Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 15 of 125
Found at i:4842122 original size:32 final size:31
Alignment explanation
Indices: 4842046--4842127 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
4842036 TTGCTAAATA
4842046 TCTTCCTTGAAATTAATGCTTTTTGCCTAAT
1 TCTTCCTTGAAATTAATGCTTTTTGCCTAAT
*
4842077 TCCTCCTTGAAATTAATGCTTTTTGCCTAATT
1 TCTTCCTTGAAATTAATGCTTTTTGCCTAA-T
*
4842109 TCTTCCTTAAAATTAATGC
1 TCTTCCTTGAAATTAATGC
4842128 CTTTATGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 29 0.62
32 18 0.38
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (31 bp):
TCTTCCTTGAAATTAATGCTTTTTGCCTAAT
Found at i:4847481 original size:16 final size:16
Alignment explanation
Indices: 4847460--4847495 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4847450 TAAAAGATTT
4847460 TCTAGCATTTATAAAA
1 TCTAGCATTTATAAAA
*
4847476 TCTAGCTTTTATAAAA
1 TCTAGCATTTATAAAA
4847492 TCTA
1 TCTA
4847496 TGATAATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (16 bp):
TCTAGCATTTATAAAA
Found at i:4849438 original size:3 final size:3
Alignment explanation
Indices: 4849430--4849460 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4849420 ACCTCCCATT
4849430 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4849461 CTAACAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4851185 original size:42 final size:42
Alignment explanation
Indices: 4851114--4851216 Score: 143
Period size: 42 Copynumber: 2.5 Consensus size: 42
4851104 AGGGAGTTGA
* * *
4851114 TCAGTTGCCAGGGTTGAATGAGTCTCCTGAATATGGAGATGC
1 TCAGTTCCCAGGGTTGAATGAGTCCCCTGAACATGGAGATGC
* * *
4851156 TGAGTTCCCAGGGTTGAATGAGTCCCCTGACCATGGAGTTGC
1 TCAGTTCCCAGGGTTGAATGAGTCCCCTGAACATGGAGATGC
*
4851198 TCAGTTCCCATGGTTGAAT
1 TCAGTTCCCAGGGTTGAAT
4851217 CAGATTCATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (42 bp):
TCAGTTCCCAGGGTTGAATGAGTCCCCTGAACATGGAGATGC
Found at i:4856032 original size:18 final size:19
Alignment explanation
Indices: 4856009--4856045 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4855999 ATGATGATCT
*
4856009 AATTTAATT-TTTACTTTA
1 AATTTAATTATTTAATTTA
4856027 AATTTAATTATTTAATTTA
1 AATTTAATTATTTAATTTA
4856046 GTCATCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTAATTATTTAATTTA
Found at i:4867085 original size:23 final size:22
Alignment explanation
Indices: 4867059--4867108 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
4867049 TCCATGATAC
4867059 TTTTA-TAGTTACTTTTATATTAA
1 TTTTACTAGTTACTTTT-TATT-A
**
4867082 TTTTACTTTTTACTTTTTATTA
1 TTTTACTAGTTACTTTTTATTA
4867104 TTTTA
1 TTTTA
4867109 GTTAAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 9 0.38
24 9 0.38
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTACTAGTTACTTTTTATTA
Found at i:4878033 original size:12 final size:12
Alignment explanation
Indices: 4878016--4878049 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4878006 AAATACAGCA
4878016 ATTATAATTAAT
1 ATTATAATTAAT
*
4878028 ATTATAATAAAT
1 ATTATAATTAAT
4878040 ATTAATAATT
1 ATT-ATAATT
4878050 TATTCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTATAATTAAT
Found at i:4888772 original size:37 final size:37
Alignment explanation
Indices: 4888730--4888811 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
4888720 TACAACAAAT
* *
4888730 TTAAAAAATA-AATAATATATAAATATACTTAAAA-ACA
1 TTAAAAAA-ACAATAA-AAATAAATAAACTTAAAATACA
* *
4888767 TTAAAACAAACATTAAAAATAAATAAATTTAAAATACA
1 TTAAAA-AAACAATAAAAATAAATAAACTTAAAATACA
4888805 TTAAAAA
1 TTAAAAA
4888812 TTATTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
37 23 0.61
38 15 0.39
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (37 bp):
TTAAAAAAACAATAAAAATAAATAAACTTAAAATACA
Found at i:4888950 original size:20 final size:20
Alignment explanation
Indices: 4888925--4888962 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4888915 GTAAAAATGC
* *
4888925 ATAAAAATAACATCCAAATA
1 ATAAAAACAACAACCAAATA
4888945 ATAAAAACAACAACCAAA
1 ATAAAAACAACAACCAAA
4888963 ATAACGGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.13
Consensus pattern (20 bp):
ATAAAAACAACAACCAAATA
Found at i:4889016 original size:19 final size:18
Alignment explanation
Indices: 4889002--4889037 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4888992 AAAAAATAAC
4889002 ACCA-AAACAGTAAAAAA
1 ACCAGAAACAGTAAAAAA
*
4889019 ACCAGAAAGAGTAAAAAA
1 ACCAGAAACAGTAAAAAA
4889037 A
1 A
4889038 AATAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.69, C:0.14, G:0.11, T:0.06
Consensus pattern (18 bp):
ACCAGAAACAGTAAAAAA
Found at i:4889016 original size:21 final size:22
Alignment explanation
Indices: 4888971--4889019 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4888961 AAATAACGGC
4888971 AAAAATAACAACAAAACAGCAA
1 AAAAATAACAACAAAACAGCAA
* *
4888993 AAAAATAACACCAAAACAGTAA
1 AAAAATAACAACAAAACAGCAA
4889015 AAAAA
1 AAAAA
4889020 CCAGAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.73, C:0.16, G:0.04, T:0.06
Consensus pattern (22 bp):
AAAAATAACAACAAAACAGCAA
Found at i:4891629 original size:2 final size:2
Alignment explanation
Indices: 4891622--4891657 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4891612 TTTTCTTTCT
4891622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4891658 ACATTCATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4893819 original size:20 final size:20
Alignment explanation
Indices: 4893794--4893832 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4893784 TATGAAATTT
4893794 ATTGAT-AATTATTTTATATA
1 ATTGATGAA-TATTTTATATA
4893814 ATTGATGAATATTTTATAT
1 ATTGATGAATATTTTATAT
4893833 TTTAAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTGATGAATATTTTATATA
Found at i:4896382 original size:20 final size:19
Alignment explanation
Indices: 4896342--4896382 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
4896332 AAAGAAAACC
4896342 TAAAATATTTTTTTATGAA
1 TAAAATATTTTTTTATGAA
4896361 TAAATATATTATTTTTAT-AA
1 TAAA-ATATT-TTTTTATGAA
4896381 TA
1 TA
4896383 TATAGCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAAAATATTTTTTTATGAA
Found at i:4898585 original size:24 final size:24
Alignment explanation
Indices: 4898540--4898585 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4898530 TTGAAAGTAA
* *
4898540 ACTTCATTTATCTATTAAATGTTT
1 ACTTCATTTATCAAATAAATGTTT
4898564 ACTTCATTT-TCAAATAAGATGT
1 ACTTCATTTATCAAATAA-ATGT
4898586 ACATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (24 bp):
ACTTCATTTATCAAATAAATGTTT
Found at i:4899085 original size:28 final size:28
Alignment explanation
Indices: 4899054--4899128 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
4899044 GGATTTAGGG
*
4899054 ATTAAAT-TCAGAAAAAAGACATTAAAAC
1 ATTAAATGTAAGAAAAAAG-CATTAAAAC
* * *
4899082 ATTAAATGTAAGAAAAATGTATTAAAGC
1 ATTAAATGTAAGAAAAAAGCATTAAAAC
*
4899110 ATTAAATGTATGAAAAAAG
1 ATTAAATGTAAGAAAAAAG
4899129 GTTATTGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 31 0.77
29 9 0.22
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (28 bp):
ATTAAATGTAAGAAAAAAGCATTAAAAC
Found at i:4899752 original size:23 final size:25
Alignment explanation
Indices: 4899726--4899771 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4899716 CCAATTAAGG
4899726 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
4899749 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
4899772 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:4902026 original size:30 final size:31
Alignment explanation
Indices: 4901951--4902026 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
4901941 TGAAAGGGAT
* *
4901951 CCAAAATGTTATTTTTTAATTGTTAAGGGAC
1 CCAAAATGTTTTTTTTTAATTGTTAAGAGAC
** * * *
4901982 CCAAAAAATATTTTTTTAGTTTTTAAGAG-C
1 CCAAAATGTTTTTTTTTAATTGTTAAGAGAC
4902012 CCAAAATGTTTTTTT
1 CCAAAATGTTTTTTT
4902027 ACAACTTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (31 bp):
CCAAAATGTTTTTTTTTAATTGTTAAGAGAC
Found at i:4902074 original size:30 final size:30
Alignment explanation
Indices: 4902015--4902077 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
4902005 TAAGAGCCCA
*
4902015 AAATGTTTTTTTACAACTTTTAAGGAACCT
1 AAATGTTTTTTTACAACTTTTAAAGAACCT
* * *
4902045 AAATTTTTTTTTCCAACTTTTAAATAACCT
1 AAATGTTTTTTTACAACTTTTAAAGAACCT
4902075 AAA
1 AAA
4902078 ACCTCTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATGTTTTTTTACAACTTTTAAAGAACCT
