Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 100 of 311
Found at i:32970901 original size:6 final size:6
Alignment explanation
Indices: 32970885--32970934 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
32970875 TTTCTTTTTA
*
32970885 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
32970934 T
1 T
32970935 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:32970917 original size:37 final size:37
Alignment explanation
Indices: 32970874--32970944 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
32970864 CTTGCCTCTC
32970874 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
32970911 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
32970945 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:32970945 original size:16 final size:16
Alignment explanation
Indices: 32970870--32970930 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
32970860 GCCTCTTGCC
*
32970870 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
32970886 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
32970902 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
32970918 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
32970931 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:32971863 original size:26 final size:26
Alignment explanation
Indices: 32971834--32971883 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
32971824 TTTTTTATAC
**
32971834 TTCGATTTTTTTTTTTTTTTTTTTTT
1 TTCGATTTTTTTTAATTTTTTTTTTT
32971860 TTCGATTTTTTTTAATTTTTTTTT
1 TTCGATTTTTTTTAATTTTTTTTT
32971884 CGAATTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.08, C:0.04, G:0.04, T:0.84
Consensus pattern (26 bp):
TTCGATTTTTTTTAATTTTTTTTTTT
Found at i:32971890 original size:23 final size:22
Alignment explanation
Indices: 32971843--32971886 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
32971833 CTTCGATTTT
**
32971843 TTTTTTTTTTTTTTTTTTTCGA
1 TTTTTTTTAATTTTTTTTTCGA
32971865 TTTTTTTTAATTTTTTTTTCGA
1 TTTTTTTTAATTTTTTTTTCGA
32971887 ATTTCCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTTTTAATTTTTTTTTCGA
Found at i:32973610 original size:30 final size:30
Alignment explanation
Indices: 32973576--32973672 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
32973566 TAAACTAAAA
32973576 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
32973606 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
32973636 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
32973665 ATGAGCTA
1 -TGAGCTA
32973673 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:32975213 original size:20 final size:20
Alignment explanation
Indices: 32975190--32975236 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32975180 GGGTTAAGAT
*
32975190 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
32975210 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
32975230 TGAGCTG
1 TGAGCTG
32975237 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:32976288 original size:52 final size:51
Alignment explanation
Indices: 32976159--32976290 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 51
32976149 ATGTGTTTTG
* *
32976159 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTAAGTTAAGTTTGCAT
1 CATTAAATAAAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCAT
* * * * *
32976210 CA-TAAATGATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTTCAT
1 CATTAAATAAAGTCATGCATTATGTAACTCCCATGTAAGTT-AAGTTTGCAT
* * *
32976261 CATTAAATTAAGTTATGCATTAAGTAACTC
1 CATTAAATAAAGTCATGCATTATGTAACTC
32976291 ATTTGTTCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
50 32 0.48
51 13 0.19
52 22 0.33
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (51 bp):
CATTAAATAAAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCAT
Found at i:32985548 original size:23 final size:22
Alignment explanation
Indices: 32985496--32985548 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
32985486 TCCACGTCTT
*
32985496 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
32985518 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
32985541 TTTCTTTT
1 TTTCTTTT
32985549 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:32986848 original size:8 final size:9
Alignment explanation
Indices: 32986826--32986850 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
32986816 TGGATTTCGT
32986826 ATTTTTTCA
1 ATTTTTTCA
32986835 ATTTTTTCA
1 ATTTTTTCA
32986844 ATTTTTT
1 ATTTTTT
32986851 GACTTTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTCA
Found at i:32988711 original size:13 final size:12
Alignment explanation
Indices: 32988685--32988741 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
32988675 TTGTAGATTC
32988685 AAAAAAAATC--
1 AAAAAAAATCGA
32988695 AAAAAAAATCGA
1 AAAAAAAATCGA
*
32988707 GAAAAAAAATTGA
1 -AAAAAAAATCGA
* *
32988720 AAAAAAATTTTGA
1 AAAAAAA-ATCGA
32988733 AAAAAAAAT
1 AAAAAAAAT
32988742 TGCATACGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.25
12 8 0.20
13 22 0.55
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:32993049 original size:11 final size:10
Alignment explanation
Indices: 32993024--32993084 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
32993014 ACCAATAAAA
32993024 TAAA-TGAGC
1 TAAATTGAGC
*
32993033 TGAATTGTAGC
1 TAAATTG-AGC
32993044 TAAATTGAGC
1 TAAATTGAGC
**
32993054 TCGATTGAGC
1 TAAATTGAGC
32993064 TGAAA-TGAGC
1 T-AAATTGAGC
*
32993074 TCAATTGAGC
1 TAAATTGAGC
32993084 T
1 T
32993085 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:32993085 original size:20 final size:20
Alignment explanation
Indices: 32993025--32993085 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
32993015 CCAATAAAAT
*
32993025 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
32993045 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
32993066 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
32993086 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:32996373 original size:30 final size:30
Alignment explanation
Indices: 32996339--32996435 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32996329 AGCTCACTCC
32996339 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
32996369 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
32996399 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
32996429 TAGCTCA
1 TAGCTCA
32996436 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32998143 original size:12 final size:12
Alignment explanation
Indices: 32998096--32998169 Score: 78
Period size: 12 Copynumber: 6.0 Consensus size: 12
32998086 AGCATATTGT
32998096 AATTGAAAAAAA
1 AATTGAAAAAAA
* *
32998108 AA-AGAAAAGAGGA
1 AATTGAAAA-A-AA
32998121 AATTCGAAAAAAA
1 AATT-GAAAAAAA
32998134 AATTGAAAAAAA
1 AATTGAAAAAAA
*
32998146 AATCGAAAAAAA
1 AATTGAAAAAAA
*
32998158 AATTTAAAAAAA
1 AATTGAAAAAAA
32998170 TCAAAAAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 5 0.10
12 32 0.63
13 8 0.16
14 1 0.02
15 5 0.10
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.14
Consensus pattern (12 bp):
AATTGAAAAAAA
Found at i:32999185 original size:30 final size:30
Alignment explanation
Indices: 32999151--32999247 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32999141 AGCTCACTCC
