Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 72 of 206
Found at i:20298815 original size:14 final size:14
Alignment explanation
Indices: 20298796--20298825 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20298786 GTTTGACTAA
20298796 AAGAATTCATTTTC
1 AAGAATTCATTTTC
20298810 AAGAATTCATTTTC
1 AAGAATTCATTTTC
20298824 AA
1 AA
20298826 AAACACGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
AAGAATTCATTTTC
Found at i:20298939 original size:16 final size:16
Alignment explanation
Indices: 20298918--20298951 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20298908 GGTCAGCCTC
*
20298918 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
20298934 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
20298950 TC
1 TC
20298952 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:20314213 original size:17 final size:17
Alignment explanation
Indices: 20314191--20314254 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
20314181 TTAATGAGAT
20314191 AAAAATAAATAAATAAC
1 AAAAATAAATAAATAAC
*
20314208 AAAAATAAATAAATACC
1 AAAAATAAATAAATAAC
* *
20314225 AAAAATAAACAAATGAC
1 AAAAATAAATAAATAAC
* *
20314242 TAAAATCAATAAA
1 AAAAATAAATAAA
20314255 CCAATCAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAATAAC
Found at i:20318390 original size:35 final size:35
Alignment explanation
Indices: 20318350--20318423 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
20318340 CCATAAAACA
* *
20318350 CCAATGCTTATAAGAGCTAATCTAACCGAAACACG
1 CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
*
20318385 CCAATGCTCATAAGAGCTAATCCAACCGAAATACG
1 CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
20318420 CCAA
1 CCAA
20318424 ATAGAGAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.18
Consensus pattern (35 bp):
CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
Found at i:20328570 original size:22 final size:22
Alignment explanation
Indices: 20328508--20328576 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
20328498 ATTGTTCAAA
* **
20328508 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
20328530 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
20328552 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
20328574 CAT
1 CAT
20328577 CCGTCTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:20331274 original size:43 final size:42
Alignment explanation
Indices: 20331211--20331336 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 42
20331201 AGGATTCCGT
*
20331211 TATGTGTTATCGTGTAAGACCACGTCTAGGACGTTGGCATCGAC
1 TATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCG-C
*
20331255 T-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGC
*
20331297 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
20331337 TGTACGATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
42 3 0.04
43 63 0.88
44 6 0.08
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGC
Found at i:20340871 original size:4 final size:4
Alignment explanation
Indices: 20340862--20340997 Score: 92
Period size: 4 Copynumber: 34.0 Consensus size: 4
20340852 GAAGGAGAGG
* *
20340862 GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA
*
20340910 GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
20340956 GAAAA GGAAAA GAGAA G-AA -AAA GAAA GAAA GAAG GAAA GAAA
1 G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20340998 AGGGAAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 30
0.74 0.05 0.20
Matches are distributed among these distances:
3 22 0.20
4 60 0.55
5 20 0.18
6 7 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20340897 original size:18 final size:17
Alignment explanation
Indices: 20340862--20340997 Score: 80
Period size: 18 Copynumber: 8.2 Consensus size: 17
20340852 GAAGGAGAGG
*
20340862 GAAAGAAAGA-AAGAAA
1 GAAAGAAAGAGAGGAAA
20340878 GAAAGAAAGGAGAGGAAA
1 GAAAGAAA-GAGAGGAAA
*
20340896 GAAAGAAAAAGAAGGAAA
1 GAAAGAAAGAG-AGGAAA
20340914 GAAAAGGAAAG-GA-GAAGA
1 G-AAA-GAAAGAGAGGAA-A
*
20340932 GAAA-AAA-A-AAGAAA
1 GAAAGAAAGAGAGGAAA
*
20340946 GAAAG-AAGA-AGAAAA
1 GAAAGAAAGAGAGGAAA
20340961 GGAAAAGAGAAGA-A--AAA
1 -G-AAAGA-AAGAGAGGAAA
20340978 GAAAGAAAGA-AGGAAA
1 GAAAGAAAGAGAGGAAA
20340994 GAAA
1 GAAA
20340998 AGGGAAAAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 32
0.73 0.04 0.24
Matches are distributed among these distances:
14 13 0.13
15 16 0.16
16 17 0.17
17 17 0.17
18 23 0.23
19 9 0.09
20 4 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAGAGGAAA
Found at i:20340914 original size:36 final size:36
Alignment explanation
Indices: 20340867--20340994 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 36
20340857 AGAGGGAAAG
20340867 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
* * *
20340903 AAAGAAGGAAAGAAAAGGAAAGGAGA--AGAGAAAAAA
1 AAAGAAAGAAAG-AAA-GAAAGGAGAGGAAAGAAAGAA
* *
20340939 AAAGAAAGAAAG-AAG-AAGAAAAGGAAAAGAGAAGAA
1 AAAGAAAGAAAGAAAGAAAGGAGAGG-AAAGA-AAGAA
*
20340975 AAAGAAAGAAAGAAGGAAAG
1 AAAGAAAGAAAGAAAGAAAG
20340995 AAAAGGGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
32 5 0.07
33 1 0.01
34 2 0.03
35 4 0.05
36 46 0.61
37 5 0.07
38 12 0.16
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (36 bp):
AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
Found at i:20340979 original size:64 final size:64
Alignment explanation
Indices: 20340853--20340997 Score: 149
Period size: 64 Copynumber: 2.3 Consensus size: 64
20340843 GGGGGGGCAG
* * * *
20340853 AAGGAGAGGGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAGGAAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGAAAAGAA
*
20340917 AAGGAAAGGAGAAGAGAAA-AAA-AAAGAAAGAAAGAAGAAG-AA-AAGGAAAAGAGAAGAAAA-
1 AAGGAAAGG-GAA-AGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAA-AGAAGAAAAG
20340977 AGA
63 A-A
20340980 AA-GAAAGAAGGAAAGAAA
1 AAGGAAAG--GGAAAGAAA
20340998 AGGGAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
62 18 0.26
63 16 0.23
64 25 0.36
65 6 0.09
66 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (64 bp):
AAGGAAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGAAAAGAA
Found at i:20340998 original size:32 final size:32
Alignment explanation
Indices: 20340871--20341042 Score: 131
Period size: 36 Copynumber: 5.2 Consensus size: 32
20340861 GGAAAGAAAG
* *
20340871 AAAGAAAGAAAGAAAGGAGAGGAAAGA-AAGAA
1 AAAGAAAGAAAG-AAGGAAAGAAAAGAGAAGAA
* * *
20340903 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAG--AAGGAAA-GAAAAGAG-AAGAA
20340939 AAAGAAAGAAAGAAGAAGAAAAGGAAAAGAGAAGAA
1 AAAGAAAGAAAGAAG--G-AAA-GAAAAGAGAAGAA
*
20340975 AAAGAAAGAAAGAAGGAAAGAAAAGGGAA-AA
1 AAAGAAAGAAAGAAGGAAAGAAAAGAGAAGAA
* * *
20341006 AAA-AAGGGAAGGAAGGAAA-AAAA-AAAAGAA
1 AAAGAA-AGAAAGAAGGAAAGAAAAGAGAAGAA
20341036 AAA-AAAG
1 AAAGAAAG
20341043 GTAATTTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.03
30 13 0.11
31 16 0.14
32 20 0.17
33 10 0.09
34 9 0.08
36 35 0.30
37 11 0.09
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (32 bp):
AAAGAAAGAAAGAAGGAAAGAAAAGAGAAGAA
Found at i:20341011 original size:44 final size:42
Alignment explanation
Indices: 20340893--20341036 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 42
20340883 AAAGGAGAGG
* * *
20340893 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAG--AAAGAA-G-AAGAAAAGAAAAAGAGAAGAAAAAAAA
*
20340939 AAAGAAAGAAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAGAAA
1 AAAGAAAGAAAGAAGAAGAAAAGAAAAAGAGAAGAAAAA-AAA
* * *
20340982 GAAAGAAGGAAAGAA-AAGGGAAAA-AAAAAGGGAAGGAAGGAAAAA
1 -AAAGAAAGAAAGAAGAA--GAAAAGAAAAAGAGAA-GAA-AAAAAA
20341027 AAA-AAAGAAA
1 AAAGAAAGAAA
20341037 AAAAAGGTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
42 22 0.26
43 12 0.14
44 30 0.35
45 11 0.13
46 10 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (42 bp):
AAAGAAAGAAAGAAGAAGAAAAGAAAAAGAGAAGAAAAAAAA
Found at i:20341043 original size:22 final size:22
Alignment explanation
Indices: 20340933--20341043 Score: 57
Period size: 22 Copynumber: 4.9 Consensus size: 22
20340923 AGGAGAAGAG
20340933 AAAAAAAAAGAAAGAAAGAA-GAA
1 AAAAAAAAAGAAA-AAA-AAGGAA
*
20340956 GAAAAGGAAAAGAGAAGAAAAA-GAA
1 -AAAA--AAAA-AGAAAAAAAAGGAA
* * * * *
20340981 AGAAAGAAGGAAAGAAAAGG-G
1 AAAAAAAAAGAAAAAAAAGGAA
** **
20341002 AAAAAAAAAGGGAAGGAAGGAA
1 AAAAAAAAAGAAAAAAAAGGAA
20341024 AAAAAAAAAGAAAAAAAAGG
1 AAAAAAAAAGAAAAAAAAGG
20341044 TAATTTTATT
Statistics
Matches: 62, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
21 19 0.31
22 20 0.32
24 7 0.11
25 5 0.08
26 7 0.11
27 4 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAGGAA
Found at i:20347558 original size:3 final size:3
Alignment explanation
Indices: 20347550--20347575 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20347540 TCTTAATACT
20347550 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
20347576 TAATAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20347663 original size:19 final size:21
Alignment explanation
Indices: 20347639--20347677 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
20347629 ACTAAAACAA
*
20347639 AAAATATTA-CAA-AATATAC
1 AAAATAATAGCAACAATATAC
20347658 AAAATAATAGCAACAATATA