Found at i:4904571 original size:42 final size:43
Alignment explanation
Indices: 4904499--4904579 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
4904489 AAACTTGCAC
4904499 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
1 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
* *
4904542 GAGATAAATATTTAATGTG-GCTACAATCAAATCAATAT
1 GAGAAAAATATTTAATATGAGCTACAATCAAATCAATAT
4904580 TTGTATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 19 0.53
43 17 0.47
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (43 bp):
GAGAAAAATATTTAATATGAGCTACAATCAAATCAATATAATA
Found at i:4906804 original size:9 final size:8
Alignment explanation
Indices: 4906786--4906824 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
4906776 TTTAATAAAA
4906786 TTTTTATT
1 TTTTTATT
4906794 TTTTTATT
1 TTTTTATT
4906802 TTTTTATTT
1 TTTTTA-TT
4906811 TTTTTATT
1 TTTTTATT
*
4906819 TGTTTA
1 TTTTTA
4906825 ATTATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:4906812 original size:17 final size:16
Alignment explanation
Indices: 4906786--4906824 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
4906776 TTTAATAAAA
4906786 TTTTTATTTTTTTATT
1 TTTTTATTTTTTTATT
4906802 TTTTTATTTTTTTTATT
1 TTTTTA-TTTTTTTATT
*
4906819 TGTTTA
1 TTTTTA
4906825 ATTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTATTTTTTTATT
Found at i:4907054 original size:31 final size:31
Alignment explanation
Indices: 4907013--4907087 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
4907003 TGAACTTTTA
* **
4907013 TAATTTTCAAGTTCAAGAA-CTAAAATGAATT
1 TAATTGTCAAGTTCAAGAATC-AAAATGAACC
*
4907044 TAATTGTCAAGTTCAAGTATCAAAATGAACC
1 TAATTGTCAAGTTCAAGAATCAAAATGAACC
*
4907075 TAGTTGTCAAGTT
1 TAATTGTCAAGTT
4907088 TCGAGGTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (31 bp):
TAATTGTCAAGTTCAAGAATCAAAATGAACC
Found at i:4907565 original size:6 final size:6
Alignment explanation
Indices: 4907554--4907593 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
4907544 TGAAAATAAA
4907554 TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGG
1 TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGGAT TTGG
4907594 CTGTCTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TTGGAT
Found at i:4910137 original size:11 final size:11
Alignment explanation
Indices: 4910123--4910187 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
4910113 ATATCCAAAT
4910123 AATAACAACAA
1 AATAACAACAA
*
4910134 AATAATAA-AA
1 AATAACAACAA
*
4910144 ATATAACAGCAA
1 A-ATAACAACAA
* *
4910156 AATTACAGCAA
1 AATAACAACAA
**
4910167 AGCAACAACAA
1 AATAACAACAA
*
4910178 AACAACAACA
1 AATAACAACA
4910188 GTGGAAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
10 3 0.07
11 37 0.86
12 3 0.07
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (11 bp):
AATAACAACAA
Found at i:4910613 original size:20 final size:19
Alignment explanation
Indices: 4910588--4910661 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 19
4910578 TCAACAAAAA
4910588 TCAAAGTATCGATACTCTTG
1 TCAAAGTATCGATACT-TTG
* *
4910608 TCAAAGTA-CTGATATTTTCC
1 TCAAAGTATC-GATACTTT-G
4910628 TCAAAGTATCGATACTTTG
1 TCAAAGTATCGATACTTTG
4910647 T-ATAAGGTATCGATA
1 TCA-AA-GTATCGATA
4910662 TCATTTCAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 37 0.82
21 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (19 bp):
TCAAAGTATCGATACTTTG
Found at i:4911846 original size:16 final size:16
Alignment explanation
Indices: 4911827--4911873 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4911817 AAATTTTAAT
4911827 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
4911843 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
4911859 AAATAATAAAATATA
1 AAATAA-AAAATATA
4911874 AATATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:4914039 original size:29 final size:30
Alignment explanation
Indices: 4913986--4914051 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
4913976 ATGTAAAAAT
4913986 AATTAAAATTTTTAATTTTCAAAAT-AATTC
1 AATTAAAATTTTTAATTTT-AAAATAAATTC
* *
4914016 AATTAAATTTTTTATATTTT-AAATAAATTT
1 AATTAAAATTTTTA-ATTTTAAAATAAATTC
4914046 AATTAA
1 AATTAA
4914052 GTAATTCAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 23 0.72
31 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTAAAATTTTTAATTTTAAAATAAATTC
Found at i:4914674 original size:2 final size:2
Alignment explanation
Indices: 4914667--4914698 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4914657 TTTAGGGTTA
4914667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4914699 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4915298 original size:62 final size:62
Alignment explanation
Indices: 4915170--4915300 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
4915160 ATCCTAAATA
* ** * *
4915170 TAAAAAATTCAACAAACTTAGCCCTCAATGTTTACAAAATTTGTCATTTTTAGTTTGAATTC
1 TAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCATTTTTAATTTGAATCC
* * *
4915232 -AAAAATAATCAATAAATTTAGCCCTCAACATTTACAAAATTTTTCA-TTTTAATTTGAATCC
1 TAAAAA-AATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCATTTTTAATTTGAATCC
4915293 TAAAAAAA
1 TAAAAAAA
4915301 ATTAATTCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
61 20 0.34
62 39 0.66
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (62 bp):
TAAAAAAATCAACAAACTTAGCCCTCAACATTTACAAAATTTGTCATTTTTAATTTGAATCC
Found at i:4915396 original size:51 final size:51
Alignment explanation
Indices: 4915321--4915417 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
4915311 AAAATTAATT
**
4915321 ATTTATTTAGAATTCAAATCAAAATGACAATTTTTGTAAACATTGATGGTA
1 ATTTATTTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGATGGTA
* *
4915372 ATTTTTTTAGAATTCAAATTAAAATGACAAAATTTGTAAACATTGA
1 ATTTATTTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGA
4915418 GGGCTAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.39
Consensus pattern (51 bp):
ATTTATTTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGATGGTA
Found at i:4915436 original size:51 final size:51
Alignment explanation
Indices: 4915327--4915436 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
4915317 AATTATTTAT
** * * *
4915327 TTAGAATTCAAATCAAAATGACAATTTTTGTAAACATTGATGGTAATTTTT
1 TTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGAGGGTAAATTTG
*
4915378 TTAGAATTCAAATTAAAATGACAAAATTTGTAAACATTGAGGGCTAAATTTG
1 TTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGAGGG-TAAATTTG
4915430 TT-GAATT
1 TTAGAATT
4915437 TTTTATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 44 0.85
52 8 0.15
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (51 bp):
TTAGAATTCAAATCAAAATGACAAAATTTGTAAACATTGAGGGTAAATTTG
Found at i:4920748 original size:16 final size:18
Alignment explanation
Indices: 4920709--4920742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4920699 TAAGTTTATA
4920709 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
4920726 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
4920743 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:4921056 original size:16 final size:16
Alignment explanation
Indices: 4921009--4921060 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
4920999 TGGTTCGCTG
* *
4921009 TAATAGAATAGAGTTG
1 TAATGGAATAGAGTTA
*
4921025 TAATGGAATAAAGTTA
1 TAATGGAATAGAGTTA
*
4921041 TAATGGAATAGGGTTA
1 TAATGGAATAGAGTTA
4921057 TAAT
1 TAAT
4921061 CAATAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGTTA
Found at i:4921294 original size:58 final size:58
Alignment explanation
Indices: 4921232--4921356 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 58
4921222 TTTTAATAAG
* * * *
4921232 ATTATTATTAAATATAATTTACTAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAACATTTTTAACATA
* *
4921290 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
4921348 ATTATTATT
1 ATTATTATT
4921357 GTTATTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 21 0.35
58 39 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.46
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:4923030 original size:51 final size:51
Alignment explanation
Indices: 4922964--4923137 Score: 287
Period size: 51 Copynumber: 3.4 Consensus size: 51
4922954 AAGGGTCTGG
* * *
4922964 TGACTAAATGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTCGA
1 TGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGA
*
4923015 TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAATA-GTCCGA
1 TGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAA-AGGTCCGA
*
4923066 TGACTAAGTGCCATCATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGA
1 TGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGA
4923117 TGACTAAGTGTCATCATGAGT
1 TGACTAAGTGTCATCATGAGT
4923138 TTATAGATTC
Statistics
Matches: 116, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
50 1 0.01
51 114 0.98
52 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (51 bp):
TGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAAGGTCCGA
Found at i:4925304 original size:30 final size:30
Alignment explanation
Indices: 4925270--4925334 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
4925260 ACTTATTTTA
* *
4925270 TTGTTAATTTTGTTATTATTATAAAGGTAT
1 TTGTTAATTTTGTTACTATTATAAAGGCAT
* *
4925300 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTATAAAGGCAT
4925330 TTGTT
1 TTGTT
4925335 TGTTAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTATAAAGGCAT
Found at i:4927040 original size:27 final size:27
Alignment explanation
Indices: 4927010--4927102 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 27
4927000 AATTTTAAAT
*
4927010 AAATAATAAAATTGTACTTTAATCTAA
1 AAATAATAAAATTGTAATTTAATCTAA
*
4927037 AAATAATAAAATTTTAATTTAATCTTTTAA
1 AAATAATAAAATTGTAATTTAATC---TAA
* * *
4927067 AAAT-ATAAAAATATAAATT-AT-T-A
1 AAATAATAAAATTGTAATTTAATCTAA
4927090 AAATAATAAAATT
1 AAATAATAAAATT
4927103 ATATTTTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.09
24 8 0.14
27 22 0.39
28 2 0.04
29 12 0.21
30 7 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (27 bp):
AAATAATAAAATTGTAATTTAATCTAA
Found at i:4927133 original size:25 final size:25
Alignment explanation
Indices: 4927056--4927133 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 25
4927046 AATTTTAATT
4927056 TAATCTTTTAAAA-ATATAAAAATATA
1 TAAT-TTTTAAAATA-ATAAAAATATA
*
4927082 -AATTATTAAAATAAT-AAAAT-TA
1 TAATTTTTAAAATAATAAAAATATA
**
4927104 T-ATTTTTATTATAATAAAAATATA
1 TAATTTTTAAAATAATAAAAATATA
4927128 TAATTT
1 TAATTT
4927134 AATTTTGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
22 13 0.30
23 10 0.23
24 12 0.28
25 8 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATTTTTAAAATAATAAAAATATA
Found at i:4930135 original size:14 final size:15
Alignment explanation
Indices: 4930111--4930141 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4930101 AATAATGTTT
4930111 TCTCTAAATCTTGAA
1 TCTCTAAATCTTGAA
4930126 TCTC-AAATCTTGAA
1 TCTCTAAATCTTGAA
4930140 TC
1 TC
4930142 CCGAAGCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (15 bp):
TCTCTAAATCTTGAA
Found at i:4930293 original size:11 final size:11
Alignment explanation
Indices: 4930274--4930305 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4930264 ATCAATAATA
*
4930274 TAAAAAATTAT
1 TAAATAATTAT
4930285 TAAATAATTAT
1 TAAATAATTAT
4930296 TAAATAATTA
1 TAAATAATTA
4930306 AAAATAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:4932061 original size:25 final size:25
Alignment explanation
Indices: 4932015--4932063 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4932005 TTTTAAATAT
* **
4932015 ATATGTTCATTCATACGTAAATTAG
1 ATATGTTAATTCATACAAAAATTAG
4932040 ATATGTTAATTCATACAAAAATTA
1 ATATGTTAATTCATACAAAAATTA
4932064 AAATATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (25 bp):
ATATGTTAATTCATACAAAAATTAG
Found at i:4947927 original size:27 final size:25
Alignment explanation
Indices: 4947875--4947923 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
4947865 ATTGAGATTT
*
4947875 AGATTTTGAGGACTCGAAAGAGGTA
1 AGATTTTGAGAACTCGAAAGAGGTA
*
4947900 AGATATTTGAGAACTCGGAAGAGG
1 AGAT-TTTGAGAACTCGAAAGAGG
4947924 GTAATGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.37, C:0.08, G:0.33, T:0.22
Consensus pattern (25 bp):
AGATTTTGAGAACTCGAAAGAGGTA
Found at i:4956433 original size:20 final size:20
Alignment explanation
Indices: 4956408--4956449 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4956398 ATTTTGCTTG
4956408 TAGGTCTCTTGTTATGAAAT
1 TAGGTCTCTTGTTATGAAAT
4956428 TAGGTCTCTTGTTATGAAAT
1 TAGGTCTCTTGTTATGAAAT
4956448 TA
1 TA
4956450 TTTTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (20 bp):
TAGGTCTCTTGTTATGAAAT
Found at i:4967569 original size:6 final size:6
Alignment explanation
Indices: 4967560--4967587 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4967550 CATGTCTTCG
4967560 CTCCCT CTCCCT CTCCCT CTCCCT CTCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCC
4967588 TTGTCTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCCCT
Found at i:4970963 original size:41 final size:42
Alignment explanation
Indices: 4970918--4971011 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
4970908 TATAATTAAA
*
4970918 AAAATATATTTT-TATTTAATTTA-GAG-TTTTTTTAAGAAGAG
1 AAAATATATTTTGGA-TTAATTTATGAGTTTTTTTTAAGAAG-G
*
4970959 AAAAT-TAATTTTGGATTAGTTTATGAGTTTTTTTTAAGAAGG
1 AAAATAT-ATTTTGGATTAATTTATGAGTTTTTTTTAAGAAGG
*
4971001 AAATTATATTT
1 AAAATATATTT
4971012 GGGTAAGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
40 1 0.02
41 17 0.38
42 13 0.29
43 14 0.31
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (42 bp):
AAAATATATTTTGGATTAATTTATGAGTTTTTTTTAAGAAGG
Found at i:4971238 original size:24 final size:24
Alignment explanation
Indices: 4971211--4971266 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
4971201 CATTCGAGTT
*
4971211 ATTCGAATTCGAAAATT-TAACTCG
1 ATTCGAATTCG-AAATTCGAACTCG
* *
4971235 ATTCGAACTCGAAATTCGAACTTG
1 ATTCGAATTCGAAATTCGAACTCG
4971259 ATTCGAAT
1 ATTCGAAT
4971267 AATTCAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (24 bp):
ATTCGAATTCGAAATTCGAACTCG
Found at i:4974380 original size:17 final size:17
Alignment explanation
Indices: 4974358--4974419 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
4974348 ATAATCACTT
4974358 TAATATTAAATTAAATA
1 TAATATTAAATTAAATA
* *
4974375 TAATATT-TATCAAGATA
1 TAATATTAAATTAA-ATA
* *
4974392 T-ATATTAGATTAAATT
1 TAATATTAAATTAAATA
4974408 TAATATTAAATT
1 TAATATTAAATT
4974420 TTATTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 12 0.33
17 24 0.67
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (17 bp):
TAATATTAAATTAAATA
Found at i:4982179 original size:20 final size:19
Alignment explanation
Indices: 4982140--4982209 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 19
4982130 AATATAAATA
4982140 TAATTTTTAT-TATTTATC
1 TAATTTTTATATATTTATC
4982158 TAAATTTTTATATATATT-TC
1 T-AATTTTTATATAT-TTATC
*
4982178 T-ATTTTTATA-ATTT-TT
1 TAATTTTTATATATTTATC
**
4982194 TAAGGTTTATATATTT
1 TAATTTTTATATATTT
4982210 TATAAGAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.09
17 9 0.20
18 14 0.32
19 9 0.20
20 6 0.14
21 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TAATTTTTATATATTTATC
Found at i:4982202 original size:17 final size:18
Alignment explanation
Indices: 4982182--4982215 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4982172 TATTTCTATT
*
4982182 TTTATA-ATTTTTTAAGG
1 TTTATATATTTTATAAGG
4982199 TTTATATATTTTATAAG
1 TTTATATATTTTATAAG
4982216 AGAATGCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (18 bp):
TTTATATATTTTATAAGG
Found at i:4983452 original size:18 final size:19
Alignment explanation
Indices: 4983407--4983453 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
4983397 ATTATGAATT
* *
4983407 TTTTTAAATATTTATTTTA
1 TTTTTATATATTTATTATA
* *
4983426 ATTTAATAT-TTTATTATA
1 TTTTTATATATTTATTATA
4983444 TTTTTATATA
1 TTTTTATATA
4983454 ATACTTGTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATATATTTATTATA
Found at i:4984481 original size:6 final size:6
Alignment explanation
Indices: 4984453--4984531 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
4984443 CCCAATGAGA
* * * ** *
4984453 TAAATT TAGATT T-ATTT TGAATT TAAATT TGCA-T AAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
4984499 T--ATT ATAAATT TAAATT TAAAAT TAAA-T TAAAT
1 TAAATT -TAAATT TAAATT TAAATT TAAATT TAAAT
4984532 GTCCATTTAC
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 3 0.05
5 11 0.20
6 38 0.69
7 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:4984492 original size:17 final size:17
Alignment explanation
Indices: 4984452--4984517 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
4984442 GCCCAATGAG
