Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 37
Found at i:5089581 original size:21 final size:21
Alignment explanation
Indices: 5089556--5089599 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5089546 AATTTAGTTA
5089556 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5089577 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5089598 AT
1 AT
5089600 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5089613 original size:28 final size:28
Alignment explanation
Indices: 5089576--5089629 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
5089566 TAGTATAAAT
*
5089576 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
5089604 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
5089630 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:5092768 original size:11 final size:10
Alignment explanation
Indices: 5092752--5093019 Score: 53
Period size: 10 Copynumber: 26.7 Consensus size: 10
5092742 AATGATTTGA
5092752 TAGTAATGATT
1 TAGTAATGA-T
5092763 TAGTAATGAT
1 TAGTAATGAT
*
5092773 TAGTAAT-AA
1 TAGTAATGAT
* *
5092782 T-GAAATTAT
1 TAGTAATGAT
* *
5092791 TATTAATTAT
1 TAGTAATGAT
*
5092801 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
5092812 TAGTAATGACT
1 TAGTAATGA-T
5092823 TAGTAATGAT
1 TAGTAATGAT
*
5092833 TAGTAAT-AA
1 TAGTAATGAT
* *
5092842 T-GAAATTAT
1 TAGTAATGAT
* *
5092851 TATTAATTAT
1 TAGTAATGAT
*
5092861 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
5092872 TAGTAATGATT
1 TAGTAATGA-T
5092883 TAGTAATGAT
1 TAGTAATGAT
*
5092893 TAGTAAT-AA
1 TAGTAATGAT
* *
5092902 T-GAAATTAT
1 TAGTAATGAT
* **
5092911 TATTAATTTT
1 TAGTAATGAT
* *
5092921 TAATGATTTGA-
1 TAGT-A-ATGAT
5092932 TAGTAATGATT
1 TAGTAATGA-T
5092943 TAGTAATGAT
1 TAGTAATGAT
*
5092953 TAGTAAT-AA
1 TAGTAATGAT
* *
5092962 T-GAAATTAT
1 TAGTAATGAT
* *
5092971 TATTAATTAT
1 TAGTAATGAT
*
5092981 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
5092992 TAGTAATGATT
1 TAGTAATGA-T
5093003 TAGTAATGAT
1 TAGTAATGAT
5093013 TAGTAAT
1 TAGTAAT
5093020 AATGAAATTA
Statistics
Matches: 191, Mismatches: 36, Indels: 61
0.66 0.12 0.21
Matches are distributed among these distances:
8 16 0.08
9 28 0.15
10 79 0.41
11 61 0.32
12 7 0.04
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:5092770 original size:60 final size:60
Alignment explanation
Indices: 5092699--5093121 Score: 651
Period size: 60 Copynumber: 7.2 Consensus size: 60
5092689 GTATTTATAA
*
5092699 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
5092759 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
* *
5092819 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
5092879 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
5092939 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
5092999 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
* *
5093059 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
5093107 GATTTAGTAATGATT
1 GATTTAGTAATGATT
5093122 TGATAGTAAT
Statistics
Matches: 343, Mismatches: 9, Indels: 27
0.91 0.02 0.07
Matches are distributed among these distances:
48 32 0.09
49 4 0.01
52 8 0.02
53 2 0.01
55 1 0.00
56 1 0.00
59 8 0.02
60 283 0.83
61 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
Found at i:5092896 original size:21 final size:20
Alignment explanation
Indices: 5092872--5093020 Score: 60
Period size: 21 Copynumber: 7.4 Consensus size: 20
5092862 TATGATTTGA
5092872 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
5092893 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
5092911 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
5092932 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
5092953 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
5092971 TATTAATTATGTA-TGATTTGA-
1 TAGTAA-TATTTAGT-A-ATGAT
5092992 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
5093013 TAGTAATA
1 TAGTAATA
5093021 ATGAAATTAT
Statistics
Matches: 89, Mismatches: 25, Indels: 29
0.62 0.17 0.20
Matches are distributed among these distances:
18 23 0.26
19 5 0.06
20 11 0.12
21 40 0.45
22 10 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:5093092 original size:21 final size:22
Alignment explanation
Indices: 5093068--5093137 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
5093058 TGATTAGTAA
5093068 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
5093089 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
5093112 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
5093136 TA
1 TA
5093138 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:5093095 original size:48 final size:49
Alignment explanation
Indices: 5093003--5093117 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
5092993 AGTAATGATT
*
5093003 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
5093052 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
5093100 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
5093118 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:5093105 original size:14 final size:14
Alignment explanation
Indices: 5093089--5093136 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5093079 TATTAATATT
*
5093089 TAATGATTTGATAT
1 TAATGATTTGATAG
5093103 TAATGA-TT--TAG
1 TAATGATTTGATAG
5093114 TAATGATTTGATAG
1 TAATGATTTGATAG
5093128 TAATGATTT
1 TAATGATTT
5093137 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:5093221 original size:7 final size:7
Alignment explanation
Indices: 5093209--5093235 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5093199 ATTTTTGGTT
5093209 CAATGAA
1 CAATGAA
5093216 CAATGAA
1 CAATGAA
5093223 CAATGAA
1 CAATGAA
5093230 CAATGA
1 CAATGA
5093236 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:5093270 original size:26 final size:26
Alignment explanation
Indices: 5093231--5093368 Score: 103
Period size: 26 Copynumber: 5.5 Consensus size: 26
5093221 AACAATGAAC
*
5093231 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
*
5093257 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAATAATAATCATTATAAA
* * * **
5093277 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAAT-A-ATAATCATTATAAA
* **
5093303 AATGATTTGATAATAATCATTATAGT
1 AATGATTTAATAATAATCATTATAAA
*
5093329 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
5093355 AATGATTTAATAAT
1 AATGATTTAATAAT
5093369 GATTTAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAATAATAATCATTATAAA
Found at i:5093400 original size:98 final size:98
Alignment explanation
Indices: 5093231--5093449 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
5093221 AACAATGAAC
5093231 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
*
5093296 ATTTAGTAATGATTTGATAATAATCATTATAGT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
5093329 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
5093394 ATTTAGTAATGATTTGATAATAATCATTATAAT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
*
5093427 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
5093450 GTTATTATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 114 0.97
99 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
ATTTAGTAATGATTTGATAATAATCATTATAAT
Found at i:5093429 original size:26 final size:26
Alignment explanation
Indices: 5093302--5093449 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
5093292 GATGATTTAG
*
5093302 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
5093328 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
5093354 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
5093377 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
5093400 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
5093426 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
5093450 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:5093483 original size:24 final size:24
Alignment explanation
Indices: 5093411--5093502 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
5093401 AATGATTTGA
*
5093411 TAATAATCATTA-TAATAATGATT
1 TAATAATTATTACTAATAATGATT
* * * * * *
5093434 TTATAATAATTATTATGTTATTATT
1 TAATAATTATTACTA-ATAATGATT
*
5093459 TAGTAATTATTTA-TAATAATGATT
1 TAATAATTA-TTACTAATAATGATT
5093483 TAATAATTATTACTAATAAT
1 TAATAATTATTACTAATAAT
5093503 TATAGAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
23 13 0.25
24 23 0.43
25 14 0.26
26 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATAATTATTACTAATAATGATT
Found at i:5093499 original size:13 final size:12
Alignment explanation
Indices: 5093410--5093505 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
5093400 TAATGATTTG
*
5093410 ATAATAATCATT
1 ATAATAATTATT
*
5093422 ATAATAATGATTTT
1 ATAATAAT--TATT
5093436 ATAATAATTATT
1 ATAATAATTATT
* *
5093448 AT-GTTATTATT
1 ATAATAATTATT
*
5093459 -TAGTAATTATTT
1 ATAATAATTA-TT
*
5093471 ATAATAATGATT
1 ATAATAATTATT
5093483 -TAATAATTATT
1 ATAATAATTATT
5093494 ACTAATAATTAT
1 A-TAATAATTAT
5093506 AGAATACTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.01
11 23 0.34
12 17 0.25
13 17 0.25
14 10 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:5093511 original size:24 final size:24
