Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 10 of 31
Found at i:2393651 original size:22 final size:22
Alignment explanation
Indices: 2393604--2393691 Score: 110
Period size: 22 Copynumber: 3.9 Consensus size: 22
2393594 TTTATAATTT
2393604 TAAATATAATATAAT-TATATAATA
1 TAAATAT-AT-TAATATAT-TAATA
2393628 TATAATA-ATATAATA-ATTAATA
1 TA-AATATAT-TAATATATTAATA
2393650 TAAATATATTAATATATTAATA
1 TAAATATATTAATATATTAATA
2393672 TAAATATATTAATATATTAA
1 TAAATATATTAATATATTAA
2393692 AATTTATATA
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.15
22 36 0.60
23 9 0.15
24 2 0.03
25 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATATTAATATATTAATA
Found at i:2395099 original size:18 final size:17
Alignment explanation
Indices: 2395061--2395099 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2395051 AAAATATATA
2395061 TTTTTTATTTTAATCAAT
1 TTTTTTATTTTAA-CAAT
2395079 TTTTTTATGTTTAA-AAT
1 TTTTTTAT-TTTAACAAT
2395096 TTTT
1 TTTT
2395100 AAATAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTTATTTTAACAAT
Found at i:2395141 original size:25 final size:25
Alignment explanation
Indices: 2395094--2395146 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2395084 TATGTTTAAA
* *
2395094 ATTTTTAAATAATGATAATTAATTT
1 ATTTTTAAATAATAATAATTAATAT
2395119 ATTTTTAAATAA-AATAATATAATAT
1 ATTTTTAAATAATAATAAT-TAATAT
2395144 ATT
1 ATT
2395147 AATATCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTTTAAATAATAATAATTAATAT
Found at i:2395947 original size:2 final size:2
Alignment explanation
Indices: 2395942--2395987 Score: 56
Period size: 2 Copynumber: 21.5 Consensus size: 2
2395932 TTAATTAAAT
*
2395942 TA TA TA TA TA TA TA TGA TCA CTA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A T-A -TA TA TA TA TA TA TA TA TA TA TA
2395985 TA T
1 TA T
2395988 CATAGCACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
2 34 0.87
3 4 0.10
4 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2396303 original size:2 final size:2
Alignment explanation
Indices: 2396298--2396323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2396288 ACTTACACAC
2396298 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
2396324 GTTGTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2396900 original size:23 final size:23
Alignment explanation
Indices: 2396864--2396909 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2396854 GAAATAAACC
* *
2396864 TTTCGTATGCTAAACATAAGCAT
1 TTTCGTATACTAAAAATAAGCAT
* *
2396887 TTTCGTATATTAAAAATAGGCAT
1 TTTCGTATACTAAAAATAAGCAT
2396910 CTTGTTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
TTTCGTATACTAAAAATAAGCAT
Found at i:2401554 original size:49 final size:48
Alignment explanation
Indices: 2401494--2401591 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 48
2401484 AAATAAAAAT
* * **
2401494 TTATATGAGATGATTAATGATATATAGGTTTATAAATTATATTAAATGA
1 TTATATGAGATGACTAATAATATATAAATTTATAAATTAT-TTAAATGA
* *
2401543 TTATATTAGATGACTAATAATATATAAATTTATATATTATTTAAATGA
1 TTATATGAGATGACTAATAATATATAAATTTATAAATTATTTAAATGA
2401591 T
1 T
2401592 ATTATTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 9 0.21
49 34 0.79
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (48 bp):
TTATATGAGATGACTAATAATATATAAATTTATAAATTATTTAAATGA
Found at i:2417717 original size:3 final size:3
Alignment explanation
Indices: 2417709--2417748 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2417699 CAAAGCAGAA
2417709 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2417749 CTGTTAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2435544 original size:15 final size:16
Alignment explanation
Indices: 2435514--2435546 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2435504 TAAATGTAGG
*
2435514 ATATAATATTTATTTA
1 ATATAATATATATTTA
2435530 ATATAA-ATATATTTA
1 ATATAATATATATTTA
2435545 AT
1 AT
2435547 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATATATATTTA
Found at i:2440605 original size:2 final size:2
Alignment explanation
Indices: 2440598--2440635 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2440588 AAGTTCATTC
2440598 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
2440636 GCTACGTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2443544 original size:17 final size:18
Alignment explanation
Indices: 2443519--2443553 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2443509 CCTCTCGAAT
*
2443519 AAAATAAAAA-GCAAAAA
1 AAAAAAAAAAGGCAAAAA
2443536 AAAAAAAAAAGGCAAAAA
1 AAAAAAAAAAGGCAAAAA
2443554 TAATTCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAGGCAAAAA
Found at i:2443545 original size:18 final size:18
Alignment explanation
Indices: 2443519--2443553 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2443509 CCTCTCGAAT
*
2443519 AAAATAAAAAGCAAAAAA
1 AAAAAAAAAAGCAAAAAA
*
2443537 AAAAAAAAAGGCAAAAA
1 AAAAAAAAAAGCAAAAA
2443554 TAATTCATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAGCAAAAAA
Found at i:2443741 original size:13 final size:13
Alignment explanation
Indices: 2443723--2443769 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
2443713 CTTAATTTTT
2443723 AAATAAATTATTA
1 AAATAAATTATTA
*
2443736 AAATAATAGTAATTTA
1 AAATAA-A-TTA-TTA
2443752 AAATAAATTATTA
1 AAATAAATTATTA
2443765 AAATA
1 AAATA
2443770 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 14 0.48
14 3 0.10
15 3 0.10
16 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:2443780 original size:29 final size:29
Alignment explanation
Indices: 2443717--2443781 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2443707 ACTACTCTTA
*
2443717 ATTTTTAAATAAATTATTAAAATAATAGT
1 ATTTTAAAATAAATTATTAAAATAATAGT
* * *
2443746 AATTTAAAATAAATTATTAAAATATTATT
1 ATTTTAAAATAAATTATTAAAATAATAGT
2443775 ATTTTAA
1 ATTTTAA
2443782 CTTATGATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
ATTTTAAAATAAATTATTAAAATAATAGT
Found at i:2444015 original size:27 final size:27
Alignment explanation
Indices: 2443980--2444042 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2443970 CTATTAAGGT
** *
2443980 TATTATTATGTTAGTATTTTGTAATTA
1 TATTATTATGTTAGTATTTTAAAATAA
*
2444007 TATTATTATGTTAGTTTTTTAAAATAA
1 TATTATTATGTTAGTATTTTAAAATAA
2444034 TATTATTAT
1 TATTATTAT
2444043 TATGAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (27 bp):
TATTATTATGTTAGTATTTTAAAATAA
Found at i:2444161 original size:14 final size:13
Alignment explanation
Indices: 2444135--2444178 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2444125 GTTATTATTA
2444135 TAAAATATTTAATT
1 TAAAAT-TTTAATT
**
2444149 TAATTTGTTTAATT
1 TAAAAT-TTTAATT
2444163 TAAAATTTTAATT
1 TAAAATTTTAATT
2444176 TAA
1 TAA
2444179 GTTATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAAATTTTAATT
Found at i:2444189 original size:28 final size:28
Alignment explanation
