Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 62 of 202
Found at i:18317055 original size:37 final size:39
Alignment explanation
Indices: 18317012--18317088 Score: 131
Period size: 37 Copynumber: 2.0 Consensus size: 39
18317002 ACTTAAGAGT
*
18317012 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAA-TGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
18317049 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
18317088 T
1 T
18317089 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 27 0.73
38 5 0.14
39 5 0.14
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:18317087 original size:13 final size:13
Alignment explanation
Indices: 18317069--18317093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18317059 TTTTAGTTTT
18317069 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
18317082 ATTGGGTTGGGT
1 ATTGGGTTGGGT
18317094 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:18318756 original size:17 final size:18
Alignment explanation
Indices: 18318724--18318757 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18318714 AGTTTCTTTT
18318724 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
18318742 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
18318758 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:18319267 original size:30 final size:28
Alignment explanation
Indices: 18319212--18319273 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
18319202 ATCATTTAAT
18319212 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
*
18319240 TAATAAATATCTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTACTT-AATAATAAA
18319270 TAAT
1 TAAT
18319274 TTAAATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 7 0.23
30 12 0.39
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:18327658 original size:27 final size:27
Alignment explanation
Indices: 18327628--18327683 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
18327618 TCTTGTAAGT
18327628 ATATGTTTGATTTCTACTAGAAATAGC
1 ATATGTTTGATTTCTACTAGAAATAGC
18327655 ATATGTTTGATTTCTACTAGAAATAGC
1 ATATGTTTGATTTCTACTAGAAATAGC
18327682 AT
1 AT
18327684 GTGGTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (27 bp):
ATATGTTTGATTTCTACTAGAAATAGC
Found at i:18329884 original size:55 final size:55
Alignment explanation
Indices: 18329816--18329975 Score: 203
Period size: 55 Copynumber: 2.9 Consensus size: 55
18329806 GGATGTTACG
* * * * *
18329816 TAACAATCGATTTAAAAATATAAACAATCGATTCAAAAGAAACAATATTTCAACA
1 TAACAATCAATTTAGACATATAAACAATCGATTCAAAAGAAATAATATTCCAACA
** * * * * *
18329871 TAACAATTTATTTAGACATATAAGCAATTGATTTAAAAGAAGTAATATTCCAATA
1 TAACAATCAATTTAGACATATAAACAATCGATTCAAAAGAAATAATATTCCAACA
*
18329926 TAACAATCAATTTAGACATATAAACAATCAATTCAAAAGAAATAATATTC
1 TAACAATCAATTTAGACATATAAACAATCGATTCAAAAGAAATAATATTC
18329976 TAAAATTTTC
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.29
Consensus pattern (55 bp):
TAACAATCAATTTAGACATATAAACAATCGATTCAAAAGAAATAATATTCCAACA
Found at i:18331405 original size:23 final size:23
Alignment explanation
Indices: 18331375--18331419 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18331365 AGAACAAAAT
18331375 GGGACAACA-CTGAAGCGCGTAAC
1 GGGACAACATC-GAAGCGCGTAAC
*
18331398 GGGACAACATCGAAGTGCGTAA
1 GGGACAACATCGAAGCGCGTAA
18331420 ACATAAAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.22, G:0.31, T:0.11
Consensus pattern (23 bp):
GGGACAACATCGAAGCGCGTAAC
Found at i:18333299 original size:23 final size:22
Alignment explanation
Indices: 18333272--18333315 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18333262 CCTCTCATTC
18333272 CTCACATCTCTCTCTCTT-TTTCA
1 CTCAC-TCTCTCT-TCTTATTTCA
*
18333295 CTCACTTTCTCTTCTTATTTC
1 CTCACTCTCTCTTCTTATTTC
18333316 CCATTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.52
Consensus pattern (22 bp):
CTCACTCTCTCTTCTTATTTCA
Found at i:18336804 original size:13 final size:12
Alignment explanation
Indices: 18336778--18336819 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
18336768 TCTTTTTCTA
18336778 TAAAAT-TCCAT
1 TAAAATATCCAT
18336789 TAAAATATCTCAT
1 TAAAATATC-CAT
18336802 TAAAATAATCC-T
1 TAAAAT-ATCCAT
18336814 TAAAAT
1 TAAAAT
18336820 GCTAATTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 9 0.32
13 10 0.36
14 3 0.11
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATATCCAT
Found at i:18337997 original size:32 final size:32
Alignment explanation
Indices: 18337928--18337997 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
18337918 TTTAAAAGAT
** *
18337928 ACATAACTATTCATCTAATATCTCTTGATTAA
1 ACATAACTATTCAAATAATATCTCTTGAATAA
* *
18337960 ACATAACTATTCAAATAATATTTTTTGAATAA
1 ACATAACTATTCAAATAATATCTCTTGAATAA
*
18337992 TCATAA
1 ACATAA
18337998 TTCTTTGTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (32 bp):
ACATAACTATTCAAATAATATCTCTTGAATAA
Found at i:18339828 original size:26 final size:26
Alignment explanation
Indices: 18339786--18339887 Score: 127
Period size: 26 Copynumber: 3.9 Consensus size: 26
18339776 TATCATCCCT
*
18339786 ATTTTACCCCTTA-TAAAATTTTGACG
1 ATTTTGCCCC-TAGTAAAATTTTGACG
*
18339812 ATTTTGCCCTTAGTAAAATTTTGACG
1 ATTTTGCCCCTAGTAAAATTTTGACG
* *
18339838 ATTTTGCCCCTAGTAAAATTTTAATG
1 ATTTTGCCCCTAGTAAAATTTTGACG
*
18339864 ATTTCT-CCCCTGGTAAAATTTTGA
1 ATTT-TGCCCCTAGTAAAATTTTGA
18339888 GAAAATTTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
25 2 0.03
26 64 0.96
27 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTGCCCCTAGTAAAATTTTGACG
Found at i:18341733 original size:21 final size:21
Alignment explanation
Indices: 18341709--18341778 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
18341699 CACTATAACA
18341709 GAAATGAATAAGACCATAGTT
1 GAAATGAATAAGACCATAGTT
* * * *
18341730 GAAA-GACACTATGGCACTATACTG
1 GAAATGA-A-TA-AG-ACCATAGTT
*
18341754 GAAATGAATAAGATCATAGTT
1 GAAATGAATAAGACCATAGTT
18341775 GAAA
1 GAAA
18341779 GAAACTACGG
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 3 0.09
23 3 0.09
24 11 0.31
25 2 0.06
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (21 bp):
GAAATGAATAAGACCATAGTT
Found at i:18341734 original size:45 final size:45
Alignment explanation
Indices: 18341665--18341831 Score: 205
Period size: 45 Copynumber: 3.7 Consensus size: 45
18341655 TTGGCTTGAA
*
18341665 AAATAAATAAGACCATAGGTGAAAGACACTATGGCACTATAACAG
1 AAATAAATAAGACCATAGTTGAAAGACACTATGGCACTATAACAG
* *
18341710 AAATGAATAAGACCATAGTTGAAAGACACTATGGCACTAT-ACTGG
1 AAATAAATAAGACCATAGTTGAAAGACACTATGGCACTATAAC-AG
* * * * *
18341755 AAATGAATAAGATCATAGTTGAAAGAAACTACGGCAAC-ATGAA-TG
1 AAATAAATAAGACCATAGTTGAAAGACACTATGGC-ACTAT-AACAG
*
18341800 AAATAAATAAAACCATAGTTGAAAGACACTAT
1 AAATAAATAAGACCATAGTTGAAAGACACTAT
18341832 AGCATCATGT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.02
45 101 0.95
46 2 0.02
47 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (45 bp):
AAATAAATAAGACCATAGTTGAAAGACACTATGGCACTATAACAG
Found at i:18341823 original size:90 final size:90
Alignment explanation
Indices: 18341665--18341831 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 90
18341655 TTGGCTTGAA
* * * *
18341665 AAATAAATAAGACCATAGGTGAAAGACACTATGGCACTATAACAGAAATGAATAAGACCATAGTT
1 AAATAAATAAGACCATAGGTGAAAGAAACTACGGCACTATAACAGAAATAAATAAAACCATAGTT
18341730 GAAAGACACTATGGCACTATACTGG
66 GAAAGACACTATGGCACTATACTGG
* * * *
18341755 AAATGAATAAGATCATAGTTGAAAGAAACTACGGCAAC-ATGAA-TGAAATAAATAAAACCATAG
1 AAATAAATAAGACCATAGGTGAAAGAAACTACGGC-ACTAT-AACAGAAATAAATAAAACCATAG
18341818 TTGAAAGACACTAT
64 TTGAAAGACACTAT
18341832 AGCATCATGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 63 0.94
91 4 0.06
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (90 bp):
AAATAAATAAGACCATAGGTGAAAGAAACTACGGCACTATAACAGAAATAAATAAAACCATAGTT
GAAAGACACTATGGCACTATACTGG
Found at i:18353270 original size:26 final size:26
Alignment explanation
Indices: 18353241--18353320 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
18353231 CTAGCAATAG
* *
18353241 TTTGACGATTTTACCTCTGGTAAAAT
1 TTTGACGATTTTGCCCCTGGTAAAAT
* *
18353267 TTTGACAATTTTGCCCCTGGTAAATT
1 TTTGACGATTTTGCCCCTGGTAAAAT
18353293 TTTGACGATTTTGCCCCTGGT-AAAT
