Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 12 of 21
Found at i:1705876 original size:18 final size:19
Alignment explanation
Indices: 1705849--1705888 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1705839 TAAATATAAA
* *
1705849 ATTAAGATATTTA-TATTT
1 ATTAAAATATTAATTATTT
1705867 ATTAAAATATTAATTATTT
1 ATTAAAATATTAATTATTT
1705886 ATT
1 ATT
1705889 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAAAATATTAATTATTT
Found at i:1705890 original size:29 final size:27
Alignment explanation
Indices: 1705856--1705921 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1705846 AAAATTAAGA
*
1705856 TATTTATATTTATTAAAATATTAATTATT
1 TATTT-TATTTATTAAAA-AATAATTATT
*
1705885 TA-TTTATTT-TTAAAAAATAATTTTT
1 TATTTTATTTATTAAAAAATAATTATT
1705910 TATTTTTATTTA
1 TA-TTTTATTTA
1705922 ACAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 10 0.31
26 6 0.19
27 12 0.38
28 2 0.06
29 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTATTTATTAAAAAATAATTATT
Found at i:1705900 original size:27 final size:26
Alignment explanation
Indices: 1705856--1705941 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 26
1705846 AAAATTAAGA
*
1705856 TATTTATATTTATTAAAATATTAATTATT
1 TATTTAT-TTT-TAAAAATA-TAATTATT
*
1705885 TATTTATTTTTAAAAA-ATAATTTTT
1 TATTTATTTTTAAAAATATAATTATT
1705910 TATTT-TTATTTAACAAATATAA-TATAT
1 TATTTATT-TTTAA-AAATATAATTAT-T
1705937 TATTT
1 TATTT
1705942 TTCAAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.04
25 17 0.34
26 6 0.12
27 15 0.30
28 3 0.06
29 7 0.14
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTATTTTTAAAAATATAATTATT
Found at i:1705905 original size:25 final size:25
Alignment explanation
Indices: 1705862--1705954 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
1705852 AAGATATTTA
*
1705862 TATTTATTAAAATATTAATTATTTATT
1 TATTT-TTAAAA-AATAATTATTTATT
*
1705889 TATTTTTAAAAAATAATTTTTTATT
1 TATTTTTAAAAAATAATTATTTATT
* * *
1705914 T-TTATTTAACAAAT-ATAATATA-T
1 TATT-TTTAAAAAATAATTATTTATT
*
1705937 TATTTTTCAAAAA-AATTA
1 TATTTTTAAAAAATAATTA
1705955 AAAAAGGGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 12 0.22
24 9 0.17
25 22 0.41
26 6 0.11
27 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTTTAAAAAATAATTATTTATT
Found at i:1705942 original size:27 final size:24
Alignment explanation
Indices: 1705870--1705943 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 24
1705860 TATATTTATT
1705870 AAAATATTAATTATTTATTTATTTTTA
1 AAAATA-TAATTA-TTATTT-TTTTTA
*
1705897 AAAA-ATAATTTTTTATTTTTATTTA
1 AAAATATAA-TTATTATTTTT-TTTA
1705922 ACAAATATAATATATTATTTTT
1 A-AAATATAAT-TATTATTTTT
1705944 CAAAAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
24 2 0.05
25 14 0.35
26 7 0.17
27 17 0.43
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
AAAATATAATTATTATTTTTTTTA
Found at i:1706362 original size:14 final size:14
Alignment explanation
Indices: 1706346--1706395 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1706336 ATTTATATAA
1706346 ATTA-TAAATTTTT
1 ATTATTAAATTTTT
*
1706359 AATTTATTAAA-TTAT
1 -A-TTATTAAATTTTT
1706374 ATTATTAAATTTTT
1 ATTATTAAATTTTT
1706388 ATTATTAA
1 ATTATTAA
1706396 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 8 0.26
14 13 0.42
15 6 0.19
16 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATTAAATTTTT
Found at i:1706362 original size:28 final size:26
Alignment explanation
Indices: 1706342--1706402 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 26
1706332 ATTAATTTAT
1706342 ATAAATTA-TAAATTTTTAATTTATTAA
1 ATAAATTATTAAATTTTTAA-TTATT-A
*
1706369 ATTATATTATTAAATTTTT-ATTATTA
1 A-TAAATTATTAAATTTTTAATTATTA
1706395 ATAAATTA
1 ATAAATTA
1706403 AATTATCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.20
26 2 0.07
27 6 0.20
28 7 0.23
29 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATAAATTATTAAATTTTTAATTATTA
Found at i:1706402 original size:30 final size:30
Alignment explanation
Indices: 1706343--1706421 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1706333 TTAATTTATA
* *
1706343 TAAATTA-TAAATTTTTAAT-TTATTAAAT
1 TAAATTATTAAATTTTTATTATTAATAAAT
*
1706371 TATATTATTAAATTTTTATTATTAATAAAT
1 TAAATTATTAAATTTTTATTATTAATAAAT
*
1706401 TAAATTATCTTAA-TTTTATTA
1 TAAATTAT-TAAATTTTTATTA
1706422 AATAATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 6 0.14
29 11 0.26
30 23 0.53
31 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
TAAATTATTAAATTTTTATTATTAATAAAT
Found at i:1706578 original size:14 final size:14
Alignment explanation
Indices: 1706559--1706585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1706549 TTAATTTATA
1706559 AATAATATAAATTT
1 AATAATATAAATTT
1706573 AATAATATAAATT
1 AATAATATAAATT
1706586 AATGAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATATAAATTT
Found at i:1707094 original size:8 final size:8
Alignment explanation
Indices: 1707070--1707156 Score: 94
Period size: 8 Copynumber: 11.1 Consensus size: 8
1707060 TATTAAAATT
1707070 TATAT-AA
1 TATATAAA
1707077 TATA-AAA
1 TATATAAA
*
1707084 TAT-TTAA
1 TATATAAA
*
1707091 -ATATAAT
1 TATATAAA
1707098 TATA-AAA
1 TATATAAA
1707105 TATATAAA
1 TATATAAA
1707113 TATATAAA
1 TATATAAA
1707121 TATATAAA
1 TATATAAA
1707129 TATATAAA
1 TATATAAA
1707137 TATAATACGAA
1 TAT-ATA--AA
1707148 TATATAAA
1 TATATAAA
1707156 T
1 T
1707157 TATCAAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
6 2 0.03
7 19 0.28
8 36 0.53
9 3 0.04
10 3 0.04
11 5 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:1708773 original size:30 final size:30
Alignment explanation
Indices: 1708738--1708830 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
1708728 ATTTAAATTA
*
1708738 GATAGTGGTGCATTAATCCTTAATTTAAGG
1 GATAGTGGTGCACTAATCCTTAATTTAAGG
* * * *
1708768 GATAGTGATGCACTAATCTTTAATCTAAGA
1 GATAGTGGTGCACTAATCCTTAATTTAAGG
* *
1708798 GATAATGGTGCACTAGTCCTTAATTTAAGG
1 GATAGTGGTGCACTAATCCTTAATTTAAGG
1708828 GAT
1 GAT
1708831 TTAAATTAGT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (30 bp):
GATAGTGGTGCACTAATCCTTAATTTAAGG
Found at i:1713044 original size:26 final size:26
Alignment explanation
Indices: 1713010--1713068 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 26
1713000 CCCTTTGATT
1713010 ACCATAACAATAAGTAATATTTTAAGA
1 ACCA-AACAATAAGTAATATTTTAAGA
1713037 ACCAAACAATAAGTAATATTTTAAGA
1 ACCAAACAATAAGTAATATTTTAAGA
1713063 ACCAAA
1 ACCAAA
1713069 TCATAGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (26 bp):
ACCAAACAATAAGTAATATTTTAAGA
Found at i:1716415 original size:35 final size:35
Alignment explanation
Indices: 1716346--1716415 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1716336 TTTCCATCTT
* *
1716346 TCACAAGTGAAGAATGACATATCATTCCATAAATA
1 TCACAAGTGAAGAATGAAATATCATTCCAAAAATA
*
1716381 TCACAAGTGAAGAATGAAACTAT-ATTTCAAAAATA
1 TCACAAGTGAAGAATGAAA-TATCATTCCAAAAATA
1716416 ATTATAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (35 bp):
TCACAAGTGAAGAATGAAATATCATTCCAAAAATA
Found at i:1720671 original size:8 final size:8
Alignment explanation
Indices: 1720619--1720677 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
1720609 GTTACATTTA
1720619 TTTTATAT
1 TTTTATAT
*
1720627 TTTTAAAT
1 TTTTATAT
1720635 TATATTATA-
1 T-T-TTATAT
1720644 TTTTA-AT
1 TTTTATAT
*
1720651 TATTAT-T
1 TTTTATAT
1720658 TATTTATAT
1 T-TTTATAT
1720667 TTTTATAT
1 TTTTATAT
1720675 TTT
1 TTT
1720678 ATCTTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
6 1 0.02
7 9 0.22
8 23 0.56
9 4 0.10
10 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTATAT
