Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 20 of 45
Found at i:3729336 original size:22 final size:21
Alignment explanation
Indices: 3729311--3729366 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
3729301 GAAAGTCTAT
3729311 TATAAATAAAATATTTTAATAA
1 TATAAATAAAATA-TTTAATAA
*
3729333 TATAAATTTAAAACATTTAATAA
1 TATAAA--TAAAATATTTAATAA
*
3729356 T-TAAAAAAAAT
1 TATAAATAAAAT
3729367 CATATGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
22 10 0.34
23 9 0.31
24 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAAATAAAATATTTAATAA
Found at i:3731087 original size:22 final size:21
Alignment explanation
Indices: 3731044--3731085 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3731034 AAGTTAAAAA
3731044 ATATTTTTTATATTAATATTT
1 ATATTTTTTATATTAATATTT
3731065 ATATTTTTTATAATTAA-ATTT
1 ATATTTTTTAT-ATTAATATTT
3731086 TAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTTTTATATTAATATTT
Found at i:3734456 original size:2 final size:2
Alignment explanation
Indices: 3734451--3734475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3734441 TATTTTTTGG
3734451 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
3734476 AAATTTATCG
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:3734959 original size:19 final size:20
Alignment explanation
Indices: 3734935--3734975 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3734925 TATTATATAA
3734935 ATTTATAAAATATTTAT-TT
1 ATTTATAAAATATTTATATT
*
3734954 ATTTATATAATATTTATATT
1 ATTTATAAAATATTTATATT
3734974 AT
1 AT
3734976 GTGTTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATAAAATATTTATATT
Found at i:3738544 original size:18 final size:18
Alignment explanation
Indices: 3738521--3738560 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
3738511 TTGATAGCTG
3738521 ATTAATATAATATATT-TA
1 ATTAATATAA-ATATTATA
3738539 ATTAATATAAATATTATA
1 ATTAATATAAATATTATA
3738557 ATTA
1 ATTA
3738561 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATAAATATTATA
Found at i:3738643 original size:2 final size:2
Alignment explanation
Indices: 3738631--3738667 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
3738621 AAAATACAAA
3738631 AT AT GAT 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
3738668 TTACACCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3739834 original size:11 final size:11
Alignment explanation
Indices: 3739748--3739841 Score: 51
Period size: 11 Copynumber: 9.1 Consensus size: 11
3739738 CATATTAATA
3739748 ATTTATATTAT
1 ATTTATATTAT
*
3739759 A--TAAATTAT
1 ATTTATATTAT
*
3739768 A-ATATCATTAT
1 ATTTAT-ATTAT
*
3739779 ATTCATATTAT
1 ATTTATATTAT
3739790 -TTT-T-TTA-
1 ATTTATATTAT
* *
3739797 CTTTATATTTT
1 ATTTATATTAT
3739808 ATTTA-ATTATT
1 ATTTATATTA-T
*
3739819 TTTTATATTAT
1 ATTTATATTAT
*
3739830 ATTTATAATAT
1 ATTTATATTAT
3739841 A
1 A
3739842 CTCCAAATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
8 6 0.10
9 10 0.16
10 9 0.14
11 32 0.51
12 6 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3740414 original size:21 final size:21
Alignment explanation
Indices: 3740390--3740433 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3740380 GGCCACAATG
3740390 TCCTAAAATCAACTCCATCAA
1 TCCTAAAATCAACTCCATCAA
3740411 TCCTAAAATCAACTCCATCAA
1 TCCTAAAATCAACTCCATCAA
3740432 TC
1 TC
3740434 ATATGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (21 bp):
TCCTAAAATCAACTCCATCAA
Found at i:3740572 original size:17 final size:17
Alignment explanation
Indices: 3740550--3740585 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3740540 TAAAAATATT
*
3740550 TTAAAAATTAATTTAAA
1 TTAAAAAATAATTTAAA
3740567 TTAAAAAATAATTTAAA
1 TTAAAAAATAATTTAAA
3740584 TT
1 TT
3740586 TAGTCTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAAATAATTTAAA
Found at i:3740927 original size:2 final size:2
Alignment explanation
Indices: 3740920--3740954 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3740910 TGCATGAGCT
3740920 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
3740955 TAATTTTGTT
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:3741224 original size:30 final size:29
Alignment explanation
Indices: 3741187--3741335 Score: 89
Period size: 30 Copynumber: 5.1 Consensus size: 29
3741177 AATTTTTTTG
3741187 TTATAATTATATTTAAATTATTTTATATT
1 TTATAATTATATTTAAATTATTTTATATT
*
3741216 TATATAATTTGATATATT-AA-TAATTTATA--
1 T-TATAA-TT-ATAT-TTAAATTATTTTATATT
* * **
3741245 -TA-AAATAAATTTTGATATATTTT-TATT
1 TTATAATTATATTTAAAT-TATTTTATATT
* * *
3741272 TTATATATTATATTTATATTATTTTTTATA
1 TTATA-ATTATATTTAAATTATTTTATATT
*
3741302 TTAT-ATTATATTTTAATTATTTTTAATATT
1 TTATAATTATATTTAAATTA-TTTT-ATATT
3741332 TTAT
1 TTAT
3741336 TTATTTTATA
Statistics
Matches: 91, Mismatches: 14, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
23 2 0.02
24 4 0.04
25 3 0.03
26 7 0.08
27 2 0.02
28 15 0.16
29 12 0.13
30 28 0.31
31 10 0.11
32 6 0.07
33 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
TTATAATTATATTTAAATTATTTTATATT
Found at i:3741293 original size:18 final size:18
Alignment explanation
Indices: 3741266--3741347 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
3741256 TTGATATATT
*
3741266 TTTATTTTATATATTATA
1 TTTATATTATATATTATA
* *
3741284 TTTATATTATTTTTTATA
1 TTTATATTATATATTATA
3741302 -TTATATTATAT-TT-TA
1 TTTATATTATATATTATA
* * *
3741317 ATTAT-TTTTAATATTTTA
1 TTTATATTAT-ATATTATA
*
3741335 TTTATTTTATATA
1 TTTATATTATATA
3741348 AATATATCGT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
15 5 0.10
16 8 0.15
17 12 0.23
18 24 0.46
19 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTATATATTATA
Found at i:3741301 original size:23 final size:22
Alignment explanation
Indices: 3741266--3741347 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
3741256 TTGATATATT
3741266 TTTATTTTATATATTATATTTA
1 TTTATTTTATATATTATATTTA
*
3741288 TATTATTTTTTATATTATATTATA
1 T-TTATTTTATATATTATATT-TA
* *
3741312 TTT-TAATTAT-TTTTAATATTTTA
1 TTTAT-TTTATATATT-ATA-TTTA
3741335 TTTATTTTATATA
1 TTTATTTTATATA
3741348 AATATATCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
22 5 0.11
23 35 0.74
24 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATTTTATATATTATATTTA
Found at i:3741325 original size:28 final size:29
Alignment explanation
Indices: 3741253--3741346 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 29
3741243 TATAAAATAA
* *
3741253 ATTTTGATA-TATTTTTATTTTATATATTAT
1 ATTTT-ATATTATTTTTAATAT-TATATTAT
*
3741283 A-TTTATATTATTTTTTATATTATATTAT
1 ATTTTATATTATTTTTAATATTATATTAT
*
3741311 ATTTTA-ATTATTTTTAATATTTTATT-T
1 ATTTTATATTATTTTTAATATTATATTAT
3741338 ATTTTATAT
1 ATTTTATAT
3741347 AAATATATCG
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 7 0.12
28 32 0.57
29 16 0.29
30 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (29 bp):
ATTTTATATTATTTTTAATATTATATTAT
Found at i:3743212 original size:19 final size:19
Alignment explanation
Indices: 3743176--3743215 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3743166 AGGATGGTGA
**
3743176 TTGCCCTAAAACTTCAAAT
1 TTGCCCTAAAACGACAAAT
*
3743195 TTGCCCTAAAGCGACAAAT
1 TTGCCCTAAAACGACAAAT
3743214 TT
1 TT
3743216 CTCAAAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (19 bp):
TTGCCCTAAAACGACAAAT
Found at i:3743436 original size:16 final size:16
Alignment explanation
Indices: 3743417--3743459 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3743407 AATTTATAAT
3743417 TAAATAATTATTATTA
1 TAAATAATTATTATTA
*
3743433 TAAATTAAATA-TATTA
1 TAAA-TAATTATTATTA
*
3743449 TAAATGATTAT
1 TAAATAATTAT
3743460 AGTAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAAATAATTATTATTA
Found at i:3743440 original size:21 final size:21
Alignment explanation
Indices: 3743410--3743449 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3743400 TTAAATAAAT
3743410 TTATAATTAAATA-ATTATTA
1 TTATAATTAAATATATTATTA
3743430 TTATAAATTAAATATATTAT
1 TTAT-AATTAAATATATTAT
3743450 AAATGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAATTAAATATATTATTA
Found at i:3745221 original size:20 final size:19
Alignment explanation
Indices: 3745187--3745227 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3745177 TAAAAAAATA
3745187 AATATATAAAATATTAATT
1 AATATATAAAATATTAATT
*
3745206 AATATTTAATAATATTAATT
1 AATATATAA-AATATTAATT
3745226 AA
1 AA
3745228 AATAATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATAAAATATTAATT
Found at i:3746610 original size:20 final size:20
Alignment explanation
Indices: 3746571--3746610 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3746561 ATTGATGTAG
*
3746571 AATAATTATAAATTATTTAA
1 AATAATTATAAATTAGTTAA
* *
3746591 AATAATTTTAATTTAGTTAA
1 AATAATTATAAATTAGTTAA
3746611 TTTACATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATAATTATAAATTAGTTAA
Found at i:3749174 original size:41 final size:41
Alignment explanation
Indices: 3749117--3749235 Score: 220
Period size: 41 Copynumber: 2.9 Consensus size: 41
3749107 ACACTTAGAC
3749117 GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCTGGAT
1 GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCTGGAT
3749158 GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCTGGAT
1 GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCTGGAT
* *
3749199 GTGCCTTTCTTGAGTTAATTCAATCTTATTAATTTCT
1 GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCT
3749236 ACTCAAGATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (41 bp):
GTGCCTTTCTTGAGTTACTTCAATCTTACTAATTTCTGGAT
Found at i:3749685 original size:8 final size:8
Alignment explanation
Indices: 3749669--3749827 Score: 188
