Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 71 of 373
Found at i:21604648 original size:16 final size:15
Alignment explanation
Indices: 21604622--21604655 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21604612 ATGAACGTAA
*
21604622 AACTCATATGTGATG
1 AACTCATATGTAATG
21604637 AACTCGATATGTAATG
1 AACTC-ATATGTAATG
21604653 AAC
1 AAC
21604656 CTTCGGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (15 bp):
AACTCATATGTAATG
Found at i:21608660 original size:19 final size:19
Alignment explanation
Indices: 21608636--21608675 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21608626 AAAATATCAT
21608636 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAATTTG
* *
21608655 ATTAATTTTATTTTATTTG
1 ATTAATTTTAATTAATTTG
21608674 AT
1 AT
21608676 CAAAATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
ATTAATTTTAATTAATTTG
Found at i:21617595 original size:38 final size:38
Alignment explanation
Indices: 21617553--21617632 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
21617543 TGTTCATGAA
* * * *
21617553 ATATCCAGGTTAAATCTCGCAGGCTTCGTGCTGGTATT
1 ATATCCAGGATAAATCTCACAGGCCTAGTGCTGGTATT
**
21617591 ATATCTGGGATAAATCTCACAGGCCTAGTGCTGGTATT
1 ATATCCAGGATAAATCTCACAGGCCTAGTGCTGGTATT
21617629 ATAT
1 ATAT
21617633 TCGGGCCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (38 bp):
ATATCCAGGATAAATCTCACAGGCCTAGTGCTGGTATT
Found at i:21617754 original size:43 final size:43
Alignment explanation
Indices: 21617630--21617741 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
21617620 GCTGGTATTA
*
21617630 TATTCGGGCCTTCGTGCTTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
21617673 TATTCGGGCCTTCGTGCCTAGCAGTCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
21617716 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
21617742 GTAATACCGG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.10, C:0.26, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:21632971 original size:20 final size:21
Alignment explanation
Indices: 21632892--21632971 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 21
21632882 TTTCTTTCTT
21632892 TTTTTATTTC-TTATTTAGATTA
1 TTTTTATTTCTTTA-TT-GATTA
*
21632914 -TTTTATTTCTTTATTGTTTA
1 TTTTTATTTCTTTATTGATTA
*
21632934 TTATTATTAAT-TAATTATT-ATTA
1 TTTTTATT--TCT--TTATTGATTA
21632957 TTTTTATTTCTTTAT
1 TTTTTATTTCTTTAT
21632972 GTGTTTCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
20 8 0.17
21 18 0.38
22 5 0.11
23 11 0.23
24 5 0.11
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTATTTCTTTATTGATTA
Found at i:21638353 original size:11 final size:12
Alignment explanation
Indices: 21638302--21638381 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 12
21638292 TTTATATTTT
21638302 TTATTTATT-TTA
1 TTATTT-TTCTTA
*
21638314 TTATTTTACTTTA
1 TTATTTTTC-TTA
21638327 CTTCATTTTTCTTA
1 -TT-ATTTTTCTTA
21638341 TTATTTTTC-TA
1 TTATTTTTCTTA
21638352 TTATATTTTTCTT-
1 -T-TATTTTTCTTA
* *
21638365 TTATATTTATTA
1 TTATTTTTCTTA
21638377 -TATTT
1 TTATTT
21638382 AGTTTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
11 15 0.27
12 15 0.27
13 13 0.24
14 6 0.11
15 6 0.11
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTTCTTA
Found at i:21638358 original size:13 final size:13
Alignment explanation
Indices: 21638342--21638372 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21638332 TTTTTCTTAT
21638342 TATTTTTCTATTA
1 TATTTTTCTATTA
*
21638355 TATTTTTCTTTTA
1 TATTTTTCTATTA
21638368 TATTT
1 TATTT
21638373 ATTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTCTATTA
Found at i:21638368 original size:27 final size:28
Alignment explanation
Indices: 21638309--21638372 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
21638299 TTTTTATTTA
21638309 TTTTATTATTTTACTTTACTTCATTTTTC
1 TTTTATTATTTTACTTTAC-TCATTTTTC
*
21638338 --TTATTATTTTTCTATTA-T-ATTTTTC
1 TTTTATTATTTTACT-TTACTCATTTTTC
21638363 TTTTA-TATTT
1 TTTTATTATTT
21638373 ATTATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
25 7 0.23
26 6 0.19
27 15 0.48
28 3 0.10
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTTATTATTTTACTTTACTCATTTTTC
Found at i:21638649 original size:13 final size:13
Alignment explanation
Indices: 21638631--21638656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21638621 CGCTCGATTG
21638631 GATTGGGTAACTA
1 GATTGGGTAACTA
21638644 GATTGGGTAACTA
1 GATTGGGTAACTA
21638657 TGTTCATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
GATTGGGTAACTA
Found at i:21642868 original size:34 final size:34
Alignment explanation
Indices: 21642825--21642897 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
21642815 AACTTCTCAA
21642825 TCTCAACTTTTTGTACAACAGGGTACCTATAAGG
1 TCTCAACTTTTTGTACAACAGGGTACCTATAAGG
21642859 TCTCAACTTTTTGTACAACAGGGTACCTATAAGG
1 TCTCAACTTTTTGTACAACAGGGTACCTATAAGG
21642893 TCTCA
1 TCTCA
21642898 TCCTTACTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (34 bp):
TCTCAACTTTTTGTACAACAGGGTACCTATAAGG
Found at i:21658740 original size:63 final size:63
Alignment explanation
Indices: 21658662--21658870 Score: 199
Period size: 64 Copynumber: 3.2 Consensus size: 63
21658652 TCATTTCTTT
* * * *
21658662 TTTTTTGTGAAGTTTTCATTTCTTTCTTTATCATTTAG-CCAAATAAAAGTAACTAAAAGCATC
1 TTTTTTGTGACGTTTT-ATTTCTTTCGTTATCATTTAGTCAAAATAAAAGTAACTAAAAGTATC
* * * *
21658725 TTTTTGGTGACGTTTTTTATTATTTCGTTATCTTTTAGTCAAAAAAATAAAAGTAACTAAAAGTA
1 TTTTTTGTGACGTTTTAT-TTCTTTCGTTATCATTTAGTC---AAAATAAAAGTAACTAAAAGTA
21658790 TC
62 TC
** * * * *
21658792 CATTTTGTGACGTTTT-TATTCTTTCGTTA-CCTTTAAGTAAAAAATAAAAGTAACTAAAAATGT
1 TTTTTTGTGACGTTTTAT-TTCTTTCGTTATCATTT-AGT-CAAAATAAAAGTAACTAAAAGTAT
21658855 C
63 C
21658856 TTTTTTGTGACGTTT
1 TTTTTTGTGACGTTT
21658871 CTAAATCGAT
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 30 0.25
64 36 0.30
65 4 0.03
66 15 0.12
67 35 0.29
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (63 bp):
TTTTTTGTGACGTTTTATTTCTTTCGTTATCATTTAGTCAAAATAAAAGTAACTAAAAGTATC
Found at i:21658862 original size:64 final size:65
Alignment explanation
Indices: 21658702--21658870 Score: 232
Period size: 64 Copynumber: 2.6 Consensus size: 65
21658692 TCATTTAGCC
* * * *
21658702 AAATAAAAGTAACTAAAAGCATCTTTTTGGTGACGTTTTTTATTATTTCGTTATCTTTTAGTCAA
1 AAATAAAAGTAACTAAAAGTATCTTTTTTGTGACG-TTTTTATTATTTCGTTACCTTTAAGT-AA
21658767 AA
64 AA
** *
21658769 AAATAAAAGTAACTAAAAGTATCCATTTTGTGACGTTTTTATTCTTTCGTTACCTTTAAGT-AAA
1 AAATAAAAGTAACTAAAAGTATCTTTTTTGTGACGTTTTTATTATTTCGTTACCTTTAAGTAAAA
* *
21658833 AAATAAAAGTAACTAAAAATGTCTTTTTTGTGACGTTT
1 AAATAAAAGTAACTAAAAGTATCTTTTTTGTGACGTTT
21658871 CTAAATCGAT
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.41
66 23 0.25
67 31 0.34
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (65 bp):
AAATAAAAGTAACTAAAAGTATCTTTTTTGTGACGTTTTTATTATTTCGTTACCTTTAAGTAAAA
Found at i:21663920 original size:43 final size:42
Alignment explanation
Indices: 21663854--21663954 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 42
21663844 AACAAGTACA
* * * *
21663854 ATGCCGACGTCCCAGA-CGTGGTCTTACATGTAACTCA-ATATCG
1 ATGCCGATGTCCCAGATAG-GGTCTTACACG-AAATCAGATA-CG
**
21663897 ATGCCTCTGTCCCAGATAGGGTCTTACACGAAATCAGATACG
1 ATGCCGATGTCCCAGATAGGGTCTTACACGAAATCAGATACG
21663939 ATGCCGATGTCCCAGA
1 ATGCCGATGTCCCAGA
21663955 CATGGTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 21 0.44
43 26 0.54
44 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (42 bp):
ATGCCGATGTCCCAGATAGGGTCTTACACGAAATCAGATACG
Found at i:21663954 original size:42 final size:43
Alignment explanation
Indices: 21663854--21663974 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 43
21663844 AACAAGTACA
* * * *
21663854 ATGCCGACGTCCCAGACGTGGTCTTACATGTAACTCAATATCG
1 ATGCCGATGTCCCAGAAGTGGTCTTACACGTAAATCAATATCG
**
21663897 ATGCCTCTGTCCCAGATAG-GGTCTTACACG-AAATCAGATA-CG
1 ATGCCGATGTCCCAGA-AGTGGTCTTACACGTAAATCA-ATATCG
* *
21663939 ATGCCGATGTCCCAGACA-TGGTTTTATACGTAAATC
1 ATGCCGATGTCCCAGA-AGTGGTCTTACACGTAAATC
21663975 TCAATCGAGG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 31 0.49
43 31 0.49
44 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (43 bp):
ATGCCGATGTCCCAGAAGTGGTCTTACACGTAAATCAATATCG
Found at i:21666321 original size:18 final size:18
Alignment explanation
Indices: 21666300--21666336 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21666290 TGAGTTTTTG
*
21666300 AATTTGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
*
21666318 AATTCGAATAATTCAAAT
1 AATTCGAATAACTCAAAT
21666336 A
1 A
21666337 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:21667019 original size:18 final size:18
Alignment explanation
Indices: 21666998--21667032 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21666988 AAAAATCACA
21666998 TTTTTACATT-TAAAATAT
1 TTTTTA-ATTCTAAAATAT
21667016 TTTTTAATTCTAAAATA
1 TTTTTAATTCTAAAATA
21667033 CATAGTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAATTCTAAAATAT
Found at i:21669026 original size:26 final size:25
Alignment explanation
Indices: 21668916--21669034 Score: 91
Period size: 26 Copynumber: 4.7 Consensus size: 25
21668906 TTTTTGTTGG
* * * *
21668916 TTTTAAACTCTTTTACATATTGTCTA
1 TTTTAAATTTTTTTATATAATGT-TA
* * *
21668942 TATTAAATTTTTATATATACTGTTTA
1 TTTTAAATTTTTTTATATAATG-TTA
* *
21668968 TTTTTAAATTTTTATT-TATTAT-CTA
1 -TTTTAAATTTTT-TTATATAATGTTA
21668993 TTTT-AATTTTTTTATATAATGTTCA
1 TTTTAAATTTTTTTATATAATGTT-A
21669018 TTTTAAATTTTTTTATA
1 TTTTAAATTTTTTTATA
21669035 CATCATTTAC
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
22 2 0.03
23 12 0.16
24 5 0.07
25 7 0.10
26 30 0.41
27 16 0.22
28 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTAAATTTTTTTATATAATGTTA
Found at i:21669030 original size:50 final size:51
Alignment explanation
Indices: 21668933--21669029 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
21668923 CTCTTTTACA
* * *
21668933 TATTGTCTATATTAAATTTTTATATATACTGTTTATTTTTAAATTTTTATT
1 TATTATCTATATTAAATTTTTATATATAATGTTCATTTTTAAATTTTTATT
* *
21668984 TATTATCTAT-TTTAATTTTTTTATATAATGTTCA-TTTTAAATTTTT
