Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 70 of 126
Found at i:20669620 original size:21 final size:21
Alignment explanation
Indices: 20669572--20669620 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20669562 ATCATTATAT
*
20669572 AAATATTAAAATATTTAATAAA
1 AAATA-TAAAAAATTTAATAAA
*
20669594 ATATATAAAAAATTTAA-AAA
1 AAATATAAAAAATTTAATAAA
20669614 ACAATAT
1 A-AATAT
20669621 TTTATACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATAAAAAATTTAATAAA
Found at i:20669779 original size:29 final size:30
Alignment explanation
Indices: 20669742--20669811 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
20669732 TTTTGAAAAA
20669742 TTAAAATTTAATTTTTATA-TTTT-TATTT
1 TTAAAATTTAATTTTTATATTTTTCTATTT
* *
20669770 TTATGAATTTAATTTTTTTATTTTTCTATTT
1 TTA-AAATTTAATTTTTATATTTTTCTATTT
20669801 TTAAAATTTAA
1 TTAAAATTTAA
20669812 ATTCAATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 14 0.39
30 11 0.31
31 8 0.22
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (30 bp):
TTAAAATTTAATTTTTATATTTTTCTATTT
Found at i:20670386 original size:26 final size:28
Alignment explanation
Indices: 20670346--20670400 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
20670336 AAAAATAAGT
*
20670346 TATAAAAATTCTTAAATTTTAA-TAAAAA
1 TATAAAAATTCTTAAA-CTTAATTAAAAA
20670374 TATAAAAA-T-TTAAACTTAATTAAAAA
1 TATAAAAATTCTTAAACTTAATTAAAAA
20670400 T
1 T
20670401 TAGAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 12 0.48
27 1 0.04
28 8 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAAAAATTCTTAAACTTAATTAAAAA
Found at i:20670678 original size:20 final size:20
Alignment explanation
Indices: 20670655--20670791 Score: 78
Period size: 20 Copynumber: 7.2 Consensus size: 20
20670645 TTTTGATGCA
*
20670655 TTTTATAATATTTTTATAAC
1 TTTTATAATATTTTTATAAT
** *
20670675 TTTTATAA-AAGTTTACAATT
1 TTTTATAATATTTTTATAA-T
* *
20670695 TTTTATAATTTTTTTATGAT
1 TTTTATAATATTTTTATAAT
**
20670715 TTTTATAA-A-AATTATAA-
1 TTTTATAATATTTTTATAAT
20670732 TTTT-TAATAATTTTTAT-AT
1 TTTTATAAT-ATTTTTATAAT
* * *
20670751 TTTTATTAA-AATATAATAAT
1 TTTTA-TAATATTTTTATAAT
20670771 TTTTAT--T-TTTTTATAAT
1 TTTTATAATATTTTTATAAT
20670788 TTTT
1 TTTT
20670792 TGTCATATGC
Statistics
Matches: 86, Mismatches: 21, Indels: 23
0.66 0.16 0.18
Matches are distributed among these distances:
16 3 0.03
17 15 0.17
18 7 0.08
19 21 0.24
20 32 0.37
21 8 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
TTTTATAATATTTTTATAAT
Found at i:20670709 original size:40 final size:39
Alignment explanation
Indices: 20670655--20670746 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 39
20670645 TTTTGATGCA
* *
20670655 TTTTATAATATTTTTATAACTTTTATAAAAGTTTACAATT
1 TTTTATAATTTTTTTATAACTTTTATAAAA-ATTACAATT
* * *
20670695 TTTTATAATTTTTTTATGATTTTTATAAAAATTATAATT
1 TTTTATAATTTTTTTATAACTTTTATAAAAATTACAATT
*
20670734 TTTAATAATTTTT
1 TTTTATAATTTTT
20670747 ATATTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 19 0.41
40 27 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (39 bp):
TTTTATAATTTTTTTATAACTTTTATAAAAATTACAATT
Found at i:20670754 original size:8 final size:9
Alignment explanation
Indices: 20670664--20670791 Score: 71
Period size: 9 Copynumber: 13.7 Consensus size: 9
20670654 ATTTTATAAT
20670664 ATTTTTATA
1 ATTTTTATA
*
20670673 ACTTTTATAA
1 ATTTTTAT-A
** *
20670683 AAGTTTACA
1 ATTTTTATA
20670692 ATTTTTTATA
1 A-TTTTTATA
*
20670702 ATTTTTTTATG
1 A--TTTTTATA
20670713 ATTTTTATA
1 ATTTTTATA
***
20670722 AAAATTATA
1 ATTTTTATA
20670731 ATTTTTAATA
1 ATTTTT-ATA
20670741 ATTTTTAT-
1 ATTTTTATA
20670749 ATTTTTATTAA
1 ATTTTTA-T-A
* * *
20670760 AATATAATA
1 ATTTTTATA
20670769 ATTTTTAT-
1 ATTTTTATA
*
20670777 TTTTTTATA
1 ATTTTTATA
20670786 ATTTTT
1 ATTTTT
20670792 TGTCATATGC
Statistics
Matches: 88, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
8 14 0.16
9 39 0.44
10 22 0.25
11 13 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20670770 original size:38 final size:36
Alignment explanation
Indices: 20670655--20670791 Score: 116
Period size: 40 Copynumber: 3.6 Consensus size: 36
20670645 TTTTGATGCA
* * * *
20670655 TTTTATAATATTTTTATAACTTTTATAAAAGTTTACAATT
1 TTTTAT-A-ATTTTTATAATTTTTATAAAA-ATAATAA-T
* *
20670695 TTTTATAATTTTTTTATGATTTTTATAAAAATTATAAT
1 TTTTATAA--TTTTTATAATTTTTATAAAAATAATAAT
20670733 TTTTAATAATTTTTAT-ATTTTTATTAAAATATAATAAT
1 TTTT-ATAATTTTTATAATTTTTA-TAAAA-ATAATAAT
*
20670771 TTTTAT-TTTTTTATAATTTTT
1 TTTTATAATTTTTATAATTTTT
20670792 TGTCATATGC
Statistics
Matches: 85, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
36 14 0.16
37 20 0.24
38 17 0.20
39 10 0.12
40 24 0.28
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (36 bp):
TTTTATAATTTTTATAATTTTTATAAAAATAATAAT
Found at i:20677900 original size:26 final size:27
Alignment explanation
Indices: 20677842--20677900 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
20677832 GACTGAAACC
*
20677842 GTAAAAAAATGCTACCTAAGAGCATAA
1 GTAAAATAATGCTACCTAAGAGCATAA
*
20677869 G-GAAATAATG-TACC-AGAGAGCATAA
1 GTAAAATAATGCTACCTA-AGAGCATAA
20677894 GTAAAAT
1 GTAAAAT
20677901 CATTAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 14 0.52
26 11 0.41
27 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.19
Consensus pattern (27 bp):
GTAAAATAATGCTACCTAAGAGCATAA
Found at i:20679531 original size:26 final size:26
Alignment explanation
Indices: 20679494--20679587 Score: 79
Period size: 26 Copynumber: 3.6 Consensus size: 26
20679484 GGTCTCTTTA
* * *
20679494 TGAGCT-TCCCTTGCGAGCTATGTTTG
1 TGAGCTCT-CCTTGCGAGCAACGCTTG
**
20679520 TGAGCTCTCCTTATGAGCAACGCTTG
1 TGAGCTCTCCTTGCGAGCAACGCTTG
20679546 TGAGCTCTCCTTGCGAGC--C-CTATCG
1 TGAGCTCTCCTTGCGAGCAACGCT-T-G
20679571 ATGAGCTCTCCTTGCGA
1 -TGAGCTCTCCTTGCGA
20679588 ACCCTATTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 1 0.02
26 51 0.89
27 1 0.02
ACGTcount: A:0.15, C:0.29, G:0.24, T:0.32
Consensus pattern (26 bp):
TGAGCTCTCCTTGCGAGCAACGCTTG
Found at i:20679592 original size:26 final size:26
Alignment explanation
Indices: 20679546--20679611 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
20679536 GCAACGCTTG
*
20679546 TGAGCTCTCCTTGCGAGCCCTATCGA
1 TGAGCTCTCCTTGCGAACCCTATCGA
* *
20679572 TGAGCTCTCCTTGCGAACCCTATTGG
1 TGAGCTCTCCTTGCGAACCCTATCGA
*
20679598 CGAGCTCTCCTTGC
1 TGAGCTCTCCTTGC
20679612 AAGTAGTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.14, C:0.35, G:0.23, T:0.29
Consensus pattern (26 bp):
TGAGCTCTCCTTGCGAACCCTATCGA
Found at i:20679655 original size:26 final size:27
Alignment explanation
Indices: 20679626--20679687 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
20679616 AGTTCCTGTG
*
20679626 AGCTGTCC-TTGTGAGCCCTATTTGCA
1 AGCTGTCCTTTGTGAGCCATATTTGCA
* * *
20679652 AGCTCTCCTTTTGTGAGCTATATTTGCG
1 AGCTGTCC-TTTGTGAGCCATATTTGCA
20679680 AGCTGTCC
1 AGCTGTCC
20679688 GTCTTCGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 7 0.24
28 22 0.76
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.37
Consensus pattern (27 bp):
AGCTGTCCTTTGTGAGCCATATTTGCA
Found at i:20684511 original size:29 final size:29
Alignment explanation
Indices: 20684268--20684591 Score: 251
Period size: 30 Copynumber: 10.9 Consensus size: 29
20684258 ATTTTAACCC
* * *
20684268 CCCTAAAC-TTTCTAAAATTTCATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
** **
20684296 CCCTCAAACAATTCCAAAATTGTATTTTTATA
1 CCCT-AAACTTTTCCAAAATTACA-TTTTA-A
* * **
20684328 CCTTAAACTTTTCCAAAATTACGTTTCGA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* * *
20684357 CCACCAAACTTCTCCAAAATTTCATTTTAA
1 CC-CTAAACTTTTCCAAAATTACATTTTAA
* * *
20684387 CCCTTAAATTTTTCTAAAATTATATTTTAA
1 CCC-TAAACTTTTCCAAAATTACATTTTAA
* * * * *
20684417 CCACCAAACTTCTCTAAAATTGCATTTTGA
1 CC-CTAAACTTTTCCAAAATTACATTTTAA
20684447 CCCTTAAACATTTT-CAAAATTACATTTTAA
1 CCC-TAAAC-TTTTCCAAAATTACATTTTAA
* *
20684477 CCCCTAAACCTTTCCAAAATCACATTTTAA
1 -CCCTAAACTTTTCCAAAATTACATTTTAA
*
20684507 CCCTAAA-TTTTCCTAAAATTGCATTTTAA
1 CCCTAAACTTTTCC-AAAATTACATTTTAA
** *
20684536 -CCTGAAACTTTTCCATGATTACATTTTTAC
1 CCCT-AAACTTTTCCAAAATTACA-TTTTAA
*
20684566 CCCTAAACTTTTCCAAAATTATATTT
1 CCCTAAACTTTTCCAAAATTACATTT
20684592 GACCTCAAAT
Statistics
Matches: 231, Mismatches: 49, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
28 12 0.05
29 44 0.19
30 143 0.62
31 28 0.12
32 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:20697093 original size:84 final size:84
Alignment explanation
Indices: 20696952--20697111 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
20696942 AACCCCATCT
*
20696952 TTCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTAATCTTCCTGATGAGATATAGA
1 TTCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTAATCTTCCTGATGAGATACAGA
* *
20697017 GAAGTAGACCAAATCTGTC
66 AAAATAGACCAAATCTGTC
* * * * * *
20697036 TTCTGATGAGATACAGAGAAGT-GGATTAAATCAATGAAGCGGTCATCTTCTTGATGAGATACAG
1 TTCTGATGAGATACAGAGAAGTAGG-TCAAAGCAATAAAGAGGTAATCTTCCTGATGAGATACAG
20697100 AAAAATAGACCA
65 AAAAATAGACCA
20697112 CTTCAACAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
83 2 0.03
84 64 0.97
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.24
Consensus pattern (84 bp):
TTCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGAGGTAATCTTCCTGATGAGATACAGA
AAAATAGACCAAATCTGTC
Found at i:20697239 original size:208 final size:209
Alignment explanation
Indices: 20696916--20697743 Score: 1137
Period size: 208 Copynumber: 3.9 Consensus size: 209
20696906 ACAATGATGA
** ** *
20696916 GAAGCTCAATAAGAGTGAAACTTTGAAACCCCATCTTTCTGATGAGATACAGAGAAGTAGGTCAA
1 GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAA
* * * ** * *
20696981 AGCAATAAAGAGGTA-ATCTTCCTGATGAGATATAGAGAAGTAGACCAAATCTGTCTT-CTGATG
66 ATCAATAAAGTGG-ACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCTGATG
*
20697044 AGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCTTGATGAGATACAGAAAAATAGA
130 AGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAATAGA
*
20697109 CCACTTCAACAAAGT
195 CCAATTCAACAAAGT
*
20697124 GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATATAGAGAAGTGGGTCAA
1 GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAA
20697189 ATCAATAAAGTGGACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCTGATGA
66 ATCAATAAAGTGGACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCTGATGA
** *
20697254 GATACAGAGAACAGGATTAAATCAATGAAGCGATCATCTTCCTGATGAGAGATACA-AAGAAATA
131 GATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGAT--GAGATACAGAA-AAATA
* *
20697318 GACCAATTAAACGAAGT
193 GACCAATTCAACAAAGT
* *
20697335 TAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTCCTGATGAGATACAGA-AAGTGGGTCAA
1 GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGG----
* * *
20697399 ATCAAATCAATAAAGTGGTCATCTTCTTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCT
62 -TCAAATCAATAAAGTGGACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCT
* * * * *
20697464 GATGAGATACAGAAAAGTGAATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATACAGAGAAG
126 GATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAA
20697529 TAGACCAATTCAACAAAGT
191 TAGACCAATTCAACAAAGT
** * * *
20697548 GAAGCTCAATGTGAGTGAAACTTCCAAACTTCATCTTTTTGATGAGATGCAGAGAAGTCGGTC-A
1 GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAA
* * * * * *
20697612 ATTAATAAAGTGGTCATCTTCTTGACGAGATGCAGAGAAATGAACCAAATCCGTCTTCTTGATGA
66 ATCAATAAAGTGGACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCTGATGA
* *
20697677 GATACAGAGAAGTGGACTAAGA-CAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGA
131 GATACAGAGAAGTGGATTAA-ATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAATAGA
20697741 CCA
195 CCA
20697744 TGAAATGAAG
Statistics
Matches: 556, Mismatches: 51, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
207 1 0.00
208 230 0.41
209 52 0.09
210 9 0.02
211 77 0.14
213 74 0.13
214 7 0.01
215 106 0.19
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
GAAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTGGGTCAA
ATCAATAAAGTGGACATCTTCCTGACGAGATGCAGAGAAGTAAACCAAATCCGTCTTCCTGATGA
GATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAAAAATAGAC
CAATTCAACAAAGT
Found at i:20697536 original size:85 final size:86
Alignment explanation
Indices: 20697368--20697529 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 86
20697358 CCAAACCCCA
* * *
20697368 TCTTCCTGATGAGATACAGAAAGTGGGTCAAATCAAATCAATAAAGTGGTCATCTTCTTGACGAG
1 TCTTCCTGATGAGATACAGAAAGT-GG--AAATCAAATCAATAAAGCGGTCATCTTCCTAACGAG
*
20697433 ATGCAGAGAAGTGAACCAAATCCG
63 ATACAGAGAAGTGAACCAAATCCG
* * *
20697457 TCTTCCTGATGAGATACAGAAAAGT-G-AATTAAATCAATGAAGCGGTCATCTTCCTAATGAGAT
1 TCTTCCTGATGAGATACAG-AAAGTGGAAATCAAATCAATAAAGCGGTCATCTTCCTAACGAGAT
