCAAACCTTTCC-AAA
*
19021623 ATCACATTTTGACCCC
63 ATCACATTTTAACCCC
19021639 GTATTCTCCG
Statistics
Matches: 160, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
117 17 0.11
118 76 0.47
119 25 0.16
120 26 0.16
121 16 0.10
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (119 bp):
AAAATCACATTTTAACCCCTAAACTTTCCCAAAATTATATTTAACCCTCAAACCTTTCCAAAATC
ACATTTTAACCCCAAAACTTCTCCAAAATTACATTTTAAACCTCAAACTTCTCC
Found at i:19021554 original size:60 final size:60
Alignment explanation
Indices: 19021323--19021638 Score: 297
Period size: 60 Copynumber: 5.3 Consensus size: 60
19021313 TTTTTCTTTA
* * * *
19021323 AAAATCATATTTTAACCCCT-AAACTTTCCCAAAATTGTA-TTTGACCCTCAAACCTTTCC
1 AAAATCACATTTTAACCCCTAAAACTTT-CCAAAATTATATTTTAACCCTCAAACTTTTCC
* * * * * *
19021382 AAAATCACATTTTAGCCTC-AAAACTTCTCTAAAATTATATTTTAATCCTCAAACTTCTCT
1 AAAATCACATTTTAACCCCTAAAACTT-TCCAAAATTATATTTTAACCCTCAAACTTTTCC
* *
19021442 AAAATTACA-TTTAACCCC--AAACTTTTCCAAAATTATATTTTAACCCTCAAACTTTTCT
1 AAAATCACATTTTAACCCCTAAAAC-TTTCCAAAATTATATTTTAACCCTCAAACTTTTCC
** * * * *
19021500 AAAATTGCATTTTAACCCCTAAAACTTTCCAAAATTACATTTTAAACCTTAAACTTGTCC
1 AAAATCACATTTTAACCCCTAAAACTTTCCAAAATTATATTTTAACCCTCAAACTTTTCC
* * * * * * *
19021560 AAAATCACATTTTAACCCTTAAACCTTTCTAAAAATCACATTTCAACCC-CAAAC-TTCCC
1 AAAATCACATTTTAACCCCTAAAACTTTC-CAAAATTATATTTTAACCCTCAAACTTTTCC
*
19021619 TAAAATCACATTTTGACCCC
1 -AAAATCACATTTTAACCCC
19021639 GTATTCTCCG
Statistics
Matches: 213, Mismatches: 35, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
58 42 0.20
59 52 0.24
60 100 0.47
61 19 0.09
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAATCACATTTTAACCCCTAAAACTTTCCAAAATTATATTTTAACCCTCAAACTTTTCC
Found at i:19021637 original size:29 final size:28
Alignment explanation
Indices: 19021331--19021638 Score: 224
Period size: 30 Copynumber: 10.4 Consensus size: 28
19021321 TAAAAATCAT
**
19021331 ATTTTAACCCCTAAACTTTCCCAAAATTGT
1 ATTTTAACCCC-AAACTTT-CCAAAATTAC
* *
19021361 A-TTTGACCCTCAAACCTTTCCAAAATCAC
1 ATTTTAACCC-CAAA-CTTTCCAAAATTAC
* * * *
19021390 ATTTTAGCCTCAAAACTTCTCTAAAATTAT
1 ATTTTAACC-CCAAACTT-TCCAAAATTAC
* *
19021420 ATTTTAATCCTCAAACTTCTCTAAAATTAC
1 ATTTTAA-CCCCAAACTT-TCCAAAATTAC
*
19021450 A-TTTAACCCCAAACTTTTCCAAAATTAT
1 ATTTTAACCCCAAAC-TTTCCAAAATTAC
* *
19021478 ATTTTAACCCTCAAACTTTTCTAAAATTGC
1 ATTTTAACCC-CAAAC-TTTCCAAAATTAC
19021508 ATTTTAACCCCTAAAACTTTCCAAAATTAC
1 ATTTTAACCCC--AAACTTTCCAAAATTAC
** *
19021538 ATTTTAAACCTTAAACTTGTCCAAAATCAC
1 ATTTT-AACCCCAAACTT-TCCAAAATTAC
* * *
19021568 ATTTTAACCCTTAAACCTTTCTAAAAATCAC
1 ATTTTAACCC-CAAA-CTTTC-CAAAATTAC
* * *
19021599 ATTTCAACCCCAAACTTCCCTAAAATCAC
1 ATTTTAACCCCAAACTTTCC-AAAATTAC
*
19021628 ATTTTGACCCC
1 ATTTTAACCCC
19021639 GTATTCTCCG
Statistics
Matches: 228, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
28 17 0.07
29 68 0.30
30 112 0.49
31 31 0.14
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (28 bp):
ATTTTAACCCCAAACTTTCCAAAATTAC
Found at i:19025991 original size:17 final size:17
Alignment explanation
Indices: 19025969--19026033 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
19025959 TTACAAGTAA
*
19025969 AAATATAAAATAATTAC
1 AAATATAAAACAATTAC
19025986 AAATATAAAACAATTAC
1 AAATATAAAACAATTAC
*
19026003 AAATACATATAAA-AATTAT
1 AAAT--ATA-AAACAATTAC
19026022 AAA-ATAAAACAA
1 AAATATAAAACAA
19026034 ATCAATACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 3 0.07
16 5 0.12
17 20 0.48
19 11 0.26
20 3 0.07
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATAAAACAATTAC
Found at i:19042446 original size:32 final size:32
Alignment explanation
Indices: 19042410--19042470 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
19042400 AAACATCTCA
*
19042410 ATTTGATTTTATTCCAATT-AAATTGATTTTTG
1 ATTTGATTTGATT-CAATTCAAATTGATTTTTG
*
19042442 ATTTGATTTGATTCTATTCAAATTGATTT
1 ATTTGATTTGATTCAATTCAAATTGATTT
19042471 AAAGGCTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (32 bp):
ATTTGATTTGATTCAATTCAAATTGATTTTTG
Found at i:19042953 original size:51 final size:48
Alignment explanation
Indices: 19042856--19042962 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 48
19042846 TCAAATCTTG
* * *
19042856 TTTATTTAATTTGTTTTTTAGATCTGATATTTTAAATAAATATAAATA
1 TTTATTTAATGTGTTTTTTAAATCTGATATTTTAAATAAACATAAATA
* * *
19042904 TTTATTTAATGTGTTTTGTTTAAATCTGGTGTTTTTACATAAACATAAATA
1 TTTATTTAATGTG-TTT-TTTAAATCTGAT-ATTTTAAATAAACATAAATA
*
19042955 TTTGTTTA
1 TTTATTTA
19042963 TATTATTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
48 12 0.24
49 3 0.06
50 10 0.20
51 24 0.49
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (48 bp):
TTTATTTAATGTGTTTTTTAAATCTGATATTTTAAATAAACATAAATA
Found at i:19043664 original size:23 final size:23
Alignment explanation
Indices: 19043591--19043721 Score: 106
Period size: 23 Copynumber: 5.7 Consensus size: 23
19043581 TATACGGAAC
* * *
19043591 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