Found at i:1721542 original size:17 final size:17
Alignment explanation
Indices: 1721520--1721591 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
1721510 AGGTTAATAT
1721520 TAAATAT-AATAAGATCA
1 TAAATATGAATAAGAT-A
*
1721537 TAAATATGAATACGATA
1 TAAATATGAATAAGATA
* *
1721554 TAAATAATTAATTAAAATA
1 TAAAT-ATGAA-TAAGATA
* *
1721573 T-AATATAAATATGATA
1 TAAATATGAATAAGATA
1721589 TAA
1 TAA
1721592 TATAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
16 6 0.14
17 18 0.41
18 14 0.32
19 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
TAAATATGAATAAGATA
Found at i:1721582 original size:11 final size:11
Alignment explanation
Indices: 1721514--1721617 Score: 51
Period size: 11 Copynumber: 9.5 Consensus size: 11
1721504 TTAAATAGGT
1721514 TAATATTAAATA
1 TAATA-TAAATA
*
1721526 TAATA-AGATCA
1 TAATATAAAT-A
*
1721537 TAAATATGAATA
1 T-AATATAAATA
**
1721549 CGATATAAATAA
1 TAATATAAAT-A
1721561 TTAAT-TAAAATA
1 -TAATAT-AAATA
1721573 TAATATAAATA
1 TAATATAAATA
*
1721584 TGATAT-AATA
1 TAATATAAATA
1721594 T-A-A-AAA-A
1 TAATATAAATA
*
1721601 TAATATAAACA
1 TAATATAAATA
1721612 TAATAT
1 TAATAT
1721618 GATACATAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 25
0.68 0.09 0.24
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 2 0.03
10 11 0.15
11 30 0.42
12 14 0.20
13 8 0.11
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1721603 original size:28 final size:24
Alignment explanation
Indices: 1721551--1721609 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 24
1721541 TATGAATACG
*
1721551 ATATAAATAATTAATTAAAATATA
1 ATATAAATAATTAATTAAAAAATA
1721575 ATATAAATATGATATAATATAAAAAATA
1 ATATAAATA--AT-TAAT-TAAAAAATA
1721603 ATATAAA
1 ATATAAA
1721610 CATAATATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.30
26 2 0.07
27 4 0.13
28 15 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATAAATAATTAATTAAAAAATA
Found at i:1721617 original size:28 final size:27
Alignment explanation
Indices: 1721557--1721617 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
1721547 TACGATATAA
* *
1721557 ATAAT-TAATTAAAATATAATATAAAT
1 ATAATATAATTAAAAAATAATATAAAC
*
1721583 ATGATATAATATAAAAAATAATATAAAC
1 ATAATATAAT-TAAAAAATAATATAAAC
1721611 ATAATAT
1 ATAATAT
1721618 GATACATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.14
27 4 0.14
28 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATATAATTAAAAAATAATATAAAC
Found at i:1723547 original size:2 final size:2
Alignment explanation
Indices: 1723540--1723573 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1723530 GTAGTGCTTG
* *
1723540 TA TA TA TA CA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1723574 AATAATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1724278 original size:26 final size:25
Alignment explanation
Indices: 1724218--1724283 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
1724208 AAATTTTGAG
* *
1724218 TAAATAAAAAATATTTAACTATTTATT
1 TAAAT-AAAAA-ATTTAACTATTAATA
*
1724245 TGATATAAAAAATTTAACTATTAAATA
1 T-AAATAAAAAATTTAACTATT-AATA
1724272 TAAATAAAAAAT
1 TAAATAAAAAAT
1724284 AATATTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 21 0.64
27 9 0.27
28 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
TAAATAAAAAATTTAACTATTAATA
Found at i:1725432 original size:14 final size:15
Alignment explanation
Indices: 1725413--1725441 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1725403 TTTTTATTTA
1725413 TTTTTATT-CAAAAT
1 TTTTTATTACAAAAT
1725427 TTTTTATTACAAAAT
1 TTTTTATTACAAAAT
1725442 AATAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTATTACAAAAT
Found at i:1725491 original size:18 final size:18
Alignment explanation
Indices: 1725444--1725495 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
1725434 TACAAAATAA
*
1725444 TAAAA-ATTTAATTAATTT
1 TAAAATATTTAA-TAAATT
1725462 TAAAATTATTTAATAAATT
1 TAAAA-TATTTAATAAATT
1725481 TAAAATATTTAATAA
1 TAAAATATTTAATAA
1725496 GTACTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATATTTAATAAATT
Found at i:1725877 original size:146 final size:145
Alignment explanation
Indices: 1725691--1725965 Score: 360
Period size: 146 Copynumber: 1.9 Consensus size: 145
1725681 TATTTTTTTG
* *
1725691 TTTTAATAAATTTCTTTATCACTAACTTTTTGAAATAATTTTGTGAATTTATTTCAAAT-AAAAA
1 TTTTAATAAATTTCTTTAACACTAACTTTTTGAAATAATTTTATGAATTTATTT-AAATAAAAAA
* *
1725755 CATAATATATTAATCTCAAAGTTAATAGATTGA-ATTAAA-AAAAATTTAAAATATTTAACATGT
65 CATAATACATTAATATCAAAGTTAATAGATT-ATATTAAAGAAAAATTTAAAATATTTAACATGT
1725818 ACTTGTATTAGAATTGA
129 ACTTGTATTAGAATTGA
* * *
1725835 TTTTAATCAATTTATTTTAACACTAAACTTCTTT-AAATAATTTTATTAATTTATTTAAATAAAA
1 TTTTAATAAATTT-CTTTAACACT-AACTT-TTTGAAATAATTTTATGAATTTATTTAAATAAAA
* * * * * *
1725899 AACATGATACATTTATATCAAAGTTAATATATTATATTAAAGATAAGTTTAAAATATTTAGCATG
63 AACATAATACATTAATATCAAAGTTAATAGATTATATTAAAGAAAAATTTAAAATATTTAACATG
1725964 TA
128 TA
1725966 TTTCAATTTA
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
144 12 0.11
145 13 0.12
146 62 0.55
147 25 0.22
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (145 bp):
TTTTAATAAATTTCTTTAACACTAACTTTTTGAAATAATTTTATGAATTTATTTAAATAAAAAAC
ATAATACATTAATATCAAAGTTAATAGATTATATTAAAGAAAAATTTAAAATATTTAACATGTAC
TTGTATTAGAATTGA
Found at i:1725999 original size:11 final size:11
Alignment explanation
Indices: 1725970--1726005 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1725960 CATGTATTTC
*
1725970 AATTTAAATAT
1 AATTTAATTAT
1725981 AATTTAATTAT
1 AATTTAATTAT
*
1725992 AATTTAATTTT
1 AATTTAATTAT
1726003 AAT
1 AAT
1726006 AGTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTAT
Found at i:1726014 original size:27 final size:28
Alignment explanation
Indices: 1725965--1726023 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1725955 TTTAGCATGT
**
1725965 ATTTCAATTTAAATATAATTTAATTATA
1 ATTTCAATTTAAATATAATTTAAAAATA
*
1725993 ATTT-AATTTTAATAGTAA-TTAAAAATA
1 ATTTCAATTTAAATA-TAATTTAAAAATA
1726020 ATTT
1 ATTT
1726024 TAAAACTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTCAATTTAAATATAATTTAAAAATA
Found at i:1726021 original size:22 final size:22
Alignment explanation
Indices: 1725996--1726037 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1725986 AATTATAATT
* *
1725996 TAATTTTAATAGTAATTAAAAA
1 TAATTTTAAAACTAATTAAAAA
1726018 TAATTTTAAAACTAATTAAA
1 TAATTTTAAAACTAATTAAA
1726038 TTCTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATTTTAAAACTAATTAAAAA
Found at i:1728880 original size:2 final size:2
Alignment explanation
Indices: 1728873--1728903 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1728863 CCACACCTAG
1728873 AT 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 AT A
1728904 GCCCTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1735265 original size:83 final size:84
Alignment explanation
Indices: 1735132--1735304 Score: 321
Period size: 83 Copynumber: 2.1 Consensus size: 84
1735122 TGATGATAGC
1735132 TGATAAGCCCATCTTAAAGAAAAAAAAAAAAACCATTAAAAATAATGCAAATAAATCAGTTTCGA
1 TGATAAGCCCATCTTAAAGAAAAAAAAAAAAACCATTAAAAATAATGCAAATAAATCAGTTTCGA
1735197 ATGGTCGAAGCACAATAAT
66 ATGGTCGAAGCACAATAAT
* *
1735216 TGATAAGCCCATCTTAAAG-AAAAAAAAAACACCATTAAAATTAATGCAAATAAATCAGTTTCGA
1 TGATAAGCCCATCTTAAAGAAAAAAAAAAAAACCATTAAAAATAATGCAAATAAATCAGTTTCGA
1735280 ATGGTCGAAGCACAATAAT
66 ATGGTCGAAGCACAATAAT
1735299 TGATAA
1 TGATAA
1735305 ATGACCTATG
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 68 0.78
84 19 0.22
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (84 bp):