Alignment explanation
Indices: 5093462--5093511 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
5093452 TATTATTTAG
**
5093462 TAATTATTTATAATAATGATTTAA
1 TAATTATTTATAATAATGATAGAA
*
5093486 TAATTA-TTACTAATAATTATAGAA
1 TAATTATTTA-TAATAATGATAGAA
5093510 TA
1 TA
5093512 CTAACAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATTATTTATAATAATGATAGAA
Found at i:5093610 original size:14 final size:13
Alignment explanation
Indices: 5093591--5093655 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
5093581 TTTAAATATT
5093591 TAATGATTTGATAC
1 TAATGATTT-ATAC
5093605 TAATGA-TT-TAC
1 TAATGATTTATAC
*
5093616 TAAT--TAT-TAC
1 TAATGATTTATAC
5093626 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
5093640 TAATTATTTGATAC
1 TAATGATTT-ATAC
5093654 TA
1 TA
5093656 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:5093627 original size:10 final size:11
Alignment explanation
Indices: 5093602--5093635 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5093592 AATGATTTGA
5093602 TACTAATGATT
1 TACTAATGATT
*
5093613 TACTAATTA-T
1 TACTAATGATT
5093623 TACTAATGATT
1 TACTAATGATT
5093634 TA
1 TA
5093636 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:5093645 original size:21 final size:21
Alignment explanation
Indices: 5093602--5093645 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5093592 AATGATTTGA
* *
5093602 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
5093623 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
5093644 TA
1 TA
5093646 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:5093662 original size:17 final size:17
Alignment explanation
Indices: 5093640--5093672 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5093630 GATTTAATAC
5093640 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
5093657 TAATTATTTGATACTA
1 TAATTATTTGATACTA
5093673 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:5095845 original size:15 final size:14
Alignment explanation
Indices: 5095822--5095852 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5095812 TACAACACTA
5095822 AACTTTAATATAAT
1 AACTTTAATATAAT
5095836 AACTTATAATATAAT
1 AACTT-TAATATAAT
5095851 AA
1 AA
5095853 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:5095860 original size:16 final size:16
Alignment explanation
Indices: 5095827--5095873 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5095817 CACTAAACTT
*
5095827 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
5095842 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
5095858 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
5095874 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:5095984 original size:32 final size:34
Alignment explanation
Indices: 5095909--5095990 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
5095899 CCAAACCCTT
* *
5095909 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
5095942 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
5095975 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
5095991 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:5095996 original size:12 final size:12
Alignment explanation
Indices: 5095971--5096023 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
5095961 TTTTTCATTA
*
5095971 TAATATACT-AC
1 TAATAAACTAAC
*
5095982 TAATAAACTTAC
1 TAATAAACTAAC
5095994 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
5096008 TAATAAACTAAC
1 TAATAAACTAAC
5096020 TAAT
1 TAAT
5096024 TTTTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:5096142 original size:44 final size:47
Alignment explanation
Indices: 5096053--5096143 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 47
5096043 CAACAAACAA
5096053 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
*
5096100 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
5096143 A
1 A
5096144 ACTATATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
43 13 0.31
44 11 0.26
45 5 0.12
46 6 0.14
47 7 0.17
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:5096154 original size:43 final size:45
Alignment explanation
Indices: 5096053--5096183 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 45
5096043 CAACAAACAA
5096053 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTA-TTAACTAACAAAAACTAATTAAATAATTTTTT
*
5096100 ATATAACTAACTATTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTAACTAACAA-AAACTAATTAAATAATTTTTT
* * *
5096143 A-ACTATA-TAACTA-T--CAAACATATACTAATTAAATAATTTTT
1 ATA-TA-ACTAACTATTAACTAACAAAAACTAATTAAATAATTTTT
5096184 AATTTATGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
40 1 0.01
41 10 0.14
42 12 0.16
43 21 0.28
44 12 0.16
45 5 0.07
46 6 0.08
47 7 0.09
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (45 bp):
ATATAACTAACTATTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:5096211 original size:41 final size:40
Alignment explanation
Indices: 5096123--5096211 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
5096113 TTAACAAAAC
* *
5096123 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
5096164 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
5096205 AAACTAA
1 AAACTAA
5096212 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:5096276 original size:16 final size:18
Alignment explanation
Indices: 5096247--5096285 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
5096237 ACTAATTAAC
*
5096247 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
5096265 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
5096281 ATTTA
1 ATTTA
5096286 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:5096568 original size:50 final size:48
Alignment explanation
Indices: 5096497--5096603 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 48
5096487 TAGGATCACA
*
5096497 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
5096546 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
5096594 TGGC-TGCATG
1 TGGCATGCATG
5096604 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:5096671 original size:29 final size:29
Alignment explanation
Indices: 5096638--5096732 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
5096628 TGGACGCCGG
5096638 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
5096667 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
5096696 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
5096725 GGCGACCT
1 GGCGACCT
5096733 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:5096761 original size:32 final size:32
Alignment explanation
Indices: 5096719--5096790 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
5096709 GTCGCCCAGA
*
5096719 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
5096751 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
5096783 CTGCATGG
1 CTGCATGG
5096791 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:5096855 original size:24 final size:19
Alignment explanation
Indices: 5096805--5096842 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5096795 TATATGGCTT
5096805 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
5096824 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
5096843 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:5102629 original size:16 final size:18
Alignment explanation
Indices: 5102610--5102647 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5102600 AATTAATATA
5102610 TTAAA-TTTATAATT-AT
1 TTAAATTTTATAATTAAT
*
5102626 TTAAATTTTATATTTAAT
1 TTAAATTTTATAATTAAT
5102644 TTAA
1 TTAA
5102648 TCACGAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTTTATAATTAAT
Found at i:5106076 original size:15 final size:16
Alignment explanation
Indices: 5106058--5106122 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
5106048 ATTTTTATGT
5106058 TAGTAT-TTTTTTAAA
1 TAGTATATTTTTTAAA
*
5106073 TAGTTATTATTTTTTATAT
1 TAG-TA-TATTTTTTA-AA
*
5106092 TAATATATTTATTTAAA
1 TAGTATATTT-TTTAAA
* *
5106109 TATTATTTTTTTTA
1 TAGTATATTTTTTA
5106123 TTAAAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.08
16 6 0.15
17 15 0.38
18 13 0.32
19 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TAGTATATTTTTTAAA
Found at i:5106107 original size:36 final size:32
Alignment explanation
Indices: 5106044--5106123 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 32
5106034 GTGGTAAGAA
* *
5106044 ATTTATTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTT-TTTTTATATTAATATTTTTTTAAATA-TT
5106078 ATTATTTTTTATATTAATATATTTATTTAAATATT
1 ATT-TTTTTTATATTAATAT-TTT-TTTAAATATT
5106113 ATTTTTTTTAT
1 ATTTTTTTTAT
5106124 TAAAATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 24 0.59
35 9 0.22
36 8 0.20
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (32 bp):
ATTTTTTTTATATTAATATTTTTTTAAATATT
Found at i:5106111 original size:20 final size:18
Alignment explanation
Indices: 5106064--5106122 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
5106054 ATGTTAGTAT
5106064 TTTTTTAAATAGTT-ATTA
1 TTTTTTAAATA-TTAATTA
5106082 TTTTTT--ATATTAATATA
1 TTTTTTAAATATTAAT-TA
5106099 TTTATTTAAATATT-ATT-