Indices: 2444135--2444189 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2444125 GTTATTATTA
* * *
2444135 TAAAATATTTAATTTAATTTGTTTAATT
1 TAAAATATTTAATTTAAGTTATATAATT
2444163 TAAAAT-TTTAATTTAAGTTATAATAAT
1 TAAAATATTTAATTTAAGTTAT-ATAAT
2444190 CTAATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
TAAAATATTTAATTTAAGTTATATAATT
Found at i:2444216 original size:37 final size:37
Alignment explanation
Indices: 2444165--2444252 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
2444155 GTTTAATTTA
* *
2444165 AAATTTTAATTTAAG-TTATAATAATCTAATTATTTGTT
1 AAATTTTAAATTAAGATTATAATAATCTAATTA-CT-TT
* *
2444203 AAA-TTTAAATTAAGAATTGTAATTATCTAATTACTTT
1 AAATTTTAAATTAAG-ATTATAATAATCTAATTACTTT
2444240 AAATTTTAAATTA
1 AAATTTTAAATTA
2444253 TTATCATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 15 0.35
38 13 0.30
39 15 0.35
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (37 bp):
AAATTTTAAATTAAGATTATAATAATCTAATTACTTT
Found at i:2444266 original size:70 final size:72
Alignment explanation
Indices: 2444174--2444307 Score: 175
Period size: 70 Copynumber: 1.9 Consensus size: 72
2444164 AAAATTTTAA
* * *
2444174 TTTAAGTTATAATAATCTAATTATTTGTTAAA-TTTAAATTAA-GAA-TTGTAATTATCTAATTA
1 TTTAAATTATAATAATCTAATTATTT-TAAAATTTTAAATTAATGAAGTTGTAATCATCTAATTA
2444236 CTTTAAAT
65 CTTTAAAT
* * * *
2444244 TTTAAATTATTATCATCTAATTATTTTAAAATTTTAATTTAATTAAGTTGTAATCATCTAATTA
1 TTTAAATTATAATAATCTAATTATTTTAAAATTTTAAATTAATGAAGTTGTAATCATCTAATTA
2444308 TTTTTAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 4 0.07
70 32 0.59
71 2 0.04
72 16 0.30
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (72 bp):
TTTAAATTATAATAATCTAATTATTTTAAAATTTTAAATTAATGAAGTTGTAATCATCTAATTAC
TTTAAAT
Found at i:2444775 original size:32 final size:32
Alignment explanation
Indices: 2444739--2444822 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
2444729 TATTAAAACG
* * * *
2444739 TTTAAAAATTTTT-CATGGAATTCATTAATTAT
1 TTTAAAAATTTTTAAATAG-ATACATTAATTAA
*
2444771 TTTAATAATTTTTAAATAGATACATTAATTAA
1 TTTAAAAATTTTTAAATAGATACATTAATTAA
2444803 TTTAATAAATTTTTATAATA
1 TTTAA-AAATTTTTA-AATA
2444823 ATATTTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 28 0.65
33 11 0.26
34 4 0.09
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (32 bp):
TTTAAAAATTTTTAAATAGATACATTAATTAA
Found at i:2444813 original size:13 final size:13
Alignment explanation
Indices: 2444797--2444869 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
2444787 TAGATACATT
*
2444797 AATTAATTTAATA
1 AATTATTTTAATA
2444810 AATT-TTTATAAT-
1 AATTATTT-TAATA
2444822 AA-TATTTTAATA
1 AATTATTTTAATA
2444834 AATTATTTTAAATAA
1 AATTATTTT-AAT-A
2444849 ATATTATTTTAATA
1 A-ATTATTTTAATA
*
2444863 ATTTATT
1 AATTATT
2444870 AAAAGTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
11 5 0.10
12 9 0.18
13 19 0.37
14 5 0.10
15 5 0.10
16 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTATTTTAATA
Found at i:2444870 original size:16 final size:14
Alignment explanation
Indices: 2444811--2444869 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
2444801 AATTTAATAA
* *
2444811 ATTTTTATAATAAT
1 ATTTTAATAATATT
2444825 ATTTTAATAA-ATT
1 ATTTTAATAATATT
2444838 ATTTTAAATAAATATT
1 ATTTT-AAT-AATATT
2444854 ATTTTAATAAT-TT
1 ATTTTAATAATATT
2444867 ATT
1 ATT
2444870 AAAAGTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 12 0.30
14 15 0.38
15 5 0.12
16 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTAATAATATT
Found at i:2444880 original size:29 final size:29
Alignment explanation
Indices: 2444818--2444881 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2444808 TAAATTTTTA
*
2444818 TAATAATATTTTAATAAATTATTTTAAAT
1 TAATAATATTTTAATAAATTATTTAAAAT
* * *
2444847 AAATATTATTTTAATAATTTA-TTAAAAGT
1 TAATAATATTTTAATAAATTATTTAAAA-T
2444876 TAATAA
1 TAATAA
2444882 GATTATGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAATAATATTTTAATAAATTATTTAAAAT
Found at i:2459892 original size:17 final size:18
Alignment explanation
Indices: 2459870--2459909 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2459860 GCTATTAAGA
2459870 AAAAGAGCTAG-T-GGACC
1 AAAAGAGC-AGCTAGGACC
2459887 AAAAGAGCAGCTAGGACC
1 AAAAGAGCAGCTAGGACC
2459905 AAAAG
1 AAAAG
2459910 CCACAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 10 0.48
ACGTcount: A:0.47, C:0.17, G:0.28, T:0.07
Consensus pattern (18 bp):
AAAAGAGCAGCTAGGACC
Found at i:2462054 original size:3 final size:3
Alignment explanation
Indices: 2462046--2462071 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2462036 TTGTCTCGGT
2462046 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2462072 TCCTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2462828 original size:22 final size:23
Alignment explanation
Indices: 2462810--2462876 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 23
2462800 TGTATATAGT
2462810 TATAT-AATAAATATAATATAAA
1 TATATAAATAAATATAATATAAA
*
2462832 TATATAAATAAATAT--TTTAAA
1 TATATAAATAAATATAATATAAA
* **
2462853 TAT-GAAATAAACGTAATATAAA
1 TATATAAATAAATATAATATAAA
2462875 TA
1 TA
2462877 ATTAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 12 0.32
23 9 0.24
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (23 bp):
TATATAAATAAATATAATATAAA
Found at i:2465275 original size:13 final size:13
Alignment explanation
Indices: 2465248--2465291 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2465238 AAATAAACTA
2465248 AATTAATTTATAT
1 AATTAATTTATAT
2465261 AATTATATTTA-AT
1 AATTA-ATTTATAT
*
2465274 AAATAATATTATAT
1 AATTAAT-TTATAT
2465288 AATT
1 AATT
2465292 TAATCTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.08
13 14 0.54
14 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTAATTTATAT
Found at i:2474833 original size:2 final size:2
Alignment explanation
Indices: 2474826--2474860 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2474816 TTATTCTCTT
2474826 TA TA TA TA 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 TA TA TA TA T
2474861 TTGCAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2475085 original size:29 final size:29
Alignment explanation
Indices: 2475050--2475116 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
2475040 AGTTTACAAT
*
2475050 ATATTTTTTTT-AATTTTCAGACTTTGAC
1 ATATTTTTTTTAAATTGTCAGACTTTGAC
2475078 ATATTTTTTTTAAATTGTCAGACTTTGAC
1 ATATTTTTTTTAAATTGTCAGACTTTGAC
2475107 ATATTTTTTT
1 ATATTTTTTT
2475117 AAAAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 11 0.30
29 26 0.70
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.58
Consensus pattern (29 bp):
ATATTTTTTTTAAATTGTCAGACTTTGAC
Found at i:2483331 original size:11 final size:11
Alignment explanation
Indices: 2483297--2483336 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2483287 AAAAGATAAC
*
2483297 ATCACGTGCAA
1 ATCACGTGCAT
*
2483308 ATCACGTGAAT
1 ATCACGTGCAT
