Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 70 of 255
Found at i:20674026 original size:12 final size:12
Alignment explanation
Indices: 20674011--20674041 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
20674001 TGCAATTTCT
20674011 TTTTCTTTTTTG
1 TTTTCTTTTTTG
20674023 TTTTC-TTTTTG
1 TTTTCTTTTTTG
20674034 TTTTCTTT
1 TTTTCTTT
20674042 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:20674054 original size:6 final size:6
Alignment explanation
Indices: 20673937--20674041 Score: 61
Period size: 6 Copynumber: 17.2 Consensus size: 6
20673927 TCATTCTCAA
* * * ** **
20673937 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
20673988 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTT-TGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
20674035 TTTCTT T
1 TTTCTT T
20674042 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 23, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
5 5 0.07
6 53 0.75
7 10 0.14
8 3 0.04
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:20675100 original size:20 final size:20
Alignment explanation
Indices: 20675054--20675100 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20675044 AGCTCGTTTC
*
20675054 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
20675074 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20675094 CAGCTCA
1 CAGCTCA
20675101 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20676612 original size:11 final size:11
Alignment explanation
Indices: 20676566--20676626 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
20676556 CTCGCAAGAC
20676566 TTTTCACTTTT
1 TTTTCACTTTT
*
20676577 TTTTCTTCTTTT
1 TTTTC-ACTTTT
* *
20676589 TTAACTCAATTTT
1 TT--TTCACTTTT
20676602 TTTTCACTTTT
1 TTTTCACTTTT
*
20676613 TTTTCAATTTT
1 TTTTCACTTTT
20676624 TTT
1 TTT
20676627 GAATATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 25 0.62
12 7 0.17
13 6 0.15
14 2 0.05
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTCACTTTT
Found at i:20678737 original size:10 final size:12
Alignment explanation
Indices: 20678720--20678791 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 12
20678710 TTCGAAACGT
*
20678720 GAAAAAAAAATC
1 GAAAAAAAATTC
20678732 -AAAAAAAATTC
1 GAAAAAAAATTC
20678743 GAAAAAAAAATTGATTC
1 G--AAAAAAA---ATTC
20678760 AGAAAAAAAATTC
1 -GAAAAAAAATTC
*
20678773 -AAAAAAAAATC
1 GAAAAAAAATTC
20678784 GAAAAAAA
1 GAAAAAAA
20678792 GGAAAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
11 20 0.40
12 7 0.14
13 4 0.08
14 7 0.14
16 7 0.14
17 4 0.08
18 1 0.02
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (12 bp):
GAAAAAAAATTC
Found at i:20678748 original size:13 final size:13
Alignment explanation
Indices: 20678720--20678791 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 13
20678710 TTCGAAACGT
20678720 GAAAAAAAAA-TC
1 GAAAAAAAAATTC
20678732 --AAAAAAAATTC
1 GAAAAAAAAATTC
20678743 GAAAAAAAAATT-
1 GAAAAAAAAATTC
20678755 GATTCAGAAAAAAAATTC
1 G----A-AAAAAAAATTC
20678773 -AAAAAAAAA-TC
1 GAAAAAAAAATTC
20678784 GAAAAAAA
1 GAAAAAAA
20678792 GGAAAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
10 8 0.16
11 4 0.08
12 16 0.32
13 11 0.22
16 1 0.02
17 10 0.20
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (13 bp):
GAAAAAAAAATTC
Found at i:20678799 original size:11 final size:11
Alignment explanation
Indices: 20678785--20678870 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
20678775 AAAAAAATCG
20678785 AAAAAAAGGAA
1 AAAAAAAGGAA
20678796 AAAAAAAGTGACA
1 AAAAAAAG-GA-A
*
20678809 AAAAAAATCGAGTTA
1 AAAAAAA--G-G-AA
20678824 AAAAAAA-GAA
1 AAAAAAAGGAA
*
20678834 AAAAAAAGTAA
1 AAAAAAAGGAA
* *
20678845 AAGAAAAGAACA
1 AAAAAAAGGA-A
20678857 AAAAAAAGTGAA
1 AAAAAAAG-GAA
20678869 AA
1 AA
20678871 GTATTGTGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 8 0.14
11 19 0.32
12 13 0.22
13 9 0.15
15 10 0.17
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (11 bp):
AAAAAAAGGAA
Found at i:20678812 original size:24 final size:24
Alignment explanation
Indices: 20678785--20678870 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 24
20678775 AAAAAAATCG
20678785 AAAAAAAG-GAAAAAAAAAGTGACA
1 AAAAAAAGAGAAAAAAAAAG-GACA
*
20678809 AAAAAAATCGAGTTAAAAAAAA-GA-A
1 AAAAAAA--GAG-AAAAAAAAAGGACA
* * *
20678834 AAAAAAAG-TAAAAGAAAAGAACA
1 AAAAAAAGAGAAAAAAAAAGGACA
*
20678857 AAAAAAAGTGAAAA
1 AAAAAAAGAGAAAA
20678871 GTATTGTGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
21 7 0.14
22 1 0.02
23 10 0.20
24 11 0.22
25 8 0.16
26 3 0.06
27 1 0.02
28 8 0.16
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (24 bp):
AAAAAAAGAGAAAAAAAAAGGACA
Found at i:20684536 original size:20 final size:20
Alignment explanation
Indices: 20684513--20684577 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
20684503 AAGCTCAAAC
20684513 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
*
20684533 GAGCTCAAA-CAAGCTAAATT
1 GAGCT-AAAGTAAGCTAAATT
* * * *
20684553 AAGCTCATGTGAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
20684573 GAGCT
1 GAGCT
20684578 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.89
21 3 0.08
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:20686002 original size:20 final size:20
Alignment explanation
Indices: 20685979--20686035 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
20685969 GGGTTAAGAT
*
20685979 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
20685999 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
20686019 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
20686036 AAATGGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:20688600 original size:21 final size:21
Alignment explanation
Indices: 20688571--20688626 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
20688561 CAAGCTCTCT
*
20688571 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
20688592 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
20688613 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
20688627 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:20688619 original size:14 final size:14
Alignment explanation
Indices: 20688570--20688626 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
20688560 TCAAGCTCTC
20688570 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
20688583 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
20688597 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
20688611 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
20688625 TT
1 TT
20688627 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:20688686 original size:18 final size:18
Alignment explanation
Indices: 20688588--20688691 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
20688578 TCTTTTTTCG
20688588 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
20688607 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
20688627 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
20688645 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
20688663 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
20688681 CTTTTTGTTTT
1 CTTTTTCTTTT
20688692 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:20688708 original size:6 final size:6
Alignment explanation
Indices: 20688588--20688695 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
20688578 TCTTTTTTCG
* * * **
20688588 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
20688639 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
20688687 -GTTTT CTTT
1 CTTTTT CTTT
20688696 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:20689803 original size:13 final size:13
Alignment explanation
Indices: 20689787--20689846 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
20689777 TTTTTTCACC
20689787 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
20689800 TTTTTTTTCAATCAAAT
1 TTTTTTTTGAAT----T
20689817 TTTTTTTTCGAA-T
1 TTTTTTTT-GAATT
20689830 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
20689842 TTTTT
1 TTTTT
20689847 GTTACTCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
11 1 0.03
12 7 0.18
13 20 0.51
17 9 0.23
18 2 0.05
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:20693218 original size:30 final size:30
Alignment explanation
Indices: 20693184--20693280 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
20693174 AAAACTAAAA
20693184 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
20693214 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
20693244 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