*
4984452 ATAAATTTAGATTTATT
1 ATAAATTTAAATTTATT
* *
4984469 TTGAATTTAAATTTGCA-T
1 ATAAATTTAAATTT--ATT
4984487 A-AAATTTAAATTTATT
1 ATAAATTTAAATTTATT
4984503 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
4984518 AAATTAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 2 0.05
17 35 0.88
18 1 0.03
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:4985219 original size:3 final size:3
Alignment explanation
Indices: 4985213--4985268 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
4985203 GATGATGATG
4985213 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4985261 ATA ATA AT
1 ATA ATA AT
4985269 GAAGTTATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4986420 original size:59 final size:58
Alignment explanation
Indices: 4986374--4986691 Score: 365
Period size: 59 Copynumber: 5.4 Consensus size: 58
4986364 CCCCAAAACA
* *
4986374 TTCA-AAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACTCCGAT
1 TTCACAAAAATTACCATTTTACCC-CAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
* *
4986431 TTCACCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGAT
1 TTCA-CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
* **
4986490 TTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTGACCCTTAT
1 TTCA-CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
* * *
4986548 TTCACCAAAAATTACCATTTTACCCCAAAACTTTCTAAAATTCTATTTTTGACCTCGAT
1 TTCA-CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
* * * *** * * * *
4986607 TTCACCAAAAATTATCGTTTCACCCTTGAACTTTCCGAAATTCTATTTTTAACCCTGAT
1 TTCA-CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
4986666 TTCACCAAAAATTA-CATTTTTACCCC
1 TTCA-CAAAAATTACCA-TTTTACCCC
4986692 TGGAAGTCAA
Statistics
Matches: 231, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
57 4 0.02
58 54 0.23
59 173 0.75
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (58 bp):
TTCACAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCGAT
Found at i:4986421 original size:29 final size:29
Alignment explanation
Indices: 4986379--4986589 Score: 133
Period size: 29 Copynumber: 7.2 Consensus size: 29
4986369 AAACATTCAA
4986379 AAAATTACCATTTTACCCTCAAACTTTCC
1 AAAATTACCATTTTACCCTCAAACTTTCC
* **
4986408 AAAATT-CCATTTTTA-ACTCCGA-TTTCACC
1 AAAATTACCA-TTTTACCCTCAAACTTT--CC
4986437 AAAAATTACCATTTTACCC-CTAAACTTTCC
1 -AAAATTACCATTTTACCCTC-AAACTTTCC
*
4986467 AAAATT-CCATTTTTAACCC-C-GA-TTTCACC
1 AAAATTACCA-TTTT-ACCCTCAAACTTT--CC
*
4986496 AAAAATTACCATTTTACCCCCAAACTTTCC
1 -AAAATTACCATTTTACCCTCAAACTTTCC
*
4986526 AAAATT-CCATTTTGACCCT--TA-TTTCACC
1 AAAATTACCATTTT-ACCCTCAAACTTT--CC
*
4986554 AAAAATTACCATTTTACCC-CAAAACTTTCT
1 -AAAATTACCATTTTACCCTC-AAACTTTCC
4986584 AAAATT
1 AAAATT
4986590 CTATTTTTGA
Statistics
Matches: 144, Mismatches: 12, Indels: 52
0.69 0.06 0.25
Matches are distributed among these distances:
26 3 0.02
27 7 0.05
28 20 0.14
29 55 0.38
30 40 0.28
31 10 0.07
32 9 0.06
ACGTcount: A:0.35, C:0.29, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCAAACTTTCC
Found at i:4986452 original size:30 final size:30
Alignment explanation
Indices: 4986378--4986576 Score: 131
Period size: 30 Copynumber: 6.8 Consensus size: 30
4986368 AAAACATTCA
4986378 AAAAATTACCATTTT-ACCCTCAAACTTT--CC
1 AAAAATT-CCATTTTAACCC-CAAA-TTTCACC
* *
4986408 -AAAATTCCATTTTTAACTCC-GATTTCACC
1 AAAAATTCCA-TTTTAACCCCAAATTTCACC
4986437 AAAAATTACCATTTT-ACCCCTAAACTTT--CC
1 AAAAATT-CCATTTTAACCCC-AAA-TTTCACC
*
4986467 -AAAATTCCATTTTTAACCCC-GATTTCACC
1 AAAAATTCCA-TTTTAACCCCAAATTTCACC
*
4986496 AAAAATTACCATTTTACCCCCAAACTTT--CC
1 AAAAATT-CCATTTTAACCCCAAA-TTTCACC
* **
4986526 -AAAATTCCATTTTGA-CCCTTATTTCACC
1 AAAAATTCCATTTTAACCCCAAATTTCACC
4986554 AAAAATTACCATTTT-ACCCCAAA
1 AAAAATT-CCATTTTAACCCCAAA
4986577 ACTTTCTAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.02
27 10 0.07
28 17 0.13
29 42 0.31
30 48 0.36
31 8 0.06
32 6 0.04
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAATTCCATTTTAACCCCAAATTTCACC
Found at i:4986596 original size:117 final size:118
Alignment explanation
Indices: 4986378--4986691 Score: 454
Period size: 117 Copynumber: 2.7 Consensus size: 118
4986368 AAAACATTCA
4986378 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACTCC-GATTTCACCAAAAA
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAAC-CCTGATTTCACCAAAAA
*
4986442 TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
65 TTACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
4986496 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTGACCCTTATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCAAAAAT
* * * *
4986560 TACCATTTTACCCCAAAACTTTCTAAAATTCTATTTTTGACCTCGATTTCACC
66 TACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * * ** * *
4986613 AAAAATTATCGTTTCACCCTTGAACTTTCCGAAATTCTATTTTTAACCCTGATTTCACCAAAAAT
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCAAAAAT
4986678 TA-CATTTTTACCCC
66 TACCA-TTTTACCCC
4986692 TGGAAGTCAA
Statistics
Matches: 175, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
116 2 0.01
117 101 0.58
118 72 0.41
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (118 bp):
AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCAAAAAT
TACCATTTTACCCCAAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:4999229 original size:201 final size:200
Alignment explanation
Indices: 4998648--4999493 Score: 1250
Period size: 200 Copynumber: 4.2 Consensus size: 200
4998638 CCAACAAAGC
*
4998648 AGCGAGGCGGTCATCTTTCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
1 AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
*
4998713 AATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
66 AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* *
4998778 TCCTGATGTGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCA
131 TCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATCA
4998843 AAACA
196 AAACA
* * * * *
4998848 AGCGAGGGGGTCATCTTCTTGATGAAATATAGAGAAGAATACCAATTCAACGCTTAACACGAGCC
1 AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
*
4998913 AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAATGGTTAGCT
66 AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
*
4998978 TTCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATCA
131 TCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATCA
4999043 AAACA
196 AAACA
* *
4999048 AGCGAGGGGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
1 AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
*
4999113 AAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAATGGTTAGC
66 -AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
* * * * *
4999178 TTCCTGATGAGATACAGAGAAGTGGACCAGATTCATCTTCTTGAAGAGATCCAGAGAAGCGAACC
130 TTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATC
*
4999243 GAAACA
195 AAAACA
* * * *
4999249 AGCGAAGCGGTCATCTTCTTGATGATATACAAAGAAGAATACCAACTT-AACGCTCAA-A-GCAG
1 AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAA-TTCAACGCTCAACACG-A-
* * *
4999311 GCAAATCTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTA
63 GCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * * * * * *
4999376 GCTTCTTGATAAGACACGGAGAAGTGAACCAAATTCGTCTTCTTGAGGAGATCCAAAGAAGCGAA
128 GCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAA
*
4999441 TTAAAAC-
193 TCAAAACA
* * * * *
4999448 AGATGATTGCGGTCATCTTCCTGATGAGACACAGGGAAGAAGACCA
1 AG-CGA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
4999494 GGTCAATGAA
Statistics
Matches: 589, Mismatches: 51, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
199 3 0.01
200 374 0.63
201 210 0.36
202 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (200 bp):
AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACACGAGCC
AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
TCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAAGAAGCGAATCA
AAACA
Found at i:4999400 original size:401 final size:399
Alignment explanation
Indices: 4998642--4999493 Score: 1298
Period size: 401 Copynumber: 2.1 Consensus size: 399
4998632 AGCAGTCCAA
* *
4998642 CAAAGCAGCGAGGCGGTCATCTTTCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACA
1 CAAAACAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACA
*
4998707 CGAGCCAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
66 CGAGCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
* * *
4998772 TTAGCTTCCTGATGTGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGC
131 TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCATCTTCCTGAAGAGATCCAGAGAAGC
* * * * *
4998837 GAATCAAAACAAGCGAGGGGGTCATCTTCTTGATGAAATATAGAGAAGAATACCAATTCAACGCT
196 GAACCAAAACAAGCGAAGCGGTCATCTTCTTGATGAAATACAAAGAAGAATACCAATTCAACGCT
* * *
4998902 TAACACGAGCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAA
261 AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
* * * * *
4998967 AATGGTTAGCTTTCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAAA
326 AAAGGTTAGCTTTCTGATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAAA
4999032 GAAGCGAAT
391 GAAGCGAAT
* *
4999041 CAAAACAAGCGAGGGGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAATTCAACGCTCAAC
1 CAAAAC-AGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAAC
*
4999106 ACGAGCCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAT
65 ACGAGCC-AATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
*
4999171 GGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCATCTTCTTGAAGAGATCCAGAGAA
129 GGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCATCTTCCTGAAGAGATCCAGAGAA
* *
4999236 GCGAACCGAAACAAGCGAAGCGGTCATCTTCTTGATGATATACAAAGAAGAATACCAACTT-AAC
194 GCGAACCAAAACAAGCGAAGCGGTCATCTTCTTGATGAAATACAAAGAAGAATACCAA-TTCAAC
*
4999300 GCTCAAAGCA-G-GCAAATCTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
258 GCT-AAA-CACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
* *
4999363 AATAAAAAGGTTAGC-TTCTTGATAAGACACGGAGAAGTGAACCAAATTCGTCTTCTTGAGGAGA
321 AATAAAAAGGTTAGCTTTC-TGATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGA
4999427 TCCAAAGAAGCGAAT
385 TCCAAAGAAGCGAAT
* * * * * *
4999442 TAAAACAGATGATTGCGGTCATCTTCCTGATGAGACACAGGGAAGAAGACCA
1 CAAAACAG-CGA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
4999494 GGTCAATGAA
Statistics
Matches: 409, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
399 5 0.01
400 67 0.16
401 297 0.73
402 38 0.09
403 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (399 bp):
CAAAACAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAACA
CGAGCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
TTAGCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCATCTTCCTGAAGAGATCCAGAGAAGC
GAACCAAAACAAGCGAAGCGGTCATCTTCTTGATGAAATACAAAGAAGAATACCAATTCAACGCT
AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
AAAGGTTAGCTTTCTGATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAAA
GAAGCGAAT
Found at i:4999835 original size:6 final size:6
Alignment explanation
Indices: 4999824--4999902 Score: 60
Period size: 6 Copynumber: 13.8 Consensus size: 6
4999814 CCCAATGAGA
* * ** *
4999824 TAAATT TAAATT T-ATTT TGAATT TAAATT TGCA-T AAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
4999870 T--ATT ATAAATT TAAATT TAAAAT TAAA-T TAAAT
1 TAAATT -TAAATT TAAATT TAAATT TAAATT TAAAT
4999903 GTCCATTTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 39 0.68
7 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:4999848 original size:17 final size:17
Alignment explanation
Indices: 4999824--4999888 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
4999814 CCCAATGAGA
4999824 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* ***
4999841 TGAATTTAAATTTGCAT
1 TAAATTTAAATTTATTT
* *
4999858 AAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
4999875 TAAATTTAAATTTA
1 TAAATTTAAATTTA
4999889 AAATTAAATT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:4999901 original size:34 final size:34
Alignment explanation
Indices: 4999824--4999902 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
4999814 CCCAATGAGA
* * **
4999824 TAAATTTAAATTTATTTTGAATTTAAATTTGCAT
1 TAAATTTAAATTTATTATAAATTTAAATTTAAAT
*
4999858 AAAATTTAAATTTATTATAAATTTAAATTTAAAAT
1 TAAATTTAAATTTATTATAAATTTAAATTT-AAAT
4999893 TAAA-TTAAAT
1 TAAATTTAAAT
4999903 GTCCATTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 33 0.87
35 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (34 bp):
TAAATTTAAATTTATTATAAATTTAAATTTAAAT
Found at i:5000533 original size:3 final size:3
Alignment explanation
Indices: 5000525--5000602 Score: 70
Period size: 3 Copynumber: 25.3 Consensus size: 3
5000515 TTAATTTATG
** *
5000525 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GCA ATA AGA ATGA AGTTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A A--TA
*
5000573 ATA ATA ATA ATAA ATA A-C ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A
5000603 AAAAGGGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
2 3 0.05
3 50 0.82
4 5 0.08
5 2 0.03
6 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:5001691 original size:30 final size:30
Alignment explanation
Indices: 5001656--5001757 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
5001646 ATTGACCTCA
5001656 AAACTTTCAAAAAATTACCATTTTACCCCC
1 AAACTTTCAAAAAATTACCATTTTACCCCC
* *
5001686 AAACTTTC-TAAAATT-CCATTTTAAACCCC
1 AAACTTTCAAAAAATTACCATTTT-ACCCCC
* * *
5001715 -GA-TTTCACCAAAAATTACCATTTTGCCCCT
1 AAACTTTCA--AAAAATTACCATTTTACCCCC
*
5001745 AAACTTTCCAAAA
1 AAACTTTCAAAAA
5001758 TCCCATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
27 4 0.07
28 8 0.14
29 11 0.20
30 21 0.38
31 8 0.14
32 4 0.07
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.31
Consensus pattern (30 bp):
AAACTTTCAAAAAATTACCATTTTACCCCC
Found at i:5001733 original size:59 final size:59
Alignment explanation
Indices: 5001665--5001803 Score: 206
Period size: 59 Copynumber: 2.3 Consensus size: 59
5001655 AAAACTTTCA
* *
5001665 AAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTAAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACC
* * * **
5001724 AAAAATTACCATTTTGCCCCTAAACTTTCCAAAATCCCATTTTTAACCGTGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACC
5001783 AAAAATTACCATTTTTACCCC
1 AAAAATTACCA-TTTTACCCC
5001804 TGAAAGTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 63 0.89
60 8 0.11
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACC
Found at i:5008076 original size:26 final size:27
Alignment explanation
Indices: 5008030--5008085 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
5008020 TTTACTCCGG
5008030 ACCTCAACCCGGAATCTTGAACCTTGA
1 ACCTCAACCCGGAATCTTGAACCTTGA
* *
5008057 ACCTGAACCC-GAATCTTGAATCTTGA
1 ACCTCAACCCGGAATCTTGAACCTTGA
5008083 ACC
1 ACC
5008086 AAAAGATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.23
Consensus pattern (27 bp):
ACCTCAACCCGGAATCTTGAACCTTGA
Found at i:5008449 original size:43 final size:43
Alignment explanation
Indices: 5008385--5008481 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
5008375 CATTAAACGT
*
5008385 CGCTAAAGAACGAGGTCTTTAGCGGCGCTTTCCCCACAAACAC
1 CGCTAAAGAACGAAGTCTTTAGCGGCGCTTTCCCCACAAACAC
* **
5008428 CGCTAAAGAAC-ATAGTTTTTAGCGGCGCTTTCCCCACAAACGT
1 CGCTAAAGAACGA-AGTCTTTAGCGGCGCTTTCCCCACAAACAC
5008471 CGCTAAAGAAC
1 CGCTAAAGAAC
5008482 TGCTAAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (43 bp):
CGCTAAAGAACGAAGTCTTTAGCGGCGCTTTCCCCACAAACAC
Found at i:5008511 original size:54 final size:54
Alignment explanation
Indices: 5008429--5008535 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
5008419 CACAAACACC
*
5008429 GCTAAAGAACATAGTTTTTAGCGGCGCTTTCCCCACAAACG-TCGCTAAAGAACT
1 GCTAAAGAACATAGTCTTTAGCGGCGCTTTCCCCACAAACGCT-GCTAAAGAACT
* *
5008483 GCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTCACAAACGCTGCTAAAGAAC
1 GCTAAAGAACATAGTCTTTAGCGGCGCTTTCCCCACAAACGCTGCTAAAGAAC
5008536 AAACACCGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
54 48 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (54 bp):
GCTAAAGAACATAGTCTTTAGCGGCGCTTTCCCCACAAACGCTGCTAAAGAACT
Found at i:5011901 original size:18 final size:19
Alignment explanation
Indices: 5011858--5011901 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5011848 TTAATAATGT
*
5011858 TAATTCTAGAAATTATCAA
1 TAATTTTAGAAATTATCAA
* *
5011877 AAATTTTAGAAA-TATTAA
1 TAATTTTAGAAATTATCAA
5011895 TAATTTT
1 TAATTTT
5011902 TTAATTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TAATTTTAGAAATTATCAA
Found at i:5012608 original size:41 final size:41
Alignment explanation
Indices: 5012562--5012668 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
5012552 CCCATAAGCT
* * *
5012562 GCTAATGCTTTGACCTTTAGCGACGTTTATTAGAAAGCGTC
1 GCTAATGCTCTAACCTTTAGCGACGTTTATTAGAAAGCGCC