1 TTT-TTTAAATATTAATTA
5106116 TTTTTTA
1 TTTTTTA
5106123 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.06
16 9 0.25
17 8 0.22
18 10 0.28
19 2 0.06
20 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTTAAATATTAATTA
Found at i:5106123 original size:20 final size:20
Alignment explanation
Indices: 5106099--5106136 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5106089 TATTAATATA
* *
5106099 TTTATTTAAATATTATTTTT
1 TTTATTAAAATAATATTTTT
5106119 TTTATTAAAATAATATTT
1 TTTATTAAAATAATATTT
5106137 ATATAATTAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTAAAATAATATTTTT
Found at i:5106135 original size:35 final size:35
Alignment explanation
Indices: 5106061--5106150 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 35
5106051 TTTATGTTAG
* *
5106061 TATTTTTTTAAATAGTTATTATTTTTTATATTAATA
1 TATTTATTTAAATA-TTATTATTTTTTATATAAATA
5106097 TATTTATTTAAATATTATT-TTTTTTAT-TAAAATAA
1 TATTTATTTAAATATTATTATTTTTTATAT-AAAT-A
* *
5106132 TATTTATATAATTATTATT
1 TATTTATTTAAATATTATT
5106151 CTTTCAAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 1 0.02
34 11 0.23
35 23 0.48
36 13 0.27
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TATTTATTTAAATATTATTATTTTTTATATAAATA
Found at i:5110560 original size:76 final size:76
Alignment explanation
Indices: 5110478--5110627 Score: 187
Period size: 76 Copynumber: 2.0 Consensus size: 76
5110468 GAGGGGGGAG
* * * *
5110478 AGAGTTAGT-ATCCATTTACATAATTTATATAAATAAA-TGGATATTATTATTTAAAAAAAAATT
1 AGAGTTA-TAATCCATGTACACAATTGATATAAATAAACAGG-TATTATTATTTAAAAAAAAATT
5110541 GTACAATTATTAT
64 GTACAATTATTAT
* * * * *
5110554 AGAGTTATAATCTATGTAGACAATTGATATAGATAAACAGGTATTATTATTTAAGAAATAATTGT
1 AGAGTTATAATCCATGTACACAATTGATATAAATAAACAGGTATTATTATTTAAAAAAAAATTGT
5110619 ACAATTATT
66 ACAATTATT
5110628 TTTTATTATG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 1 0.02
76 60 0.95
77 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (76 bp):
AGAGTTATAATCCATGTACACAATTGATATAAATAAACAGGTATTATTATTTAAAAAAAAATTGT
ACAATTATTAT
Found at i:5117963 original size:15 final size:13
Alignment explanation
Indices: 5117930--5118030 Score: 50
Period size: 15 Copynumber: 7.5 Consensus size: 13
5117920 AATAATTACA
*
5117930 AATATAACAAATA-
1 AATATAA-ATATAT
5117943 AATATAAATAATATT
1 AATATAAAT-ATA-T
5117958 AATAT-AATATAT
1 AATATAAATATAT
* *
5117970 AATATATA-ATGT
1 AATATAAATATAT
*
5117982 AAT-GAAATATAT
1 AATATAAATATAT
5117994 AACTATATAATA-AGT
1 AA-TATA-AATATA-T
5118009 AAGTATATAATAATAT
1 AA-TATA-AAT-ATAT
5118025 AATATA
1 AATATA
5118031 TATTATGTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.03
12 18 0.26
13 15 0.22
14 5 0.07
15 24 0.35
16 4 0.06
17 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:5118031 original size:15 final size:15
Alignment explanation
Indices: 5117943--5118032 Score: 71
Period size: 15 Copynumber: 5.9 Consensus size: 15
5117933 ATAACAAATA
*
5117943 AATATAA-ATAATATT
1 AATATAATAT-ATAAT
5117958 AATATAATATATAAT
1 AATATAATATATAAT
*
5117973 -ATATAATGTAATGAA-
1 AATATAATAT-AT-AAT
5117988 ATATATAACTATATAAT
1 A-ATATAA-TATATAAT
*
5118005 AAGTA-AGTATATAAT
1 AA-TATAATATATAAT
5118020 AATATAATATATA
1 AATATAATATATA
5118033 TTATGTTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.16
15 30 0.49
16 8 0.13
17 11 0.18
18 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (15 bp):
AATATAATATATAAT
Found at i:5118095 original size:36 final size:35
Alignment explanation
Indices: 5118012--5118096 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
5118002 AATAAGTAAG
*
5118012 TATATAATAATATAATATATATTATGTTTTCAAAAA
1 TATAT-ATAATATAATATATATTATGATTTCAAAAA
* *
5118048 TCATTTA-AATATATATATATATATAT-ATTTCAAAAC
1 T-ATATATAATATA-ATATATAT-TATGATTTCAAAAA
5118084 TATATATAATATA
1 TATATATAATATA
5118097 CGTTTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
35 10 0.24
36 25 0.61
37 6 0.15
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (35 bp):
TATATATAATATAATATATATTATGATTTCAAAAA
Found at i:5118136 original size:23 final size:23
Alignment explanation
Indices: 5118110--5118189 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
5118100 TTTTAAAACG
* *
5118110 TTTTCAATACCATTTATTATACA
1 TTTTCAAAACCATATATTATACA
**
5118133 TTTTCAAAAATATATATTATACA
1 TTTTCAAAACCATATATTATACA
*
5118156 CGTTTTTAAAACCATATATTATACA
1 --TTTTCAAAACCATATATTATACA
5118181 TTTTCAAAA
1 TTTTCAAAA
5118190 ATGTTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
23 27 0.57
25 20 0.43
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.44
Consensus pattern (23 bp):
TTTTCAAAACCATATATTATACA
Found at i:5118208 original size:35 final size:35
Alignment explanation
Indices: 5118157--5118329 Score: 140
Period size: 35 Copynumber: 4.9 Consensus size: 35
5118147 TATTATACAC
*
5118157 GTTTTTAAAACCATATATTATACATTTTCAAAAAT
1 GTTTTTAAAACTATATATTATACATTTTCAAAAAT
* * *
5118192 GTTTTTAAAACTATATAATATATGC-TTTT-TAAAAC
1 GTTTTTAAAACTATAT-AT-TATACATTTTCAAAAAT
* **
5118227 GTTTTCAAAA-TCATATATTATACGCTTTCAAAAAT
1 GTTTTTAAAACT-ATATATTATACATTTTCAAAAAT
* * *
5118262 GTTTTTAAAACTATATAATATATATTTTTTAAAACAT
1 GTTTTTAAAACTATATATTATACA-TTTTCAAAA-AT
* * * *
5118299 ATTTTCAAAAC--CATATTATATATTTTCAAAA
1 GTTTTTAAAACTATATATTATACATTTTCAAAA
5118330 CACCGATTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 17
0.75 0.14 0.12
Matches are distributed among these distances:
33 4 0.04
34 14 0.13
35 63 0.57
36 14 0.13
37 15 0.14
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (35 bp):
GTTTTTAAAACTATATATTATACATTTTCAAAAAT
Found at i:5118231 original size:70 final size:70
Alignment explanation
Indices: 5118155--5118329 Score: 246
Period size: 70 Copynumber: 2.5 Consensus size: 70
5118145 TATATTATAC
*
5118155 ACGTTTTTAAAACCATATATTATACATTTTCAAAAATGTTTTTAAAACTATATAATATATGCTTT
1 ACGTTTTTAAAACCATATATTATACATTTTCAAAAATGTTTTTAAAACTATATAATATATACTTT
5118220 TTAAA
66 TTAAA
* * ** *
5118225 ACGTTTTCAAAATCATATATTATACGCTTTCAAAAATGTTTTTAAAACTATATAATATATATTTT
1 ACGTTTTTAAAACCATATATTATACATTTTCAAAAATGTTTTTAAAACTATATAATATATACTTT
5118290 TTAAA
66 TTAAA
* *
5118295 ACATATTTTCAAAACC--ATATTATATATTTTCAAAA
1 ACGT-TTTT-AAAACCATATATTATACATTTTCAAAA
5118330 CACCGATTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
70 83 0.91
71 3 0.03
72 5 0.05
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.43
Consensus pattern (70 bp):
ACGTTTTTAAAACCATATATTATACATTTTCAAAAATGTTTTTAAAACTATATAATATATACTTT
TTAAA
Found at i:5118596 original size:2 final size:2
Alignment explanation
Indices: 5118589--5118636 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5118579 GCTTCGTTTA
5118589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5118631 AT AT AT
1 AT AT AT
5118637 GAAAAATTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5119340 original size:12 final size:13
Alignment explanation
Indices: 5119308--5119349 Score: 59
Period size: 12 Copynumber: 3.2 Consensus size: 13
5119298 TCTAAAATTT
*
5119308 TAAAATTGAAGATC
1 TAAAATT-AAAATC
5119322 TAAAATTAAAATC
1 TAAAATTAAAATC
5119335 -AAAATTAAAATC
1 TAAAATTAAAATC
5119347 TAA
1 TAA
5119350 TGCTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.46
13 7 0.27
14 7 0.27
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (13 bp):
TAAAATTAAAATC
Found at i:5123117 original size:18 final size:18
Alignment explanation
Indices: 5123092--5123136 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5123082 TAATTAAGAA
5123092 AAATTGTGAACAAAA-ATT
1 AAATTGTGAA-AAAATATT
*
5123110 ATATTGTGAAAAAATATT
1 AAATTGTGAAAAAATATT
5123128 AAATTGTGA
1 AAATTGTGA
5123137 GTATTTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.33
Consensus pattern (18 bp):
AAATTGTGAAAAAATATT
Found at i:5123186 original size:2 final size:2
Alignment explanation
Indices: 5123179--5123207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5123169 TGAACAAATA
5123179 AT AT 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 AT AT A
5123208 ACCGCCCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5126846 original size:26 final size:26
Alignment explanation
Indices: 5126817--5126866 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5126807 TAGTATATAG
*
5126817 TATA-TATACATTACATAATATATACA
1 TATATTATA-ATTACATAACATATACA
*
5126843 TATATTATAATTATATAACATATA
1 TATATTATAATTACATAACATATA
5126867 TCACATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATTATAATTACATAACATATACA
Found at i:5130892 original size:214 final size:214
Alignment explanation
Indices: 5130523--5131592 Score: 2140
Period size: 214 Copynumber: 5.0 Consensus size: 214
5130513 GAAGTACCAT
5130523 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
1 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
5130588 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
66 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
5130653 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
131 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
5130718 TTCATAGTTGCAACTTCAC
196 TTCATAGTTGCAACTTCAC
5130737 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
