Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 12 of 19
Found at i:1474848 original size:13 final size:13
Alignment explanation
Indices: 1474832--1474892 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
1474822 CATATACAAT
1474832 TATATTATATAAA
1 TATATTATATAAA
*
1474845 TATAATATATAAA
1 TATATTATATAAA
* *
1474858 AATAATTAAAATAAAA
1 TAT-ATT-ATAT-AAA
*
1474874 TATAATATATAAA
1 TATATTATATAAA
1474887 TTATAT
1 -TATAT
1474893 AAATACATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
13 17 0.47
14 9 0.25
15 5 0.14
16 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATTATATAAA
Found at i:1474893 original size:9 final size:8
Alignment explanation
Indices: 1474837--1474911 Score: 63
Period size: 8 Copynumber: 10.0 Consensus size: 8
1474827 ACAATTATAT
1474837 TATATAAA
1 TATATAAA
*
1474845 TATA-ATA
1 TATATAAA
*
1474852 TATAAAAA
1 TATATAAA
*
1474860 TA-ATTAA
1 TATATAAA
1474867 -A-ATAAA
1 TATATAAA
1474873 -ATAT-AA
1 TATATAAA
1474879 TATATAAA
1 TATATAAA
1474887 TTATATAAA
1 -TATATAAA
*
1474896 TACATAAA
1 TATATAAA
1474904 TATATAAA
1 TATATAAA
1474912 AAATTTTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
6 8 0.15
7 15 0.27
8 24 0.44
9 8 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (8 bp):
TATATAAA
Found at i:1474955 original size:31 final size:29
Alignment explanation
Indices: 1474840--1474989 Score: 109
Period size: 29 Copynumber: 5.2 Consensus size: 29
1474830 ATTATATTAT
* * *
1474840 ATAAATATAATATA-TAAAAATAATTAAA
1 ATAAATATAATATATTAAAATTTATAAAA
*
1474868 ATAAAATATAATATA-T-AAA-TTATATAA
1 AT-AAATATAATATATTAAAATTTATAAAA
* *
1474895 ATACATA-AATATATAAAAAATTT-TAAAAA
1 ATAAATATAATATAT-TAAAATTTAT-AAAA
1474924 ATAAATTATTAATATATTAAAATTTATAAAA
1 ATAAA-TA-TAATATATTAAAATTTATAAAA
*
1474955 A-AAATATAATATTTTAAATATGATTAT-AAA
1 ATAAATATAATATATTAAA-AT--TTATAAAA
1474985 ATAAA
1 ATAAA
1474990 AAATTTTACG
Statistics
Matches: 99, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
25 6 0.06
26 4 0.04
27 7 0.07
28 20 0.20
29 26 0.26
30 9 0.09
31 19 0.19
32 8 0.08
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
ATAAATATAATATATTAAAATTTATAAAA
Found at i:1475271 original size:16 final size:14
Alignment explanation
Indices: 1475241--1475267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1475231 ATGATAGAAA
1475241 ATTAAATGAAAAAT
1 ATTAAATGAAAAAT
1475255 ATTAAATGAAAAA
1 ATTAAATGAAAAA
1475268 AATAATTATC
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:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
ATTAAATGAAAAAT
Found at i:1479688 original size:20 final size:20
Alignment explanation
Indices: 1479668--1479704 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1479658 AAATTTAATA
*
1479668 AAATATTA-TTAAAATATAT
1 AAATATTACATAAAATATAT
1479687 AAATATTACATAAAATAT
1 AAATATTACATAAAATAT
1479705 TGTTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTACATAAAATATAT
Found at i:1479703 original size:31 final size:29
Alignment explanation
Indices: 1479648--1479711 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 29
1479638 TTTTAAAAAG
1479648 TAAAATTGATAAATTTAATAAAATATTAT
1 TAAAATTGATAAATTTAATAAAATATTAT
*
1479677 TAAAATAT-ATAAATATTACATAAAATATTGT
1 TAAAAT-TGATAAAT-TTA-ATAAAATATTAT
1479708 TAAA
1 TAAA
1479712 GATTTTAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 12 0.39
30 4 0.13
31 15 0.48
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAAATTGATAAATTTAATAAAATATTAT
Found at i:1479845 original size:10 final size:10
Alignment explanation
Indices: 1479827--1479879 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
1479817 AAATATTTTA
1479827 ATTTT-TTAT
1 ATTTTATTAT
*
1479836 GTTTTATTAT
1 ATTTTATTAT
1479846 ATTTTAATTAT
1 ATTTT-ATTAT
*
1479857 TTTTATATTAT
1 ATTT-TATTAT
*
1479868 ATTATATTAT
1 ATTTTATTAT
1479878 AT
1 AT
1479880 AATTTAATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 4 0.11
10 16 0.44
11 15 0.42
12 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:1479867 original size:25 final size:25
Alignment explanation
Indices: 1479819--1479867 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1479809 AAATTTTAAA
* *
1479819 ATATTTTAATTTTTTATGTTTTATT
1 ATATTTTAATTTTTTATATATTATT
1479844 ATATTTTAATTATTTT-TATATTAT
1 ATATTTTAATT-TTTTATATATTAT
1479868 ATTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
ATATTTTAATTTTTTATATATTATT
Found at i:1479870 original size:27 final size:25
Alignment explanation
Indices: 1479819--1479884 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 25
1479809 AAATTTTAAA
* *
1479819 ATATTTTAATTTTTTATGTTTTATT
1 ATATTTTAATTTTTTATATTATATT
1479844 ATATTTTAATTATTTTTATATTATATT
1 ATATTTTAA-T-TTTTTATATTATATT
1479871 ATATTATATAATTT
1 ATATT-T-TAATTT
1479885 AATGATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 9 0.26
26 1 0.03
27 20 0.57
28 2 0.06
29 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATATTTTAATTTTTTATATTATATT
Found at i:1480364 original size:5 final size:5
Alignment explanation
Indices: 1480354--1480519 Score: 61
Period size: 5 Copynumber: 34.4 Consensus size: 5
1480344 TATAATGTTA
* *
1480354 AATAT AATAT -A-AT AATAT AATTAA AATAA AATAT AAATAT AATAT AA-AT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT -AATAT AATAT AATAT
* * * * * * *
1480403 -ATAT AATAT -TTAA AAT-T TATAT TATA- AAT-T ATTAA AATATT AAATTT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA-T -AATAT
* * * *
1480450 AATATT AATAT ATTAT ATTTT AAATAT AATTAT AATAT AATA- AAAAT
1 AATA-T AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
1480497 AA-A- AATAT AATAT AA-AT -ATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
1480520 ATTATCATAT
Statistics
Matches: 122, Mismatches: 19, Indels: 40
0.67 0.10 0.22
Matches are distributed among these distances:
3 6 0.05
4 23 0.19
5 67 0.55
6 23 0.19
7 3 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:1480391 original size:11 final size:12
Alignment explanation
Indices: 1480353--1480532 Score: 82
Period size: 11 Copynumber: 14.2 Consensus size: 12
1480343 TTATAATGTT
1480353 AAATATAATATA
1 AAATATAATATA
1480365 ATAATATAAT-TA
1 A-AATATAATATA
*
1480377 AAATAAAATAT-
1 AAATATAATATA
1480388 AAATATAATATA
1 AAATATAATATA
1480400 AATATATAATATTTA
1 AA-ATATAATA--TA
*
1480415 AAATTTATATTATA
1 AAA--TATAATATA
* *
1480429 AATTATTAAAATATT
1 AA--A-TATAATATA
*
1480444 AAATTTAATATTA
1 AAATATAATA-TA
* * *
1480457 ATATATTATATTTT
1 AAATA-TA-ATATA
1480471 AAATATAAT-TA
1 AAATATAATATA
*
1480482 TAATATAATA-A
1 AAATATAATATA
*
1480493 AAATA-AAAATA
1 AAATATAATATA
*
1480504 TAATATAAATATA
1 AAATAT-AATATA
*
1480517 TAAATTATCATATA
1 -AAA-TATAATATA
1480531 AA
1 AA
1480533 TACATACATT
Statistics
Matches: 127, Mismatches: 22, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
10 3 0.02
11 36 0.28
12 14 0.11
13 30 0.24
14 19 0.15
15 18 0.14
16 7 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATATAATATA
Found at i:1480487 original size:20 final size:20
Alignment explanation
Indices: 1480394--1480487 Score: 51
Period size: 21 Copynumber: 4.8 Consensus size: 20
1480384 ATATAAATAT
*
1480394 AATATAAATATATAATATTTAA
1 AATAT-AAT-TATAATATTTTA
*
1480416 AATTTATATTATAA-ATTATTA
1 AATATA-ATTATAATATT-TTA
1480437 AA-AT-A-T-TAA-A-TTT-
1 AATATAATTATAATATTTTA
*
1480450 AATATTAATATATTATATTTTA
1 AATA-TAAT-TATAATATTTTA
1480472 AATATAATTATAATAT