19043613 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
19043634 AGGCAACAGAGAGCACATACAGTGCT
1 A---AACAGAGAGCACACACAGTGCT
* * *
19043660 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* *
19043683 AATCAGAGAGCACACACGGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
19043706 AATCAGAGAGTACACA
1 AAACAGAGAGCACACA
19043722 AAGCACACAC
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
21 16 0.18
22 1 0.01
23 51 0.57
25 15 0.17
26 7 0.08
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:19045463 original size:79 final size:79
Alignment explanation
Indices: 19045367--19045528 Score: 324
Period size: 79 Copynumber: 2.1 Consensus size: 79
19045357 CAAATTACTC
19045367 TTTTGCCCCTCCTCAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTA
1 TTTTGCCCCTCCTCAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTA
19045432 TTTAGTCCTCCATA
66 TTTAGTCCTCCATA
19045446 TTTTGCCCCTCCTCAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTA
1 TTTTGCCCCTCCTCAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTA
19045511 TTTAGTCCTCCATA
66 TTTAGTCCTCCATA
19045525 TTTT
1 TTTT
19045529 CTCCGCTTTA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (79 bp):
TTTTGCCCCTCCTCAATCAATCTAATTCCCATGATGACTCAAAATTCAATTTGGATAATTCGCTA
TTTAGTCCTCCATA
Found at i:19047089 original size:54 final size:56
Alignment explanation
Indices: 19047006--19047134 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 56
19046996 GAGAATTTGA
* *
19047006 AAAAAAAATTTGGTGTTGGCCATTGCATGGTCG-ACACCCACTTTTTTATCTG-A-C
1 AAAAAAATTTTGGTGTTGGCCATTACATGG-CGAACACCCACTTTTTTATCTGAAGC
* *
19047060 AAAAAAATTTTGGTGTTGGCCATTACATGGCGAACACCCCCTTTTTTATCTGATAGG
1 AAAAAAATTTTGGTGTTGGCCATTACATGGCGAACACCCACTTTTTTATCTGA-AGC
19047117 AAAAAAATTTTGGT-TTGG
1 AAAAAAATTTTGGTGTTGG
19047135 ATCATTGCAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
53 2 0.03
54 46 0.69
56 5 0.07
57 14 0.21
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (56 bp):
AAAAAAATTTTGGTGTTGGCCATTACATGGCGAACACCCACTTTTTTATCTGAAGC
Found at i:19047234 original size:60 final size:59
Alignment explanation
Indices: 19047148--19047572 Score: 341
Period size: 60 Copynumber: 7.1 Consensus size: 59
19047138 ATTGCATGTC
* * * ** * *
19047148 CGACACCTCTTTTAATCTGATAAAAAAAATCAAATTTTAGTGTGCTGGCCATGCAATGGC
1 CGACACCCCTTTTTATCAGAT-AAAAAAATCAAATTTTTTTGTGTTGGCCATGCAATGGT
* * * * *
19047208 CGACACTCCCTTTTTGTCAGATAAAAAATTC-AATTTTTTTGGTGTTGACCATGCCATAGT
1 CGACAC-CCCTTTTTATCAGATAAAAAAATCAAATTTTTTT-GTGTTGGCCATGCAATGGT
* ** *
19047268 CGACA-CCCTATTTATTTGATAAAAAAATC-AATTTTTTTG-GTTTGGCCTTGCAATGGT
1 CGACACCCCTTTTTATCAGATAAAAAAATCAAATTTTTTTGTG-TTGGCCATGCAATGGT
19047325 CGACACCCC-TTTT-TCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTGC-ATGGT
1 CGACACCCCTTTTTATCAGATAAAAAAA--TCAAATTTTTTT-GTGTTGGCCA-TGCAATGGT
* * ** * *
19047385 CGACACCACTCTTTTTATCTGA-ATAAAAAATTAAATTTTTGGGTGTTGGTCATGCCATGGT
1 CGACACC-C-CTTTTTATCAGATA-AAAAAATCAAATTTTTTTGTGTTGGCCATGCAATGGT
* * * * * *
19047446 CGACACCCCCTTTTGTCAGATAAAAAATTCAAATTTTCTTTTGTGTTGGACATGTC-ATTGC
1 CGACACCCCTTTTTATCAGATAAAAAAATCAAA-TTT-TTTTGTGTTGGCCATG-CAATGGT
* * * *
19047507 CGACACCCCCTATTTTATCTGGT-AAAAAATC-TATTTTTTTGTGTTGGTCATGCAATGGT
1 CGACA-CCCCT-TTTTATCAGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCAATGGT
19047566 CGACACC
1 CGACACC
19047573 AACTTTCCCT
Statistics
Matches: 293, Mismatches: 49, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
56 12 0.04
57 21 0.07
58 36 0.12
59 57 0.19
60 63 0.22
61 59 0.20
62 22 0.08
63 13 0.04
64 10 0.03
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (59 bp):
CGACACCCCTTTTTATCAGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCAATGGT
Found at i:19047482 original size:59 final size:59
Alignment explanation
Indices: 19047148--19047572 Score: 323
Period size: 61 Copynumber: 7.1 Consensus size: 59
19047138 ATTGCATGTC
* * * * * * *
19047148 CGACA-CCTCTTTTAATCTGATAAAAAAAATCAAA-TTTTAGTGTGCTGGCCATGCAATGGC
1 CGACACCCCCTTTT-ATCAGAT-AAAAAATTCAAATTTTTTG-GTGTTGGCCATGCCATGGT
* * * * *
19047208 CGACACTCCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGGTGTTGACCATGCCATAGT
1 CGACAC-CCCCTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGT
** * * * *
19047268 CGACA--CCCTATTTATTTGATAAAAAAATCAATTTTTTTGGT-TTGGCCTTGCAATGGT
1 CGACACCCCCT-TTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGT
19047325 CGACA-CCCCTTTT-TCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTG-CATGGT
1 CGACACCCCCTTTTATCAGAT-AAAAAA-TTCAAA-TTTTTTGGTGTTGGCCA-TGCCATGGT
* * * *
19047385 CGACACCACTCTTTTTATCTGAATAAAAAATT-AAATTTTTGGGTGTTGGTCATGCCATGGT
1 CGACACC-C-CCTTTTATCAG-ATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGT
* * * * * *
19047446 CGACACCCCCTTTTGTCAGATAAAAAATTCAAATTTTCTTTTGTGTTGGACATGTCATTGC
1 CGACACCCCCTTTTATCAGATAAAAAATTCAAA-TTT-TTTGGTGTTGGCCATGCCATGGT
* * * * * *
19047507 CGACACCCCCTATTTTATCTGGTAAAAAA-TC-TATTTTTTTGTGTTGGTCATGCAATGGT