1 TTTGACGATTTTGCCCCTGGTAAAAT
18353318 TTT
1 TTT
18353321 CAAGAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 6 0.12
26 42 0.88
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (26 bp):
TTTGACGATTTTGCCCCTGGTAAAAT
Found at i:18357150 original size:21 final size:21
Alignment explanation
Indices: 18357124--18357163 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18357114 TTTGCAGGAG
18357124 GAGGCACACAGCT-GTGTGATT
1 GAGGCACACA-CTCGTGTGATT
18357145 GAGGCACACACTCGTGTGA
1 GAGGCACACACTCGTGTGA
18357164 CCCAGGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.20
Consensus pattern (21 bp):
GAGGCACACACTCGTGTGATT
Found at i:18361080 original size:17 final size:17
Alignment explanation
Indices: 18361025--18361082 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
18361015 AATATCTACC
*
18361025 ATTTATATTATTAAATT
1 ATTTATATTATTGAATT
* *
18361042 AAATTTCATA-TATTGTACT
1 --ATTT-ATATTATTGAATT
18361061 ATTTATATTATTGAATT
1 ATTTATATTATTGAATT
18361078 ATTTA
1 ATTTA
18361083 ATCATATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.09
17 16 0.50
19 10 0.31
20 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTATATTATTGAATT
Found at i:18367430 original size:26 final size:26
Alignment explanation
Indices: 18367400--18367488 Score: 135
Period size: 26 Copynumber: 3.4 Consensus size: 26
18367390 ACAAATTTTC
18367400 TCAAAATTTTACCATGGGTAAAATCT
1 TCAAAATTTTACCATGGGTAAAATCT
*
18367426 TCAAAATTTTACCATAGGTAAAATCT
1 TCAAAATTTTACCATGGGTAAAATCT
* *
18367452 TCAAAATTTTACTAAGGGTAAAAT-T
1 TCAAAATTTTACCATGGGTAAAATCT
18367477 GTCAAAATTTTA
1 -TCAAAATTTTA
18367489 TTAAGGGTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 1 0.02
26 57 0.98
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (26 bp):
TCAAAATTTTACCATGGGTAAAATCT
Found at i:18367501 original size:26 final size:26
Alignment explanation
Indices: 18367400--18367502 Score: 113
Period size: 26 Copynumber: 4.0 Consensus size: 26
18367390 ACAAATTTTC
* *
18367400 TCAAAATTTTACCATGGGTAAAATCT-
1 TCAAAATTTTACTAAGGGTAAAAT-TG
*
18367426 TCAAAATTTTACCATA-GGTAAAATCT-
1 TCAAAATTTTACTA-AGGGTAAAAT-TG
18367452 TCAAAATTTTACTAAGGGTAAAATTG
1 TCAAAATTTTACTAAGGGTAAAATTG
* *
18367478 TCAAAATTTTATTAAGGGTGAAATT
1 TCAAAATTTTACTAAGGGTAAAATT
18367503 TGGATGAGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
25 2 0.03
26 68 0.97
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (26 bp):
TCAAAATTTTACTAAGGGTAAAATTG
Found at i:18369094 original size:50 final size:50
Alignment explanation
Indices: 18369035--18369132 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
18369025 ACTCGACCTT
18369035 GCCTGAACAATTAATAGGGTAAACATTTCTCAATTCCATTAATAAGTCGA
1 GCCTGAACAATTAATAGGGTAAACATTTCTCAATTCCATTAATAAGTCGA
18369085 GCCTGAACAATTAATAGGGTAAACATTTCTCAATTCCATTAATAAGTC
1 GCCTGAACAATTAATAGGGTAAACATTTCTCAATTCCATTAATAAGTC
18369133 AATATCTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (50 bp):
GCCTGAACAATTAATAGGGTAAACATTTCTCAATTCCATTAATAAGTCGA
Found at i:18378769 original size:20 final size:20
Alignment explanation
Indices: 18378744--18378787 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
18378734 ATTCAATTAT
18378744 TAATAAATTTTTTAATCATC
1 TAATAAATTTTTTAATCATC
18378764 TAATAAATTTTTTAATCATC
1 TAATAAATTTTTTAATCATC
18378784 TAAT
1 TAAT
18378788 TATATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATTTTTTAATCATC
Found at i:18379846 original size:21 final size:21
Alignment explanation
Indices: 18379822--18379870 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
18379812 AAGGAACTTC
*
18379822 AAAATTTATAAAAAAGT-TATT
1 AAAATTTATAAAAAA-TATATA
*
18379843 AAAATTTTTAAAAAATATATA
1 AAAATTTATAAAAAATATATA
18379864 AAAATTT
1 AAAATTT
18379871 CAAATGTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATTTATAAAAAATATATA
Found at i:18381975 original size:21 final size:19
Alignment explanation
Indices: 18381947--18382006 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
18381937 AAAATATATA
18381947 TTAA-TTTTTTTTTAATTT
1 TTAATTTTTTTTTTAATTT
**
18381965 TTATACTTTTTTTAATAATTT
1 TTA-A-TTTTTTTTTTAATTT
*
18381986 TTAATTTTTTTTTGAATTT
1 TTAATTTTTTTTTTAATTT
18382005 TT
1 TT
18382007 TAAAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.09
19 15 0.44
20 1 0.03
21 15 0.44
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTAATTTTTTTTTTAATTT
Found at i:18382007 original size:21 final size:20
Alignment explanation
Indices: 18381947--18382007 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
18381937 AAAATATATA
18381947 TTAATTTTTTTTTAATTTTT
1 TTAATTTTTTTTTAATTTTT
* * *
18381967 AT-A-CTTTTTTTAATAATTT
1 TTAATTTTTTTTTAAT-TTTT
18381986 TTAATTTTTTTTTGAATTTTT
1 TTAATTTTTTTTT-AATTTTT
18382007 T
1 T
18382008 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 2 0.06
21 11 0.35
22 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (20 bp):
TTAATTTTTTTTTAATTTTT
Found at i:18385101 original size:44 final size:43
Alignment explanation
Indices: 18385041--18385167 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 43
18385031 AGGATTTCGT
18385041 TATGTG-TTATCGTGTAAGACCACGTCTGGGACATTGGCATCGA
1 TATGTGATTA-CGTGTAAGACCACGTCTGGGACATTGGCATCGA
* * *
18385084 CT-TGTGACTTACGTGTAAAACC-CTGTCTAGGACAGTGGCATCGA
1 -TATGTGA-TTACGTGTAAGACCAC-GTCTGGGACATTGGCATCGA
* *
18385128 TATGTGATTACATGTAAGACTACGTCTGGGACATTGGCAT
1 TATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
18385168 TGTACGAGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
43 32 0.46
44 35 0.50
45 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGA
Found at i:18386543 original size:10 final size:10
Alignment explanation
Indices: 18386518--18386551 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18386508 ATTTGGATAT
*
18386518 TATATATATA
1 TATATGTATA
18386528 TATATGTATA
1 TATATGTATA
*
18386538 TATATGCATA
1 TATATGTATA
18386548 TATA
1 TATA
18386552 GCGTTTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (10 bp):
TATATGTATA
Found at i:18399035 original size:5 final size:5
Alignment explanation
Indices: 18399025--18399050 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18399015 CTAATCTTGG
18399025 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
18399051 TATCTTTTGT
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:18399535 original size:17 final size:17
Alignment explanation
Indices: 18399513--18399548 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18399503 TCCTTTTTAT
* *
18399513 CTTCTCTCTCTACTTCC
1 CTTCTCTATCTACATCC
18399530 CTTCTCTATCTACATCC
1 CTTCTCTATCTACATCC
18399547 CT
1 CT
18399549 AGTAATGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (17 bp):
CTTCTCTATCTACATCC
Found at i:18404181 original size:21 final size:20
Alignment explanation
Indices: 18404152--18404195 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
18404142 TTCAGACTAA
18404152 TAAAAATTTAAAAATAATATT
1 TAAAAATTTAAAAATAA-ATT
* * *
18404173 TAAATATTTTAGAATAAATT
1 TAAAAATTTAAAAATAAATT
18404193 TAA
1 TAA
18404196 GTAAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAAATTTAAAAATAAATT
Found at i:18417261 original size:10 final size:8
Alignment explanation
Indices: 18417235--18417259 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18417225 GTATCACATG
18417235 TTAATATA
1 TTAATATA
18417243 TTAATATA
1 TTAATATA
18417251 TTAATATA
1 TTAATATA
18417259 T
1 T
18417260 ATACATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAATATA
Found at i:18417472 original size:21 final size:21
Alignment explanation
Indices: 18417419--18417514 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
18417409 GAGCTAAACA
*
18417419 GAAACCCATAAGGGTTGAACT
1 GAAACCCATAAGAGTTGAACT
* *
18417440 GAAACTCGTAAGAGTTGAAC-
1 GAAACCCATAAGAGTTGAACT
* * *
18417460 GAAAACCCATAAGGGTTAAAAT
1 G-AAACCCATAAGAGTTGAACT
* * * * *
18417482 GAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGAGTTGAACT
18417503 GAAACCCATAAG
1 GAAACCCATAAG
18417515 GGTTAAACAA
Statistics
Matches: 54, Mismatches: 19, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
GAAACCCATAAGAGTTGAACT
Found at i:18417495 original size:42 final size:42