1 AATATAATTATAATAT
1480488 AATAAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 24
0.66 0.06 0.28
Matches are distributed among these distances:
13 2 0.04
14 3 0.05
15 2 0.04
16 5 0.09
17 1 0.02
18 2 0.04
19 2 0.04
20 12 0.21
21 17 0.30
22 10 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATAATTATAATATTTTA
Found at i:1480700 original size:28 final size:28
Alignment explanation
Indices: 1480635--1480735 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 28
1480625 TTTATATATT
*
1480635 TATATTAAATTTTATAAATATAAATA-TAA
1 TATATTAAATTTTA-AAA-ATAAATATTTA
** *
1480664 TA-AAAAAATTTTAAAAATAAATATTTT
1 TATATTAAATTTTAAAAATAAATATTTA
*
1480691 TATATTAAATTTTAAATATAAATAATTATA
1 TATATTAAATTTTAAAAATAAAT-ATT-TA
1480721 TATATTAAATATTTA
1 TATATTAAAT-TTTA
1480736 TTAAATATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
26 7 0.12
27 6 0.10
28 26 0.44
29 5 0.08
30 11 0.19
31 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATATTAAATTTTAAAAATAAATATTTA
Found at i:1481657 original size:20 final size:20
Alignment explanation
Indices: 1481632--1481674 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1481622 AAATAGGTCT
*
1481632 ATAAATATCATATAAATAAG
1 ATAAATATAATATAAATAAG
*
1481652 ATAAATATAATATAAATATG
1 ATAAATATAATATAAATAAG
1481672 ATA
1 ATA
1481675 TTATAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAATATAATATAAATAAG
Found at i:1482170 original size:20 final size:22
Alignment explanation
Indices: 1482145--1482190 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1482135 TAAGTTTTAA
*
1482145 ATAT-AATTTTAA-ATAAAAAT
1 ATATAAATATTAATATAAAAAT
1482165 ATATAAATATTAATATAAAAAT
1 ATATAAATATTAATATAAAAAT
1482187 ATAT
1 ATAT
1482191 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAAATATTAATATAAAAAT
Found at i:1483357 original size:2 final size:2
Alignment explanation
Indices: 1483352--1483381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1483342 CTCTCAAAAC
1483352 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
1483382 GATAGAATAT
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:1483639 original size:18 final size:18
Alignment explanation
Indices: 1483617--1483652 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1483607 TAACCAGTGA
1483617 TTTTTATAATTATTATAAT
1 TTTTTATAATT-TTATAAT
*
1483636 TTTTTTTAATTTTATAA
1 TTTTTATAATTTTATAA
1483653 AAATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATAATTTTATAAT
Found at i:1483947 original size:21 final size:22
Alignment explanation
Indices: 1483909--1483953 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1483899 TCGATTAATG
*
1483909 ATTATTTATAAATATTTT-TAA
1 ATTATTTAAAAATATTTTATAA
1483930 ATTATTTAAATAAT-TTTTATAA
1 ATTATTTAAA-AATATTTTATAA
1483952 AT
1 AT
1483954 AAATGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTTAAAAATATTTTATAA
Found at i:1485513 original size:2 final size:2
Alignment explanation
Indices: 1485506--1485545 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1485496 GATTATGATG
1485506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1485546 GTAGGATGAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1486055 original size:33 final size:34
Alignment explanation
Indices: 1486012--1486079 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
1486002 TTTTTATGAG
** *
1486012 TTATAATTATATATAA-ATTTTAATATTTAATAAT
1 TTATAATTATATA-AATATTAAAATATTTAAAAAT
1486046 TTAT-ATTATATAAATATTAAAATATTTAAAAAT
1 TTATAATTATATAAATATTAAAATATTTAAAAAT
1486079 T
1 T
1486080 AAGATGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 2 0.07
33 24 0.80
34 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTATAATTATATAAATATTAAAATATTTAAAAAT
Found at i:1486308 original size:11 final size:11
Alignment explanation
Indices: 1486294--1486339 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1486284 GTTTAAATAA
*
1486294 ATTTATTTTAT
1 ATTTATATTAT
1486305 ATTTATATTAT
1 ATTTATATTAT
**
1486316 ATTCGTATT-T
1 ATTTATATTAT
1486326 -TTTATATTAT
1 ATTTATATTAT
1486336 ATTT
1 ATTT
1486340 CATAGTTTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 20 0.71
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1486943 original size:2 final size:2
Alignment explanation
Indices: 1486885--1486929 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1486875 CATTCGTGTG
1486885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1486926 TA TA
1 TA TA
1486930 CTAATGGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1490470 original size:49 final size:47
Alignment explanation
Indices: 1490398--1490489 Score: 157
Period size: 49 Copynumber: 1.9 Consensus size: 47
1490388 CTTCTTTTTT
1490398 TAATTTTCTTTTATTAATGAATTATATATAATATATACATATATACATA
1 TAATTTTCTTTTATTAATGAA-T-TATATAATATATACATATATACATA
*
1490447 TAATTTTCTTTTATTAATGAATTATATAATATATATATATATA
1 TAATTTTCTTTTATTAATGAATTATATAATATATACATATATA
1490490 GTTTTCATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 20 0.48
48 1 0.02
49 21 0.50
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (47 bp):
TAATTTTCTTTTATTAATGAATTATATAATATATACATATATACATA
Found at i:1490663 original size:4 final size:4
Alignment explanation
Indices: 1490620--1490675 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
1490610 AATATCATAC
* * * * * *
1490620 ATAT ACAT ACAT ATAT ATAT ATAT ACAT AGAC ATAC ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1490668 ATAT ATAT
1 ATAT ATAT
1490676 CACATCTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:1490673 original size:6 final size:6
Alignment explanation
Indices: 1490620--1490675 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1490610 AATATCATAC
* * * * * *
1490620 ATATAC ATACAT ATATAT ATATAT ACATAG ACATAC ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1490668 ATATAT AT
1 ATATAT AT
1490676 CACATCTTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (6 bp):
ATATAT
Found at i:1490675 original size:10 final size:10
Alignment explanation
Indices: 1490611--1490674 Score: 67
Period size: 10 Copynumber: 6.5 Consensus size: 10
1490601 GGAAAATCCA
*
1490611 ATAT-CATAC
1 ATATACATAT
*
1490620 ATATACATAC
1 ATATACATAT
*
1490630 ATATATATAT
1 ATATACATAT
*
1490640 ATATACATAG
1 ATATACATAT
*
1490650 ACATACATAT
1 ATATACATAT
*
1490660 ATATATATAT
1 ATATACATAT
1490670 ATATA
1 ATATA
1490675 TCACATCTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
9 4 0.09
10 42 0.91
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (10 bp):
ATATACATAT
Found at i:1493509 original size:90 final size:89
Alignment explanation
Indices: 1493344--1493601 Score: 288
Period size: 90 Copynumber: 2.9 Consensus size: 89
1493334 ATCATTTTCT
* * * *
1493344 TTCTTGCTACTTTGGCTATTTGTTTTCTTATTTTCAAAACTTTATTAATTTAAACATCAAAGCAT
1 TTCTTGCTACTTTGACTATTTG--TTCTTATCTTCAAAACTTTATTAATTTAAATATCAAAGTAT
* *
1493409 GTTTCGAAGTATAAACTCCGACATCA
64 ATTTCAAAGTATAAACTCCGACATCA
* * *
1493435 TTCTTGCTATTTTGACTATTTGCTCTCTTATCCTC-AAACTTTATTAATTTAAATATCAAAATAT
1 TTCTTGCTACTTTGACTATTTG-T-TCTTATCTTCAAAACTTTATTAATTTAAATATCAAAGTAT
* *
1493499 ATTTTAAAGTATAAACTCCGACTTCA
64 ATTTCAAAGTATAAACTCCGACATCA
* * * * *
1493525 TTCTT-ATCACTTTAACTATTT-TTTTTATCTTCAAAACTTTATTAATTTAATTATTAAAGTATA
1 TTCTTGCT-ACTTTGACTATTTGTTCTTATCTTCAAAACTTTATTAATTTAAATATCAAAGTATA
* *
1493588 TCTCAAAATATAAA
65 TTTCAAAGTATAAA
1493602 TTTCGATAGC
