Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 66 of 120
Found at i:19471064 original size:75 final size:75
Alignment explanation
Indices: 19470931--19471069 Score: 197
Period size: 75 Copynumber: 1.9 Consensus size: 75
19470921 TAAGCTGACG
** * * *
19470931 AGCGTAAACGTATTCATGCTGACGAGCATAAATGTATACATATGTTGATGAGCGTAAATGTATTT
1 AGCGTAAACGTATTCATGCTGACGAGCATAAACATATACATATGCTGACGAGCATAAATGTATTT
19470996 ATAGCTAACA
66 ATAGCTAACA
* * * *
19471006 AGCGTAAATGTATTCATGCTGACGAGCGTAAACATATATATATGCTGACGAGTATAAATGTATT
1 AGCGTAAACGTATTCATGCTGACGAGCATAAACATATACATATGCTGACGAGCATAAATGTATT
19471070 CATGCTGACG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 55 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (75 bp):
AGCGTAAACGTATTCATGCTGACGAGCATAAACATATACATATGCTGACGAGCATAAATGTATTT
ATAGCTAACA
Found at i:19471068 original size:50 final size:50
Alignment explanation
Indices: 19470924--19471098 Score: 194
Period size: 50 Copynumber: 3.5 Consensus size: 50
19470914 TATCTGATAA
* * *
19470924 GCTGACGAGCGTAAACGTAT-T-CATGCTGACGAGCATAAATGTATACATAT
1 GCTGACGAGCGTAAACATATATATATGCTGACGAGCATAAATGTATTC--AT
* * ** * * * *
19470974 GTTGATGAGCGTAAATGTATTTATA-GCTAACAAGCGTAAATGTATTCAT
1 GCTGACGAGCGTAAACATATATATATGCTGACGAGCATAAATGTATTCAT
*
19471023 GCTGACGAGCGTAAACATATATATATGCTGACGAGTATAAATGTATTCAT
1 GCTGACGAGCGTAAACATATATATATGCTGACGAGCATAAATGTATTCAT
*
19471073 GCTGACGAGCATAAACATATATATAT
1 GCTGACGAGCGTAAACATATATATAT
19471099 ATATATATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
49 22 0.21
50 62 0.60
51 19 0.18
52 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (50 bp):
GCTGACGAGCGTAAACATATATATATGCTGACGAGCATAAATGTATTCAT
Found at i:19471096 original size:2 final size:2
Alignment explanation
Indices: 19471089--19471138 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
19471079 GAGCATAAAC
19471089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19471131 AT AT AT AT
1 AT AT AT AT
19471139 GTTGATGAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19471159 original size:24 final size:24
Alignment explanation
Indices: 19471132--19471177 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19471122 TATATATATA
* *
19471132 TATATATGTTGATGAGCGTAAATG
1 TATACATGTTGACGAGCGTAAATG
19471156 TATACATGTTGACGAGCGTAAA
1 TATACATGTTGACGAGCGTAAA
19471178 CGTACATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (24 bp):
TATACATGTTGACGAGCGTAAATG
Found at i:19471452 original size:2 final size:2
Alignment explanation
Indices: 19471440--19471470 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19471430 TATTAAACGA
*
19471440 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19471471 ATGAATATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19475538 original size:2 final size:2
Alignment explanation
Indices: 19475533--19475563 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19475523 TATATATATA
19475533 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
19475564 TTCTAAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:19478635 original size:43 final size:43
Alignment explanation
Indices: 19478582--19478712 Score: 174
Period size: 43 Copynumber: 3.0 Consensus size: 43
19478572 ACGCTGCTAT
19478582 AGAACATGGTCTTTAGCGGCG-TTTTCCTCACAAACACCACTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCC-CACAAACACCACTAA
* * *
19478625 AGAACATGGTCTTTAGTGGCGCTTTTCCCACAAACTCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACACCACTAA
* * * * *
19478668 AGAACATGGTCTTTAGCAGCACTTTTTCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACACCACTAA
19478711 AG
1 AG
19478713 TTAACATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 73 0.92
44 6 0.08
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACACCACTAA
Found at i:19478886 original size:20 final size:19
Alignment explanation
Indices: 19478851--19478888 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
19478841 TATATGATTT
19478851 AAATTTATAAATAAATAAA
1 AAATTTATAAATAAATAAA
19478870 AAATATTATACAA-AAATAA
1 AAAT-TTATA-AATAAATAA
19478889 TATTGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 11 0.65
21 2 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTTATAAATAAATAAA
Found at i:19480646 original size:92 final size:92
Alignment explanation
Indices: 19480489--19480695 Score: 387
Period size: 92 Copynumber: 2.2 Consensus size: 92
19480479 CTTGGGACGG
*
19480489 ATGAAGAGTCATATCTCCATACATGAAAAGACATAATGAATTCCAGTATGAAGGTTACAACCTTC
1 ATGAAGAGTCATATCTCCATACATGAAAAGACATAATGAATTCCAGTATGAAGCTTACAACCTTC
19480554 CATGTCTTTCATGTATTGGGAGTGCAC
66 CATGTCTTTCATGTATTGGGAGTGCAC
*
19480581 ATGAAGAGTCATATCTCCATACATGAAAAGACATAATGAATTCCAGTATGCAGCTTACAACCTTC
1 ATGAAGAGTCATATCTCCATACATGAAAAGACATAATGAATTCCAGTATGAAGCTTACAACCTTC
*
19480646 CATGTCTTTCATTTATTGGGAGTGCAC
66 CATGTCTTTCATGTATTGGGAGTGCAC
19480673 ATGAAGAGTCATATCTCCATACA
1 ATGAAGAGTCATATCTCCATACA
19480696 ACTGATTTTG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 112 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (92 bp):
ATGAAGAGTCATATCTCCATACATGAAAAGACATAATGAATTCCAGTATGAAGCTTACAACCTTC
CATGTCTTTCATGTATTGGGAGTGCAC
Found at i:19481068 original size:2 final size:2
Alignment explanation
Indices: 19481055--19481085 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19481045 ATAAGAGTGA
*
19481055 GT GT GA GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
19481086 AGGTTACATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.52, T:0.45
Consensus pattern (2 bp):
GT
Found at i:19482703 original size:41 final size:41
Alignment explanation
Indices: 19482652--19482913 Score: 278
Period size: 41 Copynumber: 6.4 Consensus size: 41
19482642 GTTTATGGGA
* * *
19482652 AAACGCCGCTATTGCT-TAACCATTAGCGGCGTATTTCTCAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCG-ATTTCTCAT
* * *
19482693 AAACGCCGCTAATGTTGTGACCTTTAGCGGCGCTTTTTCAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCGATTTCTCAT
* *
19482734 AAACGCCGCTAATGCTTTGACCTTTAGCGAC-ACTTTCTCAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCGA-TTTCTCAT
* * * *
19482775 AAACGTCGTTAATGCTGTGACCTTTAGCGAC-ACTTTCTAAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCGA-TTTCTCAT
* * *
19482816 AAACGCCGCTAATGTTGTAACCTTTAGCGGCGCTTTCTCAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCGATTTCTCAT
* * * * *
19482857 AAACGCCGTTAATGCTTTGACCTTTAACGGTGTTTTCTCAT
1 AAACGCCGCTAATGCTGTGACCTTTAGCGGCGATTTCTCAT
* *
19482898 AAATGTCGCTAATGCT
1 AAACGCCGCTAATGCT
19482914 CTTTCCCATA
Statistics
Matches: 186, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
41 173 0.93
42 13 0.07
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAATGCTGTGACCTTTAGCGGCGATTTCTCAT
Found at i:19482894 original size:123 final size:123
Alignment explanation
Indices: 19482685--19482913 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 123
19482675 TAGCGGCGTA
* * *
19482685 TTTCTCATAAACGCCGCTAATGTTGTGACCTTTAGCGGCGCTTTTTCATAAACGCCGCTAATGCT
1 TTTCTAATAAACGCCGCTAATGTTGTAACCTTTAGCGGCGCTTTCTCATAAACGCCGCTAATGCT
* *
19482750 TTGACCTTTAGCGACACTTTCTCATAAACGTCGTTAATGCTGTGACCTTTAGCGACAC
66 TTGACCTTTAACGACACTTTCTCATAAACGTCGCTAATGCTGTGACCTTTAGCGACAC
*
19482808 TTTCTAATAAACGCCGCTAATGTTGTAACCTTTAGCGGCGCTTTCTCATAAACGCCGTTAATGCT
1 TTTCTAATAAACGCCGCTAATGTTGTAACCTTTAGCGGCGCTTTCTCATAAACGCCGCTAATGCT
**** *
19482873 TTGACCTTTAACGGTGTTTTCTCATAAATGTCGCTAATGCT
66 TTGACCTTTAACGACACTTTCTCATAAACGTCGCTAATGCT
19482914 CTTTCCCATA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (123 bp):
TTTCTAATAAACGCCGCTAATGTTGTAACCTTTAGCGGCGCTTTCTCATAAACGCCGCTAATGCT
TTGACCTTTAACGACACTTTCTCATAAACGTCGCTAATGCTGTGACCTTTAGCGACAC
Found at i:19483371 original size:14 final size:14
Alignment explanation
Indices: 19483352--19483378 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19483342 CTCGAATTTT
19483352 GAATTATTCGAGTC
1 GAATTATTCGAGTC
19483366 GAATTATTCGAGT
1 GAATTATTCGAGT
19483379 TAAACGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (14 bp):
GAATTATTCGAGTC
Found at i:19483473 original size:18 final size:18
Alignment explanation
Indices: 19483437--19483474 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19483427 TGAATTTTCG
*
19483437 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
19483455 AATTCGAATAAAC-CAAAT
1 AATTCGAAT-AACTCAAAT
19483473 AA
1 AA
19483475 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:19492038 original size:61 final size:62
Alignment explanation
Indices: 19491973--19492098 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 62
19491963 ATATAATAGG
* * * * *
19491973 ATTATTATTAAATATAATTTAATAAAAATGATAATAAATAATTTAATCATATT-TTAATATA
1 ATTATTATTAAATAGAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
*
19492034 ATTATTATTAAATAGAATTTAATAAAAATAAAAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATAGAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
19492096 ATT
1 ATT
19492099 TTTTTTATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 47 0.81
62 11 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (62 bp):
ATTATTATTAAATAGAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
Found at i:19509168 original size:191 final size:191
Alignment explanation
Indices: 19508838--19509221 Score: 759
Period size: 191 Copynumber: 2.0 Consensus size: 191
19508828 AGAGGTGTCC
*
19508838 AAGAGCTGTCGAAAGCCATTACGATAGCGAAGTTTGTGGTCAAGCTTGGTCTAGGGAAAACAAGC
1 AAGAGATGTCGAAAGCCATTACGATAGCGAAGTTTGTGGTCAAGCTTGGTCTAGGGAAAACAAGC
19508903 TTGAATCTTCCAAGTTCGAGGAAAGAGGATCATGTAAAGGGAATCATGAGGAAGATGATAATGGC
66 TTGAATCTTCCAAGTTCGAGGAAAGAGGATCATGTAAAGGGAATCATGAGGAAGATGATAATGGC
19508968 GGTGGCAACGGAAACAATGGTGGTAATAGGAAACCACGAGTTGGGAAGAAGAAACCCAATA
131 GGTGGCAACGGAAACAATGGTGGTAATAGGAAACCACGAGTTGGGAAGAAGAAACCCAATA
19509029 AAGAGATGTCGAAAGCCATTACGATAGCGAAGTTTGTGGTCAAGCTTGGTCTAGGGAAAACAAGC
1 AAGAGATGTCGAAAGCCATTACGATAGCGAAGTTTGTGGTCAAGCTTGGTCTAGGGAAAACAAGC