2483319 ATCACGTGCAT
1 ATCACGTGCAT
*
2483330 ATTACGT
1 ATCACGT
2483337 ACAGTCTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (11 bp):
ATCACGTGCAT
Found at i:2483520 original size:42 final size:42
Alignment explanation
Indices: 2483472--2483554 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
2483462 ACTAATAATT
2483472 AATGTAAAGATATATTCATTATTCTATAATAAATTGATTATC
1 AATGTAAAGATATATTCATTATTCTATAATAAATTGATTATC
2483514 AATGTAAAGATATATTCATTATTCTATAATAAATTGATTAT
1 AATGTAAAGATATATTCATTATTCTATAATAAATTGATTAT
2483555 TAGTGTTGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (42 bp):
AATGTAAAGATATATTCATTATTCTATAATAAATTGATTATC
Found at i:2483555 original size:19 final size:19
Alignment explanation
Indices: 2483489--2483555 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
2483479 AGATATATTC
2483489 ATTATTCTATAATAAATTG
1 ATTATTCTATAATAAATTG
* * * *
2483508 ATTATCAATGTAAAGATATATTC
1 ATTAT---TCTATA-ATAAATTG
2483531 ATTATTCTATAATAAATTG
1 ATTATTCTATAATAAATTG
2483550 ATTATT
1 ATTATT
2483556 AGTGTTGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 17 0.47
20 4 0.11
22 4 0.11
23 11 0.31
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (19 bp):
ATTATTCTATAATAAATTG
Found at i:2484479 original size:18 final size:19
Alignment explanation
Indices: 2484456--2484491 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2484446 AAAAACTTAA
2484456 TTTTAAT-TTTAAAAAATC
1 TTTTAATCTTTAAAAAATC
*
2484474 TTTTAATCTTTTAAAAAT
1 TTTTAATCTTTAAAAAAT
2484492 TTAGAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATCTTTAAAAAATC
Found at i:2493479 original size:2 final size:2
Alignment explanation
Indices: 2493472--2493501 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2493462 TAGACAAGAA
2493472 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
2493502 TGCTTCTAAC
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):
AT
Found at i:2493585 original size:2 final size:2
Alignment explanation
Indices: 2493578--2493616 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2493568 ATCATTACCG
* *
2493578 TA TA TA TA TT TA TA TA CA 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 TA TA TA TA TA TA T
2493617 CCAGCTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2496715 original size:21 final size:22
Alignment explanation
Indices: 2496670--2496720 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2496660 ATATGGTTGG
*
2496670 TTTCAGTTTTGTATTTCAGAAA
1 TTTCAGCTTTGTATTTCAGAAA
* *
2496692 TTTCAGCTTTG-ATTTGAGACA
1 TTTCAGCTTTGTATTTCAGAAA
2496713 TTTCAGCT
1 TTTCAGCT
2496721 AAACATATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.47
Consensus pattern (22 bp):
TTTCAGCTTTGTATTTCAGAAA
Found at i:2499912 original size:22 final size:23
Alignment explanation
Indices: 2499886--2499939 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
2499876 TAAAAATAAT
2499886 ATTTTATATATTT-T-ATATTTAA
1 ATTTTATATATTTATAAT-TTTAA
2499908 ATTTTA-ATATTTATAATTTTAA
1 ATTTTATATATTTATAATTTTAA
2499930 ATTTTATATA
1 ATTTTATATA
2499940 ATATTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.21
22 18 0.62
23 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATATATTTATAATTTTAA
Found at i:2499919 original size:14 final size:15
Alignment explanation
Indices: 2499882--2499933 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
2499872 CTTTTAAAAA
2499882 TAATATTTTATATATTT
1 TAATA-TTTATA-ATTT
2499899 T-ATATTTA-AATTT
1 TAATATTTATAATTT
2499912 TAATATTTATAATTT
1 TAATATTTATAATTT
2499927 TAA-ATTT
1 TAATATTT
2499934 TATATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 5 0.15
14 12 0.36
15 12 0.36
16 3 0.09
17 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATATTTATAATTT
Found at i:2499935 original size:15 final size:15
Alignment explanation
Indices: 2499886--2499937 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2499876 TAAAAATAAT
*
2499886 ATTTTATATATTTTAT
1 ATTTTATA-ATTTTAA
2499902 A-TTTA-AATTTT-A
1 ATTTTATAATTTTAA
2499914 ATATTTATAATTTTAA
1 AT-TTTATAATTTTAA
2499930 ATTTTATA
1 ATTTTATA
2499938 TAATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
12 1 0.03
13 5 0.16
14 5 0.16
15 16 0.52
16 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTATAATTTTAA
Found at i:2500004 original size:13 final size:14
Alignment explanation
Indices: 2499986--2500014 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2499976 CTTTTTGAAA
2499986 ATTTATCAAAC-AT
1 ATTTATCAAACTAT
2499999 ATTTATCAAACTAT
1 ATTTATCAAACTAT
2500013 AT
1 AT
2500015 ATATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTATCAAACTAT
Found at i:2501889 original size:9 final size:9
Alignment explanation
Indices: 2501870--2501927 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 9
2501860 AAATATAAAA
2501870 ATAA-TTAT
1 ATAATTTAT
*
2501878 ATAATTTTT
1 ATAATTTAT
2501887 ATAAGATTTAT
1 AT-A-ATTTAT
2501898 ATAATTTATT
1 ATAATTTA-T
2501908 ATAAGATTTAT
1 AT-A-ATTTAT
2501919 ATAATTTAT
1 ATAATTTAT
2501928 TTCGACTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 4 0.10
9 16 0.38
10 6 0.14
11 11 0.26
12 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
ATAATTTAT
Found at i:2501895 original size:11 final size:11
Alignment explanation
Indices: 2501881--2501922 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2501871 TAATTATATA
*
2501881 ATTTTTATAAG
1 ATTTATATAAG
2501892 ATTTATAT-A-
1 ATTTATATAAG
2501901 ATTTATTATAAG
1 ATTTA-TATAAG
2501913 ATTTATATAA
1 ATTTATATAA
2501923 TTTATTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 13 0.48
12 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (11 bp):
ATTTATATAAG
Found at i:2501941 original size:21 final size:21
Alignment explanation
Indices: 2501874--2501928 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2501864 ATAAAAATAA
2501874 TTATATAATTT-TTATAAGAT
1 TTATATAATTTATTATAAGAT
2501894 TTATATAATTTATTATAAGAT
1 TTATATAATTTATTATAAGAT
2501915 TTATATAATTTATT
1 TTATATAATTTATT
2501929 TCGACTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 11 0.32
21 23 0.68
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTATATAATTTATTATAAGAT
Found at i:2502428 original size:35 final size:37
Alignment explanation
Indices: 2502359--2502428 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
2502349 TAAATAACTT
* *
2502359 ATTTGATTTGAGTTAAACTTTAAATAATATTTTTAAA
1 ATTTGATTTGAATTAAACTTTAAATAATAATTTTAAA
*
2502396 ATTTGATTT-AATTAAA-TTTAAATTATAATTTTA
1 ATTTGATTTGAATTAAACTTTAAATAATAATTTTA
2502429 TTTTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 15 0.50
36 6 0.20
37 9 0.30
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (37 bp):
ATTTGATTTGAATTAAACTTTAAATAATAATTTTAAA
Found at i:2510153 original size:16 final size:16
Alignment explanation
Indices: 2510132--2510163 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2510122 TAATTTTTTT
