Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 55 of 204
Found at i:17926149 original size:48 final size:47
Alignment explanation
Indices: 17926083--17926189 Score: 162
Period size: 48 Copynumber: 2.3 Consensus size: 47
17926073 TAGTCCTTTT
* *
17926083 TAATTACTTAACTATCAAAACGTTAAAATTTTCTAACT-AAACTTTAA
1 TAATAACTTAATTATCAAAACGTTAAAATTTTCTAA-TGAAACTTTAA
17926130 TAATAACTTAATTAATCAAAACGTTAAAATTTTCTAATGAAACTTTAA
1 TAATAACTTAATT-ATCAAAACGTTAAAATTTTCTAATGAAACTTTAA
*
17926178 TACTAACTTAAT
1 TAATAACTTAAT
17926190 AACACTTCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 12 0.22
48 43 0.78
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (47 bp):
TAATAACTTAATTATCAAAACGTTAAAATTTTCTAATGAAACTTTAA
Found at i:17930618 original size:23 final size:24
Alignment explanation
Indices: 17930592--17930641 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
17930582 TGATTTTTAA
17930592 ATTTTA-AATTATTTAGAGATAAT
1 ATTTTAGAATTATTTAGAGATAAT
* *
17930615 A-TTTAGATTTATTTAGTGATAAT
1 ATTTTAGAATTATTTAGAGATAAT
17930638 ATTT
1 ATTT
17930642 AGGAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 17 0.74
24 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTTAGAATTATTTAGAGATAAT
Found at i:17930642 original size:23 final size:23
Alignment explanation
Indices: 17930600--17930643 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17930590 AAATTTTAAA
17930600 TTATTTAGAGATAATATTTAGAT
1 TTATTTAGAGATAATATTTAGAT
*
17930623 TTATTTAGTGATAATATTTAG
1 TTATTTAGAGATAATATTTAG
17930644 GAAAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (23 bp):
TTATTTAGAGATAATATTTAGAT
Found at i:17932674 original size:22 final size:22
Alignment explanation
Indices: 17932644--17932686 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17932634 ACACCAAGAC
* * *
17932644 AGGCTTTTAGTGGCGTTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
17932666 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
17932687 AGTGCCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:17932840 original size:43 final size:43
Alignment explanation
Indices: 17932779--17932983 Score: 288
Period size: 43 Copynumber: 4.8 Consensus size: 43
17932769 TTTATGATAG
17932779 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
17932822 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
17932865 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTAGCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * * ** *
17932908 AAACGCCACTAAAGATCATGTTCTTTAGCGATGCTTT-CTCTAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTAC-CCAC
* *
17932951 AAACACCG-TCAAAGAACATGACCTTTAGCGGCG
1 AAACGCCGCT-AAAGAACATGATCTTTAGCGGCG
17932984 TTTTTGGTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
42 1 0.01
43 142 0.99
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:17937244 original size:102 final size:100
Alignment explanation
Indices: 17937131--17937372 Score: 251
Period size: 106 Copynumber: 2.3 Consensus size: 100
17937121 AGTGAAATTG
* * ***
17937131 TTTTTGTGGCGTTTTTTATAAAAACGCCGCAAATTTTTTTCATTTTGAACAAAATGACGTTGTTT
1 TTTTTGCGGCGTTTTTTATAAAAACGCCGC-----TATTTCATTTTGAACAAAATGACACCGTTT
*
17937196 TGCTATTCT-AAA-T-TTTT-TTTTTTACAAATTGATTTA
61 TGCTATGCTAAAATTATTTTATTTTTTACAAATTGATTTA
*
17937232 TTTTTTGCGGCG-TTTTTATAAAAAACTCCGCTATTTCATTTTGAACAAAATGACACCGTTTTGC
1 -TTTTTGCGGCGTTTTTTAT-AAAAACGCCGCTATTTCATTTTGAACAAAATGACACCGTTTTGC
*
17937296 TATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTA
64 TATGCT-AAAA----TTATTTTATTTTTTACAAATTGATTTA
*
17937338 TTTTTGCGGCGTTTTTATAAAAAAACGCCGCTATT
1 TTTTTGCGGCGTTTTT-TATAAAAACGCCGCTATT
17937373 GCTTATCTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 20
0.80 0.07 0.14
Matches are distributed among these distances:
97 34 0.29
99 3 0.03
101 7 0.06
102 20 0.17
104 1 0.01
105 15 0.13
106 36 0.31
107 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (100 bp):
TTTTTGCGGCGTTTTTTATAAAAACGCCGCTATTTCATTTTGAACAAAATGACACCGTTTTGCTA
TGCTAAAATTATTTTATTTTTTACAAATTGATTTA
Found at i:17937283 original size:97 final size:101
Alignment explanation
Indices: 17937168--17937372 Score: 267
Period size: 97 Copynumber: 2.0 Consensus size: 101
17937158 CGCAAATTTT
*** *
17937168 TTTCATTTTGAACAAAATGACGTTGTTTTGCTATTCT-AAA-T-TTTT-TTTTTTACAAATTGAT
1 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAATTATTTTATTTTTTACAAATTGAT
*
17937229 TTATTTTTTGCGGCGTTTTTAT-AAAAAACTCCGCTA
66 TTA-TTTTTGCGGCGTTTTTATAAAAAAACGCCGCTA
*
17937265 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
1 TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCT-AAAA----TTATTTTATTTTTTACAAA
17937330 TTGATTTATTTTTGCGGCGTTTTTATAAAAAAACGCCGCTA
61 TTGATTTATTTTTGCGGCGTTTTTATAAAAAAACGCCGCTA
17937371 TT
1 TT
17937373 GCTTATCTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
97 33 0.36
99 3 0.03
104 1 0.01
105 22 0.24
106 33 0.36
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (101 bp):
TTTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAATTATTTTATTTTTTACAAATTGAT
TTATTTTTGCGGCGTTTTTATAAAAAAACGCCGCTA
Found at i:17938502 original size:15 final size:15
Alignment explanation
Indices: 17938478--17938508 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17938468 AACCCCTAAT
17938478 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
17938493 CCATACTCCCTAAAC
1 CCATAATCCCTAAAC
17938508 C
1 C
17938509 TTAAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:17938955 original size:114 final size:113
Alignment explanation
Indices: 17938771--17939080 Score: 505
Period size: 114 Copynumber: 2.7 Consensus size: 113
17938761 GCACTTTTCC
* *
17938771 AAAAACGCTGCTAAATCCCTGAAAGCTCAGAAAACGACGTCATTGGACTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCC-GAAAGCTCAGAAAACGACGTCGTTGGACTTAGGTTTTTTTGCGGC
17938836 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
*
17938885 AAAAACGCCGCTAAATCCTCGAAAGCTCAGAAAACGGCGTCGTTGGACTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCC-CGAAAGCTCAGAAAACGACGTCGTTGGACTTAGGTTTTTTTGCGGC
*
17938950 GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
* * * **
17938999 AGAAACGCCGCTAAATCCCCGAAAGCTCGGGAAACGACGTCGTTTCACTTAGG-TTTTTTGCGGC
1 AAAAACGCCGCTAAAT-CCCGAAAGCTCAGAAAACGACGTCGTTGGACTTAGGTTTTTTTGCGGC
17939063 GCTTTCTCAAAAACGCCG
65 GCTTTCTCAAAAACGCCG
17939081 TTAATGCTTA
Statistics
Matches: 183, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
113 28 0.15
114 152 0.83
115 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (113 bp):
AAAAACGCCGCTAAATCCCGAAAGCTCAGAAAACGACGTCGTTGGACTTAGGTTTTTTTGCGGCG
CTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
Found at i:17939516 original size:43 final size:43
Alignment explanation
Indices: 17939452--17939578 Score: 168
Period size: 43 Copynumber: 2.9 Consensus size: 43
17939442 AGGATTTCCG
17939452 ATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGT-TTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
*
17939497 TTATGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGAT
1 ATATGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT
* * *
17939540 ATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
17939579 TGGACGAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
42 2 0.03
43 61 0.84
44 5 0.07
45 5 0.07
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
ATATGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:17941203 original size:2 final size:2
Alignment explanation
Indices: 17941196--17941265 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
17941186 ATTCTTAATG
17941196 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
*
17941238 AT AT AT GT 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
17941266 GAATGTCATG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17941798 original size:13 final size:13
Alignment explanation
Indices: 17941780--17941804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17941770 TTTGAATTAT
17941780 TTAGTGATAATAA
1 TTAGTGATAATAA
17941793 TTAGTGATAATA
1 TTAGTGATAATA
17941805 TTTAAATTTA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTAGTGATAATAA
Found at i:17943152 original size:45 final size:45
Alignment explanation
Indices: 17943103--17943225 Score: 194
Period size: 45 Copynumber: 2.7 Consensus size: 45
17943093 ATGCCAGAAA
* * *
17943103 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
1 CGAGTAAGACCATGACTGAAAGACATTATGGCATCACAATTATAT