5012603 GCTAATGCTCTAACCTTTAGC-AGCGTTTATTAGAAAGCGCC
1 GCTAATGCTCTAACCTTTAGCGA-CGTTTATTAGAAAGCGCC
* *
5012644 GCTAGTGCTCTAACTTTTAGCGACG
1 GCTAATGCTCTAACCTTTAGCGACG
5012669 CTTTTCCATA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.02
41 57 0.97
42 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
GCTAATGCTCTAACCTTTAGCGACGTTTATTAGAAAGCGCC
Found at i:5012694 original size:41 final size:41
Alignment explanation
Indices: 5012649--5012747 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
5012639 GCGCCGCTAG
* * ** ** *
5012649 TGCTCTAACTTTTAGCGACGCTTTTCCATAAACGCTGCTTA
1 TGCTCTGACCTTTAGCGACGCTTCCCCATAAACGCCACTGA
**
5012690 TGCTCTGACCTTTAGCGGTGCTTCCCCATAAACGCCACTGA
1 TGCTCTGACCTTTAGCGACGCTTCCCCATAAACGCCACTGA
5012731 TGCTCTGACCTTTAGCG
1 TGCTCTGACCTTTAGCG
5012748 GCTCTTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.32
Consensus pattern (41 bp):
TGCTCTGACCTTTAGCGACGCTTCCCCATAAACGCCACTGA
Found at i:5012809 original size:40 final size:39
Alignment explanation
Indices: 5012761--5012875 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 39
5012751 CTTTTTTTAT
* * **
5012761 AAACGCCGCTATTGCTTTACCTTTTACGGCGTTTATGGTA
1 AAACGCCGCTATTGCTTTACTTTTTGCGGCGTTT-TGCAA
*
5012801 AAACGCCGCTATTGCTTTATCTTTTTGCGGCATTTTGCAA
1 AAACGCCGCTATTGCTTTA-CTTTTTGCGGCGTTTTGCAA
**
5012841 AAACATCGCTATTGCTTTACTTTTTGCGGCGTTTT
1 AAACGCCGCTATTGCTTTACTTTTTGCGGCGTTTT
5012876 CTATCCAAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 15 0.23
40 39 0.59
41 12 0.18
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (39 bp):
AAACGCCGCTATTGCTTTACTTTTTGCGGCGTTTTGCAA
Found at i:5013161 original size:25 final size:25
Alignment explanation
Indices: 5013131--5013189 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
5013121 TTTCATAAAT
5013131 TTAATTTTAACGTTTATATTTTTTA-
1 TTAATTTTAAC-TTTATATTTTTTAG
* *
5013156 TTAATTTTATCTTTATTTTTTTTAG
1 TTAATTTTAACTTTATATTTTTTAG
5013181 TTAAGTTTT
1 TTAA-TTTT
5013190 GTTCTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 12 0.40
25 14 0.47
26 4 0.13
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (25 bp):
TTAATTTTAACTTTATATTTTTTAG
Found at i:5017725 original size:28 final size:28
Alignment explanation
Indices: 5017679--5017750 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
5017669 TCAGTTTTCC
5017679 ATTTTCTTTCTTCTTTTTTTCCCCCTCT
1 ATTTTCTTTCTTCTTTTTTTCCCCCTCT
5017707 ATTTTCTTTCTT-TTCTTTTTCCCCCTC-
1 ATTTTCTTTCTTCTT-TTTTTCCCCCTCT
* *
5017734 ATTGTTTTTTCATCTTT
1 ATT-TTCTTTCTTCTTT
5017751 CTCAAATCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.13
28 32 0.82
29 2 0.05
ACGTcount: A:0.06, C:0.28, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTTTCTTTCTTCTTTTTTTCCCCCTCT
Found at i:5039251 original size:2 final size:2
Alignment explanation
Indices: 5039244--5039268 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5039234 CCCTTTTTAA
5039244 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5039269 ATACAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5042820 original size:27 final size:27
Alignment explanation
Indices: 5042779--5042892 Score: 192
Period size: 27 Copynumber: 4.2 Consensus size: 27
5042769 GCTTGAGGAG
*
5042779 TATTCTGATTCTGGCTCAAAAGAGCGA
1 TATTCTGATTCTGGCTCAAAAGAGCGT
*
5042806 TATTCTGATTTTGGCTCAAAAGAGCGT
1 TATTCTGATTCTGGCTCAAAAGAGCGT
5042833 TATTCTGATTCTGGCTCAAAAGAGCGT
1 TATTCTGATTCTGGCTCAAAAGAGCGT
* *
5042860 TGTTCTGATTTTGGCTCAAAAGAGCGT
1 TATTCTGATTCTGGCTCAAAAGAGCGT
5042887 TATTCT
1 TATTCT
5042893 AACTATTTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (27 bp):
TATTCTGATTCTGGCTCAAAAGAGCGT
Found at i:5055968 original size:20 final size:22
Alignment explanation
Indices: 5055929--5055969 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
5055919 ATTAACAATT
5055929 GGACTAGAATTTTAAAATTTAG
1 GGACTAGAATTTTAAAATTTAG
*
5055951 GGACTA-AA-TTTCAAATTTA
1 GGACTAGAATTTTAAAATTTA
5055970 CAAAGAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (22 bp):
GGACTAGAATTTTAAAATTTAG
Found at i:5071680 original size:14 final size:14
Alignment explanation
Indices: 5071661--5071690 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5071651 TAAAAACAAC
5071661 GAATATTATAATAT
1 GAATATTATAATAT
5071675 GAATATTATAATAT
1 GAATATTATAATAT
5071689 GA
1 GA
5071691 GATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (14 bp):
GAATATTATAATAT
Found at i:5076822 original size:23 final size:25
Alignment explanation
Indices: 5076796--5076842 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5076786 TCCAATTAGG
5076796 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
5076819 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
5076843 TGGATCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:5078325 original size:23 final size:23
Alignment explanation
Indices: 5078267--5078425 Score: 128
Period size: 23 Copynumber: 6.8 Consensus size: 23
5078257 AAGTACTTAA
*
5078267 CAGTAAGCACACA-AGTGCTGGGGAAA
1 CAGTAAGCACACACAGTGC----GAAT
5078293 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCGAAT
*
5078315 CCAGTAGGCACACACAGTGC-AAT
1 -CAGTAAGCACACACAGTGCGAAT
* * * * *
5078338 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGCGAAT
* * *
5078361 CAGTAGGCACATGA-AGTGCGAAA
1 CAGTAAGCACA-CACAGTGCGAAT
* *
5078384 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACACAGTGCGAAT
5078407 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
5078426 TGAACGGTAA
Statistics
Matches: 115, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
22 19 0.17
23 77 0.67
24 1 0.01
26 13 0.11
27 5 0.04
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCGAAT
Found at i:5078437 original size:46 final size:44
Alignment explanation
Indices: 5078265--5078425 Score: 135
Period size: 45 Copynumber: 3.5 Consensus size: 44
5078255 CGAAGTACTT
*
5078265 AACAGTAAGCACACAAGTGCTGGGGAAACAGTAAGCACACACAGTGCA
1 AACAGTAAGCACACAAGTGC----GAAACAGTAAGCACACAAAGTGCA
* * * * * * *
5078313 ATCCAGTAGGCACACACAGTGC-AATCAGTAGGCGCACATAGCGCA
1 A-ACAGTAAGCACACA-AGTGCGAAACAGTAAGCACACAAAGTGCA
* *
5078358 AATCAGTAGGCACATGAAGTGCGAAACAGTAAGCACACAAAGTGCGA
1 AA-CAGTAAGCACA-CAAGTGCGAAACAGTAAGCACACAAAGTGC-A
5078405 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACA-AGTGC
5078426 TGAACGGTAA
Statistics
Matches: 90, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
45 36 0.40
46 33 0.37
47 3 0.03
48 1 0.01
49 12 0.13
50 5 0.06
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (44 bp):
AACAGTAAGCACACAAGTGCGAAACAGTAAGCACACAAAGTGCA
Found at i:5079513 original size:33 final size:35
Alignment explanation
Indices: 5079450--5079515 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
5079440 CTCTTTTACC
* *
5079450 CCTTGCTCTACTCTTTTCCTTTGTCTTCAATTTGAT
1 CCTTGCTC-ACTCTTCTCCTTTCTCTTCAATTTGAT
5079486 CCTTGCTC-CTCTTCT-CTTTCTCTTCAATTT
1 CCTTGCTCACTCTTCTCCTTTCTCTTCAATTT
5079516 CACATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.50
34 6 0.21
36 8 0.29
ACGTcount: A:0.09, C:0.32, G:0.06, T:0.53
Consensus pattern (35 bp):
CCTTGCTCACTCTTCTCCTTTCTCTTCAATTTGAT
Found at i:5083588 original size:10 final size:10
Alignment explanation
Indices: 5083573--5083615 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
5083563 TCATGTTTTT
5083573 AAAAAAATTG
1 AAAAAAATTG
*
5083583 AAAAAAATTA
1 AAAAAAATTG
*
5083593 AAAAAAAAT-
1 AAAAAAATTG
5083602 AAAAAAATTG
1 AAAAAAATTG
5083612 AAAA
1 AAAA
5083616 GTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:5083651 original size:6 final size:6
Alignment explanation
Indices: 5083637--5083696 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
5083627 AATTAGTTTA
* *
5083637 TTTATT TTCATT TTCATT TTTATT TTTATT TTTA-T TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
5083683 TTTAAT TTTATT TT
1 TTTATT TTTATT TT
5083697 AATTATGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:5084652 original size:12 final size:12
Alignment explanation
Indices: 5084637--5084690 Score: 69
Period size: 11 Copynumber: 4.6 Consensus size: 12
5084627 AGAAAAAATC
5084637 AAAAAAAAATTG
1 AAAAAAAAATTG
5084649 AAAAAAAAATTG
1 AAAAAAAAATTG
5084661 -AAAAAAAATTG
1 AAAAAAAAATTG
5084672 AGAAAAAGAAA--G
1 A-AAAAA-AAATTG
5084684 AAAAAAA
1 AAAAAAA
5084691 GACAAAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 16 0.41
12 14 0.36
13 5 0.13