1 TATTATCTATATTAAATTTTTATATATAATGTTCATTTTTAAATTTTT
21669030 TTATACATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 12 0.29
50 20 0.49
51 9 0.22
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (51 bp):
TATTATCTATATTAAATTTTTATATATAATGTTCATTTTTAAATTTTTATT
Found at i:21669071 original size:50 final size:49
Alignment explanation
Indices: 21669017--21669206 Score: 141
Period size: 52 Copynumber: 3.7 Consensus size: 49
21669007 TATAATGTTC
*
21669017 ATTTTAAATTTTTTTATACATCATTTACTTTAAAATTTTATGTATTATTT
1 ATTTTAAATTTTTTTATACATTATTTA-TTTAAAATTTTATGTATTATTT
** * * * *
21669067 ATTTT-AATTTTTCCCATATATTATTTATTTTAAATCTTTGTGTATATTATCT
1 ATTTTAAATTTTT-TTATACATTATTTATTTAAAAT-TTTATG--TATTATTT
* * ** * *
21669119 ATTTTAAAGTTTTATATACATTACTTGGTTTAAATTATTTTATATGTTATTT
1 ATTTTAAATTTTTTTATACATTA-TTTATTTAAA--ATTTTATGTATTATTT
* * *
21669171 ACTTTAAATTTCTTT-TACATTATTATTTTTAAAATT
1 ATTTTAAATTTTTTTATACATTATT-TATTTAAAATT
21669207 GTTTTATATT
Statistics
Matches: 107, Mismatches: 24, Indels: 19
0.71 0.16 0.13
Matches are distributed among these distances:
49 17 0.16
50 22 0.21
51 13 0.12
52 36 0.34
53 13 0.12
54 4 0.04
55 2 0.02
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.59
Consensus pattern (49 bp):
ATTTTAAATTTTTTTATACATTATTTATTTAAAATTTTATGTATTATTT
Found at i:21669125 original size:76 final size:75
Alignment explanation
Indices: 21668969--21669133 Score: 177
Period size: 76 Copynumber: 2.2 Consensus size: 75
21668959 TACTGTTTAT
* * ** * * *
21668969 TTTTAAATTTTTATTTATTATCTATTTTAATTTTTTTATATAATGTTCATTTTAAATTTTTTTAT
1 TTTTAAAATTTTATGTATTATCTATTTTAATTTTTCCATATAATATTCATTTTAAATCTTTGTAT
*
21669034 ACATCATTTA
66 ACATCATCTA
* * * * *
21669044 CTTTAAAATTTTATGTATTATTTATTTTAATTTTTCCCATATATTATTTATTTTAAATCTTTGTG
1 TTTTAAAATTTTATGTATTATCTATTTTAATTTTT-CCATATAATATTCATTTTAAATCTTTGTA
* *
21669109 TATATTATCTA
65 TACATCATCTA
*
21669120 TTTTAAAGTTTTAT
1 TTTTAAAATTTTAT
21669134 ATACATTACT
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
75 31 0.43
76 41 0.57
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (75 bp):
TTTTAAAATTTTATGTATTATCTATTTTAATTTTTCCATATAATATTCATTTTAAATCTTTGTAT
ACATCATCTA
Found at i:21669141 original size:26 final size:26
Alignment explanation
Indices: 21668932--21669181 Score: 135
Period size: 26 Copynumber: 9.8 Consensus size: 26
21668922 ACTCTTTTAC
* *
21668932 ATATTGTCTATATTAAATTTTTATAT
1 ATATTATCTATTTTAAATTTTTATAT
* * *
21668958 ATACTGTTTATTTTTAAATTTTTAT-T
1 ATATTATCTA-TTTTAAATTTTTATAT
*
21668984 -TATTATCTATTTT-AATTTTTTTAT
1 ATATTATCTATTTTAAATTTTTATAT
*
21669008 ATAATGT-TC-ATTTTAAATTTTTTTAT
1 AT-AT-TATCTATTTTAAATTTTTATAT
* * * * *
21669034 ACATCATTTACTTTAAA-ATTT-TAT
1 ATATTATCTATTTTAAATTTTTATAT
* * **
21669058 GTATTATTTATTTT-AATTTTTCCCAT
1 ATATTATCTATTTTAAATTTTT-ATAT
* * * *
21669084 ATATTATTTATTTTAAATCTTTGTGT
1 ATATTATCTATTTTAAATTTTTATAT
*
21669110 ATATTATCTATTTTAAAGTTTTATAT
1 ATATTATCTATTTTAAATTTTTATAT
*
21669136 ACATTA-CT-TGGTTTAAATTATTT-TAT
1 ATATTATCTAT--TTTAAATT-TTTATAT
* * *
21669162 ATGTTATTTACTTTAAATTT
1 ATATTATCTATTTTAAATTT
21669182 CTTTTACATT
Statistics
Matches: 173, Mismatches: 34, Indels: 35
0.71 0.14 0.14
Matches are distributed among these distances:
23 10 0.06
24 22 0.13
25 21 0.12
26 96 0.55
27 24 0.14
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (26 bp):
ATATTATCTATTTTAAATTTTTATAT
Found at i:21669222 original size:26 final size:26
Alignment explanation
Indices: 21669150--21669222 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 26
21669140 TACTTGGTTT
21669150 AAATTATTTTATATGTTATTTA-CTTTA
1 AAATTATTTTATAT-TT-TTTATCTTTA
* * * * *
21669177 AATTTCTTTTACA-TTATTATTTTTA
1 AAATTATTTTATATTTTTTATCTTTA
*
21669202 AAATTGTTTTATATTTTTTAT
1 AAATTATTTTATATTTTTTAT
21669223 ATATTACGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 6 0.17
27 10 0.29
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (26 bp):
AAATTATTTTATATTTTTTATCTTTA
Found at i:21669311 original size:26 final size:26
Alignment explanation
Indices: 21669282--21669366 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
21669272 TTTATATGTA
* *
21669282 ATTTTAAATTGTTTTATAAATTAGTT
1 ATTTTAAATTGTTTTATATATTAATT
* * *
21669308 ATTTTAGATCGTTTTATATATTATTTT
1 ATTTTAAATTGTTTTATATATTA-ATT
*
21669335 ATTTTAAATTGTTTTGTATATTAATT
1 ATTTTAAATTGTTTTATATATTAATT
21669361 -TTTTAA
1 ATTTTAA
21669367 TTATTATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
25 6 0.12
26 22 0.44
27 22 0.44
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.61
Consensus pattern (26 bp):
ATTTTAAATTGTTTTATATATTAATT
Found at i:21669348 original size:27 final size:27
Alignment explanation
Indices: 21669282--21669362 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
21669272 TTTATATGTA
* *
21669282 ATTTTAAATTGTTTTATAAATTA-GTT
1 ATTTTAAATTGTTTTATATATTATTTT
* *
21669308 ATTTTAGATCGTTTTATATATTATTTT
1 ATTTTAAATTGTTTTATATATTATTTT
*
21669335 ATTTTAAATTGTTTTGTATATTAATTTT
1 ATTTTAAATTGTTTTATATATT-ATTTT
21669363 TTAATTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
26 20 0.43
27 21 0.46
28 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (27 bp):
ATTTTAAATTGTTTTATATATTATTTT
Found at i:21673873 original size:4 final size:4
Alignment explanation
Indices: 21673864--21673904 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
21673854 AATGTATTTA
21673864 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
21673905 CGCTATGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:21675693 original size:5 final size:5
Alignment explanation
Indices: 21675683--21675711 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
21675673 CTTTCGCTTT
21675683 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
21675712 GTGATGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:21677801 original size:21 final size:19
Alignment explanation
Indices: 21677771--21677824 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
21677761 ATAACACTGC
21677771 ATAAACATATACATATATA
1 ATAAACATATACATATATA
*
21677790 TATTAAAGATATGTACATATATA
1 -A-TAAACATA--TACATATATA
21677813 ATAAACATATAC
1 ATAAACATATAC
21677825 TAATAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 1 0.03
21 14 0.48
22 1 0.03
23 10 0.34
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (19 bp):
ATAAACATATACATATATA
Found at i:21678055 original size:21 final size:21
Alignment explanation
Indices: 21677988--21678055 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
21677978 ATATACCCAT
* * *
21677988 ATAAT-AAAATATATGTACTA
1 ATAATAAAAATAAATATAATA
* *
21678008 ATATTAATAATAAATATAATA
1 ATAATAAAAATAAATATAATA
** *
21678029 GGAATAAAAATAGATATAATA
1 ATAATAAAAATAAATATAATA
21678050 ATAATA
1 ATAATA
21678056 TATACATAAT
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.32
Consensus pattern (21 bp):
ATAATAAAAATAAATATAATA
Found at i:21678064 original size:11 final size:10
Alignment explanation
Indices: 21678037--21678088 Score: 63
Period size: 9 Copynumber: 5.1 Consensus size: 10
21678027 TAGGAATAAA
21678037 AATAGATATAAT
1 AATA-ATAT-AT
21678049 AATAATATAT
1 AATAATATAT
21678059 ACATAATATAT
1 A-ATAATATAT
21678070 AA-AATATAT
1 AATAATATAT
21678079 -ATAATATAT
1 AATAATATAT
21678088 A
1 A
21678089 CATATGTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 14 0.38
10 4 0.11
11 14 0.38
12 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AATAATATAT
Found at i:21678086 original size:18 final size:18
Alignment explanation
Indices: 21677930--21678088 Score: 80
Period size: 18 Copynumber: 8.6 Consensus size: 18
21677920 AAATAATAGG
21677930 TATAATA-AT-AAATATA
1 TATAATATATAAAATATA
* *
21677946 -ATGATATATGAAA-ATA
1 TATAATATATAAAATATA
* * *
21677962 -ATACTATGTAAAGTATA
1 TATAATATATAAAATATA
21677979 TATACCCATATAATAAAATATA
1 TATA---ATAT-ATAAAATATA
*
21678001 TGTACTAATAT-TAATAATAAA
1 --TA-TAATATATAA-AATATA
* *
21678022 TATAATAGGAATAAAAATAGA
1 TATAATA--TAT-AAAATATA
*
21678043 TATAATA-ATAATATATA
1 TATAATATATAAAATATA
*
21678060 CATAATATATAAAATATA
1 TATAATATATAAAATATA
21678078 TATAATATATA
1 TATAATATATA
21678089 CATATGTTAG
Statistics
Matches: 109, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
15 5 0.05
16 13 0.12
17 18 0.17
18 29 0.27
19 2 0.02
20 3 0.03
21 21 0.19
22 14 0.13
24 2 0.02
25 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (18 bp):
TATAATATATAAAATATA
Found at i:21678283 original size:22 final size:22
Alignment explanation
Indices: 21678242--21678310 Score: 54
Period size: 24 Copynumber: 3.1 Consensus size: 22
21678232 GATATATAAC
21678242 TAATAATAT-TA-AAATGTATACA
1 TAATAATATATATAAA--TATACA
*
21678264 TAATAATATATATAAATATAATA
1 TAATAATATATATAAATAT-ACA
* *
21678287 TTAAAAATATATATACATA-ACA
1 -TAATAATATATATAAATATACA
21678309 TA
1 TA
21678311 TATGAAAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 2 0.05
22 14 0.36
23 4 0.10
24 19 0.49
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (22 bp):
TAATAATATATATAAATATACA
Found at i:21678295 original size:24 final size:24
Alignment explanation
Indices: 21678268--21678342 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
21678258 TATACATAAT
*
21678268 AATATATATAAATATAATATTAAA
1 AATATATATACATATAATATTAAA
21678292 AATATATATACATA-ACATATATGAAA
1 AATATATATACATATA-ATAT-T-AAA
* *
21678318 GATATATATATCATATAGTATTAAA
1 AATATATATA-CATATAATATTAAA
21678343 TATTTACAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
23 1 0.02
24 17 0.40
25 4 0.09
26 13 0.30
27 7 0.16
28 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
AATATATATACATATAATATTAAA
Found at i:21678302 original size:40 final size:38
Alignment explanation
Indices: 21678233--21678313 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 38
21678223 AGTATAAAAG
* *
21678233 ATATATAACTAATAATATTAAAATGTATACATAATAAT
1 ATATATAAATAATAATATTAAAATATATACATAATAAT
* *
21678271 ATATATAAAT-ATAATATTAAAA-ATATATATACATAAC
1 ATATATAAATAATAATATTAAAATATATACATA-ATAAT
21678308 ATATAT
1 ATATAT
21678314 GAAAGATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 7 0.18
37 22 0.58
38 9 0.24