19509094 TTGAATCTTCCAAGTTCGAGGAAAGAGGATCATGTAAAGGGAATCATGAGGAAGATGATAATGGC
66 TTGAATCTTCCAAGTTCGAGGAAAGAGGATCATGTAAAGGGAATCATGAGGAAGATGATAATGGC
19509159 GGTGGCAACGGAAACAATGGTGGTAATAGGAAACCACGAGTTGGGAAGAAGAAACCCAATA
131 GGTGGCAACGGAAACAATGGTGGTAATAGGAAACCACGAGTTGGGAAGAAGAAACCCAATA
19509220 AA
1 AA
19509222 AAATGAGGCA
Statistics
Matches: 192, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 192 1.00
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (191 bp):
AAGAGATGTCGAAAGCCATTACGATAGCGAAGTTTGTGGTCAAGCTTGGTCTAGGGAAAACAAGC
TTGAATCTTCCAAGTTCGAGGAAAGAGGATCATGTAAAGGGAATCATGAGGAAGATGATAATGGC
GGTGGCAACGGAAACAATGGTGGTAATAGGAAACCACGAGTTGGGAAGAAGAAACCCAATA
Found at i:19512777 original size:19 final size:18
Alignment explanation
Indices: 19512753--19512788 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19512743 AATGAAATTA
*
19512753 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
19512772 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
19512789 ACATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:19512814 original size:19 final size:20
Alignment explanation
Indices: 19512770--19512834 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 20
19512760 TTACAATTTT
*
19512770 ATTTTAATAATAAATTTTAAC
1 ATTTTAAAAAT-AATTTTAAC
19512791 A--TTAAAAATAATTTTAA-
1 ATTTTAAAAATAATTTTAAC
* * *
19512808 ATTTTAAATGATATTTTTAAT
1 ATTTTAAA-AATAATTTTAAC
19512829 ATTTTA
1 ATTTTA
19512835 TTGAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 8 0.22
19 12 0.32
20 9 0.24
21 7 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTAAAAATAATTTTAAC
Found at i:19513120 original size:38 final size:38
Alignment explanation
Indices: 19513078--19513153 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
19513068 ATTAAATCTA
*
19513078 TATAAGACTTTAGTTATTAAAAAATATTATTTTTTAAT
1 TATAAGACATTAGTTATTAAAAAATATTATTTTTTAAT
19513116 TATAAGACATTAGTTATTAAAAAATATTATTTTTTAAT
1 TATAAGACATTAGTTATTAAAAAATATTATTTTTTAAT
19513154 AAAATAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (38 bp):
TATAAGACATTAGTTATTAAAAAATATTATTTTTTAAT
Found at i:19513135 original size:21 final size:20
Alignment explanation
Indices: 19513077--19513135 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
19513067 TATTAAATCT
*
19513077 ATATAAGACTTTAGTTATTA
1 ATATAAGACATTAGTTATTA
* * *
19513097 A-A-AA-ATATTATTTTTTA
1 ATATAAGACATTAGTTATTA
19513114 ATTATAAGACATTAGTTATTA
1 A-TATAAGACATTAGTTATTA
19513135 A
1 A
19513136 AAAATATTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 7
0.67 0.17 0.17
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 2 0.07
20 3 0.11
21 11 0.39
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATAAGACATTAGTTATTA
Found at i:19513144 original size:17 final size:18
Alignment explanation
Indices: 19513087--19513159 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
19513077 ATATAAGACT
19513087 TTAGTTATTAA-AAAATA
1 TTAGTTATTAATAAAATA
* * *
19513104 TTATTTTTTAATTATAAGACA
1 TTAGTTATTAA-TA-AA-ATA
19513125 TTAGTTATTAA-AAAATA
1 TTAGTTATTAATAAAATA
* *
19513142 TTATTTTTTAATAAAATA
1 TTAGTTATTAATAAAATA
19513160 AATTTCAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 20 0.47
18 8 0.19
19 2 0.05
20 2 0.05
21 11 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (18 bp):
TTAGTTATTAATAAAATA
Found at i:19513695 original size:20 final size:20
Alignment explanation
Indices: 19513651--19513694 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
19513641 CAAATAATTT
*
19513651 AAAAATTAAAAAATATTCAA
1 AAAAATTAAAAAATATTAAA
*
19513671 AAAAATT-AAAATTATTAAA
1 AAAAATTAAAAAATATTAAA
19513690 AAAAA
1 AAAAA
19513695 AACACGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAATTAAAAAATATTAAA
Found at i:19520908 original size:1 final size:1
Alignment explanation
Indices: 19520902--19520927 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
19520892 GTTGAAACTT
19520902 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
19520928 AAGAATGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:19521298 original size:20 final size:20
Alignment explanation
Indices: 19521270--19521308 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19521260 TTTATACAAT
19521270 AATAGTATATTTTAATTTTAG
1 AATAGTATATTTT-ATTTTAG
19521291 AATA-TATATTTTATTTTA
1 AATAGTATATTTTATTTTA
19521309 AAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
AATAGTATATTTTATTTTAG
Found at i:19521314 original size:20 final size:20
Alignment explanation
Indices: 19521270--19521316 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
19521260 TTTATACAAT
*
19521270 AATAGTATATTTTAATTTTAG
1 AATA-TATATTTTAATTTTAA
19521291 AATATATATTTT-ATTTTAA
1 AATATATATTTTAATTTTAA
19521310 AA-ATATA
1 AATATATA
19521317 ATTATATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 8 0.32
21 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
AATATATATTTTAATTTTAA
Found at i:19521315 original size:18 final size:20
Alignment explanation
Indices: 19521275--19521316 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19521265 ACAATAATAG
*
19521275 TATATTTTAATTTTAGAATA
1 TATATTTTAATTTTAGAAAA
19521295 TATATTTT-ATTTTA-AAAA
1 TATATTTTAATTTTAGAAAA
19521313 TATA
1 TATA
19521317 ATTATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATATTTTAATTTTAGAAAA
Found at i:19523734 original size:29 final size:29
Alignment explanation
Indices: 19523701--19523776 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 29
19523691 TTTTAGTTAC
19523701 AACCTTTTCAAAGATATCCTTTCA-GATAT
1 AACCTTTTCAAAGATATCCTTT-AGGATAT
*
19523730 AACCTTTTCAAAAATAT-CTTTATGGATAT
1 AACCTTTTCAAAGATATCCTTTA-GGATAT
19523759 AACCTTTTCAAAGATATC
1 AACCTTTTCAAAGATATC
19523777 GTTTTACTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 1 0.02
28 4 0.10
29 37 0.88
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (29 bp):
AACCTTTTCAAAGATATCCTTTAGGATAT
Found at i:19524845 original size:25 final size:25
Alignment explanation
Indices: 19524793--19524844 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
19524783 ACGTTAAGCA
*
19524793 TTTGAATAAGGAAATAATTTTAATT
1 TTTGAACAAGGAAATAATTTTAATT
*
19524818 TTTGAACATGGAAATAA-TTTAATT
1 TTTGAACAAGGAAATAATTTTAATT
19524842 TTT
1 TTT
19524845 TAATTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TTTGAACAAGGAAATAATTTTAATT
Found at i:19526819 original size:40 final size:40
Alignment explanation
Indices: 19526764--19526845 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
19526754 AACCATCTCC
* *
19526764 TCAAATTTATTTTTTCAGAAGCATCAGTATTAAAAAAGCA
1 TCAAATTTATTTTTTCAGAAGCATCAATACTAAAAAAGCA
19526804 TCAAATTTATTTTTTCAGAAGCATCAATACTAAAAAAGCA
1 TCAAATTTATTTTTTCAGAAGCATCAATACTAAAAAAGCA
19526844 TC
1 TC
19526846 CACTTGGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (40 bp):
TCAAATTTATTTTTTCAGAAGCATCAATACTAAAAAAGCA
Found at i:19526962 original size:29 final size:30
Alignment explanation
Indices: 19526920--19526978 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
19526910 AAACAAAATT
19526920 CATCTCGTCAAAATTAT-TTCTT-TAGAACC
1 CATCTCGTCAAAATTATATT-TTCTAGAACC
19526949 CATCTCGTCAAAATTATATTTTCTAGAACC
1 CATCTCGTCAAAATTATATTTTCTAGAACC
19526979 ATAGTAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (30 bp):
CATCTCGTCAAAATTATATTTTCTAGAACC
Found at i:19527602 original size:31 final size:29
Alignment explanation
Indices: 19527559--19527625 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
19527549 AATATTTTAT
*
19527559 ATTTTGATATTTTTTAA-AGGATTAAATCAAA
1 ATTTT-ATA-TTTTTAAGAGG-TTAAAGCAAA
*
19527590 ATTTTATCATTTTTAAGAGGTTAAAGCACA
1 ATTTTAT-ATTTTTAAGAGGTTAAAGCAAA
19527620 ATTTTA
1 ATTTTA
19527626 CTTTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (29 bp):
ATTTTATATTTTTAAGAGGTTAAAGCAAA
Found at i:19527605 original size:30 final size:30
Alignment explanation
Indices: 19527569--19527625 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19527559 ATTTTGATAT
*
19527569 TTTTTAA-AGGATTAAATCAAAATTTTATCA
1 TTTTTAAGAGG-TTAAAGCAAAATTTTATCA
*
19527599 TTTTTAAGAGGTTAAAGCACAATTTTA
1 TTTTTAAGAGGTTAAAGCAAAATTTTA
19527626 CTTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (30 bp):
TTTTTAAGAGGTTAAAGCAAAATTTTATCA
Found at i:19530184 original size:15 final size:15
Alignment explanation
Indices: 19530164--19530193 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19530154 GGTTACATTG
19530164 CTATCAAGTGAGTAT
1 CTATCAAGTGAGTAT
19530179 CTATCAAGTGAGTAT
1 CTATCAAGTGAGTAT
19530194 TTGTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
CTATCAAGTGAGTAT
Found at i:19533507 original size:21 final size:23
Alignment explanation
Indices: 19533464--19533507 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19533454 TTGTTAAAAC
* *
19533464 AAAATATATCTTTTACAATTATT
1 AAAATATATCTCTTACAAATATT
19533487 AAAATATAT-TCTTA-AAATATT
1 AAAATATATCTCTTACAAATATT
19533508 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 9 0.47
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATATATCTCTTACAAATATT
Found at i:19543629 original size:2 final size:2
Alignment explanation
Indices: 19543622--19543648 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19543612 AATATCATAA
19543622 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19543649 ATTATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19546981 original size:29 final size:29
Alignment explanation
Indices: 19546939--19547019 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
19546929 TTTGTCTCAG
*
19546939 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
* *
19546968 GTTATGTTTTAGTCACTGATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
19546997 GTTACGTTTTAGTCACTTATGTT
1 GTTACGTTTTAGTCACTTATGTT
19547020 ATTTTGTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.49
Consensus pattern (29 bp):
GTTACGTTTTAGTCACTTATGTTTGAAAT
Found at i:19547636 original size:16 final size:16
Alignment explanation
Indices: 19547599--19547640 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