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
87 8 0.06
88 39 0.28
89 1 0.01
90 65 0.46
91 28 0.20
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (89 bp):
TTCTTGCTACTTTGACTATTTGTTCTTATCTTCAAAACTTTATTAATTTAAATATCAAAGTATAT
TTCAAAGTATAAACTCCGACATCA
Found at i:1493840 original size:8 final size:8
Alignment explanation
Indices: 1493827--1493852 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1493817 AATTATTTAT
1493827 TTAAAATA
1 TTAAAATA
1493835 TTAAAATA
1 TTAAAATA
1493843 TTAAAATA
1 TTAAAATA
1493851 TT
1 TT
1493853 TTATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAATA
Found at i:1494187 original size:20 final size:18
Alignment explanation
Indices: 1494158--1494197 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1494148 AATAGACTCG
*
1494158 ATTATTTTATATATAATATA
1 ATTATATTATAT-TAA-ATA
1494178 ATTATATTATATTAAATA
1 ATTATATTATATTAAATA
1494196 AT
1 AT
1494198 AATTAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATTATATTAAATA
Found at i:1494942 original size:15 final size:15
Alignment explanation
Indices: 1494922--1494951 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1494912 CAAACTCAAA
*
1494922 AAACTCTAATACCAT
1 AAACTCAAATACCAT
1494937 AAACTCAAATACCAT
1 AAACTCAAATACCAT
1494952 GTAAGTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACTCAAATACCAT
Found at i:1495207 original size:19 final size:18
Alignment explanation
Indices: 1495165--1495207 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1495155 AAATTAAATA
1495165 ATTTT-ATTTAATTATAT
1 ATTTTAATTTAATTATAT
*
1495182 TTGTTTAATTTAATTATTAT
1 AT-TTTAATTTAATTA-TAT
1495202 ATTTTA
1 ATTTTA
1495208 TGTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 13 0.62
20 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTAATTATAT
Found at i:1496710 original size:22 final size:20
Alignment explanation
Indices: 1496685--1496739 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1496675 TTTTTAAAAA
*
1496685 AATATTTTAAATTTATTATATT
1 AATATTTTAAA-TT-TTATAAT
1496707 AATATTTATATAATTTTATAAT
1 AATATTT-TA-AATTTTATAAT
*
1496729 AAAATTTTAAA
1 AATATTTTAAA
1496740 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 19 0.66
23 4 0.14
24 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTTAAATTTTATAAT
Found at i:1498335 original size:22 final size:22
Alignment explanation
Indices: 1498303--1498356 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1498293 TTATATAATT
*
1498303 ATTTTTATAAAATAATATTTTATA
1 ATTTTTA-AATATAA-ATTTTATA
* *
1498327 ATTTTTAAATTTAAATTTTATT
1 ATTTTTAAATATAAATTTTATA
1498349 ATTTTTAA
1 ATTTTTAA
1498357 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
23 5 0.19
24 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTTAAATATAAATTTTATA
Found at i:1499567 original size:23 final size:24
Alignment explanation
Indices: 1499541--1499603 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
1499531 AAATAAGAAA
1499541 TTTATTTTATTTAAAAATTAA-TT
1 TTTATTTTATTTAAAAATTAATTT
** *
1499564 TTTAAATTA-TAAAAAATTAATTT
1 TTTATTTTATTTAAAAATTAATTT
1499587 TTTAATTTTAATTTAAA
1 TTT-ATTTT-ATTTAAA
1499604 TTATCAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 10 0.33
23 12 0.40
24 3 0.10
25 1 0.03
26 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTTTATTTAAAAATTAATTT
Found at i:1499639 original size:20 final size:21
Alignment explanation
Indices: 1499598--1499641 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1499588 TTAATTTTAA
*
1499598 TTTAAATTATCAAAATATAAT
1 TTTAAATTATAAAAATATAAT
1499619 TTTAAA-TATAAAAAT-TAAAT
1 TTTAAATTATAAAAATAT-AAT
1499639 TTT
1 TTT
1499642 TTACTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 14 0.67
21 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTATAAAAATATAAT
Found at i:1499948 original size:18 final size:18
Alignment explanation
Indices: 1499922--1499988 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 18
1499912 TTTTTAAAAT
1499922 ATTTT-ATATTTATATAA
1 ATTTTAATATTTATATAA
1499939 ATTTTAATATATTA-AT-A
1 ATTTTAATAT-TTATATAA
1499956 A--TTAATA-TTATATAA
1 ATTTTAATATTTATATAA
*
1499971 ATATTAAAATATTTATAT
1 AT-TT-TAATATTTATAT
1499989 TATATTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 8 0.20
17 7 0.17
18 7 0.17
19 7 0.17
20 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATTTATATAA
Found at i:1499976 original size:17 final size:17
Alignment explanation
Indices: 1499905--1499977 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
1499895 TTATTACGTT
*
1499905 ATATTAAT-TTTTA-AA
1 ATATTAATATTATATAA
*
1499920 ATATTTTATATTTATATAA
1 ATA-TTAATA-TTATATAA
*
1499939 ATTTTAATA-TAT-T-A
1 ATATTAATATTATATAA
1499953 ATAATTAATATTATATAA
1 AT-ATTAATATTATATAA
1499971 ATATTAA
1 ATATTAA
1499978 AATATTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.07
15 10 0.22
16 10 0.22
17 6 0.13
18 12 0.27
19 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAATATTATATAA
Found at i:1499993 original size:25 final size:24
Alignment explanation
Indices: 1499947--1499993 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1499937 AAATTTTAAT
*
1499947 ATATTAATAATTAATATTATATAA
1 ATATTAAAAATTAATATTATATAA
*
1499971 ATATTAAAATATTTATATTATAT
1 ATATTAAAA-ATTAATATTATAT
1499994 TATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTAAAAATTAATATTATATAA
Found at i:1500250 original size:2 final size:2
Alignment explanation
Indices: 1500243--1500272 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1500233 GAAAATATTT
*
1500243 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1500273 GCAAGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1503003 original size:33 final size:32
Alignment explanation
Indices: 1502919--1503014 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 32
1502909 ATTTAGTAAA
1502919 TATTAAATATGATTATATAAATATAATAATAAAAT
1 TATTAAA-AT-ATTATAT-AATATAATAATAAAAT
* *
1502954 TATTAAAATATAATATAATATGAATATATAAATT
1 TATTAAAATATTATATAATAT-AATA-ATAAAAT
* * *
1502988 TGTTAAACT-TTATATAATATATTAATA
1 TATTAAAATATTATATAATATAATAATA
1503015 GATTAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.06
32 8 0.15
33 20 0.38
34 15 0.28
35 7 0.13
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (32 bp):
TATTAAAATATTATATAATATAATAATAAAAT
Found at i:1503041 original size:27 final size:27
Alignment explanation
Indices: 1502971--1503038 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1502961 ATATAATATA
* *
1502971 ATATGAATATATAAATTTG-TTAAACTTT
1 ATAT-AATATATAAA-TAGATTAAAATTT
*
1502999 ATATAATATATTAATAGATTAAAATTT
1 ATATAATATATAAATAGATTAAAATTT
1503026 ATATAA-ATATAAA
1 ATATAATATATAAA
1503039 ATAATATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.23
27 23 0.66
28 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (27 bp):
ATATAATATATAAATAGATTAAAATTT
Found at i:1503715 original size:20 final size:21
Alignment explanation
Indices: 1503672--1503727 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1503662 TAACTGAATA
*
1503672 AATTTAACATAAAATTAAATT
1 AATTTAACATAAAATTAAAAT
* *
1503693 AATTTCACATATAA-TAAAAT
1 AATTTAACATAAAATTAAAAT
*
1503713 AATTTATATATAAAA
1 AATTTA-ACATAAAA
1503728 CTTCATCGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTAACATAAAATTAAAAT
Found at i:1504774 original size:17 final size:17
Alignment explanation
Indices: 1504749--1504783 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1504739 ATATTAATTC