TGATAAGCCCATCTTAAAGAAAAAAAAAAAAACCATTAAAAATAATGCAAATAAATCAGTTTCGA
ATGGTCGAAGCACAATAAT
Found at i:1746931 original size:31 final size:31
Alignment explanation
Indices: 1746891--1746957 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1746881 ATAAAAAGAA
1746891 AAAGA-TAATCAAATTACCTATACTGAATTC
1 AAAGACTAATCAAATTACCTATACTGAATTC
1746921 AAAGACTAATCAAATTACCTATACTGAATTC
1 AAAGACTAATCAAATTACCTATACTGAATTC
1746952 AAAGAC
1 AAAGAC
1746958 GACGACAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (31 bp):
AAAGACTAATCAAATTACCTATACTGAATTC
Found at i:1749431 original size:2 final size:2
Alignment explanation
Indices: 1749424--1749455 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1749414 TGGAAATGTA
*
1749424 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1749456 TGGCGGTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1753759 original size:29 final size:29
Alignment explanation
Indices: 1753727--1753824 Score: 71
Period size: 29 Copynumber: 3.4 Consensus size: 29
1753717 GTAGTGGTAC
1753727 TTTTGATATAATTACTTTGATACATATAT
1 TTTTGATATAATTACTTTGATACATATAT
1753756 TTTT--TATACATGTACTTT-A-ACATAAATAT
1 TTTTGATATA-AT-TACTTTGATACAT--ATAT
* * * * *
1753785 TTTTAATACAAATATTTTGATATA-AGTAT
1 TTTTGATATAATTACTTTGATACATA-TAT
1753814 TTTTGATATAA
1 TTTTGATATAA
1753825 ACATTTTGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
27 8 0.15
28 4 0.07
29 35 0.65
30 2 0.04
31 5 0.09
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (29 bp):
TTTTGATATAATTACTTTGATACATATAT
Found at i:1753814 original size:14 final size:14
Alignment explanation
Indices: 1753777--1753838 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1753767 GTACTTTAAC
*
1753777 ATAAATATTTTTAAT
1 ATAAATA-TTTTGAT
*
1753792 ACAAATATTTTGAT
1 ATAAATATTTTGAT
*
1753806 ATAAGTATTTTTGAT
1 ATAAATA-TTTTGAT
* *
1753821 ATAAACATTTTGAC
1 ATAAATATTTTGAT
1753835 ATAA
1 ATAA
1753839 CAACTTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 21 0.54
15 18 0.46
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (14 bp):
ATAAATATTTTGAT
Found at i:1753817 original size:15 final size:15
Alignment explanation
Indices: 1753777--1753831 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1753767 GTACTTTAAC
*
1753777 ATAAATATTTTTAAT
1 ATAAATATTTTTGAT
*
1753792 ACAAATA-TTTTGAT
1 ATAAATATTTTTGAT
*
1753806 ATAAGTATTTTTGAT
1 ATAAATATTTTTGAT
*
1753821 ATAAACATTTT
1 ATAAATATTTT
1753832 GACATAACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (15 bp):
ATAAATATTTTTGAT
Found at i:1753830 original size:29 final size:29
Alignment explanation
Indices: 1753775--1753838 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1753765 ATGTACTTTA
*
1753775 ACATAAATATTTTTAATACAAATATTTTG
1 ACATAAATATTTTTAATACAAACATTTTG
* * * *
1753804 ATATAAGTATTTTTGATATAAACATTTTG
1 ACATAAATATTTTTAATACAAACATTTTG
1753833 ACATAA
1 ACATAA
1753839 CAACTTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
ACATAAATATTTTTAATACAAACATTTTG
Found at i:1756431 original size:29 final size:29
Alignment explanation
Indices: 1756391--1756446 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1756381 TAAAATGAAA
*
1756391 AAAATAATTAATT-TAAATAAAATAAAATC
1 AAAATAATTAATTGCAAA-AAAATAAAATC
1756420 AAAATCAA-TAATTGCAAAAAAATAAAA
1 AAAAT-AATTAATTGCAAAAAAATAAAA
1756447 AAAATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (29 bp):
AAAATAATTAATTGCAAAAAAATAAAATC
Found at i:1757171 original size:29 final size:29
Alignment explanation
Indices: 1757114--1757173 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1757104 ATTTATTTCT
*
1757114 ATTAAATGAATAAATAATTTTTAAGAAAA
1 ATTAAATGAATAAATAATTTTAAAGAAAA
*
1757143 ATTAAAT-AA-AAATAATTAATTAAATAAAA
1 ATTAAATGAATAAATAATT--TTAAAGAAAA
1757172 AT
1 AT
1757174 ATGAGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 2 0.07
29 17 0.63
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
ATTAAATGAATAAATAATTTTAAAGAAAA
Found at i:1760904 original size:122 final size:118
Alignment explanation
Indices: 1760687--1760927 Score: 428
Period size: 122 Copynumber: 2.0 Consensus size: 118
1760677 CCAATTACTC
1760687 GTATAACCCATGTTTAGTTTTAAAGGTAGTTTTTCTTTCATCATTCGGTTTCATTCTAATCTGAT
1 GTATAACCCATGTTTAGTTTTAAAGGTAGTTTTTCTTTCATCATTCGGTTTCATTCTAATCTGAT
*
1760752 GCTATCCATTTTTCAAATCAACTTTAGAAAATATGTAAGAACCATACAACTCATATA
66 GCTATCCACTTTTCAAATCAACTTTAG-AAA-A--TAAGAACCATACAACTCATATA
1760809 GTATAACCCATGTTTAGTTTTAAAGGTAGTTTTTCTTTCATCATTCGGTTTCATTCTAATCTGAT
1 GTATAACCCATGTTTAGTTTTAAAGGTAGTTTTTCTTTCATCATTCGGTTTCATTCTAATCTGAT
*
1760874 GCTATCCACTTTTCAAATCAATTTTAGAAAATAAGAACCATACAACTCATATA
66 GCTATCCACTTTTCAAATCAACTTTAGAAAATAAGAACCATACAACTCATATA
1760927 G
1 G
1760928 CATATCATCT
Statistics
Matches: 117, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
118 23 0.20
120 1 0.01
121 3 0.03
122 90 0.77
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (118 bp):
GTATAACCCATGTTTAGTTTTAAAGGTAGTTTTTCTTTCATCATTCGGTTTCATTCTAATCTGAT
GCTATCCACTTTTCAAATCAACTTTAGAAAATAAGAACCATACAACTCATATA
Found at i:1763361 original size:13 final size:13
Alignment explanation
Indices: 1763343--1763367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1763333 CATAAAGTGT
1763343 TGTATCGATACAA
1 TGTATCGATACAA
1763356 TGTATCGATACA
1 TGTATCGATACA
1763368 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1763383 original size:32 final size:33
Alignment explanation
Indices: 1763323--1763388 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1763313 TTCAACGATT
1763323 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
1763356 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1763388 T
1 T
1763389 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1763521 original size:52 final size:52
Alignment explanation
Indices: 1763462--1763590 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
1763452 TACTGATCTT
* *
1763462 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATTGATACATTATAAAA
1 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1763514 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1763566 TGTATCGATACATGTAGGTAAATTT
1 TGTATCGATACATGTAGGCAAATTT
1763591 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (52 bp):
TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1769113 original size:21 final size:21
Alignment explanation
Indices: 1769075--1769114 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1769065 TTTGAGCGAC
*
1769075 AAAATTTAATAAAAAATAAGT
1 AAAATTCAATAAAAAATAAGT
* *
1769096 AAAATTCAATGAATAATAA
1 AAAATTCAATAAAAAATAA
1769115 TATAGAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATTCAATAAAAAATAAGT
Found at i:1769524 original size:2 final size:2
Alignment explanation
Indices: 1769517--1769555 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1769507 TCAAAATCAA
1769517 AT AT AT AT AT 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 AT AT AT AT AT A
1769556 AATCACTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1769676 original size:19 final size:20
Alignment explanation
Indices: 1769646--1769688 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1769636 TCAAGTTAAA
1769646 AAAATCAAAATTTTGAAATC
1 AAAATCAAAATTTTGAAATC
*
1769666 AAAAT-AAAATTTTGAAATT
1 AAAATCAAAATTTTGAAATC
1769685 AAAA
1 AAAA
1769689 ATTTGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATCAAAATTTTGAAATC
Found at i:1771281 original size:18 final size:18
Alignment explanation
Indices: 1771262--1771296 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1771252 TAATATATTA
