Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 45 of 335
Found at i:16285284 original size:66 final size:66
Alignment explanation
Indices: 16285178--16285311 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
16285168 TAAATATTTT
16285178 TATAAATATTTATGGAGTGTTGATAAGTTAGTATTAAAGTTTCGTCAAGAAATTTTAAAGTTTCG
1 TATAAATATTTATGGAGTGTTGATAAGTTAGTATTAAAGTTTCGTCAAGAAATTTTAAAGTTTCG
16285243 A
66 A
16285244 TATAAATATTTATGGAGTGTTGATAAGTTAGTATTAAAGTTTCGTCAAGAAATTTTAAAGTTTCG
1 TATAAATATTTATGGAGTGTTGATAAGTTAGTATTAAAGTTTCGTCAAGAAATTTTAAAGTTTCG
16285309 A
66 A
16285310 TA
1 TA
16285312 GTTAATTGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (66 bp):
TATAAATATTTATGGAGTGTTGATAAGTTAGTATTAAAGTTTCGTCAAGAAATTTTAAAGTTTCG
A
Found at i:16286998 original size:51 final size:51
Alignment explanation
Indices: 16286920--16287083 Score: 283
Period size: 51 Copynumber: 3.2 Consensus size: 51
16286910 ACTTCTGATC
* *
16286920 AGTGACAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
* *
16286971 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
*
16287022 AGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
16287073 AGTGATAAATG
1 AGTGATAAATG
16287084 TGATCAGTGT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 105 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (51 bp):
AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
Found at i:16289728 original size:41 final size:41
Alignment explanation
Indices: 16289682--16289763 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
16289672 TCTGACCCAG
*
16289682 CTTGGTTTGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
1 CTTGGTGTGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
*
16289723 CTTGGTGTGGCATTAAATTTGTTAGGCCCCATTCCTTGACT
1 CTTGGTGTGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
16289764 TTCTTCATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (41 bp):
CTTGGTGTGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
Found at i:16293294 original size:53 final size:53
Alignment explanation
Indices: 16293153--16293303 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
16293143 ATAAGTGCGC
* * **
16293153 CCGTTTAAGACCATAGCTGGGTTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
* *
16293206 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
*
16293259 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGATATGGCATCGGTAT-A-ATGTGA
16293304 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
Found at i:16295164 original size:65 final size:67
Alignment explanation
Indices: 16295083--16295217 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 67
16295073 AAAAATTACA
*
16295083 TTAAAAAAATCACAAAACACTAAACTAA-ACACTAA-C-AATCATAAATTACTAACAAAATAA-A
1 TTAAAAAAATCACAAAACACT-AA-TAATACA-TAACCTAATCATAAACTACTAACAAAATAACA
16295144 TAATT
63 TAATT
* **
16295149 TTAAGAAAA-CACAAAACACTAATAATTTATAACCTAATCATAAACTACTAACAAAATAACTATA
1 TTAAAAAAATCACAAAACACTAATAATACATAACCTAATCATAAACTACTAACAAAATAAC-ATA
16295213 ATT
65 ATT
16295216 TT
1 TT
16295218 TTTTTTAGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
63 6 0.10
64 4 0.07
65 34 0.57
66 8 0.13
67 8 0.13
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (67 bp):
TTAAAAAAATCACAAAACACTAATAATACATAACCTAATCATAAACTACTAACAAAATAACATAA
TT
Found at i:16295367 original size:60 final size:60
Alignment explanation
Indices: 16295250--16295368 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
16295240 AAAACTCACT
*
16295250 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
16295310 AAACACAATAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
16295369 TAAAAAAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:16297532 original size:19 final size:18
Alignment explanation
Indices: 16297503--16297539 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
16297493 TTCATAATAA
16297503 TTATATATTATTATAGAT
1 TTATATATTATTATAGAT
16297521 TTATAGTATTATTATAGAT
1 TTATA-TATTATTATAGAT
16297540 AATTGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TTATATATTATTATAGAT
Found at i:16297934 original size:28 final size:29
Alignment explanation
Indices: 16297892--16297946 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
16297882 GTTATTTAAT
* *
16297892 TATTAACATATTTTTATTTTCATCATTCA
1 TATTAACAAATTTTTATTTTAATCATTCA
16297921 TATTAA-AAATTTTTATTTTAATCATT
1 TATTAACAAATTTTTATTTTAATCATT
16297947 TAATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTAACAAATTTTTATTTTAATCATTCA
Found at i:16297934 original size:29 final size:29
Alignment explanation
Indices: 16297885--16297963 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
16297875 AAAAATAGTT
* *
16297885 ATTTAATTATTAACATATTTTTATTTTCATC
1 ATTTAA-TATTAA-AAATTTTTATTTTAATC
*
16297916 A-TTCATATTAAAAATTTTTATTTTAATC
1 ATTTAATATTAAAAATTTTTATTTTAATC
**
16297944 ATTTAATATTATTAATTTTT
1 ATTTAATATTAAAAATTTTT
16297964 TGGTTTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 16 0.39
29 21 0.51
30 3 0.07
31 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTAATATTAAAAATTTTTATTTTAATC
Found at i:16298165 original size:10 final size:10
Alignment explanation
Indices: 16298150--16298196 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
16298140 AATATTTTTT
16298150 TATAAAAATA
1 TATAAAAATA
* *
16298160 TATAAAATTT
1 TATAAAAATA
16298170 TATAAAAATA
1 TATAAAAATA
*
16298180 TATTCAAAAT-
1 TA-TAAAAATA
16298190 TATAAAA
1 TATAAAA
16298197 GCATTTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 4 0.13
10 20 0.67
11 6 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
TATAAAAATA
Found at i:16298192 original size:20 final size:19
Alignment explanation
Indices: 16298148--16298196 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
16298138 AAAATATTTT
16298148 TTTATAAAAATATATAAAA
1 TTTATAAAAATATATAAAA
16298167 TTTTATAAAAATATATTCAAAA
1 -TTTATAAAAATATA-T-AAAA
16298189 -TTATAAAA
1 TTTATAAAA
16298197 GCATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 22 0.81
21 1 0.04
22 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTATAAAAATATATAAAA
Found at i:16298278 original size:20 final size:20
Alignment explanation
Indices: 16298255--16298300 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
16298245 ATTCATTTAT
**
16298255 TAAAATAAAAATTTTATAAA
1 TAAAATAAAAATACTATAAA
*
16298275 TAAAATAATAATACTATAAA
1 TAAAATAAAAATACTATAAA
16298295 TAAAAT
1 TAAAAT
16298301 TGTTTAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAAAAATACTATAAA
Found at i:16298840 original size:18 final size:18
Alignment explanation
Indices: 16298817--16298854 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
16298807 TAAAAATGAA
16298817 TTTTAAATATTTTTT-ATT
1 TTTTAAAT-TTTTTTAATT
16298835 TTTTAAATTTTTTTAATT
1 TTTTAAATTTTTTTAATT
16298853 TT
1 TT
16298855 GAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTAAATTTTTTTAATT
Found at i:16298859 original size:16 final size:16
Alignment explanation
Indices: 16298815--16298862 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
16298805 TATAAAAATG
16298815 AATTTTAAATATTTTTT
1 AATTTTAAAT-TTTTTT
*
16298832 ATTTTTTAAATTTTTTT
1 A-ATTTTAAATTTTTTT
*
16298849 AATTTTGAATTTTT
1 AATTTTAAATTTTT
16298863 AAGAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 8 0.30
18 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
AATTTTAAATTTTTTT
