Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 70 of 129
Found at i:11006005 original size:21 final size:24
Alignment explanation
Indices: 11005957--11006005 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
11005947 GGATTTTAAA
*
11005957 AAATTGATCGATCCTTTTTGTGTAC
1 AAATTGATCGAT-CTTTTTGTATAC
11005982 AAATTGATCGAT-TTTTT-TAT-C
1 AAATTGATCGATCTTTTTGTATAC
11006003 AAA
1 AAA
11006006 ATCAAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 2 0.09
23 5 0.22
25 12 0.52
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
AAATTGATCGATCTTTTTGTATAC
Found at i:11013149 original size:28 final size:29
Alignment explanation
Indices: 11013094--11013151 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
11013084 ATCAAAAAAG
11013094 AGTATTAACTCTAATACCAATTGTTACTC
1 AGTATTAACTCTAATACCAATTGTTACTC
11013123 AGTATTAACTCTAA-ACCAATTGTTACTC
1 AGTATTAACTCTAATACCAATTGTTACTC
11013151 A
1 A
11013152 AAGATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (29 bp):
AGTATTAACTCTAATACCAATTGTTACTC
Found at i:11014949 original size:70 final size:70
Alignment explanation
Indices: 11014822--11014966 Score: 175
Period size: 70 Copynumber: 2.1 Consensus size: 70
11014812 AATGCTTTGG
* * ** ** *
11014822 TTTGATAATTGCATTTGCATCATGTTTTGAACATGCATTTGCAGTACTTAGTGAACATTTGAATT
1 TTTGATAATTGCATTTCCATCATGATTTGAACATGCATCCGCAGTACTTAGCAAACATTTGAATC
11014887 ATTGT
66 ATTGT
* * * *
11014892 TTTGATAATTGTATTTCCATCATGATTTGGACCTGCATCCGCA-TCATTTAGCAAACATTTGAAT
1 TTTGATAATTGCATTTCCATCATGATTTGAACATGCATCCGCAGT-ACTTAGCAAACATTTGAAT
11014956 CATTGT
65 CATTGT
11014962 TTTGA
1 TTTGA
11014967 ATATTGGGCT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 1 0.02
70 62 0.98
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (70 bp):
TTTGATAATTGCATTTCCATCATGATTTGAACATGCATCCGCAGTACTTAGCAAACATTTGAATC
ATTGT
Found at i:11015845 original size:23 final size:23
Alignment explanation
Indices: 11015773--11015847 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 23
11015763 GAAATCTTGG
11015773 ATGTGAAT-TCTTAAAATTTTTTGA
1 ATGTGAATATC-TAAAA-TTTTTGA
** *
11015797 ATGAAAATAT-TTAAATTTTGTG-
1 ATGTGAATATCTAAAATTTT-TGA
11015819 -TGTGAATATCTAAAATTTTTGA
1 ATGTGAATATCTAAAATTTTTGA
11015841 ATGTGAA
1 ATGTGAA
11015848 CCTTTGAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
21 9 0.22
22 12 0.30
23 12 0.30
24 6 0.15
25 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (23 bp):
ATGTGAATATCTAAAATTTTTGA
Found at i:11016121 original size:17 final size:17
Alignment explanation
Indices: 11016101--11016151 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
11016091 ATCATTTTTT
*
11016101 AATTCTTACAAATCTTC
1 AATTCTTGCAAATCTTC
** *
11016118 AATTCTTGTGAATC-TA
1 AATTCTTGCAAATCTTC
11016134 AATTCTTGCAAATCTTC
1 AATTCTTGCAAATCTTC
11016151 A
1 A
11016152 TGTAAATGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTCTTGCAAATCTTC
Found at i:11016200 original size:34 final size:33
Alignment explanation
Indices: 11016162--11016333 Score: 110
Period size: 34 Copynumber: 5.1 Consensus size: 33
11016152 TGTAAATGTA
*
11016162 AAAATCTTGTGAATCTTCAATTCTTACGAATAT
1 AAAATCTTGTGAATCTTTAATTCTTACGAATAT
* * * * *
11016195 GAAAATATTGTAAATCTTTAATTTTTGCGAATCT
1 -AAAATCTTGTGAATCTTTAATTCTTACGAATAT
** * *
11016229 AAAATCTTACGAATTTTTAATTCTTACGAAATTT
1 AAAATCTTGTGAATCTTTAATTCTTACG-AATAT
* * ** ** ** *
11016263 CAATTCTTACGAATCTAAAATTCTTGTGAATCT
1 AAAATCTTGTGAATCTTTAATTCTTACGAATAT
* * * *
11016296 CAAAATCTTATGAAGCTCTAATTCTTGCGAATAT
1 -AAAATCTTGTGAATCTTTAATTCTTACGAATAT
11016330 AAAA
1 AAAA
11016334 ATATTACAAA
Statistics
Matches: 106, Mismatches: 30, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
33 29 0.27
34 77 0.73
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (33 bp):
AAAATCTTGTGAATCTTTAATTCTTACGAATAT
Found at i:11016255 original size:17 final size:17
Alignment explanation
Indices: 11016233--11016276 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
11016223 GAATCTAAAA
*
11016233 TCTTACGAATTTTTAAT
1 TCTTACGAATTTTCAAT
*
11016250 TCTTACGAAATTTCAAT
1 TCTTACGAATTTTCAAT
11016267 TCTTACGAAT
1 TCTTACGAAT
11016277 CTAAAATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (17 bp):
TCTTACGAATTTTCAAT
Found at i:11016284 original size:17 final size:17
Alignment explanation
Indices: 11016222--11016333 Score: 68
Period size: 17 Copynumber: 6.6 Consensus size: 17
11016212 TTAATTTTTG
11016222 CGAATCTAAAA-TCTTA
1 CGAATCTAAAATTCTTA
* **
11016238 CGAATTTTTAATTCTTA
1 CGAATCTAAAATTCTTA
**
11016255 CGAAAT-TTCAATTCTTA
1 CG-AATCTAAAATTCTTA
*
11016272 CGAATCTAAAATTCTTG
1 CGAATCTAAAATTCTTA
*
11016289 TGAATCTCAAAA-TCTTA
1 CGAATCT-AAAATTCTTA
* * ** *
11016306 TGAAGCTCTAATTCTTG
1 CGAATCTAAAATTCTTA
*
11016323 CGAATATAAAA
1 CGAATCTAAAA
11016334 ATATTACAAA
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
16 13 0.18
17 53 0.73
18 7 0.10
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (17 bp):
CGAATCTAAAATTCTTA
Found at i:11016464 original size:18 final size:18
Alignment explanation
Indices: 11016429--11016480 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
11016419 CTTAAGAATC
**
11016429 TTTGAAATCTTGTGAAAT
1 TTTGAAATCTTGCAAAAT
*
11016447 TTT-AATTTCTTGCAAAAT
1 TTTGAA-ATCTTGCAAAAT
11016465 TTTGAAATCTTGCAAA
1 TTTGAAATCTTGCAAA
11016481 CCTTTGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTGAAATCTTGCAAAAT
Found at i:11016486 original size:18 final size:17
Alignment explanation
Indices: 11016382--11016489 Score: 51
Period size: 18 Copynumber: 6.0 Consensus size: 17
11016372 TATCTAAAAG
*
11016382 TCTTGCAAACCTTT-AAG
1 TCTTGCAAA-CTTTGAAA
*
11016399 TCCTTGCAAACTTTCGAAT
1 T-CTTGCAAACTTT-GAAA
*
11016418 TCTTAAG-AATCTTTGAAA
1 TCTT--GCAAACTTTGAAA
* * *
11016436 TCTTGTGAAA-TTTTAATT
1 TCTTG-CAAACTTTGAA-A
*
11016454 TCTTGCAAAATTTTGAAA
1 TCTTGC-AAACTTTGAAA