32999151 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
32999181 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
32999211 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
32999241 TAGCTCA
1 TAGCTCA
32999248 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33000936 original size:37 final size:37
Alignment explanation
Indices: 33000885--33000955 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
33000875 CATTCTTGTA
33000885 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGT
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGT
*
33000922 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
33000956 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGT
Found at i:33000955 original size:6 final size:6
Alignment explanation
Indices: 33000895--33000944 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33000885 AAGAGAAAAC
*
33000895 AAAG-A AAAG-A AAAGAA AAAGAA AAAGTAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
33000944 A
1 A
33000945 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:33000955 original size:21 final size:23
Alignment explanation
Indices: 33000899--33000957 Score: 59
Period size: 27 Copynumber: 2.5 Consensus size: 23
33000889 GAAAACAAAG
33000899 AAAAGAAAAGAAAAAGAAAAAGTA
1 AAAAGAAAAGAAAAAG-AAAAGTA
*
33000923 AGAGAAGAAAAAGAAAATG-AAA-TA
1 A-A-AAG-AAAAGAAAAAGAAAAGTA
33000947 AAAAGAAAAGA
1 AAAAGAAAAGA
33000958 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 6 0.19
22 3 0.10
23 1 0.03
24 4 0.13
25 4 0.13
26 3 0.10
27 10 0.32
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (23 bp):
AAAAGAAAAGAAAAAGAAAAGTA
Found at i:33001035 original size:6 final size:6
Alignment explanation
Indices: 33001027--33001094 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
33001017 TTGAAAAGCA
* * * *
33001027 AAAAT- AAAATG AAAATG AAAATG AAAA-G AAATTTG AGAGTG AAAAAG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAA-ATG AAAATG AAAATG
* * *
33001074 AAGATG AAAAAG AAATTG AAA
1 AAAATG AAAATG AAAATG AAA
33001095 CAAAAGAATC
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
5 9 0.19
6 36 0.75
7 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:33012155 original size:12 final size:11
Alignment explanation
Indices: 33012140--33012169 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33012130 AAAAATTTTT
33012140 AAAAAATCAAA
1 AAAAAATCAAA
*
33012151 AAAAAATTAAA
1 AAAAAATCAAA
33012162 AAAAAATC
1 AAAAAATC
33012170 GAAGTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAATCAAA
Found at i:33012165 original size:22 final size:22
Alignment explanation
Indices: 33012126--33012169 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33012116 GGAAATTCGA
***
33012126 AAAAAAAAATTTTTAAAAAATC
1 AAAAAAAAATTAAAAAAAAATC
33012148 AAAAAAAAATTAAAAAAAAATC
1 AAAAAAAAATTAAAAAAAAATC
33012170 GAAGTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAAAAAATTAAAAAAAAATC
Found at i:33024964 original size:15 final size:14
Alignment explanation
Indices: 33024928--33024982 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
33024918 TCTATTGATC
33024928 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
33024942 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
33024956 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
33024971 GAAAGAAAAGAA
1 GAGA-AAAAGAA
33024983 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:33031930 original size:30 final size:30
Alignment explanation
Indices: 33031896--33031992 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33031886 TAAACTAAAA
33031896 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33031926 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
33031956 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
33031986 TGAGCTA
1 TGAGCTA
33031993 GGAGTGCGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33032738 original size:30 final size:30
Alignment explanation
Indices: 33032704--33032801 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
33032694 AGCTCACTCC
33032704 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
33032734 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
33032764 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
33032794 TAGCTCAT
1 TAGCTCAT
33032802 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:33040805 original size:13 final size:13
Alignment explanation
Indices: 33040787--33040815 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33040777 TGAATAGTTG
33040787 TGTTATTTAATTA
1 TGTTATTTAATTA
33040800 TGTTATTTAATTA
1 TGTTATTTAATTA
33040813 TGT
1 TGT
33040816 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33043002 original size:18 final size:18
Alignment explanation
Indices: 33042979--33043039 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
33042969 GAAAGAAAAA
*
33042979 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
33042997 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
*
33043015 GAAAAAGAGAATGAGAGA
1 GAAAAAGAGAATGAGAGT
33043033 GAAAAAG
1 GAAAAAG
33043040 CATGTCAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:33044960 original size:13 final size:13
Alignment explanation
Indices: 33044942--33044970 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33044932 AATAGTTGTG
33044942 TGTTATTTAATTA
1 TGTTATTTAATTA
33044955 TGTTATTTAATTA
1 TGTTATTTAATTA
33044968 TGT
1 TGT
33044971 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33049389 original size:30 final size:30
Alignment explanation
Indices: 33049355--33049451 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33049345 TAAACTAAAA
33049355 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33049385 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
33049415 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
33049444 ATGAGCTA
1 -TGAGCTA
33049452 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:33051641 original size:12 final size:12
Alignment explanation
Indices: 33051626--33051656 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33051616 TTCTTTTTGC
33051626 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33051638 TTTTCAAAGGCT
1 TTTTCAAAGGCT
33051650 TTTTCAA
1 TTTTCAA
33051657 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:33051733 original size:6 final size:6
Alignment explanation
Indices: 33051717--33051766 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33051707 TTTCTTTTTA
*
33051717 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
33051766 T
1 T
33051767 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:33051749 original size:37 final size:37
Alignment explanation
Indices: 33051706--33051776 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
33051696 CTTGCCTCTC
33051706 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
33051743 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
33051777 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:33051777 original size:16 final size:16
Alignment explanation
Indices: 33051702--33051762 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
33051692 GCCTCTTGCC
*
33051702 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
33051718 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