*
1504749 TTTACAAAAAATTAATA
1 TTTAAAAAAAATTAATA
*
1504766 TTTAAAAAATATTAATA
1 TTTAAAAAAAATTAATA
1504783 T
1 T
1504784 AAACCTAATA
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAAAAAAATTAATA
Found at i:1505201 original size:24 final size:23
Alignment explanation
Indices: 1505189--1505245 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1505179 TATCATTTAA
*
1505189 ATTAAATTAATTTATTATTAATTT
1 ATTAAAATAATTT-TTATTAATTT
*
1505213 ATTAAAATAATTTTT-TAAATTT
1 ATTAAAATAATTTTTATTAATTT
1505235 AATATAAAATA
1 -AT-TAAAATA
1505246 TATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTAAAATAATTTTTATTAATTT
Found at i:1505223 original size:13 final size:13
Alignment explanation
Indices: 1505189--1505233 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1505179 TATCATTTAA
1505189 ATTAAATTAATTT
1 ATTAAATTAATTT
1505202 ATT--ATTAATTT
1 ATTAAATTAATTT
*
1505213 ATTAAAATAATTT
1 ATTAAATTAATTT
*
1505226 TTTAAATT
1 ATTAAATT
1505234 TAATATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 11 0.41
13 16 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAAATTAATTT
Found at i:1505292 original size:19 final size:21
Alignment explanation
Indices: 1505246--1505298 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1505236 ATATAAAATA
*
1505246 TATAA-ATATTAATATATTTT
1 TATAATATTTTAATATATTTT
*
1505266 TTTAATATTTTAATATATTTT
1 TATAATATTTTAATATATTTT
*
1505287 ATATATTATTTT
1 -TATAATATTTT
1505299 GATCATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 14 0.52
22 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATAATATTTTAATATATTTT
Found at i:1505588 original size:19 final size:19
Alignment explanation
Indices: 1505565--1505602 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1505555 AAATTGATAA
*
1505565 AAAAATCAAAATAATATTAT
1 AAAAAT-AAAATAAAATTAT
1505585 AAAAATAAAATAAAATTA
1 AAAAATAAAATAAAATTA
1505603 CAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATAAAATAAAATTAT
Found at i:1505736 original size:15 final size:15
Alignment explanation
Indices: 1505698--1505736 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1505688 TAACTTATAT
*
1505698 ATATTTTTTAATATA
1 ATATTTTTTAATAAA
* *
1505713 ATAATTTTTATTAAA
1 ATATTTTTTAATAAA
1505728 ATATTTTTT
1 ATATTTTTT
1505737 TACCCATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTTTTAATAAA
Found at i:1507163 original size:34 final size:33
Alignment explanation
Indices: 1507115--1507335 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
1507105 TAGTAAAAAC
*
1507115 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1507148 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1507182 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1507216 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
1507250 CTCCCATTTAGTTAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1507284 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
1507318 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1507336 TCTCTCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1507231 original size:68 final size:68
Alignment explanation
Indices: 1507117--1507335 Score: 298
Period size: 68 Copynumber: 3.2 Consensus size: 68
1507107 GTAAAAACCA
* * *
1507117 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
1507181 TCAC
65 TCAC
* * * *
1507185 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
1507250 CTC
66 CAC
* * * * *
1507253 CCATTTAGTTAACAATGGCAAACCACCAAATCACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
1507318 CA-
66 CAC
1507320 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1507336 TCTCTCACTT
Statistics
Matches: 131, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
67 16 0.12
68 115 0.88
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:1507294 original size:102 final size:101
Alignment explanation
Indices: 1507115--1507335 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
1507105 TAGTAAAAAC
* *
1507115 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1507180 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
1507216 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
1507281 AATCACTCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1507318 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1507336 TCTCTCACTT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1511791 original size:34 final size:33
Alignment explanation
Indices: 1511743--1511962 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 33
1511733 TGGTAAAAAC
*
1511743 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1511776 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1511810 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1511844 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
1511878 CTCCCATTTAGTTAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1511912 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1511946 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1511963 ATATATCTTC
Statistics
Matches: 159, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1511859 original size:68 final size:67
Alignment explanation
Indices: 1511745--1511962 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 67
1511735 GTAAAAACCA
* * *
1511745 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1511810 CAC
65 CAC
* * * *
1511813 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1511878 CTC
65 CAC
* * * * *
1511881 CCATTTAGTTAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1511946 CA-
65 CAC
1511948 CCATTTAATCAACAA
1 CCATTTAATCAACAA
1511963 ATATATCTTC
Statistics
Matches: 129, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1511887 original size:102 final size:101
Alignment explanation
Indices: 1511743--1511962 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
1511733 TGGTAAAAAC
* *
1511743 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1511808 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
1511844 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1511909 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1511946 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1511963 ATATATCTTC
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1512696 original size:28 final size:31
Alignment explanation
Indices: 1512665--1512736 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 31
1512655 TAAAATTTTA
1512665 TTTTATTATTTAAAATATT-A-AAAAAT-A-T
1 TTTTATTATTTAAAAT-TTAATAAAAATAATT
*
1512693 TTTTA-TAATT-AAATTTAAATAAAAATAATT
1 TTTTATTATTTAAAATTT-AATAAAAATAATT
1512723 TTTTATTATTTAAA
1 TTTTATTATTTAAA
1512737 TAATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
25 2 0.06
26 4 0.11
27 5 0.14
28 11 0.31
29 1 0.03
30 6 0.17
31 4 0.11
32 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTTATTATTTAAAATTTAATAAAAATAATT
Found at i:1513698 original size:2 final size:2
Alignment explanation
Indices: 1513693--1513719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1513683 ACATGTGTGC
1513693 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
1513720 CACACCACGG
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:1515641 original size:27 final size:28
Alignment explanation
Indices: 1515611--1515694 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 28