Found at i:16300955 original size:29 final size:29
Alignment explanation
Indices: 16300913--16300968 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
16300903 CCCTTGGCCG
*
16300913 AGCACTTCAGCACACCCTTCGTCTCTGCC
1 AGCACTCCAGCACACCCTTCGTCTCTGCC
16300942 AGCACTCCAGCACACCCTTCGTCTCTG
1 AGCACTCCAGCACACCCTTCGTCTCTG
16300969 TACTTTCCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.23
Consensus pattern (29 bp):
AGCACTCCAGCACACCCTTCGTCTCTGCC
Found at i:16301025 original size:18 final size:18
Alignment explanation
Indices: 16301002--16301036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16300992 CTTCCTTTTT
* *
16301002 CTTTTCTTTTTTTTTCTC
1 CTTTTCCTTTGTTTTCTC
16301020 CTTTTCCTTTGTTTTCT
1 CTTTTCCTTTGTTTTCT
16301037 TTAGCTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (18 bp):
CTTTTCCTTTGTTTTCTC
Found at i:16314638 original size:67 final size:67
Alignment explanation
Indices: 16314567--16314769 Score: 406
Period size: 67 Copynumber: 3.0 Consensus size: 67
16314557 TATAAATTTA
16314567 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
1 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
16314632 CC
66 CC
16314634 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
1 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
16314699 CC
66 CC
16314701 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
1 TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
16314766 CC
66 CC
16314768 TT
1 TT
16314770 TTGTAAATAT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 136 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (67 bp):
TTAAATATTAAAATAAAATAAAATAAATATTTTTTAAAAAAATAATATGAATGGGCTTGAATTAG
CC
Found at i:16327648 original size:25 final size:25
Alignment explanation
Indices: 16327590--16327648 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
16327580 TTGAATGAGG
* *
16327590 TATGATTTCAAATGGAATTGTGGTA
1 TATGATTTCAAATGAAATTATGGTA
** *
16327615 CGTGTTTTCAAATGAAATTATGGTA
1 TATGATTTCAAATGAAATTATGGTA
16327640 TATGATTTC
1 TATGATTTC
16327649 TTATCTATTG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (25 bp):
TATGATTTCAAATGAAATTATGGTA
Found at i:16341001 original size:21 final size:22
Alignment explanation
Indices: 16340957--16341006 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
16340947 AATAACTTCA
* *
16340957 TAAAATATAATTTAGATAATTT
1 TAAAATATAATTAAAATAATTT
*
16340979 TAAAATGTAATTAAAAT-ATTT
1 TAAAATATAATTAAAATAATTT
16341000 TAAAATA
1 TAAAATA
16341007 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATATAATTAAAATAATTT
Found at i:16341013 original size:19 final size:20
Alignment explanation
Indices: 16340975--16341013 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16340965 AATTTAGATA
16340975 ATTTTAAAATGTAATTAAAAT
1 ATTTTAAAA-GTAATTAAAAT
*
16340996 ATTTTAAAA-TAGTTAAAA
1 ATTTTAAAAGTAATTAAAA
16341014 AAAAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAGTAATTAAAAT
Found at i:16346801 original size:16 final size:16
Alignment explanation
Indices: 16346733--16346802 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
16346723 GGTCAAATAA
16346733 AATTTT-AATTTTTAAT
1 AATTTTAAATTTTT-AT
*
16346749 AA-TTTATATTTTTAT
1 AATTTTAAATTTTTAT
**
16346764 AATTTTTAAATAATTA-
1 AA-TTTTAAATTTTTAT
16346780 AA--TTAAATTTTTAT
1 AATTTTAAATTTTTAT
16346794 AATTTTAAA
1 AATTTTAAA
16346803 ATAGTAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 7 0.17
16 15 0.36
17 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTAAATTTTTAT
Found at i:16346822 original size:30 final size:30
Alignment explanation
Indices: 16346753--16346822 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
16346743 TTTAATAATT
* * * *
16346753 TATATTTTTATAATTTTTAAATAATTAAAT
1 TATAATTTTATAATTTTAAAATAATAAAAA
*
16346783 TA-AATTTTTATAATTTTAAAATAGTAAAAA
1 TATAA-TTTTATAATTTTAAAATAATAAAAA
16346813 TATAATTTTA
1 TATAATTTTA
16346823 ATTTTACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 30 0.91
31 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATAATTTTATAATTTTAAAATAATAAAAA
Found at i:16349820 original size:69 final size:69
Alignment explanation
Indices: 16349709--16349849 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
16349699 GCAATTCTCA
*
16349709 AAAGTGCATGTCTGTCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
1 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
16349774 ATTG
66 ATTG
16349778 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
1 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
16349843 ATTG
66 ATTG
16349847 AAA
1 AAA
16349850 TTTCTACACA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (69 bp):
AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
ATTG
Found at i:16351844 original size:26 final size:27
Alignment explanation
Indices: 16351784--16351845 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
16351774 TGAGTACATC
16351784 ATAATTAATAAATAAAGTAAGAATAAA
1 ATAATTAATAAATAAAGTAAGAATAAA
* *
16351811 ATAA-TAATAATATTAA-TAATAAT-AA
1 ATAATTAATAA-ATAAAGTAAGAATAAA
*
16351836 CTAATTAATA
1 ATAATTAATA
16351846 TTGAGCGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (27 bp):
ATAATTAATAAATAAAGTAAGAATAAA
Found at i:16353975 original size:23 final size:25
Alignment explanation
Indices: 16353933--16353980 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
16353923 AAATTCATTA
16353933 AAATTATATATAAATATATTAAATT
1 AAATTATATATAAATATATTAAATT
16353958 AAATTATA-ATAAAT-TATTAAATT
1 AAATTATATATAAATATATTAAATT
16353981 TTACTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
25 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTATATATAAATATATTAAATT
Found at i:16354350 original size:2 final size:2
Alignment explanation
Indices: 16354343--16354377 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
16354333 ACAAATATTA
*
16354343 AT AT AT AT AT AT AT AT AT AT AGT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
16354378 TGATATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16355916 original size:4 final size:4
Alignment explanation
Indices: 16355907--16355948 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
16355897 AATCATTACT
*
16355907 TGTA TGTA TGTA TGTA TGTA TGTA TGTGAA TGTA CGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT--A TGTA TGTA TGTA
16355949 GTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 30 0.88
6 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:16360331 original size:32 final size:31
Alignment explanation
Indices: 16360266--16360331 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
16360256 ATTTTTTTTT
* * *
16360266 AGTTTAATTTGACCCTCAATCTTCTAAAAAG
1 AGTTAAATTTGACCATCAACCTTCTAAAAAG
16360297 AGTTAAATTTGACCATCAACCTAT-TGAAAAAG
1 AGTTAAATTTGACCATCAACCT-TCT-AAAAAG
16360329 AGT
1 AGT
16360332 CGGAATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (31 bp):
AGTTAAATTTGACCATCAACCTTCTAAAAAG
Found at i:16362662 original size:13 final size:13
Alignment explanation
Indices: 16362646--16362670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16362636 ATTACTAAAA
16362646 AAAATAAATACAT
1 AAAATAAATACAT
16362659 AAAATAAATACA
1 AAAATAAATACA
16362671 ATAATAGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATACAT
Found at i:16363735 original size:12 final size:12
Alignment explanation