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (38 bp):
ATATATAAATAATAATATTAAAATATATACATAATAAT
Found at i:21678443 original size:15 final size:15
Alignment explanation
Indices: 21678381--21678469 Score: 60
Period size: 15 Copynumber: 5.8 Consensus size: 15
21678371 AAAAAACGAC
*
21678381 TAATAATAATATTACA
1 TAATAATAATA-TAAA
*
21678397 T-A-AAT-ATATACA
1 TAATAATAATATAAA
*
21678409 TAATAAAACATATACTAA
1 TAATAATA-ATATA--AA
21678427 TAATAATAATATAAA
1 TAATAATAATATAAA
*
21678442 TAATAGTAA-ATACAA
1 TAATAATAATATA-AA
21678457 TAATAAATAATAT
1 TAAT-AATAATAT
21678470 TTAAAATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
12 5 0.08
13 4 0.07
14 8 0.14
15 17 0.29
16 10 0.17
17 7 0.12
18 8 0.14
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.33
Consensus pattern (15 bp):
TAATAATAATATAAA
Found at i:21678957 original size:2 final size:2
Alignment explanation
Indices: 21678950--21678980 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21678940 TTGAAAGAAA
21678950 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21678981 ATTCTCTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21684368 original size:11 final size:11
Alignment explanation
Indices: 21684352--21684381 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
21684342 AACATTTAAG
21684352 AAAATTTAGTT
1 AAAATTTAGTT
21684363 AAAATTTAGTT
1 AAAATTTAGTT
21684374 AAAATTTA
1 AAAATTTA
21684382 ATTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (11 bp):
AAAATTTAGTT
Found at i:21696199 original size:40 final size:40
Alignment explanation
Indices: 21696122--21696339 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
21696112 AAACCAAGTA
* *
21696122 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
21696161 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
21696201 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
21696241 CCTTCGGGACTTATCCCGAATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
21696281 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
21696321 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
21696340 TTATCATCCG
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 15 0.09
40 146 0.91
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:21700960 original size:26 final size:26
Alignment explanation
Indices: 21700929--21701036 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
21700919 TGAAATGCCC
*
21700929 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
21700955 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
21700981 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
21701007 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21701033 ATCA
1 ATCA
21701037 AATTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:21701946 original size:50 final size:49
Alignment explanation
Indices: 21701737--21702109 Score: 344
Period size: 50 Copynumber: 7.7 Consensus size: 49
21701727 CTAGGGAGTT
* *
21701737 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGGC-TTGAT-
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
* * ** * *
21701784 ATGTG-TC-AGTGTAAGACCATGTCCAGGACATGGCAT-AGCACCGATA
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
*
21701830 GATGAGAGCTAGCT-TAAGACCATGTCTGGGACATGGCATCGGC-TTGAT-
1 -ATGAGAGCTAG-TGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
* * * *
21701878 ATGTG-TC-AGTGTAAGACCATGTCCGGGACATGGCATAGGCACTGATA
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
* *
21701925 GATGAGAGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCACCGATA
1 -ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
* * * *
21701975 GATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATTGGC-CTTAATA
1 -ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-TGATA
* *
21702025 TATGAGAG-TCAGTGTAAGACCATGTTTGGGACATGGCATC-G-ACT-TTA
1 -ATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
* * *
21702072 ATGGGTGAGCCAGTGTAAGACCATGTCCGGGACATGGC
1 AT--GAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
21702110 GTTGGCACCT
Statistics
Matches: 265, Mismatches: 42, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
44 3 0.01
45 58 0.22
46 8 0.03
47 14 0.05
48 35 0.13
49 32 0.12
50 115 0.43
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (49 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
Found at i:21702031 original size:100 final size:95
Alignment explanation
Indices: 21701737--21702117 Score: 428
Period size: 94 Copynumber: 3.9 Consensus size: 95
21701727 CTAGGGAGTT
* * * *
21701737 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGGCTTGATATGTGTCAGTGTAAGACC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGATATGAGCCAGTGTAAGACC
* * *
21701802 ATGTCCAGGACATGGCA-TAGCACCGATAG
66 ATGTCCGGGACATGGCATTGGCACTGATAG
* * *
21701831 ATGAGAGCTAGCT-TAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGTCAGTGTAAGAC
1 ATGAGAGCTAG-TGTAAGACCATGTCTGGGACATGGCATCGGCTCGATATGAGCCAGTGTAAGAC
*
21701895 CATGTCCGGGACATGGCATAGGCACTGATAG
65 CATGTCCGGGACATGGCATTGGCACTGATAG
* *
21701926 ATGAGAGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCACCGATAGATGAGAGCCAGTGTA
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAT--AT--GAGCCAGTGTA
* * * *
21701991 AGACCATGTCTGGAACATGGCATTGGC-CTTAATAT
61 AGACCATGTCCGGGACATGGCATTGGCAC-TGATAG
* * ** *
21702026 ATGAGAG-TCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTTAATGGGTGAGCCAGTGTAA
1 ATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAT--ATGAGCCAGTGTAA
*
21702090 GACCATGTCCGGGACATGGCGTTGGCAC
62 GACCATGTCCGGGACATGGCATTGGCAC
21702118 CTTACCCTAT
Statistics
Matches: 249, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
94 79 0.32
95 49 0.20
96 3 0.01
98 37 0.15
99 3 0.01
100 78 0.31
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGATATGAGCCAGTGTAAGACC
ATGTCCGGGACATGGCATTGGCACTGATAG
Found at i:21705253 original size:21 final size:20
Alignment explanation
Indices: 21705227--21705271 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
21705217 GATTTTTTAA
*
21705227 AACACTTTGAAAATTACTTTG
1 AACACTTAGAAAA-TACTTTG
* *
21705248 AACACTTAGGAAATATTTTG
1 AACACTTAGAAAATACTTTG
21705268 AACA
1 AACA
21705272 AGTTCAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (20 bp):
AACACTTAGAAAATACTTTG
Found at i:21708458 original size:74 final size:73
Alignment explanation
Indices: 21708313--21708458 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 73
21708303 GGTATAAGGA
21708313 CTAAATTTGAAAAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCT
1 CTAAATTTGAAAAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCT
*
21708378 TTTTTATT
66 TCTTTATT
* * *
21708386 CTAAA-TTGTAAAAGTGGTAAAAGTTAATTTTTAATTAATTGAAGGACCAATTGAGCAATTGGCC
1 CTAAATTTG-AAAAGTGGTAAAAGTTAA-TTTTAATTAATTGAAGGACCAATTGACCAATTAGAC
21708450 CTTCTTTAT
64 CTTCTTTAT
21708459 CACGTCAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 3 0.04
73 23 0.34
74 41 0.61
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (73 bp):
CTAAATTTGAAAAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCT
TCTTTATT
Found at i:21708476 original size:74 final size:71
Alignment explanation
Indices: 21708324--21708476 Score: 182
Period size: 74 Copynumber: 2.1 Consensus size: 71
21708314 TAAATTTGAA
* *
21708324 AAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCTTTTTTATTCTA
1 AAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCTTCTTTATACTA
**
21708389 AATTGT
66 AACAGT
* * *
21708395 AAAAGTGGTAAAAGTTAATTTTTAATTAATTGAAGGACCAATTGAGCAATTGGCCCTTCTTTATC
1 --AAGTGGTAAAAGTTAA-TTTTAATTAATTGAAGGACCAATTGACCAATTAGACCTTCTTTAT-
21708460 ACGTCAAACAGT
62 AC-T-AAACAGT
21708472 -AGTGG
1 AAGTGG
21708477 ATGCAAATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
73 16 0.23
74 46 0.67
75 1 0.01
76 1 0.01
77 5 0.07
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (71 bp):
AAGTGGTAAAAGTTAATTTTAATTAATTGAAGGACCAATTGACCAATTAGACCTTCTTTATACTA
AACAGT
Found at i:21708557 original size:14 final size:14
Alignment explanation
Indices: 21708538--21708564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21708528 TTAAGATTTA
21708538 TTTAATTAATTATG
1 TTTAATTAATTATG
21708552 TTTAATTAATTAT
1 TTTAATTAATTAT
21708565 TAACTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TTTAATTAATTATG
Found at i:21709765 original size:6 final size:6
Alignment explanation
Indices: 21709754--21709780 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21709744 TAGGTTTCCA
21709754 AAATGG AAATGG AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAA
21709781 CGATTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:21711159 original size:9 final size:9
Alignment explanation
Indices: 21711145--21711169 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21711135 TTTTGTTTTT
21711145 GTTAATTCG
1 GTTAATTCG
21711154 GTTAATTCG
1 GTTAATTCG
21711163 GTTAATT
1 GTTAATT
21711170 TTTATACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (9 bp):
GTTAATTCG
Found at i:21711486 original size:26 final size:26
Alignment explanation
Indices: 21711444--21711504 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
21711434 AATTTTACCA
* *
21711444 GGGTAAAATTGTCAAAATTTTATT-G
1 GGGTAAAATCGTAAAAATTTTATTAG
21711469 GGAGTAAAATCGTAAAAATTTTATTAG
1 GG-GTAAAATCGTAAAAATTTTATTAG
21711496 GGGTAAAAT
1 GGGTAAAAT
21711505 AGGGATGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 2 0.06
26 27 0.84
27 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (26 bp):
GGGTAAAATCGTAAAAATTTTATTAG
Found at i:21713436 original size:54 final size:54
Alignment explanation
Indices: 21713368--21713472 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
21713358 CCATAATTAT
* *
21713368 CGTCCTAGTCGACTACCCCAT-TTTTATTGTCCCGATGGACTATCCCATGTTCAC
1 CGTCCTAGTCGACTA-CCCATCGTTTATTGTCCCGATGGACTATCACATGTTCAC
* * *
21713422 CGTCCTAGTGGACTACCCATCGTTTATTGTCTCGGTGGACTATCACATGTT
1 CGTCCTAGTCGACTACCCATCGTTTATTGTCCCGATGGACTATCACATGTT
21713473 TAATGTCCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (54 bp):
CGTCCTAGTCGACTACCCATCGTTTATTGTCCCGATGGACTATCACATGTTCAC