1 AAAATAATAGCAACAATATA
20347678 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAGCAACAATATAC
Found at i:20347856 original size:27 final size:27
Alignment explanation
Indices: 20347826--20347910 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
20347816 CCAATCAATA
20347826 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* **
20347853 TGGCACCATTGGTGCCGCTAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* *
20347880 TGGCACCTTTGGTGCCGCCAATGACAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
20347907 TGGC
1 TGGC
20347911 GTGACCAAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:20347991 original size:26 final size:27
Alignment explanation
Indices: 20347962--20348029 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 27
20347952 GTTTTTTTTT
*
20347962 TATATATTTTGGTAAAT-AAAAATTTA
1 TATATATTTTGGTAAATAAAAAAGTTA
20347988 TATATATTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAAT-AAAAAAGTTA
20348016 TA-ATATTTTGGTAA
1 TATATATTTTGGTAA
20348030 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 17 0.44
27 12 0.31
28 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
TATATATTTTGGTAAATAAAAAAGTTA
Found at i:20348760 original size:15 final size:15
Alignment explanation
Indices: 20348740--20348786 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
20348730 CCCCTCCTCT
20348740 TTTTTTTTCTTCTTC
1 TTTTTTTTCTTCTTC
*
20348755 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTCTTC
* *
20348770 TTCTTCTTCTTCTTC
1 TTTTTTTTCTTCTTC
20348785 TT
1 TT
20348787 CTCCTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTTCTTC
Found at i:20348773 original size:3 final size:3
Alignment explanation
Indices: 20348746--20348809 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
20348736 CTCTTTTTTT
* * * *
20348746 TTC TTC TTC TTT TTT TTC TTT TTC TTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
20348794 TT- TGC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TT
20348810 TTGCTGCCCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:20348810 original size:6 final size:6
Alignment explanation
Indices: 20348737--20348811 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
20348727 CTCCCCCTCC
* * * *
20348737 TCTTTT TTTTTCT TCTTCTT T-TTTT TCTTTT TCTTCT TCTTCT TCTTCT
1 TCTTTT TCTTT-T TCTT-TT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
**
20348786 TCTCCT TCTTTGCT TCTTTT TCTTTT
1 TCTTTT TCTTT--T TCTTTT TCTTTT
20348812 GCTGCCCAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 42 0.72
7 6 0.10
8 7 0.12
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (6 bp):
TCTTTT
Found at i:20349202 original size:21 final size:21
Alignment explanation
Indices: 20349168--20349261 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 21
20349158 TTTGGTACTA
20349168 TCTCAT-ATTCTTTTAATATTC
1 TCTCATAATT-TTTTAATATTC
20349189 TCTCATAATTTTTTCAAT-TTC
1 TCTCATAATTTTTT-AATATTC
* *
20349210 T-TCAT-TTTTTTTTATACTTC
1 TCTCATAATTTTTTAATA-TTC
* *
20349230 -ATCATAATTTTTT-ATATTT
1 TCTCATAATTTTTTAATATTC
* *
20349249 TGTCAGAATTTTT
1 TCTCATAATTTTT
20349262 ATATTCCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 24 0.40
21 20 0.33
22 6 0.10
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (21 bp):
TCTCATAATTTTTTAATATTC
Found at i:20349214 original size:20 final size:21
Alignment explanation
Indices: 20349170--20349242 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
20349160 TGGTACTATC
*
20349170 TCAT-ATTCTTTTAATA-TTCT
1 TCATAATT-TTTTCATACTTCT
*
20349190 CTCATAATTTTTTCA-ATTTCT
1 -TCATAATTTTTTCATACTTCT
* * *
20349211 TCAT-TTTTTTTTATACTTCA
1 TCATAATTTTTTCATACTTCT
20349231 TCATAATTTTTT
1 TCATAATTTTTT
20349243 ATATTTTGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.17
20 13 0.31
21 19 0.45
22 3 0.07
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATAATTTTTTCATACTTCT
Found at i:20349787 original size:18 final size:18
Alignment explanation
Indices: 20349734--20349787 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
20349724 GGTTTTTTTA
20349734 TTTTGTTA-GGTTTAGGGG
1 TTTTGTTAGGGTTTA-GGG
20349752 TTTTGTTAGGG-TTAGGG
1 TTTTGTTAGGGTTTAGGG
20349769 TTTT-TTAAGGGTTTAGGG
1 TTTTGTT-AGGGTTTAGGG
20349787 T
1 T
20349788 CAAAACTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 18 0.55
19 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (18 bp):
TTTTGTTAGGGTTTAGGG
Found at i:20357510 original size:21 final size:20
Alignment explanation
Indices: 20357467--20357511 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20357457 TCCCTTGTAA
*
20357467 TTTTGGTACTTCCTTATATT
1 TTTTGGTACTTCCTCATATT
20357487 TTTTGGTA-TTCTCTCATAATT
1 TTTTGGTACTTC-CTCAT-ATT
20357508 TTTT
1 TTTT
20357512 ATACATACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTGGTACTTCCTCATATT
Found at i:20357601 original size:20 final size:20
Alignment explanation
Indices: 20357533--20357601 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
20357523 ATACTTCCTT
* *
20357533 AGATTTCTTCGTATTCCCTC
1 AGATTTTTTGGTATTCCCTC
* *
20357553 AGAATTTTTGGTATTTCCTC
1 AGATTTTTTGGTATTCCCTC
* *
20357573 ATATTTTTTGGTACTCCCTC
1 AGATTTTTTGGTATTCCCTC
20357593 AGATTTTTT
1 AGATTTTTT
20357602 TTTGTACTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (20 bp):
AGATTTTTTGGTATTCCCTC
Found at i:20357608 original size:22 final size:22
Alignment explanation
Indices: 20357547--20357624 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
20357537 TTCTTCGTAT
*
20357547 TCCCTCAGAA--TTTTTGGTAT
1 TCCCTCAGAATTTTTTTGGTAC
* *
20357567 TTCCTCA-TA-TTTTTTGGTAC
1 TCCCTCAGAATTTTTTTGGTAC
* *
20357587 TCCCTCAGATTTTTTTTTGTAC
1 TCCCTCAGAATTTTTTTGGTAC
* *
20357609 TTCCTCATAATTTTTT
1 TCCCTCAGAATTTTTT
20357625 GTATTGTTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 21 0.47
22 23 0.51
ACGTcount: A:0.17, C:0.21, G:0.09, T:0.54
Consensus pattern (22 bp):
TCCCTCAGAATTTTTTTGGTAC
Found at i:20357624 original size:20 final size:20
Alignment explanation
Indices: 20357549--20357627 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
20357539 CTTCGTATTC
* * *
20357549 CCTCAGAATTTTTGGTATTT
1 CCTCATAATTTTTTGTACTT
*
20357569 CCTCAT-ATTTTTTGGTACTC
1 CCTCATAATTTTTT-GTACTT
**
20357589 CCTCAGATTTTTTTTTGTACTT
1 CCTC--ATAATTTTTTGTACTT
20357611 CCTCATAATTTTTTGTA
1 CCTCATAATTTTTTGTA
20357628 TTGTTTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 6 0.13
20 24 0.51
22 11 0.23
23 6 0.13
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.53
Consensus pattern (20 bp):
CCTCATAATTTTTTGTACTT
Found at i:20358192 original size:20 final size:20
Alignment explanation
Indices: 20358145--20358230 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
20358135 GTATTCCTTT
*
20358145 ATAATTTTTGGTACTTGCTC
1 ATAATTTTTGGTACTTCCTC
*
20358165 ATATTTTTTGGTA-TTCCCTC
1 ATAATTTTTGGTACTT-CCTC
* *
20358185 GTAATTTTT--TACATT-TTC
1 ATAATTTTTGGTAC-TTCCTC
20358203 ATAATTTTTGGTACTTCCTC
1 ATAATTTTTGGTACTTCCTC
20358223 A-AATTTTT
1 ATAATTTTT
20358231 TATATTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
18 12 0.23
19 11 0.21
20 30 0.57
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (20 bp):
ATAATTTTTGGTACTTCCTC
Found at i:20358205 original size:38 final size:37
Alignment explanation
Indices: 20358163--20358238 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
20358153 TGGTACTTGC
* *
20358163 TCATATTTTTTGGTA-TTCCCTCGTAATTTTTTACATTT
1 TCATAATTTTTGGTACTT-CCTC-AAATTTTTTACATTT
*
20358201 TCATAATTTTTGGTACTTCCTCAAATTTTTTATATTT
1 TCATAATTTTTGGTACTTCCTCAAATTTTTTACATTT
20358238 T
1 T
20358239 TTTCATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 14 0.41
38 18 0.53
39 2 0.06
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (37 bp):
TCATAATTTTTGGTACTTCCTCAAATTTTTTACATTT
Found at i:20358246 original size:11 final size:10
Alignment explanation
Indices: 20358226--20358255 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
20358216 CTTCCTCAAA
20358226 TTTTTTATAT
1 TTTTTTATAT
20358236 TTTTTTCATAT
1 TTTTTT-ATAT
20358247 TTTTTTATA
1 TTTTTTATA
20358256 CATTCTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:20358294 original size:20 final size:20
Alignment explanation
Indices: 20358096--20358307 Score: 77
Period size: 20 Copynumber: 10.6 Consensus size: 20
20358086 ATTCCTTCGT
20358096 GTATATCCTCA-ATTTTTTT-
1 GTAT-TCCTCATATTTTTTTG
* *
20358115 GTAATTCTTCATCTTTTTTT-
1 GT-ATTCCTCATATTTTTTTG
* *
20358135 GTATTCCT-TTATAATTTTTG
1 GTATTCCTCATAT-TTTTTTG
*
20358155 GTACTTGCTCATA-TTTTTTG
1 GTA-TTCCTCATATTTTTTTG
* *
20358175 GTATTCCCTCGTAATTTTTT-
1 GTATT-CCTCATATTTTTTTG
** * *
20358195 ACATT-TTCATA-ATTTTTG
1 GTATTCCTCATATTTTTTTG
*
20358213 GTACTTCCTCAAATTTTTTAT-
1 GTA-TTCCTCATATTTTTT-TG
* * **
20358234 ATTTTTTTCATATTTTTTT-
1 GTATTCCTCATATTTTTTTG
* *
20358253 ATACATT-CTCATGTTTTTTTTG
1 GT--ATTCCTCAT-ATTTTTTTG
*
20358275 TTATTCCTCATATTTTTTTG
1 GTATTCCTCATATTTTTTTG
20358295 GTACTTCCTCATA
1 GTA-TTCCTCATA
20358308 ATTATTGGTA
Statistics
Matches: 142, Mismatches: 32, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
17 5 0.04
18 7 0.05
19 24 0.17