2510132 AAAAATTATATATTTA
1 AAAAATTATATATTTA
*
2510148 AAAAATTATATTTTTA
1 AAAAATTATATATTTA
2510164 TCTTGAGATA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATTATATATTTA
Found at i:2527157 original size:17 final size:17
Alignment explanation
Indices: 2527131--2527164 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2527121 TTTAATCATA
* *
2527131 TAAAATATAAGATAAAT
1 TAAAACATAACATAAAT
2527148 TAAAACATAACATAAAT
1 TAAAACATAACATAAAT
2527165 ATAATATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
TAAAACATAACATAAAT
Found at i:2527173 original size:24 final size:24
Alignment explanation
Indices: 2527133--2527194 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2527123 TAATCATATA
* * *
2527133 AAATATAAGATAA-ATTAAAACAT
1 AAATAAAATATAATATTAAAAAAT
2527156 AACAT-AAATATAATATTAAAAAAT
1 AA-ATAAAATATAATATTAAAAAAT
*
2527180 AATTAAAATATAATA
1 AAATAAAATATAATA
2527195 CAACATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATAAAATATAATATTAAAAAAT
Found at i:2529893 original size:25 final size:25
Alignment explanation
Indices: 2529842--2529894 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2529832 TCTATATAAA
* *
2529842 TATATACAATATTAATAAATCAGAT
1 TATATACAATATTAATAAATAAAAT
*
2529867 TATATCACATTATTAA-AAATAAAAT
1 TATAT-ACAATATTAATAAATAAAAT
2529892 TAT
1 TAT
2529895 TTATATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (25 bp):
TATATACAATATTAATAAATAAAAT
Found at i:2535664 original size:23 final size:23
Alignment explanation
Indices: 2535635--2535682 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2535625 TGAGTTAATT
*
2535635 GTTTTTAATTAATTTTAAACTTTAA
1 GTTTATAA-TAATTTT-AACTTTAA
*
2535660 GTTTATAATCATTTTAACTTTAA
1 GTTTATAATAATTTTAACTTTAA
2535683 ATTACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (23 bp):
GTTTATAATAATTTTAACTTTAA
Found at i:2535721 original size:16 final size:16
Alignment explanation
Indices: 2535655--2535730 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
2535645 AATTTTAAAC
*
2535655 TTTAAGTTTATAATCAT
1 TTTAAATTTA-AATCAT
* *
2535672 TTTAACTTTAAATTACT
1 TTTAAATTTAAATCA-T
* *
2535689 TTT-ATTTTAAATTAT
1 TTTAAATTTAAATCAT
*
2535704 TTTAAATTTGAATCAT
1 TTTAAATTTAAATCAT
2535720 TTTAAATTTAA
1 TTTAAATTTAA
2535731 TATTTATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
15 4 0.08
16 33 0.66
17 13 0.26
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAAATCAT
Found at i:2535929 original size:16 final size:16
Alignment explanation
Indices: 2535910--2535940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2535900 TTATTATGAA
2535910 TTTAAATCAATTTAAG
1 TTTAAATCAATTTAAG
*
2535926 TTTAAATTAATTTAA
1 TTTAAATCAATTTAA
2535941 ATTATTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTAAATCAATTTAAG
Found at i:2535991 original size:17 final size:17
Alignment explanation
Indices: 2535969--2536003 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2535959 TCAATTTTGA
2535969 GTTAACCTATTTCATTT
1 GTTAACCTATTTCATTT
* *
2535986 GTTAACCTTTTTTATTT
1 GTTAACCTATTTCATTT
2536003 G
1 G
2536004 ATTTTGAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (17 bp):
GTTAACCTATTTCATTT
Found at i:2536402 original size:24 final size:24
Alignment explanation
Indices: 2536378--2536425 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2536368 CGAATGTTAA
*
2536378 TTTTTAAAAAAATTTTAAATATAATT
1 TTTTTAAAAAAA-TTAAAATATAA-T
2536404 TTTTTAAAAAAATTAAAATATA
1 TTTTTAAAAAAATTAAAATATA
2536426 TTGATATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTTTAAAAAAATTAAAATATAAT
Found at i:2536412 original size:25 final size:25
Alignment explanation
Indices: 2536378--2536425 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2536368 CGAATGTTAA
* *
2536378 TTTTTAAAAAAATTTTAAATATAAT
1 TTTTTAAAAAAAATTAAAATATAAT
*
2536403 TTTTTTAAAAAAATTAAAATATA
1 TTTTTAAAAAAAATTAAAATATA
2536426 TTGATATCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTTAAAAAAAATTAAAATATAAT
Found at i:2544396 original size:24 final size:24
Alignment explanation
Indices: 2544353--2544405 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2544343 TATAAATAAC
* *
2544353 ATAATAAGATTATTATATTATTTT
1 ATAATAAAATTATGATATTATTTT
2544377 -TAATAAAATATATGATATTATTTT
1 ATAATAAAAT-TATGATATTATTTT
2544401 ATAAT
1 ATAAT
2544406 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAATAAAATTATGATATTATTTT
Found at i:2544490 original size:24 final size:24
Alignment explanation
Indices: 2544462--2544509 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2544452 AAAAATAAAA
*
2544462 AATTATAATTTT-TTATATTTTATT
1 AATTAT-ATTTTATTATATATTATT
2544486 AATTATATTTTATTATATATTATT
1 AATTATATTTTATTATATATTATT
2544510 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
AATTATATTTTATTATATATTATT
Found at i:2544511 original size:15 final size:15
Alignment explanation
Indices: 2544474--2544516 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2544464 TTATAATTTT
2544474 TTATATTTTATTA-A
1 TTATATTTTATTATA
2544488 TTATATTTTATTATA
1 TTATATTTTATTATA
*
2544503 -TATTATTTTTTTAT
1 TTA-TATTTTATTAT
2544517 TTTTACTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTTTATTATA
Found at i:2546268 original size:18 final size:19
Alignment explanation
Indices: 2546245--2546280 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2546235 ATACTTCAAT
2546245 ACTTGAAGATAAT-GCAGC
1 ACTTGAAGATAATAGCAGC
*
2546263 ACTTGATGATAATAGCAG
1 ACTTGAAGATAATAGCAG
2546281 AAATTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (19 bp):
ACTTGAAGATAATAGCAGC
Found at i:2551579 original size:7 final size:7
Alignment explanation
Indices: 2551569--2551603 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
2551559 TTGCCAATAA
*
2551569 TCTCAAA
1 TCTCAAC
2551576 TCTCAAC
1 TCTCAAC
2551583 TCTCAAC
1 TCTCAAC
2551590 TCTCAAC
1 TCTCAAC
2551597 TCTCAAC
1 TCTCAAC
2551604 CAAAGTGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (7 bp):
TCTCAAC
Found at i:2551944 original size:25 final size:25
Alignment explanation
Indices: 2551873--2551944 Score: 60
Period size: 26 Copynumber: 2.9 Consensus size: 25
2551863 AATATTAATA
***
2551873 AAAAATATTTA-ATT-ATTATTTTT
1 AAAAATATTTACATTAATTATTCAC
* *
2551896 AAAAAAATTT-CATTTAATGAATTCAC
1 AAAAATATTTACA-TTAAT-TATTCAC
2551922 AAAAATATTTACATTAATTATTC
1 AAAAATATTTACATTAATTATTC
2551945 TATTTTATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
23 10 0.27
24 2 0.05
25 6 0.16
26 17 0.46
27 2 0.05
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (25 bp):
AAAAATATTTACATTAATTATTCAC
Found at i:2556236 original size:2 final size:2
Alignment explanation
Indices: 2556225--2556256 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2556215 TTTGCTACTG
2556225 TA TA -A 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 TA TA TA T