Indices: 16363718--16363748 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16363708 GAAGCAGGGG
16363718 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
16363730 AGAAAAAGGGAA
1 AGAAAAAGAGAA
16363742 AGAAAAA
1 AGAAAAA
16363749 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:16364752 original size:38 final size:39
Alignment explanation
Indices: 16364692--16364788 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
16364682 CGGATAGATT
* * * *
16364692 CGATGAGGTACTGGGTACCAACT-TTATTTCG-GCTAGGC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTA-GC
* * *
16364730 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
16364769 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
16364789 TATTGGTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 19 0.40
39 26 0.54
40 3 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
Found at i:16369817 original size:20 final size:20
Alignment explanation
Indices: 16369788--16369827 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16369778 ATTTAAGTAT
*
16369788 TAAAATATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
16369808 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
16369828 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:16370068 original size:20 final size:18
Alignment explanation
Indices: 16370039--16370083 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
16370029 AACGAAAAGC
16370039 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
16370057 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
16370076 AGGGAAAA
1 AGGGAAAA
16370084 TTAAGGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:16371983 original size:6 final size:6
Alignment explanation
Indices: 16371972--16371996 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16371962 CTTGTTTTTC
16371972 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
16371997 GTTATATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:16383821 original size:68 final size:68
Alignment explanation
Indices: 16383654--16383829 Score: 150
Period size: 68 Copynumber: 2.6 Consensus size: 68
16383644 TAGTACCACT
* * * * *
16383654 CATGCGACCTAGCT-GAT-T-TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
*
16383716 CACG
65 CACA
* * *
16383720 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGCGACCTAGCTACATATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
16383782 ATCACA
63 ATCACA
*
16383788 CATGTGACCTAGCTACTATATAGTATCTCGTAGC-CTTCTTGT
1 CATGCGACCTAGCTAC-ATATA-TATCTCGTAGCTC-TCTTGT
16383830 ACACATGATG
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
66 14 0.15
67 3 0.03
68 34 0.37
69 8 0.09
70 6 0.07
71 26 0.29
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (68 bp):
CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:16387542 original size:28 final size:28
Alignment explanation
Indices: 16387510--16387565 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
16387500 ATGTGAAGTT
16387510 AGGAAAAATTTTGAAATAGTGAATAGTG
1 AGGAAAAATTTTGAAATAGTGAATAGTG
*
16387538 AGGAAAATTTTTGAAATAGTGAATAGTG
1 AGGAAAAATTTTGAAATAGTGAATAGTG
16387566 TACTAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (28 bp):
AGGAAAAATTTTGAAATAGTGAATAGTG
Found at i:16388187 original size:37 final size:37
Alignment explanation
Indices: 16388137--16388210 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
16388127 AAGAAATTGA
16388137 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
*
16388174 AAGTTTCTATACATATGTGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
16388211 TTGGCATAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (37 bp):
AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
Found at i:16392557 original size:24 final size:22
Alignment explanation
Indices: 16392530--16392576 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
16392520 AGGATTTATA
16392530 ATATTCCGGGTGTGTTTGGGCTGG
1 ATATT-CGGGTGTGTTTGGG-TGG
*
16392554 ATATTCTGGTGTGTTTGGGTGG
1 ATATTCGGGTGTGTTTGGGTGG
16392576 A
1 A
16392577 ATCCGCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.11, C:0.09, G:0.40, T:0.40
Consensus pattern (22 bp):
ATATTCGGGTGTGTTTGGGTGG
Found at i:16393579 original size:40 final size:40
Alignment explanation
Indices: 16393523--16393600 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
16393513 TGTGTGAGAA
* *
16393523 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGATT
1 TGAGATAGCTTCGGCTATATACGACACTTAGTGTGCGATT
16393563 TGAGATAGCTGT-GGCTATATACGACACTTAGTGTGCGA
1 TGAGATAGCT-TCGGCTATATACGACACTTAGTGTGCGA
16393601 GATATCGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.32
Consensus pattern (40 bp):
TGAGATAGCTTCGGCTATATACGACACTTAGTGTGCGATT
Found at i:16393625 original size:28 final size:28
Alignment explanation
Indices: 16393585--16393661 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
16393575 GGCTATATAC
*
16393585 GACACTTAGTGTGCGAGATATCGAGTAT
1 GACACTTAGTGTGCGAGATATCAAGTAT
16393613 GACACTTAGTGTGC-AGGATATCAAGTAT
1 GACACTTAGTGTGCGA-GATATCAAGTAT
*
16393641 GACACTTAGTGTGCGAAATAT
1 GACACTTAGTGTGCGAGATAT
16393662 GTAGTATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 1 0.02
28 43 0.96
29 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
GACACTTAGTGTGCGAGATATCAAGTAT
Found at i:16398586 original size:27 final size:27
Alignment explanation
Indices: 16398567--16398856 Score: 402
Period size: 27 Copynumber: 10.8 Consensus size: 27
16398557 ATTACCAAAG
* *
16398567 TACCCTCAATTTACAGAATTACCGTTC
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398594 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398621 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398648 TACCCTCAATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
16398675 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
16398702 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398729 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
16398756 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398783 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398810 TACCCTTGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
16398837 TACCCTC-AATTACAAAATTA
1 TACCCTCGATTTACAGAATTA
16398857 TTGAAATACC
Statistics
Matches: 236, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
26 11 0.05
27 225 0.95
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:16398890 original size:27 final size:27
Alignment explanation
Indices: 16398860--16399164 Score: 335
Period size: 27 Copynumber: 11.3 Consensus size: 27
16398850 AAAATTATTG
**
16398860 AAATACCCTTGATTTACAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* ** *
16398887 AAATACCCTCGATCAGTAAAATTACTA
1 AAATACCCTTGATTTGTAAAATTACCA
* * * *
16398914 AAATGCCCCTGGTTTGTAAAATTACTA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
16398941 AAATACCCTTGGTTTATAAAATTGCCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
16398968 GAATACCCCTGTTTTGTAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* *
16398995 AAATACCCCT-AGTTTGTGAAATTACCA
1 AAATACCCTTGA-TTTGTAAAATTACCA
* * **
16399022 AAATACCCCTGATTTGTGAAATTACTT
1 AAATACCCTTGATTTGTAAAATTACCA
*
16399049 AAATACCCTTGACTTGTAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
* * *
16399076 AAATACCATTGGTTTATAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
*