14 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:5084664 original size:23 final size:23
Alignment explanation
Indices: 5084629--5084690 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
5084619 TTAAAAAAAG
*
5084629 AAAAAATCAAAAAAAAATTGA-AA
1 AAAAAAT-GAAAAAAAATTGAGAA
5084652 AAAAAATTGAAAAAAAATTGAGAA
1 AAAAAA-TGAAAAAAAATTGAGAA
5084676 AAAGAAA-GAAAAAAA
1 AAA-AAATGAAAAAAA
5084691 GACAAAAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 26 0.74
24 6 0.17
25 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.11
Consensus pattern (23 bp):
AAAAAATGAAAAAAAATTGAGAA
Found at i:5084670 original size:11 final size:11
Alignment explanation
Indices: 5084638--5084678 Score: 64
Period size: 12 Copynumber: 3.5 Consensus size: 11
5084628 GAAAAAATCA
5084638 AAAAAAAATTG
1 AAAAAAAATTG
5084649 AAAAAAAAATTG
1 -AAAAAAAATTG
5084661 AAAAAAAATTG
1 AAAAAAAATTG
5084672 AGAAAAA
1 A-AAAAA
5084679 GAAAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:5085747 original size:23 final size:25
Alignment explanation
Indices: 5085721--5085767 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5085711 TCCAATTAGG
5085721 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
5085744 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
5085768 TGGATTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:5086905 original size:21 final size:21
Alignment explanation
Indices: 5086881--5086920 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5086871 CGATTCTTAA
* *
5086881 TTTGTTTATGCTTTGTAATAG
1 TTTGATTATACTTTGTAATAG
*
5086902 TTTGATTCTACTTTGTAAT
1 TTTGATTATACTTTGTAAT
5086921 TGATTAGACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTGATTATACTTTGTAATAG
Found at i:5094588 original size:18 final size:18
Alignment explanation
Indices: 5094565--5094617 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
5094555 TTTTCAGTTA
5094565 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
5094583 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
5094601 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
5094617 T
1 T
5094618 TCATCCCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.28
17 7 0.22
18 16 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:5094615 original size:16 final size:17
Alignment explanation
Indices: 5094574--5094617 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
5094564 ATAATTAATT
5094574 TAAAATT-TTTAATTAA
1 TAAAATTATTTAATTAA
*
5094590 TTAAATTTATTTAATTAA
1 -TAAAATTATTTAATTAA
5094608 -AAAATTATTT
1 TAAAATTATTT
5094618 TCATCCCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 6 0.25
18 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAATTATTTAATTAA
Found at i:5100294 original size:44 final size:44
Alignment explanation
Indices: 5100244--5100330 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
5100234 ATAATATGTC
* *
5100244 AATTTAA-CTCTTTATATTTATATATT-TATTATTTTAATTTTTAA
1 AATTTAATC-CTTAATATTTATAAATTATATTATTTT-ATTTTTAA
*
5100288 AATTTAATCCTTAATATTTATAAATTATTTTATTTTATTTTTA
1 AATTTAATCCTTAATATTTATAAATTATATTATTTTATTTTTA
5100331 CATAAAATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 29 0.76
45 9 0.24
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (44 bp):
AATTTAATCCTTAATATTTATAAATTATATTATTTTATTTTTAA
Found at i:5100535 original size:26 final size:26
Alignment explanation
Indices: 5100485--5100535 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5100475 AATGAAACTC
* * *
5100485 AAATCATCTTAACCGTTAGTGTATAA
1 AAATCATCTCAACCCTCAGTGTATAA
*
5100511 AAATCATCTCAACCCTCAGTTTATA
1 AAATCATCTCAACCCTCAGTGTATA
5100536 TAAAGATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (26 bp):
AAATCATCTCAACCCTCAGTGTATAA
Found at i:5100840 original size:78 final size:78
Alignment explanation
Indices: 5100751--5100902 Score: 304
Period size: 78 Copynumber: 1.9 Consensus size: 78
5100741 TCACCAATGC
5100751 TTTTTTACTGTAAAAATGTTTTTTGATTAAAAATAATACTAAACAAGTAACTTTTGAAAGAAATT
1 TTTTTTACTGTAAAAATGTTTTTTGATTAAAAATAATACTAAACAAGTAACTTTTGAAAGAAATT
5100816 TTTAACTTTAATA
66 TTTAACTTTAATA
5100829 TTTTTTACTGTAAAAATGTTTTTTGATTAAAAATAATACTAAACAAGTAACTTTTGAAAGAAATT
1 TTTTTTACTGTAAAAATGTTTTTTGATTAAAAATAATACTAAACAAGTAACTTTTGAAAGAAATT
5100894 TTTAACTTT
66 TTTAACTTT
5100903 TTAAAAAGAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (78 bp):
TTTTTTACTGTAAAAATGTTTTTTGATTAAAAATAATACTAAACAAGTAACTTTTGAAAGAAATT
TTTAACTTTAATA
Found at i:5117697 original size:2 final size:2
Alignment explanation
Indices: 5117690--5117742 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
5117680 TAACAAAGAG
5117690 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5117732 CT CT CT CT CT C
1 CT CT CT CT CT C
5117743 CTTCCCAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5123293 original size:25 final size:25
Alignment explanation
Indices: 5123239--5123370 Score: 134
Period size: 23 Copynumber: 5.5 Consensus size: 25
5123229 ACCAAAGTAC
* * *
5123239 TAACAGAGAGCACA-TAAGTACTAGG
1 TAACAGAGAGCACACAAAGTGCTA-A
* *
5123264 CAACAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACAAAGTGCTAA
* *
5123289 TAACAGAGAGTACACAAAGTACTAA
1 TAACAGAGAGCACACAAAGTGCTAA
5123314 T--CAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACAAAGTGCTAA
*
5123337 T--CAGAGAGCACACATAGTGCTAA
1 TAACAGAGAGCACACAAAGTGCTAA
5123360 T--CAGAGAGCAC
1 TAACAGAGAGCAC
5123371 GAGACGTGCT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 53 0.56
25 35 0.37
26 6 0.06
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (25 bp):
TAACAGAGAGCACACAAAGTGCTAA
Found at i:5123303 original size:23 final size:22
Alignment explanation
Indices: 5123267--5123391 Score: 142
Period size: 23 Copynumber: 5.4 Consensus size: 22
5123257 TACTAGGCAA
5123267 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACA-AGTGCTAAT
* *
5123290 AACAGAGAGTACACAAAGTACTAAT
1 --CAGAGAGCACAC-AAGTGCTAAT
5123315 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACAC-AAGTGCTAAT
5123338 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACA-AGTGCTAAT
* * *
5123361 CAGAGAGCACGAGACGTGCTAAA
1 CAGAGAGCAC-ACAAGTGCTAAT
5123384 CAGAGAGC
1 CAGAGAGC
5123392 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
22 1 0.01
23 67 0.74
24 2 0.02
25 19 0.21
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGAGAGCACACAAGTGCTAAT
Found at i:5123324 original size:48 final size:48
Alignment explanation
Indices: 5123239--5123391 Score: 165
Period size: 46 Copynumber: 3.2 Consensus size: 48
5123229 ACCAAAGTAC
* *
5123239 TAACAGAGAGCACA-TAAGTACTAGGCAACAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACAAAGTACTA---ATCAGAGAGCACACACAGTGCTAA
* *
5123289 TAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACACAGTGCTAA
* * *
5123337 T--CAGAGAGCACACATAGTGCTAATCAGAGAGCACGAGAC-GTGCT-A
1 TAACAGAGAGCACACAAAGTACTAATCAGAGAGCAC-ACACAGTGCTAA
5123382 -AACAGAGAGC
1 TAACAGAGAGC
5123392 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
45 1 0.01
46 43 0.48
47 2 0.02
48 23 0.26
50 13 0.14
51 8 0.09
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (48 bp):
TAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACACAGTGCTAA
Found at i:5123344 original size:46 final size:45
Alignment explanation
Indices: 5123221--5123370 Score: 153
Period size: 46 Copynumber: 3.2 Consensus size: 45
5123211 ACGGAACAAG
* * *
5123221 CAGAGAGTAC-CAAAGTACTAA-CAGAGAG-CACATAAGTACTAGGCAA
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGACACA-AAGTACTA---AT
*
5123267 CAGAGAGCACACACAGTGCTAATAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT--CAGAGAG-ACACAAAGTACTAAT
* *
5123315 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAATCAGAGAG-ACACAAAGTACTAAT
5123361 CAGAGAGCAC
1 CAGAGAGCAC
5123371 GAGACGTGCT
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
46 39 0.43
47 9 0.10
48 23 0.26
50 7 0.08
51 8 0.09
52 4 0.04
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (45 bp):
CAGAGAGCACACAAAGTGCTAATCAGAGAGACACAAAGTACTAAT
Found at i:5126063 original size:17 final size:17
Alignment explanation
Indices: 5126041--5126079 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5126031 AGGTGGAGAA
* *
5126041 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
5126058 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
5126075 CTTGT
1 CTTGT