Found at i:21726370 original size:21 final size:20
Alignment explanation
Indices: 21726324--21726373 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
21726314 CTTTTTTTAG
*
21726324 AAATCATAAAAGAATCATAA
1 AAATTATAAAAGAATCATAA
* *
21726344 ATAATTATAAAAGAGTTATAGA
1 A-AATTATAAAAGAATCATA-A
21726366 AAATTATA
1 AAATTATA
21726374 TAAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (20 bp):
AAATTATAAAAGAATCATAA
Found at i:21726372 original size:10 final size:9
Alignment explanation
Indices: 21726340--21726414 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 9
21726330 TAAAAGAATC
21726340 ATAAATAATT
1 ATAAA-AATT
21726350 ATAAAAGAGTT
1 ATAAAA-A-TT
21726361 ATAGAAAATT
1 ATA-AAAATT
21726371 ATATAAAATT
1 ATA-AAAATT
*
21726381 A-ATAAAATG
1 ATA-AAAATT
21726390 ATAAAAA-T
1 ATAAAAATT
21726398 ATTAAAAATTT
1 A-TAAAAA-TT
21726409 ATAAAA
1 ATAAAA
21726415 CTAGTACTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
8 1 0.02
9 19 0.35
10 24 0.44
11 8 0.15
12 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:21726387 original size:9 final size:10
Alignment explanation
Indices: 21726346--21726414 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 10
21726336 AATCATAAAT
21726346 AATTATA-AA
1 AATTATATAA
*
21726355 AGAGTTATAGAA
1 A-A-TTATATAA
21726367 AATTATATAA
1 AATTATATAA
21726377 AATTA-ATAA
1 AATTATATAA
*
21726386 AATGATA-AA
1 AATTATATAA
21726395 AA-TAT-TAAA
1 AATTATAT-AA
21726404 AATT-TATAA
1 AATTATATAA
21726413 AA
1 AA
21726415 CTAGTACTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
8 2 0.04
9 22 0.45
10 16 0.33
11 6 0.12
12 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (10 bp):
AATTATATAA
Found at i:21726439 original size:9 final size:9
Alignment explanation
Indices: 21726425--21726478 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
21726415 CTAGTACTTC
21726425 TTTAAAAAT
1 TTTAAAAAT
21726434 TTT--AAAT
1 TTTAAAAAT
*
21726441 TTTGAAAAT
1 TTTAAAAAT
*
21726450 TTTAATAAT
1 TTTAAAAAT
*
21726459 TTCTAATAAT
1 TT-TAAAAAT
21726469 TTTAAAAAT
1 TTTAAAAAT
21726478 T
1 T
21726479 AATAAACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.18
9 23 0.59
10 9 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:21726777 original size:17 final size:17
Alignment explanation
Indices: 21726747--21726784 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21726737 TTAAAATAAT
*
21726747 TTTTTATAATTTTCACTA
1 TTTTTATAAGTTTCA-TA
21726765 TTTTTAT-AGTTTCATA
1 TTTTTATAAGTTTCATA
21726781 TTTT
1 TTTT
21726785 AATCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTATAAGTTTCATA
Found at i:21731288 original size:42 final size:42
Alignment explanation
Indices: 21731241--21731325 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
21731231 TTTACTTAGC
* *
21731241 TAAAATCTTAGTTTTTAATCTCCTAGTCAAATCAAAATATTT
1 TAAAATCTTAGTTTTTAACCACCTAGTCAAATCAAAATATTT
* *
21731283 TAAAATCTTAGTTTTTAACCACCTTGTCAAATCAATATATTT
1 TAAAATCTTAGTTTTTAACCACCTAGTCAAATCAAAATATTT
21731325 T
1 T
21731326 TCTTCATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (42 bp):
TAAAATCTTAGTTTTTAACCACCTAGTCAAATCAAAATATTT
Found at i:21737539 original size:15 final size:16
Alignment explanation
Indices: 21737521--21737550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21737511 ATTTGATCAT
21737521 ATTTTA-TTTAATAAG
1 ATTTTATTTTAATAAG
21737536 ATTTTATTTTAATAA
1 ATTTTATTTTAATAA
21737551 ATTAATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTATTTTAATAAG
Found at i:21743568 original size:40 final size:40
Alignment explanation
Indices: 21743523--21743739 Score: 226
Period size: 40 Copynumber: 5.5 Consensus size: 40
21743513 TATGCGAATG
* * *
21743523 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
21743563 ATATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAG-TGACT
* * *
21743603 ATATCCGGGCTAAGACTCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
21743643 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * * **
21743683 ATATTCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
21743722 ATATCC-GGCTAAATCCCG
1 ATATCCGGGCTAAGTCCCG
21743740 GAGATACTTG
Statistics
Matches: 145, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
38 10 0.07
39 15 0.10
40 117 0.81
41 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:21762171 original size:20 final size:21
Alignment explanation
Indices: 21762146--21762185 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21762136 CGCTTAAAGC
21762146 AGGGC-ACATGCCAGTGTGGA
1 AGGGCAACATGCCAGTGTGGA
*
21762166 AGGGCAACATGCCTGTGTGG
1 AGGGCAACATGCCAGTGTGG
21762186 CCACTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.20, G:0.40, T:0.17
Consensus pattern (21 bp):
AGGGCAACATGCCAGTGTGGA
Found at i:21763453 original size:49 final size:49
Alignment explanation
Indices: 21763374--21763497 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
21763364 AGATATCGAC
* *
21763374 GCCATGTCCCAGACATGGTCTTACACTGGCTTTGATATAGCGAG-GCCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGC-AGTGCCGAT
* * * * *
21763424 GCCATGTCCTAGACAGGTCTTATACTGGCTCTCATCTATCAGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCAGTGCCGAT
*
21763473 GTCATGTCCCAGACAGGTCTTACAC
1 GCCATGTCCCAGACAGGTCTTACAC
21763498 AAGCTTGTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.03
49 47 0.75
50 14 0.22
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCAGTGCCGAT
Found at i:21763553 original size:98 final size:95
Alignment explanation
Indices: 21763376--21763592 Score: 213
Period size: 98 Copynumber: 2.2 Consensus size: 95
21763366 ATATCGACGC
** * * * *
21763376 CATGTCCCAGACATGGTCTTACACTGGCTTTGATATAGCGAGGCCGATGCCATGTCCTAGACAGG
1 CATGTCCCAGACA-GGTCTTACACAAGCTTTGATATAGCAAGGCCGATGCCATGTCCCAAAAAGG
* * * **
21763441 TCTTATACTGGCTCTCATCTATCAGTGTCGATG
65 TCTTACACTAGCTCT--TCTATCAATACCGATG
* *
21763474 TCATGTCCCAGACAGGTCTTACACAAGC-TTG-TCTACCGCAAGGCTGATGCCATGTCCCAAAAA
1 -CATGTCCCAGACAGGTCTTACACAAGCTTTGATATA--GCAAGGCCGATGCCATGTCCCAAAAA
* * *
21763537 TGTCTTACACTAGCTCTTGTCTCAATACCGATG
63 GGTCTTACACTAGCTCTTCTATCAATACCGATG
*
21763570 CATGTCCCAGACATGTCTTACAC
1 CATGTCCCAGACAGGTCTTACAC
21763593 TAGCACACAT
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
95 22 0.22
96 14 0.14
97 3 0.03
98 47 0.47
99 13 0.13
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (95 bp):
CATGTCCCAGACAGGTCTTACACAAGCTTTGATATAGCAAGGCCGATGCCATGTCCCAAAAAGGT
CTTACACTAGCTCTTCTATCAATACCGATG
Found at i:21769272 original size:16 final size:16
Alignment explanation
Indices: 21769251--21769286 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
21769241 GATGAGGCAT
21769251 CGCATGTGGAGCTAAA
1 CGCATGTGGAGCTAAA
21769267 CGCATGTGGAGCTAAA
1 CGCATGTGGAGCTAAA
21769283 CGCA
1 CGCA
21769287 GTTTGCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.17
Consensus pattern (16 bp):
CGCATGTGGAGCTAAA
Found at i:21779234 original size:21 final size:21
Alignment explanation
Indices: 21779208--21779249 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21779198 GTAATGAGTG
21779208 AGGTTCACAAGAGTAGGTACT
1 AGGTTCACAAGAGTAGGTACT
* *
21779229 AGGTTCGCAAGAGTGGGTACT
1 AGGTTCACAAGAGTAGGTACT
21779250 TGAAATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (21 bp):
AGGTTCACAAGAGTAGGTACT
Found at i:21790346 original size:48 final size:48
Alignment explanation
Indices: 21790275--21790507 Score: 210
Period size: 48 Copynumber: 4.9 Consensus size: 48
21790265 TAAGGATATG
*
21790275 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAAA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
* * *
21790323 TGTGATCCCATGTAAGACAATGTCTTGGACATGGCATTGGCATTAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
* * * * * * * * *
21790371 TGAGA-CATCGTGTAAGACGATAAT-TGGG-C-T---ATCGACTTCGATA
1 TGTGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCAATA
* * *
21790414 TGCATAATCCCATGAAAGACCATGTCCGGGACATGGCATTGGCATCAATA
1 TG--TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
* * *
21790464 TGTGATCCCATGTAAGACCATTTTTGGGATATGGCATTGGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
21790508 CTACTATGTA
Statistics
Matches: 141, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
43 10 0.07
44 1 0.01
45 14 0.10
46 3 0.02
47 3 0.02
48 98 0.70
49 1 0.01
50 11 0.08
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATA
Found at i:21797931 original size:26 final size:26
Alignment explanation
Indices: 21797883--21797932 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
21797873 ACATATTTTC
*
21797883 TCAAAATTTTACAATGGGCAAAATTA
1 TCAAAATTTTACAAGGGGCAAAATTA
* * *
21797909 TCAAAATTTTGCTAGGGGTAAAAT
1 TCAAAATTTTACAAGGGGCAAAAT
21797933 AGGGATGAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACAAGGGGCAAAATTA
Found at i:21800047 original size:27 final size:27
Alignment explanation
Indices: 21800007--21800064 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
21799997 TAAACTTGAT
* *
21800007 ACTTTTTTTTTCTAATTTGGTACGTAA
1 ACTTTTTTTGTCTAATTTGGTACCTAA
21800034 ACTTTTTTTGTCTAATTTGGTACCTAA
1 ACTTTTTTTGTCTAATTTGGTACCTAA
21800061 ACTT
1 ACTT
21800065 GTCAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (27 bp):
ACTTTTTTTGTCTAATTTGGTACCTAA
Found at i:21800823 original size:6 final size:6
Alignment explanation
Indices: 21800812--21800838 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21800802 ACTTAATCCT
21800812 TAATTC TAATTC TAATTC TAATTC TAA
1 TAATTC TAATTC TAATTC TAATTC TAA
21800839 AGTAGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATTC
Found at i:21801201 original size:25 final size:25
Alignment explanation
Indices: 21801171--21801257 Score: 120
Period size: 25 Copynumber: 3.5 Consensus size: 25
21801161 TAGGGATTTT
* *
21801171 ATATGCGAGCCTGTATGCTAGTATA
1 ATATGCGAGCCTGTATGTTAGTGTA
* *
21801196 ATATGCAAGCATGTATGTTAGTGTA
1 ATATGCGAGCCTGTATGTTAGTGTA
* *
21801221 ATATGCGAGCCTATCTGTTAGTGTA
1 ATATGCGAGCCTGTATGTTAGTGTA
21801246 ATATGCGAGCCT
1 ATATGCGAGCCT
21801258 ATTTGTAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (25 bp):