1 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
5130802 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
66 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
5130867 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
131 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
5130932 TTCATAGTTGCAACTTCAC
196 TTCATAGTTGCAACTTCAC
5130951 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
1 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
5131016 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
66 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
5131081 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
131 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
5131146 TTCATAGTTGCAACTTCAC
196 TTCATAGTTGCAACTTCAC
5131165 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
1 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
5131230 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
66 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
5131295 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
131 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
5131360 TTCATAGTTGCAACTTCAC
196 TTCATAGTTGCAACTTCAC
5131379 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
1 TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
5131444 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
66 AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
5131509 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
131 GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
5131574 TTCATAGTTGCAACTTCAC
196 TTCATAGTTGCAACTTCAC
5131593 CATTTGATCA
Statistics
Matches: 856, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 856 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (214 bp):
TTCTGAATCCATATCCTAGCCATTCTAACTTCATTCTATGTGAGTTGACATCTGGGATAGATGCT
AAGAAATTGAAGGTACACAAGCTCCACTGCTTTGCTCTCTCGAGTTATCTTGTTCCTCGCACAGT
GTTTATGAATGGTCGTCCTTGTTCATCTCGTCTTATCTTATAGTTTTTGAAATAATTTCTAATTC
TTCATAGTTGCAACTTCAC
Found at i:5132438 original size:24 final size:25
Alignment explanation
Indices: 5132406--5132455 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
5132396 TATTTTTAAT
5132406 TTAATTTTATATTTTAAATAAAATA
1 TTAATTTTATATTTTAAATAAAATA
*
5132431 TTAA-TTTATTTTTTAAATAAAATA
1 TTAATTTTATATTTTAAATAAAATA
5132455 T
1 T
5132456 CTGTTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAATTTTATATTTTAAATAAAATA
Found at i:5132523 original size:31 final size:31
Alignment explanation
Indices: 5132441--5132526 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
5132431 TTAATTTATT
* ** *
5132441 TTTTAAATAAAATATCTGTTAAACTCTTAAA
1 TTTTAAATAAAACATCAATTTAACTCTTAAA
5132472 TTTTAAATAAAACATCAATTTAACTCTTAAA
1 TTTTAAATAAAACATCAATTTAACTCTTAAA
*
5132503 TTTTAAATAAAGCATCAATTTAAC
1 TTTTAAATAAAACATCAATTTAAC
5132527 CCTAAATCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTAAATAAAACATCAATTTAACTCTTAAA
Found at i:5154821 original size:154 final size:155
Alignment explanation
Indices: 5154646--5154926 Score: 383
Period size: 154 Copynumber: 1.8 Consensus size: 155
5154636 AATTTTATAA
* *
5154646 TAAGTATGGATACATTATTATTAACT-GTTAAAGTA-TCTATACTTTTAGAA-TAATTATCCATA
1 TAAGTATGAATACATTATTATTAA-TAGTTAAAGTATTC-ATACTTTTA-AAGTAAATATCCATA
* * * *
5154708 CTTTCGAA-TTTAAAAAAAAATATTTCAAAC-GATTAGGTTGTATATATTTTACTGTTTATATTA
63 CTTTCGAATTTTAAAAAAAAATATTTAAAACAG-TTAAGTTGTATATATTTTACCGTTTACATTA
5154771 CTTTCGAAACAATATTTATACTTTTGGAG
127 CTTTCGAAACAATATTTATACTTTTGGAG
* * *
5154800 TAAGTATGAATACATTATTATTAATATTTAGAGTATTCATACTTTTAAAGTAAATATTCATACTT
1 TAAGTATGAATACATTATTATTAATAGTTAAAGTATTCATACTTTTAAAGTAAATATCCATACTT
* *
5154865 TTGAATTTTTAAAAAAATATATTTAAAACAGTTAAGTTGTATATATTTTACCGTTTACATTA
66 TCGAA-TTTTAAAAAAAAATATTTAAAACAGTTAAGTTGTATATATTTTACCGTTTACATTA
5154927 TTATTAACCT
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
153 3 0.03
154 56 0.51
155 2 0.02
156 48 0.44
157 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (155 bp):
TAAGTATGAATACATTATTATTAATAGTTAAAGTATTCATACTTTTAAAGTAAATATCCATACTT
TCGAATTTTAAAAAAAAATATTTAAAACAGTTAAGTTGTATATATTTTACCGTTTACATTACTTT
CGAAACAATATTTATACTTTTGGAG
Found at i:5155124 original size:75 final size:75
Alignment explanation
Indices: 5154908--5155292 Score: 402
Period size: 75 Copynumber: 5.1 Consensus size: 75
5154898 AAGTTGTATA
*
5154908 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACT-AGTAGCA-AGTTTAACATAATAGG
1 TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGA-TAG-ATAGTTTAACATAATAGG
*
5154971 TAACGTCTATTT
64 TAACGCCTATTT
* * * * * * *
5154983 TATTTTACAGTTTACATTATTATTAACATTAATTAAACAAACCGATAGCTATTTTAACGTAATAG
1 TATTTTACCGTTTACATTATTAGTAAC-CT--TTAAACAAACTGATAGATAGTTTAACATAATAG
* *
5155048 GTAGCGTCTATTT
63 GTAACGCCTATTT
* * *
5155061 TATTTTACCGTTTACATTATTCGTAACATTTAAACAAACTGATAGGTAGTTTAACATAATAGGTA
1 TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGTA
*
5155126 ATGCCTATTT
66 ACGCCTATTT
* * * * **
5155136 TATTTTACTGTTTACATTATTAGTAACCTTTAAACAAA-TCGGTAGATATTTTAACGTAATAAAT
1 TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACT-GATAGATAGTTTAACATAATAGGT
* *
5155200 ATCACCTATTT
65 AACGCCTATTT
* * * * *
5155211 TATTTTA-TGTTTTATATTATTAGTAACCTTCAAACAAACCGGTAGATAGTTTAACATAATAGGT
1 TATTTTACCG-TTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGT
5155275 -ACTGCCTATTT
65 AAC-GCCTATTT
*
5155286 GATTTTA
1 TATTTTA
5155293 ACCAGTTAAG
Statistics
Matches: 261, Mismatches: 40, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
74 4 0.02
75 192 0.74
76 1 0.00
77 1 0.00
78 62 0.24
79 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (75 bp):
TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGTA
ACGCCTATTT
Found at i:5155246 original size:150 final size:152
Alignment explanation
Indices: 5154908--5155292 Score: 483
Period size: 150 Copynumber: 2.5 Consensus size: 152
5154898 AAGTTGTATA
*
5154908 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACT-AGTAGCA-AGTTTAACATAATAGG
1 TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGA-TAG-ATAGTTTAACATAATAGG
* * * * *
5154971 TAACGTCTATTTTATTTTACAGTTTACATTATTATTAACATTAATTAAACAAACCGATAGCTATT
64 TAATGCCTATTTTATTTTACAGTTTACATTATTAGTAACACT-ATTAAACAAACCGATAGATATT
** **
5155036 TTAACGTAATAGGTAGCGTCTATTT
128 TTAACGTAATAAATAGCACCTATTT
* * *
5155061 TATTTTACCGTTTACATTATTCGTAACATTTAAACAAACTGATAGGTAGTTTAACATAATAGGTA
1 TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGTA
* * *
5155126 ATGCCTATTTTATTTTACTGTTTACATTATTAGTAAC-CT-TTAAACAAATCGGTAGATATTTTA
66 ATGCCTATTTTATTTTACAGTTTACATTATTAGTAACACTATTAAACAAACCGATAGATATTTTA
*
5155189 ACGTAATAAATATCACCTATTT
131 ACGTAATAAATAGCACCTATTT
* * * * *
5155211 TATTTTA-TGTTTTATATTATTAGTAACCTTCAAACAAACCGGTAGATAGTTTAACATAATAGGT
1 TATTTTACCG-TTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGT
* *
5155275 ACTGCCTATTTGATTTTA
65 AATGCCTATTTTATTTTA
5155293 ACCAGTTAAG
Statistics
Matches: 202, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
149 1 0.00
150 108 0.53
152 1 0.00
153 91 0.45
154 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (152 bp):
TATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGATAGTTTAACATAATAGGTA
ATGCCTATTTTATTTTACAGTTTACATTATTAGTAACACTATTAAACAAACCGATAGATATTTTA
ACGTAATAAATAGCACCTATTT
Found at i:5156188 original size:14 final size:14
Alignment explanation
Indices: 5156140--5156205 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
5156130 ATTTTAAATT
5156140 ATTTTAAAATTTTAAA
1 ATTTTAAAATTTT--A
*
5156156 ATATT-AAATTATTA
1 ATTTTAAAATT-TTA
*
5156170 TTTTTAAAATTTTA
1 ATTTTAAAATTTTA
* * *
5156184 ATTTTAATATTCTC
1 ATTTTAAAATTTTA
5156198 ATTTTAAA
1 ATTTTAAA
5156206 TTAGAATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 24 0.60
15 10 0.25
16 6 0.15
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTAAAATTTTA
Found at i:5157611 original size:14 final size:14
Alignment explanation
Indices: 5157573--5157602 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5157563 ATCCGAAGCT
*
5157573 ATCCGACCGAGGGC
1 ATCCGACCGAGGCC
5157587 ATCCGACCGAGGCC
1 ATCCGACCGAGGCC
5157601 AT
1 AT
5157603 TCGAGCGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.37, G:0.30, T:0.10
Consensus pattern (14 bp):
ATCCGACCGAGGCC
Found at i:5157699 original size:29 final size:29
Alignment explanation
Indices: 5157658--5157763 Score: 185
Period size: 29 Copynumber: 3.7 Consensus size: 29
5157648 GAGGAGCAGG
*
5157658 AGGAGTGTATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
5157687 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
5157716 CGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
5157745 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
5157764 TGCTGGGAAG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:5169463 original size:2 final size:2
Alignment explanation
Indices: 5169456--5169499 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5169446 TGGATCAAGC
5169456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5169498 AT
1 AT