20697520 ACAGAGAAGT
65 ACAGAGAAGT
20697530 AGACCAATTC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
85 40 0.62
88 1 0.02
89 19 0.29
90 5 0.08
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (86 bp):
TCTTCCTGATGAGATACAGAAAGTGGAAATCAAATCAATAAAGCGGTCATCTTCCTAACGAGATA
CAGAGAAGTGAACCAAATCCG
Found at i:20702137 original size:168 final size:168
Alignment explanation
Indices: 20701819--20702153 Score: 575
Period size: 168 Copynumber: 2.0 Consensus size: 168
20701809 ATGTCTCAAG
20701819 TATATATATCCTTCCGATCCCTCTTACTTACTTTTAGATTTTTTTTTATCAAGAAAACAATATAT
1 TATATATATCCTTCCGATCCCTCTTACTTACTTTTAGA-TTTTTTTTATCAAGAAAACAATATAT
*
20701884 ATAAAAGCACAAGTTAAAAAAAAACATTTGAATAAATTAAATGATAGGTTTGAAGGAAAAAATTA
65 ATAAAAGCACAAGTTAAAAAAAAACATTTGAATAAATTAAATGATAAGTTTGAAGGAAAAAATTA
20701949 TGTCGTTCTGACACACTTTCGTCTACTTTTTGGCACAAA
130 TGTCGTTCTGACACACTTTCGTCTACTTTTTGGCACAAA
* *
20701988 TATATATATCCTTCCGATCTCTCTTACTCTTACTTTTAGA-TTTTTTTATCAGGAAAACAATATA
1 TATATATATCCTTCCGATCCCTCTTA--CTTACTTTTAGATTTTTTTTATCAAGAAAACAATATA
* * *
20702052 TATAAAAGCATAAGTT-TAAAAAAATATTTGAATAAATTAAATGATAAGTTTGAAGGAAAAAATT
64 TATAAAAGCACAAGTTAAAAAAAAACATTTGAATAAATTAAATGATAAGTTTGAAGGAAAAAATT
20702116 ATGTCGTTCTGACACACTTTCGTCTACTTTTTGGCACA
129 ATGTCGTTCTGACACACTTTCGTCTACTTTTTGGCACA
20702154 CTTTTTTGCA
Statistics
Matches: 158, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
168 83 0.53
169 63 0.40
171 12 0.08
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (168 bp):
TATATATATCCTTCCGATCCCTCTTACTTACTTTTAGATTTTTTTTATCAAGAAAACAATATATA
TAAAAGCACAAGTTAAAAAAAAACATTTGAATAAATTAAATGATAAGTTTGAAGGAAAAAATTAT
GTCGTTCTGACACACTTTCGTCTACTTTTTGGCACAAA
Found at i:20703644 original size:49 final size:49
Alignment explanation
Indices: 20703519--20703662 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 49
20703509 ACTGTGGAAA
* * * *
20703519 AATGAAGATTTGAAGGGAAAAGTTGAGGCCATAATGGCGAACCCGGTAC
1 AATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
** ** * * *
20703568 CTTAGAAGACGTGATGGG-AAGGATTGAGGCCGTAACGGTGAATCCGGTAC
1 AAT-GAAGATATGAAGGGAAAGG-TTGAGGCCGTAACGGCGAACCCGGTAC
* *
20703618 AATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCG
1 AATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCG
20703663 ATACCTTAGA
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
49 34 0.47
50 39 0.53
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.17
Consensus pattern (49 bp):
AATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
Found at i:20703827 original size:41 final size:40
Alignment explanation
Indices: 20703691--20704054 Score: 345
Period size: 41 Copynumber: 8.6 Consensus size: 40
20703681 AGACACACCG
20703691 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATCATCCA
1 ATCTTTTACCCCTAA-TCAAGA-GGGCAGATTGAAG--AT--TCCA
* * *
20703737 ATCTTTTACCCCTAAGTCAAAAGAGGCATATTGCAACCATCATCCA
1 ATCTTTTACCCCTAA-TCAAGAG-GGCAGATTG-AA-GAT--TCCA
* *
20703783 ATCTTTTACCCTTAATCAAGAGGGACAGATTGAAGATTTCA
1 ATCTTTTACCCCTAATCAAGAGGG-CAGATTGAAGATTCCA
*
20703824 ATCTTTTACCCCTAATCAAGAGGGGCAGATTTAAGATTCCA
1 ATCTTTTACCCCTAATCAAGA-GGGCAGATTGAAGATTCCA
*
20703865 ATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCA
1 ATCTTTTACCCCTAATCAAG-AGGGCAGATTGAAGATTCCA
*
20703906 ATCTTTTACCCCTAAT--AGAAGGGCAAATTGAAGATTCCA
1 ATCTTTTACCCCTAATCAAG-AGGGCAGATTGAAGATTCCA
* * * *
20703945 ATCTTTTACCCTTAATCAATAAGGGTAGATTGAAAATTCCA
1 ATCTTTTACCCCTAATCAA-GAGGGCAGATTGAAGATTCCA
* * * **
20703986 GTCTTTTACCCCTAAATCAATAAGGACAGATTGAAGACCATTCTG
1 ATCTTTTACCCCT-AATCAA-GAGGGCAGATTGAAG---ATTCCA
* *
20704031 ATCTTTTACCCCTAACCGAGAGGG
1 ATCTTTTACCCCTAATCAAGAGGG
20704055 GCAAATCCAA
Statistics
Matches: 273, Mismatches: 32, Indels: 29
0.82 0.10 0.09
Matches are distributed among these distances:
39 37 0.14
41 118 0.43
42 23 0.08
43 5 0.02
44 8 0.03
45 29 0.11
46 51 0.19
47 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (40 bp):
ATCTTTTACCCCTAATCAAGAGGGCAGATTGAAGATTCCA
Found at i:20703969 original size:80 final size:81
Alignment explanation
Indices: 20703691--20704000 Score: 372
Period size: 80 Copynumber: 3.7 Consensus size: 81
20703681 AGACACACCG
* *
20703691 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTCA
1 ATCTTTTACCCTTAA-TCAAGAAGGGCAGATTGAAG--AT--TCCAATCTTTTACCCCTAA-TCA
* * *
20703756 AAAGAGGCATATTGCAACCATCATCCA
60 GAAG-GGCAAATTG-AA-GAT--TCCA
* *
20703783 ATCTTTTACCCTTAATCAAG-AGGGACAGATTGAAGATTTCAATCTTTTACCCCTAATCAAGAGG
1 ATCTTTTACCCTTAATCAAGAAGGG-CAGATTGAAGATTCCAATCTTTTACCCCTAATC-AGAAG
* *
20703847 GGCAGATTTAAGATTCCA
64 GGCAAATTGAAGATTCCA
20703865 ATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTTTTACCCCTAAT-AGAAGGG
1 ATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTTTTACCCCTAATCAGAAGGG
20703929 CAAATTGAAGATTCCA
66 CAAATTGAAGATTCCA
* * * *
20703945 ATCTTTTACCCTTAATCAATAAGGGTAGATTGAAAATTCCAGTCTTTTACCCCTAA
1 ATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTTTTACCCCTAA
20704001 ATCAATAAGG
Statistics
Matches: 199, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
80 72 0.36
82 55 0.28
83 4 0.02
84 2 0.01
85 2 0.01
86 9 0.05
87 21 0.11
89 2 0.01
90 3 0.02
91 15 0.08
92 14 0.07
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (81 bp):
ATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTCCAATCTTTTACCCCTAATCAGAAGGG
CAAATTGAAGATTCCA
Found at i:20704901 original size:30 final size:30
Alignment explanation
Indices: 20704870--20704925 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
20704860 TCAGCCCTTC
* *
20704870 CCCG-GGCTATCAATGCATCCTTTCGAATT
1 CCCGAGGCCATCAATGCACCCTTTCGAATT
20704899 CCCGAGGCCATCAATGCACCCTTTCGA
1 CCCGAGGCCATCAATGCACCCTTTCGA
20704926 CGACTACTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (30 bp):
CCCGAGGCCATCAATGCACCCTTTCGAATT
Found at i:20707904 original size:25 final size:25
Alignment explanation
Indices: 20707874--20707939 Score: 116
Period size: 25 Copynumber: 2.6 Consensus size: 25
20707864 CTTTTAAAAG
20707874 AAACTCAAGAGCAATTCTTGAAGAA
1 AAACTCAAGAGCAATTCTTGAAGAA
20707899 AAACTCAAGAGCAATTCTTGAAGAA
1 AAACTCAAGAGCAATTCTTGAAGAA
20707924 AAACTCAAAGAG-AATT
1 AAACTC-AAGAGCAATT
20707940 ATTATTAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (25 bp):
AAACTCAAGAGCAATTCTTGAAGAA
Found at i:20710276 original size:31 final size:31
Alignment explanation
Indices: 20710240--20710309 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
20710230 AATGTCTAAA
* * * *
20710240 GGACTAAATTGAGAATATCTGATAATCTTAG
1 GGACTAAACTAAGAATATCTAAAAATCTTAG
* *
20710271 GGACTAAACTAAGAATGTCTAAAAATGTTAG
1 GGACTAAACTAAGAATATCTAAAAATCTTAG
20710302 GGACTAAA
1 GGACTAAA
20710310 GCGGACTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (31 bp):
GGACTAAACTAAGAATATCTAAAAATCTTAG
Found at i:20727892 original size:8 final size:7
Alignment explanation
Indices: 20727871--20727895 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20727861 GGCTCTTTGG
20727871 ATTAAAA
1 ATTAAAA
20727878 ATTAAAA
1 ATTAAAA
20727885 ATTAAAA
1 ATTAAAA
20727892 ATTA
1 ATTA
20727896 GGAAGGAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:20728371 original size:25 final size:24
Alignment explanation
Indices: 20728330--20728412 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 24
20728320 ATTAAATTAA
*
20728330 ATTAAA-TTTTATATATTATTTAT
1 ATTAAATTTTTAAATATTATTTAT
20728353 ATTAAATTATTTAAATATTATTTAT
1 ATTAAATT-TTTAAATATTATTTAT
*
20728378 CTTAAATTGTTTAAATATTATTTATT
1 ATTAAATT-TTTAAATATTATTTA-T
*
20728404 ATTACATTT
1 ATTAAATTT
20728413 AATTTTGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 38 0.73
26 7 0.13
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (24 bp):
ATTAAATTTTTAAATATTATTTAT
Found at i:20734386 original size:14 final size:14
Alignment explanation
Indices: 20734357--20734391 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20734347 AATGATACTT
20734357 TGAAACATCAAAAGG
1 TGAAA-ATCAAAAGG
*
20734372 TGAAAATCGAAAGG
1 TGAAAATCAAAAGG
20734386 TGAAAA
1 TGAAAA
20734392 GAAAGAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (14 bp):
TGAAAATCAAAAGG
Found at i:20734430 original size:18 final size:18
Alignment explanation
Indices: 20734393--20734431 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20734383 AGGTGAAAAG
**
20734393 AAAGAAAGAAAAAGTTTA
1 AAAGAAAGAAAAAGGGTA
*
20734411 AAAGAATGAAAAAGGGTA
1 AAAGAAAGAAAAAGGGTA
20734429 AAA
1 AAA
20734432 CAAATTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (18 bp):
AAAGAAAGAAAAAGGGTA
Found at i:20736720 original size:98 final size:98
Alignment explanation
Indices: 20736611--20736875 Score: 422
Period size: 98 Copynumber: 2.7 Consensus size: 98
20736601 TTCCTTTTAC
* * * *
20736611 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTCATTTCTTTGTGGTACTGG
1 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAG
20736676 ATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
66 ATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
* * * *
20736709 GTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCCTCGTGATACTAG
1 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAG
*
20736774 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
66 ATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
* * *
20736807 GTTTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAA
1 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAG
20736872 ATTC
66 ATTC
20736876 TCGTAAAATA
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 151 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAG
ATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
Found at i:20736850 original size:49 final size:49
Alignment explanation
Indices: 20736596--20736851 Score: 245
Period size: 49 Copynumber: 5.2 Consensus size: 49
20736586 TGGCAGCCTC
* * * *
20736596 AACCTTTCCTTTTACGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTA
1 AACCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTA
* * * * *
20736645 AACATTTCCCTTCAT-TTCTTTGTGGTACT--GGATTCACCGTTGCGGCTTA
1 AACCTTTCCCTTCATGTT-TCTGAGGTA-TAAGG-TTCGCCGTTGCGACTTA
* * *
20736694 AATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTA
1 AACCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTA
* * * * *
20736743 AACCTTTCCCTCCATATCCTCGTGA--TACT-AGATTCGCCGTTGCGGCTTA
1 AACCTTTCCCTTCATGT-TTC-TGAGGTA-TAAGGTTCGCCGTTGCGACTTA
* *
20736792 AATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCATTGCGACTTA
1 AACCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTA
20736841 AACCTTTCCCT
1 AACCTTTCCCT
20736852 CCATATCTTT
Statistics
Matches: 162, Mismatches: 33, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
47 3 0.02
48 7 0.04
49 144 0.89
50 6 0.04
51 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.37
Consensus pattern (49 bp):
AACCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTGCGACTTA
Found at i:20738897 original size:16 final size:17
Alignment explanation
Indices: 20738876--20738915 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
20738866 TCATCTTGAC
20738876 TTTCTTTTTCTTCCT-T
1 TTTCTTTTTCTTCCTCT
*
20738892 TTTC-TTTTCTTCTTCT
1 TTTCTTTTTCTTCCTCT
20738908 TTTCTTTT
1 TTTCTTTT
20738916 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTCTTCCTCT
Found at i:20738901 original size:5 final size:5
Alignment explanation
Indices: 20738891--20738925 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
20738881 TTTTCTTCCT
20738891 TTTTC TTTTC TTCTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTT
20738926 TAAAAGATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:20738901 original size:21 final size:21
Alignment explanation
Indices: 20738876--20738926 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
20738866 TCATCTTGAC
20738876 TTTCTTTTTCTTC-CTTTTTCT
1 TTTCTTTTTCTTCTC-TTTTCT
* *
20738897 TTTCTTCTTCTTTTCTTTTCT
1 TTTCTTTTTCTTCTCTTTTCT
20738918 TTTCTTTTT
1 TTTCTTTTT
20738927 AAAAGATGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTCTTCTCTTTTCT
Found at i:20738926 original size:16 final size:16
Alignment explanation
Indices: 20738876--20738926 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
20738866 TCATCTTGAC
*
20738876 TTTCTTTT-TCTTCCTT
1 TTTCTTTTCT-TTTCTT
20738892 TTTCTTTTCTTCTTC-T
1 TTTCTTTTCTT-TTCTT
20738908 TTTCTTTTCTTTTCTT
1 TTTCTTTTCTTTTCTT
20738924 TTT
1 TTT
20738927 AAAAGATGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:20743294 original size:14 final size:14
Alignment explanation
Indices: 20743265--20743299 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20743255 AATGATACTT
20743265 TGAAACATCAAAAGG
1 TGAAA-ATCAAAAGG
*
20743280 TGAAAATCGAAAGG
1 TGAAAATCAAAAGG
20743294 TGAAAA