Alignment explanation
Indices: 18417420--18417521 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
18417410 AGCTAAACAG
* * ** *
18417420 AAACCCATAAGGGTTGAACTGAAACTCGTAAGAGTTGAACGA
1 AAACCCATAAGGGTTAAAATGAAACTCAAAAGAGCTGAACGA
* *
18417462 AAACCCATAAGGGTTAAAATGAAGCTCAAAAGAGCTGAACGG
1 AAACCCATAAGGGTTAAAATGAAACTCAAAAGAGCTGAACGA
18417504 AAACCCATAAGGGTTAAA
1 AAACCCATAAGGGTTAAA
18417522 CAAAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAAATGAAACTCAAAAGAGCTGAACGA
Found at i:18423017 original size:19 final size:17
Alignment explanation
Indices: 18422995--18423055 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
18422985 TTCTTTCTCT
18422995 TTTTCTTTCTCAATTTTC
1 TTTTCTTTCTCAA-TTTC
*
18423013 GTTTTGC-TTCTCTATTTC
1 -TTTT-CTTTCTCAATTTC
18423031 -TTTCTTTCTC-ATTTC
1 TTTTCTTTCTCAATTTC
*
18423046 TATTCTTTCT
1 TTTTCTTTCT
18423056 TTTGTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.16
16 16 0.43
18 4 0.11
19 10 0.27
20 1 0.03
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTCTTTCTCAATTTC
Found at i:18423854 original size:83 final size:84
Alignment explanation
Indices: 18423726--18423987 Score: 298
Period size: 84 Copynumber: 3.1 Consensus size: 84
18423716 GTTACAAGAT
* * * *
18423726 TTTATTTAATTCAATTCAAATTAGAAAACAAAACAAAATAAAATAAAATCTTGTTAAATGGCGGG
1 TTTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGGG
18423791 AATAAATTCTGAAACAGAA
66 AATAAATTCTGAAACAGAA
* * *** * * *
18423810 -TTATTTGATT-ACGTCTTTGTTTGGAAACAAAATAACATCAAATAAAATCTTGTTAAACGGCGG
1 TTTATTTAATTCAAGTC-AAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGG
* *
18423873 GAATAAATCCCGAAACA-AA
65 GAATAAATTCTGAAACAGAA
* * * *
18423892 TTTTATTTAATTCAATTCAAATTAGGAAACAAAGTAAAATCAAATAAAATCTTATTAAATGGCGA
1 -TTTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGG
*
18423957 GAATAAA-TCTCGAAACAGAT
65 GAATAAATTCT-GAAACAGAA
18423977 TTTATTTAATT
1 TTTATTTAATT
18423988 TAATTTCTCG
Statistics
Matches: 143, Mismatches: 29, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
82 5 0.03
83 63 0.44
84 71 0.50
85 4 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (84 bp):
TTTATTTAATTCAAGTCAAATTAGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGGG
AATAAATTCTGAAACAGAA
Found at i:18424048 original size:87 final size:86
Alignment explanation
Indices: 18423752--18424156 Score: 353
Period size: 87 Copynumber: 4.8 Consensus size: 86
18423742 CAAATTAGAA
* * * * * *
18423752 AACAAAA-CAAAATAAAATAAAATCTTGTTAAATGGCGGGAATAAATTCTGAAACAGA-ATTATT
1 AACAAAATC-AAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATT
* ** * *
18423815 TGA-TT-ACGTCT-TTGTTTGGA
65 TAATTTAATTTCTCAT-TTTGGC
* *
18423835 AACAAAAT-AACATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAAATTTTATT
1 AACAAAATCAA-ATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATT
* * * * *
18423899 TAATTCAA-TTC-AAATTAGGA
65 TAATTTAATTTCTCATTTTGGC
* * * * *
18423919 AACAAAGTAAAATCAAATAAAATCTTATTAAATGGCGAGAATAAATCTCGAAACAGATTTTATTT
1 AACAAAATCAAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTT
*
18423984 AATTTAATTTCTCGTTTGTGGC
66 AATTTAATTTCTCATTT-TGGC
* * ** *
18424006 AACAAAATCAAATCAAATAAATTTTTATTAAACGTTGGGAATAAATCCCAAAACAGATTTTATTT
1 AACAAAATCAAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTT
*
18424071 TATTTAATTTCTCATTTTTGGC
66 AATTTAATTTCTCA-TTTTGGC
** * * * * *
18424093 AACAAAATCAAAATGTAAT-AAATC-CATTGAACGGCGGGAATCAATCTCGAAACATATTTTATT
1 AACAAAATC-AAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATT
18424156 T
65 T
18424157 TACTCGTTGT
Statistics
Matches: 262, Mismatches: 48, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
82 2 0.01
83 48 0.18
84 74 0.28
85 8 0.03
86 35 0.13
87 85 0.32
88 10 0.04
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (86 bp):
AACAAAATCAAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTT
AATTTAATTTCTCATTTTGGC
Found at i:18424199 original size:76 final size:78
Alignment explanation
Indices: 18424119--18424311 Score: 259
Period size: 76 Copynumber: 2.5 Consensus size: 78
18424109 AATAAATCCA
*
18424119 TTGAACGGCGGGAATCAATCTCGAAACATATTTTATTTTACTCGTTGT-TGGAAAT-AAA-AAAA
1 TTGAACGGCGGGAATCAATC-CGAAACAGATTTTATTTTACTCGTT-TCTGGAAATAAAACAAAA
18424181 TTGA-AATAAAATCG
64 TTGAGAATAAAATCG
*
18424195 TTGAACGGCGGGAATCAATCCTGAAACGGATTTTATTTTACTCGTTTCTGGAAATAAAACAAAAT
1 TTGAACGGCGGGAATCAATCC-GAAACAGATTTTATTTTACTCGTTTCTGGAAATAAAACAAAAT
*
18424260 TTAGAATAAAATCG
65 TGAGAATAAAATCG
* * * *
18424274 TTAAACGTCAGGAATCAATCCCGAAATAGATTTTATTT
1 TTGAACGGCGGGAATCAAT-CCGAAACAGATTTTATTT
18424312 ACCTTTAATT
Statistics
Matches: 103, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
75 2 0.02
76 49 0.48
77 3 0.03
78 7 0.07
79 40 0.39
80 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (78 bp):
TTGAACGGCGGGAATCAATCCGAAACAGATTTTATTTTACTCGTTTCTGGAAATAAAACAAAATT
GAGAATAAAATCG
Found at i:18424356 original size:88 final size:87
Alignment explanation
Indices: 18424245--18424411 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 87
18424235 CTCGTTTCTG
* * * *
18424245 GAAATAAAACAAAATTTAGAATAAAAT-CGTTAAACGTC-AGGAATCAATCCCGAAATAGATTTT
1 GAAATAAAACAAAATATAGAATAAAATCCGTTAAACGGCGA-GAATAAATCCCGAAACAGATTTT
18424308 ATTTACCTTTAATTTCCCGTTTT
65 ATTTACCTTTAATTTCCCGTTTT
** *
18424331 GAAATAAAATCAAAATAATAGAATAAAATCCGTTGTACGGCGAGAATAAATCCTGAAACAGATTT
1 GAAATAAAA-CAAAAT-ATAGAATAAAATCCGTTAAACGGCGAGAATAAATCCCGAAACAGATTT
*
18424396 TATTTACTTTTAATTT
64 TATTTACCTTTAATTT
18424412 TGGAAAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 9 0.13
87 6 0.09
88 11 0.16
89 42 0.61
90 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (87 bp):
GAAATAAAACAAAATATAGAATAAAATCCGTTAAACGGCGAGAATAAATCCCGAAACAGATTTTA
TTTACCTTTAATTTCCCGTTTT
Found at i:18424465 original size:73 final size:73
Alignment explanation
Indices: 18424342--18424480 Score: 181
Period size: 74 Copynumber: 1.9 Consensus size: 73
18424332 AAATAAAATC
* * ** *
18424342 AAAATAATAGAATAAAATCCGTTGTACGGCGAGAATAAATCCTGAAACAGATTTTATTTACTTTT
1 AAAAAAATAGAATAAAATCCATTAAACGGCGAGAATAAATCCCGAAACAGATTTTA-TTACTTTT
18424407 AATTTTGGA
65 AATTTTGGA
* * * *
18424416 AAAAAAATCGAATAAAATCCATTAAACGTCGGGAA-AAATCCCGAAACAGATTTTATTAGTTTTA
1 AAAAAAATAGAATAAAATCCATTAAACGGCGAGAATAAATCCCGAAACAGATTTTATTACTTTTA
18424480 A
66 A
18424481 AATTCATTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 9 0.16
73 19 0.34
74 28 0.50
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (73 bp):
AAAAAAATAGAATAAAATCCATTAAACGGCGAGAATAAATCCCGAAACAGATTTTATTACTTTTA
ATTTTGGA
Found at i:18430478 original size:19 final size:19
Alignment explanation
Indices: 18430454--18430490 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18430444 TTTTAATTTC
*
18430454 AAAATAAAATAAAGATAAT
1 AAAATAAAATAAAAATAAT
*
18430473 AAAATAAGATAAAAATAA
1 AAAATAAAATAAAAATAA
18430491 AATACAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAAAAATAAT
Found at i:18438742 original size:39 final size:39
Alignment explanation
Indices: 18438667--18438743 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
18438657 ATAAATAAGC
* * * *
18438667 ATTTTTGTTAGTAGAATTCAATAATGATTAATTTTTACA
1 ATTTTAGTTAGTAGAATTCAATAACGACTAACTTTTACA
** *
18438706 ATTTTAGTTAGTAGAATTTGATAGCGACTAACTTTTAC
1 ATTTTAGTTAGTAGAATTCAATAACGACTAACTTTTAC
18438744 GATTCTTACG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (39 bp):
ATTTTAGTTAGTAGAATTCAATAACGACTAACTTTTACA
Found at i:18441446 original size:25 final size:26
Alignment explanation
Indices: 18441406--18441454 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
18441396 GTAAAATTAT
18441406 AATAAAATTTTGAT-AAAATAATAAG
1 AATAAAATTTTGATAAAAATAATAAG
18441431 AATAAAATTATT-ATAAAAATAATA
1 AATAAAATT-TTGATAAAAATAATA
18441455 TTTCAGTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATAAAATTTTGATAAAAATAATAAG
Found at i:18442369 original size:21 final size:21
Alignment explanation
Indices: 18442345--18442389 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
18442335 TTATAAAAAA
18442345 TTTTTATAACTTTTTAA-TAAT
1 TTTTTAT-ACTTTTTAATTAAT
*
18442366 TTTTTATAGTTTTTAATTAAT
1 TTTTTATACTTTTTAATTAAT
18442387 TTT