20693273 ATGAGCTA
1 -TGAGCTA
20693281 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:20695674 original size:12 final size:12
Alignment explanation
Indices: 20695657--20695718 Score: 72
Period size: 12 Copynumber: 5.0 Consensus size: 12
20695647 AAACCGTATG
20695657 CAATTTTTTTTT
1 CAATTTTTTTTT
20695669 CAATTTTTTTTT
1 CAATTTTTTTTT
20695681 CAAATTTTTTTTT
1 C-AATTTTTTTTT
*
20695694 -ATTTTTTTTTT
1 CAATTTTTTTTT
*
20695705 GAACTCTTTTTTTT
1 CAA-T-TTTTTTTT
20695719 ATGTACCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
11 10 0.23
12 14 0.32
13 12 0.27
14 8 0.18
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:20695720 original size:25 final size:24
Alignment explanation
Indices: 20695658--20695720 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
20695648 AACCGTATGC
*
20695658 AATTTTTTTTTCAATTTTTTTTTCA
1 AATTTTTTTTT-ATTTTTTTTTTCA
*
20695683 AATTTTTTTTTATTTTTTTTTTGA
1 AATTTTTTTTTATTTTTTTTTTCA
*
20695707 ACTCTTTTTTTTAT
1 AAT-TTTTTTTTAT
20695721 GTACCTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (24 bp):
AATTTTTTTTTATTTTTTTTTTCA
Found at i:20696047 original size:22 final size:22
Alignment explanation
Indices: 20696017--20696060 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20696007 TTTGGTATTT
20696017 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
20696039 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
20696061 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:20701116 original size:18 final size:18
Alignment explanation
Indices: 20701095--20701145 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
20701085 CACTATTTTG
20701095 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTGCA
20701113 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTGCA
*
20701131 ATTTCTTTTTGTTTT
1 ATTTCTTTTTCTTTT
20701146 CTTTCAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.10, C:0.14, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTGCA
Found at i:20701155 original size:21 final size:23
Alignment explanation
Indices: 20701101--20701161 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 23
20701091 TTTGATTTCT
20701101 TTTTCTTTTGCAATTTC----T-
1 TTTTCTTTTGCAATTTCTTTTTG
20701119 TTTTCTTTTGCAATTTCTTTTTG
1 TTTTCTTTTGCAATTTCTTTTTG
20701142 TTTTC-TTT-CAATTTCTTTTT
1 TTTTCTTTTGCAATTTCTTTTT
20701162 CAATCTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 17 0.45
21 12 0.32
22 4 0.11
23 5 0.13
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTCTTTTGCAATTTCTTTTTG
Found at i:20702181 original size:11 final size:11
Alignment explanation
Indices: 20702159--20702216 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
20702149 CTCGCAAGAC
*
20702159 TTTTCACTTTT
1 TTTTCATTTTT
*
20702170 TTTTCTTCTTTT
1 TTTTCAT-TTTT
*
20702182 TTTTC--CTTT
1 TTTTCATTTTT
*
20702191 TTTTCAATTTT
1 TTTTCATTTTT
20702202 TTTTCATTTTT
1 TTTTCATTTTT
20702213 TTTT
1 TTTT
20702217 GAATTTCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 8 0.21
11 22 0.56
12 9 0.23
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:20702193 original size:9 final size:9
Alignment explanation
Indices: 20702168--20702215 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
20702158 CTTTTCACTT
20702168 TTTTTTCTTC
1 TTTTTT-TTC
20702178 TTTTTTTTC
1 TTTTTTTTC
*
20702187 CTTTTTTTC
1 TTTTTTTTC
20702196 AATTTTTTTTC
1 --TTTTTTTTC
20702207 ATTTTTTTT
1 -TTTTTTTT
20702216 TGAATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 11 0.32
10 15 0.44
11 8 0.24
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:20702216 original size:22 final size:21
Alignment explanation
Indices: 20702188--20702236 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
20702178 TTTTTTTTCC
* *
20702188 TTTTTTTCAATTTTTTTTCATT
1 TTTTTTTCAATTTCTTCTC-TT
*
20702210 TTTTTTTGAATTTCTTCTCTT
1 TTTTTTTCAATTTCTTCTCTT
20702231 TTTTTT
1 TTTTTT
20702237 AAATCCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTTTTCAATTTCTTCTCTT
Found at i:20702315 original size:12 final size:13
Alignment explanation
Indices: 20702300--20702330 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
20702290 CCAACTTAAT
20702300 TTTTTTTTTTGA-
1 TTTTTTTTTTGAC
20702312 TTTTTTTTTTGAC
1 TTTTTTTTTTGAC
20702325 TTTTTT
1 TTTTTT
20702331 CTTCGTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTGAC
Found at i:20703753 original size:20 final size:20
Alignment explanation
Indices: 20703730--20703776 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20703720 GGGTTAAGAT
*
20703730 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
20703750 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
20703770 TGAGCTG
1 TGAGCTG
20703777 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:20707757 original size:30 final size:28
Alignment explanation
Indices: 20707704--20707759 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
20707694 TTCTTCCACG
* *
20707704 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
20707732 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
20707760 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:20709775 original size:10 final size:10
Alignment explanation
Indices: 20709759--20709816 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
20709749 CAACTCCGAC
20709759 CAGCTCAATT
1 CAGCTCAATT
* *
20709769 GAGCTCATTT
1 CAGCTCAATT
20709779 CAGCTCAA-T
1 CAGCTCAATT
20709788 CAAGCTCAATT
1 C-AGCTCAATT
*
20709799 TAGCTACAATT
1 CAGCT-CAATT
20709810 CAGCTCA
1 CAGCTCA
20709817 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20714223 original size:10 final size:10
Alignment explanation
Indices: 20714207--20714284 Score: 86
Period size: 10 Copynumber: 7.7 Consensus size: 10
20714197 CAACTCCGAC
20714207 CAGCTCAATT
1 CAGCTCAATT
* *
20714217 GAGCTCATTT
1 CAGCTCAATT
20714227 CAGCTCAATT
1 CAGCTCAATT
* *
20714237 GAGCTCATTT
1 CAGCTCAATT
20714247 CAGCTCAA-T
1 CAGCTCAATT
20714256 CAAGCTCAATT
1 C-AGCTCAATT
*
20714267 TAGCTACAATT
1 CAGCT-CAATT
20714278 CAGCTCA
1 CAGCTCA
20714285 TTTATTTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
9 2 0.04
10 43 0.78
11 10 0.18
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20714230 original size:20 final size:20
Alignment explanation
Indices: 20714207--20714287 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
20714197 CAACTCCGAC
20714207 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
20714227 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
**
20714247 CAGCTCAATCAAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
20714268 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
20714288 ATTTTATTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 42 0.76
21 13 0.24
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:20716550 original size:30 final size:31
Alignment explanation
Indices: 20716514--20716610 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
20716504 CATCAACTCC
*
20716514 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
20716544 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
*
20716574 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
20716604 TAGCTCA
1 TAGCTCA
20716611 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:20719972 original size:6 final size:6
Alignment explanation
Indices: 20719940--20720047 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
20719930 AAAGAAATTG
* * ** *
20719940 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
20719987 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
20720038 AAAGAA AAAG
1 AAAGAA AAAG
20720048 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
5 4 0.05
6 61 0.79
7 8 0.10
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:20720027 original size:14 final size:13
Alignment explanation
Indices: 20720008--20720045 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
20719998 AAAAGTGAAA
20720008 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
20720020 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
20720035 GAAAAAGAAAA
1 GAAAAAGAAAA
20720046 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:20720082 original size:12 final size:12
Alignment explanation
Indices: 20720051--20720082 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
20720041 GAAAAAGCGA
*
20720051 AAAAAGAATTTG
1 AAAAAGAGTTTG
20720063 AAAAAGAGTTTG
1 AAAAAGAGTTTG
20720075 AAAAAGAG
1 AAAAAGAG
20720083 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:20722415 original size:23 final size:24