1 TGAAAA
20743300 GAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.54, C:0.09, G:0.23, T:0.14
Consensus pattern (14 bp):
TGAAAATCAAAAGG
Found at i:20746227 original size:3 final size:3
Alignment explanation
Indices: 20746219--20746251 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
20746209 CATTTAATTC
*
20746219 TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
20746252 GCTGGTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:20755185 original size:108 final size:108
Alignment explanation
Indices: 20755041--20755235 Score: 320
Period size: 108 Copynumber: 1.8 Consensus size: 108
20755031 TGATGACTGT
* *
20755041 TGTGAAAGTAAATATGTTGGTACGTTATTCATGCCATGAGACAGTAAATATGTGGGTATGTTATT
1 TGTGAAAGTAAATATGTTGGTACGTTATTCAAGCCATGAGACAATAAATATGTGGGTATGTTATT
20755106 CATGCCATGAGACAATAAATATGTGGGTATGTTATTCATGCCA
66 CATGCCATGAGACAATAAATATGTGGGTATGTTATTCATGCCA
* *
20755149 TGTGATAGTAAATATG-TGAGTATGTTATTCAAGCCATGAGACAATAAATATGTGGGTATGTTAT
1 TGTGAAAGTAAATATGTTG-GTACGTTATTCAAGCCATGAGACAATAAATATGTGGGTATGTTAT
* *
20755213 TCATGCCATGTGACAATGAATAT
65 TCATGCCATGAGACAATAAATAT
20755236 ATTATGCTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 2 0.03
108 78 0.98
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (108 bp):
TGTGAAAGTAAATATGTTGGTACGTTATTCAAGCCATGAGACAATAAATATGTGGGTATGTTATT
CATGCCATGAGACAATAAATATGTGGGTATGTTATTCATGCCA
Found at i:20755228 original size:36 final size:36
Alignment explanation
Indices: 20755049--20755235 Score: 284
Period size: 36 Copynumber: 5.2 Consensus size: 36
20755039 GTTGTGAAAG
* * *
20755049 TAAATATGTTGGTACGTTATTCATGCCATGAGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
20755085 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
* * *
20755121 TAAATATGTGGGTATGTTATTCATGCCATGTGATAG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
* *
20755157 TAAATATGTGAGTATGTTATTCAAGCCATGAGACAA
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
*
20755193 TAAATATGTGGGTATGTTATTCATGCCATGTGACAA
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
*
20755229 TGAATAT
1 TAAATAT
20755236 ATTATGCTAA
Statistics
Matches: 136, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 136 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (36 bp):
TAAATATGTGGGTATGTTATTCATGCCATGAGACAA
Found at i:20755693 original size:23 final size:23
Alignment explanation
Indices: 20755628--20755695 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
20755618 ATTAAATGTG
*
20755628 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
20755651 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
20755674 TTCAATATTAATGTGATTTATG
1 TTAAATATTAATGTGATTTATG
20755696 TGTAAATGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:20772110 original size:20 final size:20
Alignment explanation
Indices: 20772064--20772166 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
20772054 AGTTTGAAAC
*
20772064 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
* *
20772086 GATTTTAAACATGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* **
20772106 AATTTGAATTAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* **
20772126 CATTTT-AACACTTCAAAAT
1 AATTTTAAACAAGTCAAAAT
**
20772145 GTTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
20772166 A
1 A
20772167 GCTTCAGGCC
Statistics
Matches: 60, Mismatches: 19, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
19 13 0.22
20 28 0.47
21 14 0.23
22 5 0.08
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:20778107 original size:2 final size:2
Alignment explanation
Indices: 20778100--20778127 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20778090 TATTACTCTC
20778100 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
20778128 TAGCCATCTG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20778351 original size:20 final size:20
Alignment explanation
Indices: 20778326--20778393 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
20778316 TGCAATTTGG
*
20778326 TATCGATACTGATATAAAAT
1 TATCGATACTGATATAAAAA
**
20778346 TATCGATACTTCTATAAAAA
1 TATCGATACTGATATAAAAA
20778366 TATCGATACTTG-TGA-AAAAA
1 TATCGATAC-TGAT-ATAAAAA
20778386 TATCGATA
1 TATCGATA
20778394 TCACGGGCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATATAAAAA
Found at i:20780466 original size:20 final size:21
Alignment explanation
Indices: 20780443--20780489 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20780433 AGTTAAAACG
*
20780443 ATTTTAAAC-ATGTCAAAATA
1 ATTTTAAACTAAGTCAAAATA
* *
20780463 A-TTTGAACTAAGTCAAAATC
1 ATTTTAAACTAAGTCAAAATA
20780483 ATTTTAA
1 ATTTTAA
20780490 CACTTCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (21 bp):
ATTTTAAACTAAGTCAAAATA
Found at i:20784158 original size:21 final size:21
Alignment explanation
Indices: 20784134--20784181 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
20784124 GTGGCGCGTG
*
20784134 GCGACGGACGGTGACAGAGAT
1 GCGACGGACGGCGACAGAGAT
*
20784155 GCGACGGACGGCGACGGAGAT
1 GCGACGGACGGCGACAGAGAT
*
20784176 GTGACG
1 GCGACG
20784182 ATAGGCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.46, T:0.08
Consensus pattern (21 bp):
GCGACGGACGGCGACAGAGAT
Found at i:20784852 original size:30 final size:29
Alignment explanation
Indices: 20784801--20784967 Score: 135
Period size: 30 Copynumber: 5.8 Consensus size: 29
20784791 GAACTTCTCA
* * *
20784801 AAACTTTCAAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATCACATTTTGACCCCC
20784830 AAACTTCCAAAAACTCACATTTTGACCCCC
1 AAACTTCCAAAAA-TCACATTTTGACCCCC
* * *
20784860 AAACTTCCAAAAATTATATTTTG-CCCTC
1 AAACTTCCAAAAATCACATTTTGACCCCC
* * *
20784888 TAACTT-CTAAAATTACAGTTTTG--CCCC
1 AAACTTCCAAAAATCACA-TTTTGACCCCC
* * * *
20784915 GAACTTTCCAAAAAGCACATTTTTACCCCTT
1 AAAC-TTCCAAAAATCACATTTTGACCCC-C
* *
20784946 GAACTTCCAAAGATCACATTTT
1 AAACTTCCAAAAATCACATTTT
20784968 TTACCTCGAA
Statistics
Matches: 113, Mismatches: 18, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
27 15 0.13
28 20 0.18
29 28 0.25
30 46 0.41
31 4 0.04
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCACATTTTGACCCCC
Found at i:20784927 original size:28 final size:26
Alignment explanation
Indices: 20784801--20785035 Score: 110
Period size: 29 Copynumber: 8.2 Consensus size: 26
20784791 GAACTTCTCA
* *
20784801 AAACTTTCAAAAATTACATTTTTACCCCC
1 AAAC-TTCCAAAATCACA-TTTTA-CCCC
20784830 AAACTTCCAAAAACTCACATTTTGACCCCC
1 AAACTTCC-AAAA-TCACATTTT-A-CCCC
* * *
20784860 AAACTTCCAAAAATTATATTTTGCCCTC
1 AAACTTCC-AAAATCACATTTTACCC-C
* * * *
20784888 TAACTTCTAAAATTACAGTTTTGCCCC
1 AAACTTCCAAAATCACA-TTTTACCCC
* *
20784915 GAACTTTCCAAAAAGCACATTTTTACCCC
1 AAAC-TTCC-AAAATCACA-TTTTACCCC
* *
20784944 TTGAACTTCCAAAGATCACATTTTTTACCTC
1 --AAACTTCCAAA-ATCACA--TTTTACCCC
* * *
20784975 GAACTTTCCAAAATGACATTTTACCCT
1 AAAC-TTCCAAAATCACATTTTACCCC
**
20785002 AAATCTTTCCAAAATCATGTTTTAACCCC
1 AAA-C-TTCCAAAATCACATTTT-ACCCC
20785031 AAACT
1 AAACT
20785036 CTCCGAAACT
Statistics
Matches: 168, Mismatches: 24, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
27 25 0.15
28 38 0.23
29 53 0.32
30 39 0.23
31 13 0.08
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (26 bp):
AAACTTCCAAAATCACATTTTACCCC
Found at i:20784967 original size:86 final size:86
Alignment explanation
Indices: 20784810--20784967 Score: 194
Period size: 86 Copynumber: 1.8 Consensus size: 86
20784800 AAAACTTTCA
* * *
20784810 AAAATTACATTTTTACCCCCAAACTTCCAAAAACTCACATTTTGACCCCCAAACTTCCAAAAATT
1 AAAATTACAGTTTTACCCCCAAACTTCCAAAAACGCACATTTTGACCCCCAAACTTCCAAAAATC
*
20784875 ATATTTTGCCCTCTAACTTCT
66 ACATTTTGCCCTCTAACTTCT
* * * ** *
20784896 AAAATTACAGTTTT-GCCCCGAACTTTCCAAAAA-GCACATTTTTACCCCTTGAACTTCCAAAGA
1 AAAATTACAGTTTTACCCCCAAAC-TTCCAAAAACGCACATTTTGACCCC-CAAACTTCCAAAAA
20784959 TCACATTTT
64 TCACATTTT
20784968 TTACCTCGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 20 0.33
86 40 0.67
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (86 bp):
AAAATTACAGTTTTACCCCCAAACTTCCAAAAACGCACATTTTGACCCCCAAACTTCCAAAAATC
ACATTTTGCCCTCTAACTTCT
Found at i:20784968 original size:30 final size:30
Alignment explanation
Indices: 20784802--20785018 Score: 113
Period size: 30 Copynumber: 7.5 Consensus size: 30
20784792 AACTTCTCAA
* * *
20784802 AACTTTCAAAAATTACATTTTTACCCC-CA
1 AACTTTCCAAAATCACATTTTTACCCCTCG
* *
20784831 AAC-TTCCAAAAACTCACATTTTGACCCC-CA
1 AACTTTCC-AAAA-TCACATTTTTACCCCTCG
* * * *
20784861 AAC-TTCCAAAAATTATA-TTTT-GCCCTCT
1 AACTTTCC-AAAATCACATTTTTACCCCTCG
* * * *
20784889 AAC-TTCTAAAATTACAGTTTT-GCCC-CG
1 AACTTTCCAAAATCACATTTTTACCCCTCG
* *
20784916 AACTTTCCAAAAAGCACATTTTTACCCCTTG
1 AACTTTCC-AAAATCACATTTTTACCCCTCG
20784947 AAC-TTCCAAAGATCACATTTTTTA--CCTCG
1 AACTTTCCAAA-ATCACA-TTTTTACCCCTCG
* *
20784976 AACTTTCCAAAATGACA-TTTTA-CCCT-A
1 AACTTTCCAAAATCACATTTTTACCCCTCG
20785003 AATCTTTCCAAAATCA
1 AA-CTTTCCAAAATCA
20785019 TGTTTTAACC
Statistics
Matches: 153, Mismatches: 22, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
27 22 0.14
28 39 0.25
29 36 0.24
30 46 0.30
31 10 0.07
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
AACTTTCCAAAATCACATTTTTACCCCTCG
Found at i:20794571 original size:3 final size:3
Alignment explanation
Indices: 20794563--20794589 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20794553 TTATGATATT
20794563 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
20794590 AGGGATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20796945 original size:78 final size:78
Alignment explanation
Indices: 20796813--20797314 Score: 496
Period size: 78 Copynumber: 6.4 Consensus size: 78
20796803 ATTAAAGATT
* * * *
20796813 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCACTCGAGCTCTTACCTCGAACCTGAGGC
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCGAACCTGAGGC
20796878 AAATCACCATCAA
66 AAATCACCATCAA
* * * * * *
20796891 CCGATCTCTTAGCCCGAGCTTGGGGCAGATCGCAGCCATTCGATCTCTTACCTCGAGCCTAAGGC
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCGAACCTGAGGC
20796956 AAATCACCATCAA
66 AAATCACCATCAA
* * ** *
20796969 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACC-CCAAGATTGGGG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCGAA-CCTGAGG
* *
20797033 CAGATCACCATCAG
65 CAAATCACCATCAA
** * * * *
20797047 TTAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTCGATCTCTTACCTCGAGCCTGGGGC
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCGAACCTGAGGC
* *
20797112 AGATCACTATCAA
66 AAATCACCATCAA
* * * *
20797125 CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCACTT-AATCTCTTACC-CCAAGCCT-AG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCA-TTCGATCTCTTACCTCGAA-CCTGA-
* * * *
20797187 GGTAGATCACTATCAG
63 GGCAAATCACCATCAA
* * * * * * *
20797203 CCAATCTCTTACCCCAAGCCTGGGGTAGA-T-CA-CTATCAGCGAATCTCTTACCCCGAGCCTGG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT--TCG-ATCTCTTACCTCGAACCTGA
*
20797265 GGCAAATCACCATCAG
63 GGCAAATCACCATCAA
* * *
20797281 CTAATCTCTTACCCCGAGCCAGAGGCAGATTGCA
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCA
20797315 ACCTTCCAAT
Statistics
Matches: 353, Mismatches: 58, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
74 1 0.00
75 2 0.01
76 2 0.01
77 5 0.01
78 334 0.95
79 7 0.02
80 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (78 bp):
CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACCTCGAACCTGAGGC
AAATCACCATCAA
Found at i:20797054 original size:117 final size:115
Alignment explanation
Indices: 20796891--20797310 Score: 372
Period size: 117 Copynumber: 3.6 Consensus size: 115
20796881 TCACCATCAA
* * * * * *
20796891 CCGATCTCTTAGCCCGAGCTTGGGGCAGATC-GCAGCCA-TTCGATCTCTTACCTCGAGCCTAAG
1 CCGATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGTT-AATCTCTTACCCCGAGCCTAGG
* *
20796954 GCAAATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCAT
64 GCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATT-CA-CCAT
* * *
20797008 TCGATCTCTTACCCCAAGATTGGGGCAGATCACCATCAGTTAATCTCTTACCCCGAGCCTAGGGC
1 CCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTTAATCTCTTACCCCGAGCCTAGGGC
* * ** * * *
20797073 AGATTA-CAGCCATTCGATCTCTTACCTCGAGCCTGGGGCAGA-TCACTATCAA
66 AGATCACCA-TCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTCAC---CAT
* * *
20797125 CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCA-C--TTAATCTCTTACCCCAAGCCTAG
1 CCGATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGTTAATCTCTTACCCCGAGCCTAG
* * * * * *
20797187 GGTAGATCACTATCAGCCAATCTCTTACCCCAAGCCTGGGGTAGA-TCACTAT
63 GGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTCACCAT
* * *
20797239 CAGCGAATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCTAATCTCTTACCCCGAGCC-AG