19547589 TAAGGGTTTA
* *
19547599 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
19547615 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
19547629 AAATATTTATTT
1 AAATATTTATTT
19547641 TCATTGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:19550638 original size:5 final size:5
Alignment explanation
Indices: 19550618--19550654 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
19550608 TGTACAATAT
19550618 AATTA AA-T- AATATA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AAT-TA AATTA AATTA AATTA AATTA AAT
19550655 AATTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 1 0.03
5 23 0.79
6 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:19550650 original size:15 final size:15
Alignment explanation
Indices: 19550613--19550654 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19550603 CAAAATGTAC
19550613 AATAT-AATTAAA-T
1 AATATAAATTAAATT
19550626 AATATAAATTAAATT
1 AATATAAATTAAATT
19550641 AA-ATTAAATTAAAT
1 AATA-TAAATTAAAT
19550655 AATTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATTAAATT
Found at i:19553655 original size:41 final size:41
Alignment explanation
Indices: 19553605--19553758 Score: 204
Period size: 41 Copynumber: 3.8 Consensus size: 41
19553595 TTAACCATAT
*
19553605 TCTCATTCTCATCTT-GAGAGATGAGTCTTCCTTAATTAAAA
1 TCTCATTCTCAT-TTCGAGATATGAGTCTTCCTTAATTAAAA
* **
19553646 TCTCATTCTCATTTCGAGATATGAGTCTTTCTT-ATTCGTAA
1 TCTCATTCTCATTTCGAGATATGAGTCTTCCTTAATT-AAAA
* * * *
19553687 TCTTATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
1 TCTCATTCTCATTTCGAGATATGAGTCTTCCTTAATTAAAA
19553728 TCTCATTCTCATTTCGAGATATGAGTCTTCC
1 TCTCATTCTCATTTCGAGATATGAGTCTTCC
19553759 ATTTATACAA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 5 0.05
41 89 0.93
42 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (41 bp):
TCTCATTCTCATTTCGAGATATGAGTCTTCCTTAATTAAAA
Found at i:19553796 original size:43 final size:42
Alignment explanation
Indices: 19553586--19553804 Score: 135
Period size: 41 Copynumber: 5.3 Consensus size: 42
19553576 TCAAGTCATA
* * * * *
19553586 AGTCTTCCTTTA-ACCATATTCTCATTCTC-ATCTTGAGAGATG
1 AGTCTTCCTTTATA-CAAAATCTCATGCTCAATC-CGAGACATG
* * * * * *
19553628 AGTCTTCCTTAAT-TAAAATCTCATTCTCATTTCGAGATATG
1 AGTCTTCCTTTATACAAAATCTCATGCTCAATCCGAGACATG
* * ** * *
19553669 AGTCTTTC-TTATTCGTAATCTTATTCTC-ATCTCGAGACATG
1 AGTCTTCCTTTATACAAAATCTCATGCTCAATC-CGAGACATG
* * * * *
19553710 AGTCTTCCTTAAT-CAAAATCTCATTCTCATTTCGAGATATG
1 AGTCTTCCTTTATACAAAATCTCATGCTCAATCCGAGACATG
** *
19553751 AGTCTTCCATTTATACAATTTTTCATGCTCAATCCGAGACATG
1 AGTCTTCC-TTTATACAAAATCTCATGCTCAATCCGAGACATG
19553794 AGTCTTCCTTT
1 AGTCTTCCTTT
19553805 TTATACACCA
Statistics
Matches: 136, Mismatches: 33, Indels: 16
0.74 0.18 0.09
Matches are distributed among these distances:
40 4 0.03
41 80 0.59
42 23 0.17
43 29 0.21
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (42 bp):
AGTCTTCCTTTATACAAAATCTCATGCTCAATCCGAGACATG
Found at i:19559380 original size:28 final size:28
Alignment explanation
Indices: 19559355--19559416 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
19559345 ATTCAAATGT
*
19559355 TAAAAATCGTAAAAAAAATATAAAATATA
1 TAAAAAT-ATAAAAAAAATATAAAATATA
* * *
19559384 TAGAAATATAAAAAAATTATAAAACTTTA
1 TAAAAATATAAAAAAAATATAAAA-TATA
19559413 TAAA
1 TAAA
19559417 GTCATAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (28 bp):
TAAAAATATAAAAAAAATATAAAATATA
Found at i:19559760 original size:28 final size:28
Alignment explanation
Indices: 19559697--19559761 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
19559687 TACAATTTTT
19559697 TTATTTTTTACGATTTTTATAAAAAAAA
1 TTATTTTTTACGATTTTTATAAAAAAAA
* * *
19559725 TTAGTTTTTA-TATTTTTATTAAAATATAA
1 TTATTTTTTACGATTTTTA-TAAAA-AAAA
19559754 -TATTTTTT
1 TTATTTTTT
19559762 TCTAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 7 0.23
28 21 0.68
29 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTATTTTTTACGATTTTTATAAAAAAAA
Found at i:19559767 original size:20 final size:19
Alignment explanation
Indices: 19559734--19559781 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
19559724 ATTAGTTTTT
*
19559734 ATATTTTTATTAAAATATA
1 ATATTTTTTTTAAAATATA
*
19559753 ATATTTTTTTCTAAAATTTA
1 ATATTTTTTT-TAAAATATA
*
19559773 TTATTTTTT
1 ATATTTTTT
19559782 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTTTTTAAAATATA
Found at i:19559961 original size:87 final size:88
Alignment explanation
Indices: 19559809--19560074 Score: 319
Period size: 89 Copynumber: 3.0 Consensus size: 88
19559799 TTTTAATAAG
*
19559809 AGCAAGGGCTTAATTGCTTTTTTGAA-AAATTTTGAGGGAC-TTTTTGATGCATTTTGAAAGTTC
1 AGCAGGGGCTTAATTGCTTTTTTGAAGAAA-TTTGAGGG-CTTTTTTGATGCATTTTGAAAGTTC
*
19559872 AAGT-ATCCAATTGAGTGAAAAAAAA
64 AAGTGCT-CAATTGAGTGAAAAAAAA
* **
19559897 AGCAGGGGCTTAATTACTTTTTT-AAGAAATTTGAGGGCTTTTTTGATATATTTTGAAAGTTCAA
1 AGCAGGGGCTTAATTGCTTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAA
* *
19559961 GTGCTTAATTGAGTGCAAAAAAA
66 GTGCTCAATTGAGTGAAAAAAAA
* * *
19559984 AG--GGGGCTTAATTGCTTTTTTTTTGAAGAAGTTTGTGGGCTTTTTTGATGCATTTTGAAAATT
1 AGCAGGGGCTTAATTGC---TTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTT
* * *
19560047 CAAGTGCTTAATTAAGTGGAAAAAAA
63 CAAGTGCTCAATTGAGTGAAAAAAAA
19560073 AG
1 AG
19560075 GACTTAATTC
Statistics
Matches: 156, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
85 12 0.08
86 1 0.01
87 53 0.34
88 31 0.20
89 59 0.38
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.38
Consensus pattern (88 bp):
AGCAGGGGCTTAATTGCTTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAA
GTGCTCAATTGAGTGAAAAAAAA
Found at i:19560040 original size:89 final size:86
Alignment explanation
Indices: 19559814--19560105 Score: 328
Period size: 87 Copynumber: 3.4 Consensus size: 86
19559804 ATAAGAGCAA
19559814 GGGCTTAATTGCTTTTTTGAA-AAATTTTGAGGGAC-TTTTTGATGCATTTTGAAAGTTCAAGT-
1 GGGCTTAATTGCTTTTTTGAAGAAA-TTTGAGGG-CTTTTTTGATGCATTTTGAAAGTTCAAGTG
* *
19559876 ATCCAATTGAGTGAAAAAAAAAGCAG
64 CT-TAATTGAGTGAAAAAAAAAG--G
* **
19559902 GGGCTTAATTACTTTTTT-AAGAAATTTGAGGGCTTTTTTGATATATTTTGAAAGTTCAAGTGCT
1 GGGCTTAATTGCTTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGTGCT
*
19559966 TAATTGAGTGCAAAAAAAAGG
66 TAATTGAGTGAAAAAAAAAGG
* * *
19559987 GGGCTTAATTGCTTTTTTTTTGAAGAAGTTTGTGGGCTTTTTTGATGCATTTTGAAAATTCAAGT
1 GGGCTTAATTGC---TTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGT
* *
19560052 GCTTAATTAAGTGGAAAAAAAA--
63 GCTTAATTGAGTGAAAAAAAAAGG
* *
19560074 GGACTTAATTCCTTTTCTTGAA-AATATTTGAG
1 GGGCTTAATTGCTTTT-TTGAAGAA-ATTTGAG
19560106 AACTTTTTAC
Statistics
Matches: 177, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
84 6 0.03
85 22 0.12
86 1 0.01
87 63 0.36
88 27 0.15
89 58 0.33
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (86 bp):
GGGCTTAATTGCTTTTTTGAAGAAATTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAGTGCT
TAATTGAGTGAAAAAAAAAGG
Found at i:19561707 original size:21 final size:22
Alignment explanation
Indices: 19561678--19561718 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19561668 AGAAAATTTT
*
19561678 TATAATTTTA-ACTTTTTTATA
1 TATAATTTTATAATTTTTTATA
*
19561699 TATATTTTTATAATTTTTTA
1 TATAATTTTATAATTTTTTA
19561719 AAAAATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TATAATTTTATAATTTTTTATA
Found at i:19565764 original size:21 final size:19
Alignment explanation
Indices: 19565739--19565799 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 19
19565729 AAAAATATTT
19565739 ACATAAAAAATACACTTAAAA
1 ACATAAAAAA-ACA-TTAAAA
19565760 ACATAAAAACAAACATTAAAA
1 ACAT-AAAA-AAACATTAAAA
*
19565781 A-ATAAACAAACATTAAAA
1 ACATAAAAAAACATTAAAA
19565799 A
1 A
19565800 TTATTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 2 0.05
21 11 0.30
22 7 0.19
23 2 0.05
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.16
Consensus pattern (19 bp):
ACATAAAAAAACATTAAAA
Found at i:19575015 original size:10 final size:9
Alignment explanation
Indices: 19574985--19575018 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19574975 ACATCATTAT
19574985 TTTTTAAAA
1 TTTTTAAAA
*
19574994 ATTTTAAAA
1 TTTTTAAAA
19575003 TTTTTAAACA
1 TTTTTAAA-A
19575013 TTTTTA
1 TTTTTA
19575019 TATATTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:19594494 original size:16 final size:17
Alignment explanation
Indices: 19594475--19594507 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19594465 AAAATATTAA
*
19594475 ATTATTTAT-ATATTTT
1 ATTATATATAATATTTT
19594491 ATTATATATAATATTTT
1 ATTATATATAATATTTT
19594508 TAAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATATATAATATTTT
Found at i:19598392 original size:13 final size:13
Alignment explanation
Indices: 19598374--19598403 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19598364 ATTTAGTGAC
19598374 ATCACAAGTCAAT
1 ATCACAAGTCAAT
19598387 ATCACAAGTCAAT
1 ATCACAAGTCAAT
19598400 ATCA
1 ATCA
19598404 TGACATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (13 bp):
ATCACAAGTCAAT
Found at i:19607206 original size:25 final size:24
Alignment explanation
Indices: 19607164--19607215 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
19607154 TGCTAATATC
*
19607164 ATATAAATCATTACATAAGTATTAA
1 ATATAAATCATTACATAA-AATTAA
*
19607189 ATATAAATTAGTTA-ATAAAATTAA
1 ATATAAATCA-TTACATAAAATTAA
19607213 ATA
1 ATA
19607216 AATAACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 13 0.54
26 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
ATATAAATCATTACATAAAATTAA
Found at i:19608396 original size:47 final size:46
Alignment explanation
Indices: 19608345--19608438 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 46
19608335 TCACACTTCC
*
19608345 AATAAACTAGAATTTCCCTTGTAATCATTTTCTATCAAAAAAAATAT
1 AATAAACTAGAATTTCCCTTCTAATCATTTTCTATC-AAAAAAATAT
19608392 AATAAACTAGAATTTCCCTTCTAATCATTTTCTATCAAAAAAATAT
1 AATAAACTAGAATTTCCCTTCTAATCATTTTCTATCAAAAAAATAT
19608438 A
1 A