Period size: 8 Copynumber: 20.2 Consensus size: 8
3749659 TTCTTCATTT
3749669 TATA-ATA
1 TATACATA
*
3749676 TATAAATA
1 TATACATA
*
3749684 TATATATA
1 TATACATA
3749692 TATACATA
1 TATACATA
3749700 TAT--ATA
1 TATACATA
*
3749706 CATACATA
1 TATACATA
3749714 TATACATA
1 TATACATA
3749722 TATAC--A
1 TATACATA
3749728 TAT--ATA
1 TATACATA
3749734 TATACATA
1 TATACATA
3749742 TATACATATA
1 TATAC--ATA
3749752 TATACATA
1 TATACATA
3749760 TATACATA
1 TATACATA
*
3749768 TATATATA
1 TATACATA
3749776 TATACATA
1 TATACATA
3749784 TATACATA
1 TATACATA
3749792 TATACATA
1 TATACATA
3749800 TATACATACA
1 TATACAT--A
3749810 TATACATA
1 TATACATA
*
3749818 TATATATA
1 TATACATA
3749826 TA
1 TA
3749828 CTTTTATCCA
Statistics
Matches: 134, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
6 13 0.10
7 4 0.03
8 101 0.75
10 16 0.12
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (8 bp):
TATACATA
Found at i:3749714 original size:20 final size:20
Alignment explanation
Indices: 3749673--3749828 Score: 176
Period size: 20 Copynumber: 8.0 Consensus size: 20
3749663 TCATTTTATA
* *
3749673 ATATATA-A-ATATATATAT
1 ATATATACATATATACATAC
* *
3749691 ATATACATATATATACATAC
1 ATATATACATATATACATAC
*
3749711 ATATATACATATATACATAT
1 ATATATACATATATACATAC
3749731 ATATATACATATATACAT--
1 ATATATACATATATACATAC
*
3749749 ATATATACATATATACATAT
1 ATATATACATATATACATAC
* * *
3749769 ATATATATATACATATATAC
1 ATATATACATATATACATAC
3749789 ATATATACATATATACATAC
1 ATATATACATATATACATAC
* * *
3749809 ATATACATATATATATATAC
1 ATATATACATATATACATAC
3749829 TTTTATCCAT
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
18 24 0.20
19 1 0.01
20 93 0.79
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATACATATATACATAC
Found at i:3761802 original size:23 final size:23
Alignment explanation
Indices: 3761767--3761816 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3761757 CCCACATTGT
* *
3761767 CCCAACCTCCCCCTCCCCCTCCC
1 CCCAACCTCCCCCCCCCCCCCCC
*
3761790 CCCAACCCACCCCCCCCCCCCCCC
1 CCCAA-CCTCCCCCCCCCCCCCCC
3761814 CCC
1 CCC
3761817 CAAAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.10, C:0.84, G:0.00, T:0.06
Consensus pattern (23 bp):
CCCAACCTCCCCCCCCCCCCCCC
Found at i:3763801 original size:2 final size:2
Alignment explanation
Indices: 3763794--3763828 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3763784 TGTATGGAAG
3763794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3763829 GTCCCCCATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3765050 original size:2 final size:2
Alignment explanation
Indices: 3765043--3765070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3765033 TTTGTTGGAT
3765043 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3765071 GCTTTCCAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3767126 original size:19 final size:20
Alignment explanation
Indices: 3767104--3767143 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3767094 ATGTTATGAT
*
3767104 ATATATTATAT-TTTAAAAA
1 ATATATGATATATTTAAAAA
3767123 ATATATGATATATTTAAAAA
1 ATATATGATATATTTAAAAA
3767143 A
1 A
3767144 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATATATGATATATTTAAAAA
Found at i:3767126 original size:21 final size:21
Alignment explanation
Indices: 3767102--3767146 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3767092 GAATGTTATG
*
3767102 ATATAT-ATTATATTTTAAAAA
1 ATATATGA-TATATTTAAAAAA
3767123 ATATATGATATATTTAAAAAA
1 ATATATGATATATTTAAAAAA
3767144 ATA
1 ATA
3767147 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATATGATATATTTAAAAAA
Found at i:3771222 original size:28 final size:27
Alignment explanation
Indices: 3771191--3771251 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
3771181 TTTACTACAG
3771191 TAAAAAAATATTTTAATTTTTATATTAT
1 TAAAAAAATATTTTAA-TTTTATATTAT
* *
3771219 TAAATTAAATATTTTAATTTTATATTTT
1 TAAA-AAAATATTTTAATTTTATATTAT
3771247 TAAAA
1 TAAAA
3771252 TTATAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAAAAAAATATTTTAATTTTATATTAT
Found at i:3771228 original size:29 final size:29
Alignment explanation
Indices: 3771196--3771259 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3771186 TACAGTAAAA
3771196 AAATATTTTAATTTTTATATTATT-AAATT
1 AAATATTTTAA-TTTTATATTATTAAAATT
*
3771225 AAATATTTTAATTTTATATTTTTAAAATT
1 AAATATTTTAATTTTATATTATTAAAATT
3771254 ATAATA
1 A-AATA
3771260 AATAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 11 0.34
29 17 0.53
30 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATATTTTAATTTTATATTATTAAAATT
Found at i:3771396 original size:22 final size:21
Alignment explanation
Indices: 3771355--3771397 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3771345 GTTACAAGTT
* *
3771355 AAATTTAAATTTTTTTACATA
1 AAATTTAAATTTTATAACATA
3771376 AAATTTAAAATTTTATAACATA
1 AAATTT-AAATTTTATAACATA
3771398 TAATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAAATTTTATAACATA
Found at i:3771473 original size:18 final size:21
Alignment explanation
Indices: 3771398--3771459 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
3771388 TTATAACATA
* *
3771398 TAATAT-ATTAAT-ATTATAT
1 TAATATAATTAATAATTTTTT
3771417 TAATAT--TTAAATAATTTTTT
1 TAATATAATT-AATAATTTTTT
*
3771437 TAATATAATTAATTATTTTTT
1 TAATATAATTAATAATTTTTT
3771458 TA
1 TA
3771460 TTTATTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.06
19 9 0.25
20 11 0.31
21 12 0.33
22 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATATAATTAATAATTTTTT
Found at i:3773750 original size:19 final size:19
Alignment explanation
Indices: 3773722--3773758 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3773712 TTTTATAAAT
*
3773722 TTAAACATTAAATTTAATG
1 TTAAACATTAAATATAATG
*
3773741 TTAAATATTAAATATAAT
1 TTAAACATTAAATATAAT
3773759 TAATAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTAAACATTAAATATAATG
Found at i:3778349 original size:25 final size:26
Alignment explanation
Indices: 3778332--3778389 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
3778322 ATATTTAATT
3778332 AATTT-TTTTTAAAAAATAATATATA
1 AATTTATTTTTAAAAAATAATATATA
3778357 AATTTATTTTTAATAAAATAATATTATTA
1 AATTTATTTTTAA-AAAATAATA-TA-TA
3778386 AATT
1 AATT
3778390 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
26 7 0.24
27 9 0.31
28 2 0.07
29 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTTATTTTTAAAAAATAATATATA
Found at i:3778373 original size:29 final size:28
Alignment explanation
Indices: 3778317--3778393 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
3778307 TCGATAAATT
* **
3778317 AAATAATATTTAATTAATTTTTTTTAAA
1 AAATAATATTAAATTAATTTTTAATAAA
*
3778345 AAATAATATATAAATTTATTTTTAATAAA
1 AAATAATAT-TAAATTAATTTTTAATAAA
*
3778374 ATAATATTATTAAATTAATT
1 A-AATAATATTAAATTAATT
3778394 AAAAATAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.22
29 25 0.61
30 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATAATATTAAATTAATTTTTAATAAA
Found at i:3778968 original size:20 final size:20
Alignment explanation
Indices: 3778941--3779001 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
3778931 AAAAAATAAA
3778941 AAATATTTTAATATTAATTT
1 AAATATTTTAATATTAATTT
** *
3778961 TTATATTTTTATAATTAAATTT
1 AAATATTTTAAT-ATT-AATTT
3778983 AAATATTTTTAATTATTAA
1 AAATA-TTTTAA-TATTAA
3779002 ATAATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 10 0.32
23 8 0.26
24 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATATTTTAATATTAATTT
Found at i:3779161 original size:8 final size:8
Alignment explanation
Indices: 3779144--3779296 Score: 79
Period size: 8 Copynumber: 19.0 Consensus size: 8
3779134 TAATTATTAG
3779144 ATTT-TAT
1 ATTTATAT
3779151 ATTTATAT
1 ATTTATAT
*
3779159 ATTTTTAT
1 ATTTATAT
*
3779167 ATGTTGT-T
1 AT-TTATAT
3779175 A-TTATAT
1 ATTTATAT
* *
3779182 -TTAAAAT
1 ATTTATAT
3779189 A-TTATAT
1 ATTTATAT
3779196 ATTTATAT
1 ATTTATAT
3779204 ATTTAATAT
1 ATTT-ATAT
*
3779213 ATTAATA-
1 ATTTATAT
3779220 ATTTATAT
1 ATTTATAT
* *
3779228 -TATATAA
1 ATTTATAT
3779235 ATTTTGATAT
1 A-TTT-ATAT
*
3779245 ATGTATAT
1 ATTTATAT
3779253 ATTTATATT
1 ATTTATA-T
3779262 ATACTTATATT
1 AT--TTATA-T
*
3779273 ATTT-TTT
1 ATTTATAT
3779280 ATGTTATAT
1 AT-TTATAT
*
3779289 TTTTATAT
1 ATTTATAT
3779297 CATATTTTAA
Statistics
Matches: 112, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
6 3 0.03
7 28 0.25
8 46 0.41
9 22 0.20
10 4 0.04
11 9 0.08
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:3779293 original size:13 final size:13
Alignment explanation
Indices: 3779242--3779304 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
3779232 TAAATTTTGA
*
3779242 TATATGTATATATT
1 TATAT-TATATTTT
*
3779256 TATATTATA--CT
1 TATATTATATTTT
3779267 TATATTAT-TTTT
1 TATATTATATTTT
*
3779279 TATGTTATATTTT
1 TATATTATATTTT
*
3779292 TATATCATATTTT
1 TATATTATATTTT
3779305 AATTTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 9 0.22
12 8 0.20
13 19 0.46
14 5 0.12
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (13 bp):
TATATTATATTTT
Found at i:3779311 original size:20 final size:20
Alignment explanation
Indices: 3779288--3779326 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3779278 TTATGTTATA
3779288 TTTTTATATCATATTTTAAT
1 TTTTTATATCATATTTTAAT
*
3779308 TTTTTATATTATATTTTAA
1 TTTTTATATCATATTTTAA
3779327 AAATATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATATCATATTTTAAT
Found at i:3781667 original size:21 final size:20
Alignment explanation
Indices: 3781630--3781669 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3781620 CTTTTCTTTT
* *
3781630 CTTTTTTTTTTCATTTTCTC
1 CTTTTTATTTTAATTTTCTC