1515601 AAAATTTATA
*
1515611 TAATAT-AATTTATTAATATATTAAA-AT
1 TAATATAAATTTA-AAATATATTAAATAT
*
1515638 TAATATAAATTTAAAATATTTTAAATAT
1 TAATATAAATTTAAAATATATTAAATAT
*
1515666 T-ATGATAATATAATAAAATAT-TTAAATAT
1 TAAT-ATAA-AT-TTAAAATATATTAAATAT
1515695 GATATCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 18 0.37
28 13 0.27
29 10 0.20
30 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATATAAATTTAAAATATATTAAATAT
Found at i:1517549 original size:13 final size:13
Alignment explanation
Indices: 1517531--1517560 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1517521 AATATATATT
1517531 ATTTTTTACTTCA
1 ATTTTTTACTTCA
*
1517544 ATTTTTTATTTCA
1 ATTTTTTACTTCA
1517557 ATTT
1 ATTT
1517561 ACTTTTTATA
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:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTTACTTCA
Found at i:1517710 original size:20 final size:21
Alignment explanation
Indices: 1517670--1517714 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1517660 GTTGAAAAAG
1517670 TTAAAATTAAAATATAAATTT
1 TTAAAATTAAAATATAAATTT
1517691 TTAAAATTAAAATA-AAATTT
1 TTAAAATTAAAATATAAATTT
1517711 TTAA
1 TTAA
1517715 TATTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATTAAAATATAAATTT
Found at i:1519189 original size:20 final size:18
Alignment explanation
Indices: 1519166--1519210 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1519156 GTTTAGATTT
1519166 TTTTAATTTAAATTGATCTA
1 TTTTAATTTAAATT-AT-TA
*
1519186 TTTTGATTTAAATTATTA
1 TTTTAATTTAAATTATTA
1519204 -TTTAATT
1 TTTTAATT
1519211 AATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 2 0.09
20 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTAATTTAAATTATTA
Found at i:1522412 original size:5 final size:5
Alignment explanation
Indices: 1522402--1522426 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1522392 AAAAGGAGAA
1522402 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1522427 GGCATGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1525961 original size:14 final size:14
Alignment explanation
Indices: 1525942--1525971 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1525932 GTGCGACGAT
1525942 TAAATCTTAATATA
1 TAAATCTTAATATA
1525956 TAAATCTTAATATA
1 TAAATCTTAATATA
1525970 TA
1 TA
1525972 GAGTGACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATCTTAATATA
Found at i:1529619 original size:28 final size:27
Alignment explanation
Indices: 1529595--1529667 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
1529585 TAGATATCTC
*
1529595 AAAATTTATATAATATAAATTATATATA
1 AAAAATTATATAA-ATAAATTATATATA
*
1529623 AAAAATTATATAAATAAACTAATAATATA
1 AAAAATTATATAAATAAA-TTAT-ATATA
*
1529652 ATAAAA-AATATAAATA
1 A-AAAATTATATAAATA
1529668 TATAAATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.13
28 15 0.38
29 15 0.38
30 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAAATTATATAAATAAATTATATATA
Found at i:1529622 original size:16 final size:15
Alignment explanation
Indices: 1529595--1529657 Score: 69
Period size: 14 Copynumber: 4.3 Consensus size: 15
1529585 TAGATATCTC
1529595 AAAATT-TATATAAT
1 AAAATTATATATAAT
1529609 ATAAATTATATATAA-
1 A-AAATTATATATAAT
1529624 AAAATTATATA-AAT
1 AAAATTATATATAAT
* *
1529638 AAACTAATAATATAAT
1 AAAATTAT-ATATAAT
1529654 AAAA
1 AAAA
1529658 AATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 17 0.41
15 9 0.22
16 13 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTATATATAAT
Found at i:1529673 original size:33 final size:32
Alignment explanation
Indices: 1529615--1529697 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 32
1529605 TAATATAAAT
*
1529615 TATATATAAAAAATTATATAAATAAACTA-ATAA
1 TATA-ATAAAAAATTAAATAAATAAACTACA-AA
* *
1529648 TATAATAAAAAATATAAATATATAAATTACCAAA
1 TATAATAAAAAAT-TAAATAAATAAACTA-CAAA
1529682 TATAA-AAAAAATTAAA
1 TATAATAAAAAATTAAA
1529698 GCAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 13 0.30
33 23 0.52
34 7 0.16
35 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (32 bp):
TATAATAAAAAATTAAATAAATAAACTACAAA
Found at i:1529861 original size:12 final size:12
Alignment explanation
Indices: 1529844--1529868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1529834 ATTTAAAATA
1529844 ATAAATTTTTAT
1 ATAAATTTTTAT
1529856 ATAAATTTTTAT
1 ATAAATTTTTAT
1529868 A
1 A
1529869 CGTTAATAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATTTTTAT
Found at i:1530284 original size:17 final size:18
Alignment explanation
Indices: 1530238--1530297 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 18
1530228 ATAATTAATG
1530238 TAATATATTTAATATATATT
1 TAATATATTTAATA-AT-TT
* *
1530258 ATATTTATATTTATAAAATTT
1 -TA-ATATATTTA-ATAATTT
1530279 TAATATATTTAATAATTT
1 TAATATATTTAATAATTT
1530297 T
1 T
1530298 TATTATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 2 0.06
21 4 0.12
22 10 0.30
23 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATATATTTAATAATTT
Found at i:1530286 original size:41 final size:45
Alignment explanation
Indices: 1530224--1530339 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 45
1530214 TTAAATAAAA
*
1530224 TTATATAATTAATGTAATATATTTAATATA-TATTA-TA-TTTATAT
1 TTATAAAATT-AT-TAATATATTTAATATATTATTATTATTTTATAT
*
1530268 TTATAAAATT-TTAATATATTTAATA-ATTTTTATTATTTTATAT
1 TTATAAAATTATTAATATATTTAATATATTATTATTATTTTATAT
* * *
1530311 TTATATAATTATTAAAAATATTAAATATA
1 TTATAAAATTATT-AATATATTTAATATA
1530340 ATATACACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.02
41 18 0.30
42 3 0.05
43 16 0.26
44 11 0.18
45 11 0.18
46 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (45 bp):
TTATAAAATTATTAATATATTTAATATATTATTATTATTTTATAT
Found at i:1530298 original size:19 final size:19
Alignment explanation
Indices: 1530238--1530299 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
1530228 ATAATTAATG
*
1530238 TAATATATTTAATATATATTA
1 TAATATATTTAATA-AT-TTT
* *
1530259 TATTTATATTT-ATAAAATTT
1 TA-ATATATTTAAT-AATTTT
1530279 TAATATATTTAATAATTTT
1 TAATATATTTAATAATTTT
1530298 TA
1 TA
1530300 TTATTTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.42
20 6 0.18
21 5 0.15
22 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATATATTTAATAATTTT
Found at i:1531200 original size:20 final size:20
Alignment explanation
Indices: 1531168--1531217 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1531158 TTTATAAAAT
1531168 TAAAAAATT--TTAAATCAG
1 TAAAAAATTAATTAAATCAG
* *
1531186 TAAAAAATTAATTAAATTAT
1 TAAAAAATTAATTAAATCAG
*
1531206 TATAAAATTAAT
1 TAAAAAATTAAT
1531218 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAAAATTAATTAAATCAG
Found at i:1531226 original size:19 final size:20
Alignment explanation
Indices: 1531189--1531227 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1531179 AAATCAGTAA
**
1531189 AAAATTAATTAAATTATTAT
1 AAAATTAATTAAAAAATTAT
1531209 AAAATTAA-TAAAAAATTAT
1 AAAATTAATTAAAAAATTAT
1531228 TTTAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTAATTAAAAAATTAT
Found at i:1531322 original size:17 final size:17
Alignment explanation
Indices: 1531302--1531343 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
1531292 TATTAAAAAT
1531302 TATATTATTTAATTAAA
1 TATATTATTTAATTAAA
1531319 TATATT-TTT-ATTAAA
1 TATATTATTTAATTAAA
1531334 TAT-TTATTTA
1 TATATTATTTA
1531344 TTATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 3 0.13