1 C--CG-ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTTAATCTCTTACCCCGAGCCTAG
20797303 AGGCAGAT
63 -GGCAGAT
20797311 TGCAACCTTC
Statistics
Matches: 243, Mismatches: 43, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
114 6 0.02
115 5 0.02
116 7 0.03
117 213 0.88
118 6 0.02
119 3 0.01
120 3 0.01
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (115 bp):
CCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTTAATCTCTTACCCCGAGCCTAGGGC
AGATCACCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTCACCAT
Found at i:20797097 original size:156 final size:156
Alignment explanation
Indices: 20796813--20797314 Score: 591
Period size: 156 Copynumber: 3.2 Consensus size: 156
20796803 ATTAAAGATT
* * * * * * *
20796813 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCACTCGAGCTCTTACCTCGAA-CCTGAGG
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACC-CCAAGCCTGGGG
* * * * * *
20796877 CAAATCACCATCAACCGATCTCTTAGCCCGAGCTTGGGGCAGATCGCAGCCATTCGATCTCTTAC
65 CAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATCACAGCCATTCGATCTCTTAC
**
20796942 CTCGAGCCTAAGGCAAATCACCATCAA
130 CTCGAGCCTGGGGCAAATCACCATCAA
**
20796969 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACCCCAAGATTGGGGC
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACCCCAAGCCTGGGGC
** * *
20797034 AGATCACCATCAGTTAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTCGATCTCTTACC
66 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATCACAGCCATTCGATCTCTTACC
* *
20797099 TCGAGCCTGGGGCAGATCACTATCAA
131 TCGAGCCTGGGGCAAATCACCATCAA
* * * * *
20797125 CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCACTT-AATCTCTTACCCCAAGCCTAGGG
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCA-TTCGATCTCTTACCCCAAGCCTGGGG
* * * * * *
20797189 TAGATCACTATCAGCCAATCTCTTACCCCAAGCCTGGGGTAGATCACTA-TCA-GCGAATCTCTT
65 CAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATCAC-AGCCATTCG-ATCTCTT
* *
20797252 ACCCCGAGCCTGGGGCAAATCACCATCAG
128 ACCTCGAGCCTGGGGCAAATCACCATCAA
*
20797281 CTAATCTCTTACCCCGAGCC-AGAGGCAGATTGCA
1 CCAATCTCTTACCCCGAGCCTAG-GGCAGATTGCA
20797315 ACCTTCCAAT
Statistics
Matches: 293, Mismatches: 48, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
155 6 0.02
156 284 0.97
157 3 0.01
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (156 bp):
CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACCCCAAGCCTGGGGC
AGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATCACAGCCATTCGATCTCTTACC
TCGAGCCTGGGGCAAATCACCATCAA
Found at i:20797209 original size:39 final size:38
Alignment explanation
Indices: 20796813--20797310 Score: 307
Period size: 39 Copynumber: 12.8 Consensus size: 38
20796803 ATTAAAGATT
* *** *
20796813 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCA-
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCACA-TCAG
* * * * * * *
20796851 CTCGAGCTCTTACCTCGAACCTGAGGCAAATCACCATCAA
1 C-CAATCTCTTACCCCGAGCCTGGGGCAGATCA-CATCAG
* * * * * *
20796891 CCGATCTCTTAGCCCGAGCTTGGGGCAGATCGCAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCACA-TCAG
* * * ** * *
20796930 TCGATCTCTTACCTCGAGCCTAAGGCAAATCACCATCAA
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCA-CATCAG
* ** * *
20796969 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCACA-TCAG
* * * **
20797008 TCGATCTCTTACCCCAAGATTGGGGCAGATCACCATCAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCA-CATCAG
** * * * *
20797047 TTAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCACA-TCAG
* * * *
20797086 TCGATCTCTTACCTCGAGCCTGGGGCAGATCACTATCAA
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCAC-ATCAG
* * ** *
20797125 CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCA-
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCACA-TCAG
* * * *
20797163 CTTAATCTCTTACCCCAAGCCTAGGGTAGATCACTATCAG
1 C-CAATCTCTTACCCCGAGCCTGGGGCAGATCAC-ATCAG
* *
20797203 CCAATCTCTTACCCCAAGCCTGGGGTAGATCACTATCAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCAC-ATCAG
* *
20797242 CGAATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAG
1 CCAATCTCTTACCCCGAGCCTGGGGCAGATCA-CATCAG
* * *
20797281 CTAATCTCTTACCCCGAGCCAGAGGCAGAT
1 CCAATCTCTTACCCCGAGCCTGGGGCAGAT
20797311 TGCAACCTTC
Statistics
Matches: 355, Mismatches: 91, Indels: 27
0.75 0.19 0.06
Matches are distributed among these distances:
38 9 0.03
39 336 0.95
40 10 0.03
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (38 bp):
CCAATCTCTTACCCCGAGCCTGGGGCAGATCACATCAG
Found at i:20797324 original size:117 final size:117
Alignment explanation
Indices: 20796857--20797332 Score: 367
Period size: 117 Copynumber: 4.1 Consensus size: 117
20796847 GCCACTCGAG
* * * * * * *
20796857 CTCTTACCTCGAA-CCTGAGGCAAATCACCATCAACCGATCTCTTAGCCCGAGCTTGGGGCAGAT
1 CTCTTACC-CCAAGCCTGGGGCAGATCACTATCAACCAATCTCTTACCCCGAGCTTGGGGCAAAT
* * * * * * * * * **
20796921 C-GCAGCCA-TTCGATCTCTTACCTCGAGCCTAAGGCAAATCACCATCAACCAAT
65 CACCA-TCAGTT-AATCTCTTACCCCGAGCCTAGGGCAGATTACAACCTTCCAAT
* * ** * ** * * * *
20796974 CTCTTACCCCGAGCCTAGGGCAGATTGC-AGCCATTCGATCTCTTACCCCAAGATTGGGGCAGAT
1 CTCTTACCCCAAGCCTGGGGCAGATCACTA-TCAACCAATCTCTTACCCCGAGCTTGGGGCAAAT
* *
20797038 CACCATCAGTTAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATT-CGAT
65 CACCATCAGTTAATCTCTTACCCCGAGCCTAGGGCAGATTACAACC-TTCCAAT
* * * *
20797091 CTCTTACCTCGAGCCTGGGGCAGATCACTATCAACCAATCTCTTACCCCGAGCTTGGGGTAGATT
1 CTCTTACCCCAAGCCTGGGGCAGATCACTATCAACCAATCTCTTACCCCGAGCTTGGGGCA-AAT
* * * * * **
20797156 GCAGCCA-C--TTAATCTCTTACCCCAAGCCTAGGGTAGATCACTATCAGCCAAT
65 -CA-CCATCAGTTAATCTCTTACCCCGAGCCTAGGGCAGATTACAACCTTCCAAT
* * * *
20797208 CTCTTACCCCAAGCCTGGGGTAGATCACTATCAGCGAATCTCTTACCCCGAGCCTGGGGCAAATC
1 CTCTTACCCCAAGCCTGGGGCAGATCACTATCAACCAATCTCTTACCCCGAGCTTGGGGCAAATC
* *
20797273 ACCATCAGCTAATCTCTTACCCCGAGCC-AGAGGCAGATTGCAACCTTCCAAT
66 ACCATCAGTTAATCTCTTACCCCGAGCCTAG-GGCAGATTACAACCTTCCAAT
*
20797325 ATCTTACC
1 CTCTTACC
20797333 TAAACAAAAA
Statistics
Matches: 279, Mismatches: 66, Indels: 28
0.75 0.18 0.08
Matches are distributed among these distances:
114 3 0.01
115 3 0.01
116 7 0.03
117 254 0.91
118 6 0.02
119 3 0.01
120 3 0.01
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (117 bp):
CTCTTACCCCAAGCCTGGGGCAGATCACTATCAACCAATCTCTTACCCCGAGCTTGGGGCAAATC
ACCATCAGTTAATCTCTTACCCCGAGCCTAGGGCAGATTACAACCTTCCAAT
Found at i:20799533 original size:29 final size:29
Alignment explanation
Indices: 20799469--20799952 Score: 368
Period size: 29 Copynumber: 16.7 Consensus size: 29
20799459 TTGAACTTTT
*
20799469 CAAAAATCACATTTTTACCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
*
20799498 TCAAAAATTACATTTTTACACTCAAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* * *
20799528 AAAAAATCACATTTTTGCCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* *
20799557 CAAAAATTACATTTTTGCCCAT-GAACTTC
1 CAAAAATTACATTTTTACCC-TCAAACTTC
* * *
20799586 CAAAAAATCACATTTTGACCCTCGAACTTC
1 C-AAAAATTACATTTTTACCCTCAAACTTC
* *
20799616 CAAATATTACATTTTTACCCTCAAACTTT
1 CAAAAATTACATTTTTACCCTCAAACTTC
* * *
20799645 TAAAAATCACATTTTGACCC-CTAAACTTC
1 CAAAAATTACATTTTTACCCTC-AAACTTC
* * *
20799674 CAAAGATTACATTTTTTCCCTCAAACTTT
1 CAAAAATTACATTTTTACCCTCAAACTTC
* *
20799703 TAAAAATTACA-TTTTACCC-CTAAACTTT
1 CAAAAATTACATTTTTACCCTC-AAACTTC
* * *
20799731 CAAAAATCACA-TTTTACCCTCGAGCTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* * *
20799759 TCAAAAATTATAGTTTTGCCAC-CAAACTTC
1 -CAAAAATTACATTTTTACC-CTCAAACTTC
* * * *
20799789 TAAAAGTCACATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* *
20799818 TCAAAAATTATATTTTTACCC-CTAAGCTTC
1 -CAAAAATTACATTTTTACCCTC-AAACTTC
* * *
20799848 CAAAGATCACATTTTTACCC-GAAACTTAC
1 CAAAAATTACATTTTTACCCTCAAACTT-C
*
20799877 TC-AAAATGACA-TTTTACCC-CTAAATCTTTC
1 -CAAAAATTACATTTTTACCCTC-AAA-C-TTC
* *
20799907 C-AAAA-TACATTTTAACCC-CAAAATCTC
1 CAAAAATTACATTTTTACCCTCAAACT-TC
* *
20799934 CAAAACTT-CATTTTGACCC
1 CAAAAATTACATTTTTACCC
20799953 CATTTTTCTT
Statistics
Matches: 365, Mismatches: 67, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 69 0.19
29 199 0.55
30 89 0.24
31 3 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCAAACTTC
Found at i:20799537 original size:59 final size:57
Alignment explanation
Indices: 20799470--20799928 Score: 367
Period size: 59 Copynumber: 7.9 Consensus size: 57
20799460 TGAACTTTTC
*
20799470 AAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACACTCAAACTTCA
1 AAAAATCACATTTTTACCC-CAAACTTC-CAAAAATTACATTTTTACCCTCAAACTTCA
* * *
20799529 AAAAATCACATTTTTGCCCTCAAACTTCCAAAAATTACATTTTTGCCCAT-GAACTTCCA
1 AAAAATCACATTTTTACCC-CAAACTTCCAAAAATTACATTTTTACCC-TCAAACTT-CA
* * * **
20799588 AAAAATCACATTTTGACCCTCGAACTTCCAAATATTACATTTTTACCCTCAAACTTTT
1 AAAAATCACATTTTTACCC-CAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCA
* * * **
20799646 AAAAATCACATTTTGACCCCTAAACTTCCAAAGATTACATTTTTTCCCTCAAACTTTT
1 AAAAATCACATTTTTACCCC-AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCA
* * * * * *
20799704 AAAAATTACA-TTTTACCCCTAAACTTTCAAAAATCACA-TTTTACCCTCGAGCTTCTC
1 AAAAATCACATTTTTACCCC-AAACTTCCAAAAATTACATTTTTACCCTCAAACTTC-A
* * * * * * * * *
20799761 AAAAATTATAGTTTTGCCACCAAACTTCTAAAAGTCACATTTTTACCCTCGAACTTCTC
1 AAAAATCACATTTTTACC-CCAAACTTCCAAAAATTACATTTTTACCCTCAAACTTC-A
* * * * * * *
20799820 AAAAATTATATTTTTACCCCTAAGCTTCCAAAGATCACATTTTTACCC-GAAACTTACT
1 AAAAATCACATTTTTACCCC-AAACTTCCAAAAATTACATTTTTACCCTCAAACTT-CA
* * *
20799878 CAAAATGACA-TTTTACCCCTAAATCTTTCC-AAAA-TACATTTTAACCC-CAAA
1 AAAAATCACATTTTTACCCC-AAA-C-TTCCAAAAATTACATTTTTACCCTCAAA
20799929 ATCTCCAAAA
Statistics
Matches: 340, Mismatches: 48, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
56 13 0.04
57 60 0.18
58 125 0.37
59 142 0.42
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAAATCACATTTTTACCCCAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCA
Found at i:20813319 original size:193 final size:193
Alignment explanation
Indices: 20812990--20813376 Score: 749
Period size: 193 Copynumber: 2.0 Consensus size: 193
20812980 GCGTAAGAAA
20812990 TAGAAAGCCAGTGTAGCCACATCTTCAGCTGCTACAAATTGAGAGAGTTTTTCAGTTTTCAGTTT
1 TAGAAAGCCAGTGTAGCCACATCTTCAGCTGCTACAAATTGAGAGAGTTTTTCAGTTTTCAGTTT
20813055 TAATTTTCATGCATATCATGTAGTTGTAGTTTATTTGTTATTGCATCTTTTGTTTCTGCATTTTT
66 TAATTTTCATGCATATCATGTAGTTGTAGTTTATTTGTTATTGCATCTTTTGTTTCTGCATTTTT
20813120 ATTATCATTGCATCTACAATGTCATTGCATTTCCATATATATTTGTAAATTAATGTCAGTGCT
131 ATTATCATTGCATCTACAATGTCATTGCATTTCCATATATATTTGTAAATTAATGTCAGTGCT
20813183 TAGAAAGCCAGTGTAGCCACATCTTCAGCTGCTACAAATTGAGAGAGTTTTTCAGTTTTCAGTTT
1 TAGAAAGCCAGTGTAGCCACATCTTCAGCTGCTACAAATTGAGAGAGTTTTTCAGTTTTCAGTTT
*
20813248 TAATTTTCATGCATATCATTTAGTTGTAGTTTATTTGTTATTGCATCTTCTT-TTTCTGCATTTT
66 TAATTTTCATGCATATCATGTAGTTGTAGTTTATTTGTTATTGCATCTT-TTGTTTCTGCATTTT
20813312 TATTATCATTGCATCTACAATGTCATTGCATTTCCATATATATTTGTAAATTAATGTCAGTGCT
130 TATTATCATTGCATCTACAATGTCATTGCATTTCCATATATATTTGTAAATTAATGTCAGTGCT
20813376 T
1 T
20813377 TGGGATCAAT
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
193 190 0.99
194 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.45
Consensus pattern (193 bp):
TAGAAAGCCAGTGTAGCCACATCTTCAGCTGCTACAAATTGAGAGAGTTTTTCAGTTTTCAGTTT
TAATTTTCATGCATATCATGTAGTTGTAGTTTATTTGTTATTGCATCTTTTGTTTCTGCATTTTT
ATTATCATTGCATCTACAATGTCATTGCATTTCCATATATATTTGTAAATTAATGTCAGTGCT
Found at i:20819590 original size:27 final size:24
Alignment explanation
Indices: 20819526--20819590 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 24
20819516 TAGTATATCC
20819526 AAAAAGAAAAAAATGAAAAATCTGAA
1 AAAAAGAAAAAAATGAAAAATCT--A
*
20819552 AAAGAAGAAAAAGATGAGTAGAAA-CTA
1 AAA-AAGAAAAAAATGA--A-AAATCTA
20819579 AAAAAGAAAAAA
1 AAAAAGAAAAAA
20819591 TTCATGAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 11 0.33
27 16 0.48
29 3 0.09
30 3 0.09
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAAGAAAAAAATGAAAAATCTA
Found at i:20824814 original size:16 final size:16
Alignment explanation
Indices: 20824795--20824829 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20824785 TAGTAATTTT
20824795 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
20824811 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
20824827 AAT
1 AAT
20824830 TACGAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:20826362 original size:38 final size:38
Alignment explanation
Indices: 20826307--20826381 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
20826297 TTTATGGTAT
* * * * *
20826307 TTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGG
1 TTATCGAGCTTAATGCCTAACAAGCTTCGTGCAGGTGG
*
20826345 TTATCGAGCTTAATGCCTAACAAGCTTCTTGCAGGTG
1 TTATCGAGCTTAATGCCTAACAAGCTTCGTGCAGGTG
20826382 TATTGATTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (38 bp):