1 CGACACCCCC--TTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGT
19047566 CGACACC
1 CGACACC
19047573 AACTTTCCCT
Statistics
Matches: 295, Mismatches: 49, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
56 4 0.01
57 29 0.10
58 45 0.15
59 45 0.15
60 59 0.20
61 69 0.23
62 12 0.04
63 21 0.07
64 9 0.03
65 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (59 bp):
CGACACCCCCTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCCATGGT
Found at i:19047492 original size:61 final size:59
Alignment explanation
Indices: 19047193--19047572 Score: 337
Period size: 61 Copynumber: 6.4 Consensus size: 59
19047183 TTTAGTGTGC
* * * *
19047193 TGGCCATGCAATGGCCGACACTCCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGGTGT
1 TGGCCATGCCATGGTCGACAC-CCCCTTTTATCAGATAAAAAATTCAATTTTTTTGGTGT
* * ** *
19047253 TGACCATGCCATAGTCGACA--CCCTATTTATTTGATAAAAAAATCAATTTTTTTGGT-T
1 TGGCCATGCCATGGTCGACACCCCCT-TTTATCAGATAAAAAATTCAATTTTTTTGGTGT
* *
19047310 TGGCCTTGCAATGGTCGACA-CCCCTTTT-TCAGATAAAAAAATTTCAAATTTTTTTGGTGT
1 TGGCCATGCCATGGTCGACACCCCCTTTTATCAGAT-AAAAAA-TTC-AATTTTTTTGGTGT
* * * *
19047370 TGGCCATTG-CATGGTCGACACCACTCTTTTTATCTGAATAAAAAATT-AAATTTTTGGGTGT
1 TGGCCA-TGCCATGGTCGACACC-C-CCTTTTATCAG-ATAAAAAATTCAATTTTTTTGGTGT
* * *
19047431 TGGTCATGCCATGGTCGACACCCCCTTTTGTCAGATAAAAAATTCAAATTTTCTTTTGTGT
1 TGGCCATGCCATGGTCGACACCCCCTTTTATCAGATAAAAAATTC-AATTTT-TTTGGTGT
* * * * * * *
19047492 TGGACATGTCATTGCCGACACCCCCTATTTTATCTGGTAAAAAA-TCTATTTTTTT-GTGT
1 TGGCCATGCCATGGTCGACACCCCC--TTTTATCAGATAAAAAATTCAATTTTTTTGGTGT
* *
19047551 TGGTCATGCAATGGTCGACACC
1 TGGCCATGCCATGGTCGACACC
19047573 AACTTTCCCT
Statistics
Matches: 260, Mismatches: 42, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
56 4 0.02
57 29 0.11
58 43 0.17
59 41 0.16
60 43 0.17
61 65 0.25
62 3 0.01
63 21 0.08
64 9 0.03
65 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (59 bp):
TGGCCATGCCATGGTCGACACCCCCTTTTATCAGATAAAAAATTCAATTTTTTTGGTGT
Found at i:19047664 original size:23 final size:24
Alignment explanation
Indices: 19047620--19047666 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
19047610 TTTTATTTTG
* *
19047620 AAATTGTAAGTAAGAAATTAAGAT
1 AAATTGTAAGAAAAAAATTAAGAT
19047644 AAATTGTAA-AAAAAAATTAAGAT
1 AAATTGTAAGAAAAAAATTAAGAT
19047667 GATAAACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (24 bp):
AAATTGTAAGAAAAAAATTAAGAT
Found at i:19048211 original size:30 final size:30
Alignment explanation
Indices: 19048175--19048266 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
19048165 TTCGTTTACT
* * *
19048175 TTTTAAATTTAATTTGTAATTTCATTTTTA
1 TTTTAAATTTAATTTCTAATTTCATGTATA
*
19048205 TTTTAAATTTAATTTTTAATTTCATGTATA
1 TTTTAAATTTAATTTCTAATTTCATGTATA
*
19048235 TTTTAATTTTAATTTCTAATTT-ACTGTATA
1 TTTTAAATTTAATTTCTAATTTCA-TGTATA
19048265 TT
1 TT
19048267 CTAATTATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 1 0.02
30 55 0.98
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCATGTATA
Found at i:19048257 original size:18 final size:18
Alignment explanation
Indices: 19048176--19048257 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 18
19048166 TCGTTTACTT
* *
19048176 TTTAAATTTAATTTGTAA
1 TTTAATTTTAATTTCTAA
* *
19048194 TTTCATTTTTATTT-TAAA
1 TTTAATTTTAATTTCT-AA
19048212 TTTAATTTTTAATTTCATGTATA
1 TTTAA-TTTTAATTTC---TA-A
19048235 TTTTAATTTTAATTTCTAA
1 -TTTAATTTTAATTTCTAA
19048254 TTTA
1 TTTA
19048258 CTGTATATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
17 1 0.02
18 21 0.41
19 9 0.18
20 2 0.04
22 1 0.02
23 12 0.24
24 5 0.10
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATTTTAATTTCTAA
Found at i:19049136 original size:59 final size:59
Alignment explanation
Indices: 19049067--19049253 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 59
19049057 GATGGCCGAT
* * *
19049067 ACAAAAAAATTAATTTTTTACCAGATAAAAAAGGGGTGTCGGTCATGGCATGGTCAAC-
1 ACAAAAAAATTAATTTTTTATCAGATAAAAAAGGGGTGTCGATCATGGCATGGCCAACA
* *
19049125 ACAAAAAAAATTGAA-TTTTTATCTGA-CAAAAAGGGGTGTCGATCATGGCATGGCCAACA
1 AC-AAAAAAATT-AATTTTTTATCAGATAAAAAAGGGGTGTCGATCATGGCATGGCCAACA
* * * * * *
19049184 ACCAAAAATTTGATTTTTTATTCAGATAAAAAA-AGGTGTCGACCAT-GCAATGGCTAACA
1 ACAAAAAAATTAATTTTTTA-TCAGATAAAAAAGGGGTGTCGATCATGGC-ATGGCCAACA
*
19049243 TCAAAAAAATT
1 ACAAAAAAATT
19049254 TAAAATTTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
57 1 0.01
58 46 0.43
59 52 0.49
60 7 0.07
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (59 bp):
ACAAAAAAATTAATTTTTTATCAGATAAAAAAGGGGTGTCGATCATGGCATGGCCAACA
Found at i:19049335 original size:60 final size:57
Alignment explanation
Indices: 19049271--19049503 Score: 188
Period size: 60 Copynumber: 4.0 Consensus size: 57
19049261 TTTTTATCTG
* *
19049271 AAAAAATTTGATTTTTTTATCAAATAAATAGGGGTGTCGACCATGGCATGGCCAATACAA
1 AAAAAATTT-ATTTTTTTATCAAATAAAAAGGGGTGTCGACCAT-GCATGGCCAACAC-A
* * ** * * * *