1 TTT
18442390 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATACTTTTTAATTAAT
Found at i:18442389 original size:11 final size:10
Alignment explanation
Indices: 18442343--18442389 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
18442333 TTTTATAAAA
18442343 AATTTTT-AT
1 AATTTTTAAT
18442352 AACTTTTTAAT
1 AA-TTTTTAAT
*
18442363 AATTTTTTAT
1 AATTTTTAAT
*
18442373 AGTTTTTAATT
1 AATTTTTAA-T
18442384 AATTTT
1 AATTTT
18442390 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 19 0.61
11 10 0.32
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:18451455 original size:6 final size:6
Alignment explanation
Indices: 18451444--18451471 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18451434 TTATGCTGGA
18451444 AATGGC AATGGC AATGGC AATGGC AATG
1 AATGGC AATGGC AATGGC AATGGC AATG
18451472 ACAAGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (6 bp):
AATGGC
Found at i:18451483 original size:18 final size:18
Alignment explanation
Indices: 18451441--18451483 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
18451431 TAATTATGCT
* *
18451441 GGAAATGGCAATGGCAAT
1 GGAAATGGCAATGACAAG
*
18451459 GGCAATGGCAATGACAAG
1 GGAAATGGCAATGACAAG
18451477 GGAAATG
1 GGAAATG
18451484 TTGCTGGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.35, T:0.14
Consensus pattern (18 bp):
GGAAATGGCAATGACAAG
Found at i:18453492 original size:13 final size:13
Alignment explanation
Indices: 18453470--18453544 Score: 61
Period size: 13 Copynumber: 6.2 Consensus size: 13
18453460 GGCCTAGCCC
18453470 AAAT-TATATATT
1 AAATATATATATT
18453482 AAATATATATATT
1 AAATATATATATT
** * * *
18453495 TGAT-TAAAAATC
1 AAATATATATATT
18453507 AAATATATATATT
1 AAATATATATATT
*
18453520 TAATATATATA--
1 AAATATATATATT
18453531 AAATATATAT-TT
1 AAATATATATATT
18453543 AA
1 AA
18453545 TATGGGCCGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
11 9 0.19
12 13 0.28
13 25 0.53
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (13 bp):
AAATATATATATT
Found at i:18453527 original size:11 final size:11
Alignment explanation
Indices: 18453511--18453547 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
18453501 AAAATCAAAT
18453511 ATATATATTTA
1 ATATATATTTA
**
18453522 ATATATATAAA
1 ATATATATTTA
18453533 ATATATATTTA
1 ATATATATTTA
18453544 ATAT
1 ATAT
18453548 GGGCCGGGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATATTTA
Found at i:18454995 original size:5 final size:5
Alignment explanation
Indices: 18454982--18455023 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
18454972 CTCCACCTTT
* * *
18454982 CCTAG CCGAG CCGAG CCGAG CCTAG CCTAG CCTAG CCTAG CC
1 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CC
18455024 AGGCGTGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.19, C:0.43, G:0.26, T:0.12
Consensus pattern (5 bp):
CCTAG
Found at i:18455417 original size:24 final size:24
Alignment explanation
Indices: 18455390--18455443 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
18455380 TGGATTTTAT
18455390 TTTCTGTTTTTGTTTCTGGGTCTG
1 TTTCTGTTTTTGTTTCTGGGTCTG
*
18455414 TTTCTGTTTTTGTTTCTGTGTCTG
1 TTTCTGTTTTTGTTTCTGGGTCTG
18455438 TTTCTG
1 TTTCTG
18455444 GATTCGCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.00, C:0.13, G:0.22, T:0.65
Consensus pattern (24 bp):
TTTCTGTTTTTGTTTCTGGGTCTG
Found at i:18455419 original size:6 final size:6
Alignment explanation
Indices: 18455390--18455443 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
18455380 TGGATTTTAT
* ** * *
18455390 TTTCTG TTTTTG TTTCTG GGTCTG TTTCTG TTTTTG TTTCTG TGTCTG
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG
18455438 TTTCTG
1 TTTCTG
18455444 GATTCGCATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.13, G:0.22, T:0.65
Consensus pattern (6 bp):
TTTCTG
Found at i:18460049 original size:27 final size:27
Alignment explanation
Indices: 18459984--18460053 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
18459974 CAGATTTTAG
* *
18459984 ATTGTTGGATTTTGATATATGTCTTGA
1 ATTGTTGGATATTGATATATGTCTTAA
* *
18460011 ATTGGTTAGATATTGAT-TATGTTTTAA
1 ATT-GTTGGATATTGATATATGTCTTAA
18460038 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
18460054 ATTGATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (27 bp):
ATTGTTGGATATTGATATATGTCTTAA
Found at i:18460058 original size:32 final size:33
Alignment explanation
Indices: 18460022--18460089 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 33
18460012 TTGGTTAGAT
18460022 ATTG-ATTATGTTTTAA-CATTGTTGGATATTGA
1 ATTGTATTATGTTTTAAGC-TTGTTGGATATTGA
18460054 ATTGATTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTG--TATTATGTTTTAAGCTTGTTGGATATTGA
18460089 A
1 A
18460090 ATTATTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 4 0.12
35 27 0.84
36 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (33 bp):
ATTGTATTATGTTTTAAGCTTGTTGGATATTGA
Found at i:18461516 original size:34 final size:35
Alignment explanation
Indices: 18461460--18461526 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
18461450 CAAACACTAG
* *
18461460 AAAATATTTTTCAGTAAGTCATTTTACAGAAAAAT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAAT
*
18461495 AAAATATTTTCCAG-AAATCATTTTATAGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
18461527 TATTTTACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAAT
Found at i:18464693 original size:59 final size:56
Alignment explanation
Indices: 18464610--18464805 Score: 173
Period size: 56 Copynumber: 3.4 Consensus size: 56
18464600 CATTCGCACT
* * * *
18464610 TTTTTTTATCCGAATTAATCTTTGAACTTGACAATTATTCTCATATAGGGGTTTAAA
1 TTTTTTTGTCCAAATTAATTTTTGAACTTG-CAATTATTCTCATATAGGGGTTTGAA
* * * * * * *
18464667 TTTTTCTTGGTCTAAGTTGATTTTTGAACTCCGCAATTGTTCT-TTCATA-GGATTTGAA
1 TTTTT-TT-GTCCAAATTAATTTTTGAACT-TGCAATTATTCTCAT-ATAGGGGTTTGAA
* * *
18464725 TTTTTTTGTCCAAATTAATTTTTGAACTTGTCGATTAATCTCATATTGGGGTTTGAA
1 TTTTTTTGTCCAAATTAATTTTTGAACTTG-CAATTATTCTCATATAGGGGTTTGAA
* *
18464782 TTTTTTT-TTCAAATTAATTCTTGA
1 TTTTTTTGTCCAAATTAATTTTTGA
18464806 TATTTCCTTG
Statistics
Matches: 109, Mismatches: 23, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
55 1 0.01
56 42 0.39
57 23 0.21
58 15 0.14
59 27 0.25
60 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (56 bp):
TTTTTTTGTCCAAATTAATTTTTGAACTTGCAATTATTCTCATATAGGGGTTTGAA
Found at i:18464955 original size:31 final size:31
Alignment explanation
Indices: 18464917--18464983 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
18464907 ACCAAAAAAA
* *
18464917 AAGTTCAAACTCCAATGTGAGAACAATTACC
1 AAGTTCAAACTCCAATATAAGAACAATTACC
* * *
18464948 AAGTTCAAGCTCTAATATAAGAACAATTATC
1 AAGTTCAAACTCCAATATAAGAACAATTACC
18464979 AAGTT
1 AAGTT
18464984 TAGGGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (31 bp):
AAGTTCAAACTCCAATATAAGAACAATTACC
Found at i:18465100 original size:17 final size:18
Alignment explanation
Indices: 18465080--18465121 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
18465070 AAATAAACAA
18465080 TTAAAAAT-CATAAAATT
1 TTAAAAATACATAAAATT
*
18465097 TTAAAAATATATAAAATT
1 TTAAAAATACATAAAATT
18465115 TATAAAA
1 T-TAAAA
18465122 CTGGTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAATACATAAAATT
Found at i:18465723 original size:40 final size:40
Alignment explanation
Indices: 18465674--18465753 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
18465664 GATCTGGGAG
18465674 ATAGACGCTTTCTCTTTCAGTTTTTTCATGAGGTAGATAT
1 ATAGACGCTTTCTCTTTCAGTTTTTTCATGAGGTAGATAT
18465714 ATAGACGCTTTCTCTTTCAGTTTTTTCATGAGGTAGATAT
1 ATAGACGCTTTCTCTTTCAGTTTTTTCATGAGGTAGATAT
18465754 TCAAAGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (40 bp):
ATAGACGCTTTCTCTTTCAGTTTTTTCATGAGGTAGATAT
Found at i:18472406 original size:76 final size:76
Alignment explanation
Indices: 18472317--18472458 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
18472307 TGCATGATTT
18472317 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAGACCT-TTACCAAAATCTGCTCCTTCAG
1 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAA-ACCTCTT-CCAAAATCTGCTCCTTCAG
18472381 CTACCATAGCGTG
64 CTACCATAGCGTG
* * * * * *