16399103 AAATACCCTTGGTTTGTAAAATTACCA
1 AAATACCCTTGATTTGTAAAATTACCA
*
16399130 AAATACCCTTGATTTGTGAAATTACC-
1 AAATACCCTTGATTTGTAAAATTACCA
16399156 AAATACCCT
1 AAATACCCT
16399165 CAGTTTGCAA
Statistics
Matches: 236, Mismatches: 40, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
26 9 0.04
27 226 0.96
28 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
AAATACCCTTGATTTGTAAAATTACCA
Found at i:16399240 original size:27 final size:27
Alignment explanation
Indices: 16399210--16399376 Score: 217
Period size: 27 Copynumber: 6.2 Consensus size: 27
16399200 CGATTTACAA
16399210 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
** *
16399237 AATTATCAAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
16399264 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* *
16399291 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAG
* *
16399318 AATTACTGAAATACCCCTGTAGGGTAA
1 AATTATTGAAATACCCCTGTAGGGTAG
** * * * *
16399345 AATTACAGAGATACCCTTGTGGGGTAA
1 AATTATTGAAATACCCCTGTAGGGTAG
16399372 AATTA
1 AATTA
16399377 CCATTTTGCC
Statistics
Matches: 124, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 124 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
AATTATTGAAATACCCCTGTAGGGTAG
Found at i:16399359 original size:54 final size:55
Alignment explanation
Indices: 16399210--16399377 Score: 243
Period size: 54 Copynumber: 3.1 Consensus size: 55
16399200 CGATTTACAA
* * *
16399210 AATTATTGAAATACCCCTGTAGGGTAGAATTATCA-AAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATCAGAAATACCCTTGTAGGGTAG
*
16399264 AATTATTGAAATACCCCTGTAGGGTAGAATTATC-GAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATCAGAAATACCCTTGTAGGGTAG
* * * *
16399318 AATTACTGAAATACCCCTGTAGGGTAAAATTA-CAGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATCAGAAATACCCTTGTAGGGTAG
16399372 AATTAC
1 AATTAC
16399378 CATTTTGCCC
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
53 1 0.01
54 104 0.99
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (55 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTATCAGAAATACCCTTGTAGGGTAG
Found at i:16399617 original size:25 final size:25
Alignment explanation
Indices: 16399583--16399677 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
16399573 AGGAAGTGCT
* *
16399583 AAAAGTGCTTTGCCCCAGTTTACTG
1 AAAAGGGCTTTGCCCCAGTTTACCG
16399608 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
16399633 AAAAGAGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
16399658 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
16399678 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:16399933 original size:31 final size:30
Alignment explanation
Indices: 16399898--16399979 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
16399888 CGTTTACAGT
*
16399898 AAAGGCTTCAGCCCAGTGATATGATT-TACG
1 AAAGGCTTCAGCCCAGT-ATATGATTAAACG
* * **
16399928 AAAAGGCTTCGGCCTAGTA-ACCATTAAACG
1 -AAAGGCTTCAGCCCAGTATATGATTAAACG
16399958 AAAGGCTTCAGCCCAGTATATG
1 AAAGGCTTCAGCCCAGTATATG
16399980 TCGAGACCGA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 20 0.50
30 5 0.12
31 15 0.38
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (30 bp):
AAAGGCTTCAGCCCAGTATATGATTAAACG
Found at i:16403609 original size:23 final size:22
Alignment explanation
Indices: 16403549--16403613 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
16403539 CTTGATTAGT
16403549 ATACGACACATAAGTGCCTGAA
1 ATACGACACATAAGTGCCTGAA
*
16403571 ATGAC-ACACGAT--GTGCTTGAA
1 AT-ACGACAC-ATAAGTGCCTGAA
16403592 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
16403614 TCGACAAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 6 0.17
23 11 0.31
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:16403827 original size:16 final size:17
Alignment explanation
Indices: 16403801--16403834 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16403791 TTCAATACAT
16403801 ATTCATCATTCAACTCA
1 ATTCATCATTCAACTCA
*
16403818 ATTC-TCATTCAATTCA
1 ATTCATCATTCAACTCA
16403834 A
1 A
16403835 CAGTAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTCATCATTCAACTCA
Found at i:16407201 original size:17 final size:16
Alignment explanation
Indices: 16407172--16407205 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16407162 GTCCTCCCTT
16407172 ATTTATCACTTGAGCA
1 ATTTATCACTTGAGCA
*
16407188 ATTTAATCATTTGAGCA
1 ATTT-ATCACTTGAGCA
16407205 A
1 A
16407206 ATTTTGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTTATCACTTGAGCA
Found at i:16410966 original size:6 final size:6
Alignment explanation
Indices: 16410947--16410989 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
16410937 GAAGCAGGGG
* * *
16410947 AGAAAA AGAGAA AGAAAA AGGAAA AGAAAA ATAAAA GAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
16410990 CTAAGGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:16411925 original size:41 final size:42
Alignment explanation
Indices: 16411880--16411979 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 42
16411870 CGACCTCGAG
* *
16411880 TCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
** * * *
16411921 TCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
16411960 T-GATGAGACACTGGGTGTCA
1 TCGATGAGACACTGGGTGTCA
16411980 ACTATTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
38 16 0.35
39 14 0.30
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
Found at i:16411988 original size:39 final size:40
Alignment explanation
Indices: 16411880--16411991 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
16411870 CGACCTCGAG
* *
16411880 TCGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCAACT--ATTACTTCGGATAGAC
** ** * *
16411921 TCGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
16411960 T-GATGAGACACTGGGTGTCAACTATTACTTCG
1 TCGATGAGACACTGGGTGTCAACTATTACTTCG
16411992 AACTATCCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 18 0.32
39 20 0.35
41 16 0.28
42 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
Found at i:16412130 original size:11 final size:11
Alignment explanation
Indices: 16412114--16412138 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16412104 CATTGAAATA
16412114 AAAAAAAAAAG
1 AAAAAAAAAAG
16412125 AAAAAAAAAAG
1 AAAAAAAAAAG
16412136 AAA
1 AAA
16412139 TTGAATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:16412157 original size:18 final size:18
Alignment explanation
Indices: 16412134--16412174 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16412124 GAAAAAAAAA
16412134 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
16412152 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
16412170 AGAAA
1 AGAAA
16412175 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:16412686 original size:20 final size:20
Alignment explanation
Indices: 16412663--16412700 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16412653 GTTATTAAGT
16412663 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
16412683 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
16412701 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:16413761 original size:29 final size:29
Alignment explanation
Indices: 16413724--16413780 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
16413714 CACCTTGACA
* *
16413724 CGAATTCTCAATGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTTCACCG
16413753 CGAACTCTCAACGAACAAGTTCTTCACC
1 CGAACTCTCAACGAACAAGTTCTTCACC
16413781 TCTTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.25
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTTCACCG
Found at i:16424683 original size:13 final size:13
Alignment explanation
Indices: 16424665--16424690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16424655 AAGTAATCGT
16424665 ACATGGGCGTGTC
1 ACATGGGCGTGTC
16424678 ACATGGGCGTGTC
1 ACATGGGCGTGTC
16424691 TCTGCCGAGC
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:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
ACATGGGCGTGTC
Found at i:16426949 original size:39 final size:38
Alignment explanation
Indices: 16426882--16427016 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
16426872 ACCAATATGG
* *
16426882 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAAATGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGTAATAAATGA
* ** *
16426921 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGTAATAAATGA
* * * * * *
16426959 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGTAATA-AATGA
*
16427000 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
16427017 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 17 0.23
39 36 0.49
40 4 0.05
41 16 0.22
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGTAATAAATGA
Found at i:16428561 original size:17 final size:17
Alignment explanation
Indices: 16428539--16428573 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16428529 GAATGCTCTC
*
16428539 TGTTTCTTATTCTTCTT
1 TGTTTCTTATTATTCTT
*
16428556 TGTTTCTTTTTATTCTT
1 TGTTTCTTATTATTCTT
16428573 T
1 T
16428574 TTCTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTTATTATTCTT
Found at i:16430823 original size:5 final size:5
Alignment explanation
Indices: 16430805--16430839 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
16430795 CCAATTTTTG
16430805 AAAAT AAAATT AAAAT AAAAT ATAAAT AAAAT AAA
1 AAAAT AAAA-T AAAAT AAAAT A-AAAT AAAAT AAA
16430840 GAACACACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:16430826 original size:16 final size:16
Alignment explanation
Indices: 16430805--16430839 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16430795 CCAATTTTTG
16430805 AAAATA-AAATTAAAAT
1 AAAATATAAA-TAAAAT
16430821 AAAATATAAATAAAAT
1 AAAATATAAATAAAAT
16430837 AAA
1 AAA
16430840 GAACACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATAAATAAAAT
Found at i:16430837 original size:11 final size:12
Alignment explanation
Indices: 16430805--16430837 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
16430795 CCAATTTTTG
16430805 AAAATAAAAT-T
1 AAAATAAAATAT
16430816 AAAATAAAATAT
1 AAAATAAAATAT
16430828 -AAATAAAATA
1 AAAATAAAATA
16430838 AAGAACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:16432010 original size:2 final size:2
Alignment explanation
Indices: 16432005--16432037 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16431995 TGTTTTATGT
*
16432005 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16432038 TTATTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16432358 original size:17 final size:18
Alignment explanation
Indices: 16432327--16432361 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16432317 AATTTAATTA
*
16432327 TTTTATCTAATAAATATC
1 TTTTATCTAAAAAATATC
16432345 TTTTA-CTAAAAAATATC
1 TTTTATCTAAAAAATATC
16432362 ACAAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTATCTAAAAAATATC
Found at i:16432859 original size:41 final size:41
Alignment explanation
Indices: 16432808--16432889 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
16432798 AACTTAATAA
*
16432808 TGATTACACTTTTACAATTTAGTCCCCATATTATAGTTAAC
1 TGATTACACTTTTACAATTTAGTCCCCATACTATAGTTAAC
*
16432849 TGATTGCACTTTTACAATTTAGTCCCCATACTATAGTTAAC
1 TGATTACACTTTTACAATTTAGTCCCCATACTATAGTTAAC
16432890 CGCTTTCTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (41 bp):
TGATTACACTTTTACAATTTAGTCCCCATACTATAGTTAAC
Found at i:16441808 original size:24 final size:24
Alignment explanation
Indices: 16441776--16441826 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16441766 ACATCAGCTG
16441776 ATTGATTAATGTGAAAAACCATGA
1 ATTGATTAATGTGAAAAACCATGA
16441800 ATTGATTAATGTGAAAAACCATGA
1 ATTGATTAATGTGAAAAACCATGA
16441824 ATT
1 ATT
16441827 TCATACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (24 bp):
ATTGATTAATGTGAAAAACCATGA
Found at i:16446478 original size:20 final size:20
Alignment explanation
Indices: 16446453--16446495 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16446443 GTTTGCTTGC
16446453 CTTCAGTCTGCCATTTTTGG
1 CTTCAGTCTGCCATTTTTGG
16446473 CTTCAGTCTGCCATTTTTGG
1 CTTCAGTCTGCCATTTTTGG
16446493 CTT
1 CTT
16446496 GCACCCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.19, T:0.47
Consensus pattern (20 bp):
CTTCAGTCTGCCATTTTTGG
Found at i:16446602 original size:72 final size:72
Alignment explanation
Indices: 16446516--16446658 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
16446506 GGGCTTGCAT
* ** *
16446516 TTTGCTGCTCGCAACTATACACCTTTGACAGGCTCGCTTTTTTGCTTACTGTCTTCAACAGGTGT
1 TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
16446581 CTTCAAC
66 CTTCAAC
* ***
16446588 TTTGCTGCTTGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAGTTGGTGT
1 TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
16446653 CTTCAA
66 CTTCAA
16446659 TAGGCTCGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.37
Consensus pattern (72 bp):
TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
CTTCAAC
Found at i:16446706 original size:25 final size:25
Alignment explanation
Indices: 16446678--16446728 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16446668 AACTATCACT
*
16446678 TCTTGCTAAGCTTGCAGCTTTGACA
1 TCTTGCTAAGCTTGCAGCTTGGACA
16446703 TCTTGCTAAGCTTGCAGCTTGGACA
1 TCTTGCTAAGCTTGCAGCTTGGACA
16446728 T
1 T
16446729 TGGAAAGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (25 bp):
TCTTGCTAAGCTTGCAGCTTGGACA
Found at i:16449918 original size:2 final size:2
Alignment explanation
Indices: 16449913--16449944 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16449903 TTTGTATTTC
16449913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16449945 AAGTTAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16463177 original size:2 final size:2
Alignment explanation
Indices: 16463170--16463208 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16463160 CAGATGAGGC
16463170 AG AG AG AG 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 AG AG AG AG A
16463209 ATAGAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16464022 original size:13 final size:13
Alignment explanation
Indices: 16464004--16464030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16463994 AAGAAAGTAT
16464004 TGAAACATGTTTC
1 TGAAACATGTTTC
16464017 TGAAACATGTTTC
1 TGAAACATGTTTC
16464030 T
1 T
16464031 ATTACTCATT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGAAACATGTTTC
Found at i:16474413 original size:19 final size:19
Alignment explanation
Indices: 16474389--16474426 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16474379 CTTTGAACTG
16474389 AAAGAAAACTTGAACCTTT
1 AAAGAAAACTTGAACCTTT
16474408 AAAGAAAACTTGAACCTTT
1 AAAGAAAACTTGAACCTTT
16474427 CCTCGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAGAAAACTTGAACCTTT
Found at i:16476524 original size:18 final size:18
Alignment explanation
Indices: 16476501--16476540 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16476491 CATAAATTAA
*
16476501 AAAAATAAAAATCATTTT
1 AAAAATAAAAATCAATTT
* *
16476519 AAAAATATAAATTAATTT
1 AAAAATAAAAATCAATTT
16476537 AAAA
1 AAAA
16476541 TGTATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATAAAAATCAATTT
Found at i:16476587 original size:31 final size:31
Alignment explanation
Indices: 16476549--16476625 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
16476539 AATGTATAAT
* * * * *
16476549 TTTTGGACAAGTTTAAGTATCAATTAGATAC
1 TTTTGGACAAGTTCAAATACCAACTAAATAC
16476580 TTTTGGACAAGTTCAAATACCAACTAAATAC
1 TTTTGGACAAGTTCAAATACCAACTAAATAC
16476611 TTTTGGACAAGTTCA
1 TTTTGGACAAGTTCA
16476626 TAGGGCAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (31 bp):
TTTTGGACAAGTTCAAATACCAACTAAATAC
Found at i:16477974 original size:3 final size:3
Alignment explanation
Indices: 16477966--16477996 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16477956 AGTTTAGAAT
16477966 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16477997 CAAAACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16490621 original size:25 final size:25
Alignment explanation
Indices: 16490587--16490638 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16490577 CATATATGCC
16490587 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
16490612 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
16490637 AT
1 AT
16490639 ACTTTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (25 bp):
ATTGCTAATTCCCTAATGGTCTCAG
Found at i:16496873 original size:5 final size:5
Alignment explanation
Indices: 16496857--16496889 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
16496847 AATCAAAATG
16496857 GAAAA GGAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA GA
16496890 GAAACAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:16498769 original size:26 final size:27
Alignment explanation
Indices: 16498703--16498769 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
16498693 ACAACGATAT
* *
16498703 AAACTAAATCTAACTTTTTAAATCCGA
1 AAACTAAATCTAACTTTTCAAATACGA
* *
16498730 AAA-TAAAAAACTAA-TTTTCAAATATGA
1 AAACT--AAATCTAACTTTTCAAATACGA
16498757 AAACTAAATCTAA
1 AAACTAAATCTAA
16498770 AACTCATACT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.25
27 16 0.50
28 8 0.25
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (27 bp):
AAACTAAATCTAACTTTTCAAATACGA
Found at i:16505487 original size:61 final size:64
Alignment explanation
Indices: 16505358--16505487 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 64
16505348 AAAAACAAAA
* *
16505358 TAAATTATTTAAGTTTATTTTTTACCTAATTAATATTTAGAAACTATTTATACTTAGATATTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
* * *
16505422 --AATTATTAAATTTTA-TTTTTACCAAATTAATATTTAGATACTATTTCGTA-TTAG-T-TTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTT-ATACTTAGATATTAC
16505481 TAAATTA
1 TAAATTA
16505488 AACTAAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
59 4 0.07
60 1 0.02
61 38 0.66
62 15 0.26
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (64 bp):
TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
Found at i:16508425 original size:19 final size:20
Alignment explanation
Indices: 16508393--16508433 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16508383 AAAGAATAAC
16508393 ATTAATAAT-AAAAAATCAA
1 ATTAATAATAAAAAAATCAA
16508412 ATTAA-AATACAAAAAATCAA
1 ATTAATAATA-AAAAAATCAA
16508432 AT
1 AT
16508434 CAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 5 0.25
20 12 0.60
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTAATAATAAAAAAATCAA
Found at i:16508433 original size:25 final size:23
Alignment explanation
Indices: 16508405--16508456 Score: 86
Period size: 25 Copynumber: 2.2 Consensus size: 23
16508395 TAATAATAAA
16508405 AAATCAAATTAAAATACAAAAAAT
1 AAATCAAATTAAAATA-AAAAAAT
16508429 CAAATCAAATTAAAATAAAAAAAT
1 -AAATCAAATTAAAATAAAAAAAT
16508453 AAAT
1 AAAT
16508457 TCCACCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 4 0.15
24 7 0.26
25 16 0.59
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATCAAATTAAAATAAAAAAAT
Found at i:16516957 original size:39 final size:39
Alignment explanation
Indices: 16516903--16516980 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
16516893 AAAAAAAAAG
16516903 AAAACGACAGTGGTTGACTTCGGCTAAACACTTACTGCA
1 AAAACGACAGTGGTTGACTTCGGCTAAACACTTACTGCA
16516942 AAAACGACAGTGGTTGACTTCGGCTAAACACTTACTGCA
1 AAAACGACAGTGGTTGACTTCGGCTAAACACTTACTGCA
16516981 CGAACTAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (39 bp):
AAAACGACAGTGGTTGACTTCGGCTAAACACTTACTGCA
Found at i:16517932 original size:22 final size:20
Alignment explanation
Indices: 16517906--16517947 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
16517896 TTTATAAGTT
16517906 TAAAAATTAAAATTAATTTAAA
1 TAAAAATT-AAATT-ATTTAAA
16517928 TAAAAATTAAATTATTTAAA
1 TAAAAATTAAATTATTTAAA
16517948 AATTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTAAATTATTTAAA
Found at i:16517933 original size:16 final size:16
Alignment explanation
Indices: 16517909--16517954 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
16517899 ATAAGTTTAA
*
16517909 AAATTAAAATTAATTT
1 AAATAAAAATTAATTT
*
16517925 AAATAAAAATTAAATT
1 AAATAAAAATTAATTT
**
16517941 ATTTAAAAATTAAT
1 AAATAAAAATTAAT
16517955 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAAAAATTAATTT
Found at i:16517950 original size:22 final size:22
Alignment explanation
Indices: 16517905--16517965 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 22
16517895 TTTTATAAGT
16517905 TTAAAAATTAAAATTAATTTAAA
1 TTAAAAATT-AAATTAATTTAAA
16517928 -TAAAAATTAAATT-ATTTAAAAA
1 TTAAAAATTAAATTAATTT--AAA
16517950 TTAATAAAATTAAATT
1 TT-A-AAAATTAAATT
16517966 TCTTCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 11 0.33
23 1 0.03
24 1 0.03
25 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAAATTAAATTAATTTAAA
Found at i:16517959 original size:20 final size:20
Alignment explanation
Indices: 16517906--16517961 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
16517896 TTTATAAGTT
16517906 TAAAAATTAAAATTAATTTAAA
1 TAAAAA-TAAAATT-ATTTAAA
*
16517928 TAAAAATTAAATTATTTAAA
1 TAAAAATAAAATTATTTAAA
*
16517948 -AATTAATAAAATTA
1 TAA-AAATAAAATTA
16517962 AATTTCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 6 0.20
22 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATTATTTAAA
Found at i:16520936 original size:25 final size:24
Alignment explanation
Indices: 16520903--16520951 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16520893 AAAAACATAA
*
16520903 ATATGATAAGATAATAATAAAAATT
1 ATATAATAAGATAA-AATAAAAATT
* *
16520928 ATATAATAATATGAAATAAAAATT
1 ATATAATAAGATAAAATAAAAATT
16520952 TAAATTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
ATATAATAAGATAAAATAAAAATT
Found at i:16529961 original size:53 final size:53
Alignment explanation
Indices: 16529806--16529970 Score: 219
Period size: 53 Copynumber: 3.1 Consensus size: 53
16529796 GACGAAAAAT
* * **
16529806 ATGTGATAA-GTG-TGCCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
*
16529857 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* *