5169500 TATCATTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5171238 original size:60 final size:59
Alignment explanation
Indices: 5171134--5171279 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 59
5171124 TATAATTTCT
* * * **
5171134 AATAAATTTGGAATGTTCAAAAAGTTTGGGGACTAATGTAGAATGGAT-GTCATAGTTTGGG
1 AATAAA-TTGAAATATTC-AAAAGTTTGAGGACTAATGTAGAAT-GATAGTCATAGTTTAAG
* * * * *
5171195 GATGAAATTGAAATATTCAAAATTTTGAGGATTAATTTAGAATGATAGTCGTAGTTTAAG
1 AAT-AAATTGAAATATTCAAAAGTTTGAGGACTAATGTAGAATGATAGTCATAGTTTAAG
*
5171255 AATAAATTGAAATATTTAAAAGTTT
1 AATAAATTGAAATATTCAAAAGTTT
5171280 AGAGACCAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
59 23 0.33
60 33 0.47
61 11 0.16
62 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (59 bp):
AATAAATTGAAATATTCAAAAGTTTGAGGACTAATGTAGAATGATAGTCATAGTTTAAG
Found at i:5171306 original size:22 final size:22
Alignment explanation
Indices: 5171278--5171324 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5171268 ATTTAAAAGT
5171278 TTAGAGACCAATTTAAAATGAG
1 TTAGAGACCAATTTAAAATGAG
5171300 TTAGAGACCAATTTAAAATGAG
1 TTAGAGACCAATTTAAAATGAG
5171322 TTA
1 TTA
5171325 TACTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (22 bp):
TTAGAGACCAATTTAAAATGAG
Found at i:5172056 original size:16 final size:17
Alignment explanation
Indices: 5172015--5172056 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5172005 AATCAATTCT
*
5172015 TAATATTATTTATATTTT
1 TAATA-TATTTATATTTA
5172033 TAAATATATTTA-ATTTA
1 T-AATATATTTATATTTA
5172050 TAATATA
1 TAATATA
5172057 ATATATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 5 0.23
18 7 0.32
19 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATATATTTATATTTA
Found at i:5179592 original size:23 final size:23
Alignment explanation
Indices: 5179566--5179656 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
5179556 CACCACAACT
* *
5179566 CGTATAATTGCACCGAAGTGCTG
1 CGTAGAATTGCACCGAAGTGCCG
*
5179589 CGTAGAATTGCA-CTAGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCG
* * *
5179612 CGTAGAATTGTATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
5179635 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
5179657 ATATAATAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.04
23 54 0.95
24 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:5184927 original size:23 final size:23
Alignment explanation
Indices: 5184878--5184932 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
5184868 CACCACAGCT
* *
5184878 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTACCA
* * *
5184901 CGTAGAATTGTACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTACCA
5184924 CGTAGAATT
1 CGTAGAATT
5184933 ACATCGTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTACCA
Found at i:5185169 original size:21 final size:21
Alignment explanation
Indices: 5185134--5185193 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
5185124 GATGTTTCTT
*
5185134 CTTTAAATGGTGCATCGATGCA
1 CTTTGAAT-GTGCATCGATGCA
5185156 CTTTGAATGTGCATCGATGCA
1 CTTTGAATGTGCATCGATGCA
5185177 CTTTGAATGTGCATCGA
1 CTTTGAATGTGCATCGA
5185194 AACATCTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (21 bp):
CTTTGAATGTGCATCGATGCA
Found at i:5186299 original size:14 final size:16
Alignment explanation
Indices: 5186254--5186300 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5186244 TAAAATGTCA
*
5186254 ATTTATTGTTATGT-AT
1 ATTTATT-TTAAGTAAT
5186270 ATTTATTTTAAGTAAT
1 ATTTATTTTAAGTAAT
5186286 ATTT-TTTTAA-TAAT
1 ATTTATTTTAAGTAAT
5186300 A
1 A
5186301 GATTGTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 13 0.45
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTATTTTAAGTAAT
Found at i:5186405 original size:19 final size:20
Alignment explanation
Indices: 5186371--5186410 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5186361 ATTTCATCTT
* *
5186371 ATTCTAAACTTTAAATCATA
1 ATTCTAAACATTAAATAATA
5186391 ATTCTAAA-ATTAAATAATA
1 ATTCTAAACATTAAATAATA
5186410 A
1 A
5186411 ACTCTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTCTAAACATTAAATAATA
Found at i:5186461 original size:2 final size:2
Alignment explanation
Indices: 5186454--5186522 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
5186444 AAATAAATAA
5186454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5186496 AT 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 AT A
5186523 AATTAACATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5186569 original size:2 final size:2
Alignment explanation
Indices: 5186562--5186591 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5186552 GTTGATTGAT
5186562 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
5186592 AATTAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5186897 original size:20 final size:20
Alignment explanation
Indices: 5186803--5187171 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
5186793 GATTTTCCAT
* ** *
5186803 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5186823 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
5186843 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5186863 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
5186883 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
5186903 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5186923 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5186943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5186963 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
5186983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5187003 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5187023 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5187043 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
5187063 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5187083 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5187103 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5187123 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5187143 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5187163 AATCACAAC
1 AATCGCAAC
5187172 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5190400 original size:19 final size:19
Alignment explanation
Indices: 5190378--5190670 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
5190368 CGGAAAATAC
*
5190378 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5190397 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5190411 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
5190431 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5190445 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190464 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5190483 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
5190497 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
5190516 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190535 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190554 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190573 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190592 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190611 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
5190625 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190644 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5190663 AATCGCAA
1 AATCGCAA
5190671 CGAGATAATC
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 165 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5190493 original size:52 final size:55
Alignment explanation
Indices: 5190406--5190692 Score: 356
Period size: 52 Copynumber: 5.4 Consensus size: 55
5190396 AAATCCCAAC
*
5190406 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
5190459 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
5190511 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
5190568 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
5190623 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
5190673 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
5190693 TATAAACGCA
Statistics
Matches: 222, Mismatches: 2, Indels: 21
0.91 0.01 0.09
Matches are distributed among these distances:
50 2 0.01
52 127 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 64 0.29
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:5190589 original size:128 final size:128
Alignment explanation
Indices: 5190378--5190692 Score: 462
Period size: 128 Copynumber: 2.6 Consensus size: 128
5190368 CGGAAAATAC
* *
5190378 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
5190438 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
5190497 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
5190562 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
5190625 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
5190685 TGCGAAAT
66 TGCGAAAT
5190693 TATAAACGCA
Statistics
Matches: 179, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
119 24 0.13
121 1 0.01
123 34 0.19
124 17 0.09
125 2 0.01
126 2 0.01
127 1 0.01