19049331 AAAAAATTTAATTTTTGATCTGACAAAAAGGGGTGTC-AGCCATTGAATGACCAACACC
1 AAAAAATTTATTTTTTTATCAAATAAAAAGGGGTGTCGA-CCA-TGCATGGCCAACACA
* *
19049389 CAAAAATTTAATTTTTTTTATCAAATAAAAAGGGGTGTCGGCCATGCAATGGCCAACAC-
1 AAAAAATTT-A-TTTTTTTATCAAATAAAAAGGGGTGTCGACCATGC-ATGGCCAACACA
* * * *
19049448 -TAAAA-TT-TTTTTTTGTCAGATAAAATAGGGAGTGTCGGCCATGCAATGGCCAACAC
1 AAAAAATTTATTTTTTTATCAAATAAAA-AGGG-GTGTCGACCATGC-ATGGCCAACAC
19049504 CAGTTTTTTT
Statistics
Matches: 143, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
54 16 0.11
55 4 0.03
56 25 0.17
57 2 0.01
58 13 0.09
59 38 0.27
60 45 0.31
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (57 bp):
AAAAAATTTATTTTTTTATCAAATAAAAAGGGGTGTCGACCATGCATGGCCAACACA
Found at i:19049511 original size:54 final size:53
Alignment explanation
Indices: 19049400--19049516 Score: 164
Period size: 54 Copynumber: 2.2 Consensus size: 53
19049390 AAAAATTTAA
19049400 TTTTTTTTATCAAATAAAAAGGGGTGTCGGCCATGCAATGGCCAACACTAAAAT
1 TTTTTTTTATCAAATAAAAAGGGGTGTCGGCCATGCAATGGCCAACAC-AAAAT
* * * *
19049454 TTTTTTTTGTCAGATAAAATAGGGAGTGTCGGCCATGCAATGGCCAACAC-CAGT
1 TTTTTTTTATCAAATAAAA-AGGG-GTGTCGGCCATGCAATGGCCAACACAAAAT
19049508 TTTTTTTTA
1 TTTTTTTTA
19049517 AATTCTCGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 27 0.48
55 4 0.07
56 25 0.45
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (53 bp):
TTTTTTTTATCAAATAAAAAGGGGTGTCGGCCATGCAATGGCCAACACAAAAT
Found at i:19051273 original size:18 final size:20
Alignment explanation
Indices: 19051244--19051282 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19051234 AAATAAATTT
19051244 AGTAAGAAAAAA-TGAAAAC
1 AGTAAGAAAAAATTGAAAAC
19051263 AGTAA-AAAAAATTGAAAAC
1 AGTAAGAAAAAATTGAAAAC
19051282 A
1 A
19051283 AAGAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (20 bp):
AGTAAGAAAAAATTGAAAAC
Found at i:19051309 original size:17 final size:17
Alignment explanation
Indices: 19051289--19051322 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19051279 AACAAAGAAC
19051289 AAATAA-AAATCATAAAT
1 AAATAAGAAAT-ATAAAT
19051306 AAATAAGAAATATAAAT
1 AAATAAGAAATATAAAT
19051323 TTAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAAGAAATATAAAT
Found at i:19063521 original size:11 final size:11
Alignment explanation
Indices: 19063499--19063550 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
19063489 CTTGATTTTT
19063499 AATTAAAGTTTA
1 AATTAAA-TTTA
19063511 AATTAAATTTA
1 AATTAAATTTA
19063522 AATTAAATTTA
1 AATTAAATTTA
*
19063533 AATTTAATTTA
1 AATTAAATTTA
*
19063544 ATTTAAA
1 AATTAAA
19063551 ATAATATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 30 0.81
12 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:19063524 original size:6 final size:6
Alignment explanation
Indices: 19063501--19063550 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 6
19063491 TGATTTTTAA
19063501 TTAAAGT TTAAA- TTAAAT TTAAA- TTAAAT TTAAAT TT-AAT TT-AAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
19063546 TTAAA
1 TTAAA
19063551 ATAATATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 20 0.50
6 15 0.38
7 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:19063527 original size:16 final size:16
Alignment explanation
Indices: 19063508--19063550 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
19063498 TAATTAAAGT
19063508 TTAAATTAAATTTAAA
1 TTAAATTAAATTTAAA
*
19063524 TTAAATTTAAATTTAAT
1 TTAAA-TTAAATTTAAA
*
19063541 TTAATTTAAA
1 TTAAATTAAA
19063551 ATAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTAAATTTAAA
Found at i:19064746 original size:15 final size:15
Alignment explanation
Indices: 19064726--19064758 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19064716 GTTTTCGAAA
19064726 TTTCCAGATCTGGAT
1 TTTCCAGATCTGGAT
*
19064741 TTTCCAGATCTGGGT
1 TTTCCAGATCTGGAT
19064756 TTT
1 TTT
19064759 GTTTTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.45
Consensus pattern (15 bp):
TTTCCAGATCTGGAT
Found at i:19065224 original size:32 final size:33
Alignment explanation
Indices: 19065181--19065254 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
19065171 ATGTTATTTA
*
19065181 TTTAA-TTGGTCCTTCTATAT-TTTTTAATTA-T
1 TTTAATTTGGTCCTT-TATATACTTTTAATTATT
* *
19065212 TTTAATTTGGTCCTTTTTCTACTTTTAATTATT
1 TTTAATTTGGTCCTTTATATACTTTTAATTATT
19065245 TTTAATTTGG
1 TTTAATTTGG
19065255 CTCAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 8 0.22
32 18 0.49
33 11 0.30
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.62
Consensus pattern (33 bp):
TTTAATTTGGTCCTTTATATACTTTTAATTATT
Found at i:19065605 original size:30 final size:30
Alignment explanation
Indices: 19065560--19065850 Score: 281
Period size: 29 Copynumber: 9.9 Consensus size: 30
19065550 GAAAATTTTG
* *
19065560 AAAATAACA-TTTTGACCCCAAAACTTTCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
* * *
19065589 AAAATTATATTTTTGACCCTAAAACTTCCC
1 AAAATTACATTTTTGACCCCAAAACTTCCA
*
19065619 AAAATCACA-TTTTGACCCCAAAAACTTCCA