17943148 CGAGTAAGACCATGACTGAAAGACATTATGGCATCACAATTATAT
1 CGAGTAAGACCATGACTGAAAGACATTATGGCATCACAATTATAT
*
17943193 CGAGTAAGACCAT-AGCTGAAAGACACTATGGCA
1 CGAGTAAGACCATGA-CTGAAAGACATTATGGCA
17943226 ACTCGACGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.01
45 72 0.99
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACATTATGGCATCACAATTATAT
Found at i:17943304 original size:47 final size:47
Alignment explanation
Indices: 17943197--17943370 Score: 228
Period size: 47 Copynumber: 3.7 Consensus size: 47
17943187 TTATATCGAG
* *
17943197 TAAGACCATAGCTGAAAGACACTATGGCAACTCGACGAAAAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCGACG-AAAAAATGAA
17943245 TAAGACCATGGTTGAAAGACACTATGGCAACTCGACGAAAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCGACGAAAAAATGAA
* ** * *
17943292 TAAGACCATGGTTGAAAGACACTATGGCATCAAGACG--AGAATAAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCGACGAAAAAATGAA
*
17943337 TAAGTCCATGGTTGAAAGACAAC-ATGGCACACTC
1 TAAGACCATGGTTGAAAGAC-ACTATGGCA-ACTC
17943371 CGATAATTTG
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
45 31 0.27
46 3 0.03
47 44 0.39
48 35 0.31
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (47 bp):
TAAGACCATGGTTGAAAGACACTATGGCAACTCGACGAAAAAATGAA
Found at i:17943320 original size:95 final size:93
Alignment explanation
Indices: 17943197--17943370 Score: 226
Period size: 92 Copynumber: 1.8 Consensus size: 93
17943187 TTATATCGAG
* *
17943197 TAAGACCATAGCTGAAAGACACTATGGCAACTCGACGAAAAAAATGAATAAGACCATGGTTGAAA
1 TAAGACCATAGCTGAAAGACACTATGGC-A-TC-AAGAAAAAAATAAATAAGACCATGGTTGAAA
17943262 GAC-ACTATGGCA-ACTCGACGAAAAAATGAA
63 GACAAC-ATGGCACACTCGACGAAAAAATGAA
* * ** * *
17943292 TAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAATAAATAAGTCCATGGTTGAAAGAC
1 TAAGACCATAGCTGAAAGACACTATGGCATCAAGAAAAAAATAAATAAGACCATGGTTGAAAGAC
17943357 AACATGGCACACTC
66 AACATGGCACACTC
17943371 CGATAATTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 34 0.49
93 8 0.12
94 1 0.01
95 26 0.38
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (93 bp):
TAAGACCATAGCTGAAAGACACTATGGCATCAAGAAAAAAATAAATAAGACCATGGTTGAAAGAC
AACATGGCACACTCGACGAAAAAATGAA
Found at i:17948368 original size:42 final size:42
Alignment explanation
Indices: 17948322--17948410 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
17948312 GTCTCAGCCA
* *
17948322 TGTGTAACACATGGCCTACCACACGGGTGTGTGTTTTGGCCG
1 TGTGTAACACATGGCCTACCACACGGGCGCGTGTTTTGGCCG
* *
17948364 TGTGTAACACATGGCCTACCATATGGGCGCGTGTTTTGGCCG
1 TGTGTAACACATGGCCTACCACACGGGCGCGTGTTTTGGCCG
17948406 TGTGT
1 TGTGT
17948411 CCCCTACATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.30
Consensus pattern (42 bp):
TGTGTAACACATGGCCTACCACACGGGCGCGTGTTTTGGCCG
Found at i:17951067 original size:2 final size:2
Alignment explanation
Indices: 17951060--17951092 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17951050 TGATCCTCAA
17951060 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 A
17951093 AAAACTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17951661 original size:199 final size:205
Alignment explanation
Indices: 17951315--17952120 Score: 1044
Period size: 218 Copynumber: 3.9 Consensus size: 205
17951305 GGGTACAAAT
* * *
17951315 TAAAAATAAAATCGCCGTTGCCGGGGATCGAACCCGGGT-C-A-C-C-C-GCGTGACAGGCGGGA
1 TAAAATTAAAATCGCCGTT-CAGGGGATCCAACCCGGGTCCGACCGCACTGCGTGACAGGCGGGA
*
17951374 ATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATATTTTAAAACAATA
65 ATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATATTTTAAAAAAATA
17951439 TAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCTTTTCCCTATTTT
130 TAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCTTTTCCCTATTTT
17951504 GAAAGGT-TAA
195 GAAAGGTATAA
* *
17951514 TAAAATTAAAATCGCCGTTGCCGGGGATCGAACCCGGGT-C-A-C-C-C-GCGTGACAGGCGGGA
1 TAAAATTAAAATCGCCGTT-CAGGGGATCCAACCCGGGTCCGACCGCACTGCGTGACAGGCGGGA
** * *
17951573 ATACTTACCACTATACTACAACGACCTCGTTGCAAGTTTGTAACAATTGCTATTTTAAAAAAATA
65 ATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATATTTTAAAAAAATA
* *
17951638 TAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTCGGCTGTTTTTTCCCTATTTT
130 TAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCTTTTCCCTATTTT
17951703 GAAAGGTATAA
195 GAAAGGTATAA
*
17951714 TAAGATTAAAATCGCCGTTCAGGGGATCCAACCCGGGTCACCCGCGTGAACCCGGATCATCTGCG
1 TAAAATTAAAATCGCCGTTCAGGGGATCCAACCCGGGT----C-C--G-A-CC-G--CA-CTGCG
17951779 TGACAGGCGGGAATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATAT
53 TGACAGGCGGGAATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATAT
*
17951844 TTTAAAACAATATAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCT
118 TTTAAAAAAATATAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCT
17951909 TTTCCCTATTTTGAAAGGTATAA
183 TTTCCCTATTTTGAAAGGTATAA
*
17951932 TAAGATTAAAATCGCCGTTCAGGGGATCCAACCCGGGTCACCCGCGTGAACCCGGATCATCTGCG
1 TAAAATTAAAATCGCCGTTCAGGGGATCCAACCCGGGT----C-C--G-A-CC-G--CA-CTGCG
*** * * * *
17951997 TGACAGGCGGGAATACTTACCACTATACTACAACGACCTCGTTATTAATTTATAACAACTGGTGT
53 TGACAGGCGGGAATACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGAT-A
* *
17952062 TTTTAAAAAAATATGAGTATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTG
117 TTTTAAAAAAATATAAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTG
17952121 TCTGGTTTCA
Statistics
Matches: 558, Mismatches: 28, Indels: 22
0.92 0.05 0.04
Matches are distributed among these distances:
199 205 0.37
200 21 0.04
205 1 0.00
209 1 0.00
211 1 0.00
215 1 0.00
217 1 0.00
218 271 0.49
219 56 0.10
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (205 bp):
TAAAATTAAAATCGCCGTTCAGGGGATCCAACCCGGGTCCGACCGCACTGCGTGACAGGCGGGAA
TACTTACCACTATACTACAACGACCTCGTTGCAAACTTGTAACAACTGATATTTTAAAAAAATAT
AAATATGCATAAGTTTATTACATTTCAAGGAACAAAAATAAGTTGGCTGTCTTTTCCCTATTTTG
AAAGGTATAA
Found at i:17956074 original size:5 final size:5
Alignment explanation
Indices: 17956064--17956089 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17956054 TGAGCATTCG
17956064 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
17956090 AATTTTCGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:17956882 original size:30 final size:31
Alignment explanation
Indices: 17956843--17956902 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
17956833 GGAGGTGGGA
*
17956843 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
17956874 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
17956903 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:17957379 original size:19 final size:20
Alignment explanation
Indices: 17957334--17957422 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 20
17957324 CTCTCTCAAC
*
17957334 AAAAATTACAAAATAATTTTC
1 AAAAATT-CAAAATAATTTTA
17957355 AAAAATTCAAAATAATTTT-
1 AAAAATTCAAAATAATTTTA
*
17957374 AAAAATTCAAAA-CATTTATAA
1 AAAAATTCAAAATAATTT-T-A
17957395 AAAAATTCAAAATTTATATTTTA
1 AAAAATTCAAAA--TA-ATTTTA
17957418 AAAAA
1 AAAAA
17957423 ATTATAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.07
19 13 0.22
20 12 0.20
21 19 0.32
23 6 0.10
24 1 0.02
25 4 0.07
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTA
Found at i:17957420 original size:21 final size:21
Alignment explanation
Indices: 17957356--17957420 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 21
17957346 ATAATTTTCA
17957356 AAAATTCAAAA--TA-ATTTT
1 AAAATTCAAAATTTATATTTT
**
17957374 AAAAATTCAAAACATTTATA--AA
1 -AAAATTC-AAA-ATTTATATTTT
17957396 AAAATTCAAAATTTATATTTT
1 AAAATTCAAAATTTATATTTT
17957417 AAAA
1 AAAA
17957421 AAATTATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 14 0.40
20 6 0.17
21 12 0.34
23 2 0.06
24 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTCAAAATTTATATTTT
Found at i:17957440 original size:20 final size:20
Alignment explanation
Indices: 17957334--17957441 Score: 52
Period size: 20 Copynumber: 5.7 Consensus size: 20
17957324 CTCTCTCAAC
* * *
17957334 AAAAATTACAAAATAATTTT
1 AAAAATTTCAAAAAAATTAT
* *
17957354 CAAAAA-TTCAAAATAATTTT
1 -AAAAATTTCAAAAAAATTAT
* *
17957374 AAAAA-TTCAAAACATTTAT
1 AAAAATTTCAAAAAAATTAT
*
17957393 AAAAAAATTC---AAAATT-T
1 -AAAAATTTCAAAAAAATTAT
* *
17957410 --ATATTTTAAAAAAATTAT
1 AAAAATTTCAAAAAAATTAT
17957428 AAAAATTTCAAAAA
1 AAAAATTTCAAAAA
17957442 CATCTAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
14 4 0.06
17 7 0.10
18 5 0.07
19 16 0.24
20 28 0.41
21 8 0.12
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTTCAAAAAAATTAT
Found at i:17957717 original size:16 final size:16
Alignment explanation
Indices: 17957678--17957719 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
17957668 AACTCGAACA
*
17957678 ATTTCACTCG-ATTTG
1 ATTTCACTCGAATTTC
* *
17957693 ACTTGACTCGAATTTC
1 ATTTCACTCGAATTTC
17957709 ATTTCACTCGA
1 ATTTCACTCGA
17957720 CTCTATAATG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (16 bp):
ATTTCACTCGAATTTC
Found at i:17960261 original size:20 final size:19
Alignment explanation
Indices: 17960212--17960261 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
17960202 TATTTATAGT
*
17960212 TTAATTTAATTAAGTTTTA
1 TTAATTTAATTAATTTTTA
*
17960231 --ATTTTAA-TAATTCTTTA
1 TTAATTTAATTAATT-TTTA
17960248 TTAATTTAATTAAT
1 TTAATTTAATTAAT
17960262 GAAACTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 7
0.71 0.09 0.21
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
19 6 0.25
20 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAATTTAATTAATTTTTA
Found at i:17962773 original size:24 final size:24
Alignment explanation
Indices: 17962727--17962773 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17962717 TATTACGAAA
* *
17962727 AAAATATTTTAAAATAGATAAATT
1 AAAATAATTTAAAATAGAAAAATT
17962751 AAAATAATTTAAGAATA-AAAAAT
1 AAAATAATTTAA-AATAGAAAAAT
17962774 ACAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAATAATTTAAAATAGAAAAATT
Found at i:17964865 original size:16 final size:15
Alignment explanation
Indices: 17964838--17964867 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
17964828 AAGAAGAGTG
17964838 AGAGAAAAGAGAGAA
1 AGAGAAAAGAGAGAA
17964853 AGAGAAAACGAGAGA
1 AGAGAAAA-GAGAGA
17964868 TATGTGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAGAAAAGAGAGAA
Found at i:17968439 original size:18 final size:18
Alignment explanation
Indices: 17968386--17968441 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
17968376 AACTTCAACA
* *
17968386 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
17968405 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
17968423 ACCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
17968441 A
1 A
17968442 TAAAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:17971289 original size:20 final size:20
Alignment explanation
Indices: 17971264--17971301 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17971254 AAAAATTCAA
17971264 AAAAATATAAAAAT-ATTTTT
1 AAAAAT-TAAAAATCATTTTT
17971284 AAAAATTAAAAATCATTT
1 AAAAATTAAAAATCATTT
17971302 AAATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTAAAAATCATTTTT
Found at i:17977619 original size:3 final size:3
Alignment explanation
Indices: 17977611--17977639 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17977601 TTTTATTTAT
17977611 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17977640 TATTTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17978357 original size:16 final size:16
Alignment explanation
Indices: 17978336--17978366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17978326 AATTCCTTTA
17978336 AAATTAGAAATATTAT
1 AAATTAGAAATATTAT
*
17978352 AAATTAGTAATATTA
1 AAATTAGAAATATTA
17978367 AATTTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATTAGAAATATTAT
Found at i:17985909 original size:16 final size:16
Alignment explanation
Indices: 17985888--17985918 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17985878 TGGGCGGTGC
17985888 GTTTGAGATTAGATAT
1 GTTTGAGATTAGATAT
17985904 GTTTGAGATTAGATA
1 GTTTGAGATTAGATA
17985919 CTATAGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
GTTTGAGATTAGATAT
Found at i:17986299 original size:30 final size:31
Alignment explanation
Indices: 17986263--17986320 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17986253 AAAAAAAGTT
*
17986263 ACTTAAAT-AAAACTTACGAATAGTTCAGTA
1 ACTTAAATGAAAACTTACGAATAATTCAGTA
*
17986293 ACTTAAATGAAAACTTTCGAATAATTCA
1 ACTTAAATGAAAACTTACGAATAATTCA
17986321 ATGATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
ACTTAAATGAAAACTTACGAATAATTCAGTA
Found at i:17989909 original size:21 final size:21
Alignment explanation
Indices: 17989885--17989929 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17989875 AAAAATTCTC
* * * *
17989885 AATATTTAATTATTTAATTTT
1 AATATTCAAATATATAAATTT
17989906 AATATTCAAATATATAAATTT
1 AATATTCAAATATATAAATTT
17989927 AAT
1 AAT
17989930 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTCAAATATATAAATTT
Found at i:17991598 original size:16 final size:17
Alignment explanation
Indices: 17991565--17991599 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17991555 ATTTGAATCA
*
17991565 TTTTTAATTGCTATATT
1 TTTTTAATTGCTAAATT
17991582 TTTTTAATT-CTAAATT
1 TTTTTAATTGCTAAATT
17991598 TT
1 TT
17991600 CAGTCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTAATTGCTAAATT
Found at i:17996494 original size:48 final size:48
Alignment explanation
Indices: 17996428--17996561 Score: 187
Period size: 48 Copynumber: 2.8 Consensus size: 48
17996418 CGAGATAATG
* * * *
17996428 GGAATCCAAGTGGCGGCTGGAGTCGAGAACAAAGGGATAGAGATTACA
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
**
17996476 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTATG
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
* * *
17996524 GGAATCCGAGCGGTGGCTGGGGCCAAGAACAAAGGGAT
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGAT
17996562 CGGAACACCC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.32, C:0.15, G:0.40, T:0.13
Consensus pattern (48 bp):
GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
Found at i:17997019 original size:19 final size:20
Alignment explanation
Indices: 17996997--17997040 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17996987 TTGGTACATA
* *
17996997 TTTTAC-TAAATTGTTTTTT
1 TTTTACATAAATTGTGTTTC
*
17997016 TTTTACATAATTTGTGTTTC
1 TTTTACATAAATTGTGTTTC
17997036 TTTTA
1 TTTTA
17997041 TTATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTACATAAATTGTGTTTC
Found at i:17998252 original size:4 final size:4
Alignment explanation
Indices: 17998243--17998270 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17998233 CGAATACATG
17998243 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
17998271 TCAAATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:17998662 original size:3 final size:3
Alignment explanation
Indices: 17998616--17998649 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17998606 TTATATTAGT
*
17998616 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17998650 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18000854 original size:26 final size:27
Alignment explanation
Indices: 18000818--18000875 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
18000808 ATTATATATT
18000818 AAATA-TATATA-TTTTATTTTTAATC
1 AAATATTATATATTTTTATTTTTAATC
18000843 AAATATTATATATTTTTATTTTTAATC
1 AAATATTATATATTTTTATTTTTAATC
18000870 AAATAT
1 AAATAT
18000876 AAATTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 5 0.16
26 6 0.19
27 20 0.65
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATATTATATATTTTTATTTTTAATC
Found at i:18011042 original size:33 final size:34
Alignment explanation
Indices: 18010997--18011087 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 34
18010987 AATGCAACAT
* * *
18010997 ACATGC-TATAACAGATCA-ATATGGTAGCAA-TA
1 ACATGCTTATAACAGAT-ATATATAGCAACAATTA
*
18011029 ACATGCTTATAACAAATATATATAGCAACAATTA
1 ACATGCTTATAACAGATATATATAGCAACAATTA
*
18011063 TCATGCTTATAACAGAT-TATGATAG
1 ACATGCTTATAACAGATATAT-ATAG
18011088 TAGTAATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 7 0.14
33 21 0.43
34 21 0.43
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (34 bp):
ACATGCTTATAACAGATATATATAGCAACAATTA
Found at i:18011410 original size:27 final size:25
Alignment explanation
Indices: 18011380--18011461 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 25
18011370 CTGTAATTTG
18011380 TAAAACAGGGGACAAATTTGTAAAATC
1 TAAAACAGGGGA-AAA-TTGTAAAATC
* *
18011407 TAAAAAATAGGGGATAATTGTAAAATC
1 T--AAAACAGGGGAAAATTGTAAAATC
* * *
18011434 TAAAAAAATGGGAAAAACTGTAAAATC
1 T-AAAACA-GGGGAAAATTGTAAAATC
18011461 T
1 T
18011462 GAAGAATAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
26 6 0.13
27 28 0.61
28 2 0.04
29 10 0.22
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (25 bp):
TAAAACAGGGGAAAATTGTAAAATC
Found at i:18011439 original size:28 final size:28