11016472 TCTTGCAAACCTTTGAAA
1 TCTTGCAAA-CTTTGAAA
11016490 CCTTATGAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
16 1 0.01
17 13 0.19
18 41 0.59
19 14 0.20
20 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (17 bp):
TCTTGCAAACTTTGAAA
Found at i:11016964 original size:171 final size:171
Alignment explanation
Indices: 11016772--11017119 Score: 644
Period size: 171 Copynumber: 2.0 Consensus size: 171
11016762 CCCGATTGTT
*
11016772 AAATTTGGAATTTTATTATTATTTTTATTTTTCTATTCTATCTTTTGTATTTATCCTTCATTTTC
1 AAATTTGGAATTTTATTATTATTTTTATTTTTCTATTCTATCTTTTGTATTTATCCCTCATTTTC
*
11016837 TTGTTGTATATATTTATTATTTATCTCCTTTTTATCTTTATTTGTTTATTTATTTATTTATTGTT
66 TTGTTGTATATATTTATTATTTATCTCCTTTTTATCTTTATTTGTTTATTTATTTATTTACTG-T
*
11016902 TTTTTTAAACTTATTTTTACTTTTAATTATCT-AAAAAAAGG
130 TTTTTAAAACTTATTTTTACTTTTAATTATCTAAAAAAAAGG
*
11016943 AAATTTGGAATTTTTTTATTATTTTTATTTTTCTATTCTATCTTTTGTATTTATCCCTCATTTTC
1 AAATTTGGAATTTTATTATTATTTTTATTTTTCTATTCTATCTTTTGTATTTATCCCTCATTTTC
11017008 TTGTTGTATATATTTATTATTTATCTCCTTTTTATCTTTATTTGTTTATTTATTTATTTACTGTT
66 TTGTTGTATATATTTATTATTTATCTCCTTTTTATCTTTATTTGTTTATTTATTTATTTACTGTT
11017073 TTTTAAAACTTATTTTTACTTTTAATTATCTAAAAAAAAGG
131 TTTTAAAACTTATTTTTACTTTTAATTATCTAAAAAAAAGG
11017114 AAATTT
1 AAATTT
11017120 TGAAATTAAA
Statistics
Matches: 172, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
170 32 0.19
171 140 0.81
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (171 bp):
AAATTTGGAATTTTATTATTATTTTTATTTTTCTATTCTATCTTTTGTATTTATCCCTCATTTTC
TTGTTGTATATATTTATTATTTATCTCCTTTTTATCTTTATTTGTTTATTTATTTATTTACTGTT
TTTTAAAACTTATTTTTACTTTTAATTATCTAAAAAAAAGG
Found at i:11017621 original size:24 final size:23
Alignment explanation
Indices: 11017594--11017647 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
11017584 GTTATACCTT
* *
11017594 TTTTATTTATTTTTATTTATTGTG-
1 TTTTATTGATTTAT-TTTA-TGTGA
11017618 TTTTAATTGATTTATTTTATGTGA
1 TTTT-ATTGATTTATTTTATGTGA
11017642 TTTTAT
1 TTTTAT
11017648 CATATTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 12 0.46
25 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTATTGATTTATTTTATGTGA
Found at i:11019834 original size:189 final size:189
Alignment explanation
Indices: 11019514--11019892 Score: 758
Period size: 189 Copynumber: 2.0 Consensus size: 189
11019504 GCTACCATAG
11019514 ATACTTAACTGTACAAAATAAACTTAAAATTTTAGCATAAAACAAATATTAAAGAAAACTTAATT
1 ATACTTAACTGTACAAAATAAACTTAAAATTTTAGCATAAAACAAATATTAAAGAAAACTTAATT
11019579 GCATTCTTTGGCTATAGTGCATTTACTATGATGACTATAACAATAATATTAAAAAAGATTGAACA
66 GCATTCTTTGGCTATAGTGCATTTACTATGATGACTATAACAATAATATTAAAAAAGATTGAACA
11019644 ACTTTTTTGATAATTAATATGAAGAAAGCATATGTTAAAAAGTGATACTAAAAAAATTA
131 ACTTTTTTGATAATTAATATGAAGAAAGCATATGTTAAAAAGTGATACTAAAAAAATTA
11019703 ATACTTAACTGTACAAAATAAACTTAAAATTTTAGCATAAAACAAATATTAAAGAAAACTTAATT
1 ATACTTAACTGTACAAAATAAACTTAAAATTTTAGCATAAAACAAATATTAAAGAAAACTTAATT