1 AAAATTACATTTTTGACCCC-AAAACTTCCA
* *
19065649 AAAATTATATTTTTAACCCCAAAACTTCCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
** *
19065679 AAAATTACATTTTT-ACCCTTAAACTTCTA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
* **
19065708 AAAATTACATTTTTAACCTTAAAACTTCCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
* **
19065738 AAAGTTACATTTTT-ACCCCCGAACTTCCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
* ** *
19065767 AAAATTCCATTTTTG-CCCTTAAACTTTCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
* * * *
19065796 AAAATTTCATTTTTGACCTC-GAATTTCCA
1 AAAATTACATTTTTGACCCCAAAACTTCCA
*
19065825 AAAATT-CTATTTTTGACCCCGAAACT
1 AAAATTAC-ATTTTTGACCCCAAAACT
19065851 CTCGAAATTA
Statistics
Matches: 215, Mismatches: 39, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.00
29 112 0.52
30 93 0.43
31 9 0.04
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTGACCCCAAAACTTCCA
Found at i:19065623 original size:59 final size:59
Alignment explanation
Indices: 19065560--19065843 Score: 279
Period size: 59 Copynumber: 4.8 Consensus size: 59
19065550 GAAAATTTTG
* *
19065560 AAAATAACATTTTGACCCCAAAACTTTCAAAAATTATATTTTTGACCCTAAAACTTCCC
1 AAAATTACATTTTGACCCCAAAACTTTCAAAAATTATATTTTTGACCCTAAAACTTCCA
* * * *
19065619 AAAATCACATTTTGACCCCAAAAACTTCCAAAAATTATATTTTTAACCCCAAAACTTCCA
1 AAAATTACATTTTGACCCC-AAAACTTTCAAAAATTATATTTTTGACCCTAAAACTTCCA
* ** * * *
19065679 AAAATTACATTTTTACCCTTAAAC-TTCTAAAAATTACATTTTTAACCTTAAAACTTCCA
1 AAAATTACATTTTGACCCCAAAACTTTC-AAAAATTATATTTTTGACCCTAAAACTTCCA
* * ** * ** * *
19065738 AAAGTTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTG-CCCTTAAACTTTCA
1 AAAATTACATTTTGACCCCAAAACTTTCAAAAATTATATTTTTGACCCTAAAACTTCCA
* * * *
19065796 AAAATTTCATTTTTGACCTC-GAA-TTTCCAAAAATTCTATTTTTGACCC
1 AAAATTACA-TTTTGACCCCAAAACTTT-CAAAAATTATATTTTTGACCC
19065844 CGAAACTCTC
Statistics
Matches: 190, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
57 2 0.01
58 39 0.21
59 95 0.50
60 54 0.28
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTACATTTTGACCCCAAAACTTTCAAAAATTATATTTTTGACCCTAAAACTTCCA
Found at i:19065859 original size:58 final size:59
Alignment explanation
Indices: 19065644--19065904 Score: 176
Period size: 59 Copynumber: 4.5 Consensus size: 59
19065634 CCCCAAAAAC
** * * * ** *
19065644 TTCCAAAAATTATATTTTTAACCCCAAAACT-TCCAAAAATTA-CATTTTTACCCTTAAAC
1 TTCCAAAAATTCCATTTTTGACCCCGAAACTCT-CAAAAATTATCATTTTGA-CCTCGAAT
* * * *** * * * *
19065703 TTCTAAAAATTACATTTTTAACCTTAAAACT-TCCAAAAGTTA-CATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTGACCCCGAAACTCT-CAAAAATTATCATTTTGA-CCTCGAAT
** *
19065762 TTCCAAAAATTCCATTTTTG-CCCTTAAACTTTCAAAAATT-TCATTTTTGACCTCGAAT
1 TTCCAAAAATTCCATTTTTGACCCCGAAACTCTCAAAAATTATCA-TTTTGACCTCGAAT
* * * *
19065820 TTCCAAAAATTCTATTTTTGACCCCGAAACTCTC-GAAATTATCATTTTGCCCTCGGAT
1 TTCCAAAAATTCCATTTTTGACCCCGAAACTCTCAAAAATTATCATTTTGACCTCGAAT
* * *
19065878 GTCTAAAAATTCCATTTTTGATCCCGA
1 TTCCAAAAATTCCATTTTTGACCCCGA
19065905 TTTTTCTAAA
Statistics
Matches: 169, Mismatches: 28, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
58 82 0.49
59 87 0.51
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTGACCCCGAAACTCTCAAAAATTATCATTTTGACCTCGAAT
Found at i:19065896 original size:29 final size:29
Alignment explanation
Indices: 19065745--19065897 Score: 105
Period size: 29 Copynumber: 5.3 Consensus size: 29
19065735 CCAAAAGTTA
* * * *
19065745 CATTTTTACCCCCGAACTTCCAAAAATTC
1 CATTTTTGCCCTCGAATTTCTAAAAATTC
** *
19065774 CATTTTTGCCCTTAAACTTTC-AAAAATTT
1 CATTTTTGCCCTCGAA-TTTCTAAAAATTC
* *
19065803 CATTTTTGACCTCGAATTTCCAAAAATTC
1 CATTTTTGCCCTCGAATTTCTAAAAATTC
* ** ** *
19065832 TATTTTTGACCC-CGAAACTCTCGAAATTAT
1 CATTTTTG-CCCTCGAATTTCTAAAAATT-C
* *
19065862 CA-TTTTGCCCTCGGATGTCTAAAAATTC
1 CATTTTTGCCCTCGAATTTCTAAAAATTC
19065890 CATTTTTG
1 CATTTTTG
19065898 ATCCCGATTT
Statistics
Matches: 93, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
28 9 0.10
29 78 0.84
30 6 0.06
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.39
Consensus pattern (29 bp):
CATTTTTGCCCTCGAATTTCTAAAAATTC
Found at i:19066061 original size:28 final size:28
Alignment explanation
Indices: 19066030--19066129 Score: 67
Period size: 28 Copynumber: 3.5 Consensus size: 28
19066020 TATTCTTTCA
*
19066030 AAAATTACCATTTTACCCTTAAGTGTCC
1 AAAATTACCATTTTACCCTAAAGTGTCC
* * * * *
19066058 AAAA-TATCATTTTTAACCCCAAATTTTTCT
1 AAAATTACCA-TTTT-ACCCTAAA-GTGTCC
* * ** *
19066088 AAAATTAACATTTTTCCCTCGAGAGTCC
1 AAAATTACCATTTTACCCTAAAGTGTCC
19066116 AAAATTACCATTTT
1 AAAATTACCATTTT
19066130 GCCCCGGGCA
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
27 4 0.08
28 23 0.44
29 10 0.19
30 11 0.21
31 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTAAAGTGTCC
Found at i:19066119 original size:117 final size:117
Alignment explanation
Indices: 19065893--19066107 Score: 297
Period size: 117 Copynumber: 1.8 Consensus size: 117