Alignment explanation
Indices: 18011381--18011544 Score: 122
Period size: 28 Copynumber: 5.8 Consensus size: 28
18011371 TGTAATTTGT
*
18011381 AAAACAGGGGACAAATTTGTAAAATCT-AA
1 AAAATAGGGGA-AAA-TTGTAAAATCTAAA
*
18011410 AAAATAGGGGATAATTGTAAAATCTAAA
1 AAAATAGGGGAAAATTGTAAAATCTAAA
* * *
18011438 AAAAT-GGGAAAAACTGTAAAATCT-GA
1 AAAATAGGGGAAAATTGTAAAATCTAAA
* * * *
18011464 AGAATAGGTGCAAAACTATAAAA--TAAGA
1 AAAATAGG-GGAAAATTGTAAAATCTAA-A
* *
18011492 AAAGTAAGGGGAAAATTGTAAAATTTGAAAA
1 AAAAT-AGGGGAAAATTGTAAAATCT--AAA
18011523 AAAATAGGGGCAAAATTGTAAA
1 AAAATAGGGG-AAAATTGTAAA
18011545 TTTGTAAAAC
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
26 6 0.06
27 29 0.27
28 36 0.33
29 13 0.12
30 6 0.06
31 16 0.15
32 2 0.02
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (28 bp):
AAAATAGGGGAAAATTGTAAAATCTAAA
Found at i:18015164 original size:22 final size:22
Alignment explanation
Indices: 18015136--18015182 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
18015126 ATAAAATAAA
* *
18015136 TTTATTTTAATCAAATTAATAT
1 TTTATTTTAATCAAACTAAAAT
*
18015158 TTTATTTTGATCAAACTAAAAT
1 TTTATTTTAATCAAACTAAAAT
18015180 TTT
1 TTT
18015183 TCATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATTTTAATCAAACTAAAAT
Found at i:18021540 original size:77 final size:77
Alignment explanation
Indices: 18021433--18021583 Score: 198
Period size: 77 Copynumber: 2.0 Consensus size: 77
18021423 TGTTGTAGAT
* * *
18021433 AGATACTAAAAGCCATCATTGTCGAGCAACCC-AAGGTGATAGAATAAAATAGTCTCGATTCCCA
1 AGATACTAAAAGCCATCATTGTCGAGCAACCCGAA-GTGACAGAATAAAATAGTCCCAATTCCCA
*
18021497 GAGGGTCATGGGC
65 AAGGGTCATGGGC
* ** *
18021510 AGATATTAAAAGCCATTGTTGTC-AGGCAACCCGAAGTGGCAGAATAAAATAGTCCCAATTCCCA
1 AGATACTAAAAGCCATCATTGTCGA-GCAACCCGAAGTGACAGAATAAAATAGTCCCAATTCCCA
18021574 AAGGGTCATG
65 AAGGGTCATG
18021584 AATTTGTCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 1 0.02
77 61 0.95
78 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (77 bp):
AGATACTAAAAGCCATCATTGTCGAGCAACCCGAAGTGACAGAATAAAATAGTCCCAATTCCCAA
AGGGTCATGGGC
Found at i:18033806 original size:18 final size:19
Alignment explanation
Indices: 18033783--18033819 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
18033773 TAGATGGTTC
*
18033783 TCTTTTATTTA-TTATTTA
1 TCTTTTATTAATTTATTTA
18033801 TCTTTTATTAATTTATTTA
1 TCTTTTATTAATTTATTTA
18033820 ATTAAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTATTAATTTATTTA
Found at i:18037356 original size:16 final size:15
Alignment explanation
Indices: 18037335--18037378 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
18037325 CATTGAATTA
**
18037335 TTTATTCAATAATTTT
1 TTTATTCAATAA-CAT
18037351 TTTATTCAATCAACAT
1 TTTATTCAAT-AACAT
18037367 TTTATTCAATAA
1 TTTATTCAATAA
18037379 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTATTCAATAACAT
Found at i:18044705 original size:13 final size:13
Alignment explanation
Indices: 18044687--18044712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18044677 TCATGCATTT
18044687 AAAAAATTATAAA
1 AAAAAATTATAAA
18044700 AAAAAATTATAAA
1 AAAAAATTATAAA
18044713 TTTTTTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAATTATAAA
Found at i:18063630 original size:36 final size:36
Alignment explanation
Indices: 18063590--18063659 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
18063580 ATCATTTAAT
* * *
18063590 CCAAACTTAATCTCCTAACTTCTGACAAGTAATCTG
1 CCAAACTCAATCTCCTAACTTCTCACAAGAAATCTG
*
18063626 CCAAACTCAATCTCCTATCTTCTCACAAGAAATC
1 CCAAACTCAATCTCCTAACTTCTCACAAGAAATC
18063660 GACTAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (36 bp):
CCAAACTCAATCTCCTAACTTCTCACAAGAAATCTG
Found at i:18065757 original size:18 final size:17
Alignment explanation
Indices: 18065735--18065769 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18065725 TTATTATTAA
*
18065735 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18065753 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18065770 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18065830 original size:61 final size:61
Alignment explanation
Indices: 18065763--18066071 Score: 262
Period size: 61 Copynumber: 5.1 Consensus size: 61
18065753 ATATAATTTA
18065763 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
* * * * * ** * * * *
18065824 AGAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
*
18065882 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
* * * * * * ** * * *
18065944 ATAAAA-T-ATAAT-TTGAAATAATTGTTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
*
18066002 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
18066064 ATAAAATT
1 ATAAAATT
18066072 AAAATTAAGT
Statistics
Matches: 183, Mismatches: 47, Indels: 36
0.69 0.18 0.14
Matches are distributed among these distances:
58 3 0.02
59 68 0.37
60 34 0.19
61 75 0.41
62 3 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
Found at i:18065855 original size:120 final size:119
Alignment explanation
Indices: 18065715--18066070 Score: 649
Period size: 120 Copynumber: 3.0 Consensus size: 119
18065705 TTAACCATAT
18065715 TTTAATATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
18065780 CAATATTCTTATATGAATTTATTAAAATCATAATATATGATACTAGAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
18065835 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
18065900 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* *
18065955 TTTGAAATAATTGTTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTT-AAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
18066020 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAT
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAT
18066071 TAAAATTAAG
Statistics
Matches: 230, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
120 228 0.99
121 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (119 bp):
TTTAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:18065876 original size:18 final size:17
Alignment explanation
Indices: 18065855--18065889 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18065845 TTATTATTAA
*
18065855 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18065873 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18065890 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18065889 original size:59 final size:57
Alignment explanation
Indices: 18065715--18066010 Score: 188
Period size: 59 Copynumber: 5.0 Consensus size: 57
18065705 TTAACCATAT
* * *
18065715 TTTAATATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * ** * * * *
18065772 TTAATAATCA-ATATTCTTATATGAATTTATTAAAATCATAATATATGATACTAGA-AAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTA-ATAAA-ATTA
* *
18065835 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * * ** * * *
18065892 TTAATAATCA-ATATTCTTATATGAATTTACTAAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
*
18065955 TTTGAA-ATAATTGTTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
18066011 CTTAATAATC
Statistics
Matches: 175, Mismatches: 43, Indels: 41
0.68 0.17 0.16
Matches are distributed among these distances:
57 7 0.04
58 7 0.04
59 57 0.33
60 34 0.19
61 54 0.31
62 9 0.05
63 7 0.04
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
Found at i:18067464 original size:21 final size:21
Alignment explanation
Indices: 18067417--18067464 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
18067407 ACTTTACTTG
18067417 GATTTTTTTTTATTTTAACAT
1 GATTTTTTTTTATTTTAACAT
* * *
18067438 GGTTTTATTTTTCTTTTTA-AT
1 GATTTT-TTTTTATTTTAACAT
18067459 GATTTT
1 GATTTT
18067465 GACAGGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.69
Consensus pattern (21 bp):
GATTTTTTTTTATTTTAACAT
Found at i:18080041 original size:24 final size:24
Alignment explanation
Indices: 18080009--18080061 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
18079999 TATTTATAGG
**
18080009 TAAATATATTATGTTAATAAATAT
1 TAAATATATTATACTAATAAATAT
*
18080033 TAAATATATTATACTCATAAATAT
1 TAAATATATTATACTAATAAATAT
18080057 TAAAT
1 TAAAT
18080062 CTTTTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATAT
Found at i:18082142 original size:42 final size:42
Alignment explanation
Indices: 18082088--18082187 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
18082078 GCTCTCGGTA
*
18082088 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
18082130 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
18082172 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