Alignment explanation
Indices: 20722385--20722430 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
20722375 TTGATTGAAA
20722385 AAAAAAATTCA-AAAAAAAAAGTG
1 AAAAAAATTCACAAAAAAAAAGTG
*
20722408 AAAAAAATTGAGCAAAAAAAAAG
1 AAAAAAATTCA-CAAAAAAAAAG
20722431 GTGAGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (24 bp):
AAAAAAATTCACAAAAAAAAAGTG
Found at i:20722426 original size:15 final size:15
Alignment explanation
Indices: 20722408--20722446 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
20722398 AAAAAAAGTG
20722408 AAAAAAATTGAGCAA
1 AAAAAAATTGAGCAA
*
20722423 AAAAAAAGGTGAGCAA
1 AAAAAAA-TTGAGCAA
20722439 AAAAAAAT
1 AAAAAAAT
20722447 CAAGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.69, C:0.05, G:0.15, T:0.10
Consensus pattern (15 bp):
AAAAAAATTGAGCAA
Found at i:20723359 original size:18 final size:18
Alignment explanation
Indices: 20723338--20723372 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20723328 AGAAAAGAAA
20723338 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
20723356 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
20723373 AAAGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:20734823 original size:30 final size:30
Alignment explanation
Indices: 20734789--20734885 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
20734779 TAAACTAAAA
*
20734789 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
20734819 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
20734849 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
20734879 TGAGCTA
1 TGAGCTA
20734886 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:20736390 original size:17 final size:17
Alignment explanation
Indices: 20736370--20736406 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20736360 GAGGTGTTCA
20736370 TTTTT-CATTTTATTT-T
1 TTTTTACATTTT-TTTCT
20736386 TTTTTACATTTTTTTCT
1 TTTTTACATTTTTTTCT
20736403 TTTT
1 TTTT
20736407 GGTGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTACATTTTTTTCT
Found at i:20737011 original size:18 final size:18
Alignment explanation
Indices: 20736960--20737023 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
20736950 ACAAAGAAAT
20736960 GAAAGAAAAAGAGGAA-GA
1 GAAAGAAAAAGA-GAATGA
* *
20736978 G-AGGAAACA-A-AATGA
1 GAAAGAAAAAGAGAATGA
**
20736993 GATTGAAAAAGAGAATGA
1 GAAAGAAAAAGAGAATGA
20737011 GAAAGAAAAAGAG
1 GAAAGAAAAAGAG
20737024 CTTGATCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 6 0.17
17 7 0.20
18 17 0.49
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.06
Consensus pattern (18 bp):
GAAAGAAAAAGAGAATGA
Found at i:20738093 original size:189 final size:189
Alignment explanation
Indices: 20737773--20738151 Score: 758
Period size: 189 Copynumber: 2.0 Consensus size: 189
20737763 TTCAGCCAAG
20737773 AAGAGCAACTAAATTCATTCTCCAAAAGCTGGCCGATGCACTTCCCAAAACAGCACCTATGCGTT
1 AAGAGCAACTAAATTCATTCTCCAAAAGCTGGCCGATGCACTTCCCAAAACAGCACCTATGCGTT
20737838 CACATTTGGAGTTCACACCAAGGACCATTTGGCTGATCATTGTTCACACTTCCAAAGACTTTTCC
66 CACATTTGGAGTTCACACCAAGGACCATTTGGCTGATCATTGTTCACACTTCCAAAGACTTTTCC
20737903 AACTCCTTTTTCACACCTTCAAGGCTGTTCACGTTCACCTTTAATGCTGGTCTCTTTTC
131 AACTCCTTTTTCACACCTTCAAGGCTGTTCACGTTCACCTTTAATGCTGGTCTCTTTTC
20737962 AAGAGCAACTAAATTCATTCTCCAAAAGCTGGCCGATGCACTTCCCAAAACAGCACCTATGCGTT
1 AAGAGCAACTAAATTCATTCTCCAAAAGCTGGCCGATGCACTTCCCAAAACAGCACCTATGCGTT
20738027 CACATTTGGAGTTCACACCAAGGACCATTTGGCTGATCATTGTTCACACTTCCAAAGACTTTTCC
66 CACATTTGGAGTTCACACCAAGGACCATTTGGCTGATCATTGTTCACACTTCCAAAGACTTTTCC
20738092 AACTCCTTTTTCACACCTTCAAGGCTGTTCACGTTCACCTTTAATGCTGGTCTCTTTTC
131 AACTCCTTTTTCACACCTTCAAGGCTGTTCACGTTCACCTTTAATGCTGGTCTCTTTTC
20738151 A
1 A
20738152 GCCAAGAATT
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 190 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (189 bp):
AAGAGCAACTAAATTCATTCTCCAAAAGCTGGCCGATGCACTTCCCAAAACAGCACCTATGCGTT
CACATTTGGAGTTCACACCAAGGACCATTTGGCTGATCATTGTTCACACTTCCAAAGACTTTTCC
AACTCCTTTTTCACACCTTCAAGGCTGTTCACGTTCACCTTTAATGCTGGTCTCTTTTC
Found at i:20740415 original size:13 final size:13
Alignment explanation
Indices: 20740397--20740422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20740387 ACCTGAAAGC
20740397 AATTTAATTCATA
1 AATTTAATTCATA
20740410 AATTTAATTCATA
1 AATTTAATTCATA
20740423 TTAGGACACA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:20740837 original size:20 final size:21
Alignment explanation
Indices: 20740812--20740850 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20740802 TCAAACAAGC
20740812 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
20740832 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
20740851 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:20752824 original size:15 final size:15
Alignment explanation
Indices: 20752806--20752875 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
20752796 CTAGACCGTA
20752806 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
*
20752821 TGCAATTTTTTTTTC
1 TGCAATTTTTTTTTT
20752836 T-C--TTTTTTTTTT
1 TGCAATTTTTTTTTT
*
20752848 T-CGGATTTTTTTTTT
1 TGC-AATTTTTTTTTT
*
20752863 CG-AACTTTTTTTT
1 TGCAA-TTTTTTTT
20752876 AACTTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
12 11 0.24
14 2 0.04
15 33 0.72
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:20752843 original size:14 final size:14
Alignment explanation
Indices: 20752810--20752875 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
20752800 ACCGTATGCA
*
20752810 ATTTTTTTTTTTGC
1 ATTTTTTTTTTCGC
* *
20752824 AATTTTTTTTTCTC
1 ATTTTTTTTTTCGC
* *
20752838 TTTTTTTTTTTCGG
1 ATTTTTTTTTTCGC
*
20752852 ATTTTTTTTTTCGA
1 ATTTTTTTTTTCGC
20752866 ACTTTTTTTT
1 A-TTTTTTTT
20752876 AACTTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 34 0.81
15 8 0.19
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (14 bp):
ATTTTTTTTTTCGC
Found at i:20752856 original size:13 final size:14
Alignment explanation
Indices: 20752840--20752892 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
20752830 TTTTTCTCTT
* *
20752840 TTTTTTTTTCGGAT
1 TTTTTTTTTCGAAC
20752854 TTTTTTTTTCGAAC
1 TTTTTTTTTCGAAC
20752868 -TTTTTTTT--AAC
1 TTTTTTTTTCGAAC
20752879 TTTTTTTTTTCGAA
1 -TTTTTTTTTCGAA
20752893 GCTACGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 3 0.09
13 16 0.48
14 12 0.36
15 2 0.06
ACGTcount: A:0.13, C:0.09, G:0.08, T:0.70
Consensus pattern (14 bp):
TTTTTTTTTCGAAC
Found at i:20754383 original size:1 final size:1
Alignment explanation
Indices: 20754377--20754420 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
20754367 GGACCATGGG
20754377 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20754421 ATTCAATGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20778507 original size:43 final size:42
Alignment explanation
Indices: 20778458--20778554 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
20778448 CCAGATGTGC
**
20778458 TCTTACATGTAATCGAATATCGATG-CCACTATCCCAGACAGGG
1 TCTTACATGTAATAAAATA-CGATGTCCA-TATCCCAGACAGGG
* * * *
20778501 TCTTACATGAAATAAAATACGATGTCGATGTCCCAGACATGG
1 TCTTACATGTAATAAAATACGATGTCCATATCCCAGACAGGG
*
20778543 TCTTACACGTAA
1 TCTTACATGTAA
20778555 ATAATAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
42 27 0.60
43 18 0.40
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
TCTTACATGTAATAAAATACGATGTCCATATCCCAGACAGGG
Found at i:20781894 original size:43 final size:43
Alignment explanation
Indices: 20781846--20781995 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 43
20781836 GGTTATCAAG
*
20781846 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA
** *
20781889 TTGTGATTACATGTAAGACTGTGTCTGGGACATTGGCATCATA
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA
* * * * * *
20781932 TAGTGATT-CGTGTAAGACCCTTTCTAGGACAGTGGCATCG-A
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA
* *
20781973 TATGTGATAACATGTAAAACCAT
1 T-TGTGATTACATGTAAGACCAT
20781996 ATTTGGGATA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
41 2 0.02
42 30 0.34
43 56 0.64
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA
Found at i:20784953 original size:44 final size:42
Alignment explanation
Indices: 20784877--20784980 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
20784867 ATATGTGTTA
* * * * *
20784877 TCGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGTAATT
1 TCGTGTAAGACCATGTCTAGGACATTGACATCGTATATG--ATT
20784920 TGCGTGTAAGACCATGTCTAGGACATTGACATCGTATATGATT
1 T-CGTGTAAGACCATGTCTAGGACATTGACATCGTATATGATT
*
20784963 TCGTGTAAGACCCTGTCT
1 TCGTGTAAGACCATGTCT