18472394 TTGAAGTT-AAAAGCGTTGATGTTGTGCAGATGTAAAACCTCTTTCGAATTCTGCTCCTTCAGCT
1 TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAACCTCTTCCAAAATCTGCTCCTTCAGCT
18472458 A
66 A
18472459 TACCGGTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
75 23 0.40
76 28 0.48
77 7 0.12
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (76 bp):
TTGAAATTAAAAAGCATTGATGTTGTGCAAATGTAAAACCTCTTCCAAAATCTGCTCCTTCAGCT
ACCATAGCGTG
Found at i:18485710 original size:24 final size:24
Alignment explanation
Indices: 18485683--18485735 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
18485673 TATTAATTAA
*
18485683 AGAAAGGATTAAATTGTAAAAGTG
1 AGAAAGGATTAAATTGCAAAAGTG
18485707 AGAAAGGATTAAATTGCAAAAGTG
1 AGAAAGGATTAAATTGCAAAAGTG
18485731 AGAAA
1 AGAAA
18485736 ATTTTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.21
Consensus pattern (24 bp):
AGAAAGGATTAAATTGCAAAAGTG
Found at i:18488734 original size:16 final size:15
Alignment explanation
Indices: 18488708--18488737 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18488698 TATTATTTCA
18488708 TTATTTATTCTTTTG
1 TTATTTATTCTTTTG
18488723 TTATTCTATTCTTTT
1 TTATT-TATTCTTTT
18488738 CATGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTATTCTTTTG
Found at i:18491348 original size:27 final size:27
Alignment explanation
Indices: 18491313--18491373 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 27
18491303 CATTAAACCG
18491313 AAAACTTGCAATTTAACCACTTTTAATT
1 AAAA-TTGCAATTTAACCACTTTTAATT
18491341 AAAATTGCAATTTAACCACTTTTAATT
1 AAAATTGCAATTTAACCACTTTTAATT
18491368 AAAATT
1 AAAATT
18491374 CATGCTAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (27 bp):
AAAATTGCAATTTAACCACTTTTAATT
Found at i:18493668 original size:22 final size:21
Alignment explanation
Indices: 18493640--18493696 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
18493630 CCCAATTTAA
18493640 TTCTAACTAAGTT-TACTTACTT
1 TTCTAACTAA-TTATACTT-CTT
18493662 TTCTAACTTAATTCATACTTCTT
1 TTCTAAC-TAATT-ATACTTCTT
*
18493685 TTCTACCTAATT
1 TTCTAACTAATT
18493697 TCTTGCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 14 0.45
23 12 0.39
24 5 0.16
ACGTcount: A:0.26, C:0.21, G:0.02, T:0.51
Consensus pattern (21 bp):
TTCTAACTAATTATACTTCTT
Found at i:18494114 original size:17 final size:17
Alignment explanation
Indices: 18494092--18494131 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
18494082 TTGTTTTCTT
18494092 TTTACTCTTTTAGTTTC
1 TTTACTCTTTTAGTTTC
18494109 TTTACTCTTTTAGTTTC
1 TTTACTCTTTTAGTTTC
18494126 TTTACT
1 TTTACT
18494132 TTATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTACTCTTTTAGTTTC
Found at i:18495538 original size:59 final size:59
Alignment explanation
Indices: 18495466--18495583 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
18495456 TAAGTGTAAC
18495466 ACCCCTTACCTGACCCGAACACCAGGTTAAGGTACTAGGATGTCACATTCATTGCTAGA
1 ACCCCTTACCTGACCCGAACACCAGGTTAAGGTACTAGGATGTCACATTCATTGCTAGA
18495525 ACCCCTTACCTGACCCGAACACCAGGTTAAGGTACTAGGATGTCACATTCATTGCTAGA
1 ACCCCTTACCTGACCCGAACACCAGGTTAAGGTACTAGGATGTCACATTCATTGCTAGA
18495584 GCAAATTCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (59 bp):
ACCCCTTACCTGACCCGAACACCAGGTTAAGGTACTAGGATGTCACATTCATTGCTAGA
Found at i:18500820 original size:17 final size:18
Alignment explanation
Indices: 18500784--18500831 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
18500774 CTCAAAAATT
18500784 TAATTAATATAAAATATTAA
1 TAATTAA-AT-AAATATTAA
18500804 TAATTAAATAAAT-TTAA
1 TAATTAAATAAATATTAA
* *
18500821 AAATTAGATAA
1 TAATTAAATAA
18500832 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 4 0.15
19 2 0.08
20 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAATTAAATAAATATTAA
Found at i:18500821 original size:25 final size:27
Alignment explanation
Indices: 18500793--18500846 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
18500783 TTAATTAATA
18500793 TAAAATATTA-ATAATTAAA-T-AAATT
1 TAAAA-ATTAGATAATTAAATTAAAATT
18500818 TAAAAATTAGATAATTAAATTAAAATT
1 TAAAAATTAGATAATTAAATTAAAATT
18500845 TA
1 TA
18500847 GGAGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.15
25 14 0.54
26 1 0.04
27 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAAATTAGATAATTAAATTAAAATT
Found at i:18501453 original size:30 final size:30
Alignment explanation
Indices: 18501393--18501454 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
18501383 GCTTTTTGAA
* * *
18501393 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAAATTTT
18501423 AATATTTACAAAAAGA-GCAACCAAAATTTT
1 AATATTTACAAAAAGAGGC-ACCAAAATTTT
18501453 AA
1 AA
18501455 AAACAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAAATTTT
Found at i:18508356 original size:2 final size:2
Alignment explanation
Indices: 18508349--18508385 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18508339 AAATTCATGA
18508349 AT AT AT AT AT 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 AT AT AT AT AT A
18508386 AATGATAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18508661 original size:21 final size:22
Alignment explanation
Indices: 18508628--18508705 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
18508618 GATGTACGGG
18508628 CTTCACTTTGCACTGAAGTGCCA
1 CTTCAC-TTGCACTGAAGTGCCA
*
18508651 C-TCACTTGCAC-CATAGTGCCA
1 CTTCACTTGCACTGA-AGTGCCA
*
18508672 CTTTCACTTGCACTGTAGTGCCA
1 C-TTCACTTGCACTGAAGTGCCA
18508695 CTATCACTTGC
1 CT-TCACTTGC
18508706 GTGCTTAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 5 0.11
23 27 0.57
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTCACTTGCACTGAAGTGCCA
Found at i:18511201 original size:21 final size:22
Alignment explanation
Indices: 18511168--18511208 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18511158 AAATATAAGT
*
18511168 ATAAATAATATAATT-AAGAAC
1 ATAAATAACATAATTCAAGAAC
*
18511189 ATAAATAGCATAATTCAAGA
1 ATAAATAACATAATTCAAGA
18511209 GGAGAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (22 bp):
ATAAATAACATAATTCAAGAAC
Found at i:18511341 original size:26 final size:26
Alignment explanation
Indices: 18511309--18511370 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
18511299 CATGAAACTT
* **
18511309 AATACAAAA-TGATATAATCGGAGAAA
1 AATACAAAATTAATATAATCAAAG-AA
18511335 AATACAAAAATTAATATAATCAAAGAA
1 AATAC-AAAATTAATATAATCAAAGAA
18511362 AATACAAAA
1 AATACAAAA
18511371 GTGCCCATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 9 0.29
27 11 0.35
28 11 0.35
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (26 bp):
AATACAAAATTAATATAATCAAAGAA
Found at i:18517029 original size:50 final size:50
Alignment explanation
Indices: 18516914--18517162 Score: 273
Period size: 50 Copynumber: 4.8 Consensus size: 50
18516904 GATAATAACA
* * ** * **
18516914 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCAG
* *
18516965 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
* * * *
18517015 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
* * *
18517065 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-TCA-G
* *
18517120 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
18517163 TTACGCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 90 0.54
51 33 0.20
53 4 0.02
54 1 0.01
55 1 0.01
56 38 0.23
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
Found at i:18517100 original size:100 final size:104
Alignment explanation
Indices: 18516913--18517162 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
18516903 TGATAATAAC
** * *
18516913 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
18516978 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-TCA-G
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
18517015 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
18517079 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
18517120 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18517163 TTACGCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 2 0.02
105 1 0.01
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:18517278 original size:13 final size:13
Alignment explanation
Indices: 18517257--18517287 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18517247 GCTTAGATCA