20 64 0.45
21 38 0.27
22 4 0.03
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (20 bp):
GTATTCCTCATATTTTTTTG
Found at i:20358317 original size:20 final size:21
Alignment explanation
Indices: 20358278--20358317 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20358268 TTTTTTGTTA
* *
20358278 TTCCTCATATTTTTTTGGTAC
1 TTCCTCATATATTATTGGTAC
20358299 TTCCTCATA-ATTATTGGTA
1 TTCCTCATATATTATTGGTA
20358318 TTATTATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (21 bp):
TTCCTCATATATTATTGGTAC
Found at i:20358525 original size:18 final size:18
Alignment explanation
Indices: 20358484--20358525 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20358474 TATATTTCAC
*
20358484 AATAATTTTAAAAAATAT
1 AATAAATTTAAAAAATAT
20358502 AA-AAATTTAAATAAATA-
1 AATAAATTTAAA-AAATAT
20358519 AATAAAT
1 AATAAAT
20358526 AAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATTTAAAAAATAT
Found at i:20358625 original size:2 final size:2
Alignment explanation
Indices: 20358620--20358653 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20358610 TTGTACTTTC
20358620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20358654 TTGTATTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20358736 original size:20 final size:20
Alignment explanation
Indices: 20358662--20358862 Score: 131
Period size: 20 Copynumber: 10.0 Consensus size: 20
20358652 ATTTGTATTC
* * *
20358662 CCTCATGATTTTCGGTGCTT
1 CCTCATAATTTTTGGTACTT
* * *
20358682 TCTAATAATTTTTTTGTA-TT
1 CCTCATAA-TTTTTGGTACTT
*
20358702 CCTTCATAATGTTTGGTACTT
1 CC-TCATAATTTTTGGTACTT
** *
20358723 CCTCATTTTTTTTGGCA-TT
1 CCTCATAATTTTTGGTACTT
* *
20358742 CCTTTATAATTTTTGGTACAT
1 CC-TCATAATTTTTGGTACTT
*
20358763 CCTCATAATTTTTAGTACTT
1 CCTCATAATTTTTGGTACTT
* * *
20358783 CCACAAAATTTTT-CTACTT
1 CCTCATAATTTTTGGTACTT
* *
20358802 CCTCATATTTTTTAGTA-TAT
1 CCTCATAATTTTTGGTACT-T
* *
20358822 CCTCATAATTTTTGGTAATC
1 CCTCATAATTTTTGGTACTT
**
20358842 CCTCATGGTTTTTTGGTACTT
1 CCTCAT-AATTTTTGGTACTT
20358863 TCTTATATTT
Statistics
Matches: 136, Mismatches: 36, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
19 20 0.15
20 87 0.64
21 29 0.21
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.51
Consensus pattern (20 bp):
CCTCATAATTTTTGGTACTT
Found at i:20358813 original size:19 final size:19
Alignment explanation
Indices: 20358762--20358814 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
20358752 TTTTGGTACA
**
20358762 TCCTCATAATTTTTAGTACT
1 TCCTCAT-ATTTTTTCTACT
* * *
20358782 TCCACAAAATTTTTCTACT
1 TCCTCATATTTTTTCTACT
20358801 TCCTCATATTTTTT
1 TCCTCATATTTTTT
20358815 AGTATATCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.51
Consensus pattern (19 bp):
TCCTCATATTTTTTCTACT
Found at i:20358832 original size:39 final size:39
Alignment explanation
Indices: 20358689--20358835 Score: 145
Period size: 40 Copynumber: 3.7 Consensus size: 39
20358679 CTTTCTAATA
* *
20358689 ATTTTTTTGTATTCCTTCATAATGTTTGGTACTTCCTCAT
1 ATTTTTTAGTATTCCTTCATAAT-TTTTGTACTTCCTCAT
* * * * *
20358729 TTTTTTTGGCATTCCTTTATAATTTTTGGTACATCCTCAT
1 ATTTTTTAGTATTCCTTCATAATTTTT-GTACTTCCTCAT
* * * *
20358769 AATTTTTAGTACTTCC-ACAAAATTTTTCTACTTCCTCAT
1 ATTTTTTAGTA-TTCCTTCATAATTTTTGTACTTCCTCAT
20358808 ATTTTTTAGTATATCC-TCATAATTTTTG
1 ATTTTTTAGTAT-TCCTTCATAATTTTTG
20358836 GTAATCCCTC
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 35 0.41
40 45 0.53
41 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (39 bp):
ATTTTTTAGTATTCCTTCATAATTTTTGTACTTCCTCAT
Found at i:20358943 original size:20 final size:20
Alignment explanation
Indices: 20358915--20358977 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
20358905 ATTTTTTGGC
* *
20358915 ATTCTCTCATAATTTATGGT
1 ATTCCCTCATAATTTATAGT
* *
20358935 ATTCCCTCAAAATTTTTAGT
1 ATTCCCTCATAATTTATAGT
*
20358955 ACTT-CCTCATAATTTTTAGT
1 A-TTCCCTCATAATTTATAGT
20358975 ATT
1 ATT
20358978 ACCTTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTCCCTCATAATTTATAGT
Found at i:20358987 original size:19 final size:19
Alignment explanation
Indices: 20358939--20358990 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
20358929 TATGGTATTC
20358939 CCTCAAAATTTTTAGTACTT
1 CCTC-AAATTTTTAGTACTT
20358959 CCTCATAATTTTTAGTA-TT
1 CCTCA-AATTTTTAGTACTT
*
20358978 ACCTTAAATTTTT
1 -CCTCAAATTTTT
20358991 TGGTATGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (19 bp):
CCTCAAATTTTTAGTACTT
Found at i:20359228 original size:20 final size:21
Alignment explanation
Indices: 20359203--20359256 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
20359193 GTACACCCTC
**
20359203 ATAATTTTTGGTATTTCC-TT
1 ATAATTTTTGGTATCACCTTT
20359223 ATAATTTTTGGTA-CACCTTT
1 ATAATTTTTGGTATCACCTTT
20359243 ATAATTTTTGGTAT
1 ATAATTTTTGGTAT
20359257 AGTCCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (21 bp):
ATAATTTTTGGTATCACCTTT
Found at i:20359269 original size:40 final size:40
Alignment explanation
Indices: 20359193--20359271 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
20359183 ATAAATGATA
* *
20359193 GTACACCCTCATAATTTTTGGTATTTCCTTATAATTTTTG
1 GTACACCCTCATAATTTTTGGTATGTCCTTAGAATTTTTG
* *
20359233 GTACACCTTTATAATTTTTGGTATAGTCC-TAGAATTTTT
1 GTACACCCTCATAATTTTTGGTAT-GTCCTTAGAATTTTT
20359272 TGTATGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (40 bp):
GTACACCCTCATAATTTTTGGTATGTCCTTAGAATTTTTG
Found at i:20359622 original size:21 final size:21
Alignment explanation
Indices: 20359596--20359640 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20359586 AAAATTTTAC
*
20359596 AAAGGTAACTTTACCATATTG
1 AAAGGTAACTTTACCATACTG
20359617 AAAGGTAACTTTACCATACTG
1 AAAGGTAACTTTACCATACTG
20359638 AAA
1 AAA
20359641 TATTTACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (21 bp):
AAAGGTAACTTTACCATACTG
Found at i:20359969 original size:37 final size:37
Alignment explanation
Indices: 20359928--20359998 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
20359918 GAATTCTTGT
20359928 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
*
20359965 TTGGCTTTGTTTGTACTAGGACGGTTCACCACTC
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTC
20359999 AACTTGTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (37 bp):
TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
Found at i:20366763 original size:69 final size:67
Alignment explanation
Indices: 20366561--20366817 Score: 246
Period size: 69 Copynumber: 3.8 Consensus size: 67
20366551 TTTATCTGAC
* * * * * *
20366561 GTCATAGCCCAACTATGGTCTTACATAGTATAAACCCATGTTTAATGTCTTGGCAACTCCATATA
1 GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCTGACAACTCCATATG
20366626 TT
66 TT
* * * * * * *
20366628 GTCATACCCTAATTATGGTCTTAAACAATATAAACCCTTGTTTAATGTCTTGGAGAACTCCATAT
1 GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCT-GACAACTCCATAT
20366693 GTT
65 GTT
* * * * *
20366696 -TCCATAGCCTAACTATGGTCTTACATATTGTGAATCCCATGTTTAATATCCTGACAAACTTCAT
1 GT-CATAGCCTAACTATGGTCTTACACATTAT-AAACCCATGTTTAATGTCCTGAC-AACTCCAT
20366760 ATGTT
63 ATGTT
* * * * * *
20366765 GTAATAGTCTAATTATGGTCTTACACATTGTGAATCTCATGTTTAATGTCCTG
1 GTCATAGCCTAACTATGGTCTTACACATTAT-AAACCCATGTTTAATGTCCTG
20366818 GCAGACTGTA
Statistics
Matches: 157, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
67 45 0.29
68 38 0.24
69 73 0.46
70 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (67 bp):
GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCTGACAACTCCATATG
TT
Found at i:20369969 original size:41 final size:41
Alignment explanation
Indices: 20369906--20370001 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
20369896 TGATTCCAGT
* *
20369906 TGGAAGCGTTTTCAGCTGATTTG-AAGAAAATCGCGTCTAGC
1 TGGAAGCGTTTTCAGATGATTTGCAAGAAAAT-GCGTCTAGA
* * *
20369947 TGGATGCGTTTTCA-ATGTATTTGCAGGAAAATGCTTCTAGA
1 TGGAAGCGTTTTCAGATG-ATTTGCAAGAAAATGCGTCTAGA
*
20369988 TGAAAGCGTTTTCA
1 TGGAAGCGTTTTCA
20370002 TTGTGCATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.04
41 37 0.80
42 7 0.15
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
TGGAAGCGTTTTCAGATGATTTGCAAGAAAATGCGTCTAGA
Found at i:20372543 original size:41 final size:41
Alignment explanation
Indices: 20372462--20372570 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
20372452 CTTCGAGTCA
* * *
20372462 ATGAGGCACTAGGTGCCAATTTA--A-TTCAG-TTTAATCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
* *
20372499 ATGAGACACTTGGTGTCAATTTACTACTTCGGATTTATTCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
20372540 ATGAGACACTAGGTGTCAATTTACTACTTCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCG
20372571 AATTATCCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 20 0.32
39 1 0.02
40 4 0.06
41 37 0.60
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
Found at i:20376847 original size:14 final size:14
Alignment explanation
Indices: 20376828--20376857 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20376818 TGATTGTTTT
20376828 TAATCTAATTTAAC
1 TAATCTAATTTAAC
20376842 TAATCTAATTTAAC
1 TAATCTAATTTAAC
20376856 TA
1 TA
20376858 CGAACGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATCTAATTTAAC
Found at i:20379070 original size:24 final size:24
Alignment explanation
Indices: 20379043--20379092 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20379033 CCAAAGTCAA
20379043 CTTAAGATTTCAGAAACTGAAACC
1 CTTAAGATTTCAGAAACTGAAACC
*
20379067 CTTAGGATTTCAGAAACTGAAACC
1 CTTAAGATTTCAGAAACTGAAACC
20379091 CT
1 CT
20379093 AAGCGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (24 bp):
CTTAAGATTTCAGAAACTGAAACC
Found at i:20380283 original size:2 final size:2
Alignment explanation
Indices: 20380276--20380315 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
20380266 TGTTATAAAC
*
20380276 AT AT AT AT AT AT AT AT AT AC AT -T CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
20380316 TATTTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20380445 original size:17 final size:20
Alignment explanation
Indices: 20380401--20380446 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
20380391 GCATACTTAC
20380401 ATATATTTTTATATTACATA
1 ATATATTTTTATATTACATA
*
20380421 AT-T-TTTTT-TAATACA-A
1 ATATATTTTTATATTACATA
20380437 ATATATTTTT
1 ATATATTTTT
20380447 TCTTTTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 1 0.04
20 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTTATATTACATA
Found at i:20383976 original size:247 final size:247
Alignment explanation
Indices: 20383514--20384005 Score: 849
Period size: 247 Copynumber: 2.0 Consensus size: 247
20383504 CCCGATGTCG
* * *
20383514 AATCCAGAAACTACTCGATCTTTAGAGGAGTACCTACAAGTATTGCCCTCTGAGATAGAAGTAAT
1 AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
* * *
20383579 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAGGGAAGAAAATAGAGCAACTAGAATAAGAAA
66 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
20383644 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
131 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
*
20383709 AACAAGGTAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
196 AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
* *
20383761 AATCCATAAACTGCTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
1 AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
20383826 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
66 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
* * *
20383891 AAATGCAATTAGGACTTGATGTTGATGTTCAAAAATTAGAGGCTGATAAACTGAGAAAAGGGAAG
131 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
* * *
20383956 AACAAGGCAGAGGGAGATTTAGACAGTCTGAAGACGGATTACAAGAAGTT
196 AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTT
20384006 GCATAGGTCA
Statistics
Matches: 230, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
247 230 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (247 bp):
AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
Found at i:20389865 original size:68 final size:68
Alignment explanation
Indices: 20389756--20389891 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
20389746 CAAATTGAGA
20389756 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
1 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
20389821 TGG
66 TGG
20389824 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
1 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
20389889 TGG
66 TGG
20389892 TTAATCTCTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (68 bp):
AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
TGG
Found at i:20393124 original size:44 final size:44
Alignment explanation
Indices: 20393037--20393140 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
20393027 AAACCTTATC
* ** * *
20393037 CCCTAAAGTTGCAGTGGAGCAGGTTGAATATACAAGTCTTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAGTCCTACTT
*
20393081 CCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAA-TCCTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAC-AAGTCCTACTT
20393125 CCCTGAAGTTGCAGTG
1 CCCTGAAGTTGCAGTG
20393141 AAGCGGATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAGTCCTACTT
Found at i:20394889 original size:2 final size:2
Alignment explanation
Indices: 20394882--20394933 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
20394872 TGTTATAAAC
*
20394882 AT AT AT AT AT AT AT AC AT -T CAT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
20394924 AT AT AT AT AT
1 AT AT AT AT AT
20394934 TCATAACTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20395059 original size:17 final size:20
Alignment explanation
Indices: 20395015--20395060 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
20395005 GCATACTTAC
20395015 ATATATTTTTATATTACATA
1 ATATATTTTTATATTACATA
*
20395035 AT-T-TTTTT-TAATACA-A
1 ATATATTTTTATATTACATA
20395051 ATATATTTTT
1 ATATATTTTT
20395061 TCTTTTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 1 0.04
20 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTTATATTACATA
Found at i:20398526 original size:96 final size:96
Alignment explanation
Indices: 20398289--20398531 Score: 405
Period size: 96 Copynumber: 2.5 Consensus size: 96
20398279 AGCCCCTTAA
* ** **
20398289 GCCAAAACCACCGAAAGAAGAGGAATCACCTGTAACAAGGGAACGACCTCCACCACTTAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
*
20398354 CACCGCCAGTTGTTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
*
20398385 GTCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
20398450 CACCGCCAGTTATTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
* *
20398481 GCCAAAACCACCGACACAAGAGGAATCACCTATAACAAGGGAACGGTCTCC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCC
20398532 GCCAGTTATT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 137 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.13
Consensus pattern (96 bp):
GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
CACCGCCAGTTATTAAGCCCCCGACACCAGT
Found at i:20398581 original size:78 final size:78
Alignment explanation
Indices: 20398452--20398609 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
20398442 AAAATTGCCA
* *
20398452 CCGCCAGTTATTAAGCCCCCGACACCAGTGCCAAAACCACCGACACAAGAGGAATCACCTATAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
20398517 AAGGGAACGGTCT
66 AAGGGAACGGTCT
* * *
20398530 CCGCCAGTTATTAAGCCCCCGCCACCAGTGGAAAAACCACCGAAACAAGAGGAATCACCTGTAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
20398595 AAGGGAACGGTCT
66 AAGGGAACGGTCT
20398608 CC
1 CC
20398610 ACCACCAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.34, C:0.33, G:0.20, T:0.13
Consensus pattern (78 bp):
CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
AAGGGAACGGTCT
Found at i:20398675 original size:24 final size:24
Alignment explanation
Indices: 20398648--20398721 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
20398638 AAGCCCCTGA
*
20398648 CACCACCAGTCCACTCTCCACCAC
1 CACCACCAGTTCACTCTCCACCAC
*
20398672 CACCACCAATTCA-T-T-CACCAC
1 CACCACCAGTTCACTCTCCACCAC
* * *
20398693 CTCCACCTGTTCACTCTCCTCCAC
1 CACCACCAGTTCACTCTCCACCAC
20398717 CACCA
1 CACCA
20398722 GTGCATTCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 16 0.40
22 2 0.05
23 2 0.05
24 20 0.50
ACGTcount: A:0.24, C:0.54, G:0.03, T:0.19
Consensus pattern (24 bp):
CACCACCAGTTCACTCTCCACCAC
Found at i:20398719 original size:21 final size:21
Alignment explanation
Indices: 20398695--20398738 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20398685 TTCACCACCT
* * *
20398695 CCACCTGTTCACTCTCCTCCA
1 CCACCAGTGCACTCTCCGCCA
*
20398716 CCACCAGTGCATTCTCCGCCA
1 CCACCAGTGCACTCTCCGCCA
20398737 CC
1 CC
20398739 TCTTTCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.09, T:0.23
Consensus pattern (21 bp):
CCACCAGTGCACTCTCCGCCA
Found at i:20401139 original size:3 final size:3
Alignment explanation
Indices: 20401127--20401192 Score: 50
Period size: 3 Copynumber: 21.7 Consensus size: 3
20401117 CCAAAATACT
*
20401127 TAA T-A TAA TAA T-A TAA TAA TAA TGAA TAGA TAGA TAA -AA GGAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A TA-A TAA TAA -TAA TAA
20401172 TAA TAAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TA
20401193 TCAAATTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
2 8 0.15
3 32 0.58
4 15 0.27
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:20402737 original size:45 final size:44
Alignment explanation
Indices: 20402668--20403238 Score: 282
Period size: 44 Copynumber: 12.6 Consensus size: 44
20402658 TTTAATATGT
* * * *
20402668 TCCACTACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTGC
* *
20402713 TCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCGTATCTTCAATCTGC
* * ** * *
20402757 CCCACTGCAACTTCAGGGAGATAATG-TTTGTGGCTTTAATCTAC
1 TCCACTGCAACTTCAGGGAGATAA-GATTCGTATCTTCAATCTGC
* *
20402801 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T--CGTATCTTCAATCTGC
* * * * *
20402850 TCAACTGTAACTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG--TATCTTCAATCTGC
* ** * * * *
20402895 TCCACTGTAACTTCAATGAGATAAGGTTTG-AT-AT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
* * * * *
20402936 TCTACTGCAACTTTAGAGAGATAAGA-TCGATAATTTATAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTCG------TAT--CTTCAATCTGC
* * * * *