1771262 AAAT-TTTTAAATTAATT
1 AAATATTTTAAATTAATT
*
1771279 AAATATTTTGAATTAATT
1 AAATATTTTAAATTAATT
1771297 TTTAAAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATATTTTAAATTAATT
Found at i:1771566 original size:53 final size:50
Alignment explanation
Indices: 1771473--1771581 Score: 139
Period size: 53 Copynumber: 2.1 Consensus size: 50
1771463 GACTCATTTA
*
1771473 TAAAATAATATTTTAAATATCATTAAAAAATTAAATAAAATACCAATTAC
1 TAAATTAATATTTTAAATATCATTAAAAAATTAAATAAAATACCAATTAC
* * *
1771523 TAAATTAATCTTTTAAATATATCATTAAAAAAATT-AATCAAAATATCAATTAT
1 TAAATTAATATTTT-AA-ATATCATT-AAAAAATTAAAT-AAAATACCAATTAC
1771576 TAAATT
1 TAAATT
1771582 TTTAATAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 12 0.24
51 2 0.04
52 11 0.22
53 26 0.51
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (50 bp):
TAAATTAATATTTTAAATATCATTAAAAAATTAAATAAAATACCAATTAC
Found at i:1771825 original size:22 final size:21
Alignment explanation
Indices: 1771783--1771849 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1771773 AAAACTAAAA
*
1771783 AATA-AAATTTTTAAATAAATT
1 AATATAAA-TTTTAAAAAAATT
1771804 AATATAAATTTTAAAAAGAATT
1 AATATAAATTTTAAAAA-AATT
*
1771826 --T-TAAATTATTATAAAAATT
1 AATATAAATT-TTAAAAAAATT
1771845 AATAT
1 AATAT
1771850 TTTAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 13 0.34
22 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
AATATAAATTTTAAAAAAATT
Found at i:1771907 original size:19 final size:19
Alignment explanation
Indices: 1771885--1771925 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1771875 ATAAAATTTT
1771885 AAAATAATAAATAAAATAA
1 AAAATAATAAATAAAATAA
** *
1771904 AAAATTTTAAATAAATTAA
1 AAAATAATAAATAAAATAA
1771923 AAA
1 AAA
1771926 TAAATATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATAATAAATAAAATAA
Found at i:1771908 original size:32 final size:33
Alignment explanation
Indices: 1771836--1771908 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
1771826 TTAAATTATT
* * *
1771836 ATAAAAATTAATATTTTAAATATATAATTTAAA
1 ATAAAAAATAAAATTTTAAATATATAATATAAA
*
1771869 A-ACAAAATAAAATTTTAAA-ATAATAA-ATAAA
1 ATAAAAAATAAAATTTTAAATAT-ATAATATAAA
1771900 ATAAAAAAT
1 ATAAAAAAT
1771909 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
31 7 0.21
32 25 0.76
33 1 0.03
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (33 bp):
ATAAAAAATAAAATTTTAAATATATAATATAAA
Found at i:1775202 original size:17 final size:17
Alignment explanation
Indices: 1775182--1775219 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1775172 AGTTTAATTT
1775182 TTTAATG-TTATTTATAA
1 TTTAATGTTTATTTA-AA
1775199 TTT-ATGTTTATTTAAA
1 TTTAATGTTTATTTAAA
1775215 TTTAA
1 TTTAA
1775220 AAATTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTAATGTTTATTTAAA
Found at i:1775493 original size:27 final size:27
Alignment explanation
Indices: 1775454--1775506 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1775444 TTATATTTTG
* *
1775454 TCATTGTACTTTAATTTTA-AAATTTC
1 TCATTATACTTTAACTTTATAAATTTC
1775480 TCATTATACATTTAACTTTATAAATTT
1 TCATTATAC-TTTAACTTTATAAATTT
1775507 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 9 0.39
28 6 0.26
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (27 bp):
TCATTATACTTTAACTTTATAAATTTC
Found at i:1777171 original size:5 final size:5
Alignment explanation
Indices: 1777156--1777197 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
1777146 GATAGCGACG
* * *
1777156 GGGCA GAGCA GGGCA GGGCA GGGCA GGGCT GGGAA GGGCA GG
1 GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GG
1777198 CTATCAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.60, T:0.02
Consensus pattern (5 bp):
GGGCA
Found at i:1779898 original size:21 final size:21
Alignment explanation
Indices: 1779856--1779899 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1779846 TTTTGAAAAA
* *
1779856 TTCATTTATTTTCTTGAGTTT
1 TTCATTTATTTCCTTGAATTT
*
1779877 TTCATTT-TTTCCTTGAAATT
1 TTCATTTATTTCCTTGAATTT
1779897 TTC
1 TTC
1779900 TGTTTTCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.64
Consensus pattern (21 bp):
TTCATTTATTTCCTTGAATTT
Found at i:1780524 original size:10 final size:10
Alignment explanation
Indices: 1780509--1780543 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
1780499 GCTAGTGAAG
1780509 AAAAAGAAAA
1 AAAAAGAAAA
1780519 AAAAAGAAAAA
1 AAAAAG-AAAA
1780530 AAAAAGAAAA
1 AAAAAGAAAA
1780540 AAAA
1 AAAA
1780544 TTAAGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1780529 original size:11 final size:11
Alignment explanation
Indices: 1780509--1780543 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
1780499 GCTAGTGAAG
1780509 AAAAAG-AAAA
1 AAAAAGAAAAA
1780519 AAAAAGAAAAA
1 AAAAAGAAAAA
1780530 AAAAAGAAAAA
1 AAAAAGAAAAA
1780541 AAA
1 AAA
1780544 TTAAGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:1782097 original size:142 final size:143
Alignment explanation
Indices: 1781854--1782114 Score: 357
Period size: 142 Copynumber: 1.8 Consensus size: 143
1781844 ATACTTTTAC
*** * * * *
1781854 GTCGAAGGTACCCCTAGGGGCATTTTTATAATTTTTCTAGGATCGAGTCCTAGTTTGTCACTCTT
1 GTCGAAGGTACCCCTAAAAGCATTTTCATAA-TTTTCTAGAATCGAGTCCTAGGTTATCACTCTT
* *
1781919 ATGCCAAAAGTGTGCACATATGATAGATTCAATCTTTTCAACCCTTTTCAAGTCCTTTAGAAGTG
65 ACGCCAAAAGTGTGCACATATGATAGATTCAATCTTTGCAACCCTTTTCAAGTCCTTTAGAAGTG
1781984 TCGGGAACTTCTAT
130 TCGGGAACTTCTAT
* *
1781998 GTCGAAGGTACCCCTAAAAGCATTTTCATAA-TTTCTAGAATTGAGTCCTAGGTTATCACTGTTA
1 GTCGAAGGTACCCCTAAAAGCATTTTCATAATTTTCTAGAATCGAGTCCTAGGTTATCACTCTTA
* *
1782062 CGCC-GAAG-GTGCACATATAAGATAGATTCACTCTTTGCAACCCTTTTCAAGTC
66 CGCCAAAAGTGTGCACATAT--GATAGATTCAATCTTTGCAACCCTTTTCAAGTC
1782115 TCTTAGGATC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
140 10 0.10
141 3 0.03
142 62 0.61
144 27 0.26
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (143 bp):
GTCGAAGGTACCCCTAAAAGCATTTTCATAATTTTCTAGAATCGAGTCCTAGGTTATCACTCTTA
CGCCAAAAGTGTGCACATATGATAGATTCAATCTTTGCAACCCTTTTCAAGTCCTTTAGAAGTGT
CGGGAACTTCTAT
Found at i:1792508 original size:11 final size:11
Alignment explanation
Indices: 1792469--1792554 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
1792459 TTCCTTTTTT
*
1792469 TGTTTTGCTAC
1 TGTTTTGCTGC
* * *
1792480 TGCTTTGGTTGT
1 TG-TTTTGCTGC
1792492 TGTTTTGCTGC
1 TGTTTTGCTGC
* *
1792503 TGTTTTAGTTGT
1 TGTTTT-GCTGC
1792515 TGTTTTGCTGC
1 TGTTTTGCTGC
* *
1792526 TATTTTGGTTGC
1 TGTTTT-GCTGC
* *
1792538 TCTTTAGCTGC
1 TGTTTTGCTGC
1792549 TGTTTT
1 TGTTTT
1792555 TTCTTTCTTT
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
11 30 0.56
12 24 0.44
ACGTcount: A:0.05, C:0.13, G:0.24, T:0.58
Consensus pattern (11 bp):
TGTTTTGCTGC
Found at i:1792524 original size:23 final size:23
Alignment explanation
Indices: 1792468--1792554 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
1792458 ATTCCTTTTT
* *
1792468 TTGTTTTGCTACTGCTTTGGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
*
1792491 TTGTTTTGCTGCTGTTTTAGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
*
1792514 TTGTTTTGCTGCTATTTTGGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
* * *
1792537 CTCTTTAGCTGCTGTTTT
1 TTGTTTTGCTGCTGTTTT
1792555 TTCTTTCTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.05, C:0.13, G:0.24, T:0.59
Consensus pattern (23 bp):
TTGTTTTGCTGCTGTTTTGGTTG
Found at i:1792648 original size:24 final size:26
Alignment explanation
Indices: 1792604--1792655 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1792594 TATTTCAATT
1792604 TTTTTCTTTCTGTTCTGTTTTGTTTC