20784981 GGGATAGTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 16 0.30
43 5 0.09
44 28 0.53
45 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTAGGACATTGACATCGTATATGATT
Found at i:20785038 original size:43 final size:43
Alignment explanation
Indices: 20784865--20785036 Score: 156
Period size: 43 Copynumber: 4.0 Consensus size: 43
20784855 TATAGGATTC
*
20784865 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * * * * *
20784908 CGAT-TTGTAATTTGCGTGTAAGACCATGTCTAGGACATTGACAT
1 CGATATT-TGA-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
20784952 CG-TATATGATTTCGTGTAAGACC-CTGTCTGGGATAG-TGGCAT
1 CGATATTTGATTACGTGTAAGACCAC-GTCTGGGA-CGTTGGCAT
* *
20784994 TGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
20785037 TGTACAAGCT
Statistics
Matches: 100, Mismatches: 20, Indels: 18
0.72 0.14 0.13
Matches are distributed among these distances:
42 28 0.28
43 40 0.40
44 30 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
CGATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:20788188 original size:15 final size:15
Alignment explanation
Indices: 20788168--20788197 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20788158 GGTTCTTGAT
*
20788168 TTAAACTTATTCAAA
1 TTAAACTCATTCAAA
20788183 TTAAACTCATTCAAA
1 TTAAACTCATTCAAA
20788198 CTTATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAACTCATTCAAA
Found at i:20799913 original size:28 final size:28
Alignment explanation
Indices: 20799851--20799944 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
20799841 TATTAAGTCT
*
20799851 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
20799878 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * * *
20799906 GCACACTTAGTGCTGTACAATTTAAACCC
1 GCACACTTAGTGCTATATAA-TCAAACTC
20799935 GCACACTTAG
1 GCACACTTAG
20799945 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.35
28 23 0.38
29 16 0.27
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:20802661 original size:11 final size:11
Alignment explanation
Indices: 20802642--20802697 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
20802632 CATGGTATGT
20802642 ATGATATGCAC
1 ATGATATGCAC
*
20802653 ATGACATG--C
1 ATGATATGCAC
20802662 ATGATATGCAC
1 ATGATATGCAC
*
20802673 ATGATATG--T
1 ATGATATGCAC
20802682 ATGATATGCAC
1 ATGATATGCAC
20802693 ATGAT
1 ATGAT
20802698 GTATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:20802697 original size:20 final size:20
Alignment explanation
Indices: 20802631--20802697 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
20802621 ATTTTGATAA
*
20802631 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
20802651 ACATGACATGCATGATATGC
1 ACATGATATGTATGATATGC
20802671 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
20802691 ACATGAT
1 ACATGAT
20802698 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:20802791 original size:23 final size:23
Alignment explanation
Indices: 20802749--20802958 Score: 298
Period size: 23 Copynumber: 9.1 Consensus size: 23
20802739 AGGAAGTGAA
*
20802749 AAAGGGCTTACG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20802771 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
20802794 AAAGGGCTTATGCCCCA-TTATC
1 AAAGGGCTTATGCCCCAGTTATT
* *
20802816 AAAGGGCTTACGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20802839 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
20802862 AAAGGGCTTATGCCACAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
20802886 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
20802909 GAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
20802933 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20802956 AAA
1 AAA
20802959 AGAGGCTAGG
Statistics
Matches: 166, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
22 30 0.18
23 96 0.58
24 40 0.24
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:20802902 original size:47 final size:46
Alignment explanation
Indices: 20802748--20802980 Score: 301
Period size: 47 Copynumber: 5.0 Consensus size: 46
20802738 GAGGAAGTGA
*
20802748 AAAAGGGCTTACG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* * * *
20802793 TAAAGGGCTTATGCCCCA-TTATCAAAGGGCTTACGCCCTAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
20802838 TAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCACAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
20802884 CAAAAGGGCTTACGCCCCAGTTATTGAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
20802931 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
20802980 A
1 A
20802981 TAATAAAGCA
Statistics
Matches: 164, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
45 53 0.32
46 27 0.16
47 64 0.39
48 9 0.05
49 11 0.07
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:20803212 original size:31 final size:30
Alignment explanation
Indices: 20803173--20803236 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
20803163 CATTTACAGT
* *
20803173 AAAAGCTTCGGCCCAGTAATATGAAATTTG
1 AAAAGCTTCGACCCAGTAATATGAAATATG
**
20803203 AAAAGGCTTCGACCCAGTGTTATGAAATATG
1 AAAA-GCTTCGACCCAGTAATATGAAATATG
20803234 AAA
1 AAA
20803237 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (30 bp):
AAAAGCTTCGACCCAGTAATATGAAATATG
Found at i:20810789 original size:20 final size:20
Alignment explanation
Indices: 20810766--20810804 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
20810756 TAAACATGGT
20810766 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
20810786 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
20810805 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:20810888 original size:23 final size:23
Alignment explanation
Indices: 20810858--20811093 Score: 312
Period size: 23 Copynumber: 10.1 Consensus size: 23
20810848 AGGAAGTGAA
* *
20810858 AAAGGGCTTACGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
20810881 AAAGGGCTTATGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
20810904 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
**
20810928 AAAGGGCTTACACCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20810951 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
20810974 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
* * *
20810998 AAAGAGCTTACG-CCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
20811021 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
20811044 GAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
20811068 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
20811091 AAA
1 AAA
20811094 AGAGGCTAGG
Statistics
Matches: 190, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
23 131 0.69
24 59 0.31
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:20810949 original size:47 final size:46
Alignment explanation
Indices: 20810858--20811115 Score: 322
Period size: 47 Copynumber: 5.5 Consensus size: 46
20810848 AGGAAGTGAA
* * * *
20810858 AAAGGGCTTACGCCCTAGTTATTAAAGGGCTTATGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
**
20810904 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACACCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
* *
20810951 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT-T
* *
20810998 AAAGAGCTTACG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
* *
20811044 GAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
*
20811091 AAAAGAGGC-TAGGCCTCCAGTTATA
1 -AAAG-GGCTTATGCC-CCAGTTATA
20811116 TGATAAAGCA
Statistics
Matches: 184, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
46 58 0.32
47 106 0.58
48 9 0.05
49 11 0.06
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:20810971 original size:70 final size:70
Alignment explanation
Indices: 20810857--20811093 Score: 377
Period size: 70 Copynumber: 3.4 Consensus size: 70
20810847 GAGGAAGTGA
* *
20810857 AAAAGGGCTTACGCCCTAGTTATTAAAGGGCTTATGCCCTAGTTATTAAAGGGCTTATGCCCCAG
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
20810922 TTATC
66 TTATC
*
20810927 AAAAGGGCTTACACCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
20810992 TTATC
66 TTATC
* * *
20810997 AAAAGAGCTTACG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTATTGAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
*
20811061 GTTATA
65 GTTATC
**
20811067 AAAAGGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTACGCCCCAGTTATTAAA
20811094 AGAGGCTAGG
Statistics
Matches: 153, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
69 9 0.06
70 135 0.88
71 9 0.06
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (70 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAG
TTATC
Found at i:20811343 original size:31 final size:31
Alignment explanation
Indices: 20811308--20811371 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
20811298 CGTTTACAGT
*
20811308 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
20811339 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
20811370 AA
1 AA
20811372 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:20813641 original size:28 final size:28
Alignment explanation
Indices: 20813598--20813698 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 28
20813588 ATGAAACAAA
20813598 ATCT-GCACACACAGTGCCCACTGACCG
1 ATCTCGCACACACAGTGCCCACTGACCG
* * * ** * **
20813625 ATCTCGCGCACATAGTGCTCGGTTAAAG
1 ATCTCGCACACACAGTGCCCACTGACCG
*
20813653 AAT-TCACACACACAGTGCCCACTGACCG
1 -ATCTCGCACACACAGTGCCCACTGACCG
*
20813681 ATCTCGCACACATAGTGC
1 ATCTCGCACACACAGTGC
20813699 TCGGTTAAAG
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
27 6 0.12
28 44 0.85
29 2 0.04
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.19
Consensus pattern (28 bp):
ATCTCGCACACACAGTGCCCACTGACCG
Found at i:20813687 original size:56 final size:56
Alignment explanation
Indices: 20813603--20813727 Score: 241
Period size: 56 Copynumber: 2.2 Consensus size: 56
20813593 ACAAAATCTG
*
20813603 CACACACAGTGCCCACTGACCGATCTCGCGCACATAGTGCTCGGTTAAAGAATTCA
1 CACACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCA
20813659 CACACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCA
1 CACACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCA
20813715 CACACACAGTGCC
1 CACACACAGTGCC
20813728 TCAATTCATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (56 bp):
CACACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCA
Found at i:20813718 original size:28 final size:28
Alignment explanation
Indices: 20813633--20813726 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
20813623 CGATCTCGCG
*
20813633 CACATAGTGCTCGGTTAAAGAATTCACA
1 CACACAGTGCTCGGTTAAAGAATTCACA
* ** * ** *
20813661 CACACAGTGCCCACTGACCG-ATCTCGCA
1 CACACAGTGCTCGGTTAAAGAAT-TCACA
*
20813689 CACATAGTGCTCGGTTAAAGAATTCACA
1 CACACAGTGCTCGGTTAAAGAATTCACA
20813717 CACACAGTGC
1 CACACAGTGC
20813727 CTCAATTCAT
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
27 2 0.04
28 43 0.91
29 2 0.04
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (28 bp):
CACACAGTGCTCGGTTAAAGAATTCACA
Found at i:20813744 original size:25 final size:25
Alignment explanation
Indices: 20813710--20813762 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
20813700 CGGTTAAAGA
20813710 ATTCACACACACAGTGCCTCA-ATTC
1 ATTCACACACACAGTGCCT-ATATTC
* *
20813735 ATTCGCACACATAGTGCCTATATTC
1 ATTCACACACACAGTGCCTATATTC
20813760 ATT
1 ATT
20813763 TGTTATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.30
Consensus pattern (25 bp):
ATTCACACACACAGTGCCTATATTC
Found at i:20813944 original size:43 final size:43
Alignment explanation
Indices: 20813895--20814019 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
20813885 CACCGATATT
* * * *
20813895 AAGCCTGCTAGGCACGAAGACCCAAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACA
* *
20813938 AAGCCTGTTAGGAACGAAGGCCCGAATACACATCACCAGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACA
* * *
20813981 AAGCCTGCTAGGCATGAAGGCCTGATTACACATCACCAG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAG
20814020 TACGAATGCC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACA
Found at i:20814079 original size:40 final size:40
Alignment explanation
Indices: 20814014--20814151 Score: 222
Period size: 40 Copynumber: 3.5 Consensus size: 40
20814004 GATTACACAT
* * * * *
20814014 CACCAGTACGAATGCCCTTCAGGACTTAGCTCGGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
20814054 CACCAGCACGAATTCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
20814094 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
20814134 CACCAGCACGAATGCTCT
1 CACCAGCACGAATGCTCT
20814152 CCGGATGTTC
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 91 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:20818538 original size:20 final size:19
Alignment explanation
Indices: 20818515--20818561 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
20818505 TATTTCTTAA
20818515 AATTAAAACTCAATTCTACC
1 AATTAAAACTCAATTC-ACC
* *
20818535 AATTCAAAACTCCATTCAGC
1 AATT-AAAACTCAATTCACC
20818555 AATTAAA
1 AATTAAA
20818562 CATGAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTAAAACTCAATTCACC
Found at i:20823621 original size:26 final size:26
Alignment explanation
Indices: 20823582--20823634 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
20823572 CGATAAAAGC
*
20823582 TGAAATACCGAAACGTTGGTATTTTG
1 TGAAATACCAAAACGTTGGTATTTTG
20823608 TGAAATACCAAAACGTTGGTATTTTG
1 TGAAATACCAAAACGTTGGTATTTTG
20823634 T
1 T
20823635 TACACCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (26 bp):
TGAAATACCAAAACGTTGGTATTTTG
Found at i:20839117 original size:40 final size:40
Alignment explanation
Indices: 20839069--20839274 Score: 326
Period size: 40 Copynumber: 5.2 Consensus size: 40
20839059 GGACTAAGAT
20839069 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
20839109 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
20839149 CCGAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
20839189 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* * *
20839229 CCGAAGGCATTTGTGCGAGTTG-CTATATTC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
*
20839268 TCGAAGG
1 CCGAAGG
20839275 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.09
40 139 0.90
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:20845794 original size:13 final size:13
Alignment explanation
Indices: 20845776--20845801 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20845766 ATATTATAAT
20845776 TATTTTATGTTAA
1 TATTTTATGTTAA
20845789 TATTTTATGTTAA
1 TATTTTATGTTAA
20845802 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:20847221 original size:40 final size:39
Alignment explanation
Indices: 20847173--20847329 Score: 197
Period size: 40 Copynumber: 4.2 Consensus size: 39
20847163 GGACTAAGAT
20847173 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCC-GGCTAAGTC
*
20847213 CCAAAGGCATTTGTGCTAGTGACT-TAT-CGGCTAAGT-
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGCTAAGTC
20847249 CCGAAGGCA-TTGTGC-A-T-A-TATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCC-GGCTAAGTC
* *
20847284 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGCTAAGTC
20847323 CCGAAGG
1 CCGAAGG
20847330 TACTTGGGTT
Statistics
Matches: 104, Mismatches: 3, Indels: 21
0.81 0.02 0.16
Matches are distributed among these distances:
31 1 0.01
32 4 0.04
33 2 0.02
34 9 0.09
35 15 0.14
36 14 0.13
37 9 0.09
38 1 0.01
39 19 0.18
40 30 0.29
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGCTAAGTC
Found at i:20852659 original size:27 final size:27
Alignment explanation
Indices: 20852629--20852690 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
20852619 ATTTACTAAA
20852629 ATACCCCTAAGTATG-AAAATTACCATT
1 ATACCCCTAAG-ATGCAAAATTACCATT
* *
20852656 ATA-CCCTTAGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATT
20852682 ATACCCCTA
1 ATACCCCTA
20852691 GGGTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 21 0.70
27 7 0.23
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATT
Found at i:20852838 original size:27 final size:28
Alignment explanation
Indices: 20852796--20852908 Score: 153
Period size: 27 Copynumber: 4.2 Consensus size: 28
20852786 GTGGAAGCGT
20852796 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAAATATCTGTA
* *
20852823 TCTGGTGGCTCCGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCACAAATATCTGTA
*
20852851 TCTGGTGGCTCTGCCA-TAATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTA
* *
20852878 TCTGGTGACTCTGTCAC-AATATCTGT-
1 TCTGGTGGCTCTGCCACAAATATCTGTA
20852904 TCTGG
1 TCTGG
20852909 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
26 5 0.06
27 57 0.74
28 15 0.19
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:20852902 original size:54 final size:54
Alignment explanation
Indices: 20852794--20852908 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 54
20852784 TGGTGGAAGC
*
20852794 GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCCGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCCGCCACAAATATCT
* * *
20852848 GTTTCTGGTGGCTCTGCCA-TAATATCTGTATCTGGTGACTCTGTCAC-AATATCT