20402987 TCCACGGCAACTTCATGGAAATAAGATTCGCTTTCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTGC
* * * *
20403032 TCCACTGCAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCTGAC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TA---T--CTTCAATCTG-C
* * * * *
20403083 -CTACTGCAACTTCAGAGG-TATAGGATT--TATCGTTTTAATCCGC
1 TCCACTGCAACTTCAG-GGAGATAAGATTCGTATC--TTCAATCTGC
* * * ** *
20403126 TCCAATGCAACTTCAAGGAGATAGGATTAATAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
* * * *
20403170 TCTACTGCAACTTCAGGGAGATAAGATTGGTATTTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
** *
20403214 TCCGTTTCAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
20403239 GTTGGTTATC
Statistics
Matches: 398, Mismatches: 91, Indels: 75
0.71 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 25 0.06
42 1 0.00
43 8 0.02
44 160 0.40
45 94 0.24
46 8 0.02
47 8 0.02
48 1 0.00
49 33 0.08
50 27 0.07
51 28 0.07
52 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
Found at i:20403213 original size:319 final size:317
Alignment explanation
Indices: 20402607--20403216 Score: 775
Period size: 319 Copynumber: 1.9 Consensus size: 317
20402597 TTAGACTTGT
* * *
20402607 TATGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCGGTAATTTATAGTTTTAATATGTTCCA
1 TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
*
20402672 CTACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
66 CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
** * * * *
20402737 GACTTGTATCTTCAACCTACCCCACTGCAACTTCAGGGAGATAATGTTTGTGGCTTTAATCTACT
131 GACTTGTAGATTCAACCTACCCCACTGCAACTTCAGGGAGATAAGGTTTATCGCTTTAATCCACT
* * * * *
20402802 CCACTACAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGCTCAACTGTAACTTCAGG
196 CCAATACAACTTCAAGGAGATAAGA-TTGTA-CATAGCTTCAATCTGCTCAACTGCAACTTCAGG
* *
20402867 GAGATAAGATTGTTTATTTTTAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
259 GAGATAAGATTGTGTATTTTCAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
* * *
20402926 TATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCGATAATTTATAGCTTTAATCTGTTCCA
1 TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
* * * *
20402991 CGGCAACTTCATGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAA
66 CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
20403056 GACTCGTTATGGTAGATTTAATCTGA-CCTACTGCAACTTCA--GAGGTATAGGATTTATCGTTT
131 GA--C--T-T-GTAGATTCAACCT-ACCCCACTGCAACTTCAGGGAGATA-AGG-TTTATCGCTT
* * * *
20403118 TAATCCGCTCCAATGCAACTTCAAGGAGATAGGA-T-TA-ATAGCTTCAATCTGCTCTACTGCAA
187 TAATCCACTCCAATACAACTTCAAGGAGATAAGATTGTACATAGCTTCAATCTGCTCAACTGCAA
20403180 CTTCAGGGAGATAAGATTG-GTATTTTCAACCTGCTCC
252 CTTCAGGGAGATAAGATTGTGTATTTTCAACCTGCTCC
20403217 GTTTCAACTT
Statistics
Matches: 249, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
319 137 0.55
320 40 0.16
321 1 0.00
322 2 0.01
323 7 0.03
324 3 0.01
325 58 0.23
326 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (317 bp):
TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
GACTTGTAGATTCAACCTACCCCACTGCAACTTCAGGGAGATAAGGTTTATCGCTTTAATCCACT
CCAATACAACTTCAAGGAGATAAGATTGTACATAGCTTCAATCTGCTCAACTGCAACTTCAGGGA
GATAAGATTGTGTATTTTCAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
Found at i:20403508 original size:44 final size:43
Alignment explanation
Indices: 20403406--20403533 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 43
20403396 AATATGCTCC
* * *
20403406 GCTTTAGTCTGTTCCACTGCAACTTCAGAGAGATAAT-ACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-ATGA-TTGTA
* * * * *
20403450 ACTTCAATCCGCTCCACTGCAACTTTAGGGAGATATGATTATTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATT-GTA
* * * *
20403494 GCTTTAATCTGCTCCATTGTAACTTCAGGGAAATAAGATT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATT
20403534 CGCCATTTTC
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
43 4 0.06
44 62 0.94
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (43 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATTGTA
Found at i:20404840 original size:15 final size:15
Alignment explanation
Indices: 20404820--20404862 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20404810 TGGCCTCTCA
20404820 TTTTTCTTTTTCCTT
1 TTTTTCTTTTTCCTT
* *
20404835 TTTTTCTCTTCTCTTT
1 TTTTTCT-TTTTCCTT
20404851 TCTTTTCTTTTT
1 T-TTTTCTTTTT
20404863 TCATCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTCCTT
Found at i:20406304 original size:13 final size:13
Alignment explanation
Indices: 20406286--20406310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20406276 TATTTTAATA
20406286 TTATTTTGTGTGT
1 TTATTTTGTGTGT
20406299 TTATTTTGTGTG
1 TTATTTTGTGTG
20406311 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:20407548 original size:2 final size:2
Alignment explanation
Indices: 20407543--20407593 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
20407533 TAATGCTAGA
20407543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20407585 AT AT AT AT A
1 AT AT AT AT A
20407594 AGTTATTGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20408661 original size:41 final size:41
Alignment explanation
Indices: 20408480--20408633 Score: 281
Period size: 41 Copynumber: 3.8 Consensus size: 41
20408470 GACTTTAAGT
20408480 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
20408521 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
20408562 CTAGCAGGCTACATGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
20408603 CTAGCAGGCTACGTGCCGGTGATCTAAATCA
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCA
20408634 TGCTATAAGT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:20408661 original size:82 final size:82
Alignment explanation
Indices: 20408475--20408670 Score: 284
Period size: 82 Copynumber: 2.4 Consensus size: 82
20408465 TTTCAGACTT
20408475 TAAGTCTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGG
1 TAAGTCTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGG
* *
20408540 TGATCTGAATCAGGTTA
66 TGATCTAAATCAGGCTA
** * *
20408557 TAAACCTAGCAGGCTACATGCCGGTGATTTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGG
1 TAAGTCTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGG
*
20408622 TGATCTAAATCATGCTA
66 TGATCTAAATCAGGCTA
* * * *
20408639 TAAGTTTAGCAGGTTATGTGCCGTTGAATCTG
1 TAAGTCTAGCAGGCTACGTGCCGGTG-ATCTG
20408671 TTTAAATTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 94 0.96
83 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (82 bp):
TAAGTCTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGG
TGATCTAAATCAGGCTA
Found at i:20413505 original size:20 final size:21
Alignment explanation
Indices: 20413473--20413513 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20413463 TATAAAAAGC
20413473 TAAAAGTGAATAATAA-ATAA
1 TAAAAGTGAATAATAAGATAA
20413493 TAAAA-TGATATAATAAGATAA
1 TAAAAGTGA-ATAATAAGATAA
20413514 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (21 bp):
TAAAAGTGAATAATAAGATAA
Found at i:20413552 original size:14 final size:13
Alignment explanation
Indices: 20413520--20413568 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
20413510 ATAAATATAT
20413520 ATAAAAATTAAAAA
1 ATAAAAA-TAAAAA
*
20413534 TTAAAAATAAACAA
1 ATAAAAATAAA-AA
*
20413548 ATAAAATATAAAAT
1 ATAAAA-ATAAAAA
20413562 ATAAAAA
1 ATAAAAA
20413569 ATAATGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.17
14 20 0.67
15 5 0.17
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:20413559 original size:21 final size:20
Alignment explanation
Indices: 20413518--20413572 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
20413508 AGATAAATAT
*
20413518 ATATAAAAATTAAAAATTAAA
1 ATATAAAAAAT-AAAATTAAA
20413539 A-ATAAACAAATAAAATATAAA
1 ATATAAA-AAATAAAAT-TAAA
20413560 ATATAAAAAATAA
1 ATATAAAAAATAA
20413573 TGCAAAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.33
21 15 0.50
22 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
ATATAAAAAATAAAATTAAA
Found at i:20419084 original size:54 final size:54
Alignment explanation
Indices: 20418980--20419084 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
20418970 TGTATAATAT
* * * * *
20418980 AAGGTCACACGGCTGTGTGGCCAGGCCGTGTAACTCTCTATGATCGTGTGGCTC
1 AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGGCTC
* * *
20419034 AAGGTCACACGACTATGTCTCCAGGCCGTGTAATTCTCTATGCCCATGTGG
1 AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGG
20419085 ATTGACCTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (54 bp):
AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGGCTC
Found at i:20428874 original size:43 final size:43
Alignment explanation
Indices: 20428805--20428886 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
20428795 ATTGTATCTA
** *
20428805 CATTTTAAAGCTGATTTCTTATTACCTATAGGAAAGACCCAGT
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
*
20428848 CATTTTAAAGCTGACATCTTGCTACCTATAGGAAAGACC
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACC
20428887 AAGAACATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (43 bp):
CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
Found at i:20449280 original size:18 final size:19
