Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 217 of 425
Found at i:66041923 original size:20 final size:21
Alignment explanation
Indices: 66041894--66041933 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
66041884 AGGTCACTTG
*
66041894 AGCTTGTTTC-AGCTCGTTTT
1 AGCTTCTTTCTAGCTCGTTTT
*
66041914 AGCTTCTTTCTATCTCGTTT
1 AGCTTCTTTCTAGCTCGTTT
66041934 CTTTTCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.53
Consensus pattern (21 bp):
AGCTTCTTTCTAGCTCGTTTT
Found at i:66046046 original size:30 final size:31
Alignment explanation
Indices: 66045988--66046047 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
66045978 ATAGCAAAAG
* *
66045988 AAACGAGCTGGAAAGAAGCTAAATTGAGCTC
1 AAACGAGCTGGAAACAAGCTAAAGTGAGCTC
*
66046019 AAACGAGCT-GAAACAAGCTCAAGTGAGCT
1 AAACGAGCTGGAAACAAGCTAAAGTGAGCT
66046048 AATTGGAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (31 bp):
AAACGAGCTGGAAACAAGCTAAAGTGAGCTC
Found at i:66047635 original size:13 final size:13
Alignment explanation
Indices: 66047617--66047641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66047607 GTATTGATCA
66047617 TGTGTTCACACCT
1 TGTGTTCACACCT
66047630 TGTGTTCACACC
1 TGTGTTCACACC
66047642 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:66059587 original size:29 final size:29
Alignment explanation
Indices: 66059554--66059613 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66059544 ATAACCAAAC
*
66059554 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
66059583 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
66059612 CT
1 CT
66059614 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:66059606 original size:15 final size:15
Alignment explanation
Indices: 66059560--66059607 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66059550 AAACCTACAA
*
66059560 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
66059575 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
66059589 AAACTTCATATCCAT
1 AAACTTCATATCCAT
66059604 AAAC
1 AAAC
66059608 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:66061502 original size:18 final size:17
Alignment explanation
Indices: 66061449--66061503 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
66061439 TGAATAAATT
66061449 ACTCATCTTAGTTAATTGA
1 ACTCATCTTAGTTAA-T-A
**
66061468 GTTCATCTTAGTTAATA
1 ACTCATCTTAGTTAATA
66061485 ACTCATCTTAGATTAATA
1 ACTCATCTTAG-TTAATA
66061503 A
1 A
66061504 ATGAGTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 8 0.26
19 13 0.42
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCATCTTAGTTAATA
Found at i:66061829 original size:30 final size:30
Alignment explanation
Indices: 66061795--66061882 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
66061785 CTAGCTTATA
* *
66061795 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
* * *
66061825 TTCAGCTTAGGAGC-ATAATCTCAGCTCAAC
1 TTCAGCTTAAGAGCTA-AACCTTAGCTCAAC
* * *
66061855 TTTAGCTTAAGGGCTAAAGCTTAGCTCA
1 TTCAGCTTAAGAGCTAAACCTTAGCTCA
66061883 TTTTAGCTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (30 bp):
TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
Found at i:66062388 original size:30 final size:30
Alignment explanation
Indices: 66062354--66062450 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
66062344 AGCTCACTCC
66062354 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66062384 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66062414 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66062444 TAGCTCA
1 TAGCTCA
66062451 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66064176 original size:31 final size:32
Alignment explanation
Indices: 66064138--66064210 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
66064128 AATATAGTAC
*
66064138 AAAAAAAAGTT-ATACAAGTAAAAAAAAAT-T-A
1 AAAAAAAAGTTCA-AAAAG-AAAAAAAAATCTGA
*
66064169 AAAAAAAATTTCAAAAAGAAAAAAAAATCTGA
1 AAAAAAAAGTTCAAAAAGAAAAAAAAATCTGA
66064201 AAAAAAAAGT
1 AAAAAAAAGT
66064211 GTTTAATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 10 0.28
31 15 0.42
32 11 0.31
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (32 bp):
AAAAAAAAGTTCAAAAAGAAAAAAAAATCTGA
Found at i:66064203 original size:19 final size:18
Alignment explanation
Indices: 66064168--66064208 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
66064158 AAAAAAAATT
*
66064168 AAAAAAAAATTTCAAAAA
1 AAAAAAAAATCTCAAAAA
*
66064186 GAAAAAAAAATCTGAAAAA
1 -AAAAAAAAATCTCAAAAA
66064205 AAAA
1 AAAA
66064209 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAAAAAATCTCAAAAA
Found at i:66065133 original size:9 final size:10
Alignment explanation
Indices: 66065126--66065182 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66065116 AAGAGAAAAC
66065126 AAAGAAAAGA
1 AAAGAAAAGA
66065136 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
66065148 AAAGAAGA-A
1 AAAGAAAAGA
66065157 AAAGAAAATGA
1 AAAGAAAA-GA
66065168 AATA-AAAAGA
1 AA-AGAAAAGA
66065178 AAAGA
1 AAAGA
66065183 GAGGCAAGAG
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:66065149 original size:21 final size:20
Alignment explanation
Indices: 66065115--66065182 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
66065105 ACATTCTTGT
66065115 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66065136 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
66065157 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66065178 AAAGA
1 AAAGA
66065183 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66065150 original size:6 final size:5
Alignment explanation
Indices: 66065126--66065182 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66065116 AAGAGAAAAC
*
66065126 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
66065173 AAAGA AAAGA
1 AAAGA AAAGA
66065183 GAGGCAAGAG
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:66065157 original size:15 final size:14
Alignment explanation
Indices: 66065126--66065182 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66065116 AAGAGAAAAC
66065126 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66065142 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66065157 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
66065173 AAAGAAAAGA
1 AAAGAAAAGA
66065183 GAGGCAAGAG
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:66065324 original size:30 final size:30
Alignment explanation
Indices: 66065251--66065331 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
66065241 TTTGAAAAGC
* * *
66065251 AAAAAGAAAATGAAAA-AAA-ATGAGATTG
1 AAAAAGAAGATGAAAAGAAATTTGAGAGTG
*
66065279 AAAAAG-AGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAG-ATGAAAAGAAATTTGAGAGTG
66065309 AAAAAGAAGATGAAAAAGAAATT
1 AAAAAGAAGATG-AAAAGAAATT
66065332 GAAACAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.02
28 12 0.28
29 3 0.07
30 15 0.35