1 TTTTTCTTTCTGTTCTGTTTTGTTTC
* *
1792630 TTTTT-TTTCT-TTCTTTTTTTTTTC
1 TTTTTCTTTCTGTTCTGTTTTGTTTC
1792654 TT
1 TT
1792656 AATGGCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 5 0.21
26 5 0.21
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (26 bp):
TTTTTCTTTCTGTTCTGTTTTGTTTC
Found at i:1792742 original size:23 final size:25
Alignment explanation
Indices: 1792696--1792742 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1792686 TTTTTTCTCT
*
1792696 TTTTTTTTCTTCCTTTCTCTCCTTCA
1 TTTTTTTTCTT-CTTTCTCCCCTTCA
1792722 TTTTTTTTCTT-TTT-TCCCCTT
1 TTTTTTTTCTTCTTTCTCCCCTT
1792743 TTATTCTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
26 11 0.55
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTTCTTCTTTCTCCCCTTCA
Found at i:1793239 original size:17 final size:17
Alignment explanation
Indices: 1793217--1793268 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
1793207 TTTCATTTGC
1793217 ATGAAAGCATGCATGAA
1 ATGAAAGCATGCATGAA
*
1793234 ATGAAAGCATGCAAGAA
1 ATGAAAGCATGCATGAA
*
1793251 ATGAAAGTATGCATGAA
1 ATGAAAGCATGCATGAA
1793268 A
1 A
1793269 CAAACATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (17 bp):
ATGAAAGCATGCATGAA
Found at i:1793504 original size:9 final size:8
Alignment explanation
Indices: 1793433--1793532 Score: 53
Period size: 8 Copynumber: 12.0 Consensus size: 8
1793423 CTTAATTATT
*
1793433 TTATTTAA
1 TTATTTTA
* *
1793441 TTAATTAA
1 TTATTTTA
* *
1793449 TTAATTAA
1 TTATTTTA
1793457 TTATTTCTA
1 TTATTT-TA
1793466 TT-TTTTA
1 TTATTTTA
1793473 TATATCTTT-
1 T-TAT-TTTA
* *
1793482 TTACTTAA
1 TTATTTTA
1793490 TTATTTTA
1 TTATTTTA
1793498 TT-TATTTA
1 TTAT-TTTA
1793506 TTTATTATTA
1 -TTATT-TTA
1793516 TTATTATTA
1 TTATT-TTA
1793525 TTATTTTA
1 TTATTTTA
1793533 AATAACTCGA
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
7 6 0.08
8 41 0.54
9 22 0.29
10 7 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTTTA
Found at i:1793531 original size:62 final size:62
Alignment explanation
Indices: 1793368--1793501 Score: 243
Period size: 62 Copynumber: 2.2 Consensus size: 62
1793358 CACCAACATG
*
1793368 ATTTT-TTTAAATTAATTAATTAATTAATTAATTCTATTTTTTATATATCTTTTTACTTAATT
1 ATTTTATTT-AATTAATTAATTAATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATT
1793430 ATTTTATTTAATTAATTAATTAATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATT
1 ATTTTATTTAATTAATTAATTAATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATT
1793492 ATTTTATTTA
1 ATTTTATTTA
1793502 TTTATTTATT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 67 0.96
63 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (62 bp):
ATTTTATTTAATTAATTAATTAATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATT
Found at i:1794603 original size:13 final size:13
Alignment explanation
Indices: 1794585--1794614 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1794575 TTGCCCTAGC
1794585 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
*
1794598 TTTTTTTTTTTCT
1 TTTTTTCTTTTCT
1794611 TTTT
1 TTTT
1794615 GTAATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:1796603 original size:15 final size:16
Alignment explanation
Indices: 1796583--1796621 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1796573 TTTATTTATA
1796583 AAAAATAAATAAG-TT
1 AAAAATAAATAAGATT
*
1796598 AAAAATAAATGAGATT
1 AAAAATAAATAAGATT
1796614 AACAAATA
1 AA-AAATA
1796622 TTTATTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 4 0.19
17 5 0.24
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAAGATT
Found at i:1796685 original size:29 final size:30
Alignment explanation
Indices: 1796626--1796685 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1796616 CAAATATTTA
* *
1796626 TTGTATTTTAATAAAATTTTATTATTTAAT
1 TTGTATTTAAATAAAATTTTATTATTAAAT
*
1796656 TTGTATTTAAATAAATTTTTATT-TTAAAT
1 TTGTATTTAAATAAAATTTTATTATTAAAT
1796685 T
1 T
1796686 AAAATTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (30 bp):
TTGTATTTAAATAAAATTTTATTATTAAAT
Found at i:1798196 original size:27 final size:27
Alignment explanation
Indices: 1798161--1798212 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1798151 TGATCACCAA
*
1798161 AATTGAGAATCAAATTCTATCAACACC
1 AATTAAGAATCAAATTCTATCAACACC
*
1798188 AATTAAGAATCCAATTCTATCAACA
1 AATTAAGAATCAAATTCTATCAACA
1798213 GACCAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (27 bp):
AATTAAGAATCAAATTCTATCAACACC
Found at i:1798852 original size:17 final size:17
Alignment explanation
Indices: 1798830--1798862 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1798820 AAACCAGAAC
1798830 TTCTGCCTCTGGTTTGA
1 TTCTGCCTCTGGTTTGA
*
1798847 TTCTGCTTCTGGTTTG
1 TTCTGCCTCTGGTTTG
1798863 TAGTTGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.24, T:0.52
Consensus pattern (17 bp):
TTCTGCCTCTGGTTTGA
Found at i:1799113 original size:19 final size:19
Alignment explanation
Indices: 1799068--1799113 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1799058 ATGCCGATTG
*
1799068 TGATTTTTTTTTTTTTAAT
1 TGATTTTTGTTTTTTTAAT
*
1799087 TGAGTTTTGTTTTTTTAAT
1 TGATTTTTGTTTTTTTAAT
1799106 TGATTTTT
1 TGATTTTT
1799114 AATTGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (19 bp):
TGATTTTTGTTTTTTTAAT
Found at i:1799799 original size:26 final size:25
Alignment explanation
Indices: 1799748--1799815 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
1799738 ATTTGAATTA
1799748 TTATTTAATATAAAAAAAATATTTT
1 TTATTTAATATAAAAAAAATATTTT
* *
1799773 TTATTTAAATATAATTATAAATA-TTT
1 TTATTT-AATATAA-AAAAAATATTTT
*
1799799 TAATATTAATATAAAAA
1 TTAT-TTAATATAAAAA
1799816 TTTTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 7 0.20
26 20 0.57
27 8 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATTTAATATAAAAAAAATATTTT
Found at i:1799819 original size:20 final size:20
Alignment explanation
Indices: 1799775--1799819 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1799765 AATATTTTTT
* *
1799775 ATTTAAATATAATTATAAAT
1 ATTTTAATATAATTATAAAA
1799795 ATTTTAATATTAA-TATAAAA
1 ATTTTAATA-TAATTATAAAA
1799815 ATTTT
1 ATTTT
1799820 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAATATAATTATAAAA
Found at i:1800332 original size:18 final size:19
Alignment explanation
Indices: 1800309--1800351 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1800299 AAAATTAATA
1800309 AAAAATTA-AAATAAAATT
1 AAAAATTATAAATAAAATT
*
1800327 ATAAA-TATAAATAAAATT
1 AAAAATTATAAATAAAATT
1800345 AAAAATT
1 AAAAATT
1800352 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATTATAAATAAAATT
Found at i:1801602 original size:2 final size:2
Alignment explanation
Indices: 1801597--1801623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1801587 TTAATAAATG
1801597 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1801624 TAAAATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1803447 original size:17 final size:17
Alignment explanation
Indices: 1803425--1803457 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1803415 GAAACCAGAC
1803425 TTCTGCCTCTGGTTTGA
1 TTCTGCCTCTGGTTTGA
*
1803442 TTCTGCTTCTGGTTTG
1 TTCTGCCTCTGGTTTG
1803458 TAGTTGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.24, T:0.52
Consensus pattern (17 bp):
TTCTGCCTCTGGTTTGA
Found at i:1803684 original size:17 final size:17
Alignment explanation
Indices: 1803662--1803707 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1803652 CCGATTGTGA
1803662 TTTTTTTTTTT-TTGAC
1 TTTTTTTTTTTATTGAC
* *
1803678 TTTTTTTTTTAATTGAG
1 TTTTTTTTTTTATTGAC
1803695 TTTTGTTTTTTTA