TTATCGAGCTTAATGCCTAACAAGCTTCGTGCAGGTGG
Found at i:20828504 original size:17 final size:16
Alignment explanation
Indices: 20828469--20828509 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20828459 TACATATATA
* *
20828469 TTTTTCTTCTTTTTCC
1 TTTTTTTTCTTTTCCC
20828485 TTTTTTTTCTTTTCCTC
1 TTTTTTTTCTTTTCC-C
20828502 TTTTTTTT
1 TTTTTTTT
20828510 TATATGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTTTCCC
Found at i:20829099 original size:17 final size:17
Alignment explanation
Indices: 20829075--20829122 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
20829065 ATATATATGG
20829075 AAATGCAATGACAATG-A
1 AAATGCAATGACAA-GAA
*
20829092 AGATGCAATGACAAGAA
1 AAATGCAATGACAAGAA
20829109 AAATGCAATGACAA
1 AAATGCAATGACAA
20829123 ACAAAATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAAGAA
Found at i:20829128 original size:17 final size:16
Alignment explanation
Indices: 20829075--20829130 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
20829065 ATATATATGG
*
20829075 AAATGCAATGACAATGA
1 AAATGCAATGACAA-AA
*
20829092 AGATGCAATGACAAGAA
1 AAATGCAATGACAA-AA
20829109 AAATGCAATGACAAACA
1 AAATGCAATGACAAA-A
20829126 AAATG
1 AAATG
20829131 TGATGACAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 1 0.03
17 33 0.97
ACGTcount: A:0.55, C:0.12, G:0.18, T:0.14
Consensus pattern (16 bp):
AAATGCAATGACAAAA
Found at i:20836366 original size:36 final size:36
Alignment explanation
Indices: 20836106--20836353 Score: 372
Period size: 36 Copynumber: 6.9 Consensus size: 36
20836096 CTGTTGTGAA
* *
20836106 AGTAAATAAGTTGGTATGTTATTCATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
* *
20836142 AGTAAATATGTGGGTATGTTATCCATGCCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
* *
20836178 AGTAATTATGTGGGTATGTTACTCATG-CATTGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCA-TGAGAT
20836214 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
* * *
20836250 AGTAAATATGTGGGTATGTTTTTCATGTCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
20836286 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
** *
20836322 AGTAAATATGCAGGTATGTTACTCATGCCATG
1 AGTAAATATGTGGGTATGTTATTCATGCCATG
20836354 TTACAGTAAA
Statistics
Matches: 191, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
35 2 0.01
36 187 0.98
37 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGAGAT
Found at i:20836788 original size:23 final size:23
Alignment explanation
Indices: 20836762--20836950 Score: 276
Period size: 23 Copynumber: 8.3 Consensus size: 23
20836752 ATTAAATGTG
20836762 TTAAATATTAATATGATTTATGC
1 TTAAATATTAATATGATTTATGC
*
20836785 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATATGATTTATGC
*
20836808 TTAAATATTAATATGATTTGTGC
1 TTAAATATTAATATGATTTATGC
* *
20836831 TTAAATA--AATGTGATTTGTGC
1 TTAAATATTAATATGATTTATGC
*
20836852 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATATGATTTATGC
*
20836875 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATATGATTTATGC
* *
20836898 TTAAATATTAATGTAATTTATGC
1 TTAAATATTAATATGATTTATGC
20836921 TTAAATATTAATATGATTTATG-
1 TTAAATATTAATATGATTTATGC
20836943 TGTAAATA
1 T-TAAATA
20836951 GACTCATGAA
Statistics
Matches: 151, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.13
22 1 0.01
23 130 0.86
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (23 bp):
TTAAATATTAATATGATTTATGC
Found at i:20836922 original size:90 final size:89
Alignment explanation
Indices: 20836758--20836950 Score: 296
Period size: 90 Copynumber: 2.1 Consensus size: 89
20836748 TATCATTAAA
*
20836758 TGTGTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATATG
1 TGTGTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATATA
*
20836823 ATTTGTGCTTAAATAAATGTGATT
66 ATTTATGCTTAAATAAATGTGATT
* *
20836847 TGTGCTTAAATATTAATGTGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATGT
1 TGTG-TTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATAT
*
20836912 AATTTATGCTTAAATATTAATATGATT
65 AATTTATGCTTAAATA--AATGTGATT
*
20836939 TATGTGTAAATA
1 TGTGT-TAAATA
20836951 GACTCATGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
89 4 0.04
90 72 0.77
91 1 0.01
92 17 0.18
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (89 bp):
TGTGTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATATA
ATTTATGCTTAAATAAATGTGATT
Found at i:20847297 original size:18 final size:18
Alignment explanation
Indices: 20847265--20847304 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
20847255 TATCAGCATC
*
20847265 TATAATAAAATAATA-TT
1 TATAACAAAATAATAGTT
20847282 TATAACAAACATAATAGTT
1 TATAACAAA-ATAATAGTT
20847301 TATA
1 TATA
20847305 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAACAAAATAATAGTT
Found at i:20849119 original size:39 final size:39
Alignment explanation
Indices: 20849076--20849213 Score: 170
Period size: 39 Copynumber: 3.5 Consensus size: 39
20849066 AAACCGGCAA
*
20849076 TGACACTATAAACATTGCGAAGTTATACTGAATAAGCAG
1 TGACACTATAAACACTGCGAAGTTATACTGAATAAGCAG
* ***
20849115 TGACACTATAAACACTGCTGAA-CTATACTGAACCGGCAG
1 TGACACTATAAACACTGC-GAAGTTATACTGAATAAGCAG
* * * *
20849154 TGACATTGTAAACACTGTGAAGTTATACTGAATAAGTAG
1 TGACACTATAAACACTGCGAAGTTATACTGAATAAGCAG
*
20849193 TGACACTGTAAACACTGCGAA
1 TGACACTATAAACACTGCGAA
20849214 ACTATTGGGA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 3 0.04
39 76 0.93
40 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (39 bp):
TGACACTATAAACACTGCGAAGTTATACTGAATAAGCAG
Found at i:20849195 original size:78 final size:78
Alignment explanation
Indices: 20849061--20849323 Score: 262
Period size: 78 Copynumber: 3.4 Consensus size: 78
20849051 AGTGATCAAA
* * * *
20849061 ATACTAAACCGGCAATGACACTATAAACATTGCGAAGTTATACTGAATAAGCAGTGACACTATAA
1 ATACTGAACCGGCAGTGACACTGTAAACACTGCGAAGTTATACTGAATAAGCAGTGACACTATAA
20849126 ACACTGCTG-AACT
66 ACACTGC-GAAACT
* * * *
20849139 ATACTGAACCGGCAGTGACATTGTAAACACTGTGAAGTTATACTGAATAAGTAGTGACACTGTAA
1 ATACTGAACCGGCAGTGACACTGTAAACACTGCGAAGTTATACTGAATAAGCAGTGACACTATAA
20849204 ACACTGCGAAACT
66 ACACTGCGAAACT
*** * * * * * * *
20849217 ATTGGGAACCGGTAGTGACACTGTAAACACTACAAAGCTATACT-AACTTAGCAGTGACATTGTA
1 ATACTGAACCGGCAGTGACACTGTAAACACTGCGAAGTTATACTGAA-TAAGCAGTGACACTATA
* **
20849281 AACATTGC-AATGTT
65 AACACTGCGAA-ACT
* * *
20849295 ATTCTGAACTGGCGGTGACACTGTAAACA
1 ATACTGAACCGGCAGTGACACTGTAAACA
20849324 TCGCGCGACT
Statistics
Matches: 154, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
77 5 0.03
78 149 0.97
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (78 bp):
ATACTGAACCGGCAGTGACACTGTAAACACTGCGAAGTTATACTGAATAAGCAGTGACACTATAA
ACACTGCGAAACT
Found at i:20849232 original size:39 final size:39
Alignment explanation
Indices: 20849061--20849364 Score: 152
Period size: 39 Copynumber: 7.8 Consensus size: 39
20849051 AGTGATCAAA
* * * * * **
20849061 ATACTAAACCGGCAATGACACTATAAACATTGCGAAGTT
1 ATACTGAACCGGTAGTGACACTGTAAACACTGCGAAACT
*** * *
20849100 ATACTGAATAAGCAGTGACACTATAAACACTGCTG-AACT
1 ATACTGAACCGGTAGTGACACTGTAAACACTGC-GAAACT
* * * **
20849139 ATACTGAACCGGCAGTGACATTGTAAACACTGTGAAGTT
1 ATACTGAACCGGTAGTGACACTGTAAACACTGCGAAACT
***
20849178 ATACTGAATAAGTAGTGACACTGTAAACACTGCGAAACT
1 ATACTGAACCGGTAGTGACACTGTAAACACTGCGAAACT
*** *
20849217 ATTGGGAACCGGTAGTGACACTGTAAACACTAC-AAAGCT
1 ATACTGAACCGGTAGTGACACTGTAAACACTGCGAAA-CT
** * * * **
20849256 ATACT-AACTTAGCAGTGACATTGTAAACATTGC-AATGTT
1 ATACTGAAC-CGGTAGTGACACTGTAAACACTGCGAA-ACT
* * ** **
20849295 ATTCTGAACTGGCGGTGACACTGTAAACA-TCGCGCGACT
1 ATACTGAACCGGTAGTGACACTGTAAACACT-GCGAAACT
* **
20849334 ATAACTCAA-TAGTAGTGACACTGTAAACACT
1 AT-ACTGAACCGGTAGTGACACTGTAAACACT
20849365 ACTAGAACAT
Statistics
Matches: 200, Mismatches: 55, Indels: 19
0.73 0.20 0.07
Matches are distributed among these distances:
38 8 0.04
39 183 0.92
40 9 0.05
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (39 bp):
ATACTGAACCGGTAGTGACACTGTAAACACTGCGAAACT
Found at i:20849899 original size:22 final size:22
Alignment explanation
Indices: 20849874--20849917 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20849864 AGATTGAAAC
20849874 CTTGAATTTATTCATTAAATCT
1 CTTGAATTTATTCATTAAATCT
* *
20849896 CTTGATTTTATTTATTAAATCT
1 CTTGAATTTATTCATTAAATCT
20849918 GTTAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.55
Consensus pattern (22 bp):
CTTGAATTTATTCATTAAATCT
Found at i:20850531 original size:20 final size:20
Alignment explanation
Indices: 20850501--20850540 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20850491 AAAAATATAT
20850501 AAAATATAAAATATTAGTAAA
1 AAAATATAAAATATTA-TAAA
20850522 AAAATA-AAAATATTATAAA
1 AAAATATAAAATATTATAAA
20850541 GCTTTCACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATATAAAATATTATAAA
Found at i:20851305 original size:20 final size:21
Alignment explanation
Indices: 20851280--20851321 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
20851270 AATGACATTA
20851280 AATTAAAACA-TAAA-AAAAAT
1 AATTAAAA-ATTAAATAAAAAT
20851300 AATTAAAAATTAAATAAAAAT
1 AATTAAAAATTAAATAAAAAT
20851321 A
1 A
20851322 GTATGTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AATTAAAAATTAAATAAAAAT
Found at i:20852451 original size:22 final size:22
Alignment explanation
Indices: 20852423--20852464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20852413 TGAATAAACT
* *
20852423 AAATAAACTTTATTTCTGTAGA
1 AAATAAACTTAATATCTGTAGA
20852445 AAATAAACTTAATATCTGTA
1 AAATAAACTTAATATCTGTA
20852465 AACTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATAAACTTAATATCTGTAGA
Found at i:20858981 original size:6 final size:6
Alignment explanation
Indices: 20858961--20859072 Score: 60
Period size: 6 Copynumber: 19.7 Consensus size: 6
20858951 TAGATTGGTC
** * **
20858961 TTAAAT TTATTT TTAAAT TT-AAT TT-ACT TTAAAT TTATTT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
20859007 TTAAAT TT--AT GTTAAAT TTAAGT TT-AA- TTAAAT TTGAAA- -CAATT
1 TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT
* *
20859051 TTAAAC TTAACT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
20859073 TTTCAAAATT
Statistics
Matches: 77, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
4 6 0.08
5 14 0.18
6 52 0.68
7 5 0.06
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:20858984 original size:17 final size:16
Alignment explanation
Indices: 20858964--20859041 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 16
20858954 ATTGGTCTTA
20858964 AATTTATTTTTAAATTT
1 AATTTA-TTTTAAATTT
*
20858981 AATTTACTTTAAATTT
1 AATTTATTTTAAATTT
20858997 -A--T-TTTTAAATTT
1 AATTTATTTTAAATTT
*
20859009 AAATTTATGTTAAATTT
1 -AATTTATTTTAAATTT
*
20859026 AAGTTTA-ATTAAATTT
1 AA-TTTATTTTAAATTT
20859042 GAAACAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 9 0.18
13 1 0.02
14 1 0.02
15 1 0.02
16 20 0.39
17 19 0.37
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTATTTTAAATTT
Found at i:20858992 original size:28 final size:29
Alignment explanation
Indices: 20858937--20859026 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
20858927 GATTAAACTT
* * ** *
20858937 TTTAATTTTAAATTTAGATTGGTCTTAAA
1 TTTATTTTTAAATTTAAATTTATGTTAAA
20858966 TTTATTTTTAAATTT-AATTTACT-TTAAA
1 TTTATTTTTAAATTTAAATTTA-TGTTAAA
20858994 TTTATTTTTAAATTTAAATTTATGTTAAA
1 TTTATTTTTAAATTTAAATTTATGTTAAA
20859023 TTTA
1 TTTA
20859027 AGTTTAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
28 24 0.44
29 30 0.56
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTATTTTTAAATTTAAATTTATGTTAAA
Found at i:20859032 original size:29 final size:28
Alignment explanation
Indices: 20858937--20859041 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 28
20858927 GATTAAACTT
* **
20858937 TTTAATTTTAAATTTAGATTGGTCTTAAA
1 TTTAATTTTAAATTTAAATTTAT-TTAAA
*
20858966 TTTATTTTTAAATTT-AATTTACTTTAAA
1 TTTAATTTTAAATTTAAATTTA-TTTAAA
*
20858994 TTTATTTTTAAATTTAAATTTATGTTAAA
1 TTTAATTTTAAATTTAAATTTAT-TTAAA
*
20859023 TTTAAGTTT-AA-TTAAATTT
1 TTTAATTTTAAATTTAAATTT
20859042 GAAACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.12
28 26 0.39
29 33 0.49
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTAATTTTAAATTTAAATTTATTTAAA
Found at i:20859035 original size:28 final size:29
Alignment explanation
Indices: 20858961--20859026 Score: 109
Period size: 28 Copynumber: 2.3 Consensus size: 29
20858951 TAGATTGGTC
20858961 TTAAATTTATTTTTAAATTT-AATTTACT
1 TTAAATTTATTTTTAAATTTAAATTTACT
20858989 TTAAATTTATTTTTAAATTTAAATTTA-T
1 TTAAATTTATTTTTAAATTTAAATTTACT
20859017 GTTAAATTTA
1 -TTAAATTTA
20859027 AGTTTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 21 0.58
29 15 0.42
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTAAATTTATTTTTAAATTTAAATTTACT
Found at i:20861030 original size:30 final size:30