1 G-TTCTGGTGGCTCTGCCACAAATATCTG-ATCTGGTGACTCCGCCACAAATATCT
20852902 GTTCTGG
1 GTTCTGG
20852909 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
53 6 0.11
54 17 0.31
55 32 0.58
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCCGCCACAAATATCT
Found at i:20862096 original size:34 final size:34
Alignment explanation
Indices: 20862058--20862130 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
20862048 AGTGACAGTC
*
20862058 CAGTATCAGT-TAGGGCATTAGCCCAATACAGTAT
1 CAGTATCAGTGT-GGGCATTAGCCCAATACAGTAA
* * *
20862092 CAGTATCTGTGTGGGCCTTAGCCCAATTCAGTAA
1 CAGTATCAGTGTGGGCATTAGCCCAATACAGTAA
20862126 CAGTA
1 CAGTA
20862131 ACAGAAATGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCATTAGCCCAATACAGTAA
Found at i:20864563 original size:85 final size:85
Alignment explanation
Indices: 20864466--20864627 Score: 279
Period size: 85 Copynumber: 1.9 Consensus size: 85
20864456 AGTGTGTCGC
* * * * *
20864466 ACACGGCTGAGACGCGCGCCCGTATCTCTGCCTGTGTGGACAAAAATAGGCTACTTTTAAAGCTA
1 ACACGGCTGAGACACACGCCCGTATCTCTGCCTGTGTAGACAAAAATAGGCTACTTGTAAAGCCA
20864531 TTTTGCCACCCTTGTGTCAT
66 TTTTGCCACCCTTGTGTCAT
20864551 ACACGGCTGAGACACACGCCCGTATCTCTGCCTGTGTAGACAAAAATAGGCTACTTGTAAAGCCA
1 ACACGGCTGAGACACACGCCCGTATCTCTGCCTGTGTAGACAAAAATAGGCTACTTGTAAAGCCA
20864616 TTTTGCCACCCT
66 TTTTGCCACCCT
20864628 ACAATCACAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (85 bp):
ACACGGCTGAGACACACGCCCGTATCTCTGCCTGTGTAGACAAAAATAGGCTACTTGTAAAGCCA
TTTTGCCACCCTTGTGTCAT
Found at i:20869226 original size:29 final size:29
Alignment explanation
Indices: 20869185--20869301 Score: 137
Period size: 29 Copynumber: 4.1 Consensus size: 29
20869175 GTTAGCATGA
* **
20869185 ATAT-AAGGTGATTTGGGCCTAGCAGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
*
20869213 ATATGAAGGTGATTTGGGCCTAATAGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
** *
20869242 ATATGAATATGAATTGGGCCTAATTGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
* * *
20869271 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
20869300 AT
1 AT
20869302 GTGACAGCCC
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 4 0.05
29 75 0.95
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (29 bp):
ATATGAAGGTGAATTGGGCCTAATAGGCC
Found at i:20869683 original size:56 final size:56
Alignment explanation
Indices: 20869597--20869716 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
20869587 ACAAGGGATG
20869597 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
20869653 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
20869709 ATGGGCAA
1 ATGGGCAA
20869717 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:20871035 original size:40 final size:39
Alignment explanation
Indices: 20870846--20871028 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 39
20870836 GAAGGATGTC
* * * *
20870846 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAT
* * *
20870885 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTT
1 -CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-AT
* *
20870926 CGGGCTAAG-CCTGAAGGCATTGGTGCGAGTTACTAAAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
20870964 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AAT
*
20871005 CGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
20871029 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 31 0.26
40 75 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:20871050 original size:79 final size:79
Alignment explanation
Indices: 20870897--20871051 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
20870887 GGACTAAGAT
* * **
20870897 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCTGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATATCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
20870962 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
20870976 CCGAAGGCATTTGTGCGAGTTACT-ATAATCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ATCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
20871039 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
20871052 ATTTCGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.62
80 23 0.35
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATATCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:20871163 original size:14 final size:14
Alignment explanation
Indices: 20871144--20871173 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20871134 GTATGTTTCG
20871144 TATGTGCTTTGAAT
1 TATGTGCTTTGAAT
*
20871158 TATGTGTTTTGAAT
1 TATGTGCTTTGAAT
20871172 TA
1 TA
20871174 GTTGAGCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.53
Consensus pattern (14 bp):
TATGTGCTTTGAAT
Found at i:20877594 original size:56 final size:56
Alignment explanation
Indices: 20877508--20877627 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
20877498 ACAAGGGATG
20877508 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
20877564 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
20877620 ATGGGCAA
1 ATGGGCAA
20877628 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:20878993 original size:40 final size:41
Alignment explanation
Indices: 20878755--20878979 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 41
20878745 TCGAAGGATG
* * *
20878755 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20878795 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
20878835 TTCGGGCTAAG-CCTGAAGGCATTGGTGCGAGTTACTA-CA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
20878874 TCCGGGTTAATTCCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20878914 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
20878955 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20878980 AACGAGTAGC
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 30 0.19
40 116 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20882187 original size:112 final size:112
Alignment explanation
Indices: 20881986--20882209 Score: 430
Period size: 112 Copynumber: 2.0 Consensus size: 112
20881976 GGCATCAGGC
*
20881986 CATATGCCCAATGTTGGAGTAGAAGAGGCTCCGGCCTCACCTGTGGCTGGAAATGGACCGTATGA
1 CATATGCCCAATGTTGGAGTAGAAGAGGCTCCGGCCTCACCTGTGGCTGGAAATAGACCGTATGA
*
20882051 TCGGGCCGCAGGAGAAGATTCATTGTCGCAGGCAATGCTGAGGATTT
66 TCGGGCCGCAGGAGAAGATGCATTGTCGCAGGCAATGCTGAGGATTT
20882098 CATATGCCCAATGTTGGAGTAGAAGAGGCTCCGGCCTCACCTGTGGCTGGAAATAGACCGTATGA
1 CATATGCCCAATGTTGGAGTAGAAGAGGCTCCGGCCTCACCTGTGGCTGGAAATAGACCGTATGA
20882163 TCGGGCCGCAGGAGAAGATGCATTGTCGCAGGCAATGCTGAGGATTT
66 TCGGGCCGCAGGAGAAGATGCATTGTCGCAGGCAATGCTGAGGATTT
20882210 TGGAAAGGGT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (112 bp):
CATATGCCCAATGTTGGAGTAGAAGAGGCTCCGGCCTCACCTGTGGCTGGAAATAGACCGTATGA
TCGGGCCGCAGGAGAAGATGCATTGTCGCAGGCAATGCTGAGGATTT
Found at i:20884906 original size:29 final size:28
Alignment explanation
Indices: 20884864--20884924 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
20884854 GTAAGCATGA
* *
20884864 ATATAAGGTTATTTGGGCATAACGGGCC
1 ATATAAGGTGATTTGGGCATAACAGGCC
* *
20884892 ATATAAAGGTGATTTGGGCCTAATAGGCC
1 ATAT-AAGGTGATTTGGGCATAACAGGCC
20884921 ATAT
1 ATAT
20884925 GAATATGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
ATATAAGGTGATTTGGGCATAACAGGCC
Found at i:20886685 original size:24 final size:24
Alignment explanation
Indices: 20886631--20886723 Score: 102
Period size: 24 Copynumber: 3.9 Consensus size: 24
20886621 AGTCATGGTC
*
20886631 GGTAAGCTCTTACTGAGCTGATAAAT
1 GGTAAGCTC-TATTGAGCTGA-AAAT
*
20886657 AGTAAGCTCTATTGAGCTGAAAAT
1 GGTAAGCTCTATTGAGCTGAAAAT
* *
20886681 GGTAAGCTCTAATGAGCTGAACA-
1 GGTAAGCTCTATTGAGCTGAAAAT
20886704 -GTAAGCTCT-TTCGAGCTGAA
1 GGTAAGCTCTATT-GAGCTGAA
20886724 TCGGTAAGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 17 0.28
24 24 0.40
25 10 0.17
26 8 0.13
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (24 bp):
GGTAAGCTCTATTGAGCTGAAAAT
Found at i:20886710 original size:22 final size:22
Alignment explanation
Indices: 20886657--20886743 Score: 77
Period size: 24 Copynumber: 3.8 Consensus size: 22
20886647 GCTGATAAAT
* *
20886657 AGTAAGCTCTATTGAGCTGAAA
1 AGTAAGCTCTAATGAGCTGAAC
20886679 ATGGTAAGCTCTAATGAGCTGAAC
1 A--GTAAGCTCTAATGAGCTGAAC
*
20886703 AGTAAGCTCT-TTCGAGCTGAATC
1 AGTAAGCTCTAAT-GAGCTGAA-C
* * *
20886726 GGTAAGATCCAATGAGCT
1 AGTAAGCTCTAATGAGCT
20886744 AAAACCGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.02
22 18 0.34
23 13 0.25
24 21 0.40
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (22 bp):
AGTAAGCTCTAATGAGCTGAAC
Found at i:20895427 original size:14 final size:13