31 12 0.28
ACGTcount: A:0.64, C:0.01, G:0.21, T:0.14
Consensus pattern (30 bp):
AAAAAGAAGATGAAAAGAAATTTGAGAGTG
Found at i:66067197 original size:6 final size:6
Alignment explanation
Indices: 66067159--66067300 Score: 103
Period size: 6 Copynumber: 22.8 Consensus size: 6
66067149 TTGCATTCAC
* * *
66067159 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
66067209 -TTACTTG ATACTG ATTCTG ATTTTG ATTCTG -TTACCTG ATACTA ATTCTG
1 ATT-C-TG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
*
66067259 ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCT
66067301 AGTTCTTATA
Statistics
Matches: 107, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
5 7 0.07
6 79 0.74
7 17 0.16
8 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:66067205 original size:31 final size:31
Alignment explanation
Indices: 66067159--66067300 Score: 221
Period size: 31 Copynumber: 4.5 Consensus size: 31
66067149 TTGCATTCAC
66067159 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
66067191 ATTCTGATTTTGATTCTGTTACTTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
66067222 ATTCTGATTTTGATTCTGTTACCTGATACTA
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * *
66067253 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
66067284 ATTCTGATTCTGATTCT
1 ATTCTGATTTTGATTCT
66067301 AGTTCTTATA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 96 0.93
32 7 0.07
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:66067223 original size:19 final size:19
Alignment explanation
Indices: 66067170--66067227 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
66067160 TTCTGATTTT
*
66067170 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACTTGATAC
66067189 TGATTCTG--A-TT--T--
1 TGATTCTGTTACTTGATAC
66067201 TGATTCTGTTACTTGATAC
1 TGATTCTGTTACTTGATAC
66067220 TGATTCTG
1 TGATTCTG
66067228 ATTTTGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
12 8 0.26
14 2 0.06
15 2 0.06
16 1 0.03
17 2 0.06
19 16 0.52
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (19 bp):
TGATTCTGTTACTTGATAC
Found at i:66067247 original size:25 final size:25
Alignment explanation
Indices: 66067194--66067295 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
66067184 GATACTGATT
* *
66067194 CTGATTTTGATTCTG-TTACTTGATA-
1 CTGATTCTGATTCTGATT-C-TGTTAC
*
66067219 CTGATTCTGATTTTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTGTTAC
*
66067244 CTGATACTAATTCTGATTCTGATTCTGTCAC
1 CTG------ATTCTGATTCTGATTCTGTTAC
66067275 CTGATTCTGATTCTGATTCTG
1 CTGATTCTGATTCTGATTCTG
66067296 ATTCTAGTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
24 4 0.06
25 35 0.55
26 2 0.03
31 23 0.36
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGATTCTGTTAC
Found at i:66070046 original size:13 final size:13
Alignment explanation
Indices: 66070028--66070064 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
66070018 TATACAAGTT
66070028 AAAAAAAATCTGA
1 AAAAAAAATCTGA
66070041 AAAAAAAATC--A
1 AAAAAAAATCTGA
66070052 AAAAAAAAT-TGA
1 AAAAAAAATCTGA
66070064 A
1 A
66070065 GTGAAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATCTGA
Found at i:66071863 original size:13 final size:13
Alignment explanation
Indices: 66071834--66071873 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
66071824 AACCAACCAA
*
66071834 TTTGTTCATATCCC
1 TTTGTTCCTA-CCC
66071848 TTTGTTCCTACCC
1 TTTGTTCCTACCC
66071861 TTTCGTTCCTACC
1 TTT-GTTCCTACC
66071874 ATTCCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTGTTCCTACCC
Found at i:66078846 original size:13 final size:13
Alignment explanation
Indices: 66078817--66078856 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
66078807 AACTGACCAA
*
66078817 TTTGTTCATATCCC
1 TTTGTTCCTA-CCC
66078831 TTTGTTCCTACCC
1 TTTGTTCCTACCC
66078844 TTTCGTTCCTACC
1 TTT-GTTCCTACC
66078857 ATTCCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTGTTCCTACCC
Found at i:66081672 original size:30 final size:30
Alignment explanation
Indices: 66081638--66081698 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66081628 TCCTTAACTC
66081638 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
66081668 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
66081698 A
1 A
66081699 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:66086131 original size:30 final size:30
Alignment explanation
Indices: 66086097--66086157 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66086087 TCCTTAACTC
66086097 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
66086127 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
66086157 A
1 A
66086158 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:66087777 original size:6 final size:5
Alignment explanation
Indices: 66087753--66087809 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66087743 ACGAGAAAAC
*
66087753 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66087800 AAAGA AAAGA
1 AAAGA AAAGA
66087810 GAGGCAAAAG
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:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:66087784 original size:15 final size:14
Alignment explanation
Indices: 66087753--66087809 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66087743 ACGAGAAAAC
66087753 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66087769 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66087784 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
66087800 AAAGAAAAGA
1 AAAGAAAAGA
66087810 GAGGCAAAAG
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:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:66087888 original size:13 final size:12
Alignment explanation
Indices: 66087857--66087888 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
66087847 TTGAGAGAAC
*
66087857 TTGAAAAAGCCT
1 TTGAAAAAACCT
66087869 TTGAAAAAACCT
1 TTGAAAAAACCT
66087881 TTGAAAAA
1 TTGAAAAA
66087889 CAAAAAGAAA
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:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (12 bp):
TTGAAAAAACCT
Found at i:66087912 original size:12 final size:12
Alignment explanation
Indices: 66087890--66087914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66087880 TTTGAAAAAC
66087890 AAAAAGAAAATG
1 AAAAAGAAAATG
66087902 AAAAAGAAAATG
1 AAAAAGAAAATG
66087914 A
1 A
66087915 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66087921 original size:18 final size:18
Alignment explanation
Indices: 66087881--66087934 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
66087871 GAAAAAACCT
* *
66087881 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
66087899 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
66087917 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
66087935 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:66087946 original size:30 final size:30