16529910 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGATTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
16529964 TATGTGA
1 -ATGTGA
16529971 ACCGTGTAAG
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
51 9 0.09
52 4 0.04
53 81 0.80
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:16531555 original size:2 final size:2
Alignment explanation
Indices: 16531548--16531576 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16531538 AAATTGACAA
16531548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16531577 AACATCCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16531998 original size:31 final size:32
Alignment explanation
Indices: 16531939--16532003 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
16531929 TTATCAATAA
16531939 AAATTATTTAAAAATAATTTATTATTAT-ATT
1 AAATTATTTAAAAATAATTTATTATTATAATT
*
16531970 AAATTATTTAATTAA-AATTTA-TAGTTATAATT
1 AAATTATTTAA-AAATAATTTATTA-TTATAATT
16532002 AA
1 AA
16532004 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.07
31 21 0.70
32 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
AAATTATTTAAAAATAATTTATTATTATAATT
Found at i:16540015 original size:11 final size:12
Alignment explanation
Indices: 16539993--16540026 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
16539983 AGATTTTTAA
16539993 TTTTCATTTTTCC
1 TTTTC-TTTTTCC
16540006 TTTT-TTTTTCC
1 TTTTCTTTTTCC
16540017 TTTTCTTTTT
1 TTTTCTTTTT
16540027 TGTCGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 5 0.25
13 4 0.20
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTCC
Found at i:16543056 original size:19 final size:19
Alignment explanation
Indices: 16543022--16543083 Score: 90
Period size: 19 Copynumber: 3.2 Consensus size: 19
16543012 ATTACAAAAA
16543022 AAATAATTTTTAAAAATTCT
1 AAATAATTTTT-AAAATTCT
16543042 AAATAATTTTTAAAATTCT
1 AAATAATTTTTAAAATTCT
*
16543061 AAAT-ATTTATAAAAATTCT
1 AAATAATTT-TTAAAATTCT
16543080 AAAT
1 AAAT
16543084 TTTATATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 4 0.10
19 25 0.62
20 11 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATTTTTAAAATTCT
Found at i:16543083 original size:26 final size:25
Alignment explanation
Indices: 16543054--16543107 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
16543044 ATAATTTTTA
16543054 AAATTCTAAATATTTATAAAAATTCT
1 AAATTCTAAATATTTA-AAAAATTCT
* * *
16543080 AAATTTTATATTTTTAAAAAATTCT
1 AAATTCTAAATATTTAAAAAATTCT
16543105 AAA
1 AAA
16543108 AAATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTCTAAATATTTAAAAAATTCT
Found at i:16543114 original size:25 final size:26
Alignment explanation
Indices: 16543066--16543115 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
16543056 ATTCTAAATA
***
16543066 TTTATAAAAATTCTAAATTTTATATT
1 TTTATAAAAATTCTAAAAAATATATT
16543092 TTTA-AAAAATTCTAAAAAATATAT
1 TTTATAAAAATTCTAAAAAATATAT
16543116 AAAGAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTATAAAAATTCTAAAAAATATATT
Found at i:16544259 original size:9 final size:9
Alignment explanation
Indices: 16544247--16544276 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16544237 AAATATCTTA
*
16544247 CATATTGTG
1 CATACTGTG
16544256 CATACTGTG
1 CATACTGTG
16544265 CATACTGTG
1 CATACTGTG
16544274 CAT
1 CAT
16544277 CTTATACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (9 bp):
CATACTGTG
Found at i:16556979 original size:11 final size:11
Alignment explanation
Indices: 16556963--16556987 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16556953 ATATCTAGAA
16556963 TTCTCTTCATT
1 TTCTCTTCATT
16556974 TTCTCTTCATT
1 TTCTCTTCATT
16556985 TTC
1 TTC
16556988 ATCATCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:16557930 original size:8 final size:9
Alignment explanation
Indices: 16557907--16557954 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
16557897 TTATTAATAG
16557907 ATAT-TTAT
1 ATATATTAT
*
16557915 A-ATGTTAT
1 ATATATTAT
16557923 -TATATTAT
1 ATATATTAT
16557931 ATATA-TAT
1 ATATATTAT
16557939 ATATATATAT
1 ATATAT-TAT
16557949 ATATAT
1 ATATAT
16557955 AACAAAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 2 0.06
8 19 0.56
9 4 0.12
10 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATTAT
Found at i:16557935 original size:2 final size:2
Alignment explanation
Indices: 16557923--16557955 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16557913 ATAATGTTAT
16557923 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16557956 ACAAAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16559581 original size:18 final size:19
Alignment explanation
Indices: 16559530--16559590 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
16559520 AGATCGTCTA
*
16559530 TTACTGAATAATTTAATTG
1 TTACTGAATAATTTGATTG
*
16559549 TTAC--AATATATTTGATTT
1 TTACTGAATA-ATTTGATTG
*
16559567 TTACTGAATAA-TTGACTG
1 TTACTGAATAATTTGATTG
16559585 TTACTG
1 TTACTG
16559591 GGTAACCGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 4 0.11
18 22 0.63
19 5 0.14
20 4 0.11
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (19 bp):
TTACTGAATAATTTGATTG
Found at i:16559636 original size:18 final size:18
Alignment explanation
Indices: 16559612--16559666 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
16559602 AATTGATTGA
16559612 TACTGAATAACTGATTAT
1 TACTGAATAACTGATTAT
* * *
16559630 TATTGAATAATTGATTGT
1 TACTGAATAACTGATTAT
* *
16559648 TACCGAATAACTGACTAT
1 TACTGAATAACTGATTAT
16559666 T
1 T
16559667 TCTAAATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (18 bp):
TACTGAATAACTGATTAT
Found at i:16559675 original size:36 final size:36
Alignment explanation
Indices: 16559602--16559684 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
16559592 GTAACCGATC
* * * *
16559602 AATTGATTGATACTGAATAACTGATTATTATTGAAT
1 AATTGATTGTTACCGAATAACTGACTATTATTAAAT
16559638 AATTGATTGTTACCGAATAACTGACTATT-TCTAAAT
1 AATTGATTGTTACCGAATAACTGACTATTAT-TAAAT
* *
16559674 AAATAATTGTT
1 AATTGATTGTT
16559685 CTGATACGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTATTATTAAAT
Found at i:16577353 original size:16 final size:16
Alignment explanation
Indices: 16577332--16577364 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16577322 CTCTAAGGAG
16577332 CATACTTATATTTTGC
1 CATACTTATATTTTGC
16577348 CATACTTATATTTTGC
1 CATACTTATATTTTGC
16577364 C
1 C
16577365 TTTGCAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
CATACTTATATTTTGC
Found at i:16584330 original size:2 final size:2
Alignment explanation
Indices: 16584323--16584349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16584313 ATCCATTGTA
16584323 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
16584350 AGGTCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:16589139 original size:32 final size:32
Alignment explanation
Indices: 16589103--16589166 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
16589093 GGGGGAGCTT
16589103 TTGTTGAAGAGAAAACAAGGGAGGGAAAGTCA
1 TTGTTGAAGAGAAAACAAGGGAGGGAAAGTCA
16589135 TTGTTGAAGAGAAAACAAGGGAGGGAAAGTCA
1 TTGTTGAAGAGAAAACAAGGGAGGGAAAGTCA
16589167 ATGCTTGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.34, T:0.16
Consensus pattern (32 bp):
TTGTTGAAGAGAAAACAAGGGAGGGAAAGTCA
Found at i:16590811 original size:23 final size:22
Alignment explanation
Indices: 16590780--16590822 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16590770 AAATTTAAAT