19608439 CATATTTCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 11 0.24
47 35 0.76
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (46 bp):
AATAAACTAGAATTTCCCTTCTAATCATTTTCTATCAAAAAAATAT
Found at i:19608730 original size:3 final size:3
Alignment explanation
Indices: 19608722--19608762 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
19608712 TTTTATTTAT
19608722 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19608763 TTATATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19609919 original size:11 final size:11
Alignment explanation
Indices: 19609900--19609932 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19609890 TTAGGATATT
19609900 ATTTATATTTA
1 ATTTATATTTA
*
19609911 ATTTGTATTTA
1 ATTTATATTTA
19609922 ATTTATATTTA
1 ATTTATATTTA
19609933 TCTTTTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:19611030 original size:21 final size:21
Alignment explanation
Indices: 19610978--19611030 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
19610968 ACCTACAAAA
* * *
19610978 CATTTTGTTTGTAACTCTCCT
1 CATTATGTTTGCAACTCTCAT
*
19610999 CA-TAAGTTTTGCAACTCTCAT
1 CATTATG-TTTGCAACTCTCAT
19611020 CATTATGTTTG
1 CATTATGTTTG
19611031 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (21 bp):
CATTATGTTTGCAACTCTCAT
Found at i:19619533 original size:2 final size:2
Alignment explanation
Indices: 19619526--19619559 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19619516 ATAGGTAAAC
19619526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19619560 TCAAGTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19620069 original size:5 final size:5
Alignment explanation
Indices: 19620059--19620084 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19620049 AGAAGGTCCA
19620059 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
19620085 TATAGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:19621961 original size:20 final size:20
Alignment explanation
Indices: 19621897--19621964 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
19621887 CTGGTGGCAT
* *
19621897 GGTATTGATACTTTGAGGAA
1 GGTATAGATACTTTGAGTAA
* *
19621917 TGTATTGATACTTTG-GATAA
1 GGTATAGATACTTTGAG-TAA
*
19621937 AGTATAGATACTTTGAGTAA
1 GGTATAGATACTTTGAGTAA
19621957 GGTATAGA
1 GGTATAGA
19621965 AATCTTAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (20 bp):
GGTATAGATACTTTGAGTAA
Found at i:19628893 original size:24 final size:24
Alignment explanation
Indices: 19628866--19628924 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
19628856 TTTAGCCCAC
19628866 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
19628890 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
19628914 ACGAGCTCAGA
1 ACGAGCCCAGA
19628925 CAGAGTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:19629080 original size:82 final size:82
Alignment explanation
Indices: 19628943--19629160 Score: 354
Period size: 82 Copynumber: 2.7 Consensus size: 82
19628933 AACTAATATA
19628943 CGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAGACTCAGCCATCGATACGGT
1 CGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAGACTCAGCCATCGATACGGT
19629008 CCAAAATTTCTCACTCT
66 CCAAAATTTCTCACTCT
* * * *
19629025 CGATGCTGCTCACATAAGCTGATGAGAATCTGCAACATATGTGAAGACTCAGCCATCGATACGGT
1 CGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAGACTCAGCCATCGATACGGT
19629090 CCAAAATTTCTCACTCT
66 CCAAAATTTCTCACTCT
* *
19629107 CGATGCTACTCACACAAGCTGAT--G-A-CCGCAATAAATGCGAAGACTCAGCCATCG
1 CGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAGACTCAGCCATCG
19629161 GAGGAATCCA
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
78 25 0.20
79 1 0.01
80 1 0.01
82 99 0.79
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (82 bp):
CGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAGACTCAGCCATCGATACGGT
CCAAAATTTCTCACTCT
Found at i:19634702 original size:42 final size:42
Alignment explanation
Indices: 19634593--19634782 Score: 240
Period size: 42 Copynumber: 4.5 Consensus size: 42
19634583 TGATGTATAA
* * * * *
19634593 AAAGGAAGACTCATGTCTCGGGTTAAGCATGAGGATT-TG-TAT
1 AAAGGAAGACTCATGACTCGAGATGAGAATGA-GATTATGAT-T
*
19634635 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAA-GGAAGACTCATGACTCGAGATGAGAATGAGATTATGATT
* *
19634678 AAAGGAAGACTCATGACTCAAGATGAGAATGAGATTATCATT
1 AAAGGAAGACTCATGACTCGAGATGAGAATGAGATTATGATT
* *
19634720 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGACTCGAGATGAGAATGAGATTATGATT
*
19634762 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGACTCGA
19634783 TAGAGTATAA
Statistics
Matches: 132, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 100 0.76
43 31 0.23
44 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (42 bp):
AAAGGAAGACTCATGACTCGAGATGAGAATGAGATTATGATT
Found at i:19658264 original size:50 final size:50
Alignment explanation
Indices: 19658201--19658429 Score: 307
Period size: 50 Copynumber: 4.6 Consensus size: 50
19658191 AACTAATACC
* * *
19658201 CGTTTACGCTCGTCAGCTTACTTATGCATTTACGCTCGCCAGCTTGTACA
1 CGTTTACGCTCGTCAGCTTATTTATGCATTTACGCTCGCCAACTTGCACA
** *
19658251 CGTTTACATTCGTCAACTTATTTATG-AGTTTACGCTCGCCAACTTGCACA
1 CGTTTACGCTCGTCAGCTTATTTATGCA-TTTACGCTCGCCAACTTGCACA
* * *
19658301 TGTCTACGCTCGTCAGCTTATTTATGCGTTTACGCTCGCCAACTTGCACA
1 CGTTTACGCTCGTCAGCTTATTTATGCATTTACGCTCGCCAACTTGCACA
* * * * * *
19658351 CGTTTACGCTCATCAGCTTATTTATACGTTTATGCTAGTCAACTTGCACA
1 CGTTTACGCTCGTCAGCTTATTTATGCATTTACGCTCGCCAACTTGCACA
19658401 CGTTTACGCTCGTCAGCTTATTTATGCAT
1 CGTTTACGCTCGTCAGCTTATTTATGCAT
19658430 ATATTATAAT
Statistics
Matches: 155, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 154 0.99
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (50 bp):
CGTTTACGCTCGTCAGCTTATTTATGCATTTACGCTCGCCAACTTGCACA
Found at i:19658293 original size:26 final size:25
Alignment explanation
Indices: 19658202--19658345 Score: 76
Period size: 26 Copynumber: 5.7 Consensus size: 25
19658192 ACTAATACCC
* * *
19658202 GTTTACGCTCGTCAGCTTACTTATG
1 GTTTACGCTCGCCAACTTATTTATG
* * * ** *
19658227 CATTTACGCTCGCCAGCTTGTACA-C
1 -GTTTACGCTCGCCAACTTATTTATG
** *
19658252 GTTTACATTCGTCAACTTATTTATG
1 GTTTACGCTCGCCAACTTATTTATG
****
19658277 AGTTTACGCTCGCCAACTTGCACAT-
1 -GTTTACGCTCGCCAACTTATTTATG
* * *
19658302 GTCTACGCTCGTCAGCTTATTTATG
1 GTTTACGCTCGCCAACTTATTTATG
19658327 CGTTTACGCTCGCCAACTT
1 -GTTTACGCTCGCCAACTT
19658346 GCACACGTTT
Statistics
Matches: 81, Mismatches: 33, Indels: 8
0.66 0.27 0.07
Matches are distributed among these distances:
24 32 0.40
26 49 0.60
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (25 bp):
GTTTACGCTCGCCAACTTATTTATG
Found at i:19658358 original size:24 final size:24
Alignment explanation
Indices: 19658278--19658415 Score: 96
Period size: 24 Copynumber: 5.6 Consensus size: 24
19658268 TTATTTATGA
* *
19658278 GTTTACGCTCGCCAACTTGCACAT
1 GTTTACGCTCGTCAACTTGCACAC
* * ** **
19658302 GTCTACGCTCGTCAGCTTATTTATGC
1 GTTTACGCTCGTCAAC-T-TGCACAC
*
19658328 GTTTACGCTCGCCAACTTGCACAC
1 GTTTACGCTCGTCAACTTGCACAC
* * ** *
19658352 GTTTACGCTCATCAGCTTATTTATAC
1 GTTTACGCTCGTCAAC-T-TGCACAC
* *
19658378 GTTTATGCTAGTCAACTTGCACAC
1 GTTTACGCTCGTCAACTTGCACAC
19658402 GTTTACGCTCGTCA
1 GTTTACGCTCGTCA
19658416 GCTTATTTAT
Statistics
Matches: 80, Mismatches: 30, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
24 45 0.56
25 4 0.05
26 31 0.39
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (24 bp):
GTTTACGCTCGTCAACTTGCACAC
Found at i:19662631 original size:10 final size:10
Alignment explanation
Indices: 19662616--19662640 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19662606 TCTTTCTCTT
19662616 ATATTTTATA
1 ATATTTTATA
19662626 ATATTTTATA
1 ATATTTTATA
19662636 ATATT
1 ATATT
19662641 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTTATA
Found at i:19662689 original size:21 final size:20
Alignment explanation
Indices: 19662646--19662689 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19662636 ATATTAAATA
* *
19662646 ATAAAATATTATCATTTATT
1 ATAAAATATTATCAATTAAT
*
19662666 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATCAATTAAT
19662687 ATA
1 ATA
19662690 TCTTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATATTATCAATTAAT
Found at i:19669726 original size:10 final size:10
Alignment explanation
Indices: 19669711--19669735 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19669701 TCTTTCTCTT
19669711 ATATTTTATA
1 ATATTTTATA
19669721 ATATTTTATA
1 ATATTTTATA
19669731 ATATT
1 ATATT
19669736 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTTATA
Found at i:19669766 original size:18 final size:18
Alignment explanation
Indices: 19669745--19669779 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19669735 TAAATAATAA
* *
19669745 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
19669763 AATAATATTATTAATTA
1 AATAATATTATTAATTA
19669780 ATATATCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:19669769 original size:21 final size:20
Alignment explanation
Indices: 19669741--19669784 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
19669731 ATATTAAATA
* *
19669741 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
19669761 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
19669782 ATA
1 ATA
19669785 TCTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:19671314 original size:20 final size:20
Alignment explanation
Indices: 19671270--19671321 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
19671260 AATGATTATT
*
19671270 TTTTAAATATTTAAAATATAA
1 TTTTATATA-TTAAAATATAA
19671291 -TTTATATATTAAAAT-TAAA
1 TTTTATATATTAAAATAT-AA
*
19671310 TTTTATAAATTA
1 TTTTATATATTA
19671322 TTAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 17 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTATATATTAAAATATAA
Found at i:19679026 original size:17 final size:18
Alignment explanation
Indices: 19678995--19679028 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19678985 CATTTAACTT