128 98 0.55
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:5190808 original size:19 final size:19
Alignment explanation
Indices: 5190699--5190800 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5190689 AAATTATAAA
5190699 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5190718 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
5190738 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
5190754 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5190771 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5190790 CGCATTGCGAT
1 CGCATTGCGAT
5190801 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:5190926 original size:14 final size:14
Alignment explanation
Indices: 5190907--5190943 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5190897 CATCAATTAC
5190907 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5190921 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5190935 ACAAATCAA
1 ACAAATCAA
5190944 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5192887 original size:19 final size:19
Alignment explanation
Indices: 5192847--5192962 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
5192837 TAGTTTACTT
* *
5192847 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
5192867 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5192886 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5192900 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5192919 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5192933 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5192952 TCGCAATGCGA
1 TCGCAACGCGA
5192963 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5192903 original size:14 final size:14
Alignment explanation
Indices: 5192884--5192940 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5192874 GCGAAATGAA
*
5192884 AATCGCAACGACAG
1 AATCGCAACGAAAG
5192898 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5192915 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5192931 AATCGCAACG
1 AATCGCAACG
5192941 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5192911 original size:33 final size:33
Alignment explanation
Indices: 5192865--5192957 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5192855 CGAAACTTAA
*
5192865 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5192898 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5192931 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5192958 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5192980 original size:19 final size:19
Alignment explanation
Indices: 5192958--5193085 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
5192948 AAAATCGCAA
5192958 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5192977 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5192991 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5193010 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
* **
5193024 TGCGCTTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5193043 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5193061 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5193081 TGCGA
1 TGCGA
5193086 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 29 0.34
20 13 0.15
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5193000 original size:33 final size:33
Alignment explanation
Indices: 5192958--5193049 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
5192948 AAAATCGCAA
5192958 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5192991 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* **
5193024 TGCGCTTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5193050 TGGTTTCGCG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.07, C:0.20, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:5193416 original size:91 final size:93
Alignment explanation
Indices: 5193129--5193506 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
5193119 TTGAATGGAT
5193129 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5193193 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5193221 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5193286 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5193314 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5193377 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5193405 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5193470 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5193498 AAATTTACT
1 AAATTTACT
5193507 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
91 75 0.27
92 69 0.25
93 136 0.49
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5193439 original size:184 final size:185
Alignment explanation
Indices: 5193129--5193506 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 185
5193119 TTGAATGGAT
5193129 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
5193194 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
5193259 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
5193314 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATATATTTCACAGTGTTAAAGAATATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
5193378 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
5193443 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5193498 AAATTTACT
1 AAATTTACT
5193507 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
184 168 0.88
185 23 0.12
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5195228 original size:14 final size:14
Alignment explanation
Indices: 5195209--5195298 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5195199 TTGAAATGAA
5195209 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5195223 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5195240 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5195256 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5195275 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5195289 AATCGCAACG
1 AATCGCAACG
5195299 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5195246 original size:33 final size:33
Alignment explanation
Indices: 5195201--5195315 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5195191 TCTTTTGGTT
5195201 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5195234 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5195267 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5195300 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5195316 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5195247 original size:19 final size:18
Alignment explanation
Indices: 5195208--5195320 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5195198 GTTGAAATGA
5195208 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5195223 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5195240 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5195256 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5195273 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
5195289 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5195306 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5195321 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5195351 original size:14 final size:14
Alignment explanation
Indices: 5195332--5195386 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5195322 TTTGGTTTCG
5195332 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5195346 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5195365 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5195379 CGTTGCGA
1 CGTTGCGA
5195387 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5195364 original size:33 final size:33
Alignment explanation
Indices: 5195316--5195386 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5195306 AAAATCGCAA
**
5195316 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5195349 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5195382 TGCGA
1 TGCGA
5195387 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5195394 original size:33 final size:34
Alignment explanation
Indices: 5195329--5195449 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 34
5195319 GATTTTGGTT
***
5195329 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT-
1 TCGCGTTGCGATTCTCTCGTTGCGACAGTCATTC
5195362 TCGCGTTGCGATTCTCTCGTTGCGACAGTCATTC
1 TCGCGTTGCGATTCTCTCGTTGCGACAGTCATTC
*
5195396 TCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTCATTC
1 TCGCGTTGCGA--TTC-----TCTCGTTGCGACAGTCATTC
*
5195437 TCTCGTTGCGATT
1 TCGCGTTGCGATT
5195450 TTCATTTATC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
33 30 0.39
34 10 0.13
36 3 0.04
39 2 0.03
41 31 0.41
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.42
Consensus pattern (34 bp):
TCGCGTTGCGATTCTCTCGTTGCGACAGTCATTC
Found at i:5195422 original size:21 final size:21
Alignment explanation
Indices: 5195396--5195468 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
5195386 ACAGTCATTC
5195396 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