2556257 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2556261 original size:2 final size:2
Alignment explanation
Indices: 2556256--2556295 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2556246 TATATATATA
2556256 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2556296 ATAAGATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2560149 original size:2 final size:2
Alignment explanation
Indices: 2560105--2560133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2560095 AATCAAAGAA
2560105 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
2560134 CACACACATA
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:2562101 original size:25 final size:25
Alignment explanation
Indices: 2562073--2562136 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
2562063 ATTATAAAAT
2562073 GTATTGCCCAAGTTCTATTTATAAC
1 GTATTGCCCAAGTTCTATTTATAAC
2562098 GTATTGCCCAAGTTCTATTTATAAC
1 GTATTGCCCAAGTTCTATTTATAAC
2562123 GTATTGCCCAAGTT
1 GTATTGCCCAAGTT
2562137 ATATATTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (25 bp):
GTATTGCCCAAGTTCTATTTATAAC
Found at i:2563651 original size:2 final size:2
Alignment explanation
Indices: 2563644--2563669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2563634 GTAGGAGTTA
2563644 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
2563670 CTATTGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2563941 original size:2 final size:2
Alignment explanation
Indices: 2563934--2563958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2563924 GTTCAAGGCA
2563934 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2563959 GTCTCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2565447 original size:2 final size:2
Alignment explanation
Indices: 2565440--2565470 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2565430 ACGCTCAGCT
2565440 TA TA 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 TA TA T
2565471 TTGTAAGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2565793 original size:14 final size:14
Alignment explanation
Indices: 2565760--2565802 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
2565750 TTGTTGGTAA
* * *
2565760 TATATATATATATA
1 TATATGTATGTATG
2565774 TATATGTATGTATG
1 TATATGTATGTATG
2565788 TATATGTATGTATG
1 TATATGTATGTATG
2565802 T
1 T
2565803 TTCCCATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (14 bp):
TATATGTATGTATG
Found at i:2565920 original size:14 final size:15
Alignment explanation
Indices: 2565894--2565923 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2565884 TCACCTACAA
2565894 TAATTATATTATAAT
1 TAATTATATTATAAT
2565909 TAATTA-ATTATAAT
1 TAATTATATTATAAT
2565923 T
1 T
2565924 CAAAGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATATTATAAT
Found at i:2566201 original size:17 final size:18
Alignment explanation
Indices: 2566169--2566204 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2566159 AATCAAAAAA
2566169 TTAAAAAAATTAATATAT
1 TTAAAAAAATTAATATAT
*
2566187 TTAAAATAATT-ATATAT
1 TTAAAAAAATTAATATAT
2566204 T
1 T
2566205 ACAAAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAAAAATTAATATAT
Found at i:2566210 original size:18 final size:18
Alignment explanation
Indices: 2566168--2566211 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2566158 CAATCAAAAA
2566168 ATTAAAAA-AATTAATAT
1 ATTAAAAATAATTAATAT
*
2566185 ATTTAAAATAATT-ATAT
1 ATTAAAAATAATTAATAT
2566202 ATTACAAAAT
1 ATTA-AAAAT
2566212 CTTTTCTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAAAAATAATTAATAT
Found at i:2567468 original size:26 final size:27
Alignment explanation
Indices: 2567439--2567499 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2567429 AAAATTGAAT
* *
2567439 TATTTTAATTTTA-TTAAATAAGTTTA
1 TATTTTAATTTTACTCAAATAAATTTA
* *
2567465 TATTTTTATTTTACTCAAATAAATTTT
1 TATTTTAATTTTACTCAAATAAATTTA
2567492 TATTTTAA
1 TATTTTAA
2567500 ATAAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (27 bp):
TATTTTAATTTTACTCAAATAAATTTA
Found at i:2568154 original size:7 final size:7
Alignment explanation
Indices: 2568142--2568170 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2568132 TGTTAATTGC
2568142 TGAATTT
1 TGAATTT
2568149 TGAATTT
1 TGAATTT
2568156 TGAATTT
1 TGAATTT
2568163 TGAATTT
1 TGAATTT
2568170 T
1 T
2568171 TTTTAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TGAATTT
Found at i:2576015 original size:21 final size:22
Alignment explanation
Indices: 2575989--2576047 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
2575979 TAAATCGATA
2575989 TTATTT-AA-TTAATAAAATATT
1 TTATTTAAATTTAA-AAAATATT
2576010 TTATTTAAATTTAAAAAATA-T
1 TTATTTAAATTTAAAAAATATT
* * *
2576031 ATATATAAATATAAAAA
1 TTATTTAAATTTAAAAA
2576048 TAAATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 21 0.64
22 8 0.24
23 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATTTAAATTTAAAAAATATT
Found at i:2576020 original size:22 final size:21
Alignment explanation
Indices: 2575989--2576030 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2575979 TAAATCGATA
2575989 TTATTTAA-TTAATAAAATATT
1 TTATTTAATTTAA-AAAATATT
2576010 TTATTTAAATTTAAAAAATAT
1 TTATTT-AATTTAAAAAATAT
2576031 ATATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATTTAATTTAAAAAATATT
Found at i:2576522 original size:27 final size:28
Alignment explanation
Indices: 2576479--2576532 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
2576469 TATGAGTTCG
*
2576479 TTTTTAATATATTAAT-AA-TAAAAATA
1 TTTTTAATATATAAATAAATTAAAAATA
*
2576505 TTTTTAATTTTATAAATAAATTAAAAAT
1 TTTTTAA-TATATAAATAAATTAAAAAT
2576533 TATAGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 7 0.30
28 2 0.09
29 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTTAATATATAAATAAATTAAAAATA
Found at i:2576560 original size:13 final size:13
Alignment explanation
Indices: 2576542--2576581 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2576532 TTATAGTATA
2576542 TTTTATTTTATTT
1 TTTTATTTTATTT
*
2576555 TTTTATTATATTT
1 TTTTATTTTATTT
*
2576568 TATTAATTTTATTT
1 T-TTTATTTTATTT
2576582 ATAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:2576582 original size:23 final size:23
Alignment explanation
Indices: 2576538--2576583 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2576528 AAAATTATAG
*
2576538 TATATTTTATTTTATTTTTTTAT
1 TATATTTTATTTAATTTTTTTAT
2576561 TATATTTTA-TTAATTTTATTTAT
1 TATATTTTATTTAATTTT-TTTAT
2576584 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TATATTTTATTTAATTTTTTTAT
Found at i:2576590 original size:23 final size:23
Alignment explanation
Indices: 2576541--2576590 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2576531 ATTATAGTAT
* * *
2576541 ATTTTATTTTATTTTTTTATTAT
1 ATTTTATTTAATTTTTTTATAAA
2576564 ATTTTA-TTAATTTTATTTATAAA
1 ATTTTATTTAATTTT-TTTATAAA
2576587 ATTT
1 ATTT
2576591 AAAAGTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTATTTAATTTTTTTATAAA
Found at i:2577590 original size:2 final size:2
Alignment explanation
Indices: 2577583--2577630 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2577573 TGAAGGATAC
2577583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2577625 TA TA TA
1 TA TA TA
2577631 GTAGCTTTTG
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):
TA
Found at i:2578353 original size:17 final size:18
Alignment explanation
Indices: 2578331--2578364 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2578321 TATTGAATCG
2578331 AATTTAA-ATAATTTTTT
1 AATTTAAGATAATTTTTT
*
2578348 AATTTAAGTTAATTTTT
1 AATTTAAGATAATTTTT
2578365 ATTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTAAGATAATTTTTT
Found at i:2579684 original size:22 final size:24
Alignment explanation
Indices: 2579648--2579728 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 24
2579638 TTGATTTAAG
2579648 TTAATTT-AATGTAATTTAAATA-A
1 TTAATTTAAAT-TAATTTAAATATA
* *
2579671 TT-ATTTAAATTAA-TAAAAAATA
1 TTAATTTAAATTAATTTAAATATA
2579693 TTAATTTAAATTTAATTATAAATATA
1 TTAATTTAAA-TTAATT-TAAATATA
*
2579719 TAAATATTAA
1 TTAAT-TTAA
2579729 TATAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 5 0.11
22 10 0.22
23 12 0.26
24 4 0.09
25 1 0.02
26 10 0.22
27 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TTAATTTAAATTAATTTAAATATA
Found at i:2579715 original size:35 final size:33
Alignment explanation
Indices: 2579659--2579748 Score: 78
Period size: 35 Copynumber: 2.7 Consensus size: 33
2579649 TAATTTAATG
2579659 TAATTTAAA--TAATTATTTAAATTAATAAAAAATAT
1 TAATTTAAATTTAATTA-TTAAA-T-AT-AAAAATAT
*
2579694 TAATTTAAATTTAATTA-TAAATATATAAATAT
1 TAATTTAAATTTAATTATTAAATATAAAAATAT
* * *
2579726 TAATATAAAATTTATTTTTTAAA
1 TAAT-TTAAATTTAATTATTAAA
2579749 ATTTTAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 11 0.23
33 12 0.26
34 5 0.11
35 13 0.28
37 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATTTAAATTTAATTATTAAATATAAAAATAT
Found at i:2579763 original size:19 final size:19
Alignment explanation
Indices: 2579741--2579786 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2579731 TAAAATTTAT
* * *
2579741 TTTTTAAAATTTTAATATA
1 TTTTTAAAAATTAAATAAA
2579760 TTTTTAAAAATTAAATAAA
1 TTTTTAAAAATTAAATAAA
2579779 TTTTTAAA
1 TTTTTAAA
2579787 TACAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAATTAAATAAA
Found at i:2580988 original size:32 final size:32
Alignment explanation
Indices: 2580916--2581009 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 32
2580906 TTAAAATATG
* * *
2580916 ATATAAAAATTATTATTATATAAATATATAAAT
1 ATATTAAAATT-TTATAATAAAAATATATAAAT
* *
2580949 ATTTTAAAATGTTTATAATAAAAAT-TATTAAT
1 ATATTAAAAT-TTTATAATAAAAATATATAAAT
2580981 ATATTAAAATTTATATAAATATAAAATAT
1 ATATTAAAATTT-TAT-AATA-AAAATAT
2581010 TTTAATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
31 2 0.04
32 18 0.36
33 23 0.46
34 6 0.12
35 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATTAAAATTTTATAATAAAAATATATAAAT
Found at i:2581005 original size:17 final size:17
Alignment explanation
Indices: 2580916--2581020 Score: 62
Period size: 16 Copynumber: 6.4 Consensus size: 17
2580906 TTAAAATATG
* *
2580916 ATATAAAAATTATTATT
1 ATATAAAATTTATTAAT
* *
2580933 ATAT-AAATATATAAAT
1 ATATAAAATTTATTAAT
* *
2580949 ATTTTAAAATGT-TT-AT
1 A-TATAAAATTTATTAAT
*
2580965 A-ATAAAAATTATTAAT
1 ATATAAAATTTATTAAT
2580981 ATATTAAAATTTATATAA-
1 ATA-TAAAATTTAT-TAAT
2580999 ATATAAAATATT-TTAAT
1 ATATAAAAT-TTATTAAT
2581016 -TATAA
1 ATATAA
2581021 TTATAAAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 23 0.34
17 15 0.22
18 19 0.28
19 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
ATATAAAATTTATTAAT
Found at i:2581593 original size:19 final size:18
Alignment explanation
Indices: 2581561--2581599 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2581551 TATGATCATC
*
2581561 ATATAATAAAATATACGA
1 ATATAATAAAATATAAGA
2581579 ATATAATATAAATATAAGA
1 ATATAATA-AAATATAAGA
2581598 AT
1 AT
2581600 TATCACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
ATATAATAAAATATAAGA
Found at i:2583989 original size:2 final size:2
Alignment explanation
Indices: 2583982--2584019 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2583972 TAAACATTTT
2583982 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2584020 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2586118 original size:15 final size:15
Alignment explanation
Indices: 2586098--2586126 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2586088 TATCTTTCTC
2586098 TCAGATGGAAGATAT
1 TCAGATGGAAGATAT
2586113 TCAGATGGAAGATA
1 TCAGATGGAAGATA
2586127 GCAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.24
Consensus pattern (15 bp):
TCAGATGGAAGATAT
Found at i:2589113 original size:13 final size:13
Alignment explanation
Indices: 2589084--2589125 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2589074 CTTGACTCTC
*
2589084 ATTTTTGTTTAAAT
1 ATTTATGTTT-AAT
2589098 ATTTATGTTTAAT
1 ATTTATGTTTAAT
*
2589111 ATTTATATTTAAT
1 ATTTATGTTTAAT
2589124 AT
1 AT
2589126 ATTTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATTTATGTTTAAT
Found at i:2589129 original size:15 final size:14
Alignment explanation
Indices: 2589091--2589132 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
2589081 CTCATTTTTG
*
2589091 TTTAAATATTTATG
1 TTTAAATATTTATA
2589105 TTT-AATATTTATA
1 TTTAAATATTTATA
2589118 TTTAATATATTTATA
1 TTTAA-ATATTTATA
2589133 AAATAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 12 0.48
14 4 0.16
15 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTAAATATTTATA
Found at i:2590736 original size:2 final size:2
Alignment explanation
Indices: 2590729--2590755 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2590719 CGACCTAATA
2590729 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
2590756 ATACAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2591505 original size:243 final size:246
Alignment explanation
Indices: 2591032--2591506 Score: 739
Period size: 243 Copynumber: 1.9 Consensus size: 246
2591022 TCCTGAGGGT
*
2591032 GATGAAGGAGATGAGGTGCCTGAATTGATAACTATTGCTAACCGAGATGGAAGTGGATGGTTTTA
1 GATGAAGGAGATGAGGTGCCTGAATTGATAACTATTGCTAACCGAGATGGAAGTGGATGGTTCTA
*
2591097 ATGATGTTTCTGAGCCAGTTGAAGTTAATATTAATGGTTCTGCCAAGAAAGCAACGAAGAAGAGC
66 ATGATGTTTCTGAGCCAGTTGAAGTTAATATTAATGGTTCTGCCAAGAAAGCAACAAAGAAGAGC
* * *
2591162 AAGAAGGCCAAAAAGGTGACTAAGGGCAGTGTTAAAAAGATTAAGAACAGTAAGAATGCTGAATG
131 AAGAAGGCCAAAAAGGTGACTAAGGGCAGTGGTAAAAAGACTAAGAACAGCAAGAATGCTGAATG
* *
2591227 TAGCCCCGCAGATCAGGAGAATGATGTTCTGGTACCTAAGGTAATGAAGTG
196 TAGCCCCGCAGATCAGAAGAATGATGTTATGGTACCTAAGGTAATGAAGTG
* *
2591278 GATGAAGGAGATGA-GTGCCTGAATTG-TACCTATTGCT-AGCGAGATGGAAGTGGATGGTTCTA
1 GATGAAGGAGATGAGGTGCCTGAATTGATAACTATTGCTAACCGAGATGGAAGTGGATGGTTCTA