19065883 AAAATTCCAT
* ** *
19065893 TTTTGATCCCGATTTTTCTAAAAATTACCGTTTTACCCTCAAATGTTTAAAATGTCATTTCTAAC
1 TTTTGATCCCGATTTTTCTAAAAATTACCATTTTACCCTCAAATGTCCAAAATATCATTTCTAAC
* * *
19065958 TCTAAATTTTCCTAAAATTACCAATTTTCCCTCAGACATCCAAAAGGTCTCG
66 CCCAAATTTTCCTAAAATTAACAATTTTCCCTCAGACATCCAAAAGGTCTCG
* * * *
19066010 TTTTGATCCCTATTCTTTC-AAAAATTACCATTTTACCCTTAAGTGTCCAAAATATCATTTTTAA
1 TTTTGATCCCGATT-TTTCTAAAAATTACCATTTTACCCTCAAATGTCCAAAATATCATTTCTAA
* *
19066074 CCCCAAATTTTTCTAAAATTAACATTTTTCCCTC
65 CCCCAAATTTTCCTAAAATTAACAATTTTCCCTC
19066108 GAGAGTCCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 80 0.95
118 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (117 bp):
TTTTGATCCCGATTTTTCTAAAAATTACCATTTTACCCTCAAATGTCCAAAATATCATTTCTAAC
CCCAAATTTTCCTAAAATTAACAATTTTCCCTCAGACATCCAAAAGGTCTCG
Found at i:19067877 original size:18 final size:17
Alignment explanation
Indices: 19067847--19067880 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19067837 ATTATTATAA
*
19067847 TTTAAAATTTAATTATT
1 TTTAAAATATAATTATT
19067864 TTTAAATATATAATTAT
1 TTTAAA-ATATAATTAT
19067881 CACACTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATATAATTATT
Found at i:19067917 original size:16 final size:16
Alignment explanation
Indices: 19067892--19067927 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19067882 ACACTTTCTA
* *
19067892 TTAAATTATAATTATT
1 TTAAAATATAATTACT
19067908 TTAAAATATAATTACT
1 TTAAAATATAATTACT
19067924 TTAA
1 TTAA
19067928 TTTCTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATAATTACT
Found at i:19068920 original size:7 final size:7
Alignment explanation
Indices: 19068907--19068948 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
19068897 GGAAAATAAA
19068907 ATAATAT
1 ATAATAT
*
19068914 GTAATAT
1 ATAATAT
19068921 ATAATAT
1 ATAATAT
19068928 ATAATAT
1 ATAATAT
19068935 ATAATAT
1 ATAATAT
19068942 AT-ATAT
1 ATAATAT
19068948 A
1 A
19068949 GCATAATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:19068954 original size:16 final size:14
Alignment explanation
Indices: 19068907--19068968 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
19068897 GGAAAATAAA
* *
19068907 ATAATATGTAATAT
1 ATAATATATAATAC
*
19068921 ATAATATATAATAT
1 ATAATATATAATAC
19068935 ATAATATATATATAGC
1 ATAATATATA-ATA-C
*
19068951 ATAATA-AGAATA-
1 ATAATATATAATAC
19068963 ATAATA
1 ATAATA
19068969 GTAATTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
12 6 0.14
14 26 0.60
15 5 0.12
16 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (14 bp):
ATAATATATAATAC
Found at i:19073267 original size:31 final size:31
Alignment explanation
Indices: 19073232--19073294 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
19073222 TTTGAACTTG
* * * *
19073232 AAAATAATTGTTAAGTTTAAGTCTTAATGTA
1 AAAATAATTATCAAGTTCAAGTCTCAATGTA
19073263 AAAATAATTATCAAGTTCAAGTCTCAATGTA
1 AAAATAATTATCAAGTTCAAGTCTCAATGTA
19073294 A
1 A
19073295 GAGCGATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (31 bp):
AAAATAATTATCAAGTTCAAGTCTCAATGTA
Found at i:19074975 original size:24 final size:25
Alignment explanation
Indices: 19074938--19074985 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
19074928 TTCACTCTTT
*
19074938 TTAAAAAGTCAATGATCAAATTTGA
1 TTAAAAAATCAATGATCAAATTTGA
19074963 TTAAAAAAT-AATGATCAAATTTG
1 TTAAAAAATCAATGATCAAATTTG
19074986 CAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (25 bp):
TTAAAAAATCAATGATCAAATTTGA
Found at i:19074993 original size:22 final size:23
Alignment explanation
Indices: 19074948--19074995 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
19074938 TTAAAAAGTC
*
19074948 AATGATCAAATTTGATTAAAAAAT
1 AATGATCAAATTTGA-CAAAAAAT
19074972 AATGATCAAATTTG-CAAAAAAT
1 AATGATCAAATTTGACAAAAAAT
19074994 AA
1 AA
19074996 AATATTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
24 14 0.61
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (23 bp):
AATGATCAAATTTGACAAAAAAT
Found at i:19075304 original size:3 final size:3
Alignment explanation
Indices: 19075296--19075327 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
19075286 TCAATTACAC
19075296 ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
19075328 GAGAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19083863 original size:65 final size:65
Alignment explanation
Indices: 19083769--19083890 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
19083759 GTCCTCATTG
* * *
19083769 GAAGATAAACTTCAAATTTGAATTGTGATTCTAAAGCACGTCTGAGCACATATGAGTCCTTGTTA
1 GAAGATAAACTTCAAATTCGAATTATGATTCTAAAGCACGTCTGAGCAAATATGAGTCCTTGTTA
*
19083834 GAAGATAAACTTCCAAA-TCGAATTATGATTCTAAAGTACGTCTGAGCAAATATGAGT
1 GAAGATAAACTT-CAAATTCGAATTATGATTCTAAAGCACGTCTGAGCAAATATGAGT
19083891 GAGCTGACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 48 0.92
66 4 0.08
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (65 bp):
GAAGATAAACTTCAAATTCGAATTATGATTCTAAAGCACGTCTGAGCAAATATGAGTCCTTGTTA