17 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATTTAATTAAA
Found at i:1531378 original size:18 final size:17
Alignment explanation
Indices: 1531306--1531378 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 17
1531296 AAAAATTATA
*
1531306 TTATTTAATTAA-ATAT
1 TTATTTAATTAATAAAT
*
1531322 ATT-TTT-ATTAA-ATAT
1 -TTATTTAATTAATAAAT
*
1531337 TTATTT-ATTATTAAAT
1 TTATTTAATTAATAAAT
1531353 TT-TTTAATATAATAAAT
1 TTATTTAAT-TAATAAAT
1531370 TTATTTAAT
1 TTATTTAAT
1531379 CAGTTTGATC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
14 2 0.04
15 19 0.40
16 10 0.21
17 11 0.23
18 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTAATTAATAAAT
Found at i:1532176 original size:22 final size:23
Alignment explanation
Indices: 1532141--1532192 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1532131 TATTTTTATT
*
1532141 TATATCAATAA-TTTATATAAAAA
1 TATATTAATAATTTTA-ATAAAAA
*
1532164 TATATTAA-AATTTTAATATAAA
1 TATATTAATAATTTTAATAAAAA
1532186 TATATTA
1 TATATTA
1532193 TATATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATTAATAATTTTAATAAAAA
Found at i:1532201 original size:16 final size:15
Alignment explanation
Indices: 1532163--1532211 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
1532153 TTATATAAAA
*
1532163 ATATATTAAAATTTT
1 ATATATTAAAATATT
1532178 A-ATA-TAAATATATT
1 ATATATTAAA-ATATT
1532192 ATATATTAAACATATT
1 ATATATTAAA-ATATT
1532208 ATAT
1 ATAT
1532212 TAATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 4 0.14
16 13 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTAAAATATT
Found at i:1532206 original size:24 final size:23
Alignment explanation
Indices: 1532179--1532248 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 23
1532169 TAAAATTTTA
1532179 ATATAAATATATTATATATTAAAC
1 ATAT-AATATATTATATATTAAAC
1532203 ATAT--TATATTAATAATATTTAAAC
1 ATATAATATATT-AT-ATA-TTAAAC
1532227 ATATATTATCATATT-TATATTA
1 ATATA--AT-ATATTATATATTA
1532249 CATTTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
21 6 0.16
22 2 0.05
23 3 0.08
24 14 0.37
25 3 0.08
26 3 0.08
27 1 0.03
28 1 0.03
29 5 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAATATATTATATATTAAAC
Found at i:1532211 original size:29 final size:30
Alignment explanation
Indices: 1532163--1532221 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1532153 TTATATAAAA
*
1532163 ATATATTAAAATTTTAATATAAAT-ATATT
1 ATATATTAAAATATTAATATAAATAATATT
*
1532192 ATATATTAAACATATT-ATATTAATAATATT
1 ATATATTAAA-ATATTAATATAAATAATATT
1532222 TAAACATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATATTAAAATATTAATATAAATAATATT
Found at i:1532457 original size:11 final size:11
Alignment explanation
Indices: 1532441--1532493 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1532431 TAAATACAAG
1532441 AATTAAAAATT
1 AATTAAAAATT
1532452 AATTAAATCAATTT
1 AATTAAA--AA-TT
1532466 AATTAAAAATT
1 AATTAAAAATT
* *
1532477 AAATAATAATTT
1 AATTAA-AAATT
1532489 AATTA
1 AATTA
1532494 TATATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 14 0.40
12 10 0.29
13 2 0.06
14 9 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:1532470 original size:25 final size:23
Alignment explanation
Indices: 1532441--1532493 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 23
1532431 TAAATACAAG
*
1532441 AATTAAAAATTAATTAAATCAATTT
1 AATTAAAAATTAAAT-AAT-AATTT
1532466 AATTAAAAATTAAATAATAATTT
1 AATTAAAAATTAAATAATAATTT
1532489 AATTA
1 AATTA
1532494 TATATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 10 0.37
24 3 0.11
25 14 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTAAAAATTAAATAATAATTT
Found at i:1532573 original size:23 final size:21
Alignment explanation
Indices: 1532521--1532573 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
1532511 TAATTAATTG
1532521 AATTAAT-AAAAAAATATATT
1 AATTAATAAAAAAAATATATT
*
1532541 AAATAGATAAAAAAAATTATATT
1 AATTA-ATAAAAAAAA-TATATT
*
1532564 ATTTTAATAA
1 A-ATTAATAA
1532574 TTTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 2 0.08
22 7 0.27
23 11 0.42
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTAATAAAAAAAATATATT
Found at i:1533525 original size:2 final size:2
Alignment explanation
Indices: 1533518--1533564 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1533508 TGATGATTAA
1533518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1533560 AT AT A
1 AT AT A
1533565 AACAATAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1534442 original size:2 final size:2
Alignment explanation
Indices: 1534435--1534465 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1534425 TATATCTTCA
1534435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1534466 TTTCTGTTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1548127 original size:2 final size:2
Alignment explanation
Indices: 1548120--1548146 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1548110 TAATGGTTGT
1548120 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
1548147 CATTGCTGAT
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:1548434 original size:23 final size:23
Alignment explanation
Indices: 1548406--1548449 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1548396 TGCAGCCAAT
1548406 TTTAAAATAC-AATATTTAATAAA
1 TTTAAAATACAAAT-TTTAATAAA
*
1548429 TTTAAAATTCAAATTTTAATA
1 TTTAAAATACAAATTTTAATA
1548450 TTTACAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAATACAAATTTTAATAAA
Found at i:1548913 original size:2 final size:2
Alignment explanation
Indices: 1548906--1548950 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1548896 TGCTTCTATC
1548906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1548948 AT A
1 AT A
1548951 AAAGAACTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1549196 original size:2 final size:2
Alignment explanation
Indices: 1549189--1549216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1549179 TTTGTACCTA
1549189 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
1549217 TGATAGGTTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550704 original size:21 final size:22
Alignment explanation
Indices: 1550670--1550710 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1550660 ATATATTTTT
1550670 ATTTATTTAAATT-AATTTAAA
1 ATTTATTTAAATTAAATTTAAA
**
1550691 ATTTATTTTTATTAAATTTA
1 ATTTATTTAAATTAAATTTA
1550711 TTTAAGCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTATTTAAATTAAATTTAAA
Found at i:1550713 original size:26 final size:25
Alignment explanation
Indices: 1550667--1550729 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
1550657 TTAATATATT
1550667 TTTATTTATTTAAATTAATTTAAAA
1 TTTATTTATTTAAATTAATTTAAAA
* * **
1550692 TTTATTTTTATTAAATTTATTTAAGC
1 TTTATTTAT-TTAAATTAATTTAAAA
1550718 TATTATTTATTT
1 T-TTATTTATTT
1550730 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.26
26 16 0.52
27 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTATTTATTTAAATTAATTTAAAA
Found at i:1550810 original size:27 final size:28
Alignment explanation
Indices: 1550780--1550843 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
1550770 ATTATTTTTT
1550780 TATATATAACTTA-ATTT-TTTTTAATA
1 TATATATAACTTATATTTATTTTTAATA
* *
1550806 CTATATTATAATTTATATTTATTTTTTATA
1 -TATA-TATAACTTATATTTATTTTTAATA
1550836 TA-ATATAA
1 TATATATAA
1550844 ATTACATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 9 0.28