ATATGCGAGCCTGTATGTTAGTGTA
Found at i:21801559 original size:14 final size:14
Alignment explanation
Indices: 21801542--21801571 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21801532 GCCCCTATGA
21801542 GCGAACACCTTAGT
1 GCGAACACCTTAGT
*
21801556 GCGAACTCCTTAGT
1 GCGAACACCTTAGT
21801570 GC
1 GC
21801572 AAGCCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (14 bp):
GCGAACACCTTAGT
Found at i:21801742 original size:16 final size:17
Alignment explanation
Indices: 21801723--21801755 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21801713 CTTGTAGGTA
*
21801723 CGAACCATCT-TGTATG
1 CGAACCACCTGTGTATG
21801739 CGAACCACCTGTGTATG
1 CGAACCACCTGTGTATG
21801756 AGAGCCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (17 bp):
CGAACCACCTGTGTATG
Found at i:21807391 original size:47 final size:47
Alignment explanation
Indices: 21807320--21807439 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 47
21807310 TAAGGTGCCA
** *
21807320 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAGATG
1 ATGCCATGTCCCAGACAT-GTCTTACACTAACT-ATCATCTCGAAGACG
* *
21807367 ATGCCATGTCCCAGACATGATCTTACACTAACTATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATG-TCTTACACTAACTATCATCTCGAAGACG
21807415 ATG-CATGTCCCAGACATGTCTTACA
1 ATGCCATGTCCCAGACATGTCTTACA
21807440 TTCGCTTACG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
46 10 0.15
47 49 0.75
48 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGTCTTACACTAACTATCATCTCGAAGACG
Found at i:21807576 original size:140 final size:141
Alignment explanation
Indices: 21807316--21807579 Score: 333
Period size: 140 Copynumber: 1.9 Consensus size: 141
21807306 TGGGTAAGGT
*
21807316 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGATGATGCCATGTCCCAG
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTGCCTCATATCTCAAGATGATGCCATGTCCCAG
* * *
21807381 ACATGATCTTACACTAACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACATTCGCT
66 ACATGATCTTACACTAACTATCATATCATAGCCGATGCATGTCCCAAACATGTCTTACATTCGCT
21807446 TACGCCTTGGG
131 TACGCCTTGGG
* *
21807457 GCCAATG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCAT-T-TCAATG-TAGTTGCCATGTG
1 GCCAATGCCATGTCCCAGACATGGTCTTACACT-G-CCTCATATCTCAA-GAT-GATGCCATGTC
* * ** * *
21807517 CTAGACATGGTCTTACACTGGCTCTCATAAT-ATGGCCGATGCATGTCCCAAACATGTCTTACA
62 CCAGACATGATCTTACACTAACTATCAT-ATCATAGCCGATGCATGTCCCAAACATGTCTTACA
21807580 GTAGCTCACA
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
139 15 0.14
140 78 0.74
141 13 0.12
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (141 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACACTGCCTCATATCTCAAGATGATGCCATGTCCCAG
ACATGATCTTACACTAACTATCATATCATAGCCGATGCATGTCCCAAACATGTCTTACATTCGCT
TACGCCTTGGG
Found at i:21814940 original size:47 final size:44
Alignment explanation
Indices: 21814875--21815176 Score: 178
Period size: 45 Copynumber: 6.5 Consensus size: 44
21814865 GTGCCAATGC
* * *
21814875 CATGTTCCAGACATGGTCTTACACTGGTTCATATCTCAAGTCGATG
1 CATGTCCCAAACAT-GTCTTACACTGGTT-ATATCTCAAGCCGATG
* * ** ** *
21814921 CCATGTCCCAGACATGGTCTTACAGTGACTATTATCTTGTAGCTGATG
1 -CATGTCCCAAACAT-GTCTTACACTGGTTA-TATC-TCAAGCCGATG
**
21814969 CATGTCCCAAACATGTCTTACACTGGCTTA-CGCTCAAGGCCGATG
1 CATGTCCCAAACATGTCTTACACTGG-TTATATCTCAA-GCCGATG
** *
21815014 CATGTCCCAAACATGTCTTACACTGGCTTA-CGCTCGAGGCCGATG
1 CATGTCCCAAACATGTCTTACACTGG-TTATATCTC-AAGCCGATG
* *** * *
21815059 CATGTCCCAAACATGTCTTACACTAGCCCTCGTCTCAATGTCGATG
1 CATGTCCCAAACATGTCTTACACTGGTTAT-ATCTCAA-GCCGATG
* * * * * *
21815105 CCATGTCTCAAACATGGTCTTACACTAGTTCTCATAAT-ATGGCTGATG
1 -CATGTCCCAAACAT-GTCTTACACTGGTTAT-AT-CTCA-AGCCGATG
*
21815153 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAAACATGTCTTACACT
21815177 AGCTTACACA
Statistics
Matches: 207, Mismatches: 36, Indels: 25
0.77 0.13 0.09
Matches are distributed among these distances:
44 2 0.01
45 75 0.36
46 31 0.15
47 69 0.33
48 29 0.14
49 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (44 bp):
CATGTCCCAAACATGTCTTACACTGGTTATATCTCAAGCCGATG
Found at i:21815023 original size:45 final size:45
Alignment explanation
Indices: 21814965--21815183 Score: 246
Period size: 45 Copynumber: 4.8 Consensus size: 45
21814955 TCTTGTAGCT
21814965 GATGCATGTCCCAAACATGTCTTACACTGGCTTACGCTCAAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTTACGCTCAAGGCC
*
21815010 GATGCATGTCCCAAACATGTCTTACACTGGCTTACGCTCGAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTTACGCTCAAGGCC
* * * *
21815055 GATGCATGTCCCAAACATGTCTTACACTAGCCCT-CGTCTCAATGTC
1 GATGCATGTCCCAAACATGTCTTACACT-GGCTTACG-CTCAAGGCC
* * * * *
21815101 GATGCCATGTCTCAAACATGGTCTTACACTAG-TT-CTCATAATATGGCT
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACGC-TCA-A-GGCC
* *
21815149 GATGCATGTCCCAGACATGTCTTACACTAGCTTAC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTTAC
21815184 ACAAGTGACC
Statistics
Matches: 148, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
45 75 0.51
46 29 0.20
47 28 0.19
48 16 0.11
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCTTACGCTCAAGGCC
Found at i:21817416 original size:40 final size:40
Alignment explanation
Indices: 21817365--21817949 Score: 965
Period size: 40 Copynumber: 14.6 Consensus size: 40
21817355 CATTTGAATG
21817365 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
21817405 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
21817445 ATATCCGGGCTAAGACTCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
21817485 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
21817525 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
21817565 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
21817605 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
21817645 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
21817685 ATATCCGGGATAAGACCCGAAGGCATTTGTGTGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
21817725 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
21817765 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
21817805 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
21817845 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * * * *
21817885 ATACCCGGGTTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
21817925 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
21817950 ATTGAGCTTG
Statistics
Matches: 520, Mismatches: 23, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 2 0.00
40 517 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:21824819 original size:14 final size:13
Alignment explanation
Indices: 21824796--21824829 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
21824786 TTGTTTCACT
*
21824796 AAAAATATTTTTG
1 AAAAATATTTTTA
21824809 AAAAATGATTTTTA
1 AAAAAT-ATTTTTA
21824823 AAAAATA
1 AAAAATA
21824830 AGTTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
AAAAATATTTTTA
Found at i:21825127 original size:17 final size:17
Alignment explanation
Indices: 21825105--21825141 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21825095 AATCGAAATT
21825105 TATTTTATAATAATAAA
1 TATTTTATAATAATAAA
*
21825122 TATTTTGTAATAATAAA
1 TATTTTATAATAATAAA
21825139 TAT
1 TAT
21825142 CATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTTATAATAATAAA
Found at i:21825700 original size:15 final size:15
Alignment explanation
Indices: 21825680--21825731 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
21825670 ACTACAAAAC
21825680 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
21825695 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
21825714 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
21825729 ATT
1 ATT
21825732 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:21825795 original size:16 final size:16
Alignment explanation
Indices: 21825764--21825797 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
21825754 ATATAAAGAA
21825764 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
21825780 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
21825796 TA
1 TA
21825798 ATCAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:21825862 original size:16 final size:16
Alignment explanation
Indices: 21825833--21825863 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21825823 AATTTATTAA
21825833 AATAATTAATTATATC
1 AATAATTAATTATATC
21825849 AATAATTAATTATAT
1 AATAATTAATTATAT
21825864 GATTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATTAATTATATC
Found at i:21825968 original size:5 final size:6
Alignment explanation
Indices: 21825952--21825976 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21825942 TTAAATATTT
21825952 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
21825977 TTATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:21826480 original size:18 final size:17
Alignment explanation
Indices: 21826457--21826498 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
21826447 TCAAAAATAT
21826457 ATTTTT-ATAATTCTTATA
1 ATTTTTAATAATT-TT-TA
21826475 ATTTTTTAATAATTTTTA
1 A-TTTTTAATAATTTTTA
21826493 ATTTTT
1 ATTTTT
21826499 TGAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 7 0.32
20 6 0.27
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Found at i:21826499 original size:18 final size:19
Alignment explanation
Indices: 21826458--21826499 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
21826448 CAAAAATATA
21826458 TTTTTATAATTCTTATAAT
1 TTTTTATAATTCTTATAAT
21826477 TTTTTAATAATT-TT-TAAT
1 TTTTT-ATAATTCTTATAAT
21826495 TTTTT
1 TTTTT
21826500 GAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTATAATTCTTATAAT
Found at i:21826642 original size:17 final size:19
Alignment explanation
Indices: 21826620--21826663 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
21826610 TAATACAAGT
21826620 TTAAAAGTTAAA-AAA-AA
1 TTAAAAGTTAAATAAAGAA
* *
21826637 TTAAAAATTAAATAAAGAG
1 TTAAAAGTTAAATAAAGAA
21826656 TTAAAAGT
1 TTAAAAGT
21826664 GATTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
TTAAAAGTTAAATAAAGAA
Found at i:21831061 original size:17 final size:15
Alignment explanation