33051734 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
33051750 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
33051763 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:33052730 original size:13 final size:13
Alignment explanation
Indices: 33052714--33052751 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
33052704 TTTTTTTTCC
33052714 TTTTTTTT--ATT
1 TTTTTTTTGAATT
33052725 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
33052738 TTTTTTCTGAATT
1 TTTTTTTTGAATT
33052751 T
1 T
33052752 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:33054472 original size:30 final size:30
Alignment explanation
Indices: 33054438--33054534 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33054428 AAAACTAAAA
33054438 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33054468 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
33054498 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
33054527 ATGAGCTA
1 -TGAGCTA
33054535 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:33065082 original size:14 final size:14
Alignment explanation
Indices: 33065047--33065075 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33065037 GACCGTATGC
33065047 AAATTTTTTTTTCA
1 AAATTTTTTTTTCA
33065061 AAATTTTTTTTTCA
1 AAATTTTTTTTTCA
33065075 A
1 A
33065076 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
AAATTTTTTTTTCA
Found at i:33065093 original size:12 final size:12
Alignment explanation
Indices: 33065047--33065105 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
33065037 GACCGTATGC
33065047 AAATTTTTTTTT
1 AAATTTTTTTTT
33065059 CAAAATTTTTTTTT
1 --AAATTTTTTTTT
*
33065073 CAA--TTTTTTT
1 AAATTTTTTTTT
33065083 AAATTTTTTTTT
1 AAATTTTTTTTT
**
33065095 CGATTTTTTTT
1 AAATTTTTTTT
33065106 GAATCTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.23
12 18 0.46
14 12 0.31
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (12 bp):
AAATTTTTTTTT
Found at i:33065103 original size:22 final size:23
Alignment explanation
Indices: 33065052--33065104 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
33065042 TATGCAAATT
33065052 TTTTTTTCAAAATTTTTTTTTCAA
1 TTTTTTT-AAAATTTTTTTTTCAA
*
33065076 TTTTTTT-AAATTTTTTTTTCGA
1 TTTTTTTAAAATTTTTTTTTCAA
33065098 TTTTTTT
1 TTTTTTT
33065105 TGAATCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 21 0.75
24 7 0.25
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTTTTAAAATTTTTTTTTCAA
Found at i:33068721 original size:12 final size:13
Alignment explanation
Indices: 33068700--33068736 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
33068690 AAACCGTATG
33068700 CAATTTTTTTTTT
1 CAATTTTTTTTTT
33068713 CAATTTTTTTTTT
1 CAATTTTTTTTTT
33068726 CAATTTTTTTT
1 CAATTTTTTTT
33068737 ACGTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:33070526 original size:20 final size:20
Alignment explanation
Indices: 33070503--33070549 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33070493 GGGTTAAGAT
*
33070503 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33070523 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33070543 TGAGCTG
1 TGAGCTG
33070550 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:33072275 original size:48 final size:48
Alignment explanation
Indices: 33072220--33072325 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33072210 TTGTCTTTTC
*
33072220 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33072268 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33072316 TTTCTTTTTC
1 TTTCTTTTTC
33072326 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33072322 original size:18 final size:17
Alignment explanation
Indices: 33072301--33072420 Score: 73
Period size: 18 Copynumber: 6.7 Consensus size: 17
33072291 TTTTCACATC
33072301 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
* *
33072319 CTTTTTCCATGACACTCGTTT
1 CTTTTT-CA--A-TCTCATTT
* * *
33072340 CTTTTACACTCTCGTTT
1 CTTTTTCAATCTCATTT
*
33072357 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
* *
33072376 CTTTTTCAATTTCTTGTT
1 CTTTTTCAATCTCAT-TT
*
33072394 CCTTTTC-AT-TCATTT
1 CTTTTTCAATCTCATTT
33072409 CTTTTTCAATCT
1 CTTTTTCAATCT
33072421 TGATACGGGG
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.10
16 5 0.06
17 15 0.19
18 28 0.36
19 8 0.10
20 2 0.03
21 9 0.12
22 3 0.04
ACGTcount: A:0.15, C:0.27, G:0.03, T:0.55
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:33074670 original size:23 final size:22
Alignment explanation
Indices: 33074618--33074670 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33074608 TCCACGTCTT
*
33074618 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33074640 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33074663 TTTCTTTT
1 TTTCTTTT
33074671 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33075111 original size:10 final size:10
Alignment explanation
Indices: 33075096--33075120 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
33075086 CAAATCAAAT
33075096 GAGCTGAAAC
1 GAGCTGAAAC
33075106 GAGCTGAAAC
1 GAGCTGAAAC
33075116 GAGCT
1 GAGCT
33075121 CATCGAGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:33076345 original size:55 final size:55
Alignment explanation
Indices: 33076282--33076393 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
33076272 ATTGTATGGC
33076282 AGCCTTGTATTTAAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
1 AGCCTTGTATTTAAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
*
33076337 AGCCTTGTATTTGAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
1 AGCCTTGTATTTAAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
33076392 AG
1 AG
33076394 TTGACGTCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (55 bp):
AGCCTTGTATTTAAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
Found at i:33079177 original size:27 final size:26
Alignment explanation
Indices: 33079129--33079187 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
33079119 AGCAGCAACT
*
33079129 ATTAAATTTGTCCCTAAGCTAGACAC
1 ATTAAATTTGTCCCTAAACTAGACAC
33079155 ATTAAATTGATGT-CCTAAACTAGACAC
1 ATTAAATT--TGTCCCTAAACTAGACAC
33079182 ATTAAA
1 ATTAAA
33079188 ACTATGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 19 0.63
28 3 0.10
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (26 bp):
ATTAAATTTGTCCCTAAACTAGACAC
Found at i:33086464 original size:12 final size:13
Alignment explanation
Indices: 33086447--33086479 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33086437 ATAAATCACT
33086447 TTTTTTTTAG-AA
1 TTTTTTTTAGAAA
*
33086459 TTTTTTTTCGAAA
1 TTTTTTTTAGAAA
33086472 TTTTTTTT
1 TTTTTTTT
33086480 TCAAACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTTTTTAGAAA
Found at i:33090885 original size:30 final size:30
Alignment explanation
Indices: 33090851--33090947 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33090841 TAAACTAAAA
*
33090851 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGTTAAAGT
* * * * * *
33090881 TGAGCTGAGGC-TAAACTCCTAAGTTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGTTAAAGT
*
33090911 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGTT-AAAGT
33090941 TGAGCTA
1 TGAGCTA
33090948 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGTTAAAGT
Found at i:33101271 original size:30 final size:30
Alignment explanation
Indices: 33101237--33101333 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33101227 TAAACTAAAA
*
33101237 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
33101267 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33101297 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33101326 ATGAGCTA
1 -TGAGCTA
33101334 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:33103602 original size:6 final size:6
Alignment explanation
Indices: 33103588--33103637 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33103578 TTTTTTTTTA
*
33103588 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
33103637 T
1 T
33103638 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:33103648 original size:16 final size:16
Alignment explanation
Indices: 33103574--33103633 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
33103564 GCCTCTTGCC
*
33103574 TCTCTTTT-TTTTTAT
1 TCTCTTTTCTTTTTCT
33103589 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
33103605 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
33103621 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
33103634 CTTTGTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.06
15 14 0.39
16 11 0.31
17 9 0.25
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:33105344 original size:30 final size:30
Alignment explanation
Indices: 33105310--33105406 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33105300 TAAACTAAAA
*
33105310 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
33105340 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33105370 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
33105399 ATGAGCTA
1 -TGAGCTA
33105407 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:33109438 original size:13 final size:13
Alignment explanation
Indices: 33109420--33109444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33109410 AATAGTTGTG
33109420 TGTTATTTAATTA
1 TGTTATTTAATTA
33109433 TGTTATTTAATT
1 TGTTATTTAATT
33109445 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33111497 original size:14 final size:15
Alignment explanation
Indices: 33111468--33111507 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
33111458 ACCTCTTGTA
*
33111468 AAAAGCAAGAA-A-G
1 AAAAGCAAAAAGACG
33111481 AAAAG-AAAAAGACG
1 AAAAGCAAAAAGACG
33111495 AAAAGCAAAAAGA
1 AAAAGCAAAAAGA
33111508 GATCAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 6 0.26
15 7 0.30
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGCAAAAAGACG
Found at i:33111504 original size:15 final size:14
Alignment explanation
Indices: 33111468--33111509 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33111458 ACCTCTTGTA
*
33111468 AAAAGCAAGAA-AG
1 AAAAGCAAAAAGAG
33111481 AAAAG-AAAAAGACG
1 AAAAGCAAAAAGA-G
33111495 AAAAGCAAAAAGAG
1 AAAAGCAAAAAGAG
33111509 A
1 A
33111510 TCAAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 8 0.32
15 7 0.28
ACGTcount: A:0.71, C:0.07, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGCAAAAAGAG
Found at i:33112971 original size:20 final size:20
Alignment explanation
Indices: 33112946--33112992 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
33112936 AGCTCGTTTC
33112946 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
33112966 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
33112986 CAGCTCA
1 CAGCTCA
33112993 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:33112990 original size:10 final size:10
Alignment explanation
Indices: 33112957--33112994 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33112947 AGCTCACTCG
*
33112957 AGCTCAAGTC
1 AGCTCAATTC
33112967 AGCTC-ATTC
1 AGCTCAATTC
33112976 GAGCTCAATTC
1 -AGCTCAATTC
33112987 AGCTCAAT
1 AGCTCAAT
33112995 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:33118436 original size:19 final size:19
Alignment explanation
Indices: 33118412--33118451 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
33118402 AGCTCCCATG
33118412 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
33118431 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
33118450 TA
1 TA
33118452 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:33119717 original size:14 final size:14
Alignment explanation
Indices: 33119695--33119742 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
33119685 ACCTAAACCG
* *
33119695 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
33119709 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
33119723 ACC-TTTTCGTTCCT
1 ACCATTTT-GTTCCT
33119737 ACCATT
1 ACCATT
33119743 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 4 0.13
14 24 0.80
15 2 0.07
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:33120041 original size:10 final size:10
Alignment explanation
Indices: 33120028--33120062 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
33120018 AAGCTCGGTT
33120028 GAGCTCAAAC
1 GAGCTCAAAC
*
33120038 GAGCTGAAAC
1 GAGCTCAAAC
*
33120048 GAGCTCAAAT
1 GAGCTCAAAC
33120058 GAGCT
1 GAGCT
33120063 GAGTTGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:33121693 original size:18 final size:18
Alignment explanation
Indices: 33121666--33121715 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
33121656 AAACTCTTTT
33121666 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
33121684 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
33121702 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
33121716 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:33121774 original size:42 final size:42
Alignment explanation
Indices: 33121719--33121815 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
33121709 CTTTTTCTTT
* * *
33121719 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
33121760 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
* *
33121802 TCCTCTTATTTTCT
1 TTCTCTCATTTTCT
33121816 CTCATATTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:33121793 original size:21 final size:21
Alignment explanation
Indices: 33121726--33121793 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
33121716 TTTTTCTTTC
*
33121726 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
33121747 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
33121767 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
33121789 ATTTC
1 ATTTC
33121794 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:33125130 original size:29 final size:29
Alignment explanation
Indices: 33125097--33125153 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33125087 ATAACCAAAC
*
33125097 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
33125126 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
33125154 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:33125389 original size:10 final size:10
Alignment explanation
Indices: 33125374--33125410 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
33125364 TAAGTTTCAA
33125374 AAAAAAAACG
1 AAAAAAAACG
*
33125384 AAAAAAAATG
1 AAAAAAAACG
33125394 AAAAAAAACG
1 AAAAAAAACG
33125404 AAAAAAA
1 AAAAAAA
33125411 TTTCAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAACG
Found at i:33126509 original size:30 final size:28
Alignment explanation
Indices: 33126475--33126530 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
33126465 GAAGCAAAAA
* *
33126475 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
33126505 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
33126531 CGTGGAAGAA
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:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:33129233 original size:394 final size:394
Alignment explanation
Indices: 33128500--33129291 Score: 1521
Period size: 394 Copynumber: 2.0 Consensus size: 394
33128490 ATTCCACACT
*
33128500 CATGAATGAAGAAGTATTAAATGCTGGTGCATGTACGGCTAGATGCAATGTTTCTACAAATTCAT
1 CATGAATGAAGAAGTATTAAATGCTGGTGCATGTACAGCTAGATGCAATGTTTCTACAAATTCAT
33128565 GCATGTGTCGAATGCATGTATGGACATTAAAGGCTGGTCCATGAATGGATCAAATGCATGGGATG
66 GCATGTGTCGAATGCATGTATGGACATTAAAGGCTGGTCCATGAATGGATCAAATGCATGGGATG
33128630 ATAGAATGCATGAATGGCTTAAGTGCATGTATGGTGGCTGTCTCCTAACTTTCCAAGGCACTTAT
131 ATAGAATGCATGAATGGCTTAAGTGCATGTATGGTGGCTGTCTCCTAACTTTCCAAGGCACTTAT
33128695 TCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTGACCATAGAGCTCCTTGAACATGTTCACAC
196 TCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTGACCATAGAGCTCCTTGAACATGTTCACAC
*
33128760 TTTGAATTGACCTATAGGCTACTACACATGCATGGATGGGTTCAAGAACGTCCAAGGGAAGGAAT
261 TTTGAATTGACCTATAGCCTACTACACATGCATGGATGGGTTCAAGAACGTCCAAGGGAAGGAAT
*
33128825 TAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAAGGGGAGAACGAATTTACTA
326 TAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAAGGGGAGAACGAATATACTA
33128890 GGTG
391 GGTG
*
33128894 CATGTATGAAGAAGTATTAAATGCTGGTGCATGTACAGCTAGATGCAATGTTTCTACAAATTCAT
1 CATGAATGAAGAAGTATTAAATGCTGGTGCATGTACAGCTAGATGCAATGTTTCTACAAATTCAT
33128959 GCATGTGTCGAATGCATGTATGGACATTAAAGGCTGGTCCATGAATGGATCAAATGCATGGGATG
66 GCATGTGTCGAATGCATGTATGGACATTAAAGGCTGGTCCATGAATGGATCAAATGCATGGGATG
33129024 ATAGAATGCATGAATGGCTTAAGTGCATGTATGGTGGCTGTCTCCTAACTTTCCAAGGCACTTAT
131 ATAGAATGCATGAATGGCTTAAGTGCATGTATGGTGGCTGTCTCCTAACTTTCCAAGGCACTTAT
33129089 TCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTGACCATAGAGCTCCTTGAACATGTTCACAC
196 TCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTGACCATAGAGCTCCTTGAACATGTTCACAC
*
33129154 TTTGAATTGACCTCTAGCCTACTACACATGCATGGATGGGTTCAAGAACGTCCAAGGGAAGGAAT
261 TTTGAATTGACCTATAGCCTACTACACATGCATGGATGGGTTCAAGAACGTCCAAGGGAAGGAAT
*
33129219 TAACTCAATAATTCAACACATTGTTTGAATTAAGTGCATGCACAAAGGGGAGAACGAATATACTA
326 TAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAAGGGGAGAACGAATATACTA
*
33129284 GGTT
391 GGTG
33129288 CATG
1 CATG
33129292 CTGCCATTTA
Statistics
Matches: 391, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
394 391 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (394 bp):
CATGAATGAAGAAGTATTAAATGCTGGTGCATGTACAGCTAGATGCAATGTTTCTACAAATTCAT
GCATGTGTCGAATGCATGTATGGACATTAAAGGCTGGTCCATGAATGGATCAAATGCATGGGATG
ATAGAATGCATGAATGGCTTAAGTGCATGTATGGTGGCTGTCTCCTAACTTTCCAAGGCACTTAT
TCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTGACCATAGAGCTCCTTGAACATGTTCACAC
TTTGAATTGACCTATAGCCTACTACACATGCATGGATGGGTTCAAGAACGTCCAAGGGAAGGAAT
TAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAAGGGGAGAACGAATATACTA
GGTG
Found at i:33131164 original size:9 final size:10
Alignment explanation
Indices: 33131157--33131213 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
33131147 AAGAGAAAAT
33131157 AAAGAAAAGA
1 AAAGAAAAGA
33131167 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
33131179 AAAGAAGA-A
1 AAAGAAAAGA
33131188 AAAGAAAATGA
1 AAAGAAAA-GA
33131199 AATA-AAAAGA
1 AA-AGAAAAGA
33131209 AAAGA
1 AAAGA
33131214 GAGGCAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:33131181 original size:6 final size:5
Alignment explanation
Indices: 33131157--33131213 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33131147 AAGAGAAAAT
*
33131157 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
33131204 AAAGA AAAGA
1 AAAGA AAAGA
33131214 GAGGCAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:33131188 original size:15 final size:14
Alignment explanation
Indices: 33131157--33131213 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
33131147 AAGAGAAAAT
33131157 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
33131173 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
33131188 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
33131204 AAAGAAAAGA
1 AAAGAAAAGA
33131214 GAGGCAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:33131284 original size:6 final size:6
Alignment explanation
Indices: 33131275--33131308 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
33131265 TTTGAAAACC
33131275 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
33131309 TGAGATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:33131289 original size:18 final size:18
Alignment explanation
Indices: 33131268--33131308 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
33131258 AAAAGCCTTT
*
33131268 GAAAACCAAAAAGAAAAA
1 GAAAAACAAAAAGAAAAA
*
33131286 GAAAAAGAAAAAGAAAAA
1 GAAAAACAAAAAGAAAAA
33131304 GAAAA
1 GAAAA
33131309 TGAGATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAACAAAAAGAAAAA
Found at i:33131320 original size:30 final size:30
Alignment explanation
Indices: 33131286--33131367 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
33131276 AAAAGAAAAA
*
33131286 GAAAAAGAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAAAATGAGAGT
* * **
33131316 GAAAAAGAGAACGAAAATA-AATTTGAGAGT
1 GAAAAAGAAAAAGAAAA-AGAAAATGAGAGT
* *
33131346 GAAAAAGAAGATGAAAAAGAAA
1 GAAAAAGAAAAAGAAAAAGAAA
33131368 TTGAAACAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAAAAGAAAATGAGAGT
Found at i:33134694 original size:46 final size:46
Alignment explanation
Indices: 33134627--33134798 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 46
33134617 AACCTGCCCC
33134627 TAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGGCGTTCGCATCCA
*
33134673 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATC-CA
* * *
33134724 -CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
* *
33134766 TAGGTGAACTCAGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
33134799 ATGTTCAACC
Statistics
Matches: 106, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
42 4 0.04
43 4 0.04
44 1 0.01
45 2 0.02
46 56 0.53
47 27 0.25
48 1 0.01
49 1 0.01
50 5 0.05
51 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:33134745 original size:93 final size:93
Alignment explanation
Indices: 33134633--33134801 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
33134623 CCCCTAAGTG
* * *
33134633 AACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
33134697 CGAGTTCGGATGCCTAGTTACATCTCACA
65 CGAGTTCGGATGCCTAGTTACATCTCACA
*
33134726 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCAGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
33134791 GAGTTCGGATG
66 GAGTTCGGATG
33134802 TTCAACCATC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:33135259 original size:30 final size:30
Alignment explanation
Indices: 33135225--33135281 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
33135215 TAATACGAAA
33135225 TTTTGAAAAATTACACTTTTGCCCCTAAAC