3781650 CTTTTTATTTTAAGTTTTCT
1 CTTTTTATTTTAA-TTTTCT
3781670 TTAGGTCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (20 bp):
CTTTTTATTTTAATTTTCTC
Found at i:3782650 original size:14 final size:13
Alignment explanation
Indices: 3782602--3782670 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 13
3782592 TATAGCTTGA
3782602 AAAATT-AATTAT
1 AAAATTAAATTAT
* *
3782614 AGATATTAAATTTT
1 A-AAATTAAATTAT
*
3782628 AAATTTTAAAATTAT
1 AAA-ATT-AAATTAT
*
3782643 AAAATTAATTTAT
1 AAAATTAAATTAT
*
3782656 AAAAGTGAAATTAT
1 AAAA-TTAAATTAT
3782670 A
1 A
3782671 TTAATTAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.02
13 15 0.35
14 18 0.42
15 9 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (13 bp):
AAAATTAAATTAT
Found at i:3783990 original size:2 final size:2
Alignment explanation
Indices: 3783983--3784012 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3783973 CCAACCTTGT
3783983 TA TA TA TA TA TA TA -A 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
3784013 TATTTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3784002 original size:13 final size:13
Alignment explanation
Indices: 3783984--3784009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3783974 CAACCTTGTT
3783984 ATATATATATATA
1 ATATATATATATA
3783997 ATATATATATATA
1 ATATATATATATA
3784010 TATTATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:3784003 original size:15 final size:15
Alignment explanation
Indices: 3783983--3784011 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3783973 CCAACCTTGT
3783983 TATATATATATATAA
1 TATATATATATATAA
3783998 TATATATATATATA
1 TATATATATATATA
3784012 TTATTTTCGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:3784781 original size:22 final size:22
Alignment explanation
Indices: 3784756--3784818 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
3784746 GTAATTAAAT
*
3784756 TTAAAAAATTTACATTAACAAA
1 TTAAAAAATTTACATTAAAAAA
* *
3784778 TTAAAAAATAATA-TTTAAAAAA
1 TTAAAAAAT-TTACATTAAAAAA
3784800 TTAAAAAAATTTACCATTA
1 TT-AAAAAATTTA-CATTA
3784819 TTCAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 20 0.62
23 9 0.28
24 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAAAAATTTACATTAAAAAA
Found at i:3784912 original size:15 final size:16
Alignment explanation
Indices: 3784864--3784913 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
3784854 TTTATTTTAA
3784864 ATAAAAAATTATTCATT
1 ATAAAAAATTATTCA-T
*
3784881 ATAAAACTAACTATTCAT
1 ATAAAA--AATTATTCAT
3784899 -TAAAAAATTATTCAT
1 ATAAAAAATTATTCAT
3784914 CACTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 9 0.31
17 11 0.38
18 1 0.03
19 8 0.28
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAAATTATTCAT
Found at i:3787589 original size:17 final size:16
Alignment explanation
Indices: 3787567--3787602 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3787557 AATGGAATTT
*
3787567 TTTTATTATTATTATTA
1 TTTTATAATTATTA-TA
3787584 TTTTATAATTATTATA
1 TTTTATAATTATTATA
3787600 TTT
1 TTT
3787603 GTGTTAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATAATTATTATA
Found at i:3787638 original size:14 final size:14
Alignment explanation
Indices: 3787615--3787648 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3787605 GTTAGGTATT
* *
3787615 TATATAAATTTGTA
1 TATATTAATTTATA
3787629 TATATTAATTTATA
1 TATATTAATTTATA
3787643 TATATT
1 TATATT
3787649 TATAATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATATTAATTTATA
Found at i:3787733 original size:22 final size:24
Alignment explanation
Indices: 3787701--3787753 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3787691 TATTTGTGTA
* *
3787701 TTTATAATTTATT-T-ATATTATT
1 TTTATATTTTATTATAATAATATT
3787723 TTTATATTTTATTATAATAATATT
1 TTTATATTTTATTATAATAATATT
3787747 TTTATAT
1 TTTATAT
3787754 ATAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
24 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATATTTTATTATAATAATATT
Found at i:3787810 original size:20 final size:20
Alignment explanation
Indices: 3787784--3787833 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3787774 TTATTTGTAT
*
3787784 TATTTATATTTTTA-AATTA
1 TATTTATATTTATATAATTA
3787803 TGATTTAT-TTTATATAATTA
1 T-ATTTATATTTATATAATTA
3787823 TA-TTATATTTA
1 TATTTATATTTA
3787834 AAATTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTATATTTATATAATTA
Found at i:3787840 original size:17 final size:18
Alignment explanation
Indices: 3787782--3787840 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
3787772 ATTTATTTGT
*
3787782 ATTAT-TTATATTTTTAA
1 ATTATATTATATTTTAAA
3787799 ATTATGATT-TATTTTATATA
1 ATTAT-ATTATATTTTA-A-A
3787819 ATTATATTATA-TTTAAA
1 ATTATATTATATTTTAAA
3787836 ATTAT
1 ATTAT
3787841 TTGATTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 11 0.31
18 7 0.19
19 10 0.28
20 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTATATTATATTTTAAA
Found at i:3787982 original size:15 final size:16
Alignment explanation
Indices: 3787946--3787990 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
3787936 TATAGATATT
*
3787946 TTATTTTATTTTAAAAA
1 TTATTTT-TTATAAAAA
3787963 TTATTTTTTATAAAAA
1 TTATTTTTTATAAAAA
*
3787979 -TATTTTATATAA
1 TTATTTTTTATAA
3787991 TTTATGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 11 0.42
16 8 0.31
17 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTTTTATAAAAA
Found at i:3788465 original size:15 final size:14
Alignment explanation
Indices: 3788438--3788488 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
3788428 ACCTTTTTAA
*
3788438 ATTAAATTTATATT
1 ATTAAAATTATATT
3788452 ATTAACAATTATATT
1 ATTAA-AATTATATT
*
3788467 A-T-AATTTATATT
1 ATTAAAATTATATT
3788479 ATTAATAATT
1 ATTAA-AATT
3788489 TTTTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 7 0.23
15 12 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAAAATTATATT
Found at i:3788475 original size:27 final size:26
Alignment explanation
Indices: 3788438--3788488 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
3788428 ACCTTTTTAA
3788438 ATTAAATTTATATTATTAACAATTAT
1 ATTAAATTTATATTATTAACAATTAT
*
3788464 ATTATAATTTATATTATTAATAATT
1 ATTA-AATTTATATTATTAACAATT
3788489 TTTTAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAAATTTATATTATTAACAATTAT
Found at i:3789892 original size:17 final size:18
Alignment explanation
Indices: 3789870--3789903 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3789860 TAGAGATATA
3789870 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
3789887 AATTATATTATTTATTT
1 AATTATATTATTTATTT
3789904 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3789952 original size:12 final size:13
Alignment explanation
Indices: 3789872--3789952 Score: 57
Period size: 12 Copynumber: 6.5 Consensus size: 13
3789862 GAGATATAAA
3789872 TTATAT-TTTTAT
1 TTATATATTTTAT
*
3789884 TT-TA-ATTATA-
1 TTATATATTTTAT
*
3789894 TTATTTA-TTTAT
1 TTATATATTTTAT
*
3789906 TTATTAATATTTAAT
1 TTA-T-ATATTTTAT
*
3789921 TTAAAATATTTTAT
1 TT-ATATATTTTAT
3789935 TTATATATTTTA-
1 TTATATATTTTAT
3789947 TTATAT
1 TTATAT
3789953 CAAAAAATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.04
11 10 0.19
12 12 0.23
13 10 0.19
14 12 0.23
15 6 0.11
16 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATATATTTTAT
Found at i:3790624 original size:15 final size:16
Alignment explanation
Indices: 3790605--3790654 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
3790595 AAAATTAAAA
3790605 AAATTATAAATATTA-
1 AAATTATAAATATTAT
3790620 AAATT-TAAA-ATTATT
1 AAATTATAAATATTA-T
3790635 AAA-TATAAAT-TTAT
1 AAATTATAAATATTAT
3790649 AAATTA
1 AAATTA
3790655 ACTAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTATAAATATTAT
Found at i:3790632 original size:22 final size:21
Alignment explanation
Indices: 3790604--3790685 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
3790594 AAAAATTAAA
3790604 AAAATTATAAATATTAAAATTT
1 AAAATTATAAA-ATTAAAATTT
*
3790626 AAAATTATTAAA-TATAAATTT
1 AAAATTATAAAATTA-AAATTT
*
3790647 ATAAATTA-ACTAAATTAAATTTT
1 A-AAATTATA--AAATTAAAATTT
3790670 AAAATT-TAAAATTAAA
1 AAAATTATAAAATTAAA
3790686 TTTTTTTAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
20 10 0.20
21 8 0.16
22 22 0.43
23 9 0.18
24 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTATAAAATTAAAATTT
Found at i:3794696 original size:64 final size:64
Alignment explanation
Indices: 3794621--3794749 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
3794611 AGTAGTTGCC
3794621 AAAAAATTAAATAGATAAAACATTCAAGCTTCATGCAGCACAAATATTAGAACACTAATGCATG
1 AAAAAATTAAATAGATAAAACATTCAAGCTTCATGCAGCACAAATATTAGAACACTAATGCATG
3794685 AAAAAATTAAATAGATAAAACATTCAAGCTTCATGCAGCACAAATATTAGAACACTAATGCATG
1 AAAAAATTAAATAGATAAAACATTCAAGCTTCATGCAGCACAAATATTAGAACACTAATGCATG
3794749 A
1 A
3794750 GTGCATGACC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (64 bp):
AAAAAATTAAATAGATAAAACATTCAAGCTTCATGCAGCACAAATATTAGAACACTAATGCATG
Found at i:3796974 original size:2 final size:2
Alignment explanation
Indices: 3796967--3796992 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3796957 TCTTTTAAAC
3796967 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
3796993 AAGTAAGATA
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):
TA
Found at i:3798227 original size:42 final size:42
Alignment explanation
Indices: 3798167--3798260 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
3798157 ATGTGAACAA
*
3798167 GGAAATTTCCATGGGCAAGGCAATATTGAAAATCAAAGAGGG
1 GGAAATTTCCATGAGCAAGGCAATATTGAAAATCAAAGAGGG
*
3798209 GGAAATTTCCATGAGCAAGGCAATATTGAAAGTCAAAGAGGG