Alignment explanation
Indices: 66087890--66087971 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
66087880 TTTGAAAAAC
**
66087890 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGACAG
* ***
66087920 AAAAAGAGAATGAAAAAGAGTTTGAGACAG
1 AAAAAGAAAATGAAAAAGAAAATGAGACAG
** *
66087950 AAAAAGAATGTGAACAAGAAAA
1 AAAAAGAAAATGAAAAAGAAAA
66087972 AAGAGTGGAA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGACAG
Found at i:66087986 original size:18 final size:19
Alignment explanation
Indices: 66087950--66087988 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
66087940 TTTGAGACAG
*
66087950 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
66087969 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
66087987 AA
1 AA
66087989 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:66088720 original size:10 final size:10
Alignment explanation
Indices: 66088705--66088731 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66088695 TACTCCTTCA
66088705 AGCTCAAATC
1 AGCTCAAATC
66088715 AGCTCAAATC
1 AGCTCAAATC
66088725 AGCTCAA
1 AGCTCAA
66088732 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:66090715 original size:13 final size:13
Alignment explanation
Indices: 66090697--66090721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66090687 TAACCTACAA
66090697 AATTAAATAACAT
1 AATTAAATAACAT
66090710 AATTAAATAACA
1 AATTAAATAACA
66090722 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:66090980 original size:10 final size:10
Alignment explanation
Indices: 66090947--66090992 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
66090937 AAAAAGGAAT
*
66090947 GAGCTGAAAC
1 GAGCTAAAAC
*
66090957 GAGCTAAATTC
1 GAGCTAAA-AC
66090968 GAGCTAAAAC
1 GAGCTAAAAC
66090978 GAGCTAAAAC
1 GAGCTAAAAC
66090988 GAGCT
1 GAGCT
66090993 CAAGTGAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:66093085 original size:30 final size:29
Alignment explanation
Indices: 66093022--66093095 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
66093012 GTTTCTTTTG
* *
66093022 TTTCAATTTCTTTTTCACTCTCAAATTTCT
1 TTTC-ATTTCTTTTTCAATCTCAAATCTCT
66093052 TTTCATTCTCTTTTTCAATCTC-AATCTCAT
1 TTTCATT-TCTTTTTCAATCTCAAATCTC-T
*
66093082 TTTCTTTTCTTTTT
1 TTTCATTTCTTTTT
66093096 TTCTCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTCATTTCTTTTTCAATCTCAAATCTCT
Found at i:66093106 original size:17 final size:18
Alignment explanation
Indices: 66093084--66093121 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
66093074 AATCTCATTT
*
66093084 TCTTTTCTTTTTTTC-TC
1 TCTTTTCTTTGTTTCTTC
66093101 TCTTTTCTTTGTTTCTTC
1 TCTTTTCTTTGTTTCTTC
66093119 TCT
1 TCT
66093122 CGATTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (18 bp):
TCTTTTCTTTGTTTCTTC
Found at i:66095291 original size:13 final size:13
Alignment explanation
Indices: 66095273--66095297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66095263 TAACCTACAA
66095273 AATTAAATAACAT
1 AATTAAATAACAT
66095286 AATTAAATAACA
1 AATTAAATAACA
66095298 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:66095560 original size:10 final size:10
Alignment explanation
Indices: 66095531--66095573 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
66095521 GAATGAGTTG
66095531 AAACGAGCT-
1 AAACGAGCTC
66095540 AAATTCGAGCTC
1 AAA--CGAGCTC
*
66095552 AAACGAGCTA
1 AAACGAGCTC
66095562 AAACGAGCTC
1 AAACGAGCTC
66095572 AA
1 AA
66095574 GTGAGCTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 3 0.10
10 17 0.59
11 6 0.21
12 3 0.10
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (10 bp):
AAACGAGCTC
Found at i:66095580 original size:20 final size:21
Alignment explanation
Indices: 66095531--66095573 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
66095521 GAATGAGTTG
*
66095531 AAACGAGCTAAATTCGAGCTC
1 AAACGAGCTAAATACGAGCTC
66095552 AAACGAGCTAAA-ACGAGCTC
1 AAACGAGCTAAATACGAGCTC
66095572 AA
1 AA
66095574 GTGAGCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (21 bp):
AAACGAGCTAAATACGAGCTC
Found at i:66104707 original size:20 final size:19
Alignment explanation
Indices: 66104684--66104725 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
66104674 ATTTTCTCGA
66104684 TTTTCTTTGCTT-TTTCTTCT
1 TTTTCTTTG-TTATTT-TTCT
66104704 TTTTCTTTGTTATTTTTCT
1 TTTTCTTTGTTATTTTTCT
66104723 TTT
1 TTT
66104726 CACTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTCTTTGTTATTTTTCT
Found at i:66109345 original size:30 final size:30
Alignment explanation
Indices: 66109311--66109407 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66109301 AGCTCACTCC
*
66109311 TAGCTCATA-TTCAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66109341 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66109371 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66109401 TAGCTCA
1 TAGCTCA
66109408 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66117230 original size:12 final size:12
Alignment explanation
Indices: 66117213--66117243 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
66117203 TCACTTCAAA
*
66117213 TTTTTTTCGGAT
1 TTTTTTTCGAAT
66117225 TTTTTTTCGAAT
1 TTTTTTTCGAAT
66117237 TTTTTTT
1 TTTTTTT
66117244 TAAACTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:66127666 original size:17 final size:17
Alignment explanation
Indices: 66127607--66127666 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
66127597 GAGACAGCCA
* * *
66127607 CCATACATGCACTTAAG
1 CCATTCATGCATTTAAT
66127624 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TAAT
*
66127641 -CATCCCATGCATTTAAT
1 CCAT-TCATGCATTTAAT
66127658 CCATTCATG
1 CCATTCATG
66127667 GACTAGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 26 0.76
18 4 0.12
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTAAT
Found at i:66128977 original size:17 final size:17
Alignment explanation
Indices: 66128952--66128990 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
66128942 CCAAGCATAA
*
66128952 GTATAAGCAAATTATGT
1 GTATTAGCAAATTATGT
66128969 GTATTAGCAAATTATGT
1 GTATTAGCAAATTATGT
66128986 GTATT
1 GTATT
66128991 TTGTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (17 bp):
GTATTAGCAAATTATGT
Found at i:66131321 original size:21 final size:20
Alignment explanation
Indices: 66131297--66131344 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
66131287 AAAAGAAATG
*
66131297 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAA-CA
*
66131318 AGCTCAAACGAGCTGAAACA
1 AGCTCAAACGAGCTAAAACA
66131338 AGCTCAA
1 AGCTCAA
66131345 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
AGCTCAAACGAGCTAAAACA
Found at i:66131350 original size:20 final size:21
Alignment explanation
Indices: 66131297--66131353 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
66131287 AAAAGAAATG
* *
66131297 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTGAAATCA
66131318 AGCTCAAACGAGCTGAAA-CA
1 AGCTCAAACGAGCTGAAATCA
**
66131338 AGCTCAAGTGAGCTGA
1 AGCTCAAACGAGCTGA
66131354 TTGGAGCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCTCAAACGAGCTGAAATCA
Found at i:66135959 original size:16 final size:16
Alignment explanation
Indices: 66135940--66136000 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
66135930 TGCAAACAAA
66135940 CTTTTTTTTCTACTTT
1 CTTTTTTTTCTACTTT
*
66135956 CTTTTTCTTACT-CTTT
1 CTTTTT-TTTCTACTTT
*
66135972 TTTTTCTTTTCTCACTTTTT
1 CTTTT-TTTTCT-AC--TTT
66135992 CTTTTTTTT
1 CTTTTTTTT
66136001 TCTTTTTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
16 18 0.51
17 5 0.14
18 1 0.03
19 4 0.11
20 7 0.20
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTTTTTCTACTTT
Found at i:66135960 original size:15 final size:14
Alignment explanation
Indices: 66135940--66135978 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
66135930 TGCAAACAAA
66135940 CTTTTTTTTCTACT
1 CTTTTTTTTCTACT
*
66135954 -TTCTTTTTCTTACT
1 CTTTTTTTTC-TACT
66135968 CTTTTTTTTCT
1 CTTTTTTTTCT
66135979 TTTCTCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTTTTTCTACT
Found at i:66135983 original size:20 final size:20
Alignment explanation
Indices: 66135953--66136004 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
66135943 TTTTTTCTAC
66135953 TTTCTTTTTCTTACTCTTTT-T
1 TTTC-TTTTCTTACT-TTTTCT
*
66135974 TTTCTTTTCTCACTTTTTCT
1 TTTCTTTTCTTACTTTTTCT
*
66135994 TTTTTTTTCTT
1 TTTCTTTTCTT
66136005 TTTCCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCTTTTCTTACTTTTTCT
Found at i:66136025 original size:25 final size:26
Alignment explanation
Indices: 66135972--66136028 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
66135962 CTTACTCTTT
* *
66135972 TTTTTC-TTTTCTCACTTTTTCTTTT
1 TTTTTCTTTTTCTCACTTTTTCATTC
66135997 TTTTTCTTTTTC-CA-TTTTTGCATTC
1 TTTTTCTTTTTCTCACTTTTT-CATTC
66136022 TTTTTCT
1 TTTTTCT
66136029 CATTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 18 0.64
26 5 0.18
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTTCTTTTTCTCACTTTTTCATTC
Found at i:66136042 original size:20 final size:20
Alignment explanation
Indices: 66135972--66136047 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
66135962 CTTACTCTTT
66135972 TTTTTCTTTTCTCACTTTT-TC-
1 TTTTTCTTTTCT---TTTTCTCA
66135993 TTTTT-TTTTCTTTTTC-CA
1 TTTTTCTTTTCTTTTTCTCA
*
66136011 TTTTTGC-ATTCTTTTTCTCA
1 TTTTT-CTTTTCTTTTTCTCA
66136031 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTTCTTTTTC
66136048 ATTTTCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.11
18 5 0.11
19 10 0.21
20 22 0.47
21 5 0.11
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTTCTCA
Found at i:66138443 original size:10 final size:10
Alignment explanation
Indices: 66138430--66138474 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
66138420 AAAAGAAATG
66138430 AGCTGAAACA
1 AGCTGAAACA
*
66138440 AGCTAAAATCA
1 AGCTGAAA-CA
*
66138451 AGCTCAAACA
1 AGCTGAAACA
66138461 AGCTGAAACA
1 AGCTGAAACA
66138471 AGCT
1 AGCT
66138475 CCAGTGAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (10 bp):
AGCTGAAACA
Found at i:66138454 original size:21 final size:20
Alignment explanation
Indices: 66138430--66138475 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
66138420 AAAAGAAATG
*
66138430 AGCTGAAACAAGCTAAAATCA
1 AGCTCAAACAAGCTAAAA-CA
*
66138451 AGCTCAAACAAGCTGAAACA
1 AGCTCAAACAAGCTAAAACA
66138471 AGCTC
1 AGCTC
66138476 CAGTGAGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (20 bp):
AGCTCAAACAAGCTAAAACA
Found at i:66138787 original size:19 final size:19
Alignment explanation
Indices: 66138763--66138802 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
66138753 AGCTCCCATG
66138763 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
66138782 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
66138801 TA
1 TA
66138803 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:66142326 original size:30 final size:30
Alignment explanation
Indices: 66142292--66142388 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66142282 TAAACTAAAA
66142292 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
66142322 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66142352 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66142382 TGAGCTA
1 TGAGCTA
66142389 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:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66143837 original size:27 final size:26
Alignment explanation
Indices: 66143789--66143847 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
66143779 AGCAGCAACA
*
66143789 ATTAAATTTGTCCCTAAGCTAGACAC
1 ATTAAATTTGTCCCTAAACTAGACAC
66143815 ATTAAATTGATGT-CCTAAACTAGACAC
1 ATTAAATT--TGTCCCTAAACTAGACAC
66143842 ATTAAA
1 ATTAAA
66143848 GCTAGGTATT
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:66145431 original size:19 final size:19
Alignment explanation
Indices: 66145409--66145466 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
66145399 TTAATTCAGC
66145409 TATGTGAACATAATCAATT
1 TATGTGAACATAATCAATT
* * **
66145428 TATGT--A-ATGAT-TAGC
1 TATGTGAACATAATCAATT
66145443 TATGTGAACATAATCAATT
1 TATGTGAACATAATCAATT
66145462 TATGT
1 TATGT
66145467 AATGACTATG
Statistics
Matches: 27, Mismatches: 8, Indels: 8
0.63 0.19 0.19
Matches are distributed among these distances:
15 6 0.22
16 4 0.15
17 2 0.07
18 4 0.15
19 11 0.41
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (19 bp):
TATGTGAACATAATCAATT
Found at i:66145448 original size:34 final size:34
Alignment explanation
Indices: 66145406--66145471 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
66145396 GCATTAATTC
66145406 AGCTATGTGAACATAATCAATTTATGTAATGATT
1 AGCTATGTGAACATAATCAATTTATGTAATGATT
66145440 AGCTATGTGAACATAATCAATTTATGTAATGA
1 AGCTATGTGAACATAATCAATTTATGTAATGA
66145472 CTATGGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (34 bp):
AGCTATGTGAACATAATCAATTTATGTAATGATT
Found at i:66145615 original size:30 final size:30
Alignment explanation
Indices: 66145581--66145676 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
66145571 TAAACTAAAA
66145581 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
66145611 TGAGCTGAGGC--TAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
66145640 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
66145670 TGAGCTA
1 TGAGCTA
66145677 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 2 0.04
29 20 0.40
30 22 0.44
31 6 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:66146766 original size:30 final size:30
Alignment explanation
Indices: 66146671--66146767 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
66146661 AGCTCACTCC
* *
66146671 TAGCTC-ACTTTCAACTCAAGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCAAGAGCTAAAGCT
* * * **
66146701 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAG-CT
* *
66146731 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
66146761 TAGCTCA
1 TAGCTCA
66146768 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
Found at i:66148356 original size:10 final size:11
Alignment explanation
Indices: 66148328--66148357 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
66148318 ATACAAGTAA
66148328 AAAAAAATTCG
1 AAAAAAATTCG
66148339 AAAAAAATTC-
1 AAAAAAATTCG
66148349 AAAAAAATT
1 AAAAAAATT
66148358 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:66149327 original size:21 final size:20
Alignment explanation
Indices: 66149293--66149360 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
66149283 ACATTCTTGT
66149293 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66149314 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
*
66149335 AAAGAAAAAGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66149356 AAAGA
1 AAAGA
66149361 GAGGCAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.20
21 28 0.68
22 5 0.12
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66149328 original size:6 final size:5
Alignment explanation
Indices: 66149304--66149360 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66149294 AAGAGAAAAC
*
66149304 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
66149351 AAAGA AAAGA
1 AAAGA AAAGA
66149361 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:66149353 original size:25 final size:25
Alignment explanation
Indices: 66149308--66149356 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
66149298 GAAAACAAAG
66149308 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
66149334 AAAAGAAAAAGAAATA-AAAAGAA
1 AAAAG-AAAAGAAAAACAAAAGAA
66149357 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:66149439 original size:11 final size:12
Alignment explanation
Indices: 66149408--66149438 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
66149398 TTGAGAGAAC
*
66149408 TTGAAAAACCCT
1 TTGAAAAAGCCT
66149420 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66149432 TTGAAAA
1 TTGAAAA
66149439 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66149449 original size:12 final size:12
Alignment explanation
Indices: 66149441--66149465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66149431 TTTGAAAAGA
66149441 AAAAAGAAAATG
1 AAAAAGAAAATG
66149453 AAAAAGAAAATG
1 AAAAAGAAAATG
66149465 A
1 A
66149466 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:66149475 original size:30 final size:31
Alignment explanation
Indices: 66149441--66149522 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
66149431 TTTGAAAAGA
*
66149441 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
66149471 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
66149501 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66149523 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:66153125 original size:15 final size:14
Alignment explanation
Indices: 66153104--66153146 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
66153094 AGTTTTTCCA
66153104 CTCTTTTTCTTTT-
1 CTCTTTTTCTTTTG
*
66153117 CATTCTTTTTATTTTG
1 C--TCTTTTTCTTTTG
66153133 CTCTTTTTCTTTTG
1 CTCTTTTTCTTTTG
66153147 ATCTCTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 11 0.44
16 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (14 bp):
CTCTTTTTCTTTTG
Found at i:66155660 original size:11 final size:10
Alignment explanation
Indices: 66155644--66155680 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
66155634 ATACAAGTTA
66155644 AAAAAAATTCG
1 AAAAAAATT-G
66155655 AAAAAAATTG
1 AAAAAAATTG
66155665 AAAAAAATT-
1 AAAAAAATTG
66155674 AAAAAAA
1 AAAAAAA
66155681 AGTGATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 7 0.27
10 10 0.38
11 9 0.35
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:66156599 original size:9 final size:10
Alignment explanation
Indices: 66156592--66156633 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
66156582 ACGAGAAAAC
66156592 AAAGAAAAGA
1 AAAGAAAAGA
66156602 AAAGAAAAAGA
1 AAAG-AAAAGA
66156613 AAATGAAATA-A
1 AAA-GAAA-AGA
66156624 AAAGAAAAGA
1 AAAGAAAAGA
66156634 GAGGCAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.04
10 9 0.32
11 16 0.57
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66156602 original size:5 final size:5
Alignment explanation
Indices: 66156592--66156633 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
66156582 ACGAGAAAAC
66156592 AAAGA AAAGA AAAGAA AAAGA AAATGA AATA-A AAAGA AAAGA
1 AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA AAAGA AAAGA
66156634 GAGGCAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 1 0.03
5 22 0.67
6 9 0.27
7 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:66156613 original size:16 final size:16
Alignment explanation
Indices: 66156592--66156633 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
66156582 ACGAGAAAAC
66156592 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
66156608 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
66156624 AAAGAAAAGA
1 AAAGAAAAGA
66156634 GAGGCAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:66156733 original size:12 final size:12
Alignment explanation
Indices: 66156706--66156749 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
66156696 AGAAAGACTT
66156706 TGAAAAA-A-AA
1 TGAAAAAGAGAA
* *
66156716 TGAAAATGAGAT
1 TGAAAAAGAGAA
66156728 TGAAAAAGAGAA
1 TGAAAAAGAGAA
66156740 TGAAAAAGAG
1 TGAAAAAGAG
66156750 TTTGAGAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 6 0.21
11 1 0.04
12 21 0.75
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.14
Consensus pattern (12 bp):
TGAAAAAGAGAA
Found at i:66156745 original size:24 final size:22
Alignment explanation
Indices: 66156705--66156754 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
66156695 AAGAAAGACT
*
66156705 TTGAAAAAAAATGAAAATGAGA
1 TTGAAAAAAAATGAAAAAGAGA
*
66156727 TTGAAAAAGAGAATGAAAAAGAGT
1 TTGAAAAA-A-AATGAAAAAGAGA
66156751 TTGA
1 TTGA
66156755 GAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 1 0.04
24 15 0.62
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGAAAAAAAATGAAAAAGAGA
Found at i:66156796 original size:18 final size:19
Alignment explanation
Indices: 66156760--66156798 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
66156750 TTTGAGAGAG
*
66156760 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
66156779 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
66156797 AA
1 AA
66156799 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:66158927 original size:20 final size:21
Alignment explanation
Indices: 66158896--66158940 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
66158886 TCTGCTGTCC
*
66158896 AGCTCAAATCCAGCTTATTC-G