Indices: 21831027--21831070 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
21831017 TTTAATTTAT
21831027 AATA-TAAATTTAAA
1 AATATTAAATTTAAA
21831041 AATATTAAATTGTATAA
1 AATATTAAATT-TA-AA
21831058 AATATTCAAATTT
1 AATATT-AAATTT
21831071 TTTATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 6 0.23
16 2 0.08
17 9 0.35
18 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATATTAAATTTAAA
Found at i:21832759 original size:42 final size:42
Alignment explanation
Indices: 21832712--21832796 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
21832702 TTGATAACCT
21832712 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
1 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
*
21832754 CTGTTAGCATTGTTTTCTTCCTCCTTAGTTGCTTGTCTTGAC
1 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
21832796 C
1 C
21832797 AGGGGCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.09, C:0.26, G:0.16, T:0.48
Consensus pattern (42 bp):
CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
Found at i:21836201 original size:30 final size:29
Alignment explanation
Indices: 21836137--21836202 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
21836127 AATTGAATCA
**
21836137 TCCATCAAAATACAAACATAAATAAAGTG
1 TCCATCAAAATACAAACATAAATAAACCG
*
21836166 TCCATCAAAATAC-AACTATCAATTAAACCG
1 TCCATCAAAATACAAAC-AT-AAATAAACCG
21836196 TCCATCA
1 TCCATCA
21836203 TTGAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 15 0.47
30 14 0.44
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.23
Consensus pattern (29 bp):
TCCATCAAAATACAAACATAAATAAACCG
Found at i:21837128 original size:13 final size:13
Alignment explanation
Indices: 21837110--21837136 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21837100 ATAGTGCTAA
21837110 ACATAACATACAT
1 ACATAACATACAT
21837123 ACATAACATACAT
1 ACATAACATACAT
21837136 A
1 A
21837137 AACATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:21837198 original size:20 final size:19
Alignment explanation
Indices: 21837133--21837207 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
21837123 ACATAACATA
21837133 CATAAACATTAATAAACAGT
1 CATAAACA-TAATAAACAGT
* *
21837153 GATATACCACATAATATACA-T
1 CATA-A--ACATAATAAACAGT
21837174 ACATAAACATTAATAAACAGT
1 -CATAAACA-TAATAAACAGT
*
21837195 CATACACATAATA
1 CATAAACATAATA
21837208 GTAATATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 18 0.41
21 4 0.09
22 11 0.25
23 3 0.07
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.25
Consensus pattern (19 bp):
CATAAACATAATAAACAGT
Found at i:21837226 original size:12 final size:13
Alignment explanation
Indices: 21837209--21837592 Score: 177
Period size: 12 Copynumber: 28.8 Consensus size: 13
21837199 CACATAATAG
21837209 TAATATACA-ACA
1 TAATATACATACA
21837221 TAATATACATACA
1 TAATATACATACA
* *
21837234 TTAAACATGCCATACA
1 -T-AATAT-ACATACA
* *
21837250 TAGTATACAAACA
1 TAATATACATACA
* *
21837263 TAACAGTAAATAACACA
1 TAATA-TACAT---ACA
* *
21837280 TAACAAACATACA
1 TAATATACATACA
21837293 -AATATACATACA
1 TAATATACATACA
21837305 TAATATACATAACA
1 TAATATACAT-ACA
*
21837319 TTATATAACATAACA
1 TAATAT-ACAT-ACA
*
21837334 TAACATACATACA
1 TAATATACATACA
*
21837347 -AATATACAAACA
1 TAATATACATACA
*
21837359 TAACAGTA-A-ACA
1 TAATA-TACATACA
* *
21837371 TAACATACATATA
1 TAATATACATACA
* *
21837384 TAACAAAACATAACA
1 TAA-TATACAT-ACA
*
21837399 TAACATACATACA
1 TAATATACATACA
*
21837412 -AATATACAAACA
1 TAATATACATACA
*
21837424 TAAAAGTA-A-ACA
1 TAATA-TACATACA
*
21837436 TAACATACATACA
1 TAATATACATACA
*
21837449 TAACAGTACATAACA
1 TAATA-TACAT-ACA
*
21837464 TAACATACATACA
1 TAATATACATACA
*
21837477 -AATATACAAACA
1 TAATATACATACA
*
21837489 TAACATTA-A-ACA
1 TAATA-TACATACA
* *
21837501 TAACATACATGCA
1 TAATATACATACA
*
21837514 TAACAGTACATAACA
1 TAATA-TACAT-ACA
21837529 TACATA-ACATA-A
1 TA-ATATACATACA
* *
21837541 TAGTAAACATAACA
1 TAATATACAT-ACA
*
21837555 T-ACATACATAACAA
1 TAATATACAT-AC-A
21837569 TACATA-ACATACA
1 TA-ATATACATACA
21837582 TAATATACATA
1 TAATATACATA
21837593 ACAGTTTAAA
Statistics
Matches: 294, Mismatches: 41, Indels: 73
0.72 0.10 0.18
Matches are distributed among these distances:
11 8 0.03
12 85 0.29
13 82 0.28
14 60 0.20
15 38 0.13
16 13 0.04
17 8 0.03
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.23
Consensus pattern (13 bp):
TAATATACATACA
Found at i:21837302 original size:51 final size:52
Alignment explanation
Indices: 21837260--21837474 Score: 146
Period size: 51 Copynumber: 4.1 Consensus size: 52
21837250 TAGTATACAA
21837260 ACATAACAGTAAATAAC-ACATAACAAACATACAAATATACATACATAATAT
1 ACATAACAGTAAATAACAACATAACAAACATACAAATATACATACATAATAT
* * * * *
21837311 ACATAACATTATATAACATAACATAACATACATACAAATATACAAACATAACAGT
1 ACATAACAGTAAATAAC--AACATAACAAACATACAAATATACATACATAATA-T
* *
21837366 --A-AACA-TAACAT-ACATATATAACAAAACATAACATAACATACATACA-AATAT
1 ACATAACAGTAA-ATAACA-ACATAAC-AAACAT-ACA-AATATACATACATAATAT
* * *
21837417 ACA-AACA-TAAA-AGTA-AACATAACATACATACATAACAGTACATAACATAACAT
1 ACATAACAGTAAATA--ACAACATAACAAACATACA-AATA-TACAT-ACATAATAT
21837470 ACATA
1 ACATA
21837475 CAAATATACA
Statistics
Matches: 132, Mismatches: 14, Indels: 33
0.74 0.08 0.18
Matches are distributed among these distances:
49 1 0.01
50 14 0.11
51 35 0.27
52 22 0.17
53 27 0.20
54 32 0.24
55 1 0.01
ACGTcount: A:0.59, C:0.18, G:0.02, T:0.21
Consensus pattern (52 bp):
ACATAACAGTAAATAACAACATAACAAACATACAAATATACATACATAATAT
Found at i:21837314 original size:25 final size:26
Alignment explanation
Indices: 21837277--21837583 Score: 215
Period size: 25 Copynumber: 11.5 Consensus size: 26
21837267 AGTAAATAAC
*
21837277 ACATAACAAACATACA-AATATACAT
1 ACATAACATACATACATAATATACAT
* *
21837302 ACATAATATACATAACATTATATAACAT
1 ACATAACATACAT-ACATAATAT-ACAT
*
21837330 AACATAACATACATACA-AATATACAA
1 -ACATAACATACATACATAATATACAT
*
21837356 ACATAACAGTA-A-ACATAACATACAT
1 ACATAACA-TACATACATAATATACAT
* * *
21837381 ATATAACAAAACATAACATAACATACAT
1 ACATAAC-ATACAT-ACATAATATACAT
* * *
21837409 ACA-AATATACAAACATAAAAGTA-A-
1 ACATAACATACATACATAATA-TACAT
*
21837433 ACATAACATACATACATAACAGTACAT
1 ACATAACATACATACATAATA-TACAT
*
21837460 AACATAACATACATACA-AATATACAA
1 -ACATAACATACATACATAATATACAT
*
21837486 ACATAACATTA-A-ACATAACATACAT
1 ACATAACA-TACATACATAATATACAT
*
21837511 GCATAACAGTACATAACATACATA-ACAT
1 ACATAACA-TACAT-ACATA-ATATACAT
*
21837539 AATAGTAAACATAACATACATACATA-ACAAT
1 -ACA-T-AACAT-ACATACATA-ATATAC-AT
21837570 ACATAACATACATA
1 ACATAACATACATA
21837584 ATATACATAA
Statistics
Matches: 228, Mismatches: 28, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
24 9 0.04
25 84 0.37
26 24 0.11
27 18 0.08
28 52 0.23
29 16 0.07
30 15 0.07
31 10 0.04
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.22
Consensus pattern (26 bp):
ACATAACATACATACATAATATACAT
Found at i:21837328 original size:10 final size:10
Alignment explanation
Indices: 21837259--21837595 Score: 191
Period size: 9 Copynumber: 33.9 Consensus size: 10
21837249 ATAGTATACA
21837259 AACATAACAGT
1 AACATAACA-T
21837270 AA-ATAACACAT
1 AACAT-A-ACAT
21837281 AACA-AACAT
1 AACATAACAT
*
21837290 ACAAATATACAT
1 A-ACATA-ACAT
*
21837302 -ACATAATAT
1 AACATAACAT
21837311 -ACATAACAT
1 AACATAACAT
* *
21837320 TATATAACAT
1 AACATAACAT
21837330 AACATAACAT
1 AACATAACAT
*
21837340 -ACATACAAAT
1 AACATA-ACAT
21837350 ATACA-AACAT
1 A-ACATAACAT
21837360 AACAGTAAACAT
1 AACA-T-AACAT
21837372 AACAT-ACAT
1 AACATAACAT
* *
21837381 -ATATAACAA
1 AACATAACAT
21837390 AACATAACAT
1 AACATAACAT
21837400 AACAT-ACAT
1 AACATAACAT
*
21837409 ACAAATATACA-
1 A-ACATA-ACAT
*
21837420 AACATAAAAGT
1 AACATAACA-T
21837431 AAACATAACAT
1 -AACATAACAT
21837442 -ACAT-ACAT
1 AACATAACAT
21837450 AACAGT-ACAT
1 AACA-TAACAT
21837460 AACATAACAT
1 AACATAACAT
*
21837470 -ACATACAAAT
1 AACATA-ACAT
21837480 ATACA-AACAT
1 A-ACATAACAT
21837490 AACATTAAACAT
1 AACA-T-AACAT
21837502 AACAT-ACAT
1 AACATAACAT
*
21837511 -GCATAACAGT
1 AACATAACA-T
21837521 -ACATAACAT
1 AACATAACAT
21837530 -ACATAACAT
1 AACATAACAT
*
21837539 AATAGTAAACAT
1 AACA-T-AACAT
21837551 AACAT-ACAT
1 AACATAACAT
21837560 -ACATAACA-
1 AACATAACAT
21837568 ATACATAACAT
1 A-ACATAACAT
*
21837579 -ACATAATAT
1 AACATAACAT
21837588 -ACATAACA
1 AACATAACA
21837596 GTTTAAAAAC
Statistics
Matches: 262, Mismatches: 25, Indels: 80
0.71 0.07 0.22
Matches are distributed among these distances:
8 14 0.05
9 93 0.35
10 89 0.34
11 15 0.06
12 51 0.19
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (10 bp):
AACATAACAT
Found at i:21837331 original size:15 final size:14
Alignment explanation
Indices: 21837161--21837595 Score: 163
Period size: 13 Copynumber: 32.2 Consensus size: 14
21837151 GTGATATACC
21837161 ACATAATATACAT-
1 ACATAATATACATA
*
21837174 ACATAAACATTA-ATAA
1 ACAT-AATA-TACAT-A
* *
21837190 ACAGTCATACACATA
1 ACA-TAATATACATA
*
21837205 ATAGTAATATAC--A
1 ACA-TAATATACATA
21837218 ACATAATATACAT-
1 ACATAATATACATA
* *
21837231 ACATTAAACATGCCAT-
1 ACA-T-AATAT-ACATA
*
21837247 ACATAGTATACA-A
1 ACATAATATACATA
* *
21837260 ACATAACAGTAAATAA
1 ACATAATA-TACAT-A
* *
21837276 CACATAACAAACAT-
1 -ACATAATATACATA
21837290 ACA-AATATACAT-
1 ACATAATATACATA
21837302 ACATAATATACATA
1 ACATAATATACATA
*
21837316 ACATTATATAACATA
1 ACATAATAT-ACATA
*
21837331 ACATAACATACAT-
1 ACATAATATACATA
21837344 ACA-AATATACA-A
1 ACATAATATACATA
*
21837356 ACATAACAGTAAACATA
1 ACAT-A-A-TATACATA
21837373 ACATACATAT--ATA
1 ACATA-ATATACATA
21837386 AC--AA-A-ACATA
1 ACATAATATACATA
*
21837396 ACATAACATACAT-
1 ACATAATATACATA
21837409 ACA-AATATACA-A
1 ACATAATATACATA
*
21837421 ACATAA-A-A-GTAA
1 ACATAATATACAT-A
*
21837433 ACATAACATACAT-
1 ACATAATATACATA
*
21837446 ACATAACAGTACATA
1 ACATAATA-TACATA
*
21837461 ACATAACATACAT-
1 ACATAATATACATA
21837474 ACA-AATATACA-A
1 ACATAATATACATA
* *
21837486 ACATAACAT-TA-A
1 ACATAATATACATA
*
21837498 ACATAACATACAT-
1 ACATAATATACATA
* *
21837511 GCATAACAGTACATA
1 ACATAATA-TACATA
21837526 ACATACATA-ACAT-
1 ACATA-ATATACATA
* *
21837539 A-ATAGTAAACATA
1 ACATAATATACATA
*
21837552 ACAT-ACATACATA
1 ACATAATATACATA