1 GGAAATTTCCATGAGCAAGGCAATATTGAAAATCAAAGAGGG
*
3798251 GGGAATTTCC
1 GGAAATTTCC
3798261 TTGATATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (42 bp):
GGAAATTTCCATGAGCAAGGCAATATTGAAAATCAAAGAGGG
Found at i:3798525 original size:15 final size:15
Alignment explanation
Indices: 3798505--3798569 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 15
3798495 AGACGTAATA
3798505 TATATATATTAAAAT
1 TATATATATTAAAAT
3798520 TATATA-A-TATAAAT
1 TATATATATTA-AAAT
3798534 TATTAATATATT-AAAT
1 TA-T-ATATATTAAAAT
3798550 TATA-ATA--AAAAT
1 TATATATATTAAAAT
3798562 TATA-ATAT
1 TATATATAT
3798570 AATATAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
12 11 0.26
13 5 0.12
14 8 0.19
15 8 0.19
16 9 0.21
17 1 0.02
18 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATATTAAAAT
Found at i:3798543 original size:31 final size:27
Alignment explanation
Indices: 3798503--3798570 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 27
3798493 TGAGACGTAA
*
3798503 TATATATATATTAAAATTATATAATATAAAT
1 TATA-ATATATT-AAA-T-TATAATAAAAAT
3798534 TATTAATATATTAAATTATAATAAAAAT
1 TA-TAATATATTAAATTATAATAAAAAT
3798562 TATAATATA
1 TATAATATA
3798571 ATATAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 7 0.20
28 13 0.37
29 1 0.03
30 3 0.09
31 9 0.26
32 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATATATTAAATTATAATAAAAAT
Found at i:3798581 original size:28 final size:27
Alignment explanation
Indices: 3798521--3798581 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
3798511 TATTAAAATT
*
3798521 ATATAATATAAATTATTAATATATTAA
1 ATATAATAAAAATTATTAATATATTAA
3798548 ATTATAATAAAAATTA-TAATATAATATAA
1 A-TATAATAAAAATTATTAATAT-AT-TAA
3798577 ATATA
1 ATATA
3798582 CGAATAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 19 0.63
29 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAATAAAAATTATTAATATATTAA
Found at i:3803390 original size:19 final size:19
Alignment explanation
Indices: 3803353--3803390 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3803343 TACATTATTT
* *
3803353 TTTAAATTTAATAAAAAAA
1 TTTAAATGTAAAAAAAAAA
3803372 TTTAAATGTAAAAAAAAAA
1 TTTAAATGTAAAAAAAAAA
3803391 AATAATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TTTAAATGTAAAAAAAAAA
Found at i:3815392 original size:29 final size:27
Alignment explanation
Indices: 3815338--3815397 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 27
3815328 TTTTAAAGGT
3815338 AAAAAATATTTATTTTTAAAATTTTATA
1 AAAAAATATTTATTTTTAAAATTTTA-A
*
3815366 AAAAATATATTTATTTTCTAACA-TTTAA
1 AAAAA-ATATTTATTTT-TAAAATTTTAA
3815394 AAAA
1 AAAA
3815398 TACTTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.34
29 15 0.52
30 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAAAATATTTATTTTTAAAATTTTAA
Found at i:3819899 original size:21 final size:22
Alignment explanation
Indices: 3819873--3819923 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3819863 TGCTAGCTCA
3819873 TTTTCTTCCACAC-TTGCGCCC
1 TTTTCTTCCACACTTTGCGCCC
* *
3819894 TTTTCTTTCACCCTTTTGCGCCC
1 TTTTCTTCCACAC-TTTGCGCCC
3819917 TTTTCTT
1 TTTTCTT
3819924 TTTCCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
23 15 0.58
ACGTcount: A:0.06, C:0.37, G:0.08, T:0.49
Consensus pattern (22 bp):
TTTTCTTCCACACTTTGCGCCC
Found at i:3819935 original size:23 final size:23
Alignment explanation
Indices: 3819886--3819935 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
3819876 TCTTCCACAC
***
3819886 TTGCGCCCTTTTCTTTCACCCTT
1 TTGCGCCCTTTTCTTTCACCAAA
**
3819909 TTGCGCCCTTTTCTTTTTCCAAA
1 TTGCGCCCTTTTCTTTCACCAAA
3819932 TTGC
1 TTGC
3819936 TCTAATTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.08, C:0.34, G:0.10, T:0.48
Consensus pattern (23 bp):
TTGCGCCCTTTTCTTTCACCAAA
Found at i:3823270 original size:20 final size:22
Alignment explanation
Indices: 3823229--3823270 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
3823219 TGTTTTTTTC
*
3823229 AATAAAAAGTTCGAAGCGAAAA
1 AATAAAAAGTTCGAACCGAAAA
3823251 AATAAAAAG-T-GAACCGAAAA
1 AATAAAAAGTTCGAACCGAAAA
3823271 CAAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.62, C:0.10, G:0.17, T:0.12
Consensus pattern (22 bp):
AATAAAAAGTTCGAACCGAAAA
Found at i:3828381 original size:8 final size:8
Alignment explanation
Indices: 3828370--3828433 Score: 100
Period size: 8 Copynumber: 8.5 Consensus size: 8
3828360 CCTTATATAC
3828370 ATATACAT
1 ATATACAT
3828378 ATATACAT
1 ATATACAT
3828386 ATATAC--
1 ATATACAT
3828392 ATATACAT
1 ATATACAT
3828400 ATATACAT
1 ATATACAT
3828408 ATATAC--
1 ATATACAT
3828414 ATATACAT
1 ATATACAT
3828422 ATATACAT
1 ATATACAT
3828430 ATAT
1 ATAT
3828434 CTTTGCAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.23
8 40 0.77
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:3828382 original size:14 final size:14
Alignment explanation
Indices: 3828363--3828432 Score: 104
Period size: 14 Copynumber: 4.9 Consensus size: 14
3828353 GTGGTCTCCT
3828363 TATATACATATACA
1 TATATACATATACA
3828377 TATATACATATATACA
1 TATATAC--ATATACA
* *
3828393 TATACATATATACA
1 TATATACATATACA
3828407 TATATACATATACA
1 TATATACATATACA
3828421 TATATACATATA
1 TATATACATATA
3828433 TCTTTGCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
14 38 0.76
16 12 0.24
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATACATATACA
Found at i:3828390 original size:22 final size:22
Alignment explanation
Indices: 3828363--3828433 Score: 142
Period size: 22 Copynumber: 3.2 Consensus size: 22
3828353 GTGGTCTCCT
3828363 TATATACATATACATATATACA
1 TATATACATATACATATATACA
3828385 TATATACATATACATATATACA
1 TATATACATATACATATATACA
3828407 TATATACATATACATATATACA
1 TATATACATATACATATATACA
3828429 TATAT
1 TATAT
3828434 CTTTGCAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATACATATACATATATACA
Found at i:3831079 original size:16 final size:16
Alignment explanation
Indices: 3831058--3831088 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3831048 TTGAACTCAA
3831058 AATGATTAAAATTTAG
1 AATGATTAAAATTTAG
*
3831074 AATGATTCAAATTTA
1 AATGATTAAAATTTA
3831089 ATTAACTCGA
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:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (16 bp):
AATGATTAAAATTTAG
Found at i:3833642 original size:2 final size:2
Alignment explanation
Indices: 3833635--3833672 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3833625 CTACTGCACA
*
3833635 AT AT AT AT AT AT AT AT AT AT AT AT GT 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
3833673 GACGCCGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3836985 original size:2 final size:2
Alignment explanation
Indices: 3836978--3837008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3836968 AGCCCAGAAA
3836978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3837009 AGTCAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3837038 original size:12 final size:12
Alignment explanation
Indices: 3837021--3837045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3837011 TCAATTTATT
3837021 TTAAGCAACCTG
1 TTAAGCAACCTG
3837033 TTAAGCAACCTG
1 TTAAGCAACCTG
3837045 T
1 T
3837046 AAAATAGTGT
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:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TTAAGCAACCTG
Found at i:3839848 original size:33 final size:33
Alignment explanation
Indices: 3839806--3839870 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3839796 ATCCTAACAA
*
3839806 TCCTACCTACAACCATCAAATGCCAGAAAGAAT
1 TCCTACCTACAACCATCAAAGGCCAGAAAGAAT
*
3839839 TCCTACCTACAATCATCAAAGGCCAGAAAGAA
1 TCCTACCTACAACCATCAAAGGCCAGAAAGAA
3839871 AATCAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (33 bp):
TCCTACCTACAACCATCAAAGGCCAGAAAGAAT
Found at i:3845885 original size:39 final size:39
Alignment explanation
Indices: 3845816--3845916 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 39
3845806 GATAAAGAGT
* * ** *
3845816 AATGTATAAATTATTTATTGGAATATAAAAAATATGACC
1 AATGCATAAATTTTTTATTAAAATATAAAAAATAAGACC
**
3845855 AATGCATAAATTTTTTATTAAAAT-TCAAAAAATAAGATT
1 AATGCATAAATTTTTTATTAAAATAT-AAAAAATAAGACC
* *
3845894 AATGCATAGATTTTATTTTTAAA
1 AATGCATAAATTTT-TTATTAAA
3845917 TAAATATGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.02
39 43 0.84
40 7 0.14
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (39 bp):
AATGCATAAATTTTTTATTAAAATATAAAAAATAAGACC
Found at i:3846206 original size:22 final size:20
Alignment explanation
Indices: 3846168--3846207 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3846158 TATGATGCAT
*
3846168 AGATTTTTTTTATTGAAATC
1 AGATTTTTTTGATTGAAATC
3846188 AGATTTCTTTTGATATGAAA
1 AGATTT-TTTTGAT-TGAAA
3846208 GATATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (20 bp):
AGATTTTTTTGATTGAAATC
Found at i:3847827 original size:2 final size:2
Alignment explanation
Indices: 3847820--3847848 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3847810 TATTTGGCTC
3847820 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
3847849 ACATGAATAA
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:3847935 original size:45 final size:44
Alignment explanation
Indices: 3847882--3847969 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
3847872 AAAATAAGTT
*
3847882 TTAATTA-TTTTATTAAAATATT-TAA-AATTTTTATTTATTATTAA
1 TTAATTATTTTTA-TAAAAAATTATAATAA-TTTT-TTTATTATTAA
3847926 TTAAGTTATTTTTATAAAAAATTATAATAATTTTTTTATTATTA
1 TTAA-TTATTTTTATAAAAAATTATAATAATTTTTTTATTATTA
3847970 TGATTTACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
44 4 0.10
45 21 0.54
46 12 0.31
47 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (44 bp):