* **
2591340 ATGATGTTTCTGAGCCAGTTGAAGTTAATATTAATGGTTCTGCCAAGAAGGCGTCAAAGAAGAGC
66 ATGATGTTTCTGAGCCAGTTGAAGTTAATATTAATGGTTCTGCCAAGAAAGCAACAAAGAAGAGC
* *
2591405 AAGAAGGCCAAAAA-G-G-CTATGGGGATCAGTGGTAAAATGACTAAGAACAGCAAGAATGCTGA
131 AAGAAGGCCAAAAAGGTGACTA-AGGG--CAGTGGTAAAAAGACTAAGAACAGCAAGAATGCTGA
2591467 ATGTA-CCCCTGCAGATCAGAAGAATGATGTTATGGTACCT
193 ATGTAGCCCC-GCAGATCAGAAGAATGATGTTATGGTACCT
2591507 GCAGAAACGA
Statistics
Matches: 211, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
240 3 0.01
241 4 0.02
242 5 0.02
243 163 0.77
244 10 0.05
245 12 0.06
246 14 0.07
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (246 bp):
GATGAAGGAGATGAGGTGCCTGAATTGATAACTATTGCTAACCGAGATGGAAGTGGATGGTTCTA
ATGATGTTTCTGAGCCAGTTGAAGTTAATATTAATGGTTCTGCCAAGAAAGCAACAAAGAAGAGC
AAGAAGGCCAAAAAGGTGACTAAGGGCAGTGGTAAAAAGACTAAGAACAGCAAGAATGCTGAATG
TAGCCCCGCAGATCAGAAGAATGATGTTATGGTACCTAAGGTAATGAAGTG
Found at i:2595247 original size:23 final size:21
Alignment explanation
Indices: 2595197--2595250 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2595187 GATATGAGTG
*
2595197 TACTCAATATTTTTTAATATT
1 TACTCAATATTTTTGAATATT
*
2595218 TATTCAATATATTTTGAGA-ATCT
1 TACTCAATAT-TTTTGA-ATAT-T
2595241 TACTCAATAT
1 TACTCAATAT
2595251 CCATGTCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (21 bp):
TACTCAATATTTTTGAATATT
Found at i:2599565 original size:2 final size:2
Alignment explanation
Indices: 2599558--2599585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2599548 ATCTTTCTGT
2599558 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2599586 ACTGTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2601864 original size:20 final size:21
Alignment explanation
Indices: 2601834--2601872 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2601824 TTAAAAAATA
2601834 AATATAAATAATTTTATTTTT
1 AATATAAATAATTTTATTTTT
2601855 AATA-AAATAATTTTATTT
1 AATATAAATAATTTTATTT
2601873 AATTTATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATAAATAATTTTATTTTT
Found at i:2601896 original size:24 final size:23
Alignment explanation
Indices: 2601869--2601925 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2601859 AAATAATTTT
*
2601869 ATTTAATTTATTGGT-ATTATATAA
1 ATTTAATTTATT-ATCA-TATATAA
*
2601893 ATTTAATATATTATCATATATAA
1 ATTTAATTTATTATCATATATAA
2601916 ATATTAATTT
1 AT-TTAATTT
2601926 TTAAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTAATTTATTATCATATATAA
Found at i:2602016 original size:15 final size:15
Alignment explanation
Indices: 2601998--2602084 Score: 52
Period size: 15 Copynumber: 5.5 Consensus size: 15
2601988 TATATTTATT
2601998 TATTTTATTATATAA
1 TATTTTATTATATAA
*
2602013 TATTTTTATT-TAAAA
1 TA-TTTTATTATATAA
2602028 TATTTTATATTTATATAA
1 TA-TTT-TA-TTATATAA
* * *
2602046 AATTTTAATATTTAAA
1 TATTTTATTATAT-AA
2602062 TAATTTATATTATA-AA
1 T-ATTT-TATTATATAA
*
2602078 AATTTTA
1 TATTTTA
2602085 AAATATATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
14 2 0.04
15 20 0.36
16 15 0.27
17 9 0.16
18 10 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTATTATATAA
Found at i:2602021 original size:16 final size:16
Alignment explanation
Indices: 2602000--2602051 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
2601990 TATTTATTTA
2602000 TTTTATTATATAATAT
1 TTTTATTATATAATAT
*
2602016 TTTTATT-TAAAATAT
1 TTTTATTATATAATAT
*
2602031 TTTATATTTATATAAAAT
1 TTT-TA-TTATATAATAT
2602049 TTT
1 TTT
2602052 AATATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 10 0.33
16 9 0.30
17 2 0.07
18 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTATTATATAATAT
Found at i:2602030 original size:20 final size:20
Alignment explanation
Indices: 2602007--2602058 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
2601997 TTATTTTATT
*
2602007 ATATAATATTTTTATTTAAA
1 ATATAATATTTTTATATAAA
** *
2602027 ATATTTTATATTTATATAAA
1 ATATAATATTTTTATATAAA
*
2602047 ATTTTAATATTT
1 A-TATAATATTT
2602059 AAATAATTTA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATAATATTTTTATATAAA
Found at i:2602058 original size:19 final size:20
Alignment explanation
Indices: 2602017--2602064 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2602007 ATATAATATT
* *
2602017 TTTATTTAAAATATTTTATA
1 TTTATATAAAATATTTAATA
2602037 TTTATATAAAAT-TTTAATA
1 TTTATATAAAATATTTAATA
*
2602056 TTTAAATAA
1 TTTATATAA
2602065 TTTATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATATAAAATATTTAATA
Found at i:2602075 original size:33 final size:34
Alignment explanation
Indices: 2601999--2602085 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 34
2601989 ATATTTATTT
*
2601999 ATTT-TATTATATAATATTTT--TATTTAAAATA
1 ATTTATATTATATAAAATTTTAATATTTAAAATA
*
2602030 TTTTATATTTATATAAAATTTTAATATTT-AAATA
1 ATTTATA-TTATATAAAATTTTAATATTTAAAATA
2602064 ATTTATATTATA-AAAATTTTAA
1 ATTTATATTATATAAAATTTTAA
2602086 AATATATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 3 0.06
32 12 0.24
33 18 0.37
34 11 0.22
35 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
ATTTATATTATATAAAATTTTAATATTTAAAATA
Found at i:2602125 original size:16 final size:18
Alignment explanation
Indices: 2602087--2602128 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
2602077 AAATTTTAAA
2602087 ATATATATTTAAATAATT
1 ATATATATTTAAATAATT
* *
2602105 TTATAT-TTTTAAT-ATT
1 ATATATATTTAAATAATT
2602121 ATATATAT
1 ATATATAT
2602129 CATATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATATTTAAATAATT
Found at i:2604085 original size:10 final size:11
Alignment explanation
Indices: 2604059--2604089 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2604049 AATTAAACTT
2604059 ATTTTTATTTA
1 ATTTTTATTTA
2604070 ATTTTTATTTA
1 ATTTTTATTTA
2604081 ATTTTTATT
1 ATTTTTATT
2604090 ATAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTA
Found at i:2604184 original size:57 final size:59
Alignment explanation
Indices: 2604082--2604193 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 59
2604072 TTTTATTTAA
*
2604082 TTTTTATTATAAAATATATAAATATTAATATAAAATAAATTTTATTATTTTAAATAATAT
1 TTTTTATTATAAAATATATAAATATAAATATAAAATAAATTTTATTA-TTTAAATAATAT
*
2604142 TTTTTATTA-AAAA-AT-TAAATA-AAAT-TTAAATAAATTTTTTATTATTTAAATA
1 TTTTTATTATAAAATATATAAATATAAATATAAAATAAA--TTTTATTATTTAAATA
2604194 TAATCTAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
55 8 0.17
56 11 0.23
57 14 0.29
58 2 0.04
59 4 0.08
60 9 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (59 bp):
TTTTTATTATAAAATATATAAATATAAATATAAAATAAATTTTATTATTTAAATAATAT
Found at i:2605770 original size:24 final size:24
Alignment explanation
Indices: 2605730--2605781 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2605720 TCCTCACACA
*
2605730 TTTTTTTAAAATTAATTTAATTTC
1 TTTTTTTAAAATCAATTTAATTTC
2605754 TTTTTTTATAAA-CAATTTAATTTC
1 TTTTTTTA-AAATCAATTTAATTTC
2605778 TTTT
1 TTTT