1 TTTTGAAAAATTACACTTTTGCCCCTAAAC
* *
33135255 TTTTGCATAATTACACTTTTGCCCCTA
1 TTTTGAAAAATTACACTTTTGCCCCTA
33135282 GGCTCAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACACTTTTGCCCCTAAAC
Found at i:33136522 original size:30 final size:30
Alignment explanation
Indices: 33136488--33136584 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
33136478 AGCTCACTCC
33136488 TAGCTCATA-TTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
33136518 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
33136548 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
33136578 TAGCTCA
1 TAGCTCA
33136585 TTTTAGTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:33138298 original size:13 final size:13
Alignment explanation
Indices: 33138282--33138327 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
33138272 AAGAGAGAAG
33138282 AAAATCGAAAAAA
1 AAAATCGAAAAAA
33138295 AAAATCGAAAAAA
1 AAAATCGAAAAAA
* *
33138308 AAAGT-GACAAAA
1 AAAATCGAAAAAA
33138320 AAAATCGA
1 AAAATCGA
33138328 GTTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.72, C:0.09, G:0.11, T:0.09
Consensus pattern (13 bp):
AAAATCGAAAAAA
Found at i:33139276 original size:37 final size:37
Alignment explanation
Indices: 33139225--33139295 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
33139215 CATTCTTGTA
33139225 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
33139262 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
33139296 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:33139295 original size:6 final size:6
Alignment explanation
Indices: 33139235--33139284 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33139225 AAGAGAAAAC
*
33139235 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
33139284 A
1 A
33139285 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:33141515 original size:30 final size:30
Alignment explanation
Indices: 33141481--33141577 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33141471 AGCTCACTCC
33141481 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33141511 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33141541 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33141571 TAGCTCA
1 TAGCTCA
33141578 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33151970 original size:14 final size:14
Alignment explanation
Indices: 33151926--33151979 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
33151916 ACTCTCCTCA
*
33151926 TTCTTTTCTTTCTTT
1 TTCTTTT-TCTCTTT
*
33151941 TTC-TTTTCACTCTT
1 TTCTTTTTCTCT-TT
*
33151955 TTGTTTTTCTCTTT
1 TTCTTTTTCTCTTT
33151969 TTCTTTTTCTC
1 TTCTTTTTCTC
33151980 GATCAATAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.09
14 19 0.59
15 10 0.31
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:33155798 original size:47 final size:47
Alignment explanation
Indices: 33155730--33156025 Score: 502
Period size: 47 Copynumber: 6.3 Consensus size: 47
33155720 GCTCATATCA
33155730 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
33155777 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
33155824 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
33155871 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
33155918 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * * * * * * *
33155965 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
33156012 ATAAATGTGATAAG
1 ATATATGTGATAAG
33156026 TCCCGAAGGG
Statistics
Matches: 236, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 236 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
Found at i:33156200 original size:37 final size:37
Alignment explanation
Indices: 33156144--33156222 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
33156134 CCGAGCTCTA
* * *
33156144 AAGACCCGATGACTACGTGTGG-GAATTTTGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
33156181 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
33156218 AAGAC
1 AAGAC
33156223 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:33158164 original size:29 final size:29
Alignment explanation
Indices: 33158129--33158202 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
33158119 GTTGTGAGAT
* *
33158129 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
33158158 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
33158187 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
33158203 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:33160187 original size:29 final size:28
Alignment explanation
Indices: 33160151--33160228 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
33160141 TCATGAGATT
33160151 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
33160181 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
33160208 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
33160229 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:33161821 original size:39 final size:40
Alignment explanation
Indices: 33161758--33161848 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 40
33161748 TTACAAAGAT
* *
33161758 CCGAAGGCATTTGTGTGAGATACT-AATTCCGGGCTAAG-C
1 CCGAAGGCATTGGTGCGAGATACTAAATT-CGGGCTAAGTC
*
33161797 CCGAAGGCATTGGTGCGAGTTACTAAATTCGGGCTAAGTC
1 CCGAAGGCATTGGTGCGAGATACTAAATTCGGGCTAAGTC
33161837 CCGAAGAGCATT
1 CCGAAG-GCATT
33161849 CATGCTAGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 30 0.65
40 11 0.24
41 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTGGTGCGAGATACTAAATTCGGGCTAAGTC
Found at i:33161870 original size:40 final size:40
Alignment explanation
Indices: 33161785--33161979 Score: 196
Period size: 40 Copynumber: 4.9 Consensus size: 40
33161775 AGATACTAAT
** * * *
33161785 TCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
* *
33161824 TTCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
33161864 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * *
33161904 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
33161944 TCCGGGCTAGGTCTCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
33161980 CGTGTATTCG
Statistics
Matches: 129, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
39 10 0.08
40 107 0.83
41 12 0.09
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:33166255 original size:4 final size:4
Alignment explanation
Indices: 33166246--33166272 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33166236 AAGTTTTATT
33166246 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
33166273 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:33173221 original size:22 final size:24
Alignment explanation
Indices: 33173187--33173230 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
33173177 AAACAAATTC
*
33173187 TTTTTTTCATTTT-CATCACTCGT
1 TTTTTTTCATTTTGAATCACTCGT
33173210 TTTTTTTC-TTTTGAATCACTC
1 TTTTTTTCATTTTGAATCACTC
33173231 TCTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.14, C:0.20, G:0.05, T:0.61
Consensus pattern (24 bp):
TTTTTTTCATTTTGAATCACTCGT
Found at i:33175514 original size:15 final size:14
Alignment explanation
Indices: 33175494--33175560 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
33175484 GACCGTATGC
33175494 AATTTTTTTTTTTG
1 AATTTTTTTTTTTG
33175508 TAA-TTTTTTTTTTG
1 -AATTTTTTTTTTTG
* ***
33175522 GATTTTTTTTTCAA