Found at i:19085467 original size:25 final size:27
Alignment explanation
Indices: 19085404--19085468 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
19085394 TAAAATATAA
* *
19085404 TAATGTATTATATATTTATTTAAAATTT
1 TAAT-TATTATATAATTATGTAAAATTT
*
19085432 TAATTAATATATAATTATGT-AAA-TT
1 TAATTATTATATAATTATGTAAAATTT
*
19085457 TATTTATTATAT
1 TAATTATTATAT
19085469 TCAATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 12 0.38
26 3 0.09
27 13 0.41
28 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
TAATTATTATATAATTATGTAAAATTT
Found at i:19089816 original size:31 final size:31
Alignment explanation
Indices: 19089781--19089843 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
19089771 TTGAATGACT
*
19089781 ATTTATGTAATTTATCTAAGTATTAAATATG
1 ATTTATGTAATTTATATAAGTATTAAATATG
19089812 ATTTATGTAATTTATATAAGTATTAAATATG
1 ATTTATGTAATTTATATAAGTATTAAATATG
19089843 A
1 A
19089844 CGTACTCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.48
Consensus pattern (31 bp):
ATTTATGTAATTTATATAAGTATTAAATATG
Found at i:19090201 original size:24 final size:24
Alignment explanation
Indices: 19090174--19090223 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
19090164 TTATTTGCTT
19090174 TCTTCATTCATTTCAGGTCTGCGA
1 TCTTCATTCATTTCAGGTCTGCGA
*
19090198 TCTTCATTCATTTCAGTTCTGCGA
1 TCTTCATTCATTTCAGGTCTGCGA
19090222 TC
1 TC
19090224 AATCACTGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.26, G:0.14, T:0.44
Consensus pattern (24 bp):
TCTTCATTCATTTCAGGTCTGCGA
Found at i:19094768 original size:26 final size:26
Alignment explanation
Indices: 19094732--19094785 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
19094722 AGTTTAATGA
19094732 AACTTTACTATAGCTGAAAATATGGC
1 AACTTTACTATAGCTGAAAATATGGC
19094758 AACTTTACTATAGCTGAAAATATGGC
1 AACTTTACTATAGCTGAAAATATGGC
19094784 AA
1 AA
19094786 ACCAACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (26 bp):
AACTTTACTATAGCTGAAAATATGGC
Found at i:19109322 original size:213 final size:213
Alignment explanation
Indices: 19108955--19109383 Score: 795
Period size: 213 Copynumber: 2.0 Consensus size: 213
19108945 TCAGAGTATC
*
19108955 TGCCCCAACCATACCAGGAATTCTACACGGCAAACCCTTCCTATGAATTAAACCAGTAAGAGACA
1 TGCCCCAACCATACCAGGAATTCCACACGGCAAACCCTTCCTATGAATTAAACCAGTAAGAGACA
* *
19109020 GAGCTGATCTTCTCATTTCAGGCTTCATATTTGTTCCAAATTAATGTTAATTCTCACTTAAATGT
66 GAGCAGATCTTCTCATTTCAGGCTTCATATTTGTTCCAAATTAATGTTAATTCTCACTTAAATAT
* *
19109085 ATCTTTTAAATTCTAATAAGAATAAGTGAGATTGCAAACTGGCTTTCTTTTTTGCGGTAGTAGGA
131 ATCTTTCAAATTCTAATAAGAATAAGTGAGATTGCAAACTGGCTTTCTTCTTTGCGGTAGTAGGA
19109150 AACTAATTATCCTCTATT
196 AACTAATTATCCTCTATT
19109168 TGCCCCAACCATACCAGGAATTCCACACGGCAAACCCTTCCTATGAATTAAACCAGTAAGAGACA
1 TGCCCCAACCATACCAGGAATTCCACACGGCAAACCCTTCCTATGAATTAAACCAGTAAGAGACA
* *
19109233 GAGCAGATCTTCTCATTTCAGGTTTCGTATTTGTTCCAAATTAATGTTAATTCTCACTTAAATAT
66 GAGCAGATCTTCTCATTTCAGGCTTCATATTTGTTCCAAATTAATGTTAATTCTCACTTAAATAT
19109298 ATCTTTCAAATTCTAATAAGAATAAGTGAGATTGCAAACTGGCTTTCTTCTTTGCGGTAGTAGGA
131 ATCTTTCAAATTCTAATAAGAATAAGTGAGATTGCAAACTGGCTTTCTTCTTTGCGGTAGTAGGA
19109363 AACTAATTATCCTCTATT
196 AACTAATTATCCTCTATT
19109381 TGC
1 TGC
19109384 TTCAAATTGA
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 209 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (213 bp):
TGCCCCAACCATACCAGGAATTCCACACGGCAAACCCTTCCTATGAATTAAACCAGTAAGAGACA
GAGCAGATCTTCTCATTTCAGGCTTCATATTTGTTCCAAATTAATGTTAATTCTCACTTAAATAT
ATCTTTCAAATTCTAATAAGAATAAGTGAGATTGCAAACTGGCTTTCTTCTTTGCGGTAGTAGGA
AACTAATTATCCTCTATT
Found at i:19110582 original size:20 final size:20
Alignment explanation
Indices: 19110557--19110594 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19110547 AATGTGACAG
19110557 TAAATTTAAAGGAAAATAAA
1 TAAATTTAAAGGAAAATAAA
*
19110577 TAAATTTTAAGGAAAATA
1 TAAATTTAAAGGAAAATA
19110595 TGAGGAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (20 bp):
TAAATTTAAAGGAAAATAAA
Found at i:19113440 original size:22 final size:24
Alignment explanation
Indices: 19113403--19113446 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
19113393 TAGTTTTTAG
19113403 TTTTTATTATTATTAACATAAATT
1 TTTTTATTATTATTAACATAAATT
*
19113427 TTTTTATT-TT-TTAACGTAAA
1 TTTTTATTATTATTAACATAAA
19113447 ATTATCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTTATTATTATTAACATAAATT
Found at i:19114076 original size:19 final size:19
Alignment explanation
Indices: 19114052--19114088 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19114042 TTATATAAAT
19114052 AAAAGTT-GTAACATATTTG
1 AAAAGTTAGTAA-ATATTTG
19114071 AAAAGTTAGTAAATATTT
1 AAAAGTTAGTAAATATTT
19114089 AACAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.38
Consensus pattern (19 bp):
AAAAGTTAGTAAATATTTG
Found at i:19126354 original size:3 final size:3
Alignment explanation
Indices: 19126341--19126378 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
19126331 ATACAAGCAT