21837565 ACAATACATA-ACAT-
1 AC-ATA-ATATACATA
21837579 ACATAATATACATA
1 ACATAATATACATA
21837593 ACA
1 ACA
21837596 GTTTAAAAAC
Statistics
Matches: 326, Mismatches: 41, Indels: 109
0.68 0.09 0.23
Matches are distributed among these distances:
9 1 0.00
10 6 0.02
11 4 0.01
12 79 0.24
13 85 0.26
14 58 0.18
15 50 0.15
16 29 0.09
17 14 0.04
ACGTcount: A:0.57, C:0.18, G:0.03, T:0.23
Consensus pattern (14 bp):
ACATAATATACATA
Found at i:21837422 original size:65 final size:65
Alignment explanation
Indices: 21837302--21837539 Score: 352
Period size: 65 Copynumber: 3.6 Consensus size: 65
21837292 AAATATACAT
* * * *
21837302 ACATAATATACATAACATTATATAACATAACATAACATACATACAAATATACAAACATAACAGTA
1 ACATAACATACAT-ACATAACAGAACATAACATAACATACATACAAATATACAAACATAACAGTA
21837367 A
65 A
* * *
21837368 ACATAACATACATATATAACAAAACATAACATAACATACATACAAATATACAAACATAAAAGTAA
1 ACATAACATACATACATAACAGAACATAACATAACATACATACAAATATACAAACATAACAGTAA
* *
21837433 ACATAACATACATACATAACAGTACATAACATAACATACATACAAATATACAAACATAACATTAA
1 ACATAACATACATACATAACAGAACATAACATAACATACATACAAATATACAAACATAACAGTAA
* *
21837498 ACATAACATACATGCATAACAGTACATAACAT-ACATAACATA
1 ACATAACATACATACATAACAGAACATAACATAACAT-ACATA
21837540 ATAGTAAACA
Statistics
Matches: 159, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
64 4 0.03
65 143 0.90
66 12 0.08
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (65 bp):
ACATAACATACATACATAACAGAACATAACATAACATACATACAAATATACAAACATAACAGTAA
Found at i:21837548 original size:49 final size:49
Alignment explanation
Indices: 21837296--21837638 Score: 116
Period size: 49 Copynumber: 7.1 Consensus size: 49
21837286 ACATACAAAT
* *
21837296 ATACATACATAA-TATACATAACATTATATAACATAACA-T-AACAT-AC
1 ATACATACATAACAATACATAACA-TACATAACATAACAGTAAACATAAC
* *
21837342 ATACA-A-ATATACAA-ACATAACAGTAAACATAACAT-ACATATATAACAAAAC
1 ATACATACATA-ACAATACATAACA-T--ACATAACATAACA-GTA-AACATAAC
* *
21837393 ATAACATAACAT-AC-ATACA-AATATACA-AACATAAAAGTAAACATAAC
1 AT-ACAT-ACATAACAATACATAACATACATAACATAACAGTAAACATAAC
* * *
21837440 ATACATACATAACAGTACATAACATAACAT-ACAT-ACAAATATACA-AAC
1 ATACATACATAACAATACATAACAT-ACATAACATAAC-AGTAAACATAAC
* *
21837488 ATAACATTAAACATAACATACATGCATAACAGTACATAACAT-ACA-T-AACATAAT
1 AT-ACA-T--ACATAAC--A-ATACATAACA-TACATAACATAACAGTAAACATAAC
*
21837542 AGTA-A-ACATAAC-ATACAT-ACATAACA-ATACATAACA-T--ACATAAT
1 A-TACATACATAACAATACATAACAT-ACATA-ACATAACAGTAAACATAAC
*
21837586 ATACATAACAGTTTAA-AA-ACATAACATACAT-ACATAAACAGTAAAGA-AAC
1 ATACAT-ACA---TAACAATACATAACATACATAACAT-AACAGTAAACATAAC
21837636 ATA
1 ATA
21837639 AATAACAGAC
Statistics
Matches: 229, Mismatches: 20, Indels: 92
0.67 0.06 0.27
Matches are distributed among these distances:
43 4 0.02
44 22 0.10
45 24 0.10
46 18 0.08
47 25 0.11
48 29 0.13
49 37 0.16
50 10 0.04
51 7 0.03
52 14 0.06
53 9 0.04
54 7 0.03
55 16 0.07
56 7 0.03
ACGTcount: A:0.57, C:0.18, G:0.03, T:0.22
Consensus pattern (49 bp):
ATACATACATAACAATACATAACATACATAACATAACAGTAAACATAAC
Found at i:21837613 original size:5 final size:5
Alignment explanation
Indices: 21837259--21837595 Score: 191
Period size: 5 Copynumber: 67.8 Consensus size: 5
21837249 ATAGTATACA
*
21837259 AACAT AACAGT AA-AT AACACAT AACA- AACAT ACAAAT ATACAT -ACAT
1 AACAT AACA-T AACAT -A-ACAT AACAT AACAT A-ACAT A-ACAT AACAT
* * * *
21837306 AATAT -ACAT AACAT TATAT AACAT AACAT AACAT -ACAT ACAAAT ATACA-
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT A-ACAT A-ACAT
* *
21837355 AACAT AACAGT AAACAT AACAT -ACAT -ATAT AACAA AACAT AACAT AACAT
1 AACAT AACA-T -AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
* *
21837405 -ACAT ACAAAT ATACA- AACAT AAAAGT AAACAT AACAT -ACAT -ACAT
1 AACAT A-ACAT A-ACAT AACAT AACA-T -AACAT AACAT AACAT AACAT
*
21837450 AACAGT -ACAT AACAT AACAT -ACAT ACAAAT ATACA- AACAT AACATT
1 AACA-T AACAT AACAT AACAT AACAT A-ACAT A-ACAT AACAT AACA-T
* *
21837496 AAACAT AACAT -ACAT -GCAT AACAGT -ACAT AACAT -ACAT AACAT AATAGT
1 -AACAT AACAT AACAT AACAT AACA-T AACAT AACAT AACAT AACAT AACA-T
*
21837545 AAACAT AACAT -ACAT -ACAT AACA- ATACAT AACAT -ACAT AATAT -ACAT
1 -AACAT AACAT AACAT AACAT AACAT A-ACAT AACAT AACAT AACAT AACAT
21837592 AACA
1 AACA
21837596 GTTTAAAAAC
Statistics
Matches: 264, Mismatches: 30, Indels: 76
0.71 0.08 0.21
Matches are distributed among these distances:
4 77 0.29
5 130 0.49
6 41 0.16
7 16 0.06
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (5 bp):
AACAT
Found at i:21838767 original size:22 final size:22
Alignment explanation
Indices: 21838742--21838784 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21838732 TAACATAGTC
21838742 AAATTACTTGTAATTTATTTTT
1 AAATTACTTGTAATTTATTTTT
21838764 AAATTACTTGTAATTTATTTT
1 AAATTACTTGTAATTTATTTT
21838785 GTGACTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (22 bp):
AAATTACTTGTAATTTATTTTT
Found at i:21841139 original size:42 final size:43
Alignment explanation
Indices: 21841035--21841191 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 43
21841025 TGCATTATTG
* *
21841035 TGTAAGACCACATCTGGGACGTTGGCAT--TTACTTATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATA-TT-TGATTT-CA
* * * *
21841079 TGTAAGACCACGTATGGGACGTTGTCATCG-TGTTTGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTCA
*
21841121 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTTCA
21841164 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
21841192 TGTATGAGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 26 0.27
43 40 0.42
44 28 0.29
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTCA
Found at i:21842306 original size:30 final size:30
Alignment explanation
Indices: 21842272--21842332 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
21842262 TTCCCGAGCC
*
21842272 TAGGGGTAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
21842302 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
21842332 T
1 T
21842333 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:21844992 original size:40 final size:40
Alignment explanation
Indices: 21844936--21845112 Score: 228
Period size: 40 Copynumber: 4.4 Consensus size: 40
21844926 ATTGTGAAAT
* *
21844936 ACAGAGCAATAACGGCGTTTTTAGTAAAACACCGCTAAAA
1 ACAGAGCAATAGCGGCGTTTTTAGTAAAACGCCGCTAAAA
21844976 ACAGAGCAATAGCGGCGTTTTTAGTAAAACGCCGCTAAAA
1 ACAGAGCAATAGCGGCGTTTTTAGTAAAACGCCGCTAAAA
* * *
21845016 ACAGAGCAATAACGGCGTTTTTTGCTAAAATGCCGCTAAAA
1 ACAGAGCAATAGCGGCGTTTTTAG-TAAAACGCCGCTAAAA
* * * * *
21845057 ACAGAGCAATAGCAGCGCTTTCAGTAAAATGCTGCTAAAA
1 ACAGAGCAATAGCGGCGTTTTTAGTAAAACGCCGCTAAAA
* *
21845097 ACCACAGCATTAGCGG
1 A-CAGAGCAATAGCGG
21845113 TGCTTTCGGT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 76 0.63
41 45 0.37
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (40 bp):
ACAGAGCAATAGCGGCGTTTTTAGTAAAACGCCGCTAAAA
Found at i:21845083 original size:81 final size:80
Alignment explanation
Indices: 21844936--21845098 Score: 245
Period size: 81 Copynumber: 2.0 Consensus size: 80
21844926 ATTGTGAAAT
* * *
21844936 ACAGAGCAATAACGGCGTTTTTAGTAAAACACCGCTAAAAACAGAGCAATAGCGGCGTTTTTAGT
1 ACAGAGCAATAACGGCGTTTTTAGTAAAACACCGCTAAAAACAGAGCAATAGCAGCGCTTTCAGT
21845001 AAAACGCCGCTAAAA
66 AAAACGCCGCTAAAA
* **
21845016 ACAGAGCAATAACGGCGTTTTTTGCTAAAATGCCGCTAAAAACAGAGCAATAGCAGCGCTTTCAG
1 ACAGAGCAATAACGGCGTTTTTAG-TAAAACACCGCTAAAAACAGAGCAATAGCAGCGCTTTCAG
* *
21845081 TAAAATGCTGCTAAAA
65 TAAAACGCCGCTAAAA
21845097 AC
1 AC
21845099 CACAGCATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 23 0.31
81 51 0.69
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (80 bp):
ACAGAGCAATAACGGCGTTTTTAGTAAAACACCGCTAAAAACAGAGCAATAGCAGCGCTTTCAGT
AAAACGCCGCTAAAA
Found at i:21845132 original size:41 final size:40
Alignment explanation
Indices: 21844969--21845133 Score: 141
Period size: 41 Copynumber: 4.1 Consensus size: 40
21844959 GTAAAACACC
* * * * * *
21844969 GCTAAAAACAGAGCAATAGCGGCGTTTTTAGTAAAACGCC
1 GCTAAAAACACAGCAATAGCAGCGCTTTCAGTAAAATGCT
* * * * ** *
21845009 GCTAAAAACAGAGCAATAACGGCGTTTTTTGCTAAAATGCC
1 GCTAAAAACACAGCAATAGCAGCGCTTTCAG-TAAAATGCT
*
21845050 GCTAAAAACAGAGCAATAGCAGCGCTTTCAGTAAAATGCT
1 GCTAAAAACACAGCAATAGCAGCGCTTTCAGTAAAATGCT
* * * * *
21845090 GCTAAAAACCACAGCATTAGCGGTGCTTTCGGTAAAACGCT
1 GCTAAAAA-CACAGCAATAGCAGCGCTTTCAGTAAAATGCT
21845131 GCT
1 GCT
21845134 GAAAGTCATA
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
40 45 0.42
41 63 0.58
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (40 bp):
GCTAAAAACACAGCAATAGCAGCGCTTTCAGTAAAATGCT
Found at i:21845325 original size:7 final size:7
Alignment explanation
Indices: 21845309--21845355 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
21845299 TATCATTATA
21845309 GTTTAAG
1 GTTTAAG
*
21845316 GTTTATG
1 GTTTAAG
21845323 GTTTAAG
1 GTTTAAG
* * *
21845330 ATATATG
1 GTTTAAG
21845337 GTTTAAG
1 GTTTAAG
21845344 GTTTAAG
1 GTTTAAG
21845351 GTTTA
1 GTTTA
21845356 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:21845326 original size:14 final size:14
Alignment explanation
Indices: 21845304--21845355 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
21845294 TTAATTATCA
*
21845304 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
21845318 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
*
21845332 ATATGGTTTAAGGT
1 TTATGGTTTAAGGT
*
21845346 TTAAGGTTTA
1 TTATGGTTTA
21845356 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:21845420 original size:7 final size:7
Alignment explanation
Indices: 21845393--21845528 Score: 80
Period size: 7 Copynumber: 19.1 Consensus size: 7
21845383 GATGAATTAT
21845393 GGGTTTA
1 GGGTTTA
* *
21845400 GAGATTA
1 GGGTTTA
*
21845407 TGGTTTA
1 GGGTTTA
21845414 GGGTTTA
1 GGGTTTA
21845421 GGG-TT-
1 GGGTTTA
21845426 GGAGTTTA
1 GG-GTTTA
* *
21845434 AGGTGTCA
1 GGGT-TTA
21845442 GGGTTTA
1 GGGTTTA
21845449 GGGTTTA
1 GGGTTTA
*
21845456 GGGTTAA
1 GGGTTTA
*
21845463 GGATTTA
1 GGGTTTA
*
21845470 AGGTTTA
1 GGGTTTA
*
21845477 GGGTTAA
1 GGGTTTA
*
21845484 GTGTTTA
1 GGGTTTA
*
21845491 GTGTTTA
1 GGGTTTA
*
21845498 TGGG-ATA
1 -GGGTTTA
*
21845505 GGGGTTAA