1 AGCTCAAATCCAACTT-TTCTG
66158917 AGCTC-AATCCAACTTTTCTG
1 AGCTCAAATCCAACTTTTCTG
66158937 AGCT
1 AGCT
66158941 AAACCGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (21 bp):
AGCTCAAATCCAACTTTTCTG
Found at i:66161874 original size:10 final size:10
Alignment explanation
Indices: 66161859--66161886 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
66161849 TATATTTCTT
66161859 TTTTTTTGAA
1 TTTTTTTGAA
66161869 TTTTTTTGAA
1 TTTTTTTGAA
66161879 TTTTTTTG
1 TTTTTTTG
66161887 GCTAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:66163195 original size:30 final size:31
Alignment explanation
Indices: 66163161--66163257 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66163151 AGCTCACTCC
*
66163161 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66163191 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66163221 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66163251 TAGCTCA
1 TAGCTCA
66163258 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66166252 original size:20 final size:20
Alignment explanation
Indices: 66166228--66166268 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
66166218 TTTATTTCTT
66166228 TTTTTCACAATTTTTTTTAAA
1 TTTTTCA-AATTTTTTTTAAA
*
66166249 TTTTTTAAATTTTTTTTAAA
1 TTTTTCAAATTTTTTTTAAA
66166269 GATACGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTCAAATTTTTTTTAAA
Found at i:66166264 original size:11 final size:11
Alignment explanation
Indices: 66166226--66166268 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
66166216 TATTTATTTC
*
66166226 TTTTTTTCACAA
1 TTTTTTTTA-AA
66166238 TTTTTTTTAAA
1 TTTTTTTTAAA
66166249 --TTTTTTAAA
1 TTTTTTTTAAA
66166258 TTTTTTTTAAA
1 TTTTTTTTAAA
66166269 GATACGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 9 0.32
11 11 0.39
12 8 0.29
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:66168673 original size:24 final size:24
Alignment explanation
Indices: 66168623--66168673 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
66168613 ATGAATCGGT
* *
66168623 AAAAGCCGAAATGCCGAAATGCTG
1 AAAAGCCGAAATGCCGAAAAGCAG
* *
66168647 AAAAGTCGAAATGGCGAAAAGCAG
1 AAAAGCCGAAATGCCGAAAAGCAG
66168671 AAA
1 AAA
66168674 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.16, G:0.25, T:0.10
Consensus pattern (24 bp):
AAAAGCCGAAATGCCGAAAAGCAG
Found at i:66170281 original size:29 final size:29
Alignment explanation
Indices: 66170248--66170307 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66170238 ATAACCAAAC
*
66170248 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
66170277 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
66170306 CT
1 CT
66170308 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:66170300 original size:15 final size:15
Alignment explanation
Indices: 66170254--66170301 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66170244 AAACCTACAA
*
66170254 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
66170269 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
66170283 AAACTTCATATCCAT
1 AAACTTCATATCCAT
66170298 AAAC
1 AAAC
66170302 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:66171639 original size:30 final size:28
Alignment explanation
Indices: 66171603--66171658 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
66171593 AAGCGAAAAA
* *
66171603 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
66171633 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
66171659 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:66174906 original size:29 final size:29
Alignment explanation
Indices: 66174874--66174933 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66174864 ATAACCAAAC
*
66174874 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
66174903 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
66174932 CT
1 CT
66174934 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:66174926 original size:15 final size:15
Alignment explanation
Indices: 66174880--66174927 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66174870 AAACCTACAA
*
66174880 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
66174895 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
66174909 AAACTTCATATCCAT
1 AAACTTCATATCCAT
66174924 AAAC
1 AAAC
66174928 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:66175140 original size:29 final size:29
Alignment explanation
Indices: 66175080--66175193 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 29
66175070 GTGAGCATGA
* * * *
66175080 ATATGAATGTGA-CTGGGCCTAACGGGCT
1 ATATAAATGTGATTTGGGCCTAATGGGCC
*
66175108 ATATAAATGTGATTTGAGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
66175137 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* * *
66175166 AT-TGAATATGA-TTGGGCTTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
66175193 A
1 A
66175194 GATACAAGTA
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.22
28 16 0.22
29 40 0.56
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:66176519 original size:46 final size:47
Alignment explanation
Indices: 66176457--66176552 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 47
66176447 GAGCTGCTAG
* * *
66176457 TGCATGGATGACATTAAATGATCTGCTGAAGCATTAAAG-CAAAGCA
1 TGCATGGACGACATTAAATGAGCTGCTGAAGCATTAAAGAAAAAGCA
*
66176503 TGCATGGACGATATTAAATGAGCTGCTGAAGCATTAAAGAAAAAGCA
1 TGCATGGACGACATTAAATGAGCTGCTGAAGCATTAAAGAAAAAGCA
66176550 TGC
1 TGC
66176553 TAGGATCAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 36 0.80
47 9 0.20
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (47 bp):
TGCATGGACGACATTAAATGAGCTGCTGAAGCATTAAAGAAAAAGCA
Found at i:66178097 original size:11 final size:11
Alignment explanation
Indices: 66178081--66178105 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66178071 TGTTTGCTCG
66178081 TTTTGAATTTA
1 TTTTGAATTTA
66178092 TTTTGAATTTA
1 TTTTGAATTTA
66178103 TTT
1 TTT
66178106 CATTTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGAATTTA
Found at i:66181017 original size:21 final size:20
Alignment explanation
Indices: 66180970--66181024 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
66180960 CCCAGCTCAT
* * *
66180970 TTCCAGCTCCA-CAAGCTTC
1 TTCCAGCTCAATCCAGCTTA
66180989 TTCCAGCTCAAATCCAGCTTA
1 TTCCAGCTC-AATCCAGCTTA
*
66181010 TTCGAGCTCAATCCA
1 TTCCAGCTCAATCCA
66181025 ACTTGCCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.30
20 7 0.23
21 14 0.47
ACGTcount: A:0.25, C:0.36, G:0.11, T:0.27
Consensus pattern (20 bp):
TTCCAGCTCAATCCAGCTTA
Found at i:66182721 original size:13 final size:13
Alignment explanation
Indices: 66182703--66182759 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
66182693 TATACAAGTC
66182703 AAAAAAAATTTTG
1 AAAAAAAATTTTG
66182716 AAAAAAAAATTTT-
1 -AAAAAAAATTTTG
*
66182729 -AAAAAAA-TTCG