18082188 GTTCATATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:18083034 original size:4 final size:4
Alignment explanation
Indices: 18083025--18083050 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18083015 ACATAATAGC
18083025 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
18083051 ATCACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:18087570 original size:24 final size:24
Alignment explanation
Indices: 18087543--18087594 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
18087533 AATCAAAGTC
* *
18087543 AAATATATTATATTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
18087567 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
18087591 AAAT
1 AAAT
18087595 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:18089041 original size:35 final size:35
Alignment explanation
Indices: 18088997--18089063 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
18088987 ATAAAAGTAC
18088997 ATAAATTATAATAAATTAAAAT-AATA-GAATGTCTA
1 ATAAATTATAA-AAA-TAAAATAAATACGAATGTCTA
* *
18089032 ATAATTTATAAACATAAAATAAATACGAATGT
1 ATAAATTATAAAAATAAAATAAATACGAATGT
18089064 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 6 0.21
35 16 0.57
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (35 bp):
ATAAATTATAAAAATAAAATAAATACGAATGTCTA
Found at i:18089079 original size:35 final size:33
Alignment explanation
Indices: 18089013--18089079 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
18089003 TATAATAAAT
*
18089013 TAAAATAATAGAATGTCTAATAATTTATAAACA
1 TAAAATAATAGAATGTCTAATAATATATAAACA
*
18089046 TAAAATAAATACGAATGTTTAA-AATATATTAAAC
1 TAAAAT-AATA-GAATGTCTAATAATATA-TAAAC
18089080 CATTATTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 6 0.21
34 9 0.31
35 14 0.48
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (33 bp):
TAAAATAATAGAATGTCTAATAATATATAAACA
Found at i:18095688 original size:29 final size:29
Alignment explanation
Indices: 18095632--18095688 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
18095622 TGACATTTCA
*
18095632 ATAAATTATATTTTTACATAAATTTTTTT
1 ATAAATTATATTTTTACATAAATCTTTTT
* *
18095661 ATAAA-TATATTTTTTATATAACTCTTTT
1 ATAAATTATA-TTTTTACATAAATCTTTT
18095689 AACCTAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
ATAAATTATATTTTTACATAAATCTTTTT
Found at i:18095948 original size:20 final size:20
Alignment explanation
Indices: 18095923--18095972 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
18095913 CACCTGCCTC
*
18095923 TTCCTTGTTTGCTTTTCTCT
1 TTCCTTGTTTGCTTTTCCCT
**
18095943 TTCCTT-TTTTTTTTTCCCT
1 TTCCTTGTTTGCTTTTCCCT
18095962 TTCCATTGTTT
1 TTCC-TTGTTT
18095973 AATTAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.56
20 8 0.32
21 3 0.12
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.68
Consensus pattern (20 bp):
TTCCTTGTTTGCTTTTCCCT
Found at i:18104216 original size:27 final size:29
Alignment explanation
Indices: 18104166--18104234 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 29
18104156 AAATTAAAAA
*
18104166 TTATCAAAATGT-TATAAATTTTTTTTAT
1 TTATCAAAATATATATAAATTTTTTTTAT
18104194 TTATCAAAATATATAT-AA-TTTTTTTAT
1 TTATCAAAATATATATAAATTTTTTTTAT
*
18104221 TTACCAAAATATAT
1 TTATCAAAATATAT
18104235 CAAAAAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 22 0.58
28 13 0.34
29 3 0.08
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (29 bp):
TTATCAAAATATATATAAATTTTTTTTAT
Found at i:18104328 original size:27 final size:27
Alignment explanation
Indices: 18104298--18104377 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
18104288 ACTCCCTGGG
*
18104298 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
18104325 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
18104352 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
18104378 CTCGTGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.30, T:0.14
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:18104672 original size:3 final size:3
Alignment explanation
Indices: 18104664--18104728 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
18104654 AATTTTATAG
18104664 TAT TAT 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 TAT TAT
18104712 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
18104729 AGATGTTACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18104838 original size:12 final size:12
Alignment explanation
Indices: 18104664--18104838 Score: 88
Period size: 12 Copynumber: 14.3 Consensus size: 12
18104654 AATTTTATAG
*
18104664 TATTATTATTAT
1 TATTAATATTAT
*
18104676 TATTATTATTAT
1 TATTAATATTAT
*
18104688 TATTATTATTAT
1 TATTAATATTAT
*
18104700 TATTATTATTAT
1 TATTAATATTAT
*
18104712 TATTATTATTAT
1 TATTAATATTAT
* *
18104724 TATTAAGA-TGT
1 TATTAATATTAT
*
18104735 TACTTAGTATTAT
1 TA-TTAATATTAT
* * * *
18104748 TGTTAGTA-AAA
1 TATTAATATTAT
* *
18104759 AATTAGTATTAT
1 TATTAATATTAT
*
18104771 T-TTTATAGTTAGT
1 TATTAATA-TTA-T
18104784 TATTAATAATT-T
1 TATTAAT-ATTAT
*
18104796 TAGTTAGTATTAT
1 TA-TTAATATTAT
* **
18104809 TTTGTATATAAAAT
1 TAT-TA-ATATTAT
18104823 TATTAATATTAT
1 TATTAATATTAT
18104835 TATT
1 TATT
18104839 GTGTTAGTTA
Statistics
Matches: 127, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
11 15 0.12
12 84 0.66
13 15 0.12
14 12 0.09
15 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:18105487 original size:18 final size:18
Alignment explanation
Indices: 18105459--18105503 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
18105449 TTGATATGGT
* *
18105459 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
18105477 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
18105495 TGGTGGCGA
1 TGGTGGCGA
18105504 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:18106932 original size:19 final size:19
Alignment explanation
Indices: 18106908--18106950 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
18106898 CCGTGGCAAT
18106908 GGGCTCAAAGTTTTGACGA
1 GGGCTCAAAGTTTTGACGA
18106927 GGGCTCAAAGTTTTGACGA
1 GGGCTCAAAGTTTTGACGA
18106946 GGGCT
1 GGGCT
18106951 TTCGTTATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (19 bp):
GGGCTCAAAGTTTTGACGA
Found at i:18108228 original size:27 final size:27
Alignment explanation
Indices: 18108155--18108234 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
18108145 ATAACACGAG
**
18108155 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
18108182 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
18108209 TGGTGCCGCCAACAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
18108235 CCCAGGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:18108343 original size:26 final size:25
Alignment explanation
Indices: 18108286--18108343 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 25
18108276 TTTTTGTTTT
18108286 TTTATATATTTTGGTAAATAAAAAA
1 TTTATATATTTTGGTAAATAAAAAA
18108311 TTATATATATTTTGGTAAATAAAAAAA
1 TT-TATATATTTTGGTAAAT-AAAAAA
18108338 TTTATA
1 TTTATA
18108344 ACATTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTATATATTTTGGTAAATAAAAAA
Found at i:18108349 original size:27 final size:26
Alignment explanation
Indices: 18108288--18108351 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
18108278 TTTGTTTTTT
*
18108288 TATATATTTTGGTAAATAAAAAATTA
1 TATACATTTTGGTAAATAAAAAATTA
*
18108314 TATATATTTTGGTAAATAAAAAAATT-
1 TATACATTTTGGTAAAT-AAAAAATTA
18108340 TATAACATTTTG
1 TAT-ACATTTTG
18108352 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TATACATTTTGGTAAATAAAAAATTA
Found at i:18112931 original size:30 final size:30
Alignment explanation
Indices: 18112897--18112964 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
18112887 GAGACACGGA
* *
18112897 CATGTGTCTCAGCCGTGTGTGACACATGGC
1 CATGTGTCTCAACCGTGTATGACACATGGC
18112927 CATGTGTCTCAACCGTGTATGACACATGGC
1 CATGTGTCTCAACCGTGTATGACACATGGC
18112957 CATGTGTC
1 CATGTGTC
18112965 CCTTGTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (30 bp):
CATGTGTCTCAACCGTGTATGACACATGGC
Found at i:18114933 original size:14 final size:15
Alignment explanation
Indices: 18114914--18114945 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
18114904 TCATCATAGT
18114914 AATATTTTATA-AAA
1 AATATTTTATATAAA
18114928 AATATTTTATATAAA
1 AATATTTTATATAAA
18114943 AAT
1 AAT
18114946 GCCCTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTTATATAAA
Found at i:18115546 original size:14 final size:14
Alignment explanation