Alignment explanation
Indices: 20449244--20449284 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
20449234 TCTCATTGCA
*
20449244 TCATTTTATATTTCATTTC
1 TCATTTTATATTCCATTTC
20449263 TCATTTTATA-TCCATTTC
1 TCATTTTATATTCCATTTC
20449281 TCAT
1 TCAT
20449285 CTTTTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (19 bp):
TCATTTTATATTCCATTTC
Found at i:20450532 original size:11 final size:11
Alignment explanation
Indices: 20450516--20450568 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
20450506 TTTCTATTTC
*
20450516 TTTTATTATGT
1 TTTTATTATAT
*
20450527 TTTTATTATGT
1 TTTTATTATAT
20450538 TTTTATTATAT
1 TTTTATTATAT
20450549 TTATTATTATAT
1 TT-TTATTATAT
*
20450561 TATTATTA
1 TTTTATTA
20450569 ACCTTATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 29 0.74
12 10 0.26
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:20456138 original size:58 final size:59
Alignment explanation
Indices: 20456055--20456168 Score: 176
Period size: 58 Copynumber: 1.9 Consensus size: 59
20456045 ACAGACAAGA
* * **
20456055 ACTAATTTGGAACAGTTCTAAAAGTTTTAGCGCAATCTCTAAAATACCTA-AAACAGAG
1 ACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATCTAAAAAATACCTAGAAACAGAG
*
20456113 ACTAATTTGGAAAAATTCTAAAAGTTTTAGGGCAATCTAAAAAATACCTAGAAACA
1 ACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATCTAAAAAATACCTAGAAACA
20456169 AGGGACACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 45 0.90
59 5 0.10
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (59 bp):
ACTAATTTGGAAAAATTCTAAAAGTTTTAGCGCAATCTAAAAAATACCTAGAAACAGAG
Found at i:20456764 original size:23 final size:24
Alignment explanation
Indices: 20456738--20456782 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
20456728 CAAATTTGAA
20456738 GCTAAGC-A-CATACCAAGCATTAG
1 GCTAAGCTATCATACCAA-CATTAG
20456761 GCTAAGCTATCATACCAACATT
1 GCTAAGCTATCATACCAACATT
20456783 GCCTCAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (24 bp):
GCTAAGCTATCATACCAACATTAG
Found at i:20470937 original size:16 final size:17
Alignment explanation
Indices: 20470908--20470954 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
20470898 CAGGTTAACA
20470908 TTTAAAAGTTTATA-ATT
1 TTTAAAA-TTTATATATT
20470925 TTTAAAATTTATATATT
1 TTTAAAATTTATATATT
*
20470942 TTT-TAATTTATAT
1 TTTAAAATTTATAT
20470955 TTATCACGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAAAATTTATATATT
Found at i:20470947 original size:18 final size:17
Alignment explanation
Indices: 20470908--20470944 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20470898 CAGGTTAACA
20470908 TTTAAAAGTTTATAATT
1 TTTAAAAGTTTATAATT
20470925 TTTAAAA-TTTATATATT
1 TTTAAAAGTTTATA-ATT
20470942 TTT
1 TTT
20470945 TAATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAAAGTTTATAATT
Found at i:20474444 original size:11 final size:11
Alignment explanation
Indices: 20474411--20474458 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 11
20474401 GAAATTTTGG
20474411 ATTTTTT-TAT
1 ATTTTTTATAT
20474421 A-TTTTTA-A-
1 ATTTTTTATAT
*
20474429 GTTTTTTATAT
1 ATTTTTTATAT
20474440 ATTTTTTATAT
1 ATTTTTTATAT
20474451 AATTTTTT
1 -ATTTTTT
20474459 GAGATGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 12 0.39
10 2 0.06
11 10 0.32
12 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:20477757 original size:114 final size:114
Alignment explanation
Indices: 20477557--20477785 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
20477547 TAACTAATTG
*
20477557 AGAATAAAATTTTAAGAAGAAATCCCGATTGTATTGATTGATTGAAGTGCAAAAATCCACAAAAT
1 AGAATAAAAGTTTAAGAAGAAATCCCGATTGTATTGATTGATTGAAGTGCAAAAATCCACAAAAT
20477622 GTTTGGCTGAAACCATAAATTAGATTCTCTGAATGTCATGAATGAAAAC
66 GTTTGGCTGAAACCATAAATTAGATTCTCTGAATGTCATGAATGAAAAC
*
20477671 AGAATAAAAGTTTAAGAATAAATCCCGATTGTATTGATTGATTGAAGTGCAAAAATCCACAAAAT
1 AGAATAAAAGTTTAAGAAGAAATCCCGATTGTATTGATTGATTGAAGTGCAAAAATCCACAAAAT
20477736 GTTTGGCTGAAACCATAAATTAGATTCTCTGAATGTCATGAATGAAAAC
66 GTTTGGCTGAAACCATAAATTAGATTCTCTGAATGTCATGAATGAAAAC
20477785 A
1 A
20477786 AACTTAAATA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (114 bp):
AGAATAAAAGTTTAAGAAGAAATCCCGATTGTATTGATTGATTGAAGTGCAAAAATCCACAAAAT
GTTTGGCTGAAACCATAAATTAGATTCTCTGAATGTCATGAATGAAAAC
Found at i:20482324 original size:11 final size:11
Alignment explanation
Indices: 20482310--20482337 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20482300 TGAGGGAAAT
20482310 TTGAGAGATAG
1 TTGAGAGATAG
20482321 TTGAGAGATAG
1 TTGAGAGATAG
20482332 TTGAGA
1 TTGAGA
20482338 CTGAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (11 bp):
TTGAGAGATAG
Found at i:20484125 original size:18 final size:18
Alignment explanation
Indices: 20484084--20484126 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20484074 TTATAATTCT
* *
20484084 ATTTTTTATATTTTTACA
1 ATTTTTAATAATTTTACA
* *
20484102 ACTTTTAATAATTTTATA
1 ATTTTTAATAATTTTACA
20484120 ATTTTTA
1 ATTTTTA
20484127 TAGCATTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTAATAATTTTACA
Found at i:20486705 original size:2 final size:2
Alignment explanation
Indices: 20486698--20486765 Score: 70
Period size: 2 Copynumber: 35.5 Consensus size: 2
20486688 ATATTTCTTT
* * *
20486698 TA TA TA TA TG TA CA TA TA TA TA TA TA TA TA TT TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
20486739 GA -A TA T- TC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20486766 GTACGTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20488409 original size:5 final size:5
Alignment explanation
Indices: 20488394--20488425 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20488384 AGGGGTGAGC
20488394 AATCG -ATCG AATCG AATCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AATCG AAT
20488426 TGAAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
AATCG
Found at i:20489473 original size:9 final size:9
Alignment explanation
Indices: 20489459--20489495 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20489449 TATAGTTTGA
20489459 TATTCGAAT
1 TATTCGAAT
20489468 TATTCGAAT
1 TATTCGAAT
*
20489477 TATTCGAGT
1 TATTCGAAT
20489486 TATTCGAAT
1 TATTCGAAT
20489495 T
1 T
20489496 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20495095 original size:35 final size:35
Alignment explanation
Indices: 20495012--20495100 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
20495002 TACACGGTTA
* ** *
20495012 ACCATCCAACATACCAGATTTTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAAT
* * * * *
20495047 ATCATCTAGCACACTAGATGCTCATAAGAGTCAAT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAAT
20495082 ACCATCCAACACACCAGAT
1 ACCATCCAACACACCAGAT
20495101 AACACTATAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.21
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAAT
Found at i:20499768 original size:21 final size:23
Alignment explanation
Indices: 20499723--20499768 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
20499713 ATTATTCAAT
*
20499723 TACATTATGAATACATAATAACA
1 TACATTATGAATACAAAATAACA
*
20499746 TACATT-TGAATA-AAAATAGCA
1 TACATTATGAATACAAAATAACA
20499767 TA
1 TA
20499769 ATAACGTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 6 0.29
23 6 0.29
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (23 bp):
TACATTATGAATACAAAATAACA
Found at i:20503239 original size:25 final size:25
Alignment explanation
Indices: 20503203--20503251 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20503193 TTTTTTTGGC
20503203 TTTTATTCTCCCAATGAAACTCTGT
1 TTTTATTCTCCCAATGAAACTCTGT
* *
20503228 TTTTAGTT-TCCCACTTAAACTCTG
1 TTTTA-TTCTCCCAATGAAACTCTG
20503252 ATTAGTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.45
Consensus pattern (25 bp):
TTTTATTCTCCCAATGAAACTCTGT
Found at i:20503293 original size:44 final size:44
Alignment explanation
Indices: 20503230--20503320 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
20503220 AACTCTGTTT
* *
20503230 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGCCTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAGTATAGCCTATTTTAATA
* **
20503274 TTAGTTTCTCACTTAAACTCTAATTAGTATAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAGTATAGCCTATTTTAATA
20503318 TTA
1 TTA
20503321 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAATTAGTATAGCCTATTTTAATA
Found at i:20505244 original size:44 final size:44
Alignment explanation
Indices: 20505176--20505266 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
20505166 AACTCTGTTT
* *
20505176 TTAGTTTCTCACTTAAAATTTGATTAGGGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAAATCTGATTAGGGTAGGTTATTTTAATA
* *
20505220 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAAATCTGATTAGGGTAGGTTATTTTAATA
20505264 TTA
1 TTA
20505267 TTTAACTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAAATCTGATTAGGGTAGGTTATTTTAATA
Found at i:20508471 original size:77 final size:78
Alignment explanation
Indices: 20508319--20508591 Score: 374
Period size: 78 Copynumber: 3.5 Consensus size: 78
20508309 TGTATTCTAT
* * * *
20508319 TTCAAACAGAAATTCAATTGAACAATCCTGTTTCAGGA-TTTATTCCTGTCGTTTAACAAGACTT
1 TTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATTT
*
20508383 GTTTAATTTTTTG
66 GTTTGATTTTTTG
* * * *
20508396 TTCAAACAGAAAATCAATTGAACAATCTTGTTTTAGGATTTTATTTCTGACGTCTAACATGATTT
1 TTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATTT
20508461 GTTTGA-TTTTTG
66 GTTTGATTTTTTG
* *
20508473 TTTCAAACAGAAAATCAATTGAATAATTTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATT
1 -TTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATT
*
20508538 TGTTTGATTTTTTAT
65 TGTTTGATTTTTT-G
*
20508553 TTCAAACA-AAAATCAATTGAATAAAT-TTGTTTCAGGATT
1 TTCAAACAGAAAATCAATTGAA-CAATCTTGTTTCAGGATT
20508592 CTTTTCTTGT
Statistics
Matches: 174, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
77 41 0.24
78 117 0.67
79 16 0.09
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (78 bp):
TTCAAACAGAAAATCAATTGAACAATCTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATTT
GTTTGATTTTTTG
Found at i:20508626 original size:78 final size:79
Alignment explanation
Indices: 20508316--20508626 Score: 271
Period size: 78 Copynumber: 4.0 Consensus size: 79
20508306 AATTGTATTC
* * * * * *
20508316 TATTTCAAACAGAAATTCAATTGAA-CAATCCTGTTTCAGGATT-TATTCCTGTCGTTTAACAAG
1 TATTTCAAACAGAAAATCAATTGAATAAAT-TTGTTTCAGGATTCTATTTCTGTCATTCAACAAG
* * *
20508379 ACTTGTTTAATTTTT
65 ATTTATTCAATTTTT
* * * * * * *
20508394 T-GTTCAAACAGAAAATCAATTGAA-CAATCTTGTTTTAGGATTTTATTTCTGAC-GTCTAACAT
1 TATTTCAAACAGAAAATCAATTGAATAAAT-TTGTTTCAGGATTCTATTTCTGTCATTC-AACAA
* **
20508456 GATTTGTTTGA-TTTT
64 GATTTATTCAATTTTT
* * * * *
20508471 TGTTTCAAACAGAAAATCAATTGAATAATTTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGA
1 TATTTCAAACAGAAAATCAATTGAATAAATTTGTTTCAGGATTCTATTTCTGTCATTCAACAAGA
* **
20508536 TTTGTTTGATTTTT
66 TTTATTCAATTTTT
20508550 TATTTCAAACA-AAAATCAATTGAATAAATTTGTTTCAGGATTCT-TTTCTTGTCATTCAAC-AG
1 TATTTCAAACAGAAAATCAATTGAATAAATTTGTTTCAGGATTCTATTTC-TGTCATTCAACAAG
20508612 AATTTATTCAATTTT
65 -ATTTATTCAATTTT
20508627 CGTTGTTACC
Statistics
Matches: 198, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
77 49 0.25
78 132 0.67
79 17 0.09
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (79 bp):
TATTTCAAACAGAAAATCAATTGAATAAATTTGTTTCAGGATTCTATTTCTGTCATTCAACAAGA
TTTATTCAATTTTT
Found at i:20508641 original size:156 final size:155
Alignment explanation
Indices: 20508318--20508630 Score: 384
Period size: 156 Copynumber: 2.0 Consensus size: 155
20508308 TTGTATTCTA
*
20508318 TTTCAAACAGAAATTCAATTGAACAATCCTGTTTCAGGATTTATTCCTGTCGTTTAACAAGACTT
1 TTTCAAACAGAAAATCAATTGAACAATCCTGTTTCAGGATTTATTCCTGTCGTTTAACAAGACTT
* * *
20508383 GTTTAATTTTTTGTTCAAACAGAAAATCAATTGAACAATCTTGTTTTAGGATTTTATTTCTGACG
66 GTTTAATTTTTTGTTCAAACAGAAAATCAATTGAAAAATCTTGTTTCAGGATTCTATTTCTGACG
* ** *
20508448 TCTAACATGATTTGTTTGATTTTTG
131 TCTAACATGATTTATTCAATTTTCG
* ** * *
20508473 TTTCAAACAGAAAATCAATTGAATAATTTTGTTTCAGGATTTTATTTCTGTCGTTTAACAAGATT
1 TTTCAAACAGAAAATCAATTGAACAATCCTGTTTCAGGA-TTTATTCCTGTCGTTTAACAAGACT
* *
20508538 TGTTTGATTTTTTATTTCAAACA-AAAATCAATTGAATAAAT-TTGTTTCAGGATTCT-TTTCTT
65 TGTTTAATTTTTT-GTTCAAACAGAAAATCAATTGAA-AAATCTTGTTTCAGGATTCTATTTC-T
* *
20508600 GTCAT-TCAACA-GAATTTATTCAATTTTCG
127 GACGTCT-AACATG-ATTTATTCAATTTTCG
20508629 TT
1 TT
20508631 GTTACCAGAA
Statistics
Matches: 135, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
155 41 0.30
156 83 0.61
157 11 0.08
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (155 bp):
TTTCAAACAGAAAATCAATTGAACAATCCTGTTTCAGGATTTATTCCTGTCGTTTAACAAGACTT
GTTTAATTTTTTGTTCAAACAGAAAATCAATTGAAAAATCTTGTTTCAGGATTCTATTTCTGACG
TCTAACATGATTTATTCAATTTTCG
Found at i:20512593 original size:39 final size:39
Alignment explanation
Indices: 20512535--20512646 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
20512525 ATACACCGGC
* *
20512535 ACACAACCTGCTAGGCACATAGCCCGACTAATCACCAGT
1 ACACAACCTGCTAGGCACATAGCCTGAATAATCACCAGT
* *
20512574 ACACAACCTGCTAGACACATAGCCTGAATAATCATCAGT
1 ACACAACCTGCTAGGCACATAGCCTGAATAATCACCAGT
* * *
20512613 AGACAGCCTGCTAGGCATATAGCCTGAATAATCA
1 ACACAACCTGCTAGGCACATAGCCTGAATAATCA
20512647 GCCTGCTAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (39 bp):
ACACAACCTGCTAGGCACATAGCCTGAATAATCACCAGT
Found at i:20512658 original size:29 final size:29
Alignment explanation
Indices: 20512616--20512675 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
20512606 CATCAGTAGA
* *
20512616 CAGCCTGCTAGGCATATAGCCTGAATAAT
1 CAGCCTGCTAGGCACATAGCCCGAATAAT
20512645 CAGCCTGCTAGGCACATAGCCCGAATAAT
1 CAGCCTGCTAGGCACATAGCCCGAATAAT
20512674 CA
1 CA
20512676 CCGGCACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (29 bp):
CAGCCTGCTAGGCACATAGCCCGAATAAT
Found at i:20512689 original size:68 final size:68
Alignment explanation
Indices: 20512580--20512714 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 68
20512570 CAGTACACAA
* * * * * * *
20512580 CCTGCTAGACACATAGCCTGAATAATCATCAGTAGACAGCCTGCTAGGCATATAGCCTGAATAAT
1 CCTGCTAGACACATAGCCCGAATAATCACCAGCACACAGCCTGCTAGACACATAGCCCGAATAAT
20512645 CAG
66 CAG
* *
20512648 CCTGCTAGGCACATAGCCCGAATAATCACCGGCACACAGCCTGCTAGACACATAGCCCGAATAAT
1 CCTGCTAGACACATAGCCCGAATAATCACCAGCACACAGCCTGCTAGACACATAGCCCGAATAAT
20512713 CA
66 CA
20512715 CCGGATTTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (68 bp):
CCTGCTAGACACATAGCCCGAATAATCACCAGCACACAGCCTGCTAGACACATAGCCCGAATAAT
CAG
Found at i:20516903 original size:113 final size:113
Alignment explanation
Indices: 20516703--20516918 Score: 306
Period size: 113 Copynumber: 1.9 Consensus size: 113
20516693 TGCAGTCTTG
* * * * * * * *
20516703 CTACTGTCGTGTTCATCTTGTTGTTGTATCCTGGGATACAGTCGACCAATATTTCTCCAACACCA
1 CTACTATCGTGCTCATCTTGATGTTATATCCTGGCAGACAATCGACCAACATTTCTCCAACACCA
* * *
20516768 TAGGAGCAACCGAATCTGTCTTAAGGAAACTGTGAAAACAGGCCCCAA
66 TAGAAGCAACCGAATCTATCTTAAGGAAACTATGAAAACAGGCCCCAA
*
20516816 CTACTATCGTGCTCATCTTGATGTTATATCTTGGCAGACAATCGACCAACATTTCTCCAACACCA
1 CTACTATCGTGCTCATCTTGATGTTATATCCTGGCAGACAATCGACCAACATTTCTCCAACACCA
**
20516881 TAGAAGCGGCCGAATCTATCTTAAGGAAACTATGAAAA
66 TAGAAGCAACCGAATCTATCTTAAGGAAACTATGAAAA
20516919 TATACCTCAA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 89 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (113 bp):
CTACTATCGTGCTCATCTTGATGTTATATCCTGGCAGACAATCGACCAACATTTCTCCAACACCA
TAGAAGCAACCGAATCTATCTTAAGGAAACTATGAAAACAGGCCCCAA
Found at i:20519490 original size:3 final size:3
Alignment explanation
Indices: 20519482--20519582 Score: 93
Period size: 3 Copynumber: 34.3 Consensus size: 3
20519472 ATTTAAGCTC
*
20519482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT GTT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
20519528 AGA ATT ATA ATAT ATT ATT ATC ATT ATT ATA AAT -TT ATT ATGT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
20519574 ATT A-T ATT A
1 ATT ATT ATT A
20519583 AGTTTCTTCA
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
2 7 0.09
3 68 0.85
4 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:20519493 original size:25 final size:25
Alignment explanation
Indices: 20519448--20519499 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
20519438 GTACTATTAT
*
20519448 TTTAAGTTATTATTATATATTAGTA
1 TTTAAGTCATTATTATATATTAGTA
*
20519473 TTTAAGCTCATTATTAT-TATTATTA
1 TTTAAG-TCATTATTATATATTAGTA
20519498 TT
1 TT
20519500 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTAAGTCATTATTATATATTAGTA
Found at i:20519553 original size:19 final size:20
Alignment explanation
Indices: 20519531--20519568 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20519521 TTGTTTTAGA
*
20519531 ATTATAATATA-TTATTATC
1 ATTATAATAAATTTATTATC
*
20519550 ATTATTATAAATTTATTAT
1 ATTATAATAAATTTATTAT
20519569 GTATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATAATAAATTTATTATC
Found at i:20519604 original size:23 final size:22
Alignment explanation
Indices: 20519573--20519620 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
20519563 TATTATGTAT
*
20519573 TATTATA-TTAAGTTTCTTCATA
1 TATTATATTTAA-TTTCATCATA
20519595 TATTAATATTTAATTTCATCATA
1 TATT-ATATTTAATTTCATCATA
20519618 TAT
1 TAT
20519621 CATCTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTATATTTAATTTCATCATA
Found at i:20519640 original size:29 final size:29
Alignment explanation
Indices: 20519608--20519666 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20519598 TAATATTTAA
20519608 TTTCATCATATATCATCTTATATATTTTC
1 TTTCATCATATATCATCTTATATATTTTC
20519637 TTTCATCATATATCATCTTATATATTTTC
1 TTTCATCATATATCATCTTATATATTTTC
20519666 T
1 T
20519667 ATGTAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTCATCATATATCATCTTATATATTTTC
Found at i:20519655 original size:17 final size:17
Alignment explanation
Indices: 20519608--20519655 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
20519598 TAATATTTAA
20519608 TTTCATCATATATCATC
1 TTTCATCATATATCATC
*
20519625 -TT-AT-ATAT-T-TTC
1 TTTCATCATATATCATC
20519637 TTTCATCATATATCATC
1 TTTCATCATATATCATC
20519654 TT
1 TT
20519656 ATATATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
12 2 0.08
13 3 0.12
14 6 0.25
15 6 0.25
16 3 0.12
17 4 0.17
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTCATCATATATCATC
Found at i:20526976 original size:17 final size:17
Alignment explanation
Indices: 20526954--20526986 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20526944 TTCACTTGAT
20526954 CATATAGGCTCGCATGG
1 CATATAGGCTCGCATGG
20526971 CATATAGGCTCGCATG
1 CATATAGGCTCGCATG
20526987 CACCTAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (17 bp):
CATATAGGCTCGCATGG
Found at i:20527051 original size:29 final size:28
Alignment explanation
Indices: 20526990--20527113 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 28
20526980 TCGCATGCAC
* ** * *
20526990 CTAGGGATTTTATATAGGCTTTCAAGTTT
1 CTAGGG-TTTTACATAGGCTCACATGTTA
*
20527019 CTAGGGTTTTCACATAGGCTCGCATGTTA
1 CTAGGGTTTT-ACATAGGCTCACATGTTA
* * *
20527048 CTAGGGTTCTCACATAAGCTCACATGTTC
1 CTAGGGTT-TTACATAGGCTCACATGTTA
*
20527077 CTCA-GGTTTGTACATAGGCTCACATGTTC
1 CT-AGGGTTT-TACATAGGCTCACATGTTA
20527106 CTAGGGTT
1 CTAGGGTT
20527114 CGCATATCAC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 6 0.08
29 71 0.90
30 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (28 bp):
CTAGGGTTTTACATAGGCTCACATGTTA
Found at i:20534669 original size:24 final size:24
Alignment explanation
Indices: 20534634--20534691 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
20534624 AAATGTATAT
*
20534634 TATTTTTA-AT-TTAATATT-TTA
1 TATTTTTATATATTTATATTATTA
*
20534655 TATTTTTATATATTTTTATTATTA
1 TATTTTTATATATTTATATTATTA
* *
20534679 AAATTTTATATAT
1 TATTTTTATATAT
20534692 AATCATCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.27
22 2 0.07
23 6 0.20
24 14 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTTATATATTTATATTATTA
Found at i:20534684 original size:15 final size:14
Alignment explanation
Indices: 20534634--20534685 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
20534624 AAATGTATAT
*
20534634 TATTTTTAATTTAA
1 TATTTTTATTTTAA
20534648 TATTTTATATTTTTATA
1 TATTTT-TA-TTTTA-A
20534665 TATTTTTATTATTAA
1 TATTTTTATT-TTAA
*
20534680 AATTTT
1 TATTTT
20534686 ATATATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 6 0.19
15 10 0.31
16 9 0.28
17 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:20534691 original size:34 final size:32
Alignment explanation
Indices: 20534629--20534689 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
20534619 AAAATAAATG
*
20534629 TATATTATTTTTAATTTAATATTTTATATTTT
1 TATATTATTTTTAATTTAAAATTTTATATTTT
*
20534661 TATA-TATTTTTATTATTAAAATTTTATAT
1 TATATTATTTTTAAT-TTAAAATTTTATAT
20534690 ATAATCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TATATTATTTTTAATTTAAAATTTTATATTTT
Found at i:20534800 original size:16 final size:17
Alignment explanation
Indices: 20534760--20534803 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
20534750 ATTACGTAAT
20534760 ATATATAAAAATAACATA
1 ATATA-AAAAATAACATA
*
20534778 ATATAAAAAATTACA-A
1 ATATAAAAAATAACATA
*
20534794 ATTTAAAAAA
1 ATATAAAAAA
20534804 GGGTTGGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATAAAAAATAACATA
Found at i:20538841 original size:42 final size:43
Alignment explanation
Indices: 20538782--20538884 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
20538772 CGAGATTACT
* * *
20538782 TGTAAGACCATATCTGGGATA-TGGCATTGATATGAGAATTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGAATTCG
* *
20538824 TGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGAATTCG
* *
20538867 TGTAAGATCATGGCTGGG
1 TGTAAGACCATGTCTGGG
20538885 CTAAGAAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 19 0.36
43 34 0.64
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGAATTCG
Found at i:20541358 original size:26 final size:27
Alignment explanation
Indices: 20541329--20541384 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20541319 TCAACTTCTC
20541329 TTTTAAGTTTATA-AA-TTCTCTTTGAG
1 TTTTAAGTTTA-AGAATTTCTCTTTGAG
**
20541355 TTTTATTTTTAAGAATTTCTCTTTGAG
1 TTTTAAGTTTAAGAATTTCTCTTTGAG
20541382 TTT
1 TTT
20541385 GTTTTAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 11 0.42
27 14 0.54
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (27 bp):
TTTTAAGTTTAAGAATTTCTCTTTGAG
Found at i:20541395 original size:27 final size:27
Alignment explanation
Indices: 20541344--20541395 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20541334 AGTTTATAAA
**
20541344 TTCTCTTTGAGTTTTATTTTTAAGAAT
1 TTCTCTTTGAGTTTTATTTAGAAGAAT
20541371 TTCTCTTTGAGTTTGT-TTTAGAAGA
1 TTCTCTTTGAGTTT-TATTTAGAAGA
20541396 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTATTTAGAAGAAT
Found at i:20543539 original size:45 final size:45
Alignment explanation
Indices: 20543467--20543625 Score: 178
Period size: 45 Copynumber: 3.5 Consensus size: 45
20543457 ATATGCCAAT
20543467 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
1 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
* * ** * * *
20543512 ATGAATAAGACCCTAGCTGAAAA-ATGTTATGGCATCAAAACAGAT
1 ATGAGTAAGACCATAGCT-AAAAGATGTTATGGCATCATGATAAAA
* * *
20543557 ATGAGTAAGACCATGGCTAAAAGACGTTATGGCATCATGGTAAACA
1 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAA-A
* *
20543603 A-GACTAAGACCATAGCTGAAAGA
1 ATGAGTAAGACCATAGCTAAAAGA
20543626 CTCTATAGTA
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
44 4 0.04
45 82 0.90
46 5 0.05
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (45 bp):
ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATAAAA
Found at i:20543844 original size:27 final size:27
Alignment explanation
Indices: 20543785--20543847 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
20543775 GCATCATAGT
* * *
20543785 TAGTCCAACGGGACATTAAACATGAGA
1 TAGTCCGATGGGACATTAAACAAGAGA
* *
20543812 TCGTCCGATGGGACATTAAACAAGGGA
1 TAGTCCGATGGGACATTAAACAAGAGA
20543839 TAGTCCGAT
1 TAGTCCGAT
20543848 AAGACGTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (27 bp):
TAGTCCGATGGGACATTAAACAAGAGA
Found at i:20543857 original size:27 final size:27
Alignment explanation
Indices: 20543796--20543858 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
20543786 AGTCCAACGG
* * **
20543796 GACATTAAACATGAGATCGTCCGATGG
1 GACATTAAACAAGAGATAGTCCGATAA
*
20543823 GACATTAAACAAGGGATAGTCCGATAA
1 GACATTAAACAAGAGATAGTCCGATAA
*
20543850 GACGTTAAA
1 GACATTAAA
20543859 TACGGGGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (27 bp):
GACATTAAACAAGAGATAGTCCGATAA
Found at i:20553068 original size:18 final size:18
Alignment explanation
Indices: 20553031--20553096 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
20553021 GTTTTGACTC
20553031 AAATTTTTCAATAAATTTTTT
1 AAATTTTTC-AT--ATTTTTT
**
20553052 AAATTTTTTTTA-TTTTT
1 AAATTTTTCATATTTTTT
20553069 ATAATTTTTCATATTTTTAT
1 A-AATTTTTCATATTTTT-T
20553089 AAAATTTT
1 -AAATTTT
20553097 AAGTACTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 6 0.16
18 10 0.27
19 4 0.11
20 8 0.22
21 9 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
AAATTTTTCATATTTTTT
Found at i:20554235 original size:9 final size:9
Alignment explanation
Indices: 20554174--20554308 Score: 55
Period size: 9 Copynumber: 14.1 Consensus size: 9
20554164 ATTTCTTTTC
20554174 TATTTTTAA
1 TATTTTTAA
20554183 TAATTTATTAA
1 T-ATTT-TTAA
*
20554194 CT-TTTGTAA
1 -TATTTTTAA
*
20554203 T-TTTTAAA
1 TATTTTTAA
*
20554211 TAATTCTTTTA
1 T-ATT-TTTAA
20554222 TATTTTTAA
1 TATTTTTAA
20554231 TATTTTTTGTAA
1 TA--TTTT-TAA
**
20554243 TATTTTTTTC
1 TA-TTTTTAA
20554253 TATTTTTAA
1 TATTTTTAA
*
20554262 TAATTTTAA
1 TATTTTTAA
*
20554271 TAATTATGT-A
1 T-ATT-TTTAA
20554281 TATTTTGT-A
1 TATTTT-TAA
20554290 TATTTTTAA
1 TATTTTTAA
20554299 T-TTTTGTAA
1 TATTTT-TAA
20554308 T
1 T
20554309 TTAATATAGT
Statistics
Matches: 98, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
8 13 0.13
9 41 0.42
10 19 0.19
11 19 0.19
12 6 0.06
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
TATTTTTAA
Found at i:20554245 original size:21 final size:22
Alignment explanation
Indices: 20554195--20554249 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
20554185 ATTTATTAAC
*
20554195 TTTTGTAAT-TTTTAAATAATT
1 TTTTGTAATATTTTTAATAATT
*
20554216 CTTT-T-ATATTTTTAAT-ATT
1 TTTTGTAATATTTTTAATAATT
20554235 TTTTGTAATATTTTT
1 TTTTGTAATATTTTT
20554250 TTCTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.29
20 9 0.32
21 11 0.39
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTGTAATATTTTTAATAATT
Found at i:20554269 original size:40 final size:40
Alignment explanation
Indices: 20554164--20554299 Score: 104
Period size: 40 Copynumber: 3.5 Consensus size: 40
20554154 CAATTTTATA
*
20554164 ATTTCTTTTCTATTTTTAATAA-TTTATTAACTTTTGTAAT
1 ATTT-TTTTCTATTTTTAATAATTTTAATAACTTTTGTAAT
** * * * **
20554204 -TTTTAAAT-AATTCTTTTATATTTTTAATATTTTTTGTAAT
1 ATTTT-TTTCTATT-TTTAATAATTTTAATAACTTTTGTAAT
*
20554244 ATTTTTTTCTATTTTTAATAATTTTAATAA-TTATGT-AT
1 ATTTTTTTCTATTTTTAATAATTTTAATAACTTTTGTAAT
* *
20554282 A-TTTTGTATATTTTTAAT
1 ATTTTTTTCTATTTTTAAT
20554300 TTTTGTAATT
Statistics
Matches: 74, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
37 15 0.20
38 7 0.09
39 15 0.20
40 30 0.41
41 7 0.09
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (40 bp):
ATTTTTTTCTATTTTTAATAATTTTAATAACTTTTGTAAT
Done.