19678995 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
19679013 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
19679029 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:19679266 original size:20 final size:21
Alignment explanation
Indices: 19679243--19679291 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
19679233 TTAAAGGTTC
19679243 GGGTTTAATG-TTTAGGTTTA
1 GGGTTTAATGATTTAGGTTTA
19679263 GGGTTTAATGATTTAGGTTTA
1 GGGTTTAATGATTTAGGTTTA
19679284 GGGTTTAA
1 GGGTTTAA
19679292 GGGTTTGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (21 bp):
GGGTTTAATGATTTAGGTTTA
Found at i:19680749 original size:13 final size:13
Alignment explanation
Indices: 19680731--19680755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19680721 TTAAGGGTCG
19680731 TAAATATTTTTAT
1 TAAATATTTTTAT
19680744 TAAATATTTTTA
1 TAAATATTTTTA
19680756 GAGTCTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:19682424 original size:60 final size:60
Alignment explanation
Indices: 19682323--19682721 Score: 510
Period size: 60 Copynumber: 6.6 Consensus size: 60
19682313 GGAAATGCAA
** *
19682323 AAAGGTCTAATGACTTTGTGTCATCGTGAGTATTACATGCAATGAATCCAATTACGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
* * * *
19682383 AAAGCTCCAATGACTTTGTGTCATCATGAATATTAAATGCAATGAATCCAATTACGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
* * *
19682443 AAAGGTCTGATGACTTTGTGTCATCGTGAGTATTAAATGTAATGAATCAAATTACGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
* * * *
19682503 AAAGGTCCGATGACTTTGTGTTATTGTGAGTATTAAATGCGATGAATCCAATCACGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
* * * *
19682563 AAGGGTCTGATGACTTTGTGTCATCGTGAGTATTAAATGCGATGAATCTAATTACGGATTT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGA-TT
* * * * * * *
19682624 AAGGGTCTGATGACTTTGTGTCCTCGTGAGTTTTAAATGAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
* * * * * *
19682684 ATAGGTGCAATGACTCTCTGTCATCGTGAGTATCAAAT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAAT
19682722 ATGAATTGAA
Statistics
Matches: 296, Mismatches: 42, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
60 243 0.82
61 53 0.18
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (60 bp):
AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGCAATGAATCCAATTACGGATT
Found at i:19683325 original size:16 final size:16
Alignment explanation
Indices: 19683303--19683341 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
19683293 TTTTGGTTCG
19683303 CTATAATGGAATAGAGA
1 CTATAATGGAATAG-GA
19683320 -TATAATGGAATAGGA
1 CTATAATGGAATAGGA
19683335 CTATAAT
1 CTATAAT
19683342 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (16 bp):
CTATAATGGAATAGGA
Found at i:19683579 original size:58 final size:58
Alignment explanation
Indices: 19683513--19683662 Score: 164
Period size: 57 Copynumber: 2.6 Consensus size: 58
19683503 TTTTAATAAG
*
19683513 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAAT-TATATTTTAACAT-
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAAT-TTTTAACATA
* ** * *
19683570 ATTGATTATTAAATACAATTTAAT-GTAATAATATATAATTTAATAAATTTTTAATATA
1 ATT-ATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAATTTTTAACATA
* *
19683628 ATTATTATTAAAATATGAA-TTAGTAAAAATCATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
19683663 TATATAATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
57 34 0.45
58 33 0.44
59 8 0.11
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAAATTTTTAACATA
Found at i:19683635 original size:57 final size:58
Alignment explanation
Indices: 19683499--19683639 Score: 166
Period size: 57 Copynumber: 2.5 Consensus size: 58
19683489 TTATTATTAT
*
19683499 TAAA-TTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAA
1 TAAATTTTTAATATA-ATTATTATTAAATACAATTTAATAAAAATAATAAATAATTTAA
* * ** *
19683556 T-TATATTTTAACAT-ATTGATTATTAAATACAATTTAAT-GTAATAATATATAATTTAA
1 TAAAT-TTTTAATATAATT-ATTATTAAATACAATTTAATAAAAATAATAAATAATTTAA
19683613 TAAATTTTTAATATAATTATTATTAAA
1 TAAATTTTTAATATAATTATTATTAAA
19683640 ATATGAATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
56 1 0.01
57 38 0.54
58 31 0.44
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (58 bp):
TAAATTTTTAATATAATTATTATTAAATACAATTTAATAAAAATAATAAATAATTTAA
Found at i:19698430 original size:16 final size:16
Alignment explanation
Indices: 19698409--19698458 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
19698399 TTGTTAATTT
19698409 AAAGGGTTTGGGTTTA
1 AAAGGGTTTGGGTTTA
* * *
19698425 AAAGGGTTGTTGGATCA
1 AAAGGGTT-TGGGTTTA
*
19698442 AAAAGGTTTGGGTTTA
1 AAAGGGTTTGGGTTTA
19698458 A
1 A
19698459 TATTGGGTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (16 bp):
AAAGGGTTTGGGTTTA
Found at i:19704637 original size:14 final size:15
Alignment explanation
Indices: 19704618--19704648 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19704608 ATGTATTTTT
19704618 TTATTT-ACTTTTAG
1 TTATTTCACTTTTAG
19704632 TTATTTCACTTTTAG
1 TTATTTCACTTTTAG
19704647 TT
1 TT
19704649 GTGTTGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTATTTCACTTTTAG
Found at i:19713712 original size:41 final size:41
Alignment explanation
Indices: 19713659--19713862 Score: 232
Period size: 41 Copynumber: 5.0 Consensus size: 41
19713649 CTTTTCCCAT
* * * *
19713659 AAACGCTGCAAAAGGTAA-AGAAATAACGGCGTTTATGGGAA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGG-A
* * * *
19713700 AAACGTCGCAAAAGGT-AGAGTATTAGCGGCGTTTACGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
** * * *
19713740 AAACTTCGCAAAAGCTAAGAGCATTAGTGGTGTTTATGGGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
* *
19713781 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGCTTATGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
**
19713822 AAACGCCGTGAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
19713863 GAAATACCAC
Statistics
Matches: 136, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
40 16 0.12
41 120 0.88
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGGGA
Found at i:19713885 original size:82 final size:80
Alignment explanation
Indices: 19713659--19713893 Score: 222
Period size: 82 Copynumber: 2.9 Consensus size: 80
19713649 CTTTTCCCAT
* * * * * *
19713659 AAACGCTGCAAAAGGTAA-AGAAATAACGGCGTTTATGGGAAAAACGTCGCAAAAGGTAGAGTAT
1 AAACGCCGCAAAAGCTAAGAGCATTAGCGGCGTTTATGGGAAAAAC--CGCAAAAGGTAGAGCAT
*
19713723 TAGCGGCGTTTACGAGA
64 TAGCGGCGCTTACGAGA
** * * *
19713740 AAACTTCGCAAAAGCTAAGAGCATTAGTGGTGTTTATGGGAAAACGCCGCAAAAGGTAAGAGCAT
1 AAACGCCGCAAAAGCTAAGAGCATTAGCGGCGTTTATGGGAAAA-ACCGCAAAAGGT-AGAGCAT
*
19713805 TAGCGGCGCTTATGAGA
64 TAGCGGCGCTTACGAGA
** * * * *
19713822 AAACGCCGTGAAAGGTAAGAGCATTAGCGGCGTTTATGGGAGAAATACCACTAAAGGTTGAGCAA
1 AAACGCCGCAAAAGCTAAGAGCATTAGCGGCGTTTATGGGA-AAA-ACCGCAAAAGGTAGAGC-A
19713887 TT-GCGGC
63 TTAGCGGC
19713894 ATTTTCCCAT
Statistics
Matches: 124, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
81 24 0.19
82 84 0.68
83 16 0.13
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (80 bp):
AAACGCCGCAAAAGCTAAGAGCATTAGCGGCGTTTATGGGAAAAACCGCAAAAGGTAGAGCATTA
GCGGCGCTTACGAGA
Found at i:19715471 original size:43 final size:43
Alignment explanation
Indices: 19715410--19715551 Score: 141
Period size: 42 Copynumber: 3.4 Consensus size: 43
19715400 TTAGAGGTCA
*
19715410 AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAAAGG-AATAT
1 AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAAAGGTAA-AG
* * **
19715453 AGCAATAGCGGCATTTATGAG-AAAACGCCAAAAAAGGTAAAG
1 AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAAAGGTAAAG
* * * * *
19715495 AGCATTAGCGACGTTTATAGAAAAAACGCCGCTAAAA-GT-CA-
1 AGCAATAGCGGCGTTTATGGGAAAAACGCCGC-AAAAGGTAAAG
19715536 AGCAATAGCGGCGTTT
1 AGCAATAGCGGCGTTT
19715552 TTCCATAAAC
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
41 14 0.17
42 31 0.39
43 31 0.39
44 4 0.05
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.18
Consensus pattern (43 bp):
AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAAAGGTAAAG
Found at i:19715504 original size:42 final size:42
Alignment explanation
Indices: 19715410--19715524 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
19715400 TTAGAGGTCA
* ** *
19715410 AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAAAGGAATAT
1 AGCAATAGCGGCGTTTATGAG-AAAACGCCAAAAAAGGAATAG
*
19715453 AGCAATAGCGGCATTTATGAGAAAACGCCAAAAAAGGTAA-AG
1 AGCAATAGCGGCGTTTATGAGAAAACGCCAAAAAAGG-AATAG
* * *
19715495 AGCATTAGCGACGTTTATAGAAAAAACGCC
1 AGCAATAGCGGCGTTTAT-GAGAAAACGCC
19715525 GCTAAAAGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 30 0.49
43 31 0.51
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
AGCAATAGCGGCGTTTATGAGAAAACGCCAAAAAAGGAATAG
Found at i:19723665 original size:42 final size:42
Alignment explanation
Indices: 19723618--19723723 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 42
19723608 TCAAAAAGAT
*
19723618 TATTTAATTATTTAAATATTTAATAATTAAAAATAACTCAAA
1 TATTTAATTATTTAAATATTTAATAATTAAAAACAACTCAAA
* * * *
19723660 TATTTAATTATTTAATTAGTGAATTATTAAAAACAACTCAAA
1 TATTTAATTATTTAAATATTTAATAATTAAAAACAACTCAAA
**
19723702 TATTT-ATT-TCAAAATATTTAAT
1 TATTTAATTATTTAAATATTTAAT
19723724 TATTTAATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 9 0.17
41 3 0.06
42 42 0.78
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (42 bp):
TATTTAATTATTTAAATATTTAATAATTAAAAACAACTCAAA
Found at i:19723728 original size:18 final size:18
Alignment explanation
Indices: 19723705--19723743 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19723695 ACTCAAATAT
19723705 TTATTTCAA-AATATTTAA
1 TTATTT-AATAATATTTAA
*
19723723 TTATTTAATTATATTTAA
1 TTATTTAATAATATTTAA
19723741 TTA
1 TTA
19723744 AAGATGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTTAATAATATTTAA
Found at i:19723802 original size:48 final size:48
Alignment explanation
Indices: 19723750--19723906 Score: 129
Period size: 48 Copynumber: 3.1 Consensus size: 48