1 AAAAAAAATTTTG
* *
66182740 AAAAAAAAATCTG
1 AAAAAAAATTTTG
66182753 AAAAAAA
1 AAAAAAA
66182760 GTGTTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.05
11 7 0.19
12 7 0.19
13 9 0.24
14 12 0.32
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTTG
Found at i:66182722 original size:14 final size:13
Alignment explanation
Indices: 66182703--66182759 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
66182693 TATACAAGTC
*
66182703 AAAAAAAATTTTG
1 AAAAAAAAATTTG
66182716 AAAAAAAAATTT-
1 AAAAAAAAATTTG
* *
66182728 -TAAAAAAATTCG
1 AAAAAAAAATTTG
*
66182740 AAAAAAAAATCTG
1 AAAAAAAAATTTG
66182753 AAAAAAA
1 AAAAAAA
66182760 GTGTTTAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 9 0.25
13 27 0.75
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:66182732 original size:24 final size:24
Alignment explanation
Indices: 66182704--66182759 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
66182694 ATACAAGTCA
* * *
66182704 AAAAAAATTTTGAAAAAAAAATTTT
1 AAAAAAA-TTCGAAAAAAAAATCTG
66182729 AAAAAAATTCGAAAAAAAAATCTG
1 AAAAAAATTCGAAAAAAAAATCTG
66182753 AAAAAAA
1 AAAAAAA
66182760 GTGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (24 bp):
AAAAAAATTCGAAAAAAAAATCTG
Found at i:66182747 original size:12 final size:13
Alignment explanation
Indices: 66182703--66182759 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
66182693 TATACAAGTC
* *
66182703 AAAAAAAATTTTG
1 AAAAAAAAATCTG
*
66182716 AAAAAAAAAT-TT
1 AAAAAAAAATCTG
* *
66182728 TAAAAAAATTC-G
1 AAAAAAAAATCTG
66182740 AAAAAAAAATCTG
1 AAAAAAAAATCTG
66182753 AAAAAAA
1 AAAAAAA
66182760 GTGTTTAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
12 18 0.51
13 17 0.49
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAAAAAAATCTG
Found at i:66183684 original size:16 final size:15
Alignment explanation
Indices: 66183663--66183730 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
66183653 ACATTCTTGT
66183663 AAAGAAAAAACAAAGA
1 AAAGAAAAAA-AAAGA
*
66183679 AAAGAAAAGTAAAAGTA
1 AAAGAAAA-AAAAAG-A
*
66183696 AAAG-AAGAAAAAGA
1 AAAGAAAAAAAAAGA
*
66183710 AAATGAAATAAAAAGA
1 AAA-GAAAAAAAAAGA
66183726 AAAGA
1 AAAGA
66183731 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
14 4 0.09
15 8 0.18
16 26 0.59
17 6 0.14
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAGAAAAAAAAAGA
Found at i:66183694 original size:6 final size:5
Alignment explanation
Indices: 66183663--66183730 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
66183653 ACATTCTTGT
* *
66183663 AAAGA AAAAA CAAAGA AAAGA AAAGTA AAAGTA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
66183710 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
66183731 GAGGCAAGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.55
6 19 0.36
7 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (5 bp):
AAAGA
Found at i:66183802 original size:11 final size:12
Alignment explanation
Indices: 66183778--66183808 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
66183768 TTGAGAGAAC
66183778 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66183790 TTGAAAAAG-CT
1 TTGAAAAAGCCT
66183801 TTGAAAAA
1 TTGAAAAA
66183809 TAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66183842 original size:24 final size:24
Alignment explanation
Indices: 66183815--66183878 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
66183805 AAAATAAAAA
*
66183815 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
66183839 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
66183863 GAGAGAGAAAAAGAAA
1 GAAAAAGAAAAAGAAA
66183879 GTGAACAAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:66183844 original size:13 final size:12
Alignment explanation
Indices: 66183815--66183859 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
66183805 AAAATAAAAA
* *
66183815 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
66183827 GAAAATGAGATT
1 GAAAAAGAGAAT
66183839 GAAAAAGAGAAT
1 GAAAAAGAGAAT
66183851 GAAAAAGAG
1 GAAAAAGAG
66183860 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:66183891 original size:17 final size:18
Alignment explanation
Indices: 66183868--66183908 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66183858 AGTTTGAGAG
*
66183868 AGAAAAAGAAAGT-GAACA
1 AGAAAAA-AAAGTGGAAAA
66183886 AGAAAAAAAAGTGGAAAA
1 AGAAAAAAAAGTGGAAAA
66183904 AGAAA
1 AGAAA
66183909 TTGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (18 bp):
AGAAAAAAAAGTGGAAAA
Found at i:66186236 original size:30 final size:30
Alignment explanation
Indices: 66186141--66186237 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66186131 AGCTCACTCC
*
66186141 TAGCTCATA-TTCAGCTCACAAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66186171 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66186201 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66186231 TAGCTCA
1 TAGCTCA
66186238 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66187223 original size:30 final size:30
Alignment explanation
Indices: 66187189--66187285 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
66187179 AGCTCACTCC
66187189 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66187219 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66187249 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66187279 TAGCTCA
1 TAGCTCA
66187286 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66189012 original size:17 final size:16
Alignment explanation
Indices: 66188989--66189026 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
66188979 AAAAAAATTC
*
66188989 AAAAAAATATTCGAAA
1 AAAAAAAAATTCGAAA
66189005 AGAAAAAAAATTCGAAA
1 A-AAAAAAAATTCGAAA
66189022 AAAAA
1 AAAAA
66189027 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATTCGAAA
Found at i:66189026 original size:12 final size:11
Alignment explanation
Indices: 66188968--66189010 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
66188958 AATATAGTAC
66188968 AAAAAAATTCA
1 AAAAAAATTCA
66188979 AAAAAAATTCA
1 AAAAAAATTCA
66188990 AAAAAATATTCGA
1 AAAAAA-ATTC-A
66189003 AAAGAAAA
1 AAA-AAAA
66189011 AAAATTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 5 0.17
14 3 0.10
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:66189946 original size:9 final size:10
Alignment explanation
Indices: 66189939--66189995 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66189929 AAGAGAAAAC
66189939 AAAGAAAAGA
1 AAAGAAAAGA
66189949 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
66189961 AAAGAAGA-A
1 AAAGAAAAGA
66189970 AAAGAAAATGA
1 AAAGAAAA-GA
66189981 AATA-AAAAGA
1 AA-AGAAAAGA
66189991 AAAGA
1 AAAGA
66189996 GAGGCAAGAG
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:66189962 original size:21 final size:20
Alignment explanation
Indices: 66189928--66189995 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