*
18517257 TCATCAAATAAAT
1 TCATAAAATAAAT
18517270 TCATAAAATAAAT
1 TCATAAAATAAAT
18517283 TCATA
1 TCATA
18517288 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:18524367 original size:25 final size:25
Alignment explanation
Indices: 18524339--18524403 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
18524329 TTAAGTGTTT
*
18524339 TCAGTATAGT-CTATCTATAGTAGTC
1 TCAGTATA-TACTATCTATAGAAGTC
*
18524364 TCAGTATATACTATCTATAGAAGTT
1 TCAGTATATACTATCTATAGAAGTC
*
18524389 TCAGGATATACTATC
1 TCAGTATATACTATC
18524404 AAAGACAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (25 bp):
TCAGTATATACTATCTATAGAAGTC
Found at i:18524413 original size:25 final size:25
Alignment explanation
Indices: 18524349--18524417 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
18524339 TCAGTATAGT
* * * *
18524349 CTATCTATAGTAGTCTCAGTATATA
1 CTATCTAAAGAAGTTTCAGGATATA
*
18524374 CTATCTATAGAAGTTTCAGGATATA
1 CTATCTAAAGAAGTTTCAGGATATA
18524399 CTATC-AAAGACAGTTTCAG
1 CTATCTAAAGA-AGTTTCAG
18524418 TTTCAGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.10
25 35 0.90
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (25 bp):
CTATCTAAAGAAGTTTCAGGATATA
Found at i:18524537 original size:15 final size:14
Alignment explanation
Indices: 18524503--18524537 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
18524493 TAAAAAAAAT
18524503 TTAAAAATCAGTTC
1 TTAAAAATCAGTTC
18524517 TTAAAAATCACG-TC
1 TTAAAAATCA-GTTC
18524531 TTAAAAA
1 TTAAAAA
18524538 CCCACATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.95
15 1 0.05
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (14 bp):
TTAAAAATCAGTTC
Found at i:18540715 original size:49 final size:49
Alignment explanation
Indices: 18540529--18540707 Score: 182
Period size: 50 Copynumber: 3.6 Consensus size: 49
18540519 GGGTAAAGAG
* * *
18540529 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGAAAC
* ** * * *
18540579 GTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGA-AAC
* * * * *
18540630 -TCCCATGTAAGACCATATCTGGGATATAGTATTGGCA-GTACAGGAAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-ACATGAAAC
18540678 ATCCCATGTAAGACCATGTCTGGGACATGG
1 ATCCCATGTAAGACCATGTCTGGGACATGG
18540708 TTTTGGCATG
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 3 0.03
49 30 0.29
50 71 0.68
51 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (49 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGACATGAAAC
Found at i:18543397 original size:6 final size:7
Alignment explanation
Indices: 18543380--18543405 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18543370 AAGCAATAAG
18543380 AAAAAAC
1 AAAAAAC
18543387 AAAAAAC
1 AAAAAAC
18543394 AAAAAAC
1 AAAAAAC
18543401 AAAAA
1 AAAAA
18543406 TAAAGCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:18546054 original size:47 final size:47
Alignment explanation
Indices: 18545916--18546055 Score: 163
Period size: 47 Copynumber: 3.0 Consensus size: 47
18545906 TTATTGCATT
* * * * * * *
18545916 ATTGGCAGCTTGTTTACATATATTGGCATTTTCTTTGCATTATCGTT
1 ATTGGCAGCTTGTTTGCATATATTGACAATTTATCTGCATTACCGTC
* * * *
18545963 ACTGGCAGCTTGTCTGTATATATTGACAATTTATCTACATTACCGTC
1 ATTGGCAGCTTGTTTGCATATATTGACAATTTATCTGCATTACCGTC
* *
18546010 ATTGGCAGCTTGTTTGCATATATTGACAATTTATCCGCACTACCGT
1 ATTGGCAGCTTGTTTGCATATATTGACAATTTATCTGCATTACCGT
18546056 ACTGGTGGTT
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 76 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (47 bp):
ATTGGCAGCTTGTTTGCATATATTGACAATTTATCTGCATTACCGTC
Found at i:18548668 original size:18 final size:18
Alignment explanation
Indices: 18548647--18548684 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18548637 AGAAAATTCT
*
18548647 AAAAATTAAAAATAGATA
1 AAAAATCAAAAATAGATA
*
18548665 AAAACTCAAAAATAGATA
1 AAAAATCAAAAATAGATA
18548683 AA
1 AA
18548685 GTAAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAATCAAAAATAGATA
Found at i:18557245 original size:31 final size:29
Alignment explanation
Indices: 18557210--18557299 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 29
18557200 TTTTGTAAGC
*
18557210 ATTTAAATTTGGTTTCAATATTGAATTTGGT
1 ATTTAAATTT-GTTTCAAT-TTCAATTTGGT
18557241 ATTT-AATTT-TTTC--TTCTCAATTTGGT
1 ATTTAAATTTGTTTCAATT-TCAATTTGGT
* *
18557267 ATTTAAGTTTGTTTTCAATGTTCAATATGGT
1 ATTTAAATTTG-TTTCAAT-TTCAATTTGGT
18557298 AT
1 AT
18557300 CTAGATCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
25 1 0.02
26 14 0.29
27 4 0.08
28 4 0.08
29 4 0.08
30 5 0.10
31 16 0.33
32 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (29 bp):
ATTTAAATTTGTTTCAATTTCAATTTGGT
Found at i:18560266 original size:13 final size:13
Alignment explanation
Indices: 18560248--18560277 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18560238 CAATAAAAAG
*
18560248 ATATATAATTTAT
1 ATATATAAGTTAT
18560261 ATATATAAGTTAT
1 ATATATAAGTTAT
18560274 ATAT
1 ATAT
18560278 GTTATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
ATATATAAGTTAT
Found at i:18566586 original size:2 final size:2
Alignment explanation
Indices: 18566579--18566618 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18566569 TGATAATACC
18566579 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
18566619 CAAAACATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18567836 original size:21 final size:20
Alignment explanation
Indices: 18567812--18567860 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
18567802 TAAATTTAAC
*
18567812 TCAATTTAATACAATTCATAT
1 TCAATTTAATACAATCCA-AT
* *
18567833 TCAATTCAATCCAATCCAAT
1 TCAATTTAATACAATCCAAT
18567853 TCATATTT
1 TCA-ATTT
18567861 TAGGCAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (20 bp):
TCAATTTAATACAATCCAAT
Found at i:18569451 original size:81 final size:81
Alignment explanation
Indices: 18569355--18569503 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
18569345 TTAGATTATG
* * * ** * * * *
18569355 CCACAAATGTTATTCTTTTAGAGTATGCCACAAAA-TCTATTCTTTCATAGTACGCCATAAAGAT
1 CCACAAAGGTTATTCTTTCAGAGAACACCA-AAAAGGCTATTCTTTCAAAATACGCCACAAAGAT
18569419 TATTCTTTCATAGTACA
65 TATTCTTTCATAGTACA
*
18569436 CCACAAAGGTTATTCTTTCAGAGAACACCAAAAAGGCTATTCTTTCAAAATACGCCACAAAGGTT
1 CCACAAAGGTTATTCTTTCAGAGAACACCAAAAAGGCTATTCTTTCAAAATACGCCACAAAGATT
18569501 ATT
66 ATT
18569504 TCTTAGCTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 4 0.07
81 53 0.93
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (81 bp):
CCACAAAGGTTATTCTTTCAGAGAACACCAAAAAGGCTATTCTTTCAAAATACGCCACAAAGATT
ATTCTTTCATAGTACA
Found at i:18569463 original size:27 final size:27
Alignment explanation
Indices: 18569327--18569503 Score: 167
Period size: 27 Copynumber: 6.6 Consensus size: 27
18569317 ATCAGAACAT
* * * *
18569327 GCCACAAAGGCTATTCTTTTAGATTAT
1 GCCACAAAGGTTATTCTTTCAGAGTAC
* * *
18569354 GCCACAAATGTTATTCTTTTAGAGTAT
1 GCCACAAAGGTTATTCTTTCAGAGTAC
* *
18569381 GCCACAAA-ATCTATTCTTTCATAGTAC
1 GCCACAAAGGT-TATTCTTTCAGAGTAC
* * *
18569408 GCCATAAAGATTATTCTTTCATAGTAC
1 GCCACAAAGGTTATTCTTTCAGAGTAC
* *
18569435 ACCACAAAGGTTATTCTTTCAGAGAAC
1 GCCACAAAGGTTATTCTTTCAGAGTAC
* * * * *
18569462 ACCAAAAAGGCTATTCTTTCAAAATAC
1 GCCACAAAGGTTATTCTTTCAGAGTAC
18569489 GCCACAAAGGTTATT
1 GCCACAAAGGTTATT
18569504 TCTTAGCTGT
Statistics
Matches: 127, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
26 1 0.01
27 124 0.98
28 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (27 bp):
GCCACAAAGGTTATTCTTTCAGAGTAC
Found at i:18570950 original size:27 final size:27
Alignment explanation
Indices: 18570891--18570950 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
18570881 CAACCAATAG
* *
18570891 AGTCCGTCGAGATATTAAAAGCGAGGC
1 AGTCTGTCGAGATAGTAAAAGCGAGGC
* *
18570918 AATCTGTCGAGATAGTAAACA-CGAGGT
1 AGTCTGTCGAGATAGTAAA-AGCGAGGC
18570945 AGTCTG
1 AGTCTG
18570951 CTAGAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (27 bp):
AGTCTGTCGAGATAGTAAAAGCGAGGC
Found at i:18576373 original size:4 final size:4
Alignment explanation
Indices: 18576366--18576420 Score: 89
Period size: 4 Copynumber: 14.5 Consensus size: 4
18576356 TCAGTCACCC
18576366 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC- TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