Indices: 18115512--18115540 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18115502 TCTTGTAAGT
18115512 AAAC-AAGTTTTTC
1 AAACTAAGTTTTTC
18115525 AAACTAAGTTTTTC
1 AAACTAAGTTTTTC
18115539 AA
1 AA
18115541 GGTAAGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
AAACTAAGTTTTTC
Found at i:18119004 original size:19 final size:20
Alignment explanation
Indices: 18118980--18119023 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
18118970 CGGAGGTAAC
*
18118980 AAAATGCATAACAAAA-ATT
1 AAAATGCATAAAAAAACATT
*
18118999 AAAATGTATAAAAAAACATT
1 AAAATGCATAAAAAAACATT
18119019 AAAAT
1 AAAAT
18119024 AAAGTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATGCATAAAAAAACATT
Found at i:18121092 original size:42 final size:42
Alignment explanation
Indices: 18121022--18121114 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
18121012 TGTTGCTTTA
*
18121022 CTCTTTCT-TTTCTTGACCAATTTCAGTACGTCTCTCTCTCT
1 CTCTCTCTCTTTCTTGACCAATTTCAGTACGTCTCTCTCTCT
*
18121063 CTCTCTCTCTTTCTTGACCAATTTGAGTACGTCTCTCTCTCT
1 CTCTCTCTCTTTCTTGACCAATTTCAGTACGTCTCTCTCTCT
18121105 CTCTCTCTCT
1 CTCTCTCTCT
18121115 CTCTCTCGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 7 0.14
42 42 0.86
ACGTcount: A:0.11, C:0.34, G:0.08, T:0.47
Consensus pattern (42 bp):
CTCTCTCTCTTTCTTGACCAATTTCAGTACGTCTCTCTCTCT
Found at i:18121101 original size:2 final size:2
Alignment explanation
Indices: 18121094--18121121 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18121084 TTTGAGTACG
18121094 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18121122 GCACGCGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18123554 original size:9 final size:9
Alignment explanation
Indices: 18123537--18123573 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18123527 TATAGTTTGA
*
18123537 TATTTGAAT
1 TATTCGAAT
18123546 TATTCGAAT
1 TATTCGAAT
*
18123555 TATTCGAGT
1 TATTCGAAT
18123564 TATTCGAAT
1 TATTCGAAT
18123573 T
1 T
18123574 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:18123642 original size:9 final size:9
Alignment explanation
Indices: 18123615--18123657 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
18123605 CGAAAAAAAT
*
18123615 TCGAGTTAAT
1 TCGA-TTAAC
*
18123625 TCGAATAAC
1 TCGATTAAC
18123634 TCGATTAAC
1 TCGATTAAC
*
18123643 TCGAATAAC
1 TCGATTAAC
18123652 TCGATT
1 TCGATT
18123658 CGTTTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:18123646 original size:18 final size:18
Alignment explanation
Indices: 18123615--18123657 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
18123605 CGAAAAAAAT
*
18123615 TCGAGTTAATTCGAATAAC
1 TCGA-TTAACTCGAATAAC
18123634 TCGATTAACTCGAATAAC
1 TCGATTAACTCGAATAAC
18123652 TCGATT
1 TCGATT
18123658 CGTTTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCGATTAACTCGAATAAC
Found at i:18126169 original size:63 final size:63
Alignment explanation
Indices: 18126035--18126187 Score: 175
Period size: 63 Copynumber: 2.4 Consensus size: 63
18126025 CATGGAGAAT
* * * * * * *
18126035 GTGTTGATGCA-AAGAATGATTGTGCGTGTTGTGGAGCTTGTGTAAAATAAACTGGTGTTAAAT
1 GTGTTGATGCAGGA-AATGATTGTGTGTGTTGTGGAGCTTATGTAAAATAAACTAGAGCTAAAG
* *
18126098 GTGCTGATGCAGGAAATGATTGTGTGTGTTGT-GATGCTTATGTAAAATAAACTAGAGCTGAAG
1 GTGTTGATGCAGGAAATGATTGTGTGTGTTGTGGA-GCTTATGTAAAATAAACTAGAGCTAAAG
* *
18126161 GTGTTGATGCAGGGAATTATTGTGTGT
1 GTGTTGATGCAGGAAATGATTGTGTGT
18126188 CTTATTATGT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
62 2 0.03
63 73 0.96
64 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.35
Consensus pattern (63 bp):
GTGTTGATGCAGGAAATGATTGTGTGTGTTGTGGAGCTTATGTAAAATAAACTAGAGCTAAAG
Found at i:18129045 original size:45 final size:44
Alignment explanation
Indices: 18128995--18129087 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
18128985 GGTTCGCTGT
*
18128995 AATGGAATAGAGGC-GTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
18129040 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
18129084 AATG
1 AATG
18129088 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:18129258 original size:24 final size:21
Alignment explanation
Indices: 18129181--18129288 Score: 71
Period size: 18 Copynumber: 4.9 Consensus size: 21
18129171 GTTATTAAAT
18129181 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
18129203 -ATAATAAATTATTTAATCATAT
1 TTTAATAAATTA-TTAAT-ATAA
18129225 TTTAACATAATTATTATTAAATATAA
1 TTT-A-ATAA--ATTATT-AATATAA
*
18129251 TTTAATAAA--AAT-ATATAA
1 TTTAATAAATTATTAATATAA
*
18129269 TTTAATAAAATTCTTAATAT
1 TTTAAT-AAATTATTAATAT
18129289 TAAATATTCT
Statistics
Matches: 67, Mismatches: 7, Indels: 24
0.68 0.07 0.24
Matches are distributed among these distances:
18 12 0.18
19 3 0.04
20 6 0.09
21 12 0.18
22 8 0.12
23 1 0.01
24 5 0.07
25 5 0.07
26 8 0.12
27 7 0.10
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:18129309 original size:38 final size:37
Alignment explanation
Indices: 18129261--18129444 Score: 124
Period size: 37 Copynumber: 4.8 Consensus size: 37
18129251 TTTAATAAAA
18129261 ATATATAATTTAATAAAATTCTTAATATTAAATATTC
1 ATATATAATTTAATAAAATTCTTAATATTAAATATTC
* * * *
18129298 TTATATGAATTTACTAAAA-TCATAATA-TATAATACTAC
1 ATATAT-AATTTAATAAAATTCTTAATATTA-AATA-TTC
* * * * *
18129336 AAAATATAATTTAA-AATAATTATTATAAATATAATTTAATAATA
1 -ATATATAATTTAATAA-AATT-CT-T--A-AT-ATTAAATATTC
18129380 ATATATAATTTAATAAAATTCTTAATATTAAATATTC
1 ATATATAATTTAATAAAATTCTTAATATTAAATATTC
* * *
18129417 TTATATGAATTTACTAAAA-TCATAATAT
1 ATATAT-AATTTAATAAAATTCTTAATAT
18129445 ATAATACTAT
Statistics
Matches: 111, Mismatches: 21, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
36 2 0.02
37 39 0.35
38 34 0.31
39 6 0.05
41 2 0.02
42 1 0.01
43 17 0.15
44 4 0.04
45 5 0.05
46 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (37 bp):
ATATATAATTTAATAAAATTCTTAATATTAAATATTC
Found at i:18129376 original size:119 final size:120
Alignment explanation
Indices: 18129225--18129466 Score: 450
Period size: 119 Copynumber: 2.0 Consensus size: 120
18129215 TTAATCATAT
*
18129225 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
18129290 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTACAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTACAAAATATAA
*
18129345 TTTAAAATAATTATTA-TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
18129409 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTACAAAATATAA
18129464 TTT
1 TTT
18129467 TAACATANNN
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 104 0.87
120 15 0.13
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTACAAAATATAA
Found at i:18129387 original size:18 final size:17
Alignment explanation
Indices: 18129360--18129395 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
18129350 AATAATTATT
18129360 ATAAATATAATTTAATA
1 ATAAATATAATTTAATA
18129377 ATAATATATAATTTAATA
1 ATAA-ATATAATTTAATA
18129395 A
1 A
18129396 AATTCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATTTAATA
Found at i:18129457 original size:61 final size:61
Alignment explanation
Indices: 18129260--18129459 Score: 225
Period size: 61 Copynumber: 3.3 Consensus size: 61
18129250 ATTTAATAAA
*
18129260 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * ** *
18129321 AATATATAATACT-ACAAAA-T-ATAAT-TTAAAATAATTATTATA--AATATAATTTAATAAT
1 AATATATAAT-CTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
*
18129379 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
18129440 AATATATAATACT-ATAAAAT
1 AATATATAAT-CTAATAAAAT
18129460 ATAATTTTAA
Statistics
Matches: 110, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
57 1 0.01
58 28 0.25
59 17 0.15
60 17 0.15
61 45 0.41
62 2 0.02
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (61 bp):
AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:18129767 original size:21 final size:20
Alignment explanation
Indices: 18129742--18129788 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18129732 TATATGAATT
*
18129742 TACTAAAATCATAATATATAA
1 TACTAAAA-AATAATATATAA
*
18129763 TACTATAAAAATAATGTATAA
1 TACTA-AAAAATAATATATAA
18129784 T-CTAA
1 TACTAA
18129789 TTTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 16 0.70
22 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (20 bp):
TACTAAAAAATAATATATAA
Found at i:18129790 original size:64 final size:62
Alignment explanation
Indices: 18129598--18129777 Score: 200
Period size: 54 Copynumber: 3.0 Consensus size: 62
18129588 AATAAAATTC
*