66189918 ACATTCTTGT
66189928 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66189949 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
66189970 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66189991 AAAGA
1 AAAGA
66189996 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66189963 original size:6 final size:5
Alignment explanation
Indices: 66189939--66189995 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66189929 AAGAGAAAAC
*
66189939 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
66189986 AAAGA AAAGA
1 AAAGA AAAGA
66189996 GAGGCAAGAG
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:66189970 original size:15 final size:14
Alignment explanation
Indices: 66189939--66189995 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66189929 AAGAGAAAAC
66189939 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66189955 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66189970 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
66189986 AAAGAAAAGA
1 AAAGAAAAGA
66189996 GAGGCAAGAG
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:66190098 original size:30 final size:31
Alignment explanation
Indices: 66190064--66190145 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
66190054 TTTGAAAAGC
*
66190064 AAAAAGAAAATGAAAAAGAAA-ATAAGATTG
1 AAAAAGAAAATGAAAAAGAAATATAAGAGTG
* * * *
66190094 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATAAGAGTG
*
66190124 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
66190146 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATAAGAGTG
Found at i:66193984 original size:30 final size:30
Alignment explanation
Indices: 66193950--66194046 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
66193940 AGCTCACTCC
66193950 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
66193980 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
66194010 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
66194040 TAGCTCA
1 TAGCTCA
66194047 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:66197071 original size:30 final size:31
Alignment explanation
Indices: 66197037--66197133 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
66197027 AGCTCACTCC
*
66197037 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
66197067 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
66197097 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
66197127 TAGCTCA
1 TAGCTCA
66197134 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:66201514 original size:30 final size:30
Alignment explanation
Indices: 66201480--66201576 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66201470 TAAACTAAAA
*
66201480 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
66201510 TGAGCTGAGGTTAAACTCCTAAGCTGAATT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
66201540 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAGT
66201570 TGAGCTA
1 TGAGCTA
66201577 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 48 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:66201618 original size:20 final size:21
Alignment explanation
Indices: 66201593--66201637 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
66201583 AGCTCGGTTT
*
66201593 AGCTCAGACAAGATGGA-TTG
1 AGCTCAAACAAGATGGATTTG
* *
66201613 AGCTCAAATAAGCTGGATTTG
1 AGCTCAAACAAGATGGATTTG
66201634 AGCT
1 AGCT
66201638 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
AGCTCAAACAAGATGGATTTG
Found at i:66202037 original size:20 final size:21
Alignment explanation
Indices: 66201988--66202030 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
66201978 GAATGAGCTG
66201988 AAACGAGCTAAATTCGAACTC
1 AAACGAGCTAAATTCGAACTC
*
66202009 AAACGAGCTAAATT-GAGCTC
1 AAACGAGCTAAATTCGAACTC
66202029 AA
1 AA
66202031 GTGAGCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (21 bp):
AAACGAGCTAAATTCGAACTC
Found at i:66206474 original size:24 final size:24
Alignment explanation
Indices: 66206447--66206492 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
66206437 ACACTTTTTC
* *
66206447 CTTTCTTTTTTTCATTTTTCTTGA
1 CTTTCTATTTTTCAATTTTCTTGA
66206471 CTTTCTATTTTTCAATTTTCTT
1 CTTTCTATTTTTCAATTTTCTT
66206493 TTTCTTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (24 bp):
CTTTCTATTTTTCAATTTTCTTGA
Found at i:66206497 original size:30 final size:30
Alignment explanation
Indices: 66206455--66206517 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
66206445 TCCTTTCTTT
*
66206455 TTTTCATTTTTCTTG-ACTTTCTATTTTTCAA
1 TTTTCATTTTTCTTGTACTTT-T-TCTTTCAA
66206486 TTTTC-TTTTTCTTGTACTTTTTCTTTCAA
1 TTTTCATTTTTCTTGTACTTTTTCTTTCAA
66206515 TTT
1 TTT
66206518 AGTTGATCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 10 0.33
30 10 0.33
31 10 0.33
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (30 bp):
TTTTCATTTTTCTTGTACTTTTTCTTTCAA
Found at i:66210915 original size:20 final size:20
Alignment explanation
Indices: 66210869--66210916 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
66210859 AATAAGCTCG
66210869 GTTGAGCTCAAACGACCTGA
1 GTTGAGCTCAAACGACCTGA
*** * *
66210889 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGACCTGA
66210909 GTTGAGCT
1 GTTGAGCT
66210917 AGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGACCTGA
Found at i:66212798 original size:21 final size:19
Alignment explanation
Indices: 66212760--66212828 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 19
66212750 TGCTCAAATT
66212760 TTTTTC-TTTTTCAATTTC
1 TTTTTCTTTTTTCAATTTC
*
66212778 GTTTTTCTTTTTCTCACTTTC
1 -TTTTTCTTTTT-TCAATTTC
*
66212799 TTTTTGCTTTCTTTCACA-CTC
1 TTTTT-CTTT-TTTCA-ATTTC
66212820 TTTTTCTTT
1 TTTTTCTTT
66212829 CATTTCTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 6 0.14
20 13 0.31
21 21 0.50
22 2 0.05
ACGTcount: A:0.07, C:0.22, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTCTTTTTTCAATTTC
Found at i:66212829 original size:20 final size:20
Alignment explanation
Indices: 66212779--66212834 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
66212769 TTCAATTTCG
**
66212779 TTTTTCTTT-TTCTCACTTTC
1 TTTTTCTTTCTT-TCACACTC
66212799 TTTTTGCTTTCTTTCACACTC
1 TTTTT-CTTTCTTTCACACTC
66212820 TTTTTCTTTCATTTC
1 TTTTTCTTTC-TTTC
66212835 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
21 19 0.61
22 2 0.06
ACGTcount: A:0.07, C:0.25, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTCTTTCTTTCACACTC
Found at i:66215347 original size:9 final size:10
Alignment explanation
Indices: 66215327--66215360 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
66215317 AAGCTCGGTT
66215327 GAGCTCAAAC
1 GAGCTCAAAC
66215337 GAGCT-AAAC
1 GAGCTCAAAC
*
66215346 GAGCTCAAAT
1 GAGCTCAAAC
66215356 GAGCT
1 GAGCT
66215361 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (10 bp):
GAGCTCAAAC
Done.