Alignment explanation
Indices: 20860946--20861356 Score: 396
Period size: 30 Copynumber: 13.9 Consensus size: 30
20860936 CCCTGAAGGT
* *
20860946 CCTTAAAC-TATCAAAAAATTACATTTTTAC
1 CCTTAAACTTTTC-AAAAATTACATTTTGAC
* * *
20860976 CCCTAAAC-TTTCCAAAATTCCATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
20861005 CCTTAAACTTTTCAAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
** *
20861035 CCCCAAACTTTACAAAAATTACATTTTGA-
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
*
20861064 CCTTAAACTTTCCAAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
* * *
20861094 CCTCAAACTTTCCAAAAATTACATTTTAAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
* *
20861124 CC-TAAAC-TTTCCAAAATTACATTTTAAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
20861152 CCTTAAACTTTTCAAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
* * *
20861182 ACC-TAAACTATCCAAAAATTATATTTTGAC
1 -CCTTAAACTTTTCAAAAATTACATTTTGAC
20861212 CCTTAAAC-TTTCAAAAAATTACATTTTGAC
1 CCTTAAACTTTTC-AAAAATTACATTTTGAC
* * * *
20861242 CTTTAAAC-TCTCTAAAAATTATATTGTGAC
1 CCTTAAACTTTTC-AAAAATTACATTTTGAC
* * * * *
20861272 CCTCAAACTTTCCAAAAACTCCATTTTTA-
1 CCTTAAACTTTTCAAAAATTACATTTTGAC
* * *
20861301 CCTT-GATTTTTCTTAAAATTACCATTTT-AC
1 CCTTAAACTTTTC-AAAAATTA-CATTTTGAC
* * *
20861331 CCTCAAAC-TTCCAAAAATTCCATTTT
1 CCTTAAACTTTTCAAAAATTACATTTT
20861357 TAAACCTCGA
Statistics
Matches: 315, Mismatches: 54, Indels: 26
0.80 0.14 0.07
Matches are distributed among these distances:
28 32 0.10
29 75 0.24
30 203 0.64
31 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
CCTTAAACTTTTCAAAAATTACATTTTGAC
Found at i:20861061 original size:60 final size:60
Alignment explanation
Indices: 20860946--20861356 Score: 441
Period size: 59 Copynumber: 7.0 Consensus size: 60
20860936 CCCTGAAGGT
* * *
20860946 CCTTAAAC-TATCAAAAAATTACATTTTTACCC-CTAAACTTTCC-AAAATTCCATTTTGAC
1 CCTTAAACTTTTC-AAAAATTACATTTTGACCCTC-AAACTTTCCAAAAATTACATTTTGAC
* *
20861005 CCTTAAACTTTTCAAAAATTACATTTTGACCCCCAAACTTTACAAAAATTACATTTTGA-
1 CCTTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* *
20861064 CCTTAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTAAC
1 CCTTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * *
20861124 CC-TAAAC-TTTCCAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * * *
20861182 ACC-TAAACTATCCAAAAATTATATTTTGACCCTTAAACTTTCAAAAAATTACATTTTGAC
1 -CCTTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * * * * *
20861242 CTTTAAAC-TCTCTAAAAATTATATTGTGACCCTCAAACTTTCCAAAAACTCCATTTTTA-
1 CCTTAAACTTTTC-AAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * *
20861301 CCTT-GATTTTTCTTAAAATTACCATTTT-ACCCTCAAAC-TTCCAAAAATTCCATTTT
1 CCTTAAACTTTTC-AAAAATTA-CATTTTGACCCTCAAACTTTCCAAAAATTACATTTT
20861357 TAAACCTCGA
Statistics
Matches: 303, Mismatches: 39, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
58 63 0.21
59 127 0.42
60 113 0.37
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (60 bp):
CCTTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
Found at i:20861312 original size:29 final size:29
Alignment explanation
Indices: 20861280--20861452 Score: 109
Period size: 29 Copynumber: 5.8 Consensus size: 29
20861270 ACCCTCAAAC
*
20861280 TTTCCAAAAACTCCATTTTTACCTTGATT
1 TTTCCAAAAATTCCATTTTTACCTTGATT
** * * **
20861309 TTTCTTAAAATTACCA-TTTTACCCTCAAA
1 TTTCCAAAAATT-CCATTTTTACCTTGATT
* *
20861338 CTTCCAAAAATTCCATTTTTAAACCTCGATT
1 TTTCCAAAAATTCCATTTTT--ACCTTGATT
* * * **
20861369 TTTCCAAAAATTACCA-TTTTGCCGTCAAA
1 TTTCCAAAAATT-CCATTTTTACCTTGATT
* **
20861398 CTTCCAAAAGCTCCATTTTTTATCC-TGATT
1 TTTCCAAAAATTCCA-TTTTTA-CCTTGATT
20861428 TTTCCAAAAATTCCATTTTTGACCT
1 TTTCCAAAAATTCCATTTTT-ACCT
20861453 CAAATTATTC
Statistics
Matches: 102, Mismatches: 32, Indels: 19
0.67 0.21 0.12
Matches are distributed among these distances:
28 6 0.06
29 50 0.49
30 22 0.22
31 21 0.21
32 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTCCAAAAATTCCATTTTTACCTTGATT
Found at i:20861385 original size:60 final size:59
Alignment explanation
Indices: 20860949--20861456 Score: 419
Period size: 59 Copynumber: 8.6 Consensus size: 59
20860939 TGAAGGTCCT
* * * * * *
20860949 TAAACTATCAAAAAATTACATTTTTACCC-CTAAACTTTCC-AAAATTCCATTTTGACCC
1 TAAACTTTCCAAAAATTACATTTTGACCCTC-AAACTTTCCAAAAATTACATTTTTAACC
* * * *
20861007 TTAAACTTTTCAAAAATTACATTTTGACCCCCAAACTTTACAAAAATTACA-TTTTGACC
1 -TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTAACC
20861066 TTAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACA-TTTTAACCC
1 -TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTAA-CC
* * * *
20861126 TAAACTTTCC-AAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTGACACC
1 TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTA-ACC
* * * * *
20861185 TAAACTATCCAAAAATTATATTTTGACCCTTAAACTTTCAAAAAATTACA-TTTTGACC
1 TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTAACC
* * * * * *
20861243 TTTAAACTCTCTAAAAATTATATTGTGACCCTCAAACTTTCCAAAAACTCCATTTTT-ACC
1 --TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTAACC
* ** ** *
20861303 TTGATTTTTCTTAAAATTACCATTTT-ACCCTCAAAC-TTCCAAAAATTCCATTTTTAAACC
1 -TAAACTTTCCAAAAATTA-CATTTTGACCCTCAAACTTTCCAAAAATTACATTTTT-AACC
* ** * ** * *
20861363 TCGATTTTTCCAAAAATTACCATTTTG-CCGTCAAAC-TTCCAAAAGCTCCATTTTTTATCC
1 T-AAACTTTCCAAAAATTA-CATTTTGACCCTCAAACTTTCCAAAAATTACA-TTTTTAACC
* ** *
20861423 TGATTTTTCCAAAAATTCCATTTTTGA-CCTCAAA
1 TAAACTTTCCAAAAATTACA-TTTTGACCCTCAAA
20861457 TTATTCAAAA
Statistics
Matches: 385, Mismatches: 47, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
58 59 0.15
59 171 0.44
60 146 0.38
61 9 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.37
Consensus pattern (59 bp):
TAAACTTTCCAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTTTAACC
Found at i:20861456 original size:59 final size:58
Alignment explanation
Indices: 20861255--20861456 Score: 225
Period size: 60 Copynumber: 3.4 Consensus size: 58
20861245 TAAACTCTCT
* * *
20861255 AAAAATTA-TATTGTGACCCTCAAACTTTCCAAAAACTCCA-TTTTTACCTTGATTTTTCT
1 AAAAATTACCATTTTGA-CCTCAAAC-TTCCAAAAACTCCATTTTTTACC-TGATTTTTCC
* * *
20861314 TAAAATTACCATTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTAAACCTCGATTTTTCC
1 AAAAATTACCATTTTGA-CCTCAAACTTCCAAAAACTCCATTTTT-TACCT-GATTTTTCC
*
20861374 AAAAATTACCATTTTG-CCGTCAAACTTCCAAAAGCTCCATTTTTTATCCTGATTTTTCC
1 AAAAATTACCATTTTGACC-TCAAACTTCCAAAAACTCCATTTTTTA-CCTGATTTTTCC
20861433 AAAAATT-CCATTTTTGACCTCAAA
1 AAAAATTACCA-TTTTGACCTCAAA
20861457 TTATTCAAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
58 16 0.13
59 51 0.41
60 57 0.46
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAAATTACCATTTTGACCTCAAACTTCCAAAAACTCCATTTTTTACCTGATTTTTCC
Found at i:20871048 original size:28 final size:28
Alignment explanation
Indices: 20871016--20871073 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
20871006 AAAAGTTGGT
20871016 AAAAA-GA-ATCTGCTTATAAAAATTAAAA
1 AAAAATGAGATCT-CTTA-AAAAATTAAAA
* *
20871044 AAAAATTAGATCTCTTAAAAAATTGAAA
1 AAAAATGAGATCTCTTAAAAAATTAAAA
20871072 AA
1 AA
20871074 TAATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 17 0.65
29 5 0.19
30 4 0.15
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (28 bp):
AAAAATGAGATCTCTTAAAAAATTAAAA
Found at i:20871532 original size:19 final size:19
Alignment explanation
Indices: 20871510--20871548 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20871500 ACCACTGTCA
*
20871510 TCCACTGTAATCAAAATTG
1 TCCACCGTAATCAAAATTG
*
20871529 TCCACCGTAATCAAATTTG
1 TCCACCGTAATCAAAATTG
20871548 T
1 T
20871549 TATTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (19 bp):
TCCACCGTAATCAAAATTG
Found at i:20873894 original size:29 final size:30
Alignment explanation
Indices: 20873859--20873980 Score: 126
Period size: 29 Copynumber: 4.2 Consensus size: 30
20873849 TCAAAAATGC
**
20873859 AATTTTTGGATGCTCGGGGGGTAAAATGGT
1 AATTTTTGGACACTCGGGGGGTAAAATGGT
** * *
20873889 AA-TTTTGGACACT-TTGGGGCAAAATGAT
1 AATTTTTGGACACTCGGGGGGTAAAATGGT
**
20873917 AATTTTTGGACACTCGGGGGCAAAAAT-GT
1 AATTTTTGGACACTCGGGGGGTAAAATGGT
* *
20873946 AATTTTTGGACATTC-GAGGGTAAAATGGT
1 AATTTTTGGACACTCGGGGGGTAAAATGGT
20873975 AATTTT
1 AATTTT
20873981 CAAAAGTTTG
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 21 0.28
29 43 0.58
30 10 0.14
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.34
Consensus pattern (30 bp):
AATTTTTGGACACTCGGGGGGTAAAATGGT
Found at i:20873943 original size:58 final size:58
Alignment explanation
Indices: 20873859--20873980 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 58
20873849 TCAAAAATGC
** ** *
20873859 AATTTTTGGATGCTCGGGGGGTAAAATGGTAA-TTTTGGACACTTTG-GGGCAAAATGAT
1 AATTTTTGGACACTCGGGGGCAAAAAT-GTAATTTTTGGACA-TTCGAGGGCAAAATGAT
* *
20873917 AATTTTTGGACACTCGGGGGCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGT
1 AATTTTTGGACACTCGGGGGCAAAAATGTAATTTTTGGACATTCGAGGGCAAAATGAT
20873975 AATTTT
1 AATTTT
20873981 CAAAAGTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 7 0.13
58 48 0.87
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.34
Consensus pattern (58 bp):
AATTTTTGGACACTCGGGGGCAAAAATGTAATTTTTGGACATTCGAGGGCAAAATGAT
Found at i:20873997 original size:87 final size:86
Alignment explanation
Indices: 20873845--20874057 Score: 227
Period size: 87 Copynumber: 2.4 Consensus size: 86
20873835 CAAAACAAAC
* * ** *
20873845 GGAGTCAAAAATGCAATTTTTGG-ATGCTCGGGGGGTAAAATGGTAATTTTGGACACTTTGGGGC
1 GGAG-CAAAAATGTAATTTTTGGAAT--TC-GAGGGTAAAATGGTAATTTTCAAAACTTTGGGGC
* *
20873909 -AAAATGATAATTTTTGG-ACACTCG
62 AAAAAT-ATAATTTTTGGAAAAATCG
* *
20873933 GGGGCAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTCAAAAGTTTGGGGGCAA
1 GGAGCAAAAATGTAATTTTTGGA-ATTCGAGGGTAAAATGGTAATTTTCAAAACTTT-GGGGCAA
*
20873998 AAATATGATTTTTGGAAAAATCG
64 AAATATAATTTTTGGAAAAATCG
*
20874021 GGATC-AAAATGTAATTTTTGGAAGTTCGAGGGTAAAA
1 GGAGCAAAAATGTAATTTTTGGAA-TTCGAGGGTAAAA
20874058 ATGTGATTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
86 25 0.23
87 64 0.60
88 16 0.15
89 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (86 bp):
GGAGCAAAAATGTAATTTTTGGAATTCGAGGGTAAAATGGTAATTTTCAAAACTTTGGGGCAAAA
ATATAATTTTTGGAAAAATCG
Found at i:20874058 original size:29 final size:29
Alignment explanation
Indices: 20873909--20874188 Score: 196
Period size: 29 Copynumber: 9.6 Consensus size: 29
20873899 ACTTTGGGGC
* * *
20873909 AAAATGATAATTTTTGGACA-CTCGGGGGCA
1 AAAATG-TAATTTTTGGA-AGTTCGAGGGTA
20873939 AAAATGTAATTTTTGGACA-TTCGAGGGT-
1 AAAATGTAATTTTTGGA-AGTTCGAGGGTA
*** * * *
20873967 AAAATGGTAATTTTCAAAAGTTTGGGGGCA
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTA
* * ** * *
20873997 AAAATATGATTTTTGGAAAAATCG-GGATC
1 AAAATGTAATTTTTGG-AAGTTCGAGGGTA
20874026 AAAATGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGTA
*
20874055 AAAATGTGATTTTTGGAAAGTTC-AGGGTCA
1 AAAATGTAATTTTTGG-AAGTTCGAGGGT-A
* *
20874085 AAAATGTAA-TTTTAGAAGTT-TAGGAGTA
1 AAAATGTAATTTTTGGAAGTTCGAGG-GTA
* ** *
20874113 AAAATGTAATTTTCGTGAAGTTTAAGGGTT
1 AAAATGTAATTTTTG-GAAGTTCGAGGGTA
* *
20874143 AAAATGTAATTTTTGGAAGTTCGGGGGTC
1 AAAATGTAATTTTTGGAAGTTCGAGGGTA
* *
20874172 AAAATATGATTTTTGGA
1 AAAATGTAATTTTTGGA
20874189 CAATTCAGAG
Statistics
Matches: 198, Mismatches: 40, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
28 29 0.15
29 114 0.58
30 52 0.26
31 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTA
Found at i:20876091 original size:29 final size:29
Alignment explanation
Indices: 20876059--20876114 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
20876049 GGACTTTTAT
20876059 TAAAATTAAA-GTAATTTTAAATTTAAAAG
1 TAAAATTAAACGTAA-TTTAAATTTAAAAG
* *
20876088 TAAACTTAAACTTAATTTAAATTTAAA
1 TAAAATTAAACGTAATTTAAATTTAAA
20876115 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (29 bp):
TAAAATTAAACGTAATTTAAATTTAAAAG
Found at i:20876126 original size:17 final size:18
Alignment explanation
Indices: 20876106--20876148 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
20876096 AACTTAATTT
*
20876106 AAATTTAAATTTTA-AAA
1 AAATTTAAATCTTAGAAA
*
20876123 AAATTT-AATCTTAGAAT
1 AAATTTAAATCTTAGAAA
20876140 AAATTTAAA
1 AAATTTAAA
20876149 AAAGGTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 14 0.64
18 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATTTAAATCTTAGAAA
Found at i:20877174 original size:203 final size:204
Alignment explanation
Indices: 20876757--20877275 Score: 774
Period size: 203 Copynumber: 2.5 Consensus size: 204
20876747 ATATGGTTCA
* **
20876757 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACTTTGAGCCCGGCTTCATTG
1 CTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAG-TTC-TTG
* *