Alignment explanation
Indices: 20895407--20895438 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20895397 AATATTTGAC
20895407 TTGTTCTTAATTA
1 TTGTTCTTAATTA
20895420 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
20895434 TTGTT
1 TTGTT
20895439 TTGATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:20896068 original size:30 final size:30
Alignment explanation
Indices: 20896034--20896095 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
20896024 TTTCAAGAAT
20896034 GATTCATTATAAATATTTAAAACCTGTCAC
1 GATTCATTATAAATATTTAAAACCTGTCAC
20896064 GATTCATTATAAATATTTAAAACCTGTCAC
1 GATTCATTATAAATATTTAAAACCTGTCAC
20896094 GA
1 GA
20896096 ATATCACGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (30 bp):
GATTCATTATAAATATTTAAAACCTGTCAC
Found at i:20896255 original size:22 final size:22
Alignment explanation
Indices: 20896225--20896266 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20896215 TCTGGCAACG
*
20896225 GATACAGGTTAGGGGTGTTATA
1 GATACAGGTTAAGGGTGTTATA
* *
20896247 GATATAGGTTAAGTGTGTTA
1 GATACAGGTTAAGGGTGTTA
20896267 CAGGATTACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (22 bp):
GATACAGGTTAAGGGTGTTATA
Found at i:20921595 original size:43 final size:43
Alignment explanation
Indices: 20921531--20921705 Score: 196
Period size: 43 Copynumber: 4.1 Consensus size: 43
20921521 TCACATAAAG
* * * *
20921531 CTCATA-CAATGCC-ATATCCCAGATATGGTCTTACATGTTAT
1 CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* *
20921572 CTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAAT
1 CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* * * *
20921615 CAT-ATAACGATGCCAATGTCCCAAACATGGTCTTATACGTAAT
1 C-TCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
* *
20921658 CACA-ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAAT
1 CTCATAT-CAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
20921701 CTCAT
1 CTCAT
20921706 GTCGGTAATC
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
41 6 0.05
42 7 0.06
43 97 0.87
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (43 bp):
CTCATATCAATGCCAATGTCCCAGACATGGTCTTACACGTAAT
Found at i:20923027 original size:18 final size:19
Alignment explanation
Indices: 20923004--20923044 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
20922994 CATTCACATC
20923004 TTTTCTCTCTTCTCTT-CA
1 TTTTCTCTCTTCTCTTCCA
*
20923022 TTTTCTCTCTTCTTTTCCA
1 TTTTCTCTCTTCTCTTCCA
20923041 TTTT
1 TTTT
20923045 AAATTCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTCTCTCTTCTCTTCCA
Found at i:20936432 original size:24 final size:23
Alignment explanation
Indices: 20936404--20936455 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
20936394 AGGCCTACCT
20936404 CTTTTAAT-AACTGGGGCAAAAGC
1 CTTTTAATAAACTGGGGC-AAAGC
*
20936427 CATTTTGATAAACTGGGGCAAAGC
1 C-TTTTAATAAACTGGGGCAAAGC
20936451 CTTTT
1 CTTTT
20936456 CGGTAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 12 0.46
25 9 0.35
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (23 bp):
CTTTTAATAAACTGGGGCAAAGC
Found at i:20936462 original size:24 final size:25
Alignment explanation
Indices: 20936412--20936464 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
20936402 CTCTTTTAAT
20936412 AACTGGGGCAAAAGCCATTTTGATA
1 AACTGGGGCAAAAGCCATTTTGATA
*
20936437 AACTGGGGC-AAAGCC-TTTTCGGTA
1 AACTGGGGCAAAAGCCATTTT-GATA
20936461 AACT
1 AACT
20936465 AGGGTATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 13 0.50
25 9 0.35
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAAGCCATTTTGATA
Found at i:20936546 original size:9 final size:9
Alignment explanation
Indices: 20936532--20936588 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
20936522 ACATCATGTG
20936532 CATATCATA
1 CATATCATA
*
20936541 CATATCATGTG
1 CATATCA--TA
* *
20936552 CGTATCACA
1 CATATCATA
20936561 CATATCATGA
1 CATATCAT-A
20936571 GCATATCATA
1 -CATATCATA
20936581 CATATCAT
1 CATATCAT
20936589 GTGCATATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 21 0.55
10 2 0.05
11 15 0.39
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.32
Consensus pattern (9 bp):
CATATCATA
Found at i:20936547 original size:20 final size:20
Alignment explanation
Indices: 20936524--20936610 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
20936514 TTATGAATAC
20936524 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
20936544 ATCATGTGCGTATCACACAT
1 ATCATGTGCATATCATACAT
*
20936564 ATCATGAGCATATCATACAT
1 ATCATGTGCATATCATACAT
20936584 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
20936604 ATCATGT
1 ATCATGT
20936611 ATACCAAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:20936575 original size:11 final size:11
Alignment explanation
Indices: 20936524--20936599 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
20936514 TTATGAATAC
*
20936524 ATCATGTGCAT
1 ATCATGAGCAT
20936535 ATCAT-A-CAT
1 ATCATGAGCAT
* *
20936544 ATCATGTGCGT
1 ATCATGAGCAT
*
20936555 ATCA-CA-CAT
1 ATCATGAGCAT
20936564 ATCATGAGCAT
1 ATCATGAGCAT
20936575 ATCAT-A-CAT
1 ATCATGAGCAT
*
20936584 ATCATGTGCAT
1 ATCATGAGCAT
20936595 ATCAT
1 ATCAT
20936600 ATCAATCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 22 0.43
10 2 0.04
11 27 0.53
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (11 bp):
ATCATGAGCAT
Found at i:20940111 original size:40 final size:40
Alignment explanation
Indices: 20940049--20940306 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
20940039 AAGCCAAGTA
* * * *
20940049 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
20940088 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
20940128 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20940168 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
20940208 CCTTCGGGACTTAACCCAGATACAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
20940248 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
20940288 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
20940307 TTATCATCCG
Statistics
Matches: 200, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
39 13 0.06
40 187 0.94
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:20948232 original size:40 final size:40
Alignment explanation
Indices: 20948153--20948409 Score: 340
Period size: 40 Copynumber: 6.5 Consensus size: 40
20948143 AAGCCAAGTA
* * * * *
20948153 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
20948192 CCTTTGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
20948232 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20948272 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
20948312 CCTACGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
20948352 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
20948392 CCTTTGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
20948410 TTATCATCCG
Statistics
Matches: 197, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 12 0.06
40 185 0.94
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:20955759 original size:31 final size:30
Alignment explanation
Indices: 20955703--20955766 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
20955693 CCTTTACATA
*
20955703 TTTCATATTTCATAACCCTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAG-CT
** *
20955734 TTTCATATTTCATATTACTGTGCCGAAGCT
1 TTTCATATTTCATAACACTGGGCCGAAGCT
20955764 TTT
1 TTT
20955767 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTCATATTTCATAACACTGGGCCGAAGCT
Found at i:20956003 original size:25 final size:25
Alignment explanation
Indices: 20955975--20956046 Score: 94
Period size: 24 Copynumber: 2.9 Consensus size: 25
20955965 CTAGAGGCCT
*
20955975 AGCCTATTTTAAT-AACTGGGGCAAA
1 AGCCT-TTTTGATAAACTGGGGCAAA
*
20956000 AGCCCTTTTGATAAACTGGGGC-AA
1 AGCCTTTTTGATAAACTGGGGCAAA
*
20956024 AGCCTTTTCGATAAACTGGGGCA
1 AGCCTTTTTGATAAACTGGGGCA
20956047 TAGCCCTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 28 0.68
25 13 0.32
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (25 bp):
AGCCTTTTTGATAAACTGGGGCAAA
Found at i:20956013 original size:24 final size:24
Alignment explanation
Indices: 20955988--20956056 Score: 104
Period size: 24 Copynumber: 2.8 Consensus size: 24
20955978 CTATTTTAAT
20955988 AACTGGGGCAAAAGCCCTTTTGATA
1 AACTGGGGC-AAAGCCCTTTTGATA
20956013 AACTGGGGCAAAG-CCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTT-GATA
*
20956037 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20956057 TGCACTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 6 0.15
24 20 0.49
25 15 0.37