1 -GGGTTTA
21845513 GAGGTTTA
1 G-GGTTTA
*
21845521 AGGTTTA
1 GGGTTTA
21845528 G
1 G
21845529 ATTAATTAGT
Statistics
Matches: 95, Mismatches: 27, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 76 0.80
8 14 0.15
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:21850271 original size:15 final size:15
Alignment explanation
Indices: 21850251--21850282 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21850241 TTATTAAATT
*
21850251 ATATATTTAATTATA
1 ATATATTTAATAATA
21850266 ATATATTTAATAATA
1 ATATATTTAATAATA
21850281 AT
1 AT
21850283 TATGTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATTTAATAATA
Found at i:21850528 original size:16 final size:16
Alignment explanation
Indices: 21850507--21850574 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
21850497 GATTTGCTAT
* *
21850507 TACACCTCTATTCTAA
1 TACACCTCTAATCCAA
*
21850523 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
21850539 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21850555 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21850571 TACA
1 TACA
21850575 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:21857819 original size:52 final size:53
Alignment explanation
Indices: 21857711--21857840 Score: 183
Period size: 52 Copynumber: 2.5 Consensus size: 53
21857701 CTTACGGCGA
*
21857711 GATTACCAGTCCAGGCTAAATCCC-CATATCGTAAACTCATAAGGTGATGCCAG
1 GATTACCAGTCCAGGCTAAATCCCTCATATAGT-AACTCATAAGGTGATGCCAG
* * * * *
21857764 GATTACTAGTTCAGGCTAAATCCCTCGTATAGT-ACTCATAAGGTGATGTCGG
1 GATTACCAGTCCAGGCTAAATCCCTCATATAGTAACTCATAAGGTGATGCCAG
21857816 GATTACCAGTCCAGGCTAAATCCCT
1 GATTACCAGTCCAGGCTAAATCCCT
21857841 TATAATGACA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
52 40 0.59
53 22 0.32
54 6 0.09
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (53 bp):
GATTACCAGTCCAGGCTAAATCCCTCATATAGTAACTCATAAGGTGATGCCAG
Found at i:21859062 original size:45 final size:44
Alignment explanation
Indices: 21858998--21859087 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 44
21858988 AAAAACTTAG
* *
21858998 AATTTGGGCAAATTGCTCTCCAAGGCTTTCTAATTCATAACCCAA
1 AATTTGGGAAAATTGCTCTCCAAGGCCTTCTAATT-ATAACCCAA
21859043 AATTTGGGAAAATTGCTCTCCAAGGCCTTCTAATTATAACCCAA
1 AATTTGGGAAAATTGCTCTCCAAGGCCTTCTAATTATAACCCAA
21859087 A
1 A
21859088 GCAATTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 10 0.23
45 33 0.77
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (44 bp):
AATTTGGGAAAATTGCTCTCCAAGGCCTTCTAATTATAACCCAA
Found at i:21862651 original size:28 final size:29
Alignment explanation
Indices: 21862601--21862682 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 29
21862591 TAAAGTGATT
* *
21862601 TTTGACAAAAA-GTCAATTAGGGA-TT-AA
1 TTTGA-AAAAATGTAAATTGGGGAGTTAAA
21862628 TTTGAGAAAAATGTAAATTGGGGAGTTAAA
1 TTTGA-AAAAATGTAAATTGGGGAGTTAAA
21862658 TTGTGAAACAAATGATAAATATGGG
1 TT-TGAAA-AAATG-TAAAT-TGGG
21862683 CTGATATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
27 10 0.22
28 10 0.22
29 2 0.04
30 6 0.13
31 8 0.18
32 5 0.11
33 4 0.09
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (29 bp):
TTTGAAAAAATGTAAATTGGGGAGTTAAA
Found at i:21865194 original size:29 final size:28
Alignment explanation
Indices: 21865152--21865252 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
21865142 ATCCATACTT
* * *
21865152 ATTCATTTGGCCCATTTAGGCCTAATCTC
1 ATTCATATGGCCCA-TTAGGCCAAATCAC
*
21865181 ATTCATATGGCCCATTAGACTCAAATCAC
1 ATTCATATGGCCCATTAGGC-CAAATCAC
* * * *
21865210 TTTCATATGACCCA-TCGGCCCCAATCAC
1 ATTCATATGGCCCATTAGG-CCAAATCAC
21865238 ATTCATATGGCCCAT
1 ATTCATATGGCCCAT
21865253 CGACCCCAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 26 0.45
29 32 0.55
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCAAATCAC
Found at i:21865244 original size:28 final size:28
Alignment explanation
Indices: 21865175--21865272 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 28
21865165 ATTTAGGCCT
* * * * *
21865175 AATCTCATTCATATGGCCCATTAGACTCA
1 AATCACATTCATATGACCCA-TCGACCCC
* *
21865204 AATCACTTTCATATGACCCATCGGCCCC
1 AATCACATTCATATGACCCATCGACCCC
*
21865232 AATCACATTCATATGGCCCATCGACCCC
1 AATCACATTCATATGACCCATCGACCCC
21865260 AATCACATTCATA
1 AATCACATTCATA
21865273 GTCATGCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
28 42 0.71
29 17 0.29
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.27
Consensus pattern (28 bp):
AATCACATTCATATGACCCATCGACCCC
Found at i:21866912 original size:23 final size:24
Alignment explanation
Indices: 21866867--21866922 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
21866857 ATGGTATATT
*
21866867 TTGGTATGATTTATAGATGATGAA
1 TTGGTATGATTTATAGAAGATGAA
*
21866891 TTGGTATG-TTTA-AGAAGCATGAT
1 TTGGTATGATTTATAGAAG-ATGAA
21866914 TTGGT-TGAT
1 TTGGTATGAT
21866923 AGAAAGGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 14 0.50
24 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (24 bp):
TTGGTATGATTTATAGAAGATGAA
Found at i:21871138 original size:46 final size:46
Alignment explanation
Indices: 21871086--21871481 Score: 526
Period size: 46 Copynumber: 8.6 Consensus size: 46
21871076 GTTTTCTGAA
*
21871086 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
21871132 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGGAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
21871178 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
21871224 ATAAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
21871270 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
21871316 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** ** * *
21871362 A-GGAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * *
21871407 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
21871453 A-GAAAATGAATAAGACCATAGTTGAAAGA
1 ATG-AAATGTGTAAGACCATGGTTGAAAGA
21871482 CACTATGACA
Statistics
Matches: 325, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 39 0.12
46 286 0.88
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:21871798 original size:16 final size:17
Alignment explanation
Indices: 21871777--21871809 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21871767 ATGATGGAGC
21871777 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
21871793 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
21871810 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:21874725 original size:28 final size:29
Alignment explanation
Indices: 21874611--21874735 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
21874601 GAAGGCATGT
21874611 ATATGAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
* * * *
21874640 GTACGAATGTGATTTGGGCCCAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
* * *
21874669 ATACGAATGTGATTTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
* *
21874698 ATATGAATGAGA-TTGGGCCTAGTAGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
*
21874726 ATATGCATGT
1 ATATGAATGT
21874736 ATGTAGACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 23 0.27
29 61 0.73
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATAGGCC
Found at i:21880549 original size:77 final size:77
Alignment explanation
Indices: 21880422--21880578 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
21880412 TTTAATTGAG
*
21880422 GATCCATAGGTGTAGATGCTAGTATATAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
1 GATCCATAGGTGTAGATGCTAGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
21880487 TAATGTGATTGT
66 TAATGTGATTGT
*
21880499 GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
1 GATCCATAGGTGTAGATGCTAGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
21880564 TAATGTGATTGT
66 TAATGTGATTGT
21880576 GAT
1 GAT
21880579 AAAGCTATAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (77 bp):
GATCCATAGGTGTAGATGCTAGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
TAATGTGATTGT
Found at i:21885671 original size:22 final size:22
Alignment explanation
Indices: 21885641--21885690 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 22
21885631 TAGGTAAATG
21885641 AGTTATATTTTATGAGATATTTA
1 AGTT-TATTTTATGAGATATTTA
21885664 AGTTTATTTTATGAGATATTTA
1 AGTTTATTTTATGAGATATTTA
21885686 AGTTT
1 AGTTT
21885691 TGGTGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (22 bp):
AGTTTATTTTATGAGATATTTA
Found at i:21890254 original size:17 final size:17
Alignment explanation
Indices: 21890222--21890254 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21890212 GATAAACATA
21890222 TACTAAATATATAATAC
1 TACTAAATATATAATAC
21890239 TACTATAATATA-AATA
1 TACTA-AATATATAATA
21890255 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TACTAAATATATAATAC
Found at i:21892530 original size:61 final size:62
Alignment explanation
Indices: 21892460--21892577 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
21892450 CTAAAAAATT
* * * * * *
21892460 AATAAATTTAACCCTTAATATTTACAAA-ATTTATTATTTTAGTTCTAATTCTAATAAACTC
1 AATAAATTTAACCCTCAAAAATTACAAATAATTATTAATTTAGTTATAATTCTAATAAACTC
* * *
21892521 AATAAATTTATCTCTCAAAAATTACAAATAATTATTAATTTAGTTATAATTTTAATA
1 AATAAATTTAACCCTCAAAAATTACAAATAATTATTAATTTAGTTATAATTCTAATA
21892578 TTTAAAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
61 23 0.49
62 24 0.51
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (62 bp):
AATAAATTTAACCCTCAAAAATTACAAATAATTATTAATTTAGTTATAATTCTAATAAACTC
Found at i:21895502 original size:48 final size:46
Alignment explanation
Indices: 21895389--21895510 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 46
21895379 ATAGTTTTTG
* * *
21895389 AGCTAGTGTAAGACATGTTTGGGACATGCATCGGTCGCATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGTCGCAATATGAA
21895435 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCG-AGATAT-ACA
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGG--TCGCA-ATATGA-A
* *
21895483 AGCTAGTATAAGACCTGTCTGGGACATG
1 AGCTAGTGTAAGACATGTCTGGGACATG
21895511 GCGTCAGCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 33 0.49
47 2 0.03
48 32 0.48
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGTCGCAATATGAA
Done.