2605782 CTGAGAGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTTTAAAATCAATTTAATTTC
Found at i:2615581 original size:14 final size:14
Alignment explanation
Indices: 2615557--2615611 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
2615547 TATGTTCGTT
*
2615557 TTTAAACATAATTA
1 TTTAAATATAATTA
* *
2615571 TATAAATATAATAA
1 TTTAAATATAATTA
*
2615585 TTTAAAAAATAATTA
1 TTT-AAATATAATTA
2615600 TTTAAATATAAT
1 TTTAAATATAAT
2615612 ATAATACGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAATATAATTA
Found at i:2615602 original size:15 final size:15
Alignment explanation
Indices: 2615564--2615605 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2615554 GTTTTTAAAC
* *
2615564 ATAATTATAT-AAAT
1 ATAATTATTTAAAAA
*
2615578 ATAATAATTTAAAAA
1 ATAATTATTTAAAAA
2615593 ATAATTATTTAAA
1 ATAATTATTTAAA
2615606 TATAATATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTATTTAAAAA
Found at i:2615685 original size:15 final size:15
Alignment explanation
Indices: 2615635--2615686 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2615625 ATGGATATTT
2615635 TAAAATTTATATAATA
1 TAAAATTTATATAA-A
* *
2615651 TAAATTATTA-ATATAT
1 TAAAAT-TTATATA-AA
2615667 TAAAATTTATATAAA
1 TAAAATTTATATAAA
2615682 TAAAA
1 TAAAA
2615687 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.31
16 16 0.55
17 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTTATATAAA
Found at i:2615699 original size:35 final size:35
Alignment explanation
Indices: 2615660--2615742 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
2615650 ATAAATTATT
**
2615660 AATAT-ATTAAAATTTATATAAATAAAAAAATTTAA
1 AATATAATTAAAAGATA-ATAAATAAAAAAATTTAA
* * *
2615695 AATATAATTATAAGATAATAAATATATAAATTTAA
1 AATATAATTAAAAGATAATAAATAAAAAAATTTAA
* *
2615730 AATAAAAATAAAA
1 AATATAATTAAAA
2615743 ATTATAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 31 0.79
36 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (35 bp):
AATATAATTAAAAGATAATAAATAAAAAAATTTAA
Found at i:2615727 original size:53 final size:54
Alignment explanation
Indices: 2615643--2615745 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 54
2615633 TTTAAAATTT
* * *
2615643 ATATAATATAAATTATTAATATATTAAAATTT-ATATAAATAA-AAAAATTTAAA
1 ATATAATATAAATAATAAATATATTAAAATTTAAAATAAA-AATAAAAATTTAAA
2615696 ATATAATTATAAGATAATAAATATA-T-AAATTTAAAATAAAAATAAAAATT
1 ATATAA-TATAA-ATAATAAATATATTAAAATTTAAAATAAAAATAAAAATT
2615746 ATAATTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
53 14 0.33
54 19 0.44
55 10 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (54 bp):
ATATAATATAAATAATAAATATATTAAAATTTAAAATAAAAATAAAAATTTAAA
Found at i:2615734 original size:22 final size:22
Alignment explanation
Indices: 2615692--2615749 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
2615682 TAAAAAAATT
*
2615692 TAAA-ATATAATTATAAGATAA
1 TAAATATATAATTATAAAATAA
2615713 TAAATATATAAATT-TAAAATAA
1 TAAATATAT-AATTATAAAATAA
*
2615735 -AAATA-AAAATTATAA
1 TAAATATATAATTATAA
2615750 TTATTAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 9 0.28
22 11 0.34
23 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATATAATTATAAAATAA
Found at i:2616014 original size:20 final size:20
Alignment explanation
Indices: 2615962--2616030 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
2615952 TTTTGTACAA
*
2615962 TATT-TTTAATAATTTATAT
1 TATTATTTAATAATTTAAAT
*
2615981 TAGTTAAATT--TAATTTAAAT
1 TA-TT-ATTTAATAATTTAAAT
**
2616001 TATTATTTAATAATAAAAAT
1 TATTATTTAATAATTTAAAT
*
2616021 TTTTATTTAA
1 TATTATTTAA
2616031 ATTTAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 4 0.10
20 30 0.77
22 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
TATTATTTAATAATTTAAAT
Found at i:2616076 original size:18 final size:20
Alignment explanation
Indices: 2616039--2616078 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2616029 AAATTTAATT
2616039 ATAAAAATATTTAATATTTA
1 ATAAAAATATTTAATATTTA
2616059 ATAAAAAT-TTTAAT-TTTA
1 ATAAAAATATTTAATATTTA
2616077 AT
1 AT
2616079 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATATTTAATATTTA
Found at i:2617369 original size:34 final size:34
Alignment explanation
Indices: 2617328--2617396 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
2617318 AAATTAATTT
2617328 AAATTATT-TATTTATAAATATAAA-TAAATCTAAA
1 AAATTATTATATTT-TAAAT-TAAATTAAATCTAAA
*
2617362 AAATTATTAATATTTTAAATTAAATTAAATTTAAA
1 AAATTATT-ATATTTTAAATTAAATTAAATCTAAA
2617397 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 12 0.39
35 14 0.45
36 5 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATTATTATATTTTAAATTAAATTAAATCTAAA
Found at i:2617413 original size:11 final size:11
Alignment explanation
Indices: 2617399--2617426 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2617389 AATTTAAATA
2617399 AAATTTTATTC
1 AAATTTTATTC
2617410 AAATTTTATTC
1 AAATTTTATTC
2617421 AAATTT
1 AAATTT
2617427 ATCCTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (11 bp):
AAATTTTATTC
Found at i:2618192 original size:17 final size:17
Alignment explanation
Indices: 2618166--2618207 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2618156 ACTCGATTGA
*
2618166 AAATAAATATTAAATAT
1 AAATATATATTAAATAT
**
2618183 AAATATATATTTTATAT
1 AAATATATATTAAATAT
2618200 AAATATAT
1 AAATATAT
2618208 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATATATTAAATAT
Found at i:2618203 original size:23 final size:23
Alignment explanation
Indices: 2618176--2618257 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
2618166 AAATAAATAT
*
2618176 TAAATATAAATATATATTTTATA
1 TAAATATAAATATATTTTTTATA
* *
2618199 TAAATAT--ATTTATTTTTTAAA
1 TAAATATAAATATATTTTTTATA
*
2618220 AAAATATAAATATATTTTTTATA
1 TAAATATAAATATATTTTTTATA
** *
2618243 TGTATTTAAATATAT
1 TAAATATAAATATAT
2618258 GATATGTATA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 17 0.36
23 30 0.64
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TAAATATAAATATATTTTTTATA
Found at i:2618226 original size:19 final size:19
Alignment explanation
Indices: 2618183--2618227 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2618173 TATTAAATAT
*
2618183 AAATATATATTTTATATAA
1 AAATATATATTTTATAAAA
* * *
2618202 ATATATTTATTTTTTAAAA
1 AAATATATATTTTATAAAA
2618221 AAATATA
1 AAATATA
2618228 AATATATTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATATTTTATAAAA
Found at i:2618237 original size:21 final size:21
Alignment explanation
Indices: 2618177--2618237 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2618167 AATAAATATT
* *
2618177 AAATATAAATATATATTTTATAT
1 AAATAT-AA-ATATATTTTAAAA
** *
2618200 AAATATATTTATTTTTTAAAA
1 AAATATAAATATATTTTAAAA
2618221 AAATATAAATATATTTT
1 AAATATAAATATATTTT
2618238 TTATATGTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 23 0.77
22 1 0.03
23 6 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATAAATATATTTTAAAA
Done.