*** *
5195417 TCTCGTTGCGACAGTCA-TTC
1 TCTCGTTGCGATTTTCATTTA
5195437 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
5195458 TCTCGTTGCGA
1 TCTCGTTGCGA
5195469 CTCTTCTGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTA
Found at i:5195433 original size:41 final size:41
Alignment explanation
Indices: 5195376--5195469 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
5195366 GTTGCGATTC
5195376 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
5195417 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
5195458 TCTCGTTGCGAC
1 TCTCGTTGCGAC
5195470 TCTTCTGCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.43
Consensus pattern (41 bp):
TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
Found at i:5195454 original size:20 final size:20
Alignment explanation
Indices: 5195339--5195468 Score: 112
Period size: 20 Copynumber: 6.8 Consensus size: 20
5195329 TCGCGTTGCG
5195339 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
5195359 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
5195372 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
5195392 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
5195412 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
5195433 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
5195453 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
5195469 CTCTTCTGCA
Statistics
Matches: 87, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
13 3 0.03
14 9 0.10
19 9 0.10
20 37 0.43
21 29 0.33
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:5195590 original size:33 final size:33
Alignment explanation
Indices: 5195548--5195618 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5195538 AATACTAACT
*
5195548 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5195581 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5195614 TGAAA
1 TGAAA
5195619 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5195851 original size:22 final size:22
Alignment explanation
Indices: 5195799--5195853 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5195789 TGGTTGTGAG
**
5195799 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5195821 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5195843 GGATTTCTTCG
1 GGATTTCTTCG
5195854 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5196024 original size:20 final size:20
Alignment explanation
Indices: 5195999--5196191 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
5195989 CTTTAAATAT
5195999 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5196019 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5196041 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5196060 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5196080 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5196100 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5196120 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5196140 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5196160 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5196180 CGCGTTGCGATT
1 CGCGTTGCGATT
5196192 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5196186 original size:60 final size:60
Alignment explanation
Indices: 5195999--5196191 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
5195989 CTTTAAATAT
**
5195999 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
5196060 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
5196120 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
5196180 CGCGTTGCGATT
1 CGCGTTGCGATT
5196192 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:5196272 original size:20 final size:20
Alignment explanation
Indices: 5196247--5196298 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5196237 AAGAATCGCG
*
5196247 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5196267 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5196287 TTGCGATTCTGG
1 TTGCGATTCTGG
5196299 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:5196992 original size:22 final size:23
Alignment explanation
Indices: 5196949--5196992 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5196939 GATGTTGTTT
* *
5196949 TAAAAATAATAAATAATTTTATA
1 TAAAAATAAGAAATAATATTATA
*
5196972 TAAAATTAAGAAAT-ATATTAT
1 TAAAAATAAGAAATAATATTAT
5196993 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAATAAGAAATAATATTATA
Found at i:5213254 original size:8 final size:8
Alignment explanation
Indices: 5213237--5213276 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5213227 TAAAATTTTA
5213237 TTTTAA-T
1 TTTTAATT
5213244 TTTTAA-T
1 TTTTAATT
5213251 TTTTAATT
1 TTTTAATT
5213259 TTTTAATT
1 TTTTAATT
*
5213267 TTTTTATT
1 TTTTAATT
5213275 TT
1 TT
5213277 AAACTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Found at i:5213276 original size:7 final size:7
Alignment explanation
Indices: 5213237--5213269 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5213227 TAAAATTTTA
5213237 TTTTAAT
1 TTTTAAT
5213244 TTTTAAT
1 TTTTAAT
5213251 TTTTAATT
1 TTTTAA-T
5213259 TTTTAAT
1 TTTTAAT
5213266 TTTT
1 TTTT
5213270 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:5213276 original size:15 final size:14
Alignment explanation
Indices: 5213237--5213269 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
5213227 TAAAATTTTA
5213237 TTTTAATTTTTAAT
1 TTTTAATTTTTAAT
5213251 TTTTAATTTTTTAAT
1 TTTTAA-TTTTTAAT
5213266 TTTT
1 TTTT
5213270 TTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTAATTTTTAAT
Found at i:5214233 original size:21 final size:20
Alignment explanation
Indices: 5214147--5214304 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
5214137 AAATGACCAA
**
5214147 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5214166 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5214186 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5214206 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5214227 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* ** *
5214248 CAAATTCGCATTGTGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5214268 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5214289 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5214305 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5214333 original size:20 final size:20
Alignment explanation
Indices: 5214271--5214540 Score: 260
Period size: 20 Copynumber: 13.5 Consensus size: 20
5214261 TGATTTTCCA
* ** *
5214271 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5214291 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5214311 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5214331 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5214351 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5214371 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
5214391 ATATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5214411 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5214431 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5214451 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5214471 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5214491 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5214511 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
5214531 AAATCACAAC
1 AAATCGCAAC
5214541 ACTGAAATTT
Statistics
Matches: 209, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 205 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5214357 original size:40 final size:40
Alignment explanation
Indices: 5214310--5214540 Score: 297
Period size: 40 Copynumber: 5.8 Consensus size: 40
5214300 CGCGAACACA
* * *
5214310 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCG
* * *
5214350 TATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAA--CGATAATCCG
* * *
5214390 TATATCGCAACGTGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
5214430 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
5214470 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
5214510 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCCGTAAATCGCAAC
5214541 ACTGAAATTT
Statistics
Matches: 180, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 174 0.97
42 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
Found at i:5214357 original size:60 final size:60
Alignment explanation
Indices: 5214291--5214540 Score: 290
Period size: 60 Copynumber: 4.2 Consensus size: 60
5214281 GCGAATATGA
* *
5214291 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
* * * * *
5214351 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
* * * * *
5214411 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
* * * * *
5214471 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGTGTATCCGT
*
5214531 AAATCACAAC
1 AAATCGCAAC
5214541 ACTGAAATTT
Statistics
Matches: 163, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
60 161 0.99
61 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
Found at i:5215262 original size:24 final size:24