1 TTTT-TTTTTTTA
1803708 ATTAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
17 8 0.32
18 7 0.28
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTTTATTGAC
Found at i:1803717 original size:19 final size:19
Alignment explanation
Indices: 1803681--1803716 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1803671 TTTTGACTTT
*
1803681 TTTTTTTAATTGAGTTTTG
1 TTTTTTTAATTAAGTTTTG
1803700 TTTTTTTAATTAA-TTTT
1 TTTTTTTAATTAAGTTTT
1803717 TAATTGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTTTTAATTAAGTTTTG
Found at i:1804339 original size:11 final size:11
Alignment explanation
Indices: 1804300--1804385 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
1804290 TTCCTTTTTT
*
1804300 TGTTTTGCTAC
1 TGTTTTGCTGC
* * *
1804311 TGCTTTGGTTGT
1 TG-TTTTGCTGC
1804323 TGTTTTGCTGC
1 TGTTTTGCTGC
* *
1804334 TGTTTTAGTTGT
1 TGTTTT-GCTGC
1804346 TGTTTTGCTGC
1 TGTTTTGCTGC
* *
1804357 TATTTTGGTTGC
1 TGTTTT-GCTGC
* *
1804369 TCTTTAGCTGC
1 TGTTTTGCTGC
1804380 TGTTTT
1 TGTTTT
1804386 TTCTTTCTTT
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
11 30 0.56
12 24 0.44
ACGTcount: A:0.05, C:0.13, G:0.24, T:0.58
Consensus pattern (11 bp):
TGTTTTGCTGC
Found at i:1804355 original size:23 final size:23
Alignment explanation
Indices: 1804299--1804385 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
1804289 ATTCCTTTTT
* *
1804299 TTGTTTTGCTACTGCTTTGGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
*
1804322 TTGTTTTGCTGCTGTTTTAGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
*
1804345 TTGTTTTGCTGCTATTTTGGTTG
1 TTGTTTTGCTGCTGTTTTGGTTG
* * *
1804368 CTCTTTAGCTGCTGTTTT
1 TTGTTTTGCTGCTGTTTT
1804386 TTCTTTCTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.05, C:0.13, G:0.24, T:0.59
Consensus pattern (23 bp):
TTGTTTTGCTGCTGTTTTGGTTG
Found at i:1804479 original size:24 final size:26
Alignment explanation
Indices: 1804435--1804486 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1804425 TATTTCAATT
1804435 TTTTTCTTTCTGTTCTGTTTTGTTTC
1 TTTTTCTTTCTGTTCTGTTTTGTTTC
* *
1804461 TTTTT-TTTCT-TTCTTTTTTTTTTC
1 TTTTTCTTTCTGTTCTGTTTTGTTTC
1804485 TT
1 TT
1804487 AATGGCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 5 0.21
26 5 0.21
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (26 bp):
TTTTTCTTTCTGTTCTGTTTTGTTTC
Found at i:1804574 original size:23 final size:25
Alignment explanation
Indices: 1804528--1804574 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1804518 TTTTTCTCTT
*
1804528 TTTTTTTTCTTCCTTTCTCTCCTTCA
1 TTTTTTTTCTT-CTTTCTCCCCTTCA
1804554 TTTTTTTTCTT-TTT-TCCCCTT
1 TTTTTTTTCTTCTTTCTCCCCTT
1804575 TTATTCTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
26 11 0.55
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTTCTTCTTTCTCCCCTTCA
Found at i:1805020 original size:34 final size:34
Alignment explanation
Indices: 1804982--1805053 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
1804972 ATTGCAAGCC
* **
1804982 TGAATTTGACGTTTGTT-CTTTTATTTAATTTGCA
1 TGAA-TTGACATTTGTTACTTGCATTTAATTTGCA
* *
1805016 TGAATTGGCATTTGTTACTTGCATTTCATTTGCA
1 TGAATTGACATTTGTTACTTGCATTTAATTTGCA
1805050 TGAA
1 TGAA
1805054 AGCATGCATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (34 bp):
TGAATTGACATTTGTTACTTGCATTTAATTTGCA
Found at i:1805071 original size:17 final size:17
Alignment explanation
Indices: 1805049--1805100 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
1805039 TTTCATTTGC
1805049 ATGAAAGCATGCATGAA
1 ATGAAAGCATGCATGAA
*
1805066 ATGAAAGCATGCAAGAA
1 ATGAAAGCATGCATGAA
*
1805083 ATGAAAGTATGCATGAA
1 ATGAAAGCATGCATGAA
1805100 A
1 A
1805101 CAAACATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (17 bp):
ATGAAAGCATGCATGAA
Found at i:1805249 original size:33 final size:32
Alignment explanation
Indices: 1805211--1805322 Score: 103
Period size: 33 Copynumber: 3.6 Consensus size: 32
1805201 TTTTTTTAAA
1805211 TTAATTAATTCTATTTTTTATATATCTTTTTAC
1 TTAATT-ATTCTATTTTTTATATATCTTTTTAC
* ** *
1805244 TTAATTA---T-TTTATT-TA-AT-TAATTAA
1 TTAATTATTCTATTTTTTATATATCTTTTTAC
1805269 TTAATTATTTCTATTTTTTATATATCTTTTTAC
1 TTAATTA-TTCTATTTTTTATATATCTTTTTAC
*
1805302 TTAATTATTTTATTTATTTAT
1 TTAATTATTCTATTT-TTTAT
1805323 TATTATTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
25 11 0.18
26 2 0.03
27 2 0.03
28 5 0.08
29 2 0.03
30 5 0.08
31 2 0.03
32 10 0.16
33 22 0.36
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (32 bp):
TTAATTATTCTATTTTTTATATATCTTTTTAC
Found at i:1805343 original size:58 final size:58
Alignment explanation
Indices: 1805209--1805332 Score: 209
Period size: 58 Copynumber: 2.2 Consensus size: 58
1805199 GATTTTTTTA
*
1805209 AATTAATTAATTCTATTTTTTATATATCTTTTTACTTAATTATTTTATTTAATTAATT
1 AATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATTATTTTATTTAATTAATT
*
1805267 AATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATTATTTTATTT-ATTTATT
1 AATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATTATTTTATTTAATTAATT
1805324 -ATT-ATTATT
1 AATTAATTATT
1805333 ATTATTATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
55 6 0.09
56 3 0.05
57 6 0.09
58 49 0.77
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (58 bp):
AATTAATTATTTCTATTTTTTATATATCTTTTTACTTAATTATTTTATTTAATTAATT
Found at i:1806413 original size:12 final size:12
Alignment explanation
Indices: 1806396--1806425 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1806386 TTTGCCCTAG
1806396 CTTTTTTCTTTT
1 CTTTTTTCTTTT
*
1806408 CTTTTTTTTTTT
1 CTTTTTTCTTTT
1806420 CTTTTT
1 CTTTTT
1806426 GTAATCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:1808054 original size:17 final size:17
Alignment explanation
Indices: 1808032--1808064 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1808022 AAACCAGAAC
1808032 TTCTGCCTCTGGTTTGA
1 TTCTGCCTCTGGTTTGA
*
1808049 TTCTGCTTCTGGTTTG
1 TTCTGCCTCTGGTTTG
1808065 TAGTTGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.24, T:0.52
Consensus pattern (17 bp):
TTCTGCCTCTGGTTTGA
Found at i:1808307 original size:18 final size:17
Alignment explanation
Indices: 1808274--1808312 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1808264 CCGATTGTGA
*
1808274 TTTTTTTTTTTTTTGAC
1 TTTTTTTTTTTATTGAC
*
1808291 TTTTTTTTTTTAATTGAG
1 TTTTTTTTTTT-ATTGAC
1808309 TTTT
1 TTTT
1808313 GTAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTTATTGAC
Found at i:1809027 original size:20 final size:22
Alignment explanation
Indices: 1808990--1809038 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1808980 AAAATATTTT
1808990 TATTTAA-ATATAATTATAAAA
1 TATTTAATATATAATTATAAAA
1809011 TATTTAATAT-TAA-TATAAAA
1 TATTTAATATATAATTATAAAA
*
1809031 TTTTTAAT
1 TATTTAAT
1809039 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.54
21 10 0.38
22 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAATATATAATTATAAAA
Found at i:1809222 original size:30 final size:29
Alignment explanation
Indices: 1809144--1809259 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 29
1809134 TTATTTAAAT
*
1809144 TAAAAAGTATATTTAAATTTAAATT-AAAGA
1 TAAAAA-T-TATTTAAATATAAATTAAAAGA
* *
1809174 TTAAAATT-TTTATGAATATAATTTAAAAGA
1 TAAAAATTATTTA--AATATAAATTAAAAGA
*
1809204 TAAAAATTGATTTAAATAT-CA-TAAAAGTA
1 TAAAAATT-ATTTAAATATAAATTAAAAG-A
1809233 TAAAAATTTATTTAAATA-AAATTAAAA
1 TAAAAA-TTATTTAAATATAAATTAAAA
1809260 TTTTTGTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.06
28 7 0.10
29 26 0.37
30 29 0.41
32 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAAAATTATTTAAATATAAATTAAAAGA