28 9 0.28
29 6 0.19
30 8 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATATAACTTATATTTATTTTTAATA
Found at i:1552422 original size:2 final size:2
Alignment explanation
Indices: 1552415--1552439 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1552405 TAACAGTGCT
1552415 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1552440 CCGTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1552642 original size:21 final size:22
Alignment explanation
Indices: 1552618--1552659 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1552608 TTTTTATATT
1552618 TTATTATTAAAT-TTAAATAAA
1 TTATTATTAAATATTAAATAAA
* *
1552639 TTATTTTTAATTATTAAATAA
1 TTATTATTAAATATTAAATAA
1552660 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTATTAAATATTAAATAAA
Found at i:1552675 original size:31 final size:27
Alignment explanation
Indices: 1552611--1552667 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1552601 AGTTAAATTT
*
1552611 TTATATTTTATTATTAAATTTAAATAAA
1 TTAT-TTTTATTATTAAATATAAATAAA
*
1552639 TTATTTTTAATTATTAAATAATAATTAAA
1 TTATTTTT-ATTATTAAAT-ATAAATAAA
1552668 ATCTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTTTTATTATTAAATATAAATAAA
Found at i:1552687 original size:24 final size:25
Alignment explanation
Indices: 1552651--1552701 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
1552641 ATTTTTAATT
1552651 ATTAAATAATAATTAAAA-TCTATTTA
1 ATTAAAT-ATAA-TAAAATTCTATTTA
*
1552677 ATTAAAT-TAATAAAATTTTATTTA
1 ATTAAATATAATAAAATTCTATTTA
1552701 A
1 A
1552702 AGCTAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
26 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTAAATATAATAAAATTCTATTTA
Found at i:1553250 original size:27 final size:27
Alignment explanation
Indices: 1553220--1553296 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
1553210 AAATATTTTG
*
1553220 ACACATATATTTTGACATAAATACTTA
1 ACACAAATATTTTGACATAAATACTTA
** * *
1553247 ACACAGGTATTTTGATATAGATACTTA
1 ACACAAATATTTTGACATAAATACTTA
1553274 AC-CTAAATATTTTGACATAAATA
1 ACAC-AAATATTTTGACATAAATA
1553297 TTTTGATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (27 bp):
ACACAAATATTTTGACATAAATACTTA
Found at i:1553296 original size:14 final size:14
Alignment explanation
Indices: 1553210--1553302 Score: 64
Period size: 14 Copynumber: 6.8 Consensus size: 14
1553200 TATTTAGTAC
*
1553210 AAATATTTTGACAC
1 AAATATTTTGACAT
*
1553224 ATATATTTTGACAT
1 AAATATTTTGACAT
* * *
1553238 AAATA-CTTAACAC
1 AAATATTTTGACAT
** *
1553251 AGGTATTTTGATAT
1 AAATATTTTGACAT
* * * *
1553265 AGATA-CTTAACCT
1 AAATATTTTGACAT
1553278 AAATATTTTGACAT
1 AAATATTTTGACAT
1553292 AAATATTTTGA
1 AAATATTTTGA
1553303 TAAAAATAGT
Statistics
Matches: 56, Mismatches: 21, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
13 16 0.29
14 40 0.71
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40
Consensus pattern (14 bp):
AAATATTTTGACAT
Found at i:1553633 original size:31 final size:28
Alignment explanation
Indices: 1553587--1553654 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
1553577 TGTTAAATTT
1553587 TAATTTTAATAATTAAAGATTAAATTTTAA
1 TAATTTTAATAATTAAA-A-TAAATTTTAA
*
1553617 TAATCTTTAATTATTAAAATAAATTTTAAA
1 TAAT-TTTAATAATTAAAATAAATTTT-AA
*
1553647 AAATTTTA
1 TAATTTTA
1553655 CGAGTAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 12 0.35
30 10 0.29
31 12 0.35
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
TAATTTTAATAATTAAAATAAATTTTAA
Found at i:1553758 original size:21 final size:21
Alignment explanation
Indices: 1553734--1553773 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1553724 TAATGGACTA
*
1553734 TTTAAAAAAATTGATAATTTT
1 TTTAAAAAAATAGATAATTTT
1553755 TTTAAAAAAATAGATAATT
1 TTTAAAAAAATAGATAATT
1553774 ATTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAATAGATAATTTT
Found at i:1553778 original size:20 final size:21
Alignment explanation
Indices: 1553732--1553778 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1553722 TTTAATGGAC
*
1553732 TATTTAAAAAAATTGATAATT
1 TATTTAAAAAAATAGATAATT
*
1553753 TTTTTAAAAAAATAGATAA-T
1 TATTTAAAAAAATAGATAATT
1553773 TATTTA
1 TATTTA
1553779 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
TATTTAAAAAAATAGATAATT
Found at i:1555114 original size:29 final size:30
Alignment explanation
Indices: 1555082--1555139 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1555072 TAATAAAAAA
* *
1555082 AATATTTTAGTTTTTATA-TTATTAAATTT
1 AATATTTTAATCTTTATACTTATTAAATTT
*
1555111 AATATTTTAATCTTTATACTTTTTAAATT
1 AATATTTTAATCTTTATACTTATTAAATT
1555140 ATAGCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (30 bp):
AATATTTTAATCTTTATACTTATTAAATTT
Found at i:1555772 original size:29 final size:29
Alignment explanation
Indices: 1555671--1555799 Score: 115
Period size: 30 Copynumber: 4.4 Consensus size: 29
1555661 TTTTACTTAG
* *
1555671 ATAAATTTTATAATTTT-AC-TACAATTAA
1 ATAAATTTT-TAATTTTAACTTATATTTAA
* * *
1555699 ATAAGTTTTTATTTTTAA-TT-TATGTAAA
1 ATAAATTTTTAATTTTAACTTATAT-TTAA
1555727 ATAAA-TTTTACATTTTTAACTTATATTTAA
1 ATAAATTTTTA-A-TTTTAACTTATATTTAA
*
1555757 ATAAATTTTTAATTTTTAATTTATATTTAA
1 ATAAATTTTTAA-TTTTAACTTATATTTAA
*
1555787 ATAATTTTTTAAT
1 ATAAATTTTTAAT
1555800 ATAAATCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
27 12 0.14
28 17 0.20
29 7 0.08
30 39 0.47
31 8 0.10
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
ATAAATTTTTAATTTTAACTTATATTTAA
Found at i:1555797 original size:18 final size:18
Alignment explanation
Indices: 1555776--1555827 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1555766 TAATTTTTAA
1555776 TTTATATTTAAATAATTT
1 TTTATATTTAAATAATTT
*
1555794 TTTA-ATATAAATCAATTT
1 TTTATATTTAAAT-AATTT
1555812 TTT-TATTTAAAATAAT
1 TTTATATTT-AAATAAT
1555828 CACTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 7 0.24
18 18 0.62
19 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATTTAAATAATTT
Found at i:1555799 original size:30 final size:29
Alignment explanation
Indices: 1555695--1555795 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 29
1555685 TTTACTACAA
*
1555695 TTAAATAAGTTTTT-ATTTTTAATTTAT-G
1 TTAAATAA-TTTTTAATTTTTAATTTATAT
* * *
1555723 TAAAATAAATTTTACATTTTTAACTTATAT
1 TTAAATAATTTTTA-ATTTTTAATTTATAT
1555753 TTAAATAAATTTTTAATTTTTAATTTATAT
1 TTAAAT-AATTTTTAATTTTTAATTTATAT
1555783 TTAAATAATTTTT
1 TTAAATAATTTTT
1555796 TAATATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.06
28 7 0.11
29 19 0.31
30 25 0.40
31 7 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTAAATAATTTTTAATTTTTAATTTATAT
Found at i:1560474 original size:17 final size:17
Alignment explanation
Indices: 1560452--1560494 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1560442 TATTTTTTTA
1560452 TTTTATTTTTAAAAATC
1 TTTTATTTTTAAAAATC
** *
1560469 TTTTATCCTTAAAATTC
1 TTTTATTTTTAAAAATC
1560486 TTTTATTTT
1 TTTTATTTT
1560495 GTAATGAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATTTTTAAAAATC
Found at i:1561579 original size:21 final size:21
Alignment explanation
Indices: 1561544--1561598 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1561534 TGATTAATAA
1561544 AAATTTAAA-AAATTAT-ATT
1 AAATTTAAATAAATTATAATT
*
1561563 AATATTTATATAAATTATAATT
1 AA-ATTTAAATAAATTATAATT
1561585 AAATTTAAATAAAT
1 AAATTTAAATAAAT
1561599 AAAAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 18 0.58