19723740 ATTAAAGATG
*
19723750 TAATTATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATT
1 TAATTATTAAAAACAACTCAAATATTTATACCAAAATATTTAATTATT
* ** * * * *
19723798 TAATTATATTTAATTAAA-TA-TTTAATAATTAAAAAACCTAAATATTTAATTAGT
1 TAA-T-TA-TTAA--AAACAACTCAAAT-ATT--TATACCAAAATATTTAATTATT
* **
19723852 TAATTATTAAAAACAACCCAAATATTTATTTCAAAATATTTAATTATT
1 TAATTATTAAAAACAACTCAAATATTTATACCAAAATATTTAATTATT
19723900 TAATTAT
1 TAATTAT
19723907 ATTCAATTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
48 26 0.32
49 4 0.05
50 6 0.07
51 15 0.19
52 6 0.07
53 4 0.05
54 20 0.25
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (48 bp):
TAATTATTAAAAACAACTCAAATATTTATACCAAAATATTTAATTATT
Found at i:19723829 original size:70 final size:70
Alignment explanation
Indices: 19723685--19723845 Score: 254
Period size: 70 Copynumber: 2.3 Consensus size: 70
19723675 TTAGTGAATT
**
19723685 ATTAAAAACAACTCAAATATTTATTTCAAAATATTTAATTATTTAATTATATTTAATTAAAGATG
1 ATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTTAATTAAAGATG
*
19723750 TAATT
66 TAATA
* *
19723755 ATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTTAATTAAATATT
1 ATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTTAATTAAAGATG
19723820 TAATA
66 TAATA
*
19723825 ATTAAAAA-ACCT-AAATATTTA
1 ATTAAAAACAACTCAAATATTTA
19723846 ATTAGTTAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
68 9 0.11
69 3 0.04
70 73 0.86
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (70 bp):
ATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTTAATTAAAGATG
TAATA
Found at i:19723856 original size:102 final size:104
Alignment explanation
Indices: 19723750--19723958 Score: 323
Period size: 102 Copynumber: 2.0 Consensus size: 104
19723740 ATTAAAGATG
* *
19723750 TAATTATTAAAAACAACTCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTTAATTAA
1 TAATTATTAAAAACAACCCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTCAATTAA
* * *
19723815 ATATTTAATAATT-AAAA-AACCTAAATATTTAATTAGT
66 AAATTTAATAATTAAAAACAACCCAAATAATTAATTAGT
**
19723852 TAATTATTAAAAACAACCCAAATATTTATTTCAAAATATTTAATTATTTAATTATATTCAATTAA
1 TAATTATTAAAAACAACCCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTCAATTAA
* *
19723917 AAATTTAATTATTAAAAACAACCCAAATAATTAATTATT
66 AAATTTAATAATTAAAAACAACCCAAATAATTAATTAGT
19723956 TAA
1 TAA
19723959 ATCTAAACAT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 72 0.75
103 4 0.04
104 20 0.21
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (104 bp):
TAATTATTAAAAACAACCCAAATATTTATGCCAAAATATTTAATTATTTAATTATATTCAATTAA
AAATTTAATAATTAAAAACAACCCAAATAATTAATTAGT
Found at i:19724093 original size:26 final size:26
Alignment explanation
Indices: 19724026--19724094 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
19724016 CAAATATTAG
* *
19724026 TCAAATTTTTAATTAGTAAAAACAAC
1 TCAAATATTTAATTATTAAAAACAAC
*
19724052 CCAAATATTTAATTATTAAAAACAAC
1 TCAAATATTTAATTATTAAAAACAAC
19724078 TCAAATATTTAATTATT
1 TCAAATATTTAATTATT
19724095 TAATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (26 bp):
TCAAATATTTAATTATTAAAAACAAC
Found at i:19729818 original size:66 final size:66
Alignment explanation
Indices: 19729746--19729870 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
19729736 CTTAAAGAGG
* **
19729746 AGGCAGCAGCAAGAGAAGCAGAGACTCAAAGAAAATATGATGAACTTTAGCTACAACTTGAAGCC
1 AGGCAGCAGCAAGAGAAGCAGAGACTCAAAGAAAATATGACGAACTGCAGCTACAACTTGAAGCC
19729811 A
66 A
* * * *
19729812 AGGCAGCAGCGAGGGAAGCAGAGTCTCAAAGAAAGTATGACGAACTGCAGCTACAACTT
1 AGGCAGCAGCAAGAGAAGCAGAGACTCAAAGAAAATATGACGAACTGCAGCTACAACTT
19729871 CAAAATATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (66 bp):
AGGCAGCAGCAAGAGAAGCAGAGACTCAAAGAAAATATGACGAACTGCAGCTACAACTTGAAGCC
A
Found at i:19730225 original size:43 final size:43
Alignment explanation
Indices: 19730178--19730383 Score: 259
Period size: 43 Copynumber: 4.8 Consensus size: 43
19730168 TATCATGTCT
* * *
19730178 TTTAGCGGCATTTGTGGGATAAGCGCCGTTAAAGACCATATTC
1 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
** *
19730221 TTTAGCGGCATTTGTATGAAAAGCGCTGCTAAAGACCATGTTC
1 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * *
19730264 TTTAGTGGCATTTGTGGAAAAAGCGCCGCTAAAAACCATGTTC
1 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
19730307 TTTAGCGACGTTTGTGGGAAAAGCGCCACTAAAGGCCATGTTC
1 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
19730350 TTTAGCGGCGTTTTTGGGAAAAGCACTGCTAAAG
1 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAG
19730384 CGGCGTTTGT
Statistics
Matches: 139, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 139 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:19731006 original size:61 final size:59
Alignment explanation
Indices: 19730868--19731025 Score: 169
Period size: 61 Copynumber: 2.6 Consensus size: 59
19730858 TAGAATATTA
* * *
19730868 TATATTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAAT
1 TATA-TATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAGAATATGATTAAAT
* *
19730929 TATATATTA-TTTTATTAAATTTTATTTAATAATAATTATGTTAA-AATATGATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAT
* * *
19730986 TATTTATTTTTATTTTTATTAAAATATATTTGATAATAAT
1 TA--TA-TATTATTTTTATTAAATTATATTTAATAATAAT
19731026 CTTTTTAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
57 13 0.16
58 19 0.23
59 11 0.13
60 12 0.14
61 28 0.34
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (59 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAT
Found at i:19731234 original size:16 final size:16
Alignment explanation
Indices: 19731215--19731262 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
19731205 CTGATTACTC
19731215 CTCTATTCCATTACAA
1 CTCTATTCCATTACAA
* *
19731231 CTCTATTTCATTACAT
1 CTCTATTCCATTACAA
19731247 CTCTATTCCATTACAA
1 CTCTATTCCATTACAA
19731263 TGAACCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (16 bp):
CTCTATTCCATTACAA
Found at i:19738065 original size:86 final size:86
Alignment explanation
Indices: 19737954--19738145 Score: 210
Period size: 86 Copynumber: 2.2 Consensus size: 86
19737944 GACAATATTC
* * * * ** *
19737954 ATATATGTGTGCTCAACACTAGTTGGTTAAACCAACAATATAAATA-AGTGTGTGCCCAGCAAT-
1 ATATATGTGTGCCCAGCACTAGTTGGCTAAACCAAAAATATAAATATA-TAAGTGCCCAACAATG
*
19738017 GATCGGTTA-ACTCGATAATATAA
65 GAT-GGTTAGACT-AATAATATAA
* * * * *
19738040 ATATATGTGTGCCCAGCATTGGTTGGCTAACCCAAAAATATACATATATAAGTGCCCAACATTGG
1 ATATATGTGTGCCCAGCACTAGTTGGCTAAACCAAAAATATAAATATATAAGTGCCCAACAATGG
19738105 ATGGTTAGACTAATAATATAA
66 ATGGTTAGACTAATAATATAA
*
19738126 ATATATATGTGCCCAGCACT
1 ATATATGTGTGCCCAGCACT
19738146 GATCGATTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
86 81 0.92
87 7 0.08
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (86 bp):
ATATATGTGTGCCCAGCACTAGTTGGCTAAACCAAAAATATAAATATATAAGTGCCCAACAATGG
ATGGTTAGACTAATAATATAA
Found at i:19738080 original size:43 final size:43
Alignment explanation
Indices: 19737917--19738143 Score: 170
Period size: 43 Copynumber: 5.3 Consensus size: 43
19737907 CAACATTAGA
* * * * * **
19737917 TGTGCCCCGCATTGGTCGGATTAAACCGACAATATTCATATATG
1 TGTGCCCAGCATTGGTTGG-TTAACCCAATAATATAAATATATG
* * * * * *
19737961 TGTGCTCAACACTAGTTGGTTAAACCAACAATATAAATA-AGTG
1 TGTGCCCAGCATTGGTTGGTTAACCCAATAATATAAATATA-TG
* * * * *
19738004 TGTGCCCAGCAATGATCGGTTAACTCGATAATATAAATATATG
1 TGTGCCCAGCATTGGTTGGTTAACCCAATAATATAAATATATG
* * * *
19738047 TGTGCCCAGCATTGGTTGGCTAACCCAAAAATATACATATATA
1 TGTGCCCAGCATTGGTTGGTTAACCCAATAATATAAATATATG
* * * * *
19738090 AGTGCCCAACATTGGATGGTTAGA-CTAATAATATAAATATATA
1 TGTGCCCAGCATTGGTTGGTTA-ACCCAATAATATAAATATATG
19738133 TGTGCCCAGCA
1 TGTGCCCAGCA
19738144 CTGATCGATT
Statistics
Matches: 143, Mismatches: 37, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
42 1 0.01
43 127 0.89
44 15 0.10
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (43 bp):
TGTGCCCAGCATTGGTTGGTTAACCCAATAATATAAATATATG
Found at i:19741918 original size:20 final size:19
Alignment explanation
Indices: 19741882--19742008 Score: 62
Period size: 20 Copynumber: 7.1 Consensus size: 19
19741872 ACACATATTG
* *
19741882 ATCACATTTGATTACATATA
1 ATCACATTTAATCACAT-TA
19741902 ATCACATTTAATCACATTA
1 ATCACATTTAATCACATTA
* *
19741921 GTCACA-TGAAT---ATT-
1 ATCACATTTAATCACATTA
19741935 -TCAACATTT-ATCAC----
1 ATC-ACATTTAATCACATTA
19741949 ATCACATATTAATCACATTTA
1 ATCACAT-TTAATCACA-TTA
* *
19741970 GTCATATTTAATCACATTA
1 ATCACATTTAATCACATTA
* *
19741989 GTCACA-TGAATCACATTA
1 ATCACATTTAATCACATTA
19742007 AT
1 AT
19742009 ATTTAAGCAT
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
13 2 0.02
14 9 0.11
15 8 0.10
16 5 0.06
18 16 0.19
19 15 0.18
20 24 0.29
21 5 0.06
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (19 bp):
ATCACATTTAATCACATTA
Found at i:19741919 original size:10 final size:10
Alignment explanation
Indices: 19741882--19742005 Score: 56
Period size: 10 Copynumber: 11.8 Consensus size: 10
19741872 ACACATATTG
*
19741882 ATCACATTTG
1 ATCACATTTA
* *
19741892 ATTACATATA
1 ATCACATTTA
19741902 ATCACATTTA
1 ATCACATTTA
19741912 ATCACA-TTA
1 ATCACATTTA
* *
19741921 GTCACATGAATA
1 ATCACAT--TTA
*
19741933 TTTCAACATTTATCA
1 -ATC-ACA-TT-T-A
19741948 CATCACATATTA
1 -ATCACAT-TTA
19741960 ATCACATTTA
1 ATCACATTTA
* *
19741970 GTCATATTTA
1 ATCACATTTA
19741980 ATCACA-TTA
1 ATCACATTTA
* *
19741989 GTCACA-TGA
1 ATCACATTTA
19741998 ATCACATT
1 ATCACATT
19742006 AATATTTAAG
Statistics
Matches: 86, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
9 23 0.27
10 37 0.43
11 7 0.08
12 3 0.03
13 4 0.05
14 8 0.09
15 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (10 bp):
ATCACATTTA
Found at i:19741927 original size:9 final size:9
Alignment explanation
Indices: 19741895--19742008 Score: 53
Period size: 9 Copynumber: 12.9 Consensus size: 9
19741885 ACATTTGATT
19741895 ACATATAATC
1 ACAT-TAATC
19741905 ACATTTAATC
1 ACA-TTAATC
*
19741915 ACATTAGTC
1 ACATTAATC
*
19741924 ACATGAAT-
1 ACATTAATC