20876822 ACTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTCGTTTTGATCACTTCTCT
64 ATTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACTGCAT--CTCGTTTTGATCACTTCTCT
* * * *
20876887 GTTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTAGTACTCATCAAGAAGCTAACCATTTTA
127 GTTATCTCATCAGGAAGACGGATCCGATTCACTTCTCAGTACTCATCAAGAAGCTAACCATTTTA
20876952 TTGCTTCGACCTG
192 TTGCTTCGACCTG
*
20876965 CTTCTCAGTATCTCATCTGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAG-T-TTGAT
1 CTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAGTTCTTGAT
* **
20877028 TTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCATCTTTTTTTGATCCACTTCTCTG-T
66 TTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACTGCATCTCGTTTTGAT-CACTTCTCTGTT
* * *
20877092 ATCTCATCAGGAAGACGGATCCGATTCTCTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATT
130 ATCTCATCAGGAAGACGGATCCGATTCACTTCTCAGTA-CTCATCAAGAAGCTAACCATTTTATT
20877157 GCTTCGACCTG
194 GCTTCGACCTG
* **
20877168 CTTCTCAATATCTCATCAGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAGTTTCTTGA
1 CTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAG-TTCTTGA
*
20877233 TGTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACTGCATC
65 TTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACTGCATC
20877276 ACTTGTTTCA
Statistics
Matches: 284, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
202 43 0.15
203 98 0.35
204 43 0.15
205 1 0.00
206 46 0.16
208 53 0.19
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (204 bp):
CTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAGTTCTTGAT
TTGGTCTACTTCTCAGTATCTCATCAGAAAGATGACTGCATCTCGTTTTGATCACTTCTCTGTTA
TCTCATCAGGAAGACGGATCCGATTCACTTCTCAGTACTCATCAAGAAGCTAACCATTTTATTGC
TTCGACCTG
Found at i:20877363 original size:374 final size:377
Alignment explanation
Indices: 20876918--20877655 Score: 1045
Period size: 379 Copynumber: 2.0 Consensus size: 377
20876908 ATCTGGTTCA
* * *
20876918 CTTCTTAGTACTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCT
1 CTTCTCAGTACTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCACCA
20876983 GGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAG-T-TTGATTTGGTCTACTTCTCAGTA
66 GGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAGTTCTTGATTTGGTCTACTTCTCAGTA
* * ** *
20877046 TCTCATCAGGAAGATGACTGCAT-CTTTTTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGG
131 TCTCATCAGGAAGATGACCGCATACTTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGA
* * *
20877110 ATCCGATTCTCTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
196 ATCCGATCCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCA
* * ** * ** *
20877175 ATATCTCATCAGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAG-TTTC-TTGATGTGG
261 ATATCTCATCAAGAAGCT-GGGTTCGAAGATTCGCTCACATCAAGCCTAGACTTCATTGATGTGG
* *
20877238 TCTACTTCTCAGTATCTCATCAGAAAGATGACTGCATCACTTGTTTCAATATG
325 TCTACTGCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATATG
* * *
20877291 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACTTGCTTCTCAGTATCTCACC
1 CTTCTCAGTA-CTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCACC
** *
20877356 AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTGGTTTCTTGATTTGGTCTACTTCTCAG
65 AGGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAG-TTCTTGATTTGGTCTACTTCTCAG
** *
20877421 TATCTTTTCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGA
129 TATCTCATCAGGAAGATGACCGCAT-ACTTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGA
** * *
20877486 CGAATTTGGTCCACTTCTTAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTACTTC
193 CGAATCCGATCCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTACTTC
* * * * *
20877551 TTAGTATCTCATCAAGAAGCTGGGTTCGAAGATTCGCTCACATCAAGCTTTGACTTCATTGATTT
258 TCAATATCTCATCAAGAAGCTGGGTTCGAAGATTCGCTCACATCAAGCCTAGACTTCATTGATGT
*
20877616 GGTCTACTGCTCAGTATCTCATCTGAAAGATGACCGCATC
323 GGTCTACTGCTCAGTATCTCATCAGAAAGATGACCGCATC
20877656 TTTATTTTGA
Statistics
Matches: 317, Mismatches: 40, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
373 9 0.03
374 86 0.27
376 1 0.00
377 43 0.14
378 24 0.08
379 111 0.35
380 43 0.14
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (377 bp):
CTTCTCAGTACTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCACCA
GGAAGTTGGGGTTCGAAGATTCGCTCACTTTGAGCCTAGTTCTTGATTTGGTCTACTTCTCAGTA
TCTCATCAGGAAGATGACCGCATACTTGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGA
ATCCGATCCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCA
ATATCTCATCAAGAAGCTGGGTTCGAAGATTCGCTCACATCAAGCCTAGACTTCATTGATGTGGT
CTACTGCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATATG
Found at i:20877412 original size:171 final size:171
Alignment explanation
Indices: 20877120--20877484 Score: 604
Period size: 171 Copynumber: 2.1 Consensus size: 171
20877110 ATCCGATTCT
* *
20877120 CTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCACC
20877185 AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAGTTTCTTGATGTGGTCTACTTCTCAG
66 AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAGTTTCTTGATGTGGTCTACTTCTCAG
* *
20877250 TATCTCATCAGAAAGATGACTGCATCACTTGTTTCAATATG
131 TATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATACG
* * *
20877291 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACTTGCTTCTCAGTATCTCACC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCACC
* *
20877356 AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTGGTTTCTTGATTTGGTCTACTTCTCAG
66 AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAGTTTCTTGATGTGGTCTACTTCTCAG
** * *
20877421 TATCTTTTCAGGAAGATGACCGCATCACTTGTTTCAATCCG
131 TATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATACG
*
20877462 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
20877485 ACGAATTTGG
Statistics
Matches: 180, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 180 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (171 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCACC
AGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTAGTTTCTTGATGTGGTCTACTTCTCAG
TATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATACG
Found at i:20877676 original size:208 final size:209
Alignment explanation
Indices: 20877291--20878065 Score: 851
Period size: 208 Copynumber: 3.8 Consensus size: 209
20877281 TTTCAATATG
* * *
20877291 CTTCTC-AGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACTTGCTTCTCAGTATCTCAC
1 CTTCTCTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * ** * * *
20877355 CAGGAAGTTGGGGTTCGAAGATTTTCTCACTTTGAGCCTGGTTTC-TTGATTTGGTCTACTTCTC
66 CAAGAAGCTGGGGTTCGAAGATTCGCTCACATTGAG-CTTGCTTCATTGATTTGGTCTACTTCTC
** ** *
20877419 AGTATCTTTTCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAA
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAA
* *
20877484 GACGAATTTGGTCCA
195 GACGGATTTGGTTCA
* * *
20877499 CTTCT-TAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTTAGTATCTCAT
1 CTTCTCTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
** *
20877563 CAAGAAGCT-GGGTTCGAAGATTCGCTCACATCAAGCTTTGACTTCATTGATTTGGTCTACTGCT
66 CAAGAAGCTGGGGTTCGAAGATTCGCTCACATTGAGC-TTG-CTTCATTGATTTGGTCTACTTCT
* * * * * *
20877627 CAGTATCTCATCTGAAAGATGACCGCATC-TTTATTTTGATCCACTTCTCTGTATCTCATTAGAA
129 CAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGA
20877691 AGACGGATTTGGTTCA
194 AGACGGATTTGGTTCA
* * * ** * *
20877707 GTTCTCT-GTATCTCATCAAGAAGGTAACTGTTTTATTGCTTCGACCTGCTTTTCAGTATCTTAT
1 CTTCTCTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * *
20877771 C-AGAAAGCT-GGGTTCGAAG--T---T----TT--GC-T-C-GCATTGAGTTGGTATACTTCTC
66 CAAG-AAGCTGGGGTTCGAAGATTCGCTCACATTGAGCTTGCTTCATTGATTTGGTCTACTTCTC
* * * *
20877820 TGTATCTCATCAGGAAGATGACCTCATCGCTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAA
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAA
20877885 GACGGATTTGGTTCA
195 GACGGATTTGGTTCA
* * ** *
20877900 CTTCTCTA-TACCTCATCAGGAAGGTAACCGCTTTATTGCTTCAACCTGCTTCTCAGTATCTCAT
1 CTTCTCTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * * * *
20877964 CAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTCTACTTATC
66 CAAGAAGCTGGGGTTCGAAGATTCGCTCACATTGAGC-TTGCTTCATTGATTTGGTCTACTTCTC
*
20878029 AGTATCTCCTCAGGAAGATGACC-CATCACTTGTTTTG
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
20878066 GATAATCGCA
Statistics
Matches: 472, Mismatches: 70, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
192 42 0.09
193 108 0.23
194 11 0.02
195 1 0.00
196 1 0.00
197 2 0.00
199 2 0.00
203 3 0.01
205 2 0.00
206 2 0.00
207 26 0.06
208 190 0.40
209 82 0.17
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (209 bp):
CTTCTCTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAAGAAGCTGGGGTTCGAAGATTCGCTCACATTGAGCTTGCTTCATTGATTTGGTCTACTTCTCA
GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAG
ACGGATTTGGTTCA
Found at i:20877958 original size:193 final size:193
Alignment explanation
Indices: 20877607--20877991 Score: 547
Period size: 193 Copynumber: 2.0 Consensus size: 193
20877597 GCTTTGACTT
* * * *
20877607 CATTGATTTGGTCTACTGCTCAGTATCTCATCTGAAAGATGACCGCATCTTTATTTTGATCCACT
1 CATTGAGTTGGTATACTGCTCAGTATCTCATCAGAAAGATGACCGCATCCTTATTTTGATCCACT
* * * * *
20877672 TCTCTGTATCTCATTAGAAAGACGGATTTGGTTCAGTTCTCTGTATCTCATCAAGAAGGTAACTG
66 TCTCTGTATCTCATCAGAAAGACGGATTTGGTTCACTTCTCTATACCTCATCAAGAAGGTAACCG
* * * * *
20877737 TTTTATTGCTTCGACCTGCTTTTCAGTATCTTATCAGAAAGCT-GGGTTCGAAGTTTTGCTCG
131 CTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGTTTCGCTCG
* * * * *
20877799 CATTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCTCATCGCTTGTTTTGATCCAC
1 CATTGAGTTGGTATACTGCTCAGTATCTCATCAGAAAGATGACCGCATC-CTTATTTTGATCCAC
* * *
20877864 TTCTCTGTGTCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATACCTCATCAGGAAGGTAACC
65 TTCTCTGTATCTCATCAGAAAGACGGATTTGGTTCACTTCTCTATACCTCATCAAGAAGGTAACC
*
20877929 GCTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTC
130 GCTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGTTTCGCTC
20877992 ATATTGAGCT
Statistics
Matches: 168, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
192 42 0.25
193 109 0.65
194 17 0.10
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (193 bp):
CATTGAGTTGGTATACTGCTCAGTATCTCATCAGAAAGATGACCGCATCCTTATTTTGATCCACT
TCTCTGTATCTCATCAGAAAGACGGATTTGGTTCACTTCTCTATACCTCATCAAGAAGGTAACCG
CTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGTTTCGCTCG
Found at i:20887435 original size:29 final size:29
Alignment explanation
Indices: 20887403--20887471 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
20887393 TTCGAGGCAC
**
20887403 AATGGTAATTTTTGGACA-CTCAGGGGAAA
1 AATGGTAATTTTTGGACATC-CAAAGGAAA
* *
20887432 AAT-GTAACTTTTGGACATCCAAAGGTAA
1 AATGGTAATTTTTGGACATCCAAAGGAAA
20887460 AATGGTAATTTT
1 AATGGTAATTTT
20887472 CGAAAGTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (29 bp):
AATGGTAATTTTTGGACATCCAAAGGAAA
Found at i:20887545 original size:28 final size:29
Alignment explanation
Indices: 20887514--20887588 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
20887504 AATCGGGATC
20887514 AAAATGTATTTTTTGGATG-TCGGGGT-AA
1 AAAATGTA-TTTTTGGATGTTCGGGGTCAA
*
20887542 AAAATGTGATTTTTGGAAAGTTCGGGGTCAA
1 AAAATGT-ATTTTTGG-ATGTTCGGGGTCAA
*
20887573 AATATG-ATTTTTGGAT
1 AAAATGTATTTTTGGAT
20887589 TTAGAATTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 15 0.38
29 11 0.28
30 7 0.17
31 7 0.17
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (29 bp):
AAAATGTATTTTTGGATGTTCGGGGTCAA
Found at i:20887554 original size:29 final size:28
Alignment explanation
Indices: 20887514--20887588 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
20887504 AATCGGGATC
20887514 AAAATGT-ATTTTTTGGATG-TCGGGGTAA
1 AAAATGTGA-TTTTTGGATGTTCGGGGT-A
* *
20887542 AAAATGTGATTTTTGGAAAGTTCGGGGTC
1 AAAATGTGATTTTTGG-ATGTTCGGGGTA
*
20887571 AAAATATGATTTTTGGAT
1 AAAATGTGATTTTTGGAT
20887589 TTAGAATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.38
29 18 0.45
30 7 0.17
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (28 bp):
AAAATGTGATTTTTGGATGTTCGGGGTA
Found at i:20893794 original size:21 final size:21
Alignment explanation
Indices: 20893765--20893811 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20893755 GTTTCATTTG
* *
20893765 GTATAGGTAGCACCCATCAAA
1 GTATCGGTAGAACCCATCAAA
*
20893786 GTATCGGTAGAACCCATCAGA
1 GTATCGGTAGAACCCATCAAA
20893807 GTATC
1 GTATC
20893812 AGTAAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GTATCGGTAGAACCCATCAAA
Found at i:20895641 original size:12 final size:12
Alignment explanation
Indices: 20895624--20895648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20895614 TGGCCTATGA
20895624 TGGAAGAAGTGG
1 TGGAAGAAGTGG