TTAATTATTTTTATAAAAAATTATAATAATTTTTTTATTATTAA
Found at i:3853264 original size:2 final size:2
Alignment explanation
Indices: 3853257--3853285 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3853247 TCTGCTGTCA
3853257 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3853286 TGTAAGAGAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3853457 original size:2 final size:2
Alignment explanation
Indices: 3853452--3853484 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3853442 AGTGTGTGTG
3853452 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 T
3853485 TACTTTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3854422 original size:14 final size:15
Alignment explanation
Indices: 3854389--3854434 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
3854379 TTGATCGAAT
3854389 AAATTTATTTAAATC
1 AAATTTATTTAAATC
*
3854404 -GATTTATTT-AATC
1 AAATTTATTTAAATC
*
3854417 AAATTTTATTGAAATC
1 AAA-TTTATTTAAATC
3854433 AA
1 AA
3854435 TTAACTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 6 0.24
16 6 0.24
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (15 bp):
AAATTTATTTAAATC
Found at i:3860821 original size:18 final size:19
Alignment explanation
Indices: 3860800--3860847 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
3860790 TTTTAAAATA
*
3860800 AAATAATATTTTATT-TTG
1 AAATAATATTATATTGTTG
* *
3860818 AAATAAAATTATATTGTTT
1 AAATAATATTATATTGTTG
*
3860837 AAGTAATATTA
1 AAATAATATTA
3860848 AATAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (19 bp):
AAATAATATTATATTGTTG
Found at i:3861609 original size:25 final size:24
Alignment explanation
Indices: 3861555--3861600 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3861545 ATATTTTCAT
3861555 TAAATTATATAATCAACACATAACA
1 TAAATTATATAA-CAACACATAACA
*
3861580 TAAATTATATAA-AAGACATAA
1 TAAATTATATAACAACACATAA
3861601 TATAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (24 bp):
TAAATTATATAACAACACATAACA
Found at i:3863472 original size:40 final size:40
Alignment explanation
Indices: 3863402--3863481 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
3863392 TGTTAGTGTT
*
3863402 TAAATAATAAAAAATTAATTAAATTATAAATTATATAAATA
1 TAAATAATAAAAAATTAATTAAATTATAAATAATA-AAATA
* **
3863443 TAAAT-ATAAAATATTTTTTAATATT-TAAATAATAAAATA
1 TAAATAATAAAAAATTAATTAA-ATTATAAATAATAAAATA
3863482 ATTTGATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.15
40 21 0.62
41 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (40 bp):
TAAATAATAAAAAATTAATTAAATTATAAATAATAAAATA
Found at i:3863664 original size:24 final size:25
Alignment explanation
Indices: 3863623--3863670 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3863613 TTTCATTTTG
3863623 TATTTTAATTGATTTTTAATTTTTCA
1 TATTTTAATTGA-TTTTAATTTTTCA
3863649 TATTTTAATTGA-TTTAATTTTT
1 TATTTTAATTGATTTTAATTTTT
3863671 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
TATTTTAATTGATTTTAATTTTTCA
Found at i:3863670 original size:25 final size:25
Alignment explanation
Indices: 3863623--3863683 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
3863613 TTTCATTTTG
*
3863623 TATTTTAATTGATTTTTAATTTTTCA
1 TATTTTAATTGA-TTTTAATTTTTAA
3863649 TATTTTAATTGA-TTTAATTTTTTAA
1 TATTTTAATTGATTTTAA-TTTTTAA
*
3863674 TTTTTTAATT
1 TATTTTAATT
3863684 TTGAATGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 5 0.16
25 15 0.47
26 12 0.38
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (25 bp):
TATTTTAATTGATTTTAATTTTTAA
Found at i:3863678 original size:9 final size:8
Alignment explanation
Indices: 3863635--3863685 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
3863625 TTTTAATTGA
3863635 TTTTTAA-
1 TTTTTAAT
*
3863642 TTTTTCAT
1 TTTTTAAT
*
3863650 ATTTTAAT
1 TTTTTAAT
*
3863658 TGATTTAAT
1 T-TTTTAAT
3863667 TTTTTAAT
1 TTTTTAAT
3863675 TTTTTAAT
1 TTTTTAAT
3863683 TTT
1 TTT
3863686 GAATGAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
7 6 0.17
8 23 0.64
9 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTTAAT
Found at i:3869825 original size:26 final size:29
Alignment explanation
Indices: 3869795--3869853 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 29
3869785 CAAGTGTATT
*
3869795 TGCAAA-GTACAAATTA-TATAT-ATT-CA
1 TGCAAATGT-CAAATGAGTATATGATTGCA
3869821 TGCAAATGTCAAATGAGTATATGATTGCA
1 TGCAAATGTCAAATGAGTATATGATTGCA
3869850 TGCA
1 TGCA
3869854 TTGCTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 3 0.11
29 6 0.21
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (29 bp):
TGCAAATGTCAAATGAGTATATGATTGCA
Found at i:3872955 original size:24 final size:23
Alignment explanation
Indices: 3872910--3872956 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3872900 TTTATATTTT
3872910 TATTATTTTTTTAATTAAATTAA
1 TATTATTTTTTTAATTAAATTAA
3872933 TATTATTTATTTTAA-TAATATTAA
1 TATTATTT-TTTTAATTAA-ATTAA
3872957 ATTTAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTTTTTTAATTAAATTAA
Found at i:3873734 original size:22 final size:22
Alignment explanation
Indices: 3873693--3873734 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3873683 TTAGGTGAAT
* *
3873693 AATAATAATTAATATCTTAAAA
1 AATAATAAATAAAATCTTAAAA
*
3873715 AATAATAAATAAAATTTTAA
1 AATAATAAATAAAATCTTAA
3873735 TTTTAAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAATAAATAAAATCTTAAAA
Found at i:3874539 original size:22 final size:22
Alignment explanation
Indices: 3874514--3874555 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3874504 ATTTAATGAA
3874514 ATTAAT-ATAAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
*
3874536 ATTAATAATAAAATTTTAAT
1 ATTAATAATAAAAATTTAAT
3874556 GATGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:3879146 original size:31 final size:31
Alignment explanation
Indices: 3879108--3879170 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3879098 GGTGGATATA
*
3879108 TTGCTTTCTTCTACAACGATTAAATTCTTTT
1 TTGCTTTCTTCTACAACGATTAAATCCTTTT
* *
3879139 TTGCTTTCTTCTGCGACGATTAAATCCTTTT
1 TTGCTTTCTTCTACAACGATTAAATCCTTTT
3879170 T
1 T
3879171 GCAAGTACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.51
Consensus pattern (31 bp):
TTGCTTTCTTCTACAACGATTAAATCCTTTT
Found at i:3879996 original size:30 final size:31
Alignment explanation
Indices: 3879932--3880005 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
3879922 GATTCAATCG
* *
3879932 ATTAAAT-TATT-TAATCATTTAAATAAGAT
1 ATTAAATATATTAAAATAATTTAAATAAGAT
* * *
3879961 TTTAAATATTTTAAAATAATTTTAATAA-AT
1 ATTAAATATATTAAAATAATTTAAATAAGAT
3879991 ATTAAATATATTAAA
1 ATTAAATATATTAAA
3880006 TTATTAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 6 0.17
30 18 0.50
31 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
ATTAAATATATTAAAATAATTTAAATAAGAT
Found at i:3880798 original size:16 final size:15
Alignment explanation
Indices: 3880762--3880810 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3880752 TTTATATTTA
3880762 ATATAATAATTAAATTT
1 ATATAATAATT-AA-TT
*
3880779 ATATAATTATATAATT
1 ATATAATAAT-TAATT
3880795 ATATAATAATTAATT
1 ATATAATAATTAATT
3880810 A
1 A
3880811 AAATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.21
16 11 0.38
17 11 0.38
18 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAATAATTAATT
Found at i:3880804 original size:33 final size:32
Alignment explanation
Indices: 3880746--3880807 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
3880736 AGTAAAAAAC
*
3880746 TATATATTTATATTTAATATAATAATTAAATT
1 TATATATTTATAATTAATATAATAATTAAATT
3880778 TATATAATTATATAATT-ATATAATAATTAA
1 TATAT-ATT-TATAATTAATATAATAATTAA
3880808 TTAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 5 0.19
33 16 0.59
34 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATATTTATAATTAATATAATAATTAAATT
Found at i:3881831 original size:2 final size:2
Alignment explanation
Indices: 3881824--3881849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3881814 TGGTAATCTA
3881824 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3881850 AATTTTCTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3884222 original size:28 final size:27
Alignment explanation
Indices: 3884186--3884238 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3884176 TGACGGTGAG
* *
3884186 AATCACGCGACACCCATAACCGCAAGA
1 AATCACGCGAAACCCACAACCGCAAGA
*
3884213 AATCTACGCGAAACCCACAACTGCAA
1 AATC-ACGCGAAACCCACAACCGCAA
3884239 AGCATCGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.42, C:0.36, G:0.13, T:0.09
Consensus pattern (27 bp):
AATCACGCGAAACCCACAACCGCAAGA
Found at i:3885042 original size:23 final size:18
Alignment explanation
Indices: 3884989--3885031 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
3884979 AACTAATTAC
3884989 TTTTAATGATAATGCCAT
1 TTTTAATGATAATGCCAT
3885007 TTTTAATGATAATGCCAT
1 TTTTAATGATAATGCCAT
3885025 TATTTAA
1 T-TTTAA
3885032 GTTGTGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTTAATGATAATGCCAT
Found at i:3888542 original size:21 final size:20
Alignment explanation
Indices: 3888516--3888575 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
3888506 TTGTTAAGTT
3888516 ATTATTTTTTACTTATTATCA
1 ATTATTTTTTA-TTATTATCA
* **
3888537 ATTATTACTTTATTATTATTT
1 ATTATT-TTTTATTATTATCA
*
3888558 ATTATTTATTAATTATTA
1 ATTATTT-TTTATTATTA
3888576 ATTAATCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATTTTTTATTATTATCA
Found at i:3889019 original size:23 final size:25
Alignment explanation
Indices: 3888993--3889042 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
3888983 TTTAACAAAT
3888993 TAATAATTAGTAAAATA-AT-ATTA
1 TAATAATTAGTAAAATATATAATTA
* *
3889016 TAATAATTATTATAATATATAATTA