Found at i:1809439 original size:2 final size:2
Alignment explanation
Indices: 1809434--1809467 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1809424 CGAAAAAATC
1809434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1809468 AAAATTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1809527 original size:6 final size:6
Alignment explanation
Indices: 1809518--1809570 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
1809508 TTAATTTAAT
1809518 TTAAAA TTAATAA --AAAA TT-AAA TTAAAA TTATAAA TATAAAA -TAAAA
1 TTAAAA TTAA-AA TTAAAA TTAAAA TTAAAA TTA-AAA T-TAAAA TTAAAA
1809565 TTAAAA
1 TTAAAA
1809571 ATTTTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
4 2 0.05
5 12 0.30
6 15 0.38
7 9 0.22
8 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:1809529 original size:22 final size:22
Alignment explanation
Indices: 1809513--1809568 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1809503 TAATATTAAT
*
1809513 TTAATTTAAAATTAATAAAAAA
1 TTAAATTAAAATTAATAAAAAA
*
1809535 TTAAATTAAAATT-AT-AAATA
1 TTAAATTAAAATTAATAAAAAA
*
1809555 -TAAAATAAAATTAA
1 TTAAATTAAAATTAA
1809569 AAATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.37
20 5 0.17
21 2 0.07
22 12 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATTAAAATTAATAAAAAA
Found at i:1809563 original size:19 final size:18
Alignment explanation
Indices: 1809530--1809573 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1809520 AAAATTAATA
*
1809530 AAAAATTAAATTAAAATT
1 AAAAATTAAAATAAAATT
*
1809548 ATAAATATAAAATAAAATT
1 AAAAAT-TAAAATAAAATT
1809567 AAAAATT
1 AAAAATT
1809574 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTAAAATAAAATT
Found at i:1811836 original size:11 final size:12
Alignment explanation
Indices: 1811820--1811886 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 12
1811810 TTACTTTTTC
1811820 ATATTTTAAAT-
1 ATATTTTAAATA
*
1811831 ATATTTAAAATA
1 ATATTTTAAATA
1811843 ATATTTTAAAAATA
1 ATATTTT--AAATA
*
1811857 ATATTTTTAAAAA
1 ATA-TTTTAAATA
1811870 ATATTTT-AATA
1 ATATTTTAAATA
1811881 ATATTT
1 ATATTT
1811887 ACTTTTCCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 19 0.40
12 10 0.21
13 7 0.15
14 8 0.17
15 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTTTAAATA
Found at i:1811850 original size:38 final size:39
Alignment explanation
Indices: 1811808--1811920 Score: 99
Period size: 38 Copynumber: 2.9 Consensus size: 39
1811798 ATTATTTTAC
1811808 TTTTACTTTTTCATATTTT-AAATATATTTAAAATAATA
1 TTTTACTTTTTCATATTTTAAAATATATTTAAAATAATA
**** * * *
1811846 TTTTA-AAAATAATATTTTTAAAAAATATTT-TAATAATA
1 TTTTACTTTTTCATA-TTTTAAAATATATTTAAAATAATA
*
1811884 -TTTACTTTTCCATATTTTAAAAATAATATTTAAAATA
1 TTTTACTTTTTCATATTTT-AAAAT-ATATTTAAAATA
1811921 TTTTAATTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
37 12 0.22
38 23 0.43
39 15 0.28
40 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.50
Consensus pattern (39 bp):
TTTTACTTTTTCATATTTTAAAATATATTTAAAATAATA
Found at i:1811871 original size:16 final size:14
Alignment explanation
Indices: 1811828--1811883 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
1811818 TCATATTTTA
1811828 AATATATTT-AAAAT
1 AATAT-TTTAAAAAT
1811842 AATATTTTAAAAAT
1 AATATTTTAAAAAT
*
1811856 AATATTTTTAAAA-
1 AATATTTTAAAAAT
*
1811869 AATATTTTAATAAT
1 AATATTTTAAAAAT
1811883 A
1 A
1811884 TTTACTTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 14 0.38
14 23 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATTTTAAAAAT
Found at i:1811883 original size:27 final size:28
Alignment explanation
Indices: 1811828--1811883 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1811818 TCATATTTTA
1811828 AATATATTTAAAATAATATTTTAAAAAT
1 AATATATTTAAAATAATATTTTAAAAAT
* *
1811856 AATATTTTTAAAA-AATATTTTAATAAT
1 AATATATTTAAAATAATATTTTAAAAAT
1811883 A
1 A
1811884 TTTACTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATATTTAAAATAATATTTTAAAAAT
Found at i:1812057 original size:22 final size:22
Alignment explanation
Indices: 1812032--1812073 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1812022 TTTTTTTTAG
* *
1812032 TTGATCATTTTTTTTTAAAATT
1 TTGATCATTTCTTTTGAAAATT
1812054 TTGATCATTTCTTTTGAAAA
1 TTGATCATTTCTTTTGAAAA
1812074 ATTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTGATCATTTCTTTTGAAAATT
Found at i:1812217 original size:2 final size:2
Alignment explanation
Indices: 1812204--1812239 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1812194 AAAAGATAAG
*
1812204 AT AT AT AC 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
1812240 GATTTCGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1813676 original size:22 final size:22
Alignment explanation
Indices: 1813631--1813676 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1813621 TTATAAAACA
* *
1813631 AATTAAATATAATTAATATGAT
1 AATTAAATAAAATTAATATAAT
1813653 AATTAAATAAAATTTAATA-AAT
1 AATTAAATAAAA-TTAATATAAT
1813675 AA
1 AA
1813677 AAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAAATAAAATTAATATAAT
Found at i:1814021 original size:49 final size:49
Alignment explanation
Indices: 1813968--1814070 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
1813958 AAAATGATAA
* * * *
1813968 AATTATGA-ACGATTATATTA-ATATAATACAATTACAATGCATTTATATT
1 AATTATGATACAATTATATTATAT-TAA-ACAATTAAAATACAATTATATT
* *
1814017 AATTATGATATAATTATATTATATTAAATAATTAAAATACAATTATATT
1 AATTATGATACAATTATATTATATTAAACAATTAAAATACAATTATATT
1814066 AATTA
1 AATTA
1814071 AAAACAAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 31 0.67
50 13 0.28
51 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (49 bp):
AATTATGATACAATTATATTATATTAAACAATTAAAATACAATTATATT
Found at i:1817451 original size:17 final size:17
Alignment explanation
Indices: 1817429--1817461 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1817419 AAACCAGAAC
1817429 TTCTGCCTCTGGTTTGA
1 TTCTGCCTCTGGTTTGA
*
1817446 TTCTGCTTCTGGTTTG
1 TTCTGCCTCTGGTTTG
1817462 TAGTTGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.24, T:0.52
Consensus pattern (17 bp):
TTCTGCCTCTGGTTTGA
Found at i:1818407 original size:21 final size:21
Alignment explanation
Indices: 1818383--1818431 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1818373 AAAATATTTT
1818383 TATTTAAATA-TAATTATAAAA
1 TATTTAAATATTAA-TATAAAA
1818404 TATTTAAATATTAATATAAAA
1 TATTTAAATATTAATATAAAA
*
1818425 TTTTTAA
1 TATTTAA
1818432 TTTTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTAAATATTAATATAAAA
Found at i:1818615 original size:30 final size:29
Alignment explanation
Indices: 1818537--1818652 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 29
1818527 TTATTTAAAT
*
1818537 TAAAAAGTATATTTAAATTTAAATT-AAAGA
1 TAAAAA-T-TATTTAAATATAAATTAAAAGA
* *
1818567 TTAAAATT-TTTATGAATATAATTTAAAAGA
1 TAAAAATTATTTA--AATATAAATTAAAAGA
*
1818597 TAAAAATTGATTTAAATAT-CA-TAAAAGTA
1 TAAAAATT-ATTTAAATATAAATTAAAAG-A
1818626 TAAAAATTTATTTAAATA-AAATTAAAA
1 TAAAAA-TTATTTAAATATAAATTAAAA
1818653 TTTTTGTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.06
28 7 0.10
29 26 0.37
30 29 0.41
32 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAAAATTATTTAAATATAAATTAAAAGA
Found at i:1818832 original size:2 final size:2
Alignment explanation
Indices: 1818827--1818862 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1818817 CGAAAAAATC
1818827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1818863 AAAATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1818922 original size:6 final size:6