1 AATTTTTTTTTTTG
*
33175536 AACTTTTTTTTTT-
1 AATTTTTTTTTTTG
33175549 AACTTTTTTTTT
1 AA-TTTTTTTTT
33175561 GAAGCTACGA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
13 3 0.07
14 36 0.88
15 2 0.05
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.75
Consensus pattern (14 bp):
AATTTTTTTTTTTG
Found at i:33175516 original size:14 final size:14
Alignment explanation
Indices: 33175497--33175561 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 14
33175487 CGTATGCAAT
33175497 TTTTTTTTTTGTAA
1 TTTTTTTTTTGTAA
*
33175511 TTTTTTTTTTG-GA
1 TTTTTTTTTTGTAA
***
33175524 TTTTTTTTTCAAAA
1 TTTTTTTTTTGTAA
*
33175538 CTTTTTTTTT-TAA
1 TTTTTTTTTTGTAA
*
33175551 CTTTTTTTTTG
1 TTTTTTTTTTG
33175562 AAGCTACGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
13 22 0.52
14 20 0.48
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTTGTAA
Found at i:33178358 original size:49 final size:47
Alignment explanation
Indices: 33178235--33178682 Score: 725
Period size: 47 Copynumber: 9.4 Consensus size: 47
33178225 CAGCCAAGAC
33178235 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
33178282 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTAAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
33178329 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
33178378 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
33178427 AGTGTATATATAGGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATAT--GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
33178476 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
33178523 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
33178570 AGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
33178617 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
33178664 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
33178683 TCCCGAAGGG
Statistics
Matches: 378, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 237 0.63
49 141 0.37
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:33178875 original size:37 final size:37
Alignment explanation
Indices: 33178801--33178879 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
33178791 CCGAGCTCTA
* *
33178801 AAGACCCGATGACTACGTGTGGGAATTTTGTTCGGGT
1 AAGACCCGATAACTACGTGTGGGAATTATGTTCGGGT
*
33178838 AAGACCCGATAACTTCGTGT-GGAGATTATG-TCTGGGT
1 AAGACCCGATAACTACGTGTGGGA-ATTATGTTC-GGGT
33178875 AAGAC
1 AAGAC
33178880 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 5 0.14
37 32 0.86
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGGAATTATGTTCGGGT
Found at i:33187162 original size:23 final size:22
Alignment explanation
Indices: 33187110--33187162 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33187100 TCCACGTCTT
*
33187110 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33187132 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33187155 TTTCTTTT
1 TTTCTTTT
33187163 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33190679 original size:27 final size:27
Alignment explanation
Indices: 33190624--33190718 Score: 63
Period size: 27 Copynumber: 3.4 Consensus size: 27
33190614 AAAAGAAAAT
* *
33190624 GAAAAAGAAATGAGAAATGAGAAATGA
1 GAAAAAGAAATGAAAAATGAGAAAAGA
33190651 GAAAAAGAACAT-AAAAAT-AGCAAAAGA
1 GAAAAAGAA-ATGAAAAATGAG-AAAAGA
33190678 GAGAGAAGAGGAAATGATAAAA-GA-AAAAGAA
1 GA-A-AA-A-GAAATGA-AAAATGAGAAAAG-A
*
33190709 GAAGAAGAAA
1 GAAAAAGAAA
33190719 AAGAAAATGG
Statistics
Matches: 55, Mismatches: 3, Indels: 20
0.71 0.04 0.26
Matches are distributed among these distances:
26 2 0.04
27 25 0.45
28 4 0.07
29 3 0.05
30 9 0.16
31 7 0.13
32 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.07
Consensus pattern (27 bp):
GAAAAAGAAATGAAAAATGAGAAAAGA
Found at i:33192504 original size:29 final size:29
Alignment explanation
Indices: 33192471--33192530 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
33192461 ATAACCGAAC
33192471 CTACAAAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
33192500 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
33192529 CT
1 CT
33192531 TTGAACCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:33192523 original size:15 final size:15
Alignment explanation
Indices: 33192477--33192524 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
33192467 GAACCTACAA
33192477 AAACTTCATATCCAT
1 AAACTTCATATCCAT
* * *
33192492 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
33192506 AAACTTCATATCCAT
1 AAACTTCATATCCAT
33192521 AAAC
1 AAAC
33192525 CCATCTTTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:33192773 original size:11 final size:11
Alignment explanation
Indices: 33192759--33192837 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
33192749 AAAAGGTTTC
33192759 AAAAAAATTCA
1 AAAAAAATTCA
33192770 AAAAAAA-T-A
1 AAAAAAATTCA
33192779 AAAAAAAGTTC-
1 AAAAAAA-TTCA
*
33192790 ---AAAATTCG
1 AAAAAAATTCA
33192798 AAAAAAATTCTGA
1 AAAAAAATTC--A
*
33192811 AAAAAATTTCA
1 AAAAAAATTCA
33192822 GAAAAAAAGTTCA
1 -AAAAAAA-TTCA
33192835 AAA
1 AAA
33192838 TTTGAATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
7 3 0.06
8 4 0.07
9 8 0.15
10 1 0.02
11 16 0.30
12 9 0.17
13 13 0.24
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:33192834 original size:13 final size:12
Alignment explanation
Indices: 33192790--33192834 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
33192780 AAAAAAGTTC
33192790 AAAATTC-GAAA
1 AAAATTCAGAAA
*
33192801 AAAATTCTGAAA
1 AAAATTCAGAAA
33192813 AAAATTTCAGAAA
1 AAAA-TTCAGAAA
33192826 AAAAGTTCA
1 AAAA-TTCA
33192835 AAATTTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 7 0.23
12 8 0.27
13 15 0.50
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (12 bp):
AAAATTCAGAAA
Found at i:33194015 original size:39 final size:40
Alignment explanation
Indices: 33193966--33194114 Score: 139
Period size: 39 Copynumber: 3.8 Consensus size: 40
33193956 TAAACTCGGT
* * *
33193966 ATAATACCAGCTCGAAGCCTGCGGGA-CTTTAGCCCGGAC
1 ATAATTCCAGCACGAAGCCTGCGGGACCTTAAGCCCGGAC
* * * *
33194005 ATATTTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGAT
1 ATAATTCCAGCACGAAGCCTGCGGGACCTTAAGCCCGGAC
* * *
33194044 ATAATTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCCGGAT
1 ATAATTCCAGCACGA-AGCCTGCGGGACCTTAAGCCCGGAC
*
33194083 ATAATTCCAGCAC-ATAGCCTGC-GGACCCTAAG
1 ATAATTCCAGCACGA-AGCCTGCGGGACCTTAAG
33194115 TCCAGATATA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
38 3 0.03
39 95 0.97
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (40 bp):
ATAATTCCAGCACGAAGCCTGCGGGACCTTAAGCCCGGAC
Found at i:33194115 original size:39 final size:39
Alignment explanation
Indices: 33193999--33194124 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
33193989 GGACTTTAGC
* * * *
33193999 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
33194038 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
33194077 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
33194116 CCAGATATA
1 CCGGATATA
33194125 CACCACTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:33200828 original size:22 final size:22
Alignment explanation
Indices: 33200800--33200843 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
33200790 TTTTGAACCA