18129598 TTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
1 TTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAAT
* * * *
18129662 TTAAAATAATTATTATTAAATAT-AA-TT--T--AATAATAATATATAAT--T-TAATAA-AAT
1 TTAATATAATTATTCTT--ATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
*
18129716 TCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
1 TTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
18129778 GTATAATCTA
Statistics
Matches: 94, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
52 4 0.04
53 2 0.02
54 19 0.20
55 1 0.01
56 5 0.05
57 1 0.01
58 15 0.16
59 15 0.16
60 1 0.01
61 6 0.06
62 3 0.03
63 11 0.12
64 7 0.07
65 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (62 bp):
TTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
Found at i:18131235 original size:49 final size:49
Alignment explanation
Indices: 18131163--18131267 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
18131153 CTTAAGAAAA
* * *
18131163 AAAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
18131212 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
18131261 AAAATTA
1 AAAATTA
18131268 TAACACATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (49 bp):
AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
Found at i:18133424 original size:27 final size:28
Alignment explanation
Indices: 18133385--18133455 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 28
18133375 TCAATAATAA
*
18133385 ATGTAATTAAATTATAAGTATTT-TTAAAT
1 ATGTAA-T-AATTATAAATATTTGTTAAAT
18133414 ATGTAATAATTATCACAATATTTGTTAAAT
1 ATGTAATAATTAT-A-AATATTTGTTAAAT
18133444 -T-T-ATAATTATAA
1 ATGTAATAATTATAA
18133456 CAAATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 14 0.37
28 3 0.08
29 13 0.34
30 6 0.16
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (28 bp):
ATGTAATAATTATAAATATTTGTTAAAT
Found at i:18137326 original size:14 final size:15
Alignment explanation
Indices: 18137288--18137329 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
18137278 GGACATGATC
18137288 TAATATAAAATATAA
1 TAATATAAAATATAA
18137303 TAATATAAAATA-AA
1 TAATATAAAATATAA
18137317 TACATA-AAAATAT
1 TA-ATATAAAATAT
18137330 TAATTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
TAATATAAAATATAA
Found at i:18137569 original size:24 final size:25
Alignment explanation
Indices: 18137515--18137569 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
18137505 AATAATTAAG
* * **
18137515 GAATAACATTTGATGCATTATCTGT
1 GAATAACATTTCATGCATGATCAAT
*
18137540 GCATAA-ATTTCATGCATGATCAAT
1 GAATAACATTTCATGCATGATCAAT
18137564 GAATAA
1 GAATAA
18137570 TAACATGACA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (25 bp):
GAATAACATTTCATGCATGATCAAT
Found at i:18139811 original size:17 final size:17
Alignment explanation
Indices: 18139794--18139826 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
18139784 ATAAAATAAT
18139794 TTTAAAAAA-TTTAAAA
1 TTTAAAAAACTTTAAAA
18139810 TTTAAAAAACTTTAAAA
1 TTTAAAAAACTTTAAAA
18139827 CTTCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAAAACTTTAAAA
Found at i:18139834 original size:17 final size:17
Alignment explanation
Indices: 18139797--18139835 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18139787 AAATAATTTT
*
18139797 AAAAAATTTAAAATTTA
1 AAAAAATTTAAAACTTA
* *
18139814 AAAAACTTTAAAACTTC
1 AAAAAATTTAAAACTTA
18139831 AAAAA
1 AAAAA
18139836 TAACTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAATTTAAAACTTA
Found at i:18141419 original size:17 final size:17
Alignment explanation
Indices: 18141381--18141420 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
18141371 TATACATTTC
* *
18141381 TTTTGATTTTATTTTAA
1 TTTTTATTTTATTTCAA
*
18141398 ATTTTATTTTATTTCAA
1 TTTTTATTTTATTTCAA
18141415 TTTTTA
1 TTTTTA
18141421 ATATTTGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTATTTTATTTCAA
Found at i:18141803 original size:15 final size:16
Alignment explanation
Indices: 18141783--18141815 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18141773 ATAGAGGCAT
18141783 AATAAA-ATATTAAAA
1 AATAAATATATTAAAA
*
18141798 AATAAATATTTTAAAA
1 AATAAATATATTAAAA
18141814 AA
1 AA
18141816 GATGCATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATATATTAAAA
Found at i:18142118 original size:16 final size:16
Alignment explanation
Indices: 18142097--18142130 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
18142087 ACTACTTTTC
18142097 TTATAAA-AGTTATATA
1 TTATAAATA-TTATATA
18142113 TTATAAATATTATATA
1 TTATAAATATTATATA
18142129 TT
1 TT
18142131 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATAAATATTATATA
Found at i:18142485 original size:6 final size:6
Alignment explanation
Indices: 18142476--18142503 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18142466 CTTTTCTTTG
18142476 AGATTC AGATTC AGATTC AGATTC AGAT
1 AGATTC AGATTC AGATTC AGATTC AGAT
18142504 CTTATTTTCT
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:0.18, T:0.32
Consensus pattern (6 bp):
AGATTC
Found at i:18148360 original size:26 final size:25
Alignment explanation
Indices: 18148331--18148380 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18148321 TTGGTTTTTT
*
18148331 TTTAAATCTTATTAAACTCCTAAAAA
1 TTTAAATCTTA-TAAACCCCTAAAAA
* *
18148357 TTTACATTTTATAAACCCCTAAAA
1 TTTAAATCTTATAAACCCCTAAAA
18148381 GTACACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAAATCTTATAAACCCCTAAAAA
Found at i:18155432 original size:20 final size:20
Alignment explanation
Indices: 18155409--18155450 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18155399 TTAATAATAA
* * *
18155409 AATATTAAATTTATTCATTT
1 AATAGTAAATATATTAATTT
18155429 AATAGTAAATATATTAATTT
1 AATAGTAAATATATTAATTT
18155449 AA
1 AA
18155451 CAAAATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AATAGTAAATATATTAATTT
Found at i:18155823 original size:22 final size:22
Alignment explanation
Indices: 18155795--18155845 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
18155785 CTCTCTAATC
18155795 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
18155817 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
18155839 CTCTCAA
1 CTCTCAA
18155846 ACTCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:18155871 original size:51 final size:51
Alignment explanation
Indices: 18155815--18155929 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
18155805 CCTTCCAAAA
*
18155815 TTCTCTCAATTTCCTTCCAAAATTCTCTCAAA-CTCATATTTAATTTCAATT
1 TTCTCTCAATTTCCTTCCAAAAATCTCTCAAATC-CATATTTAATTTCAATT
18155866 TTCTCTCAATTTCCTTCCAAAAATCTCTCAAATCCATATTTAATTTCAATT
1 TTCTCTCAATTTCCTTCCAAAAATCTCTCAAATCCATATTTAATTTCAATT
* *
18155917 TCCCCTCAATTTC
1 TTCTCTCAATTTC
18155930 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.00, T:0.43
Consensus pattern (51 bp):
TTCTCTCAATTTCCTTCCAAAAATCTCTCAAATCCATATTTAATTTCAATT
Found at i:18157057 original size:7 final size:7
Alignment explanation
Indices: 18157045--18157069 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18157035 AGTCGATTGA
18157045 TATTTAG
1 TATTTAG
18157052 TATTTAG
1 TATTTAG
18157059 TATTTAG
1 TATTTAG
18157066 TATT
1 TATT
18157070 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:18158293 original size:23 final size:23
Alignment explanation
Indices: 18158252--18158296 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18158242 TAAAAATCCA
* *
18158252 AATTTAATTACAAACCCTAACCT
1 AATTTAACTAAAAACCCTAACCT
*
18158275 AATTTAACTAAAAAGCCTAACC
1 AATTTAACTAAAAACCCTAACC
18158297 CTAACCTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (23 bp):
AATTTAACTAAAAACCCTAACCT
Found at i:18158306 original size:29 final size:29
Alignment explanation
Indices: 18158264--18158505 Score: 356
Period size: 29 Copynumber: 8.6 Consensus size: 29
18158254 TTTAATTACA
*
18158264 AACCCTAACCTAATTTAACTAAAAAGCCT
1 AACCCTAACCTAATTTAACTAAAAACCCT
*
18158293 AACCCTAACCTAATTTAA-TCACAAACCCT
1 AACCCTAACCTAATTTAACT-AAAAACCCT
* *
18158322 AACCCTAACCTAATTTAA-TAAAAAATCAT
1 AACCCTAACCTAATTTAACT-AAAAACCCT
18158351 AACCCTAACCTAATTTAACTAAAAACCCT
1 AACCCTAACCTAATTTAACTAAAAACCCT
*
18158380 AACCCTAACTTAATTTAACTAAAAACCCT
1 AACCCTAACCTAATTTAACTAAAAACCCT
18158409 AACCCTAACCTAATTTAACTAAAAACCCT
1 AACCCTAACCTAATTTAACTAAAAACCCT
18158438 AACCCTAACCTAATTTAA-T-AAAA----
1 AACCCTAACCTAATTTAACTAAAAACCCT
*
18158461 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAACTAAAAACCCT
18158490 AACCCTAACCTAATTT
1 AACCCTAACCTAATTT
18158506 TACATAATTT