*
19126341 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
19126379 GTAGAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:19129251 original size:15 final size:16
Alignment explanation
Indices: 19129216--19129254 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
19129206 ATTATTCAAT
*
19129216 ATAAAAAAAATCAGAA
1 ATAAAAAAAATCAAAA
*
19129232 TTAAAAAAAAT-AAAA
1 ATAAAAAAAATCAAAA
19129247 ATAAAAAA
1 ATAAAAAA
19129255 TTCAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
ATAAAAAAAATCAAAA
Found at i:19130283 original size:60 final size:59
Alignment explanation
Indices: 19130218--19130370 Score: 243
Period size: 59 Copynumber: 2.6 Consensus size: 59
19130208 GCTTAGGTAC
*
19130218 AATTAGGAAAAAATGTCAAGTTTAGGTACCAAATTGGATCCAAAAAAAGATTAAGTACCA
1 AATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGAT-CAAAAAAAGATTAAGTACCA
* * *
19130278 AATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCAAAAAAAGTTTAGGTACCA
1 AATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGATCAAAAAAAGATTAAGTACCA
* *
19130337 AATTAGTAAAAAATGTCAAGTTCAAGTACCAAAT
1 AATTAGGAAAAAATGTCAAGTTCAGGTACCAAAT
19130371 GTTATATTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
59 49 0.57
60 37 0.43
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (59 bp):
AATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGATCAAAAAAAGATTAAGTACCA
Found at i:19130310 original size:31 final size:30
Alignment explanation
Indices: 19130218--19130370 Score: 99
Period size: 31 Copynumber: 5.1 Consensus size: 30
19130208 GCTTAGGTAC
*
19130218 AATTAGGAAAAAATGTCAAGTTTAGGTACCA
1 AATTAGG-AAAAATGTCAAGTTCAGGTACCA
* *
19130249 AATT-GGATCCAAAA---AAAGATT-AAGTACCA
1 AATTAGGA---AAAATGTCAAG-TTCAGGTACCA
19130278 AATTAGGAAAAAGTGTCAAGTTCAGGTACCA
1 AATTAGGAAAAA-TGTCAAGTTCAGGTACCA
* *
19130309 AATT-GGATCAAAA---AAAGTTTAGGTACCA
1 AATTAGGA--AAAATGTCAAGTTCAGGTACCA
* *
19130337 AATTAGTAAAAAATGTCAAGTTCAAGTACCA
1 AATTAG-GAAAAATGTCAAGTTCAGGTACCA
19130368 AAT
1 AAT
19130371 GTTATATTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 34
0.68 0.07 0.24
Matches are distributed among these distances:
27 4 0.04
28 21 0.22
29 16 0.17
30 13 0.14
31 33 0.35
32 8 0.08
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (30 bp):
AATTAGGAAAAATGTCAAGTTCAGGTACCA
Found at i:19160452 original size:30 final size:30
Alignment explanation
Indices: 19160416--19160480 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
19160406 GCAAATGATT
19160416 TTAAAATTATTTTTTTAAAAT-ATAAAATTA
1 TTAAAATTA-TTTTTTAAAATAATAAAATTA
19160446 TTAAAATTATTTTTTAAAATAATAAAATTA
1 TTAAAATTATTTTTTAAAATAATAAAATTA
19160476 TTAAA
1 TTAAA
19160481 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAAAATTATTTTTTAAAATAATAAAATTA
Found at i:19160486 original size:29 final size:29
Alignment explanation
Indices: 19160416--19160487 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
19160406 GCAAATGATT
*
19160416 TTAAAATTATTTTTTTAAAATATAAAATTA
1 TTAAAA-TAATTTTTTAAAATATAAAATTA
*
19160446 TTAAAATTATTTTTTAAAATAATAAAATTA
1 TTAAAATAATTTTTTAAAAT-ATAAAATTA
19160476 TT-AAATAATTTT
1 TTAAAATAATTTT
19160488 AATTTCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAATAATTTTTTAAAATATAAAATTA
Found at i:19161530 original size:21 final size:22
Alignment explanation
Indices: 19161491--19161534 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19161481 GAAAATCAGA
19161491 AATTTTATTATTTCAAAAAAAT
1 AATTTTATTATTTCAAAAAAAT
*
19161513 AATTTTA-TATTTTTAAAAAAAT
1 AATTTTATTA-TTTCAAAAAAAT
19161535 TAAAATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTTATTATTTCAAAAAAAT
Found at i:19167452 original size:23 final size:22
Alignment explanation
Indices: 19167422--19167524 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 22
19167412 ACATTAGCGC
19167422 GCTTACTGTTTAGCACTGTGTGT
1 GCTTACTGTTT-GCACTGTGTGT
* *
19167445 GCTTACTGATTTGCATTTTGTGT
1 GCTTACTG-TTTGCACTGTGTGT
*
19167468 GCTTACTGTTTTGCACTGCGTGT
1 GCTTACTG-TTTGCACTGTGTGT
* *
19167491 GCCTATTGATTTGCACTGTGTGT
1 GCTTACTG-TTTGCACTGTGTGT
*
19167514 GTTTACTGTTT
1 GCTTACTGTTT
19167525 CCCCAGCACT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
22 3 0.05
23 60 0.91
24 3 0.05
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.48
Consensus pattern (22 bp):
GCTTACTGTTTGCACTGTGTGT
Found at i:19167491 original size:46 final size:46
Alignment explanation
Indices: 19167422--19167524 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
19167412 ACATTAGCGC
* * * *
19167422 GCTTACTGTTTAGCACTGTGTGTGCTTACTGATTTGCATTTTGTGT
1 GCTTACTGTTTAGCACTGCGTGTGCCTACTGATTTGCACTGTGTGT
* *
19167468 GCTTACTGTTTTGCACTGCGTGTGCCTATTGATTTGCACTGTGTGT
1 GCTTACTGTTTAGCACTGCGTGTGCCTACTGATTTGCACTGTGTGT
*
19167514 GTTTACTGTTT
1 GCTTACTGTTT
19167525 CCCCAGCACT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.48
Consensus pattern (46 bp):
GCTTACTGTTTAGCACTGCGTGTGCCTACTGATTTGCACTGTGTGT
Done.