19741932 --ATT--TC
1 ACATTAATC
*
19741937 AACATTTATC
1 -ACATTAATC
*
19741947 ACA-TCA-C
1 ACATTAATC
*
19741954 ATATTAATC
1 ACATTAATC
*
19741963 ACATTTAGTC
1 ACA-TTAATC
*
19741973 ATATTTAATC
1 ACA-TTAATC
*
19741983 ACATTAGTC
1 ACATTAATC
*
19741992 ACATGAATC
1 ACATTAATC
19742001 ACATTAAT
1 ACATTAAT
19742009 ATTTAAGCAT
Statistics
Matches: 78, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
4 1 0.01
6 2 0.03
7 3 0.04
8 7 0.09
9 36 0.46
10 28 0.36
11 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (9 bp):
ACATTAATC
Found at i:19741964 original size:78 final size:76
Alignment explanation
Indices: 19741828--19742018 Score: 215
Period size: 78 Copynumber: 2.5 Consensus size: 76
19741818 ATTCTTTTAA
** * * *
19741828 ACATTAATTGCATTAATCACATGAGTACTTAAGCATTTAACACAACACATATTGATCACATTTGA
1 ACATTAATCACATTAATCACATGAATATTTAAGCATTTAACACAACACATATTAATCACATTT-A
*
19741893 TTACATA-TAATC
65 GT-CATATTAATC
* * *
19741905 ACATTTAATCACATTAGTCACATGAATATTTCAA-CATTTATCACATCACATATTAATCACATTT
1 ACA-TTAATCACATTAATCACATGAATATTT-AAGCATTTAACACAACACATATTAATCACATTT
19741969 AGTCATATTTAATC
64 AGTCATA-TTAATC
* * *
19741983 ACATTAGTCACATGAATCACATTAATATTTAAGCAT
1 ACATTAATCACATTAATCACATGAATATTTAAGCAT
19742019 AAATCACATT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
76 6 0.06
77 31 0.32
78 57 0.59
79 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (76 bp):
ACATTAATCACATTAATCACATGAATATTTAAGCATTTAACACAACACATATTAATCACATTTAG
TCATATTAATC
Found at i:19742002 original size:18 final size:19
Alignment explanation
Indices: 19741959--19742006 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
19741949 ATCACATATT
* *
19741959 AATCACATTTAGTCATATTT
1 AATCACA-TTAGTCACATTG
19741979 AATCACATTAGTCACA-TG
1 AATCACATTAGTCACATTG
19741997 AATCACATTA
1 AATCACATTA
19742007 ATATTTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 7 0.27
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (19 bp):
AATCACATTAGTCACATTG
Found at i:19742027 original size:23 final size:23
Alignment explanation
Indices: 19741997--19742285 Score: 159
Period size: 23 Copynumber: 11.6 Consensus size: 23
19741987 TAGTCACATG
19741997 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
19742020 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* * * *
19742043 AATTATATTAACATTTAAGCTTA
1 AATCACATTAATATTTAAGCATA
*
19742066 AATCACATTAATACTTGACA-CATA
1 AATCACATTAATA-TTTA-AGCATA
* *
19742090 TAATCACATTTAATCACATATAACCACATA
1 -AATCACA-TTAAT---ATTTAA--GCATA
* * * *
19742120 TAGTCACGTATAATCACATTTAACCAAATTT
1 -AATCACAT-TAAT---ATTTAAGC--A-TA
* * *
19742151 AATCACATTTAGTCACATTTAATATCATTT
1 AATCACA-TTA---ATATTT-A-AGCA-TA
* * *
19742181 AATCAAATAAATATTTCAA-CACA
1 AATCACATTAATATTT-AAGCATA
19742204 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
*
19742227 AATCGCATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
19742250 AATCATATTAATATTTAAGCTTA
1 AATCACATTAATATTTAAGCATA
19742273 AATCACATTAATA
1 AATCACATTAATA
19742286 CTTGACACAT
Statistics
Matches: 211, Mismatches: 34, Indels: 42
0.74 0.12 0.15
Matches are distributed among these distances:
22 2 0.01
23 123 0.58
24 8 0.04
25 9 0.04
26 11 0.05
27 1 0.00
28 3 0.01
29 4 0.02
30 44 0.21
31 3 0.01
32 2 0.01
33 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:19742103 original size:10 final size:10
Alignment explanation
Indices: 19742084--19742185 Score: 98
Period size: 10 Copynumber: 10.2 Consensus size: 10
19742074 TAATACTTGA
*
19742084 CACATATAAT
1 CACATTTAAT
19742094 CACATTTAAT
1 CACATTTAAT
* *
19742104 CACATATAAC
1 CACATTTAAT
* *
19742114 CACATATAGT
1 CACATTTAAT
* *
19742124 CACGTATAAT
1 CACATTTAAT
*
19742134 CACATTTAAC
1 CACATTTAAT
*
19742144 CAAATTTAAT
1 CACATTTAAT
*
19742154 CACATTTAGT
1 CACATTTAAT
19742164 CACATTTAAT
1 CACATTTAAT
19742174 -ATCATTTAAT
1 CA-CATTTAAT
19742184 CA
1 CA
19742186 AATAAATATT
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
9 1 0.01
10 73 0.97
11 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (10 bp):
CACATTTAAT
Found at i:19742169 original size:30 final size:30
Alignment explanation
Indices: 19742087--19742172 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
19742077 TACTTGACAC
* *
19742087 ATATAATCACATTTAATCACATATAACCAC
1 ATATAATCACATTTAATCACATTTAACCAA
* * *
19742117 ATATAGTCACGTATAATCACATTTAACCAA
1 ATATAATCACATTTAATCACATTTAACCAA
* *
19742147 ATTTAATCACATTTAGTCACATTTAA
1 ATATAATCACATTTAATCACATTTAA
19742173 TATCATTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (30 bp):
ATATAATCACATTTAATCACATTTAACCAA
Found at i:19742788 original size:36 final size:36
Alignment explanation
Indices: 19742715--19742789 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
19742705 TAATCAGTCT
* *
19742715 CATGGCATGAAGAAAATACCCACATATTTTTTATCA
1 CATGGCATGAAGAAAATACCCACATATTATATATCA
* *
19742751 CATGGCATGAATAAAATACCTACATATTCATAT-TCA
1 CATGGCATGAAGAAAATACCCACATATT-ATATATCA
19742787 CAT
1 CAT
19742790 TCACAACAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 32 0.94
37 2 0.06
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (36 bp):
CATGGCATGAAGAAAATACCCACATATTATATATCA
Found at i:19743710 original size:9 final size:9
Alignment explanation
Indices: 19743678--19743708 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19743668 CACGTTTGGA
19743678 GAAGATGAT
1 GAAGATGAT
19743687 GAAGATGAT
1 GAAGATGAT
*
19743696 GAAGGTGAT
1 GAAGATGAT
19743705 GAAG
1 GAAG
19743709 GTTTGTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (9 bp):
GAAGATGAT
Found at i:19749328 original size:6 final size:7
Alignment explanation
Indices: 19749311--19749338 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19749301 ATAGAAGGCC
19749311 AAAAAAT
1 AAAAAAT
19749318 AAAAAAT
1 AAAAAAT
19749325 AAAAAAT
1 AAAAAAT
19749332 AAAAAAT
1 AAAAAAT
19749339 TGCAAGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:19755065 original size:29 final size:29
Alignment explanation
Indices: 19755018--19755249 Score: 159
Period size: 29 Copynumber: 7.9 Consensus size: 29
19755008 TAAATTTAGA
*
19755018 AAAGTTTAGGGGGTGAAAATGTAATTTTGGG
1 AAAGTTTA--GGGTTAAAATGTAATTTTGGG
** * *
19755049 AAAGTTCGGGGTCAAAATACT-ATTTT-GG
1 AAAGTTTAGGGTTAAAAT-GTAATTTTGGG
* ** * *
19755077 AGAAGTTTAGGGTCAAAACATGATTTTAGG
1 A-AAGTTTAGGGTTAAAATGTAATTTTGGG
* * * *
19755107 AAGGTTTAAGGTCAAAATGTGATTTTGGAG
1 AAAGTTTAGGGTTAAAATGTAATTTTGG-G
* * * *
19755137 AAA-TTTAAGGTTAAAATGTGATTTTTGA
1 AAAGTTTAGGGTTAAAATGTAATTTTGGG
* **
19755165 AAAGTTTAAGGTTAAAATGTAATTTTGAA
1 AAAGTTTAGGGTTAAAATGTAATTTTGGG
19755194 AAAGTTT-GGAAGTTAAAATGTAATTTT-GG
1 AAAGTTTAGG--GTTAAAATGTAATTTTGGG
*
19755223 AAAGTTTTGGGGTTAAAATGTAATTTT
1 AAAG-TTTAGGGTTAAAATGTAATTTT
19755250 ATAAAAGTTT
Statistics
Matches: 168, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
28 8 0.05
29 126 0.75
30 26 0.15
31 8 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAGTTTAGGGTTAAAATGTAATTTTGGG
Found at i:19755238 original size:59 final size:59
Alignment explanation
Indices: 19755146--19755259 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
19755136 GAAATTTAAG
*
19755146 GTTAAAATGTGATTTTTGAAAAGTTTAAGGTTAAAATGTAATTTTGA-AAAAGTTTGGAA
1 GTTAAAATGTGAATTTTGAAAAGTTTAAGGTTAAAATGTAATTTT-ATAAAAGTTTGGAA
* **
19755205 GTTAAAATGT-AATTTTGGAAAGTTTTGGGGTTAAAATGTAATTTTATAAAAGTTT
1 GTTAAAATGTGAATTTTGAAAAG-TTTAAGGTTAAAATGTAATTTTATAAAAGTTT
19755260 AAGGGTCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 11 0.22
59 38 0.78
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (59 bp):
GTTAAAATGTGAATTTTGAAAAGTTTAAGGTTAAAATGTAATTTTATAAAAGTTTGGAA
Found at i:19755287 original size:59 final size:58
Alignment explanation
Indices: 19755159--19755287 Score: 131
Period size: 59 Copynumber: 2.2 Consensus size: 58
19755149 AAAATGTGAT
** * *
19755159 TTTTGAAAAG-TTTAAGGTTAAAATGTAATTTTGAAAAAGTTTGGAAGTTAAAATGTAA
1 TTTTGAAAAGTTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTGG-AGTCAAAATATAA
*
19755217 TTTTGGAAAGTTTTGGGGTTAAAATGTAATTTT-ATAAAAGTTTAAGG-GTCAAAA-ATAA
1 TTTTGAAAAGTTTTGGGGTTAAAATGTAATTTTGA-AAAAGTTT--GGAGTCAAAATATAA
*
19755275 TTTTTAAGAAGTT
1 TTTTGAA-AAGTT
19755288 CGGGGCTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
58 18 0.31
59 39 0.66
61 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (58 bp):
TTTTGAAAAGTTTTGGGGTTAAAATGTAATTTTGAAAAAGTTTGGAGTCAAAATATAA
Found at i:19757473 original size:39 final size:40
Alignment explanation
Indices: 19757430--19757924 Score: 283
Period size: 39 Copynumber: 12.7 Consensus size: 40
19757420 GATGGTTACA
*
19757430 ATCTGCCCTTA-GCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * **
19757469 ATCTGCCCT-AGGCTCGAGGTAAGAGATCGGACAGCT-GCA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGG-CTGATGGTG
* * *
19757508 ATCT-TCCTCAGGCTCAGGGTAAGAGATTGGCTGATGATG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
** * * * *
19757547 ATCTATCC-CAGGCTCGGGGTAAGAGATCGGATAGCT-GTA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCT-GATGGTG
*
19757586 ATCTGCCC-CAGGCTCGGGGTTAGAGATTGGCTGATGGTG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * *
19757625 ATCTG-CCTCAGGCTCGGGGTAAGAGATCGAAT-A-GCTACA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGT--G
* * * *
19757664 ATCTG-CCTCAAGCTCAGGGTAAGAGATTGACTAATGGTG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * *
19757703 ATCTGCCC-CAGGCTTGGGGTAAGAGATCAAG-TGCCT-GTA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGAT-TGGCTG-ATGGTG
* * * *
19757742 ATTTGCCC-CAAGCTCGGGGTAAGAGATTGACTGATGATG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * * **
19757781 ATTTGCCCT-GGGCTCGAGGTAAAAAATTGGATGACT-GCA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* * *
19757820 ATCT-ACCTCAAGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * ** * * *
19757859 ATTTGCCC-CAGGCTTGGGGTAACAGATCGAATGGTTGTA
1 ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
*
19757898 ATTTGCCC-CAGGCTCGGGGTAAGAGAT