Statistics
Matches: 195, Mismatches: 10, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
23 18 0.09
24 1 0.01
25 4 0.02
27 4 0.02
28 2 0.01
29 165 0.85
30 1 0.01
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.26
Consensus pattern (29 bp):
AACCCTAACCTAATTTAACTAAAAACCCT
Found at i:18158320 original size:23 final size:23
Alignment explanation
Indices: 18158252--18158325 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 23
18158242 TAAAAATCCA
*
18158252 AATTTAATTACAAACCCTAACCT
1 AATTTAATAACAAACCCTAACCT
*
18158275 AATTTAACTAAAAAGCCTAACCCTAACCT
1 AATTTAA-T---AA--CAAACCCTAACCT
*
18158304 AATTTAATCACAAACCCTAACC
1 AATTTAATAACAAACCCTAACC
18158326 CTAACCTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
25 1 0.02
27 1 0.02
28 1 0.02
29 19 0.46
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (23 bp):
AATTTAATAACAAACCCTAACCT
Found at i:18158608 original size:55 final size:55
Alignment explanation
Indices: 18158500--18158676 Score: 311
Period size: 55 Copynumber: 3.2 Consensus size: 55
18158490 AACCCTAACC
18158500 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAA-TTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
*
18158554 TAAATTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
* *
18158609 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTTGGGCTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAA-TTTTTGGACTTAA
18158665 TAATTTTACATA
1 TAATTTTACATA
18158677 GTTTTACATA
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
54 41 0.35
55 52 0.44
56 24 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.44
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:18159943 original size:20 final size:20
Alignment explanation
Indices: 18159898--18159935 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18159888 GATCTGAAAT
18159898 AACACAGATATCAGGTTGGG
1 AACACAGATATCAGGTTGGG
18159918 AACACAGATATCAGGTTG
1 AACACAGATATCAGGTTG
18159936 AGGGCACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AACACAGATATCAGGTTGGG
Found at i:18162052 original size:123 final size:122
Alignment explanation
Indices: 18161823--18162164 Score: 533
Period size: 123 Copynumber: 2.8 Consensus size: 122
18161813 ACTTGCTACT
* * * * *
18161823 TAGCAAAATTGCGTCCACGAAGGCGCGATTTCACACTTTCTTCTCAAATAGCATCCTGGTAAAAG
1 TAGCGAAATCGCGTCCACG-AGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
18161888 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTG
65 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTG
18161946 TAGCGAAATCGCGTCCACGATGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
1 TAGCGAAATCGCGTCCACGA-GGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
* * *
18162011 CAATTTTATACTATTTGCTCTGAAACGTCAAAAAAATTATTTCTTACATGACCTACTG
65 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTG
* * *
18162069 TAGCGAAATCACGTTCACGAGGGAGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
1 TAGCGAAATCGCGTCCACGAGGCA-CGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAG
*
18162134 TGATTTTATACTATTTGAC-CAGAAACGTCAA
65 CGATTTTATACTATTTG-CTCAGAAACGTCAA
18162165 TTCGAAATAA
Statistics
Matches: 202, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
122 4 0.02
123 197 0.98
124 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (122 bp):
TAGCGAAATCGCGTCCACGAGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGC
GATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTG
Found at i:18165735 original size:20 final size:20
Alignment explanation
Indices: 18165708--18165745 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
18165698 ATTTCTTTAT
18165708 TTTATTTTTCT-TCTTCTCC
1 TTTATTTTTCTCTCTTCTCC
18165727 TTTATTTTTCTCTCTTCTC
1 TTTATTTTTCTCTCTTCTC
18165746 ATATTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTTTTCTCTCTTCTCC
Found at i:18166850 original size:31 final size:30
Alignment explanation
Indices: 18166814--18166887 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
18166804 TTAACGACTC
*
18166814 AGTGACTAAAATGTTACAACACGTT-AACGTA
1 AGTGACTAAAATGTT--AACACGTTAAACATA
**
18166845 AGTGACTAAAATG-TAACATTTTAAACATA
1 AGTGACTAAAATGTTAACACGTTAAACATA
18166874 AGTGACTAAAATGT
1 AGTGACTAAAATGT
18166888 AATCTGAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 6 0.16
29 18 0.47
30 1 0.03
31 13 0.34
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (30 bp):
AGTGACTAAAATGTTAACACGTTAAACATA
Found at i:18167304 original size:31 final size:31
Alignment explanation
Indices: 18167222--18167305 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
18167212 ACATAACGGG
* * *
18167222 CTTAAATGATCTTTAATTA-TTTTACAAAGG
1 CTTAATTGATTTTTAATTATTTTTACAAAGA
* * * **
18167252 TTTAATTGCTTATTTATTTATTTTTAGGAAGA
1 CTTAATTGATT-TTTAATTATTTTTACAAAGA
18167284 CTTAATTGATTTTTAATTATTT
1 CTTAATTGATTTTTAATTATTT
18167306 AAGTCTAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 7 0.17
31 17 0.41
32 17 0.41
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.54
Consensus pattern (31 bp):
CTTAATTGATTTTTAATTATTTTTACAAAGA
Found at i:18167361 original size:19 final size:20
Alignment explanation
Indices: 18167337--18167374 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18167327 TTATTTTTTT
18167337 GGAAAA-TATAAATATTATA
1 GGAAAACTATAAATATTATA
18167356 GGAAAACTATAAATATTAT
1 GGAAAACTATAAATATTAT
18167375 TAAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (20 bp):
GGAAAACTATAAATATTATA
Found at i:18167496 original size:16 final size:17
Alignment explanation
Indices: 18167436--18167506 Score: 54
Period size: 18 Copynumber: 4.0 Consensus size: 17
18167426 AAAAATATGC
*
18167436 AAAATATTACATAAATAAT
1 AAAA-ATTATATAAA-AAT
* * *
18167455 TAAAATTATAGAAATTAT
1 AAAAATTATATAAA-AAT
*
18167473 AGAAAATT-TTTAAAAAT
1 A-AAAATTATATAAAAAT
18167490 AAAAATTATATAAAAAT
1 AAAAATTATATAAAAAT
18167507 TATAGAAGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 6 0.15
17 11 0.27
18 15 0.37
19 9 0.22
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATTATATAAAAAT
Found at i:18167535 original size:20 final size:20
Alignment explanation
Indices: 18167488--18167571 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 20
18167478 ATTTTTAAAA
*
18167488 ATAAAAATTATATAAAAATT
1 ATAAAAGTTATATAAAAATT
* *
18167508 ATAGAAGTTATAT-AAACTT
1 ATAAAAGTTATATAAAAATT
18167527 ACTAAAAG-TATA-AAAAAGTT
1 A-TAAAAGTTATATAAAAA-TT
*
18167547 TTAAAAGTT-T-TAAAAATAT
1 ATAAAAGTTATATAAAAAT-T
18167566 ATAAAA
1 ATAAAA
18167572 AAAATTATAC
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
18 1 0.02
19 31 0.61
20 19 0.37
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (20 bp):
ATAAAAGTTATATAAAAATT
Found at i:18167884 original size:9 final size:9
Alignment explanation
Indices: 18167844--18167945 Score: 50
Period size: 9 Copynumber: 11.4 Consensus size: 9
18167834 ATTTTTTTAA
*
18167844 AAAAATTAA
1 AAAAATTAT
18167853 AAAAATTAT
1 AAAAATTAT
*
18167862 -AAAATTTT
1 AAAAATTAT
*
18167870 AGAAAATTGT
1 A-AAAATTAT
18167880 AAAAA-TA-
1 AAAAATTAT
* *
18167887 GAAAGTTAT
1 AAAAATTAT
*
18167896 AAAAAATTAC
1 -AAAAATTAT
* *
18167906 ATAAGTTAT
1 AAAAATTAT
* *
18167915 TAAAATTGTT
1 AAAAATT-AT
*
18167925 AAATATTAT
1 AAAAATTAT
18167934 AAAAATT-T
1 AAAAATTAT
18167942 AAAA
1 AAAA
18167946 TCATTGGCCC
Statistics
Matches: 67, Mismatches: 20, Indels: 13
0.67 0.20 0.13
Matches are distributed among these distances:
7 3 0.04
8 15 0.22
9 29 0.43
10 20 0.30
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18172832 original size:27 final size:29
Alignment explanation
Indices: 18172775--18172832 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
18172765 AACTTTTAAC
*
18172775 TTTTAAAAATAAAAAATATATGTATTGTA
1 TTTTAAAAATAAAAAATATATGTATTATA
*
18172804 TTTTAAAAATAAAGAATATA-GT-TTATA
1 TTTTAAAAATAAAAAATATATGTATTATA
18172831 TT
1 TT
18172833 CGGTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 2 0.07
29 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTAAAAATAAAAAATATATGTATTATA
Found at i:18180973 original size:25 final size:25
Alignment explanation
Indices: 18180945--18180998 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
18180935 CTCCTCCAAT
18180945 CTGAGTAACGGTAAGCTCA-TACGAG
1 CTGAGTAACGGTAAGCTCATTA-GAG
*
18180970 CTGAGTATCGGTAAGCTCATTAGAG
1 CTGAGTAACGGTAAGCTCATTAGAG
18180995 CTGA
1 CTGA
18180999 AATTGGTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (25 bp):
CTGAGTAACGGTAAGCTCATTAGAG
Done.