11019768 GCATTCTTTGGCTATAGTGCATTTACTATGATGACTATAACAATAATATTAAAAAAGATTGAACA
66 GCATTCTTTGGCTATAGTGCATTTACTATGATGACTATAACAATAATATTAAAAAAGATTGAACA
11019833 ACTTTTTTGATAATTAATATGAAGAAAGCATATGTTAAAAAGTGATACTAAAAAAATTA
131 ACTTTTTTGATAATTAATATGAAGAAAGCATATGTTAAAAAGTGATACTAAAAAAATTA
11019892 A
1 A
11019893 ATATAAACAG
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 190 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (189 bp):
ATACTTAACTGTACAAAATAAACTTAAAATTTTAGCATAAAACAAATATTAAAGAAAACTTAATT
GCATTCTTTGGCTATAGTGCATTTACTATGATGACTATAACAATAATATTAAAAAAGATTGAACA
ACTTTTTTGATAATTAATATGAAGAAAGCATATGTTAAAAAGTGATACTAAAAAAATTA
Found at i:11030275 original size:15 final size:15
Alignment explanation
Indices: 11030257--11030294 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11030247 AACTCGAATG
*
11030257 ATTTGAATTTAAATA
1 ATTTGAATTCAAATA
11030272 ATTTGAATTCAAATA
1 ATTTGAATTCAAATA
*
11030287 ATTCGAAT
1 ATTTGAAT
11030295 ACTTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (15 bp):
ATTTGAATTCAAATA
Found at i:11031468 original size:96 final size:96
Alignment explanation
Indices: 11031304--11031509 Score: 367
Period size: 96 Copynumber: 2.1 Consensus size: 96
11031294 TCAATAGATT
* *
11031304 CCAACGATGCTGAAGCAATTGATCAAAGTCAAGGTATTGCTGATTCTGCTGATAATTGCAATCAA
1 CCAACGATGCTGAAGCAATTGATCAAAGTCAAGGTATTACCGATTCTGCTGATAATTGCAATCAA
* *
11031369 ACGTTAGAGTCGCAAAATGATTATGAAATAA
66 ACGTTAGAGTCGCAAAATCATGATGAAATAA
*
11031400 CCAACGATACTGAAGCAATTGATCAAAGTCAAGGTATTACCGATTCTGCTGATAATTGCAATCAA
1 CCAACGATGCTGAAGCAATTGATCAAAGTCAAGGTATTACCGATTCTGCTGATAATTGCAATCAA
11031465 ACGTTAGAGTCGCAAAATCATGATGAAATAA
66 ACGTTAGAGTCGCAAAATCATGATGAAATAA
11031496 CCAACGATGCTGAA
1 CCAACGATGCTGAA
11031510 TTTGTGCCTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (96 bp):
CCAACGATGCTGAAGCAATTGATCAAAGTCAAGGTATTACCGATTCTGCTGATAATTGCAATCAA
ACGTTAGAGTCGCAAAATCATGATGAAATAA
Found at i:11033517 original size:19 final size:20
Alignment explanation
Indices: 11033481--11033518 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11033471 GTCATAAATA
**
11033481 TAAAAATAACAATTAATAAT
1 TAAAAATAACAACCAATAAT
11033501 TAAAAAT-ACAACCAATAA
1 TAAAAATAACAACCAATAA
11033519 AATCATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATAACAACCAATAAT
Found at i:11033787 original size:9 final size:9
Alignment explanation
Indices: 11033764--11033804 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
11033754 TTATTAACAT
11033764 AATTATTAA
1 AATTATTAA
11033773 AA-TATTAA
1 AATTATTAA
11033781 AATTATT--
1 AATTATTAA
*
11033788 TATTATTAA
1 AATTATTAA
11033797 AATTATTA
1 AATTATTA
11033805 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
7 6 0.22
8 8 0.30
9 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:11033996 original size:22 final size:22
Alignment explanation
Indices: 11033962--11034003 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11033952 ATTAAAAATA