Alignment explanation
Indices: 1818913--1818965 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
1818903 TTAATTTAAT
1818913 TTAAAA TTAATAA --AAAA TT-AAA TTAAAA TTATAAA TATAAAA -TAAAA
1 TTAAAA TTAA-AA TTAAAA TTAAAA TTAAAA TTA-AAA T-TAAAA TTAAAA
1818960 TTAAAA
1 TTAAAA
1818966 ATTTTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
4 2 0.05
5 12 0.30
6 15 0.38
7 9 0.22
8 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:1818924 original size:22 final size:22
Alignment explanation
Indices: 1818908--1818963 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1818898 TAATATTAAT
*
1818908 TTAATTTAAAATTAATAAAAAA
1 TTAAATTAAAATTAATAAAAAA
*
1818930 TTAAATTAAAATT-AT-AAATA
1 TTAAATTAAAATTAATAAAAAA
*
1818950 -TAAAATAAAATTAA
1 TTAAATTAAAATTAA
1818964 AAATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.37
20 5 0.17
21 2 0.07
22 12 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATTAAAATTAATAAAAAA
Found at i:1818958 original size:19 final size:18
Alignment explanation
Indices: 1818925--1818968 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1818915 AAAATTAATA
*
1818925 AAAAATTAAATTAAAATT
1 AAAAATTAAAATAAAATT
*
1818943 ATAAATATAAAATAAAATT
1 AAAAAT-TAAAATAAAATT
1818962 AAAAATT
1 AAAAATT
1818969 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTAAAATAAAATT
Found at i:1821233 original size:11 final size:12
Alignment explanation
Indices: 1821217--1821283 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 12
1821207 TTACTTTTTC
1821217 ATATTTTAAAT-
1 ATATTTTAAATA
*
1821228 ATATTTAAAATA
1 ATATTTTAAATA
1821240 ATATTTTAAAAATA
1 ATATTTT--AAATA
*
1821254 ATATTTTTAAAAA
1 ATA-TTTTAAATA
1821267 ATATTTT-AATA
1 ATATTTTAAATA
1821278 ATATTT
1 ATATTT
1821284 ACTTTTCCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 19 0.40
12 10 0.21
13 7 0.15
14 8 0.17
15 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTTTAAATA
Found at i:1821247 original size:38 final size:39
Alignment explanation
Indices: 1821205--1821317 Score: 99
Period size: 38 Copynumber: 2.9 Consensus size: 39
1821195 ATTATTTTAC
1821205 TTTTACTTTTTCATATTTT-AAATATATTTAAAATAATA
1 TTTTACTTTTTCATATTTTAAAATATATTTAAAATAATA
**** * * *
1821243 TTTTA-AAAATAATATTTTTAAAAAATATTT-TAATAATA
1 TTTTACTTTTTCATA-TTTTAAAATATATTTAAAATAATA
*
1821281 -TTTACTTTTCCATATTTTAAAAATAATATTTAAAATA
1 TTTTACTTTTTCATATTTT-AAAAT-ATATTTAAAATA
1821318 TTTTAATTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
37 12 0.22
38 23 0.43
39 15 0.28
40 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.50
Consensus pattern (39 bp):
TTTTACTTTTTCATATTTTAAAATATATTTAAAATAATA
Found at i:1821268 original size:16 final size:14
Alignment explanation
Indices: 1821225--1821280 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
1821215 TCATATTTTA
1821225 AATATATTT-AAAAT
1 AATAT-TTTAAAAAT
1821239 AATATTTTAAAAAT
1 AATATTTTAAAAAT
*
1821253 AATATTTTTAAAA-
1 AATATTTTAAAAAT
*
1821266 AATATTTTAATAAT
1 AATATTTTAAAAAT
1821280 A
1 A
1821281 TTTACTTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 14 0.38
14 23 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATTTTAAAAAT
Found at i:1821280 original size:27 final size:28
Alignment explanation
Indices: 1821225--1821280 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1821215 TCATATTTTA
1821225 AATATATTTAAAATAATATTTTAAAAAT
1 AATATATTTAAAATAATATTTTAAAAAT
* *
1821253 AATATTTTTAAAA-AATATTTTAATAAT
1 AATATATTTAAAATAATATTTTAAAAAT
1821280 A
1 A
1821281 TTTACTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATATTTAAAATAATATTTTAAAAAT
Found at i:1821453 original size:21 final size:22
Alignment explanation
Indices: 1821429--1821469 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1821419 TTTTTTTTAG
*
1821429 TTGATCATTT-TTTTTAAAATT
1 TTGATCATTTCTTTTGAAAATT
1821450 TTGATCATTTCTTTTGAAAA
1 TTGATCATTTCTTTTGAAAA
1821470 ATTATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGATCATTTCTTTTGAAAATT
Found at i:1821613 original size:2 final size:2
Alignment explanation
Indices: 1821600--1821633 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1821590 AAAAGATAAG
*
1821600 AT AT AT AC 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
1821634 GATTTCGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1823071 original size:22 final size:22
Alignment explanation
Indices: 1823026--1823071 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1823016 TTATAAAACA
* *
1823026 AATTAAATATAATTAATATGAT
1 AATTAAATAAAATTAATATAAT
1823048 AATTAAATAAAATTTAATA-AAT
1 AATTAAATAAAA-TTAATATAAT
1823070 AA
1 AA
1823072 AAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAAATAAAATTAATATAAT
Found at i:1823416 original size:49 final size:49
Alignment explanation
Indices: 1823363--1823465 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
1823353 AAAATGATAA
* * * *
1823363 AATTATGA-ACGATTATATTA-ATATAATACAATTACAATGCATTTATATT
1 AATTATGATACAATTATATTATAT-TAA-ACAATTAAAATACAATTATATT
* *
1823412 AATTATGATATAATTATATTATATTAAATAATTAAAATACAATTATATT
1 AATTATGATACAATTATATTATATTAAACAATTAAAATACAATTATATT
1823461 AATTA
1 AATTA
1823466 AAAACAAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 31 0.67
50 13 0.28
51 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (49 bp):
AATTATGATACAATTATATTATATTAAACAATTAAAATACAATTATATT
Found at i:1825744 original size:16 final size:16
Alignment explanation
Indices: 1825723--1825754 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1825713 CAAAATTAAT
*
1825723 AAAAGAGAAAGAAAAG
1 AAAAGAAAAAGAAAAG
1825739 AAAAGAAAAAGAAAAG
1 AAAAGAAAAAGAAAAG
1825755 GTAGCCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:1826102 original size:12 final size:12
Alignment explanation
Indices: 1826085--1826109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1826075 CATTTATCAA
1826085 ATTACAAATAAT
1 ATTACAAATAAT
1826097 ATTACAAATAAT
1 ATTACAAATAAT
1826109 A
1 A
1826110 ATAAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTACAAATAAT
Found at i:1827325 original size:43 final size:43
Alignment explanation
Indices: 1827235--1827327 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
1827225 TTTTTATATT
1827235 ACAAT-TT-TTAATTTATAAAATTTCACAAAATATTTATACAA
1 ACAATATTATTAATTTATAAAATTTCACAAAATATTTATACAA
** * *
1827276 TTAATATTATTAATTTATAATATTT-A-AAAATATTTATAATAA
1 ACAATATTATTAATTTATAAAATTTCACAAAATATTTAT-ACAA
1827318 CACAATATTA
1 -ACAATATTA
1827328 ACTCAAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
41 14 0.33
42 6 0.14
43 22 0.52
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (43 bp):
ACAATATTATTAATTTATAAAATTTCACAAAATATTTATACAA
Found at i:1833251 original size:2 final size:2
Alignment explanation
Indices: 1833244--1833284 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1833234 AGCATTAGTA
* *
1833244 AT AT AT AT AT AT AT AT AT AT AT AT AT -T GT AT AT AA 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
1833285 GCATTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1833789 original size:20 final size:20
Alignment explanation
Indices: 1833740--1833789 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1833730 ATTTTGCATG
1833740 AAATTGCAAAATCTTATATTA
1 AAATTG-AAAATCTTATATTA
*
1833761 AAA-TAAAAATCTTA-ATTA
1 AAATTGAAAATCTTATATTA
1833779 TAAATTGAAAA
1 -AAATTGAAAA
1833790 CCTTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 4 0.16
19 12 0.48
20 6 0.24
21 3 0.12
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (20 bp):
AAATTGAAAATCTTATATTA
Done.