5126080 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:5128185 original size:5 final size:5
Alignment explanation
Indices: 5128175--5128221 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
5128165 TAAAACGGTT
*
5128175 AATTG AATTG AATTAG TATT- AATTG AATT- AATTG AATT- AATTG AATT
1 AATTG AATTG AATT-G AATTG AATTG AATTG AATTG AATTG AATTG AATT
5128222 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 11 0.31
5 21 0.58
6 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.45
Consensus pattern (5 bp):
AATTG
Found at i:5128206 original size:9 final size:9
Alignment explanation
Indices: 5128173--5128221 Score: 71
Period size: 9 Copynumber: 5.2 Consensus size: 9
5128163 ATTAAAACGG
5128173 TTAATTGAA
1 TTAATTGAA
*
5128182 TTGAATTAGTA
1 TT-AATT-GAA
5128193 TTAATTGAA
1 TTAATTGAA
5128202 TTAATTGAA
1 TTAATTGAA
5128211 TTAATTGAA
1 TTAATTGAA
5128220 TT
1 TT
5128222 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 24 0.67
10 8 0.22
11 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (9 bp):
TTAATTGAA
Found at i:5129695 original size:21 final size:23
Alignment explanation
Indices: 5129655--5129697 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
5129645 ATTTAAATTT
5129655 AATTATAAAATATATATAATATC
1 AATTATAAAATATATATAATATC
*
5129678 AATTA-AAAATAT-TTTAATAT
1 AATTATAAAATATATATAATAT
5129698 TTTATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTATAAAATATATATAATATC
Found at i:5131002 original size:23 final size:21
Alignment explanation
Indices: 5130975--5131028 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
5130965 ATTTATATCT
5130975 ATTAAATTAAAATTTAATTAATA
1 ATTAAA-TAAAA-TTAATTAATA
*
5130998 ATTAAATCAAATTAATTAAGT-
1 ATTAAATAAAATTAATTAA-TA
5131019 -TTAAATAAAA
1 ATTAAATAAAA
5131029 AGTTAGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 9 0.32
21 8 0.29
22 5 0.18
23 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTAAATAAAATTAATTAATA
Found at i:5132335 original size:22 final size:23
Alignment explanation
Indices: 5132293--5132337 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5132283 CAATTTTCTT
*
5132293 TTTCTTCTTTGATGTTATGTGAA
1 TTTCGTCTTTGATGTTATGTGAA
*
5132316 TTTCGTCTTTGGT-TTATGTGAA
1 TTTCGTCTTTGATGTTATGTGAA
5132338 AATTGGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.56
Consensus pattern (23 bp):
TTTCGTCTTTGATGTTATGTGAA
Found at i:5140740 original size:16 final size:16
Alignment explanation
Indices: 5140706--5140743 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5140696 ACCAGATTTT
*
5140706 TTTTTATTTTTAATGA
1 TTTTTATTTTTAATAA
5140722 TTTTTATTTTATAA-AA
1 TTTTTATTTT-TAATAA
5140738 TTTTTA
1 TTTTTA
5140744 ATAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTTAATAA
Found at i:5143610 original size:18 final size:19
Alignment explanation
Indices: 5143587--5143625 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5143577 ATTTCGGTTA
5143587 AAATCAAAT-TAA-TCGATT
1 AAATC-AATCTAATTCGATT
5143605 AAATCAATCTAATTCGATT
1 AAATCAATCTAATTCGATT
5143624 AA
1 AA
5143626 TCGATCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (19 bp):
AAATCAATCTAATTCGATT
Found at i:5146511 original size:5 final size:5
Alignment explanation
Indices: 5146496--5146534 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
5146486 GAAGGTGAGT
*
5146496 TTTTG TTTT- TTGTTT TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TT-TTG TTTTG TTTTG TTTTG TTTTG TTTT
5146535 TTTGCATGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 2 0.06
5 27 0.87
6 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:5146512 original size:13 final size:13
Alignment explanation
Indices: 5146494--5146538 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5146484 CTGAAGGTGA
5146494 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
5146507 GTTTTT-TTGTTTT
1 GTTTTTGTT-TTTT
5146520 G-TTTTGTTTTGTT
1 GTTTTTGTTTT-TT
5146533 -TTTTTG
1 GTTTTTG
5146539 CATGCCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (13 bp):
GTTTTTGTTTTTT
Found at i:5146515 original size:15 final size:14
Alignment explanation
Indices: 5146495--5146537 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
5146485 TGAAGGTGAG
5146495 TTTTTGTTTTTTGTT
1 TTTTTGTTTTTT-TT
5146510 TTTTTGTTTTGTTTT
1 TTTTTGTTTT-TTTT
*
5146525 GTTTTGTTTTTTT
1 TTTTTGTTTTTTT
5146538 GCATGCCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTTTT
Found at i:5146958 original size:2 final size:2
Alignment explanation
Indices: 5146951--5146980 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5146941 CTGTGTATTG
*
5146951 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5146981 TTGTACCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5148550 original size:2 final size:2
Alignment explanation
Indices: 5148543--5148567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5148533 GCTTGACAAG
5148543 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5148568 TAAAGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5149587 original size:13 final size:13
Alignment explanation
Indices: 5149567--5149600 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5149557 AAAAAGTGTG
5149567 TTGAAAAATGAATT
1 TTGAAAAAT-AATT
*
5149581 TTGAAAAATACTT
1 TTGAAAAATAATT
5149594 TTGAAAA
1 TTGAAAA
5149601 GTTTGGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (13 bp):
TTGAAAAATAATT
Found at i:5155399 original size:14 final size:14
Alignment explanation
Indices: 5155382--5155434 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
5155372 TTTTGTCATG
5155382 TTATTTTATTTTTT
1 TTATTTTATTTTTT
*
5155396 TTATTTTATATTTT
1 TTATTTTATTTTTT
*
5155410 ATAGTTTTATTTTTT
1 TTA-TTTTATTTTTT
5155425 TATATTTTAT
1 T-TATTTTAT
5155435 AGGTTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 15 0.45
15 16 0.48
16 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTATTTTATTTTTT
Found at i:5155435 original size:7 final size:7
Alignment explanation
Indices: 5155383--5155456 Score: 69
Period size: 7 Copynumber: 10.1 Consensus size: 7
5155373 TTTGTCATGT
5155383 TATTTTA
1 TATTTTA
* *
5155390 TTTTTTT
1 TATTTTA
5155397 TATTTTA
1 TATTTTA
5155404 TATTTTA
1 TATTTTA
5155411 TAGTTTTA
1 TA-TTTTA
*
5155419 TTTTTTTA
1 -TATTTTA
5155427 TATTTTA
1 TATTTTA
5155434 TAGGTTTTA
1 TA--TTTTA
*
5155443 TAATTT-
1 TATTTTA
5155449 TATTTTA
1 TATTTTA
5155456 T
1 T
5155457 TTAATAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.09
7 31 0.57
8 10 0.19
9 8 0.15
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:5155436 original size:23 final size:24
Alignment explanation
Indices: 5155383--5155451 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
5155373 TTTGTCATGT
5155383 TATTTTAT--TTTT-TTTATTTTA
1 TATTTTATAGTTTTATTTATTTTA
5155404 TATTTTATAGTTTTATTT-TTTTA
1 TATTTTATAGTTTTATTTATTTTA
*
5155427 TATTTTATAGGTTTTA-TAATTTTA
1 TATTTTATA-GTTTTATTTATTTTA
5155451 T
1 T
5155452 TTTATTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
21 8 0.19
23 19 0.45
24 15 0.36
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (24 bp):
TATTTTATAGTTTTATTTATTTTA
Found at i:5156044 original size:24 final size:25
Alignment explanation
Indices: 5155999--5156045 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
5155989 TCATTATTTT
*
5155999 AAATATTCAAAAAATTACAATTATA
1 AAATATTCAAAAAATTAAAATTATA
5156024 AAATATT--AAAAATATAAAATTA
1 AAATATTCAAAAAAT-TAAAATTA
5156046 AAACAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATATTCAAAAAATTAAAATTATA
Found at i:5156098 original size:22 final size:22
Alignment explanation
Indices: 5156070--5156111 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5156060 TTTTTATTAA
5156070 ATAAAATA-AAATTATAAAAACT
1 ATAAAATAGAAA-TATAAAAACT
5156092 ATAAAATAGAAATATAAAAA
1 ATAAAATAGAAATATAAAAA
5156112 TAAAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAAATAGAAATATAAAAACT
Found at i:5156105 original size:28 final size:28
Alignment explanation
Indices: 5156068--5156126 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5156058 CTTTTTTATT
*
5156068 AAATAAAATA-AAATTATAAAAAC-TATA
1 AAATAAAATATAAA-AATAAAAACATATA
5156095 AAATAGAAATATAAAAATAAAAACATATA
1 AAATA-AAATATAAAAATAAAAACATATA
5156124 AAA
1 AAA
5156127 ATTGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.18
28 13 0.46
29 10 0.36
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (28 bp):
AAATAAAATATAAAAATAAAAACATATA
Done.