1 TAATAATTAGTAAAATATATAATTA
3889041 TA
1 TA
3889043 TTATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 2 0.09
25 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATAATTAGTAAAATATATAATTA
Found at i:3889026 original size:12 final size:12
Alignment explanation
Indices: 3888993--3889042 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
3888983 TTTAACAAAT
*
3888993 TAATAATTAGTA
1 TAATAATTATTA
*
3889005 AAATAA-TATTA
1 TAATAATTATTA
3889016 TAATAATTATTA
1 TAATAATTATTA
*
3889028 TAATATATAATTA
1 TAATA-ATTATTA
3889041 TA
1 TA
3889043 TTATAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 9 0.28
12 15 0.47
13 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
TAATAATTATTA
Found at i:3889039 original size:16 final size:16
Alignment explanation
Indices: 3889018--3889065 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
3889008 TAATATTATA
3889018 ATAATTATTATAATAT
1 ATAATTATTATAATAT
*
3889034 ATAATTATATTATAAAAT
1 ATAA-T-TATTATAATAT
3889052 ATAAATT-TTATAAT
1 AT-AATTATTATAAT
3889066 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 10 0.37
17 2 0.07
18 13 0.48
19 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATTATTATAATAT
Found at i:3889046 original size:18 final size:19
Alignment explanation
Indices: 3889007--3889055 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3888997 AATTAGTAAA
3889007 ATAATATTATAATAATTATT
1 ATAATA-TATAATAATTATT
*
3889027 ATAATATATAATTA-TATT
1 ATAATATATAATAATTATT
*
3889045 ATAAAATATAA
1 ATAATATATAA
3889056 ATTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
19 7 0.26
20 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATATATAATAATTATT
Found at i:3889069 original size:20 final size:21
Alignment explanation
Indices: 3889003--3889070 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 21
3888993 TAATAATTAG
3889003 TAAAATA-AT-ATTATAATAAT
1 TAAAATATATAATTAT-ATAAT
*
3889023 TATTATAATATATAATTATATTA-
1 TA--A-AATATATAATTATATAAT
*
3889046 TAAAATATA-AATTTTATAAT
1 TAAAATATATAATTATATAAT
3889066 TAAAA
1 TAAAA
3889071 AAATTTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 8 0.21
20 13 0.33
21 1 0.03
22 1 0.03
23 6 0.15
24 5 0.13
25 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATATATAATTATATAAT
Found at i:3890096 original size:2 final size:2
Alignment explanation
Indices: 3890089--3890125 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3890079 TAACTGGTGC
3890089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3890126 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3891929 original size:19 final size:18
Alignment explanation
Indices: 3891899--3891935 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3891889 CAATTATAAC
3891899 ATAATAAAATATATAAAT
1 ATAATAAAATATATAAAT
3891917 ATAATATAAATATATAAAT
1 ATAATA-AAATATATAAAT
3891936 TATCAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATAAAATATATAAAT
Found at i:3891938 original size:43 final size:45
Alignment explanation
Indices: 3891863--3891959 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 45
3891853 ATCAATAATT
*
3891863 TATATAAATATAAAATAATTTAAACACAATTAT-AACATAATAA-AA
1 TATATAAATATAAAATAATATAAACACAATTATCAA-AT-ATAATAA
* * * *
3891908 TATATAAATATAATATAA-ATATATA-AATTATCAAATTTAATAA
1 TATATAAATATAAAATAATATAAACACAATTATCAAATATAATAA
3891951 TATATAAAT
1 TATATAAAT
3891960 TTATTCTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
42 3 0.07
43 19 0.42
44 6 0.13
45 17 0.38
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (45 bp):
TATATAAATATAAAATAATATAAACACAATTATCAAATATAATAA
Found at i:3892261 original size:3 final size:3
Alignment explanation
Indices: 3892253--3892288 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3892243 AAATAACCCT
3892253 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3892289 ATAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3895242 original size:3 final size:3
Alignment explanation
Indices: 3895234--3895259 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3895224 AAGAGAAAAC
3895234 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3895260 AAAAAAACAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3904136 original size:68 final size:68
Alignment explanation
Indices: 3904053--3904212 Score: 173
Period size: 68 Copynumber: 2.4 Consensus size: 68
3904043 ACAACAACAT
* * *
3904053 AACAA-CAAGTAACACCAAGTCACCTTCT-CTAATCAAAGA-CCTCAAGGGTTTGCTCTCCACAA
1 AACAAGCAAGTGACACCAAGTCACCTT-TGCTAATCAAAGATCC-CAAGGGTTTGATCGCCACAA
3904115 TGGTA
64 TGGTA
* * * * *
3904120 AACCAGCAAGTGACACCAAGTCACCTTTGCTAATTAATGATCCCATGGGTTTGATCGCCACATTG
1 AACAAGCAAGTGACACCAAGTCACCTTTGCTAATCAAAGATCCCAAGGGTTTGATCGCCACAATG
*
3904185 GTG
66 GTA
* **
3904188 TACAAGCACTTGACACCAAGTCACC
1 AACAAGCAAGTGACACCAAGTCACC
3904213 AATACAAAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
67 5 0.06
68 70 0.91
69 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (68 bp):
AACAAGCAAGTGACACCAAGTCACCTTTGCTAATCAAAGATCCCAAGGGTTTGATCGCCACAATG
GTA
Found at i:3912260 original size:506 final size:504
Alignment explanation
Indices: 3911180--3912556 Score: 1605
Period size: 506 Copynumber: 2.7 Consensus size: 504
3911170 GGGTTTGTGG
* * * * * **
3911180 CAAGTTAATTATAGATGGGAGCTCGGTAAGTATGTTAGCCACA-CTTTTTGTTCAAGTTCCCACA
1 CAAGTCAATTATAGGTGGGAGCTCAGTAAGTATGTTAGCCATAGTTTTTTGTTCAAGTTTTCACA
* * * * *
3911244 GACGACGCCAAATTATT-AATGTCTTCTATTGATGTCTTTCTTAGATGGGAGCT-GAAAATTGTT
66 GACGATGCCAAATTATTGAA-GTCTTCTGTCGATGTCTTTCTTAGATGGCAGCTAAAAAATTGTT
* * *
3911307 CCACCGAACCTAAAAGCAGACAGAGATTAGAAGAGCGTCGAAGTTTAAGACT-TCAAAAGCACTT
130 CCACCGAACCTAAAAGCAGACAGAGGTTAGAAGAGCGTTGAAGTTTAAGACTCT-AAACGCACTT
3911371 CGATACTTAAGTCAGACAGAGCCCAAA-AGAAATGAAAATGGAACCAATGAGAAATATGAAAAAG
194 CGATACTTAAGTCAGACAGAGCCCAAAGA-AAATGAAAATGGAACCAATGAGAAATATGAAAAAG
* * * * * * *
3911435 ACGATAAAATCGAAAGGGGTA-TTCTTTCCTCTTTTGGACTTACCTCTTTAGGGTGTTTGCTTCT
258 ACGGTAAAACCGAAAGGGGCATTTTTTTCAT-TTTTGGACTCACCTCTCTAGGGTGTTTGCTTCT
* * * * * * *
3911499 TTTTATTTATACCTGGGCCACTTGACGGGAGTTGTGTGATTTCCTTATGCTGTGGAGTGTAACTT
322 CTTTATTTATACTTGGGCCACTTGACGGGAGTTGTATGGTTTCC-T-TGCAGTGCAATGTAACTT
** * * ** * *
3911564 TTTGTCATGCTCCAAGCATATGTCATTCTAATTGTCAGATTATCATTTTTTTGGTCTTTTTGATG
385 GCTGTCAAGCTCCAACCATATGTCATTCTAATTGTCAGATTATCATTTTTTTAATCTGTTTGATA
* ** * *
3911629 GTTTTAAAGTCAGTTTGATTTAATACGATGAGACTTCTATCAGTGTGGTTTAATA
450 GCTCCAAAGTCAGTGTGATTTAATACGAGGAGACTTCTATCAGTGTGGTTTAATA
* * * *
3911684 TAAGTCAGTTATAGGTGGGAGCTCAGTAAGTATGTTAGCCATGGTTTTCTGTTCAAG-TTTCTAC
1 CAAGTCAATTATAGGTGGGAGCTCAGTAAGTATGTTAGCCATAGTTTTTTGTTCAAGTTTTC-AC
* * * *
3911748 AGACGATGACAAATTATTGAAGTCTTCTGTCGATGTCTTTCTTGGATGGCAGTTAAAAAATTGCT
65 AGACGATGCCAAATTATTGAAGTCTTCTGTCGATGTCTTTCTTAGATGGCAGCTAAAAAATTGTT
* * * * * * * *
3911813 CCACCAAACCCAAAAGCAGACAAAGGTTAGAAAAACGTTAAAGTTTAAGACTCTGAACGCACTCC
130 CCACCGAACCTAAAAGCAGACAGAGGTTAGAAGAGCGTTGAAGTTTAAGACTCTAAACGCACTTC
* * * *
3911878 GACACTTAAGTTAGACAGAG-CCAAAGATAAATGGAAATGGAACCAATAAGAAATATGAAAAAGA
195 GATACTTAAGTCAGACAGAGCCCAAAGA-AAATGAAAATGGAACCAATGAGAAATATGAAAAAGA
*
3911942 TGGTAAAACCGAAAGGGGCATTTTTTTCATTTTTGGACTCACCTCTCTAGGGTGTTTGCTTCTCT
259 CGGTAAAACCGAAAGGGGCATTTTTTTCATTTTTGGACTCACCTCTCTAGGGTGTTTGCTTCTCT
* * * **
3912007 TTATTTATATTTGGGCCACTT-AGCGGAAGTTGTATGGTTTCCTTGGAGTGCAAT-TTTCTGTCA
324 TTATTTATACTTGGGCCACTTGA-CGGGAGTTGTATGGTTTCCTTGCAGTGCAATGTAACT-T--
*
3912070 GGCTGTCAAGCTCCAACCATATGTCATTCTAATTGTCAGGTTATCATTTTTTTAATCTGTTTGAT
385 -GCTGTCAAGCTCCAACCATATGTCATTCTAATTGTCAGATTATCATTTTTTTAATCTGTTTGAT
* *
3912135 AGCTCCAAAGTCAGTGTGATTTAATGCGAGGGGACTTCTATCAGTGTGGTTTAATA
449 AGCTCCAAAGTCAGTGTGATTTAATACGAGGAGACTTCTATCAGTGTGGTTTAATA
* * * * *
3912191 CAAGTCAATTATAGGTGAGAGCTCAGT-GGTAGGTTAGCCATAGTTTTTTGTTGAAGTTTTCATA
1 CAAGTCAATTATAGGTGGGAGCTCAGTAAGTATGTTAGCCATAGTTTTTTGTTCAAGTTTTCACA
* *
3912255 GACGATGCCAAATTATTGATGTCTTCTGTCGATGTCTTTCTTCA-ATTGCAGCTAAAAAATTGTT
66 GACGATGCCAAATTATTGAAGTCTTCTGTCGATGTCTTTCTT-AGATGGCAGCTAAAAAATTGTT
* * * * * *
3912319 CCGCCGAACCTGAAATCAGATAGAGGTTAGAAGAGCGTTGAAGTTTAAAACTCAAAACGCACTTC
130 CCACCGAACCTAAAAGCAGACAGAGGTTAGAAGAGCGTTGAAGTTTAAGACTCTAAACGCACTTC
* *
3912384 GATGCTTAAGTCAGACAAAGCCCACAAG-AAAT-AAGAATGGAACCAATGAGAAATATGAAAAAG
195 GATACTTAAGTCAGACAGAGCCCA-AAGAAAATGAA-AATGGAACCAATGAGAAATATGAAAAAG
* * * * * * * * *
3912447 ACGGTAAAACCGACATGAGCGTTCTTTCCTTTTTTGGACTCACCTC-CTTAAGGTGTTTGCTTAT
258 ACGGTAAAACCGAAAGGGGCATTTTTTTCATTTTTGGACTCACCTCTC-TAGGGTGTTTGCTTCT
* * * *
3912511 CTTTATTTATACTTGAGTCACTTGACGGGAGTTGCATAGTTTCCTT
322 CTTTATTTATACTTGGGCCACTTGACGGGAGTTGTATGGTTTCCTT
3912557 ATGCTGTGGA
Statistics
Matches: 731, Mismatches: 123, Indels: 36
0.82 0.14 0.04
Matches are distributed among these distances:
503 3 0.00
504 46 0.06
505 66 0.09
506 469 0.64
507 144 0.20
508 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (504 bp):
CAAGTCAATTATAGGTGGGAGCTCAGTAAGTATGTTAGCCATAGTTTTTTGTTCAAGTTTTCACA
GACGATGCCAAATTATTGAAGTCTTCTGTCGATGTCTTTCTTAGATGGCAGCTAAAAAATTGTTC
CACCGAACCTAAAAGCAGACAGAGGTTAGAAGAGCGTTGAAGTTTAAGACTCTAAACGCACTTCG
ATACTTAAGTCAGACAGAGCCCAAAGAAAATGAAAATGGAACCAATGAGAAATATGAAAAAGACG
GTAAAACCGAAAGGGGCATTTTTTTCATTTTTGGACTCACCTCTCTAGGGTGTTTGCTTCTCTTT
ATTTATACTTGGGCCACTTGACGGGAGTTGTATGGTTTCCTTGCAGTGCAATGTAACTTGCTGTC
AAGCTCCAACCATATGTCATTCTAATTGTCAGATTATCATTTTTTTAATCTGTTTGATAGCTCCA
AAGTCAGTGTGATTTAATACGAGGAGACTTCTATCAGTGTGGTTTAATA
Found at i:3914222 original size:509 final size:508
Alignment explanation
Indices: 3912592--3914309 Score: 2046
Period size: 509 Copynumber: 3.4 Consensus size: 508