1 ATCTGCCCTCAGGCTCGGGGTAAGAGAT
19757925 CGAAATTTTC
Statistics
Matches: 343, Mismatches: 91, Indels: 44
0.72 0.19 0.09
Matches are distributed among these distances:
37 2 0.01
38 17 0.05
39 307 0.90
40 15 0.04
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (40 bp):
ATCTGCCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:19757537 original size:78 final size:78
Alignment explanation
Indices: 19757440--19757924 Score: 503
Period size: 78 Copynumber: 6.2 Consensus size: 78
19757430 ATCTGCCCTT
* *
19757440 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAGGTAAGAGATCGGACAGCT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGGATAGCT
*
19757505 GCAATCTTCCTCA
66 GCAATCTGCCTCA
* * * *
19757518 GGCTCAGGGTAAGAGATTGGCTGATGATGATCTATCCC-AGGCTCGGGGTAAGAGATCGGATAGC
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCTAGGCTCGGGGTAAGAGATCGGATAGC
* *
19757582 TGTAATCTGCCCCA
65 TGCAATCTGCCTCA
* * *
19757596 GGCTCGGGGTTAGAGATTGGCTGATGGTGATCTG-CCTCAGGCTCGGGGTAAGAGATCGAATAGC
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AGGCTCGGGGTAAGAGATCGGATAGC
*
19757660 TACAATCTGCCTCA
65 TGCAATCTGCCTCA
* * * * * *
19757674 AGCTCAGGGTAAGAGATTGACTAATGGTGATCTGCCCCAGGCTTGGGGTAAGAGATC-AAGT-GC
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGGA-TAG-
* * *
19757737 CTGTAATTTGCCCCA
64 CTGCAATCTGCCTCA
* * * * * * * *
19757752 AGCTCGGGGTAAGAGATTGACTGATGATGATTTGCCCTGGGCTCGAGGTAAAAAATTGGAT-GAC
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGGATAG-C
*
19757816 TGCAATCTACCTCA
65 TGCAATCTGCCTCA
* * * * * * * *
19757830 AGCTCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCCAGGCTTGGGGTAACAGATCGAATGGTT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGGATAGCT
* * *
19757895 GTAATTTGCCCCA
66 GCAATCTGCCTCA
*
19757908 GGCTCGGGGTAAGAGAT
1 AGCTCGGGGTAAGAGAT
19757925 CGAAATTTTC
Statistics
Matches: 337, Mismatches: 62, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
76 2 0.01
77 3 0.01
78 325 0.96
79 7 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (78 bp):
AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGGATAGCT
GCAATCTGCCTCA
Found at i:19757691 original size:156 final size:155
Alignment explanation
Indices: 19757441--19757924 Score: 632
Period size: 156 Copynumber: 3.1 Consensus size: 155
19757431 TCTGCCCTTA
*
19757441 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAGGTAAGAGATCGGACAGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAGGTAAGAGATCGGATAGCTG
* * * ** *
19757506 CAATCTTCCTCAGGCTCAGGGTAAGAGATTGGCTGATGATGATCTATCCCAGGCTCGGGGTAAGA
66 CAATCTACCTCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAGA
* *
19757571 GATCGGATAGCTGTAATCTGCCCCAG
131 GATCGAAT-GCTGTAATTTGCCCCAG
* * *
19757597 GCTCGGGGTTAGAGATTGGCTGATGGTGATCTG-CCTCAGGCTCGGGGTAAGAGATCGAATAGCT
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AGGCTCGAGGTAAGAGATCGGATAGCT
* * * *
19757661 ACAATCTGCCTCAAGCTCAGGGTAAGAGATTGACTAATGGTGATCTGCCCCAGGCTTGGGGTAAG
65 GCAATCTACCTCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAG
*
19757726 AGATC-AAGTGCCTGTAATTTGCCCCAA
130 AGATCGAA-TG-CTGTAATTTGCCCCAG
* * * * * * *
19757753 GCTCGGGGTAAGAGATTGACTGATGATGATTTGCCCTGGGCTCGAGGTAAAAAATTGGAT-GACT
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAGGTAAGAGATCGGATAG-CT
* * * *
19757817 GCAATCTACCTCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCCAGGCTTGGGGTAAC
65 GCAATCTACCTCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAG
*
19757882 AGATCGAATGGTTGTAATTTGCCCCAG
130 AGATCGAAT-GCTGTAATTTGCCCCAG
19757909 GCTCGGGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
19757925 CGAAATTTTC
Statistics
Matches: 285, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
155 6 0.02
156 273 0.96
157 6 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (155 bp):
GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAGGTAAGAGATCGGATAGCTG
CAATCTACCTCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAGA
GATCGAATGCTGTAATTTGCCCCAG
Found at i:19769499 original size:29 final size:29
Alignment explanation
Indices: 19769467--19769655 Score: 193
Period size: 29 Copynumber: 6.4 Consensus size: 29
19769457 GCTCAAGGTC
* *
19769467 AAAATGTGATTTTAGAGAATTTTAGGGTT
1 AAAATGTGATTTTAGAAAAGTTTAGGGTT
** * * *
19769496 AAAACATGATTTTAGGAAAGTTTGGGGTC
1 AAAATGTGATTTTAGAAAAGTTTAGGGTT
* *
19769525 AAAATGTGATTTTGGAGAAA-TTTAAGGTT
1 AAAATGTGATTTTAGA-AAAGTTTAGGGTT
*
19769554 AAAATGTGATTTTTGAAAAGTTTAGGGTT
1 AAAATGTGATTTTAGAAAAGTTTAGGGTT
* *
19769583 AAAATATAATTTT-GAAAAAGTTTAGGGGTT
1 AAAATGTGATTTTAG-AAAAGTTTA-GGGTT
* *
19769613 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
1 AAAATGTGATTTTAGAAAAGTTT-AGGGTT
*
19769643 AAAATATGATTTT
1 AAAATGTGATTTT
19769656 TAAGAAGTTC
Statistics
Matches: 132, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.03
29 83 0.63
30 43 0.33
31 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAATGTGATTTTAGAAAAGTTTAGGGTT
Found at i:19769525 original size:58 final size:57
Alignment explanation
Indices: 19769463--19769655 Score: 224
Period size: 58 Copynumber: 3.3 Consensus size: 57
19769453 GAAAGCTCAA
* * ** * *
19769463 GGTCAAAATGTGATTTTAGAGAATTTTAGGGTTAAAACATGATTTTAGGAAAGTTTGG
1 GGTCAAAATATGATTTT-GAGAAATTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * *
19769521 GGTCAAAATGTGATTTTGGAGAAATTTAAGGTTAAAATGTGATTTTTGAAAAGTTTAG
1 GGTCAAAATATGATTTT-GAGAAATTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAG
* * * *
19769579 GGTTAAAATATAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAAG
1 GGTCAAAATATGATTTTGAGAAA-TTTA-GGGTTAAAATGTGATTTTAGAAAAGTTT-AG
19769639 GGTCAAAATATGATTTT
1 GGTCAAAATATGATTTT
19769656 TAAGAAGTTC
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
57 5 0.04
58 68 0.59
59 25 0.22
60 17 0.15
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (57 bp):
GGTCAAAATATGATTTTGAGAAATTTAGGGTTAAAATGTGATTTTAGAAAAGTTTAG
Found at i:19769531 original size:87 final size:88
Alignment explanation
Indices: 19769407--19769655 Score: 279
Period size: 87 Copynumber: 2.8 Consensus size: 88
19769397 ATACGGGATC
* * * * * *
19769407 AAAACATAAATTTGGAAAAGTTGAGGGGGTGAAAATGTAATTTTGGGAAAGCTCAAGGTCAAAAT
1 AAAACATAATTTTGAAAAAGTTTA-GGGGTCAAAATGTAATTTTGGGAAAGTTTAAGGTCAAAAT
* *
19769472 GTGATTTTAGAGAATTTTAGGGTT
65 GTGATTTTAGAAAAGTTTAGGGTT
* * * *
19769496 AAAACATGATTTT-AGGAAAGTTT-GGGGTCAAAATGTGATTTTGGAGAAA-TTTAAGGTTAAAA
1 AAAACATAATTTTGA-AAAAGTTTAGGGGTCAAAATGTAATTTTGG-GAAAGTTTAAGGTCAAAA
*
19769558 TGTGATTTTTGAAAAGTTTAGGGTT
64 TGTGATTTTAGAAAAGTTTAGGGTT
* * * *
19769583 AAAATATAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAAT
1 AAAACATAATTTTGAAAAAGTTTAGGGGTCAAAATGTAATTTTGGGAAAGTTTAA-GGTCAAAAT
*
19769648 ATGATTTT
65 GTGATTTT
19769656 TAAGAAGTTC
Statistics
Matches: 132, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
87 72 0.55
88 28 0.21
89 32 0.24
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (88 bp):
AAAACATAATTTTGAAAAAGTTTAGGGGTCAAAATGTAATTTTGGGAAAGTTTAAGGTCAAAATG
TGATTTTAGAAAAGTTTAGGGTT
Found at i:19771452 original size:29 final size:28
Alignment explanation
Indices: 19771420--19771543 Score: 74
Period size: 29 Copynumber: 4.3 Consensus size: 28
19771410 AAAACGGGGT
19771420 TAAAAATGAGATTTAGGGAAGTTTGAGGG
1 TAAAAATG-GATTTAGGGAAGTTTGAGGG
* * * *
19771449 T-AAAATGGTAATTTTAGTGAA-ATCGAGGT
1 TAAAAATGG--A-TTTAGGGAAGTTTGAGGG
* *
19771478 TAAAAATGGGATTTAAGGAAGTTTGGGGG
1 TAAAAAT-GGATTTAGGGAAGTTTGAGGG
** * *
19771507 T-AAAATGGTAATTTTTGAAAGTTTCAGGG
1 TAAAAATGG--ATTTAGGGAAGTTTGAGGG
19771536 TAAAAATG
1 TAAAAATG
19771544 CAATTTTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 17
0.69 0.15 0.17
Matches are distributed among these distances:
27 3 0.04
28 18 0.25
29 29 0.41
30 19 0.27
31 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (28 bp):
TAAAAATGGATTTAGGGAAGTTTGAGGG
Found at i:19771479 original size:58 final size:58
Alignment explanation
Indices: 19771391--19771521 Score: 199
Period size: 58 Copynumber: 2.2 Consensus size: 58
19771381 ACTCGGGGGC
* * *
19771391 AAAATGGTAGATTTTGGTGAAAACGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAAACGAGGTTAAAAATGAGATTTAAGGAAGTTTGAGGGT
* * *
19771450 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAAGGAAGTTTGGGGGT
1 AAAATGGTAATTTTAGTGAAAACGAGGTTAAAAATGAGATTTAAGGAAGTTTGAGGGT
19771508 AAAATGGTAATTTT
1 AAAATGGTAATTTT
19771522 TGAAAGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 57 0.86
59 9 0.14
ACGTcount: A:0.37, C:0.02, G:0.31, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAAACGAGGTTAAAAATGAGATTTAAGGAAGTTTGAGGGT
Found at i:19771484 original size:30 final size:31
Alignment explanation
Indices: 19771391--19771486 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 31
19771381 ACTCGGGGGC
* * *
19771391 AAAATGGTAGATTTTGGTGAAAACGGGGTTA
1 AAAATGGTAGATTTTAGTGAAATCGAGGTTA
* * * *
19771422 AAAAT-G-AGA-TTTAGGGAAGTTTGAGGGT-
1 AAAATGGTAGATTTTAGTGAA-ATCGAGGTTA
19771450 AAAATGGTA-ATTTTAGTGAAATCGAGGTTA
1 AAAATGGTAGATTTTAGTGAAATCGAGGTTA
19771480 AAAATGG
1 AAAATGG
19771487 GATTTAAGGA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
28 12 0.24
29 15 0.31
30 17 0.35
31 5 0.10
ACGTcount: A:0.39, C:0.02, G:0.30, T:0.29
Consensus pattern (31 bp):
AAAATGGTAGATTTTAGTGAAATCGAGGTTA
Found at i:19771511 original size:28 final size:28
Alignment explanation
Indices: 19771422--19771514 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
19771412 AACGGGGTTA
* *
19771422 AAAATGAGATTTAGGGAAGTTTGAGGGT
1 AAAATGGGATTTAAGGAAGTTTGAGGGT
* * * * *
19771450 AAAATGGTAATTTTAGTGAA-ATCGAGGTT
1 AAAATGG-GATTTAAG-GAAGTTTGAGGGT
*
19771479 AAAAATGGGATTTAAGGAAGTTTGGGGGT
1 -AAAATGGGATTTAAGGAAGTTTGAGGGT
19771508 AAAATGG
1 AAAATGG
19771515 TAATTTTTGA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
28 16 0.33
29 22 0.46
30 10 0.21
ACGTcount: A:0.38, C:0.01, G:0.32, T:0.29
Consensus pattern (28 bp):
AAAATGGGATTTAAGGAAGTTTGAGGGT
Done.