18576412 TT-T TTCT TT
1 TTCT TTCT TT
18576421 TTATTTTGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 7 0.15
4 41 0.85
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTCT
Found at i:18577791 original size:81 final size:81
Alignment explanation
Indices: 18577656--18577821 Score: 314
Period size: 81 Copynumber: 2.0 Consensus size: 81
18577646 AACCAGATAC
18577656 CTCAAGCTACCAAGTAATTTGCCATCTTCTCTAGAATGGTTAGGCAAATGTACAATGGTGTCCTT
1 CTCAAGCTACCAAGTAATTTGCCATCTTCTCTAGAATGGTTAGGCAAATGTACAATGGTGTCCTT
18577721 ACTGAGGTACTAGTCT
66 ACTGAGGTACTAGTCT
* *
18577737 CTCAAGCTACCAAGTAATTTGCCATCTTCTTTAGAATGGTTAGGCAAATGTACAATGGTGTTCTT
1 CTCAAGCTACCAAGTAATTTGCCATCTTCTCTAGAATGGTTAGGCAAATGTACAATGGTGTCCTT
18577802 ACTGAGGTACTAGTCT
66 ACTGAGGTACTAGTCT
18577818 CTCA
1 CTCA
18577822 GGACTGTGGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (81 bp):
CTCAAGCTACCAAGTAATTTGCCATCTTCTCTAGAATGGTTAGGCAAATGTACAATGGTGTCCTT
ACTGAGGTACTAGTCT
Found at i:18585506 original size:21 final size:21
Alignment explanation
Indices: 18585468--18585507 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18585458 TTAGATATAA
* *
18585468 TAAAAATGAAAAATAGATATT
1 TAAAAAAGAAAAACAGATATT
*
18585489 TAAAAAAGAGAAACAGATA
1 TAAAAAAGAAAAACAGATA
18585508 CTAATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (21 bp):
TAAAAAAGAAAAACAGATATT
Found at i:18586786 original size:30 final size:30
Alignment explanation
Indices: 18586752--18586814 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
18586742 ACTTAACAAG
18586752 CAAATGCATATAAAATAATAACAAAATTAA
1 CAAATGCATATAAAATAATAACAAAATTAA
* * *
18586782 CAAATGCCTTTAAAATAATAATAAAATTAA
1 CAAATGCATATAAAATAATAACAAAATTAA
18586812 CAA
1 CAA
18586815 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCATATAAAATAATAACAAAATTAA
Found at i:18586862 original size:14 final size:14
Alignment explanation
Indices: 18586839--18586875 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18586829 TACAATATTC
18586839 AAATAATAACAACA
1 AAATAATAACAACA
*
18586853 AAATAGTAACAACA
1 AAATAATAACAACA
*
18586867 TAATAATAA
1 AAATAATAA
18586876 AATGGTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:18590094 original size:12 final size:12
Alignment explanation
Indices: 18590077--18590101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18590067 TAGGTCACCG
18590077 TTTCTTTTCTTT
1 TTTCTTTTCTTT
18590089 TTTCTTTTCTTT
1 TTTCTTTTCTTT
18590101 T
1 T
18590102 CCCGATTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:18600148 original size:38 final size:38
Alignment explanation
Indices: 18600104--18600227 Score: 239
Period size: 38 Copynumber: 3.3 Consensus size: 38
18600094 GAAAATCCAC
*
18600104 CTCCACCAATCCACCATTCCACCTTCGGTCCTCCACGG
1 CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
18600142 CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
1 CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
18600180 CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
1 CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
18600218 CTCCACCCAT
1 CTCCACCCAT
18600228 TTCCAGAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 85 1.00
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (38 bp):
CTCCACCCATCCACCATTCCACCTTCGGTCCTCCACGG
Found at i:18601874 original size:3 final size:3
Alignment explanation
Indices: 18601866--18601907 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
18601856 AATATTTTTG
18601866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18601908 CATTTTCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18602363 original size:36 final size:39
Alignment explanation
Indices: 18602300--18602372 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 39
18602290 ACAATATCCA
*
18602300 AACAATAACAACAGAAAAGTGGTAAT-AACAA-AATGGC
1 AACAATAACAACAGAAAAGTGGAAATAAACAACAATGGC
*
18602337 AACAA-AACAACATTAAAA-TGGAAATAAACAACAATG
1 AACAATAACAACA-GAAAAGTGGAAATAAACAACAATG
18602373 AAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 13 0.42
37 14 0.45
38 4 0.13
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (39 bp):
AACAATAACAACAGAAAAGTGGAAATAAACAACAATGGC
Found at i:18603306 original size:19 final size:20
Alignment explanation
Indices: 18603284--18603327 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18603274 ATTTATTTAT
*
18603284 TAAAATAAT-ATTTTATAAA
1 TAAAATAATAATCTTATAAA
*
18603303 TAAAATAATAATCTTATACA
1 TAAAATAATAATCTTATAAA
18603323 TAAAA
1 TAAAA
18603328 CAATTTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATAATAATCTTATAAA
Found at i:18612660 original size:16 final size:16
Alignment explanation
Indices: 18612626--18612673 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
18612616 GGTTAGGGTT
* *
18612626 TTTAATATTGTTA-GG
1 TTTAGTATTTTTAGGG
18612641 TTTAGTATTTTTAGGG
1 TTTAGTATTTTTAGGG
* *
18612657 TTTAGGATTTTTTGGG
1 TTTAGTATTTTTAGGG
18612673 T
1 T
18612674 ATTGGGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (16 bp):
TTTAGTATTTTTAGGG
Found at i:18633106 original size:66 final size:66
Alignment explanation
Indices: 18632922--18633107 Score: 223
Period size: 66 Copynumber: 2.8 Consensus size: 66
18632912 AGCCTAACAG
* * ** * * * *
18632922 GGCCTAGCACACGGCCGTGTGGCTTGGATGTGTGTTACAAGTCAGTATACTCACCATTTTTCACA
1 GGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAATTCAGTATGCTCACCATATTTCACA
*
18632987 T
66 C
* * *
18632988 GGCCTAGAACACGGGTATGTGGCTTGGCCATGTGTCACAAGTT-AGTATGCTCACCATATTTCAC
1 GGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAA-TTCAGTATGCTCACCATATTTCAC
18633052 AC
65 AC
*
18633054 GGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGACACAATTCAGTGA-GCTCAC
1 GGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAATTCAGT-ATGCTCAC
18633108 TAGTTTGGAC
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.02
66 97 0.96
67 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (66 bp):
GGCCTAGCACACGGGCATGTGGCTTGGCCGTGTGTCACAATTCAGTATGCTCACCATATTTCACA
C
Found at i:18640364 original size:27 final size:28
Alignment explanation
Indices: 18640334--18640401 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
18640324 ATATTAAATA
*
18640334 CAATATCCAACAAGGTT-AAAACATA-AT
1 CAATATCCAACAA-ATTCAAAACATATAT
* *
18640361 CAATATCTAACAAATTCAAGACATATAT
1 CAATATCCAACAAATTCAAAACATATAT
*
18640389 CAAAATCCAACAA
1 CAATATCCAACAA
18640402 TCTAAATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 19 0.56
28 13 0.38
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.22
Consensus pattern (28 bp):
CAATATCCAACAAATTCAAAACATATAT
Found at i:18642473 original size:2 final size:2
Alignment explanation
Indices: 18642466--18642504 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18642456 ACCACATGTG
18642466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18642505 TTTTTGGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18646964 original size:54 final size:54
Alignment explanation
Indices: 18646851--18646968 Score: 159
Period size: 54 Copynumber: 2.2 Consensus size: 54
18646841 CATGACCTAA
* * *
18646851 CACACGGGCATGTGGCTTGGCCGTGTGTCACAAGTCAGTATGCTCACCTTTTTT
1 CACACGGGCATGTGGCTTGGCCGTGTGACACAAGTCAGTATGCTCACCTGTTTG
*
18646905 CACACGGGCATGTGGCTTGGCCGTGTGACCCAAGTCAGTGA-GCTCA-CTAGTTTG
1 CACACGGGCATGTGGCTTGGCCGTGTGACACAAGTCAGT-ATGCTCACCT-GTTTG
*
18646959 GACACGGGCA
1 CACACGGGCA
18646969 GGGACACGGC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.04
54 54 0.95
55 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (54 bp):
CACACGGGCATGTGGCTTGGCCGTGTGACACAAGTCAGTATGCTCACCTGTTTG
Found at i:18669724 original size:95 final size:95
Alignment explanation
Indices: 18669593--18669771 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 95
18669583 CATGGCGTCA
* * * * *
18669593 TTTATAGTAGTGGAATTCATAGTCCAATAAAAGGTAAATGATGTCATCTCGTGGGCATTACATGG
1 TTTATAGTAGTGAAATTCATACTCCAATAAAAGGTAAATGATATCATCTCATGAGCATTACATGG
18669658 TTGATAGAAAAGTAACATGACATGACTTCC
66 TTGATAGAAAAGTAACATGACATGACTTCC
* * *
18669688 TTTATAGTAGTGAAATTCATAACT-CGATAAAAGGTAAATGATATCCTCTCATTAGCATTACATG