11033962 TTTACTATTAAAATACTTATAT
1 TTTACTATTAAAATACTTATAT
*
11033984 TTTA-TATTGAAAATATTTAT
1 TTTACTATT-AAAATACTTAT
11034004 TATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTACTATTAAAATACTTATAT
Found at i:11034440 original size:8 final size:8
Alignment explanation
Indices: 11034388--11034440 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
11034378 AGCTTGATTA
*
11034388 AAAATATG
1 AAAATATT
11034396 AAAATATT
1 AAAATATT
11034404 AAAA-ATT
1 AAAATATT
11034411 --AATA-T
1 AAAATATT
11034416 AGAAATATT
1 A-AAATATT
11034425 AAAA-ATT
1 AAAATATT
11034432 AAAATATT
1 AAAATATT
11034440 A
1 A
11034441 TATGACTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
5 3 0.08
6 1 0.03
7 10 0.26
8 22 0.58
9 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (8 bp):
AAAATATT
Found at i:11034634 original size:16 final size:18
Alignment explanation
Indices: 11034613--11034646 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
11034603 GTAGATAGGT
11034613 TTTTTTAA-AAAA-AAAA
1 TTTTTTAAGAAAAGAAAA
11034629 TTTTTTAAGAAAAGAAAA
1 TTTTTTAAGAAAAGAAAA
11034647 GTCAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TTTTTTAAGAAAAGAAAA
Found at i:11036868 original size:15 final size:15
Alignment explanation
Indices: 11036850--11036883 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11036840 AGTTGTTCAT
* *
11036850 TAAATAGTTGTTTTG
1 TAAATAGTTATTTTA
11036865 TAAATAGTTATTTTA
1 TAAATAGTTATTTTA
11036880 TAAA
1 TAAA
11036884 AAAAGTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TAAATAGTTATTTTA
Found at i:11038593 original size:14 final size:14
Alignment explanation
Indices: 11038574--11038600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11038564 TAATTAAAAA
11038574 ATTAATTAATTAAT
1 ATTAATTAATTAAT
11038588 ATTAATTAATTAA
1 ATTAATTAATTAA
11038601 AAAATAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAATTAATTAAT
Found at i:11039136 original size:21 final size:22
Alignment explanation
Indices: 11039091--11039141 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 22
11039081 ACTAACTCTC
*
11039091 CTTTTTT-CCTTTTCTTTCTAT
1 CTTTTTTGGCTTTTCTTTCTAT
*
11039112 -TTTTTTGGCTTTTC-TTCTTT
1 CTTTTTTGGCTTTTCTTTCTAT
11039132 CTTTTCTTGG
1 CTTTT-TTGG
11039142 TTGTGACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 11 0.44
21 10 0.40
22 4 0.16
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.71
Consensus pattern (22 bp):
CTTTTTTGGCTTTTCTTTCTAT
Found at i:11043796 original size:22 final size:22
Alignment explanation
Indices: 11043766--11043807 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11043756 CCCTTTTTCC
*
11043766 TTTTCTCTTTATTTTTTTGGCT
1 TTTTCTCTTTATTTTCTTGGCT
* *
11043788 TTTTTTCTTTCTTTTCTTGG
1 TTTTCTCTTTATTTTCTTGG
11043808 TTTGTGACAC
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:0.02, C:0.14, G:0.10, T:0.74
Consensus pattern (22 bp):