20895636 TGGAAGAAGTGG
1 TGGAAGAAGTGG
20895648 T
1 T
20895649 AGAATGAACT
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:0.32, C:0.00, G:0.48, T:0.20
Consensus pattern (12 bp):
TGGAAGAAGTGG
Found at i:20896467 original size:21 final size:23
Alignment explanation
Indices: 20896418--20896474 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
20896408 CAAGTATACA
*
20896418 AACTACCGATACATCATACATAT
1 AACTACCGATACATCACACATAT
20896441 AACTACCGATAC-TCACA-AT-T
1 AACTACCGATACATCACACATAT
*
20896461 CAACTACGGATACA
1 -AACTACCGATACA
20896475 ACTCAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 13 0.43
22 4 0.13
23 12 0.40
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (23 bp):
AACTACCGATACATCACACATAT
Found at i:20897135 original size:52 final size:52
Alignment explanation
Indices: 20897052--20897297 Score: 321
Period size: 52 Copynumber: 4.7 Consensus size: 52
20897042 CTTTCACTTC
*
20897052 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCTGTAAGGG
1 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
* * *
20897104 ATTCATATACTCATGATGATACATAGCCATCGGACCTTATAATCCGTAAGGG
1 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
* * * * * *
20897156 ATTCATATACTCACGATGACACATAGCCATTGGACCTCATAGTTCGTAAGAG
1 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
*** * * *
20897208 ATTCATATACTCATGATGACATGGAGTCATCAGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
* * *
20897260 ATTCATATACACATGATGACACAGAGTCACCGGACCTC
1 ATTCATATACTCATGATGACACATAGTCATCGGACCTC
20897298 TTCGTTTACG
Statistics
Matches: 166, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 166 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAGGG
Found at i:20903152 original size:25 final size:25
Alignment explanation
Indices: 20903124--20903171 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20903114 TAGCAGATGC
*
20903124 AATATTTTATATCCCCAATAGTACG
1 AATAATTTATATCCCCAATAGTACG
*
20903149 AATAATTTATATCCCTAATAGTA
1 AATAATTTATATCCCCAATAGTA
20903172 ACAGATGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (25 bp):
AATAATTTATATCCCCAATAGTACG
Found at i:20905022 original size:45 final size:45
Alignment explanation
Indices: 20904970--20905071 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
20904960 TTCAAGTCAA
20904970 ATACATCAAGGAAAAGGCTTGATAATTTTAAACTTATTCATCTTT
1 ATACATCAAGGAAAAGGCTTGATAATTTTAAACTTATTCATCTTT
20905015 ATACATCAAGGAAAAGGCTTGATAATTTTAAACTTATTCATCTTT
1 ATACATCAAGGAAAAGGCTTGATAATTTTAAACTTATTCATCTTT
20905060 ATACATCAAGGA
1 ATACATCAAGGA
20905072 CCAAATCATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (45 bp):
ATACATCAAGGAAAAGGCTTGATAATTTTAAACTTATTCATCTTT
Found at i:20915437 original size:20 final size:19
Alignment explanation
Indices: 20915390--20915467 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
20915380 AAAAACAACT
*
20915390 TATAAAAAATATTTAAAAAA
1 TATAAAAATTA-TTAAAAAA
20915410 T-T-AAAATTATTAAAAAGA
1 TATAAAAATTATTAAAAA-A
20915428 TATAAAAATTATTAAAATAA
1 TATAAAAATTATTAAAA-AA
* * * *
20915448 TTTTAAATTTTTTAAAAAA
1 TATAAAAATTATTAAAAAA
20915467 T
1 T
20915468 GAATTGCCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.14
18 8 0.16
19 5 0.10
20 28 0.57
21 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
TATAAAAATTATTAAAAAA
Found at i:20917347 original size:36 final size:36
Alignment explanation
Indices: 20917307--20917405 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
20917297 GTGAAAGTGG
20917307 ATATGTGAGTATGTTATTCATGCCAT-ATGACAGTAA
1 ATATGTGAGTATGTTATTCATGCCATGA-GACAGTAA
*
20917343 ATATGTGAGTATGTTATTCATGTCATGAGACAGTAA
1 ATATGTGAGTATGTTATTCATGCCATGAGACAGTAA
*
20917379 ATATGTGGGTATGTTATTCATGCCATG
1 ATATGTGAGTATGTTATTCATGCCATG
20917406 TACTAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 58 0.98
37 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.37
Consensus pattern (36 bp):
ATATGTGAGTATGTTATTCATGCCATGAGACAGTAA
Found at i:20917781 original size:66 final size:66
Alignment explanation
Indices: 20917665--20917800 Score: 191
Period size: 66 Copynumber: 2.1 Consensus size: 66
20917655 GGGAAATAAA
** * * * *
20917665 GAGAGTGTTAGCTTTATGCTTCACTTTTAGGACATGTTTGACTCTGTGAGTCTTTTGGTGTGTTT
1 GAGAGTGTTAGCTAGATGCTTCACTTTTAGGACATGTTCGAATCTATGAGTCTTTTGATGTGTTT
20917730 G
66 G
* **
20917731 GAGAGTGTTAGCTAGATGCTTCACTTTTGGGGTATGTTCGAATCTATGAGTCTTTTGATGTGTTT
1 GAGAGTGTTAGCTAGATGCTTCACTTTTAGGACATGTTCGAATCTATGAGTCTTTTGATGTGTTT
20917796 G
66 G
20917797 GAGA
1 GAGA
20917801 TTCGTGTATC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.43
Consensus pattern (66 bp):
GAGAGTGTTAGCTAGATGCTTCACTTTTAGGACATGTTCGAATCTATGAGTCTTTTGATGTGTTT
G
Found at i:20917906 original size:23 final size:23
Alignment explanation
Indices: 20917880--20917938 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
20917870 AAATGTGTTG
*
20917880 AATATTAATGTGATTTATTCTTA
1 AATATTAATGTGATTTATGCTTA
*
20917903 AATATTAATGTGATTTGTGCTTA
1 AATATTAATGTGATTTATGCTTA
*
20917926 AATATTCATGTGA
1 AATATTAATGTGA
20917939 CTAATGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
AATATTAATGTGATTTATGCTTA
Found at i:20917952 original size:25 final size:23
Alignment explanation
Indices: 20917872--20917973 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 23
20917862 TTATCATTAA
*
20917872 ATGTG-TTGAATATTAATGTGAT
1 ATGTGATTAAATATTAATGTGAT
* * **
20917894 TTATTCTTAAATATTAATGTGAT
1 ATGTGATTAAATATTAATGTGAT
* * *
20917917 TTGTGCTTAAATATTCATGTGACT
1 ATGTGATTAAATATTAATGTGA-T
* *
20917941 AATGTGATTAAAT-GTGAT-T-AT
1 -ATGTGATTAAATATTAATGTGAT
20917962 ATGTGATTAAAT
1 ATGTGATTAAAT
20917974 GTGACTAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 12 0.18
21 1 0.02
22 3 0.05
23 36 0.55
24 4 0.06
25 10 0.15
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (23 bp):
ATGTGATTAAATATTAATGTGAT
Found at i:20917956 original size:10 final size:10
Alignment explanation
Indices: 20917941--20917999 Score: 91
Period size: 10 Copynumber: 5.8 Consensus size: 10
20917931 TCATGTGACT
20917941 AATGTGATTA
1 AATGTGATTA
20917951 AATGTGATTA
1 AATGTGATTA
*
20917961 TATGTGATTA
1 AATGTGATTA
*
20917971 AATGTGACTA
1 AATGTGATTA
20917981 AATGTGATTA
1 AATGTGATTA
20917991 ATATGTGAT
1 A-ATGTGAT
20918000 GTGATAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
10 37 0.84
11 7 0.16
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (10 bp):
AATGTGATTA
Found at i:20917967 original size:20 final size:19
Alignment explanation
Indices: 20917933--20917998 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 19
20917923 TTAAATATTC
20917933 ATGTGACTAATGTGATTAA
1 ATGTGACTAATGTGATTAA
*
20917952 ATGTGATTATATGTGATTAA
1 ATGTGACTA-ATGTGATTAA
20917972 ATGTGACTAAATGTGATTAA
1 ATGTGACT-AATGTGATTAA
20917992 TATGTGA
1 -ATGTGA
20917999 TGTGATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.19
20 27 0.64
21 7 0.17
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.39
Consensus pattern (19 bp):
ATGTGACTAATGTGATTAA
Found at i:20917977 original size:30 final size:30
Alignment explanation
Indices: 20917933--20917999 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
20917923 TTAAATATTC
* *
20917933 ATGTGACTAATGTGATTAAATGTGATT-AT
1 ATGTGATTAATGTGACTAAATGTGATTAAT
20917962 ATGTGATTAAATGTGACTAAATGTGATTAAT
1 ATGTGATT-AATGTGACTAAATGTGATTAAT
20917993 ATGTGAT
1 ATGTGAT
20918000 GTGATAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 7 0.21
30 18 0.53
31 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (30 bp):
ATGTGATTAATGTGACTAAATGTGATTAAT
Found at i:20918036 original size:68 final size:68
Alignment explanation
Indices: 20917964--20918123 Score: 257
Period size: 68 Copynumber: 2.3 Consensus size: 68
20917954 GTGATTATAT
*
20917964 GTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACC
1 GTGATTAAATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTAAAATATTCATGTGACC
20918029 AAG
66 AAG
* * *
20918032 GTGATTAAATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTGAAATATTCATGTTACT
1 GTGATTAAATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTAAAATATTCATGTGACC
*
20918097 AAT
66 AAG
*
20918100 GTGATTAAATGTGATTAATATGTG
1 GTGATTAAATGTGACTAA-ATGTG
20918124 TTGTGTTAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 80 0.94
69 5 0.06
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (68 bp):
GTGATTAAATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTAAAATATTCATGTGACC
AAG
Found at i:20918043 original size:58 final size:58
Alignment explanation
Indices: 20917974--20918140 Score: 172
Period size: 68 Copynumber: 2.7 Consensus size: 58
20917964 GTGATTAAAT
*
20917974 GTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAAG
1 GTGATTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAAG
* * *
20918032 GTGATTAAATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTGAAATATTCATGTTACT
1 GTGATTAAATGTG-----A--T--T-AATATGTGATGTGATAAATGTTAAAATATTCATGTGACC
*
20918097 AAT
56 AAG
* *
20918100 GTGATTAAATGTGATTAATATGTGTTGTGTTAAATGCTTAA
1 GTGATTAAATGTGATTAATATGTGATGTGATAAATG-TTAA
20918141 GTACTCATGT
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
58 30 0.33
59 4 0.04
61 1 0.01
63 2 0.02
65 1 0.01
67 1 0.01
68 51 0.57
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (58 bp):
GTGATTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAAG
Found at i:20918149 original size:58 final size:58
Alignment explanation
Indices: 20918039--20918164 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 58
20918029 AAGGTGATTA
* * *
20918039 AATGTGACTAAATGTGATGAATATGTGATGTGATAAATGTTGAAATATTCATGTTACT
1 AATGTGATTAAATGTGATGAATATGTGATGTGATAAATGTTGAAATACTCATGTGACT
* * * * *
20918097 AATGTGATTAAATGTGATTAATATGTGTTGTGTTAAATGCTT-AAGTACTCATGTGATT
1 AATGTGATTAAATGTGATGAATATGTGATGTGATAAATG-TTGAAATACTCATGTGACT
20918155 AATGTGATTA
1 AATGTGATTA
20918165 GTGCGATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 57 0.97
59 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (58 bp):
AATGTGATTAAATGTGATGAATATGTGATGTGATAAATGTTGAAATACTCATGTGACT
Found at i:20922204 original size:26 final size:26
Alignment explanation
Indices: 20922168--20922240 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
20922158 TATTTTCTCG
* *
20922168 AAAA-TTTACTAGAGGTGAAATCGTC
1 AAAATTTTACTAGAGGTAAAATCATC
*
20922193 AAAATTTTACTAGGGGTAAAATCATC
1 AAAATTTTACTAGAGGTAAAATCATC
* ** *
20922219 AAAGTTTTGTTAGGGGTAAAAT
1 AAAATTTTACTAGAGGTAAAAT
20922241 AAAGATGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 4 0.10
26 37 0.90
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (26 bp):
AAAATTTTACTAGAGGTAAAATCATC
Found at i:20945625 original size:14 final size:14
Alignment explanation
Indices: 20945606--20945633 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20945596 GGTTTTCGTC
20945606 ACACTATTAATGGA
1 ACACTATTAATGGA
20945620 ACACTATTAATGGA
1 ACACTATTAATGGA
20945634 GGGTAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ACACTATTAATGGA
Found at i:20952708 original size:15 final size:16
Alignment explanation
Indices: 20952684--20952733 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
20952674 CTCCTCCATT
20952684 TCATCATCCTCTTCATC
1 TCATC-TCCTCTTCATC
20952701 TC-TCTCCTCTTCACTC
1 TCATCTCCTCTTCA-TC
*
20952717 TCAGTCTCCTCCTCATC
1 TCA-TCTCCTCTTCATC
20952734 ATGCTCCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 9 0.31
16 6 0.21
17 4 0.14
18 10 0.34
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.40
Consensus pattern (16 bp):
TCATCTCCTCTTCATC
Found at i:20962157 original size:58 final size:58
Alignment explanation
Indices: 20962089--20962208 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 58
20962079 ACCCATCAAC
* * * *
20962089 AAACTAAACCCAAATTTTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
*
20962147 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
20962205 AAAC
1 AAAC
20962209 AACTCCTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
Found at i:20968703 original size:61 final size:61
Alignment explanation
Indices: 20968605--20968740 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
20968595 TTTTTTATAC
* *
20968605 TTGGTGCTGGCCATCAATGCCTAACACCACAAAAAAAT-TAAAGATTTTATATC-GATAAAG
1 TTGGTGCCGGCCATCAATGCCCAACACCACAAAAAAATAT-AAGATTTTATATCTGATAAAG
* * * * ***
20968665 TTGGTGCCGGTCATCAGTGTCCCAACACCCCAGAAAAATATATTTTTTTATATCTGATAAAG
1 TTGGTGCCGGCCATCAATG-CCCAACACCACAAAAAAATATAAGATTTTATATCTGATAAAG
*
20968727 TTGGTGTCGGCCAT
1 TTGGTGCCGGCCAT
20968741 AGTGGACCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 16 0.26
61 26 0.42
62 20 0.32
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (61 bp):
TTGGTGCCGGCCATCAATGCCCAACACCACAAAAAAATATAAGATTTTATATCTGATAAAG
Done.