1 TTTATAGTAGTGAAATTCAT-ACTCCAATAAAAGGTAAATGATATCATCTCATGAGCATTACATG
*
18669752 GTTGATGGAAAAGTAACATG
65 GTTGATAGAAAAGTAACATG
18669772 GTCATGGGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 72 0.97
96 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (95 bp):
TTTATAGTAGTGAAATTCATACTCCAATAAAAGGTAAATGATATCATCTCATGAGCATTACATGG
TTGATAGAAAAGTAACATGACATGACTTCC
Found at i:18673407 original size:13 final size:13
Alignment explanation
Indices: 18673391--18673415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18673381 ATGTTTAGAT
18673391 GAAATGGTTATAC
1 GAAATGGTTATAC
18673404 GAAATGGTTATA
1 GAAATGGTTATA
18673416 TGAGATGATT
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:0.04, G:0.24, T:0.32
Consensus pattern (13 bp):
GAAATGGTTATAC
Found at i:18673407 original size:26 final size:26
Alignment explanation
Indices: 18673353--18673418 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
18673343 ATTATGTATT
* *
18673353 AAATGTGTAAATGAAATGGTAAAATG
1 AAATGTTTAAATGAAATGGTAAAACG
* * *
18673379 AAATGTTTAGATGAAATGGTTATACG
1 AAATGTTTAAATGAAATGGTAAAACG
* *
18673405 AAATGGTTATATGA
1 AAATGTTTAAATGA
18673419 GATGATTGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.32
Consensus pattern (26 bp):
AAATGTTTAAATGAAATGGTAAAACG
Found at i:18676579 original size:6 final size:6
Alignment explanation
Indices: 18676568--18676592 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18676558 GAATATTGAT
18676568 TATTTA TATTTA TATTTA TATTTA T
1 TATTTA TATTTA TATTTA TATTTA T
18676593 TTTTGAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:18682932 original size:21 final size:22
Alignment explanation
Indices: 18682908--18682950 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18682898 TTCTTTTATA
18682908 TTTTA-ATTTTGATATATTAAAT
1 TTTTATATTTTGATAT-TTAAAT
*
18682930 TTTTATATTTTTATATTTAAA
1 TTTTATATTTTGATATTTAAA
18682951 AATCTTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTATATTTTGATATTTAAAT
Found at i:18690985 original size:15 final size:15
Alignment explanation
Indices: 18690965--18691004 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
18690955 GTTATCATTA
18690965 TTTTTACTATTATTG
1 TTTTTACTATTATTG
18690980 TTTTTA--A-TATTG
1 TTTTTACTATTATTG
*
18690992 TTATTACTATTAT
1 TTTTTACTATTAT
18691005 CATGCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.48
13 1 0.05
14 1 0.05
15 9 0.43
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTACTATTATTG
Found at i:18691411 original size:2 final size:2
Alignment explanation
Indices: 18691404--18691483 Score: 60
Period size: 2 Copynumber: 41.5 Consensus size: 2
18691394 CATATACATC
* * *
18691404 TA TA TA TA TA TA TA TC TA CA TA TA TA TA TA TA TA T- TA TA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
18691446 TA TA -A T- TT TA -A TA TA CA TA CA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18691484 TTTTTTATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
1 4 0.07
2 55 0.92
3 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:18691418 original size:36 final size:36
Alignment explanation
Indices: 18691342--18691418 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
18691332 ACATATCTTT
* * *
18691342 TATATTTTATAATTCACATATACATATATATTTTCC
1 TATATTTTACAATTCACATATACATATATATTATCA
*
18691378 TATATTTTACAACTT-ACATATACATCTATATATAT-A
1 TATATTTTACAA-TTCACATATACATATATAT-TATCA
18691414 TATAT
1 TATAT
18691419 CTACATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (36 bp):
TATATTTTACAATTCACATATACATATATATTATCA
Found at i:18691432 original size:16 final size:16
Alignment explanation
Indices: 18691395--18691434 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
18691385 TACAACTTAC
* *
18691395 ATATACATCTATATAT
1 ATATATATCTACATAT
18691411 ATATATATCTACATAT
1 ATATATATCTACATAT
18691427 ATATATAT
1 ATATATAT
18691435 ATATTATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATATCTACATAT
Found at i:18691449 original size:20 final size:22
Alignment explanation
Indices: 18691395--18691482 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
18691385 TACAACTTAC
*
18691395 ATATACATCTATATATATATAT
1 ATATACATATATATATATATAT
*
18691417 ATCTACATATATATATATATAT
1 ATATACATATATATATATATAT
* *
18691439 -TATAC-TTTATA-AT-TTTA-
1 ATATACATATATATATATATAT
* *
18691456 ATATACATACATATATACATAT
1 ATATACATATATATATATATAT
18691478 ATATA
1 ATATA
18691483 TTTTTTTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
18 8 0.15
19 6 0.12
20 7 0.13
21 6 0.12
22 25 0.48
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATACATATATATATATATAT
Found at i:18691884 original size:19 final size:19
Alignment explanation
Indices: 18691860--18691899 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
18691850 AATGCTCTTT
18691860 AATCAAAAACATAAATAAA
1 AATCAAAAACATAAATAAA
18691879 AATCAAAAACATAAATAAA
1 AATCAAAAACATAAATAAA
18691898 AA
1 AA
18691900 GCTCATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AATCAAAAACATAAATAAA
Found at i:18695221 original size:36 final size:38
Alignment explanation
Indices: 18695161--18695231 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
18695151 CTATCCTAAG
*
18695161 AAGAAAAGAAAAAACCTAATCTAAAA-AATGAAAAGAA
1 AAGAAAAGAAAAAACCTAACCTAAAACAATGAAAAGAA
*
18695198 AAGAAAAG-AAAAACCTAACCTAAAACTATGAAAA
1 AAGAAAAGAAAAAACCTAACCTAAAACAATGAAAA
18695232 CTAAAGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 16 0.52
37 15 0.48
ACGTcount: A:0.68, C:0.11, G:0.10, T:0.11
Consensus pattern (38 bp):
AAGAAAAGAAAAAACCTAACCTAAAACAATGAAAAGAA
Found at i:18695244 original size:36 final size:36
Alignment explanation
Indices: 18695161--18695246 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
18695151 CTATCCTAAG
* *
18695161 AAGAAAAGAAAAAACCTAATCTAAAAAATGAAAAGAA
1 AAGAAAAG-AAAAACCTAACCTAAAAAATGAAAACAA
* *
18695198 AAGAAAAGAAAAACCTAACCTAAAACTATGAAAACTA
1 AAGAAAAGAAAAACCTAACCTAAAA-AATGAAAACAA
*
18695235 AAG-AGAGAAAAA
1 AAGAAAAGAAAAA
18695247 TTGTTTAGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 24 0.56
37 19 0.44
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.10
Consensus pattern (36 bp):
AAGAAAAGAAAAACCTAACCTAAAAAATGAAAACAA
Found at i:18697420 original size:3 final size:3
Alignment explanation
Indices: 18697405--18697460 Score: 69
Period size: 3 Copynumber: 18.0 Consensus size: 3
18697395 TTTTCGTTGC
*
18697405 TAT TAT TACT TAT TAT TAT TAT TAAT TAT TAT TA- TAT TACT TAC TAT
1 TAT TAT TA-T TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT
18697452 TAT TAT TAT
1 TAT TAT TAT
18697461 ACTTACATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 2 0.04
3 36 0.77
4 9 0.19
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:18697423 original size:13 final size:12
Alignment explanation
Indices: 18697405--18697460 Score: 69
Period size: 13 Copynumber: 4.5 Consensus size: 12
18697395 TTTTCGTTGC
18697405 TATTATTACTTAT
1 TATTATTA-TTAT
18697418 TATTATTATTAAT
1 TATTATTATT-AT
18697431 TATTATTA-TAT
1 TATTATTATTAT
*
18697442 TACTTACTATTAT
1 TA-TTATTATTAT
18697455 TATTAT
1 TATTAT
18697461 ACTTACATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.11
12 11 0.29
13 23 0.61
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:18697452 original size:18 final size:18
Alignment explanation
Indices: 18697405--18697466 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 18
18697395 TTTTCGTTGC
*
18697405 TATTATTACTTATTATTAT
1 TATTA-TACTTACTATTAT
*
18697424 TATTA-A-TTATTATTA-
1 TATTATACTTACTATTAT
18697439 TA-T-TACTTACTATTAT
1 TATTATACTTACTATTAT
18697455 TATTATACTTAC
1 TATTATACTTAC
18697467 ATATATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.05
15 10 0.27
16 11 0.30
17 2 0.05
18 7 0.19
19 5 0.14
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATACTTACTATTAT
Found at i:18698330 original size:21 final size:21
Alignment explanation
Indices: 18698304--18698343 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18698294 AAAATATAAA
*
18698304 TAAAAATAAGTAT-AAAATATT
1 TAAAAA-AAATATGAAAATATT
18698325 TAAAAAAAATATGAAAATA
1 TAAAAAAAATATGAAAATA
18698344 AAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAAAATATGAAAATATT
Done.