22 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTAAATAAATTATAATT
Found at i:1563110 original size:7 final size:7
Alignment explanation
Indices: 1563098--1563132 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1563088 ATTAAATTAA
1563098 ATTTTTT
1 ATTTTTT
1563105 ATTTTTT
1 ATTTTTT
*
1563112 ATTTTTA
1 ATTTTTT
*
1563119 AATTTTT
1 ATTTTTT
1563126 ATTTTTT
1 ATTTTTT
1563133 CAAGTTTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
ATTTTTT
Found at i:1563423 original size:14 final size:15
Alignment explanation
Indices: 1563395--1563423 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1563385 TATTATTACG
1563395 ATTGATTATAAAAAT
1 ATTGATTATAAAAAT
1563410 ATTGATTA-AAAAAT
1 ATTGATTATAAAAAT
1563424 TAAAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTGATTATAAAAAT
Found at i:1564800 original size:140 final size:140
Alignment explanation
Indices: 1564548--1564825 Score: 493
Period size: 140 Copynumber: 2.0 Consensus size: 140
1564538 TAACTTAGCT
* * *
1564548 TATGAGAATATCCGAGTTCTCTTGAATCAATAGATTTAATAATTTTAAACACGAAATAAAAATAT
1 TATGAGAATATCCGAATTCTCCTGAATCAATAAATTTAATAATTTTAAACACGAAATAAAAATAT
* *
1564613 GACACGATTTATTATAATAAACATTAAATATGACAGCTTTCTATCATATTAAAATAAATGTAAGT
66 GACACGATTTATTATAATAAACATTAAATATGACAACTTTCTATCATACTAAAATAAATGTAAGT
1564678 ACATATAGTC
131 ACATATAGTC
*
1564688 TATGAGAATATCTGAATTCTCCTGAATCAATAAATTTAATAATTTTAAACACGAAATAAAAATAT
1 TATGAGAATATCCGAATTCTCCTGAATCAATAAATTTAATAATTTTAAACACGAAATAAAAATAT
*
1564753 GACACGGTTTATTATAATAAACATTAAATATGACAACTTTCTATCATACTAAAATAAATGTAAGT
66 GACACGATTTATTATAATAAACATTAAATATGACAACTTTCTATCATACTAAAATAAATGTAAGT
1564818 ACATATAG
131 ACATATAG
1564826 ATTGATTTCT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 131 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (140 bp):
TATGAGAATATCCGAATTCTCCTGAATCAATAAATTTAATAATTTTAAACACGAAATAAAAATAT
GACACGATTTATTATAATAAACATTAAATATGACAACTTTCTATCATACTAAAATAAATGTAAGT
ACATATAGTC
Found at i:1570215 original size:24 final size:24
Alignment explanation
Indices: 1570170--1570215 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1570160 TTGGTTACAT
**
1570170 TAAAATTAAAAATAATGGTGATAG
1 TAAAATTAAAAATAATAATGATAG
**
1570194 TAAAATTAATTATAATAATGAT
1 TAAAATTAAAAATAATAATGAT
1570216 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (24 bp):
TAAAATTAAAAATAATAATGATAG
Found at i:1571260 original size:2 final size:2
Alignment explanation
Indices: 1571247--1571276 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1571237 TCTTTAGTTC
*
1571247 AT AT AC 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
1571277 GTTAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1576207 original size:22 final size:22
Alignment explanation
Indices: 1576180--1576225 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1576170 TTAAGTAGTA
1576180 TGTTAGATAAACATATTAAGTG
1 TGTTAGATAAACATATTAAGTG
* *
1576202 TGTTAGGTAAACATATTAGGTG
1 TGTTAGATAAACATATTAAGTG
1576224 TG
1 TG
1576226 GTAAGTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (22 bp):
TGTTAGATAAACATATTAAGTG
Found at i:1576539 original size:2 final size:2
Alignment explanation
Indices: 1576532--1576558 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1576522 ATGCTCTACA
1576532 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
1576559 ACTATGACTG
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:1577580 original size:15 final size:15
Alignment explanation
Indices: 1577549--1577577 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1577539 AAAAAGTTAA
1577549 AATATTTTTTATATT
1 AATATTTTTTATATT
1577564 AATA-TTTTTATATT
1 AATATTTTTTATATT
1577578 TAAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:1577900 original size:5 final size:5
Alignment explanation
Indices: 1577890--1577928 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
1577880 TTGAATAAAA
*
1577890 AATTT AATTT AAATTT AATTT AATTT AAATTA AATTT AA
1 AATTT AATTT -AATTT AATTT AATTT -AATTT AATTT AA
1577929 ATAAACTACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:1577905 original size:11 final size:11
Alignment explanation
Indices: 1577889--1577928 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1577879 ATTGAATAAA
1577889 AAATTTAATTT
1 AAATTTAATTT
1577900 AAATTTAATTT
1 AAATTTAATTT
*
1577911 -AATTTAAATT
1 AAATTTAATTT
1577921 AAATTTAA
1 AAATTTAA
1577929 ATAAACTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:1577911 original size:16 final size:16
Alignment explanation
Indices: 1577889--1577928 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1577879 ATTGAATAAA
1577889 AAATTTAATTTAAATT
1 AAATTTAATTTAAATT
*
1577905 TAATTTAATTTAAATT
1 AAATTTAATTTAAATT
1577921 AAATTTAA
1 AAATTTAA
1577929 ATAAACTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTAATTTAAATT
Found at i:1579194 original size:53 final size:51
Alignment explanation
Indices: 1579137--1579276 Score: 131
Period size: 53 Copynumber: 2.7 Consensus size: 51
1579127 TCCAAAATTA
*
1579137 TCGAACTCAATAAATTTAAATATTAAACTTAATTTA-CTGAAACTCGAAATGAT
1 TCGAA-TCAATTAATTTAAATATTAAA-TTAATTTATCTG-AACTCGAAATGAT
* * * *
1579190 TCGAATCTGATTAACTTAAGTGTTAAATCTAATTTATCTGAACTCGAAATGAT
1 TCGAATC-AATTAATTTAAATATTAAAT-TAATTTATCTGAACTCGAAATGAT
* * * *
1579243 ACAAATTTAATTAATTTAAA-ATTAAAATAATTTA
1 TCGAA-TCAATTAATTTAAATATTAAATTAATTTA
1579277 AATTTAAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
51 7 0.10
52 8 0.11
53 51 0.73
54 4 0.06
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (51 bp):
TCGAATCAATTAATTTAAATATTAAATTAATTTATCTGAACTCGAAATGAT
Found at i:1579273 original size:16 final size:16
Alignment explanation
Indices: 1579254--1579297 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1579244 CAAATTTAAT
1579254 TAATTTAAAATTAAAA
1 TAATTTAAAATTAAAA
*
1579270 TAATTTAAATTTAAAA
1 TAATTTAAAATTAAAA
1579286 TAATTTAAAATT
1 TAATTTAAAATT
1579298 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAAATTAAAA
Found at i:1579280 original size:31 final size:31
Alignment explanation
Indices: 1579245--1579311 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1579235 GAAATGATAC
*
1579245 AAATTT-AATTAATTTAAAATTAAAATAATTT
1 AAATTTAAAATAATTTAAAATTAAAA-AATTT
**
1579276 AAATTTAAAATAATTTAAAATTTTAAAATTT
1 AAATTTAAAATAATTTAAAATTAAAAAATTT
1579307 AAATT
1 AAATT
1579312 AGTCTAATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AAATTTAAAATAATTTAAAATTAAAAAATTT
Found at i:1581167 original size:40 final size:40
Alignment explanation
Indices: 1581104--1581185 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 40
1581094 TTTGAATAAA
1581104 ATTTTTATAAATTTAAATTATAATTTAATA-ATTAAAAAT
1 ATTTTTATAAATTTAAATTATAATTTAATATATTAAAAAT
* *
1581143 ATTTTTATTTAAATTT-AATTATAATTTATTATTTTAAAAAT
1 ATTTTTA--TAAATTTAAATTATAATTTAATATATTAAAAAT
1581184 AT
1 AT
1581186 AAAAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 7 0.18
40 14 0.37
41 17 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (40 bp):
ATTTTTATAAATTTAAATTATAATTTAATATATTAAAAAT
Found at i:1582527 original size:3 final size:3
Alignment explanation
Indices: 1582521--1582576 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1582511 ATTAAATTAT
1582521 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1582569 TAC TAC TA
1 TAC TAC TA
1582577 TTATTATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Done.