Alignment explanation
Indices: 5215223--5215269 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5215213 AAATTTGGTC
5215223 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5215247 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5215270 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5217747 original size:33 final size:34
Alignment explanation
Indices: 5217696--5217911 Score: 201
Period size: 33 Copynumber: 6.2 Consensus size: 34
5217686 CGGAAATTAC
* *
5217696 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
5217729 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
5217763 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* * *
5217801 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
5217840 AAT-GCGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
5217872 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
5217905 AATCGCA
1 AATCGCA
5217912 TTGCGATTCT
Statistics
Matches: 157, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.01
32 7 0.04
33 68 0.43
34 16 0.10
36 1 0.01
38 41 0.26
39 22 0.14
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:5217779 original size:19 final size:19
Alignment explanation
Indices: 5217710--5217917 Score: 257
Period size: 19 Copynumber: 11.7 Consensus size: 19
5217700 GCAACGAGAG
5217710 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5217729 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5217743 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5217763 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5217782 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5217801 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5217820 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5217834 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5217853 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5217872 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
5217886 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
5217905 AATCGCATTGCGA
1 AATCGCAATGCGA
5217918 TTCTCCCGTT
Statistics
Matches: 165, Mismatches: 8, Indels: 32
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.19
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 103 0.62
20 16 0.10
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5217849 original size:52 final size:52
Alignment explanation
Indices: 5217738--5217917 Score: 279
Period size: 52 Copynumber: 3.3 Consensus size: 52
5217728 AAATCCCAAC
*
5217738 ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
5217796 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
5217848 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
5217900 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
5217918 TTCTCCCGTT
Statistics
Matches: 119, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
52 84 0.71
53 1 0.01
55 2 0.02
57 16 0.13
58 16 0.13
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.16
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:5217966 original size:19 final size:19
Alignment explanation
Indices: 5217926--5218023 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5217916 GATTCTCCCG
5217926 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5217946 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5217965 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5217979 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5217998 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5218017 TTGCGAT
1 TTGCGAT
5218024 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5218020 original size:52 final size:53
Alignment explanation
Indices: 5217907--5218023 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
5217897 GAAATTAAAA
5217907 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
5217960 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5218012 TCGCATTGCGAT
1 TCGCATTGCGAT
5218024 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:5218149 original size:14 final size:14
Alignment explanation
Indices: 5218130--5218166 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5218120 CATCAATTAC
5218130 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5218144 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5218158 ACAAATCAA
1 ACAAATCAA
5218167 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5220125 original size:19 final size:20
Alignment explanation
Indices: 5220085--5220131 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5220075 TAGTTTACTT
* *
5220085 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
5220105 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
5220124 TCGCAACG
1 TCGCAACG
5220132 ACAGAATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:5220141 original size:14 final size:14
Alignment explanation
Indices: 5220122--5220178 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5220112 GCGAAACCAA
*
5220122 AATCGCAACGACAG
1 AATCGCAACGAAAG
5220136 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5220153 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5220169 AATCGCAACG
1 AATCGCAACG
5220179 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5220149 original size:33 final size:33
Alignment explanation
Indices: 5220103--5220195 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5220093 CGAAACTTAA
** *
5220103 AATCGCAACGCGAAACCAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5220136 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5220169 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5220196 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5220160 original size:19 final size:19
Alignment explanation
Indices: 5220136--5220200 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
5220126 GCAACGACAG
5220136 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5220155 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
*
5220169 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5220188 AATCGCAATGCGA
1 AATCGCAATGCGA
5220201 TTTTGGTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 8 0.20
16 6 0.15
17 6 0.15
19 20 0.50
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5220250 original size:20 final size:19
Alignment explanation
Indices: 5220196--5220258 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
5220186 AAAATCGCAA
5220196 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5220215 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5220234 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5220254 TGCGA
1 TGCGA
5220259 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.10, C:0.14, G:0.30, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5220422 original size:93 final size:93
Alignment explanation
Indices: 5220306--5220773 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
5220296 ATGGATTGCA
5220306 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
5220370 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
5220398 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
5220462 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
5220490 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
5220555 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
5220583 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
5220648 TAGCAAAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
5220676 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
5220741 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
5220769 TTACT
1 TTACT
5220774 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 96 0.26
93 274 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:5222496 original size:14 final size:14
Alignment explanation
Indices: 5222477--5222533 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5222467 TTGAAATGAA
5222477 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5222491 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
5222510 AATCGCAACTAGAG
1 AATCGCAACGAGAG
5222524 AATCGCAACG
1 AATCGCAACG
5222534 CGAAAGGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5222509 original size:33 final size:33
Alignment explanation
Indices: 5222469--5222550 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
5222459 TCTTTTGGTT
5222469 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5222502 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5222535 GAAAGGAAAATCGCAA
1 GAAATGAAAATCGCAA
5222551 TGCGATTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5222515 original size:19 final size:18
Alignment explanation
Indices: 5222491--5222555 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
5222481 GCAACGAGAG
5222491 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
* *
5222510 AATCGCAA--C--TAGAG
1 AATCGCAACGCGAAAGAA
5222524 AATCGCAACGCGAAAGGAA
1 AATCGCAACGCGAAA-GAA
*
5222543 AATCGCAATGCGA
1 AATCGCAACGCGA
5222556 TTTTGGTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 22 0.61
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Done.