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (24 bp):
AACTGGGGCAAAGCCCTTTTGATA
Found at i:20956122 original size:9 final size:9
Alignment explanation
Indices: 20956108--20956164 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
20956098 ACATCATGTG
20956108 CATATCATA
1 CATATCATA
*
20956117 CATATCATGTG
1 CATATCA--TA
20956128 CATATCATA
1 CATATCATA
20956137 CATATCATGA
1 CATATCAT-A
20956147 GCATATCATA
1 -CATATCATA
20956157 CATATCAT
1 CATATCAT
20956165 GTGCATATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 24 0.57
10 2 0.05
11 16 0.38
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (9 bp):
CATATCATA
Found at i:20956123 original size:20 final size:20
Alignment explanation
Indices: 20956100--20956186 Score: 149
Period size: 20 Copynumber: 4.3 Consensus size: 20
20956090 TTATGGATAC
20956100 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
20956120 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
20956140 ATCATGAGCATATCATACAT
1 ATCATGTGCATATCATACAT
20956160 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
20956180 ATCATGT
1 ATCATGT
20956187 ATACCAAAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:20956130 original size:40 final size:40
Alignment explanation
Indices: 20956086--20956185 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
20956076 CCCAACCCAA
* *
20956086 TGCATTATGGATAC-ATCATGTGCATATCATACATATCATG
1 TGCATTAT-CATACAATCATGAGCATATCATACATATCATG
20956126 TGCA-TATCATACATATCATGAGCATATCATACATATCATG
1 TGCATTATCATACA-ATCATGAGCATATCATACATATCATG
20956166 TGCA-TATCATATCAATCATG
1 TGCATTATCATA-CAATCATG
20956186 TATACCAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
38 4 0.07
39 3 0.05
40 46 0.84
41 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (40 bp):
TGCATTATCATACAATCATGAGCATATCATACATATCATG
Found at i:20956131 original size:11 final size:11
Alignment explanation
Indices: 20956100--20956175 Score: 74
Period size: 11 Copynumber: 7.5 Consensus size: 11
20956090 TTATGGATAC
20956100 ATCATGTGCAT
1 ATCATGTGCAT
*
20956111 ATCA--TACAT
1 ATCATGTGCAT
20956120 ATCATGTGCAT
1 ATCATGTGCAT
*
20956131 ATCA--TACAT
1 ATCATGTGCAT
*
20956140 ATCATGAGCAT
1 ATCATGTGCAT
*
20956151 ATCA--TACAT
1 ATCATGTGCAT
20956160 ATCATGTGCAT
1 ATCATGTGCAT
20956171 ATCAT
1 ATCAT
20956176 ATCAATCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 23 0.45
11 28 0.55
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:20962062 original size:47 final size:47
Alignment explanation
Indices: 20962008--20962100 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
20961998 AATGAGTTAG
* *
20962008 GTGGAGAGTAATTTGAACGAGAAGTTCAACAAGGATAACCCATTACT
1 GTGGAGAGTAATTTCAACAAGAAGTTCAACAAGGATAACCCATTACT
20962055 GTGGAGAGTAATTTCAACAAGAAGTTCAACAAGGATAACCCATTAC
1 GTGGAGAGTAATTTCAACAAGAAGTTCAACAAGGATAACCCATTAC
20962101 AAGTTAACTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (47 bp):
GTGGAGAGTAATTTCAACAAGAAGTTCAACAAGGATAACCCATTACT
Found at i:20964628 original size:49 final size:49
Alignment explanation
Indices: 20964541--20964640 Score: 132
Period size: 49 Copynumber: 2.0 Consensus size: 49
20964531 TTATTTTATT
* *
20964541 TTAGAATAAGGTTCTTCAACCTTATTACACTTAATCTATTTG-ATATTGA
1 TTAGAATAAGGTTCTTCAACCTTACTACACTCAATCTATTTGAATA-TGA
**
20964590 TTAGAATAAGGTGT-TTCAACCTTACTACACTCCTTCTATTTGAATATGA
1 TTAGAATAAGGT-TCTTCAACCTTACTACACTCAATCTATTTGAATATGA
20964639 TT
1 TT
20964641 TTACAAGCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
49 41 0.91
50 4 0.09
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (49 bp):
TTAGAATAAGGTTCTTCAACCTTACTACACTCAATCTATTTGAATATGA
Found at i:20965556 original size:42 final size:42
Alignment explanation
Indices: 20965493--20965576 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
20965483 AAAATCGTAA
* * *
20965493 TGCTGATGATAGTTATAGAAGGATAGAGGAAAGAAATCCTCG
1 TGCTGATGATAGTAATAGAAGGACACAGGAAAGAAATCCTCG
* *
20965535 TGCTGATGAT-GATAATGGAAGGACACAGGAATGAAATCCTCG
1 TGCTGATGATAG-TAATAGAAGGACACAGGAAAGAAATCCTCG
20965577 CGGTAAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.23
Consensus pattern (42 bp):
TGCTGATGATAGTAATAGAAGGACACAGGAAAGAAATCCTCG
Found at i:20974572 original size:25 final size:26
Alignment explanation
Indices: 20974508--20974575 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
20974498 ACGATCGATA
*
20974508 TCGCACACTTAGTGCTCAATTTGAGGT
1 TCGCACACTTAGTGCTCAACTTGA-GT
* *
20974535 TCGCACACATAGTGCTCTTACTT-A-T
1 TCGCACACTTAGTGCTC-AACTTGAGT
20974560 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
20974576 ACGTTTTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.44
27 17 0.47
28 3 0.08
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (26 bp):
TCGCACACTTAGTGCTCAACTTGAGT
Found at i:20974596 original size:24 final size:24
Alignment explanation
Indices: 20974535--20974598 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
20974525 AATTTGAGGT
*
20974535 TCGCACACATAGTGCTCTTACTTAT
1 TCGCACACATAGTGCTCTTA-TTAC
*
20974560 TCGCACACTTAGTGCTACGTT-TT-C
1 TCGCACACATAGTGCT-C-TTATTAC
20974584 TCGCACACATAGTGC
1 TCGCACACATAGTGC
20974599 CATAGTTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 14 0.41
25 17 0.50
26 1 0.03
27 2 0.06
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.33
Consensus pattern (24 bp):
TCGCACACATAGTGCTCTTATTAC
Found at i:20974615 original size:32 final size:32
Alignment explanation
Indices: 20974569--20974633 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
20974559 TTCGCACACT
20974569 TAGTGCTACGTTTTCTCGCACACATAGTGCCA
1 TAGTGCTACGTTTTCTCGCACACATAGTGCCA
*
20974601 TAGTTCTACGTTTTCTCGCACACATAGTGCCA
1 TAGTGCTACGTTTTCTCGCACACATAGTGCCA
20974633 T
1 T
20974634 GTAATCTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (32 bp):
TAGTGCTACGTTTTCTCGCACACATAGTGCCA
Found at i:20974645 original size:24 final size:24
Alignment explanation
Indices: 20974618--20974678 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
20974608 ACGTTTTCTC
* *
20974618 GCACACATAGTGCCATGTAATCTT
1 GCACACATAGTGCCATATAACCTT
* *
20974642 GCACACATAGTGCCGTATAGCCTT
1 GCACACATAGTGCCATATAACCTT
20974666 GCACACATAGTGC
1 GCACACATAGTGC
20974679 TGTATTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (24 bp):
GCACACATAGTGCCATATAACCTT
Found at i:20975975 original size:20 final size:21
Alignment explanation
Indices: 20975950--20975988 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20975940 TAATTTCTTC
*
20975950 TTTTATTCCTATT-TTTATTT
1 TTTTATTCATATTGTTTATTT
20975970 TTTTATTCATATTGTTTAT
1 TTTTATTCATATTGTTTAT
20975989 GATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTATTCATATTGTTTATTT
Found at i:20981634 original size:15 final size:17
Alignment explanation
Indices: 20981616--20981647 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20981606 TAGCATAATT
20981616 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
20981631 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
20981648 CAAGTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:20990895 original size:9 final size:9
Alignment explanation
Indices: 20990878--20990912 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
20990868 AATAGTTTGG
*
20990878 TATTTGAAT
1 TATTCGAAT
20990887 TATTCGAAT
1 TATTCGAAT
*
20990896 TATTCGAGT
1 TATTCGAAT
20990905 TATTCGAA
1 TATTCGAA
20990913 ATTGAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21002035 original size:47 final size:47
Alignment explanation
Indices: 21001981--21002479 Score: 845
Period size: 47 Copynumber: 10.6 Consensus size: 47
21001971 TATTTGAATA
*
21001981 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21002028 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21002075 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21002124 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21002171 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21002218 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGGGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21002265 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21002312 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21002359 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
21002406 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21002453 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
21002480 TCCCGAAGGG
Statistics
Matches: 427, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 382 0.89
49 45 0.11
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Done.