3912582 AGGCTGTCAG
* * *** * *
3912592 ACTTCTATTAGTGTGGTTTAATACAAGTTAGTTAT-GGTAAAAGCTAGATAGATAGGTTAGCCAT
1 ACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCG-TAGGTAGGTTAGCCAT
* * * * * * * *
3912656 GGCTTTTTGTTCAAATTCCCAC-AGGCGATGCCAAATTATTAATGTCTTCTATTCGTGTCTTTCT
65 TGTTTTTTGTTCAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTCATGTCTTTCT
* * ** *
3912720 TAGATGGCAGCTGAAAAATTGTTCCACCGAACTTGAAAGCAGACAGAGGTTAGAAGAGCATCGAA
130 TAGATGGCAGCTGAAAAATTATTCCACCGAACCTGAAAATAGACAGAGGTTAGAAGAGCGTCGAA
* * * *
3912785 GTTTAAGACTCCGAACGTACTCCGATGCTTAAATCAGACAGAGCCCAAGAGATATGGGAATGGAA
195 GTTTAAGACTCCGAACGTACTCCGAAGCTTAAGTCAGACAGAGCCAAAGAGAAATGGGAATGGAA
* * * *
3912850 CCAATGAGAAATATGAAAAAGACGGTAAAACCGAAAGGGGCGTTCTTTCCTTTTTTTAGACTCAC
260 CCAATGAGAAATATGAAAAAGACGATAAAATCGAAAGGGGCATTCTTTCCTTTTTTGA-ACTCAC
* * * * * *
3912915 CTCTTTAGGGTGTTTACTTCTCTTTATTTATACCTAAGCCACTTTGCGGGAGTCGCGTGGTTTTC
324 C-C--TAAGGTGTTTGCTTCTCTTTATTTATACCTGAGCCACTTGGCGGGAGTTGCGTGGTTTCC
* *
3912980 TTATACTGTGGAGTGCAAC--TT-T---CTGTCAAGCTCCAAGCATATGTCATTCTAATTGTCAA
386 TTATGCTGTGGAGTGCAACTTTTGTAGGCTGTCAAGCTCCAAGCATATGTAATTCTAATTGTCAA
* * * * * * *
3913039 ATTAAT-ATTTTTTTAGTCTTTTTGACGACTCCAAAGTTAATGTGGCTTAATGCGAGAGG
451 ATT-ATCATTTTTTT-GTCTGTTTGATGGCTCCAAAGTTAGTGTGGTTTAATGCAAGAGA
* *
3913098 ACTTCTATTAGTGTGGTTTAATATAAGTCAGTTATAGGTGGGAGCTCGATAGGTAGGTTAGCCAT
1 ACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCG-TAGGTAGGTTAGCCAT
* **
3913163 TGTTTTTTTGTTTAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTGGTGTCTTTC
65 TG-TTTTTTGTTCAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTCATGTCTTTC
* * * * *
3913228 TTGGATGGTAGTTGAAAAATTATTCCACTGAACCTGAAAGTAGACAGAGGTTAGAAGAGCGTCGA
129 TTAGATGGCAGCTGAAAAATTATTCCACCGAACCTGAAAATAGACAGAGGTTAGAAGAGCGTCGA
* * * *
3913293 AGCTTAAGACTCCGAACGTACTCC-AATGCCTAAGTCAAACAGAGCCTAAGAGAAATGGGAATGG
194 AGTTTAAGACTCCGAACGTACTCCGAA-GCTTAAGTCAGACAGAGCCAAAGAGAAATGGGAATGG
* * * * * *
3913357 AACCAATGAGAAATATGAAAAAGGCGTTAAAATCGAATGGTGCATTCTTTCATTTTTTGGACTCA
258 AACCAATGAGAAATATGAAAAAGACGATAAAATCGAAAGGGGCATTCTTTCCTTTTTTGAACTCA
* * * *
3913422 CCTCCCTAAGTTGTTTGCTTCTCTTTATTTATACCTGAGCCACTTGGTGGGAGTTGTGTCGTTTC
323 ---CCCTAAGGTGTTTGCTTCTCTTTATTTATACCTGAGCCACTTGGCGGGAGTTGCGTGGTTTC
* * * *
3913487 CTTAAGCTGTGGAGTGGAACTTTTTGTTAGGCTGTCATGCTCCAAGCATATGTAATTCCAATTGT
385 CTTATGCTGTGGAGTGCAAC-TTTTG-TAGGCTGTCAAGCTCCAAGCATATGTAATTCTAATTGT
* * *
3913552 CAGATTATCATTTTTTAGTCTGTTTGATGGCTCCAAAGTTAGTGTGGTTTAATGCAATA-A
448 CAAATTATCATTTTTTTGTCTGTTTGATGGCTCCAAAGTTAGTGTGGTTTAATGCAAGAGA
* * * * * *
3913612 GACTTATATCAGTGTGGCTTAATACAAGTCAGTTATAGGTAGGAGCTTGGCAGGTAGGTTGGCCA
1 -ACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGC-TCGTAGGTAGGTTAGCCA
* * * * *
3913677 TTGCTTTTTGTTCAAGTT-CCAATAGACGACGCTAAATTATTGATGTCTTCTGTTCATGTCTTTC
64 TTGTTTTTTGTTCAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTCATGTCTTTC
* * * * * *
3913741 TTGGATGGCACCTGAAAAATTATTCCACCGAACCTGAAAATGGATAGAGGTTAAAAAAGCGTC-A
129 TTAGATGGCAGCTGAAAAATTATTCCACCGAACCTGAAAATAGACAGAGGTTAGAAGAGCGTCGA
* * * * * *
3913805 GAGTTTAAGACTCCGAACGCACTCCGAAGCTTAAGTTAGATAGAGTCAAAAAGAAATAGGAATGG
194 -AGTTTAAGACTCCGAACGTACTCCGAAGCTTAAGTCAGACAGAGCCAAAGAGAAATGGGAATGG
*
3913870 AACCAATGAGAAATATGAAAAAGATGATAAAATCGAAAGGGGCATTCTTTCCTTTTTTGAACTCA
258 AACCAATGAGAAATATGAAAAAGACGATAAAATCGAAAGGGGCATTCTTTCCTTTTTTGAACTCA
* *
3913935 -CCTAAGGTGTTTGCCTCTCTTTATTTATACCTGCGCCACTTGGCGGGAGTTGCGTGGTTTCCTT
323 CCCTAAGGTGTTTGCTTCTCTTTATTTATACCTGAGCCACTTGGCGGGAGTTGCGTGGTTTCCTT
* * *
3913999 ATGCTGTGAAGTGTAACTTTCTGTCAGGCTGTCAAGCTCCAAGCATATGTTATTCTAATTGTCAA
388 ATGCTGTGGAGTGCAACTTT-TGT-AGGCTGTCAAGCTCCAAGCATATGTAATTCTAATTGTCAA
* * * *
3914064 ATTATCATTTTTTTTTCTGCTTAATGGCTCCAAAGTCAGTGTGGTTTAATGCAAGAGA
451 ATTATCATTTTTTTGTCTGTTTGATGGCTCCAAAGTTAGTGTGGTTTAATGCAAGAGA
* * * * *
3914122 ACTTCTATCAATATTGTTTAATACAAGTCAAG-TATAGGTGGGAGCTCAGTAGGTTGGTTAGCTA
1 ACTTCTATCAGTGTGGTTTAATACAAGTC-AGTTATAGGTGGGAGCTC-GTAGGTAGGTTAGCCA
* * * * *
3914186 TTGTTTTTTGTTCTAGTTCCCA-TGGACGATGCTAAATTATTGATGCCTTTTGTTGATGTCTTTC
64 TTGTTTTTTGTTCAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTCATGTCTTTC
* * *
3914250 TTAGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAACAGACAGAGGTTAGAAGAGC
129 TTAGATGGCAGCTGAAAAATTATTCCACCGAACCTGAAAATAGACAGAGGTTAGAAGAGC
3914310 ATTGAGGTTG
Statistics
Matches: 1033, Mismatches: 153, Indels: 49
0.84 0.12 0.04
Matches are distributed among these distances:
506 33 0.03
507 25 0.02
508 94 0.09
509 512 0.50
510 7 0.01
511 4 0.00
512 1 0.00
513 204 0.20
514 15 0.01
515 93 0.09
516 45 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (508 bp):
ACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGTAGGTAGGTTAGCCATT
GTTTTTTGTTCAAGTTCCCACTAGACGATGCCAAATTATTGATGCCTTCTGTTCATGTCTTTCTT
AGATGGCAGCTGAAAAATTATTCCACCGAACCTGAAAATAGACAGAGGTTAGAAGAGCGTCGAAG
TTTAAGACTCCGAACGTACTCCGAAGCTTAAGTCAGACAGAGCCAAAGAGAAATGGGAATGGAAC
CAATGAGAAATATGAAAAAGACGATAAAATCGAAAGGGGCATTCTTTCCTTTTTTGAACTCACCC
TAAGGTGTTTGCTTCTCTTTATTTATACCTGAGCCACTTGGCGGGAGTTGCGTGGTTTCCTTATG
CTGTGGAGTGCAACTTTTGTAGGCTGTCAAGCTCCAAGCATATGTAATTCTAATTGTCAAATTAT
CATTTTTTTGTCTGTTTGATGGCTCCAAAGTTAGTGTGGTTTAATGCAAGAGA
Found at i:3915428 original size:494 final size:492
Alignment explanation
Indices: 3914769--3916955 Score: 2272
Period size: 494 Copynumber: 4.3 Consensus size: 492
3914759 CCACTTGGCC
* * * * *
3914769 GGAGTTGCGTGGTTT-CTTAATGCTGTGAAGTGCAACTTTCTGTTAAGCTGTCAAGTTCCAAACA
1 GGAGTTGCGTGGTTTCCTT-ATGCTGTGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGCA
* * * * *
3914833 TATGTCATTTTAATTGTGAGATTATTAATTTTTTGATTTGTTTGACGGCTGCAAAGTCAGTGTGG
65 TATGTCATTCTAATTGTTAGATTA-TCATTTTTTTATTTGTTTGACGGCTCCAAAGTCAGTGTGG
* ** *
3914898 TTTAATGCGAAAAGACTTCTAAAAGTATGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGATA
129 TTTAATGCGATAAGACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGATA
*
3914963 GGTAGGTTAGCCATGGTTTTTTGTACAAGTTCCCACAGACGACG-TCAAATTATTGATGTCTTCT
194 GGTAGGTTAGCCATGGTTTTTTGTTCAAGTTCCCACAGACGACGCT-AAATTATTGATGTCTTCT
* * * * * *
3915027 GTTGATGTCTTTCTTAGATGGCAATTGAAAAATTGTTCCATCGAACTTGAAAGTAGATAGAGGTT
258 GTTGATGTCTTTCTTGGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAGCAGACAGAGGTT
** * *
3915092 AGAAAAGCATTGAAGTTTAAGACTCCGAACACACTCTGATACTTAAATCAGACAGAATG-AAGAG
323 AGAAAAGCATCAAAGTTTAAGACTCCGAACGCACTCTGATACTTAAGTCAGACAGAA-GCAAGAG
*
3915156 AAATAAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACCGAAAGGGACATTCTTTCCT
387 AAATGAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACCGAAAGGG-CATTCTTTCCT
*
3915221 TTTTTGGACTCACTTCCTTAAGGTGTTTGCTTC-TCTTTGGTG
451 TTTTTGGACTCAC-TCCTTAGGGTGTTTGCTTCTTCTTTGGTG
* * * * * *
3915263 GGAGTTGTGGGGTTTCCTTATGTTGTGAAGTGCAACTTTCTGTCAGGCTGTTAGGCTCCAAGCAT
1 GGAGTTGCGTGGTTTCCTTATGCTGTGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGCAT
* * * * *
3915328 ATGTAATTCTAATTGTCATATTATCATTTTTTTAGTTTGTTTGACGGCTCCAAAATCAGTATGGT
66 ATGTCATTCTAATTGTTAGATTATCATTTTTTTA-TTTGTTTGACGGCTCCAAAGTCAGTGTGGT
* ** * * * *
3915393 TTAATACGAGGAGACTTCTATCATTGTGTTTTAATACAAGTCAATTATAGGTGAGAGCTCGATAG
130 TTAATGCGATAAGACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGATAG
** * * * *
3915458 GTAGGTTAGCCATGGTTTTTTGTTCAAGTTTTCACAGACGACGCCAAATGATTGATGCCTTCTAT
195 GTAGGTTAGCCATGGTTTTTTGTTCAAGTTCCCACAGACGACGCTAAATTATTGATGTCTTCTGT
* * * * * * *
3915523 TGATGTTTTTCCTGAATGGCAGCTGAAAAATTATTCCA-CGAACCTAAAAGCAGATAGAGGTTAG
260 TGATGTCTTTCTTGGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAGCAGACAGAGGTTAG
* * * * * * * *
3915587 AAGAGCGTCAAAGTTTGAGACTCTGAACGCAAT-TCGATGCTTGAGTCAGATAG-AGCCCAAGAG
325 AAAAGCATCAAAGTTTAAGACTCCGAACGCACTCT-GATACTTAAGTCAGACAGAAG--CAAGAG
* * *
3915650 AAATGAGAATGGAACTAATGAGAAATATGAAAAAGACAGTAAAATCGAAAAGGCATTCTTT-CTT
387 AAATGAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACCGAAAGGGCATTCTTTCCTT
* *
3915714 TTCTTGGACTCAACTCCATAGGGTGTTTGCTTCTTTTTATTTATACTTGGGCCACTTGG
452 TT-TTGGACTC-ACTCCTTAGGGTGTTTGCTTC--------T-T-CTTTGG-----T-G
* * * * * *
3915773 CGAGAGTTACGCGGTTTCCTTATGCTGTGGAGTGCAACTCTCTATCAAGCTATTAGGCTCCAAGC
1 -G-GAGTTGCGTGGTTTCCTTATGCTGTGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGC
* * * * * *
3915838 ATATGTCATTCCAATTGTTAGATTATCATTTTTTTATCTGTTTGATGGCTCTAAAGCCAGTGTGA
64 ATATGTCATTCTAATTGTTAGATTATCATTTTTTTATTTGTTTGACGGCTCCAAAGTCAGTGTGG
* * *
3915903 TTTAATGCGATAAGACTTTTATTAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGGTA
129 TTTAATGCGATAAGACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGATA
* * * * *
3915968 GGTAAGTTAGCCATAGTTTTTTGTTCAAGTTCCTACAAACGACGCTAAATTATTGATGTCTTTTG
194 GGTAGGTTAGCCATGGTTTTTTGTTCAAGTTCCCACAGACGACGCTAAATTATTGATGTCTTCTG
* * *
3916033 TTGATGTCTTTCTTGGATGGCAACTAAAAAATTGTTCCACCGAACCTGCAAGTAGACAGAGGTTA
259 TTGATGTCTTTCTTGGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAGCAGACAGAGGTTA
* * * * ** * *
3916098 GAAGAGCATCAAAGTTTTAGACTCCAAACGTACTCTGATACTTAAGTTGGATAGAGGCCAAGAGA
324 GAAAAGCATCAAAGTTTAAGACTCCGAACGCACTCTGATACTTAAGTCAGACAGAAG-CAAGAGA
* * * * * * * * *
3916163 AATGGGAATGAAACCGATAAGTAATATGAAAATGACGGTAAAACCAAAAAGGGCGTTCTTTCCTT
388 AATGAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACC-GAAAGGGCATTCTTTCCTT
*
3916228 TTTTGGACTCACCTCCTTAGGGTGTTTGTTTCTCTTTATTTATACGTGCGTCATTTGGCG
452 TTTTGGACTCA-CTCCTTAGGGTGTTTG-----C------T-T-C-T---TC-TTTGGTG
* *
3916288 GGAGTTGCGTGGTTTTCTTATGCTGTTG-AGTGCAACTTTCTGTCAGGCTATCAGGCTCCAAGCA
1 GGAGTTGCGTGGTTTCCTTATGCTG-TGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGCA
* *