33200800 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
33200822 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
33200844 AAATACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33201292 original size:30 final size:30
Alignment explanation
Indices: 33201258--33201354 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33201248 AGCTCACTCC
33201258 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33201288 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33201318 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33201348 TAGCTCA
1 TAGCTCA
33201355 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33203575 original size:20 final size:20
Alignment explanation
Indices: 33203537--33203575 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33203527 TTTGTTCTTC
*
33203537 TTTTCTTATTTCAATTAATA
1 TTTTCTTATTTCAAATAATA
33203557 TTTT-TTATTTCAAAATAAT
1 TTTTCTTATTTC-AAATAAT
33203576 GCAAATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTCTTATTTCAAATAATA
Found at i:33210956 original size:18 final size:18
Alignment explanation
Indices: 33210935--33210969 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33210925 TTTTTCTTTT
33210935 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
33210953 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
33210970 TTTTTTTTTC
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:33211060 original size:6 final size:6
Alignment explanation
Indices: 33210994--33211047 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
33210984 ACTATTTTGA
* ** * *
33210994 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
33211041 TTTCTT T
1 TTTCTT T
33211048 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:33212032 original size:12 final size:11
Alignment explanation
Indices: 33212007--33212052 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
33211997 TTGTCACTTC
*
33212007 TTTTTTTTC-C
1 TTTTTTTTCAA
33212017 TTTTTTTTCAA
1 TTTTTTTTCAA
*
33212028 TTTTTTTTGAA
1 TTTTTTTTCAA
*
33212039 TTTTTTTTGAA
1 TTTTTTTTCAA
33212050 TTT
1 TTT
33212053 CTTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:33212144 original size:12 final size:12
Alignment explanation
Indices: 33212129--33212160 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
33212119 CCAACTCAAA
33212129 TTTTTTTTTGA-
1 TTTTTTTTTGAC
33212140 TTTTTTTTTGAC
1 TTTTTTTTTGAC
33212152 TTTTTTTTT
1 TTTTTTTTT
33212161 CGTTACGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAC
Found at i:33215295 original size:20 final size:20
Alignment explanation
Indices: 33215270--33215324 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
33215260 TGTGGTTCAA
*
33215270 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
33215290 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
* *
33215310 CTTATTCAAGCTCAA
1 CTCATTCGAGCTCAA
33215325 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:33215889 original size:59 final size:63
Alignment explanation
Indices: 33215826--33215967 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
33215816 ATTTAAAGGG
* *
33215826 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
*
33215885 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
33215950 ATGTA
59 ATGTA
33215955 AAGCATAGACATG
1 AAGCATAGACATG
33215968 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
Found at i:33215930 original size:70 final size:70
Alignment explanation
Indices: 33215847--33215983 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
33215837 TGAATTAAAT
*
33215847 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
33215912 TTCAA
66 TTCAA
* *
33215917 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
33215982 TT
66 TT
33215984 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (70 bp):
CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:33217148 original size:12 final size:13
Alignment explanation
Indices: 33217133--33217165 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
33217123 TAAAAAAAGG
33217133 AAAAAAATTC-AA
1 AAAAAAATTCGAA
33217145 AAAAAAA-TCGAA
1 AAAAAAATTCGAA
33217157 AAAAAAATT
1 AAAAAAATT
33217166 GTATTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.84
13 1 0.05
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:33218214 original size:15 final size:16
Alignment explanation
Indices: 33218194--33218225 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
33218184 AGAAAATGAA
33218194 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
33218209 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
33218225 A
1 A
33218226 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:33218949 original size:20 final size:20
Alignment explanation
Indices: 33218924--33218978 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
33218914 TGTGGTTCAA
*
33218924 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
33218944 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
33218964 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
33218979 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:33219543 original size:59 final size:63
Alignment explanation
Indices: 33219480--33219621 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
33219470 ATTTAAGGGG
* *
33219480 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
*
33219539 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
33219604 ATGTA
59 ATGTA
33219609 AAGCATAGACATG
1 AAGCATAGACATG
33219622 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
Found at i:33219584 original size:70 final size:70
Alignment explanation
Indices: 33219501--33219637 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
33219491 TGAATTAAAT
*
33219501 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
33219566 TTCAA
66 TTCAA
* *
33219571 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
33219636 TT
66 TT
33219638 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (70 bp):
CAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:33227867 original size:24 final size:25
Alignment explanation
Indices: 33227814--33227867 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
33227804 AACAAATTCT
* *
33227814 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
33227839 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
33227862 TTTTTT
1 TTTTTT
33227868 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:33230143 original size:15 final size:14
Alignment explanation
Indices: 33230118--33230146 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33230108 CTAGACCGTA
33230118 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
33230132 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
33230146 T
1 T
33230147 CAAAACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:33233225 original size:30 final size:30
Alignment explanation
Indices: 33233191--33233287 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33233181 AGCTCACTCC
33233191 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33233221 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33233251 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33233281 TAGCTCA
1 TAGCTCA
33233288 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Done.