*
16590780 TTATCTATTTTTATTTTAAAAAA
1 TTATCTATTTAT-TTTTAAAAAA
*
16590803 TTATTTATTTATTTTTAAAA
1 TTATCTATTTATTTTTAAAA
16590823 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATCTATTTATTTTTAAAAAA
Found at i:16606758 original size:20 final size:21
Alignment explanation
Indices: 16606719--16606769 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
16606709 TCTAAATTCT
*
16606719 ATATAAAT-TTTTAAATAATA
1 ATATAAATAATTTAAATAATA
16606739 ATATAAATAATTTAAA-AATA
1 ATATAAATAATTTAAATAATA
*
16606759 TTA-AAATAATT
1 ATATAAATAATT
16606770 AGACATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAATAATTTAAATAATA
Found at i:16608058 original size:19 final size:19
Alignment explanation
Indices: 16608025--16608073 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
16608015 CGTAAATATG
*
16608025 AAAAAAATTAGGTAC-AAA
1 AAAAAAATTAAGTACGAAA
16608043 AAAAAAATGTAAGTACGAAA
1 AAAAAAAT-TAAGTACGAAA
16608063 ATGAAAAAATT
1 A--AAAAAATT
16608074 GATACATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
20 4 0.15
21 1 0.04
22 7 0.27
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.18
Consensus pattern (19 bp):
AAAAAAATTAAGTACGAAA
Found at i:16610776 original size:24 final size:25
Alignment explanation
Indices: 16610749--16610797 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16610739 GTCCCATTAA
16610749 TTTCTTAGAT-TCTTCCCTTTTTTT
1 TTTCTTAGATCTCTTCCCTTTTTTT
** *
16610773 TTTCTTTTATCTTTTCCCTTTTTTT
1 TTTCTTAGATCTCTTCCCTTTTTTT
16610798 CTGGTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTCTTAGATCTCTTCCCTTTTTTT
Found at i:16612408 original size:3 final size:3
Alignment explanation
Indices: 16612402--16612608 Score: 149
Period size: 3 Copynumber: 68.7 Consensus size: 3
16612392 AATAGAAGAC
* * * *
16612402 AAT AAT AAT AAT -AT ATT AAT AAA AAT AAT AAT -AT AAA AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** **
16612448 AAT AAA AAT -AT GTT TCT AAT AAT AAT AAT AAAT CAAT AAT GAA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT -AAT AAT
* * * *
16612494 AAAT ATAT ACAA AAT AAT AGT AAC AGT AAT AA- AAT AAGT -AT AAT -AT
1 -AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
16612540 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
16612586 AAT AAT AAC AAT ATT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
16612609 CACTCTCCCT
Statistics
Matches: 160, Mismatches: 31, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
2 13 0.08
3 127 0.79
4 20 0.12
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16612863 original size:17 final size:17
Alignment explanation
Indices: 16612841--16612915 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
16612831 TTTGTAGGCA
16612841 AGTGGGGTGATGGAGTT
1 AGTGGGGTGATGGAGTT
*
16612858 AGT--GG-GATGG-TTT
1 AGTGGGGTGATGGAGTT
* *
16612871 AATTGGGTGATGGAGTT
1 AGTGGGGTGATGGAGTT
16612888 AGTGGGGTGATGGAGTT
1 AGTGGGGTGATGGAGTT
16612905 AGTGGGGTGAT
1 AGTGGGGTGAT
16612916 TTAGTAGGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 4 0.08
16 5 0.10
17 31 0.63
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (17 bp):
AGTGGGGTGATGGAGTT
Found at i:16614098 original size:29 final size:29
Alignment explanation
Indices: 16614056--16614115 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
16614046 ACGAAATGAA
* *
16614056 AACCGAATATATGGTCAATCAATATTTTG
1 AACCGAATATATGGTCAAACAATATTATG
*
16614085 AACCGAGTATATGGTCAAACAATATTATG
1 AACCGAATATATGGTCAAACAATATTATG
16614114 AA
1 AA
16614116 ACTTCAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (29 bp):
AACCGAATATATGGTCAAACAATATTATG
Found at i:16614327 original size:21 final size:21
Alignment explanation
Indices: 16614301--16614341 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16614291 TAACAGGAGT
16614301 GCTGACGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
16614322 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCAAGTTAACT
16614342 TGCCACGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:16623816 original size:53 final size:53
Alignment explanation
Indices: 16623675--16623825 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
16623665 ACAAGTGTGC
* **
16623675 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
16623728 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
16623781 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
16623826 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:16625784 original size:20 final size:20
Alignment explanation
Indices: 16625747--16625784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16625737 TGATGGGGAG
*
16625747 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
16625767 CAAGAA-ATCTAAGCTGGA
1 CAAGAATATC-AAGCTGGA
16625785 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:16627775 original size:25 final size:25
Alignment explanation
Indices: 16627741--16627791 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16627731 CTGATATGAA
16627741 ATGTGTAAGACCATGGTTGAAAGAT
1 ATGTGTAAGACCATGGTTGAAAGAT
16627766 ATGTGTAAGACCATGGTTGAAAGAT
1 ATGTGTAAGACCATGGTTGAAAGAT
16627791 A
1 A
16627792 CCATGGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.27
Consensus pattern (25 bp):
ATGTGTAAGACCATGGTTGAAAGAT
Found at i:16627811 original size:71 final size:71
Alignment explanation
Indices: 16627695--16627837 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
16627685 CTGATATGAA
* ***
16627695 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTG
16627760 AAAGAT
66 AAAGAT
*
16627766 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTG
16627831 AAAGAT
66 AAAGAT
16627837 A
1 A
16627838 CCATGGCAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (71 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTG
AAAGAT
Found at i:16627822 original size:46 final size:46
Alignment explanation
Indices: 16627772--16627896 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
16627762 AGATATGTGT
* *
16627772 AAGACCATGGTTGAAAGATACCATGGCAACGTGATATG-AAATGAAC
1 AAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAAC
**
16627818 AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAAC
* * * *
16627864 AAGACCATAGTTGAAAGACACTATGGCATCATG
1 AAGACCATGGTTGAAAGATACCATGGCAACATG
16627897 TCAAAGATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (46 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAAC
Found at i:16634047 original size:13 final size:13
Alignment explanation
Indices: 16634029--16634055 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16634019 CAATAGCCAG
16634029 TTATTTCATTCAA
1 TTATTTCATTCAA
16634042 TTATTTCATTCAA
1 TTATTTCATTCAA
16634055 T
1 T
16634056 GATCCAAAGA
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:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTCATTCAA
Found at i:16634533 original size:30 final size:30
Alignment explanation
Indices: 16634492--16634563 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
16634482 CGGTTGGCCT
* *
16634492 GGTGCTGGTGGCGGCT-TAGGTGGTGGGGGA
1 GGTGGTGGTGGCGG-TGGAGGTGGTGGGGGA
* *
16634522 GGTGGTGGTGGCGGTGGCGGTGGTGGTGGA
1 GGTGGTGGTGGCGGTGGAGGTGGTGGGGGA
*
16634552 GGTGGGGGTGGC
1 GGTGGTGGTGGC
16634564 AAAGGAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.04, C:0.08, G:0.65, T:0.22
Consensus pattern (30 bp):
GGTGGTGGTGGCGGTGGAGGTGGTGGGGGA
Done.