3916352 TATGTTATTCTAATTGTTAGATTATCATTTTTTTATTCTATTTGACGGGCTCCAAAGTCAGTGTG
65 TATGTCATTCTAATTGTTAGATTATCATTTTTTTATT-TGTTTGAC-GGCTCCAAAGTCAGTGTG
* * *
3916417 GTTTAATGCGATGAGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCAAT
128 GTTTAATGCGATAAGACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGAT
**
3916482 AGGTAGGTTAGCCATGG-TTTTAATTCAAGTTCCCACAGACGACGCTAAATTATTGATGTCTTCT
193 AGGTAGGTTAGCCATGGTTTTTTGTTCAAGTTCCCACAGACGACGCTAAATTATTGATGTCTTCT
* * * *
3916546 GTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTTCACCGAACCTGATAGCAGACAAAGGTT
258 GTTGATGTCTTTCTTGGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAGCAGACAGAGGTT
* * *
3916611 AGAAAAGCGTCAAAGTTTAAGACTCTGAATGCACTCTGATACTTAAGTCAGACA-AAGCCTAAGA
323 AGAAAAGCATCAAAGTTTAAGACTCCGAACGCACTCTGATACTTAAGTCAGACAGAAG-C-AAGA
* *
3916675 GAAATGAGAATGGAACCAATGAGAAATATGAAAGAGACGGTAAAACCGAAATGGGCATTCTTTCC
386 GAAATGAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACCGAAA-GGGCATTCTTTCC
* *
3916740 TTTTTTGGACTCACCACCTCTTTAGGGTGTTCGCTTCTTTTTCTTTCTACTGCGCCACTTGTCG
450 TTTTTTGGACT---CA-CTCCTTAGGGTGTTTGCTTC---TTC--T-T--T--G------GT-G
* * * * * * *
3916804 GGAGTTGCCTGGTTTCCTTATGCTATGGAGCGCAACTTTCTGTCAAGCTGTCAAGTTCCAAGCAT
1 GGAGTTGCGTGGTTTCCTTATGCTGTGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGCAT
* ** * * *
3916869 ATGTTATTCTAATTGTTAGATTATCATTTTTTGGTCTGTTTGACAGCTCCAAAGTCAGTGTGATT
66 ATGTCATTCTAATTGTTAGATTATCATTTTTTTATTTGTTTGACGGCTCCAAAGTCAGTGTGGTT
* *
3916934 TAATGTGAGAAGACTTCTATCA
131 TAATGCGATAAGACTTCTATCA
3916956 AAGTCTGATA
Statistics
Matches: 1399, Mismatches: 220, Indels: 128
0.80 0.13 0.07
Matches are distributed among these distances:
491 1 0.00
492 7 0.01
493 104 0.07
494 297 0.21
495 3 0.00
503 3 0.00
504 7 0.01
505 2 0.00
506 2 0.00
507 1 0.00
509 2 0.00
510 1 0.00
511 165 0.12
512 194 0.14
513 131 0.09
514 263 0.19
515 100 0.07
516 88 0.06
517 17 0.01
518 1 0.00
519 1 0.00
520 1 0.00
521 5 0.00
524 1 0.00
525 1 0.00
526 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (492 bp):
GGAGTTGCGTGGTTTCCTTATGCTGTGAAGTGCAACTTTCTGTCAAGCTATCAGGCTCCAAGCAT
ATGTCATTCTAATTGTTAGATTATCATTTTTTTATTTGTTTGACGGCTCCAAAGTCAGTGTGGTT
TAATGCGATAAGACTTCTATCAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCTCGATAGG
TAGGTTAGCCATGGTTTTTTGTTCAAGTTCCCACAGACGACGCTAAATTATTGATGTCTTCTGTT
GATGTCTTTCTTGGATGGCAACTGAAAAATTGTTCCACCGAACCTGAAAGCAGACAGAGGTTAGA
AAAGCATCAAAGTTTAAGACTCCGAACGCACTCTGATACTTAAGTCAGACAGAAGCAAGAGAAAT
GAGAATGGAACCAATGAGAAATATGAAAAAGACAGTAAAACCGAAAGGGCATTCTTTCCTTTTTT
GGACTCACTCCTTAGGGTGTTTGCTTCTTCTTTGGTG
Found at i:3916377 original size:513 final size:510
Alignment explanation
Indices: 3915257--3916956 Score: 2131
Period size: 514 Copynumber: 3.3 Consensus size: 510
3915247 TTGCTTCTCT
* * * * * * * *
3915257 TTGGTGGGAGTTGTGGGGTTTCCTTATGTTGTGAAGTGCAACTTTCTGTCAGGCTGTTAGGCTCC
1 TTGGCGGGAGTTGCGTGGTTTCCTTATGCTGTGGAGTGCAACTTTCTGTCAAGCTATCAGGCTCC
* * * * *
3915322 AAGCATATGTAATTCTAATTGTCATATTATCATTTTTTTAGTTTGTTTGACGGCTCCAAAATCAG
66 AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTAGTCTGTTTGACGGCTCCAAAGTCAG
* * * * * * * *
3915387 TATGGTTTAATACGAGGAGACTTCTATCATTGTGTTTTAATACAAGTCAATTATAGGTGAGAGCT
131 TGTGATTTAATGCGAGAAGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCT
* * * *
3915452 CGATAGGTAGGTTAGCCATGGTTTTTTGTTCAAGTT-TTCACAGACGACGCCAAATGATTGATGC
196 CGATAGGTAGGTTAGCCAT-GTTTTTTGTTCAAGTTCCT-ACAGACGACGCTAAATTATTGATGT
* * * * * * *
3915516 CTTCTATTGATGTTTTTCCTGAATGGCAGCTGAAAAATTATTCCA-CGAACCTAAAAGCAGATAG
259 CTTCTGTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTCCACCGAACCT-GAAGCAGACAG
* * * * *
3915580 AGGTTAGAAGAGCGTCAAAGTTTGAGACTCTGAACGCAAT-TCGATGCTTGAGTCAGATAGAGCC
323 AGGTTAGAAGAGCGTCAAAGTTTAAGACTCTGAACGCACTCT-GATACTTAAGTCAGATAGAGGC
* * *
3915644 CAAGAGAAATGAGAATGGAACTAATGAGAAATATGAAAAAGACAGTAAAATCGAAAA-GGCATTC
387 CAAGAGAAATGAGAATGGAACCAATGAGAAATATG-AAAAGACGGTAAAACCGAAAAGGGCATTC
* * *
3915708 TTT-CTTTTCTTGGACTCAACTCCATAGGGTGTTTGCTTCTTTTTATTTATACTTGGGCCAC
451 TTTCCTTTT-TTGGACTCACCTCCTTAGGGTGTTTGCTTCTTTTTATTTATAC-TGCGCCAC
* * * * * *
3915769 TTGGCGAGAGTTACGCGGTTTCCTTATGCTGTGGAGTGCAACTCTCTATCAAGCTATTAGGCTCC
1 TTGGCGGGAGTTGCGTGGTTTCCTTATGCTGTGGAGTGCAACTTTCTGTCAAGCTATCAGGCTCC
* * * * *
3915834 AAGCATATGTCATTCCAATTGTTAGATTATCATTTTTTTA-TCTGTTTGATGGCTCTAAAGCCAG
66 AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTAGTCTGTTTGACGGCTCCAAAGTCAG
* * * *
3915898 TGTGATTTAATGCGATAAGACTTTTATTAGTGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCT
131 TGTGATTTAATGCGAGAAGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCT
* * *
3915963 CGGTAGGTAAGTTAGCCATAGTTTTTTGTTCAAGTTCCTACAAACGACGCTAAATTATTGATGTC
196 CGATAGGTAGGTTAGCCAT-GTTTTTTGTTCAAGTTCCTACAGACGACGCTAAATTATTGATGTC
* * * *
3916028 TTTTGTTGATGTCTTTCTTGGATGGCAACTAAAAAATTGTTCCACCGAACCTGCAAGTAGACAGA
260 TTCTGTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTCCACCGAACCTG-AAGCAGACAGA
* * ** * **
3916093 GGTTAGAAGAGCATCAAAGTTTTAGACTCCAAACGTACTCTGATACTTAAGTTGGATAGAGGCCA
324 GGTTAGAAGAGCGTCAAAGTTTAAGACTCTGAACGCACTCTGATACTTAAGTCAGATAGAGGCCA
* * * * * * *
3916158 AGAGAAATGGGAATGAAACCGATAAGTAATATGAAAATGACGGTAAAACCAAAAAGGGCGTTCTT
389 AGAGAAATGAGAATGGAACCAATGAGAAATATGAAAA-GACGGTAAAACCGAAAAGGGCATTCTT
* * * *
3916223 TCCTTTTTTGGACTCACCTCCTTAGGGTGTTTGTTTCTCTTTATTTATACGTGCGTCAT
453 TCCTTTTTTGGACTCACCTCCTTAGGGTGTTTGCTTCTTTTTATTTATAC-TGCGCCAC
* * *
3916282 TTGGCGGGAGTTGCGTGGTTTTCTTATGCTGTTGAGTGCAACTTTCTGTCAGGCTATCAGGCTCC
1 TTGGCGGGAGTTGCGTGGTTTCCTTATGCTGTGGAGTGCAACTTTCTGTCAAGCTATCAGGCTCC
* *
3916347 AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTATTCTATTTGACGGGCTCCAAAGTCA
66 AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTAGTCTGTTTGAC-GGCTCCAAAGTCA
*
3916412 GTGTGGTTTAATGCGATG-AGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAG
130 GTGTGATTTAATGCGA-GAAGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAG
* * ** *
3916476 CTCAATAGGTAGGTTAGCCATGGTTTTAATTCAAGTTCCCACAGACGACGCTAAATTATTGATGT
194 CTCGATAGGTAGGTTAGCCATGTTTTTTGTTCAAGTTCCTACAGACGACGCTAAATTATTGATGT
* *
3916541 CTTCTGTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTTCACCGAACCTGATAGCAGACAA
259 CTTCTGTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTCCACCGAACCTGA-AGCAGACAG
* * * *
3916606 AGGTTAGAAAAGCGTCAAAGTTTAAGACTCTGAATGCACTCTGATACTTAAGTCAGACA-AAGCC
323 AGGTTAGAAGAGCGTCAAAGTTTAAGACTCTGAACGCACTCTGATACTTAAGTCAGATAGAGGCC
*
3916670 TAAGAGAAATGAGAATGGAACCAATGAGAAATATGAAAGAGACGGTAAAACCGAAATGGGCATTC
388 -AAGAGAAATGAGAATGGAACCAATGAGAAATATGAAA-AGACGGTAAAACCGAAAAGGGCATTC
* * * *
3916735 TTTCCTTTTTTGGACTCACCACCTCTTTAGGGTGTTCGCTTCTTTTTCTTTCTACTGCGCCAC
451 TTTCCTTTTTTGGACT---CACCTCCTTAGGGTGTTTGCTTCTTTTTATTTATACTGCGCCAC
* * * * * * *
3916798 TTGTCGGGAGTTGCCTGGTTTCCTTATGCTATGGAGCGCAACTTTCTGTCAAGCTGTCAAGTTCC
1 TTGGCGGGAGTTGCGTGGTTTCCTTATGCTGTGGAGTGCAACTTTCTGTCAAGCTATCAGGCTCC
* *
3916863 AAGCATATGTTATTCTAATTGTTAGATTATCA-TTTTTTGGTCTGTTTGACAGCTCCAAAGTCAG
66 AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTAGTCTGTTTGACGGCTCCAAAGTCAG
*
3916927 TGTGATTTAATGTGAGAAGACTTCTATCAA
131 TGTGATTTAATGCGAGAAGACTTCTATCAA
3916957 AGTCTGATAG
Statistics
Matches: 1015, Mismatches: 156, Indels: 32
0.84 0.13 0.03
Matches are distributed among these distances:
511 168 0.17
512 200 0.20
513 154 0.15
514 267 0.26
515 103 0.10
516 93 0.09
517 30 0.03
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (510 bp):
TTGGCGGGAGTTGCGTGGTTTCCTTATGCTGTGGAGTGCAACTTTCTGTCAAGCTATCAGGCTCC
AAGCATATGTTATTCTAATTGTTAGATTATCATTTTTTTAGTCTGTTTGACGGCTCCAAAGTCAG
TGTGATTTAATGCGAGAAGACTTCTATCAATGTGGTTTAATACAAGTCAGTTATAGGTGGGAGCT
CGATAGGTAGGTTAGCCATGTTTTTTGTTCAAGTTCCTACAGACGACGCTAAATTATTGATGTCT
TCTGTTGATGTCTTTCTTGGATGGCAGCTGAAAAATTGTTCCACCGAACCTGAAGCAGACAGAGG
TTAGAAGAGCGTCAAAGTTTAAGACTCTGAACGCACTCTGATACTTAAGTCAGATAGAGGCCAAG
AGAAATGAGAATGGAACCAATGAGAAATATGAAAAGACGGTAAAACCGAAAAGGGCATTCTTTCC
TTTTTTGGACTCACCTCCTTAGGGTGTTTGCTTCTTTTTATTTATACTGCGCCAC
Found at i:3922149 original size:10 final size:9
Alignment explanation
Indices: 3922134--3922166 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3922124 TATCACATTT
3922134 TTTTTAATTA
1 TTTTT-ATTA
3922144 TTTTTATT-
1 TTTTTATTA
3922152 TTTTTATTA
1 TTTTTATTA
3922161 TTTTTA
1 TTTTTA
3922167 ATAGATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 9 0.41
10 5 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3922155 original size:17 final size:17
Alignment explanation
Indices: 3922133--3922166 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3922123 ATATCACATT
3922133 TTTTTTAATTATTTTTA
1 TTTTTTAATTATTTTTA
*
3922150 TTTTTTTATTATTTTTA
1 TTTTTTAATTATTTTTA
3922167 ATAGATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTAATTATTTTTA
Found at i:3924629 original size:29 final size:30
Alignment explanation
Indices: 3924597--3924654 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
3924587 TTATTATAGT
* *
3924597 AATTATATTTATTATATTA-TTTTTATTTG
1 AATTAAATATATTATATTATTTTTTATTTG
*
3924626 AATTAAATATATTATTTTATTTTTTATTT
1 AATTAAATATATTATATTATTTTTTATTT
3924655 TTACATCACA
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:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (30 bp):
AATTAAATATATTATATTATTTTTTATTTG
Found at i:3924745 original size:1 final size:1
Alignment explanation
Indices: 3924739--3924766 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3924729 AGCCAACATG
3924739 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
3924767 CAAAGAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.