TTTTCTCTTTATTTTCTTGGCT
Found at i:11052177 original size:15 final size:15
Alignment explanation
Indices: 11052159--11052190 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11052149 AACTCGAATG
*
11052159 ATTTGAATTTAAATA
1 ATTTGAATTCAAATA
11052174 ATTTGAATTCAAATA
1 ATTTGAATTCAAATA
11052189 AT
1 AT
11052191 CCGAATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTGAATTCAAATA
Found at i:11053388 original size:96 final size:97
Alignment explanation
Indices: 11053198--11053406 Score: 350
Period size: 96 Copynumber: 2.1 Consensus size: 97
11053188 TCAATAGATT
*
11053198 CCAACGATGCTGATAGCAATTGATGACAAAGTCAAGTAGTTACTGATTCTGCTGATAATTGCAAT
1 CCAACGATGCTGA-AGCAATTGAT-ACAAAGTCAAGTAGTTACCGATTCTGCTGATAATTGCAAT
*
11053263 CAAACGTTAGAGTCGCAAAATCATTATGAAATAA
64 CAAACGTTAGAGTCGCAAAATCATGATGAAATAA
*
11053297 CCAACGATACTGAAGCAATTGAT-CAAAGTCAAGGTA-TTACCGATTCTGCTGATAATTGCAATC
1 CCAACGATGCTGAAGCAATTGATACAAAGTCAA-GTAGTTACCGATTCTGCTGATAATTGCAATC
11053360 AAACGTTAGAGTCGCAAAATCATGATGAAATAA
65 AAACGTTAGAGTCGCAAAATCATGATGAAATAA
11053393 CCAACGATGCTGAA
1 CCAACGATGCTGAA
11053407 TTTGTGCCTA
Statistics
Matches: 105, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
96 80 0.76
97 3 0.03
98 10 0.10
99 12 0.11
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (97 bp):
CCAACGATGCTGAAGCAATTGATACAAAGTCAAGTAGTTACCGATTCTGCTGATAATTGCAATCA
AACGTTAGAGTCGCAAAATCATGATGAAATAA
Found at i:11055431 original size:19 final size:20
Alignment explanation
Indices: 11055395--11055432 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11055385 TTCATAAATA
**
11055395 TAAAAATAACAATTAATAAT
1 TAAAAATAACAACCAATAAT
11055415 TAAAAAT-ACAACCAATAA
1 TAAAAATAACAACCAATAA
11055433 AATCATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATAACAACCAATAAT
Found at i:11055890 original size:22 final size:22
Alignment explanation
Indices: 11055856--11055897 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11055846 ATTAAAAATA
11055856 TTTACTATTAAAATACTTATAT
1 TTTACTATTAAAATACTTATAT
*
11055878 TTTA-TATTGAAAATATTTAT
1 TTTACTATT-AAAATACTTAT
11055898 TATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTACTATTAAAATACTTATAT
Found at i:11056142 original size:25 final size:27
Alignment explanation
Indices: 11056096--11056147 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
11056086 AAATATTTAT
11056096 TATTTATTATTAAATTATAATAAAATAA
1 TATTTATTATTAAA-TATAATAAAATAA
*
11056124 TATTTATTATTGAA-A-AATAAAATA
1 TATTTATTATTAAATATAATAAAATA
11056148 TTTATGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
28 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TATTTATTATTAAATATAATAAAATAA
Found at i:11056317 original size:21 final size:21
Alignment explanation
Indices: 11056287--11056330 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
11056277 CTTGATTAAA
*
11056287 AATATGAAAATATTAAAAATT
1 AATATAAAAATATTAAAAATT
11056308 AATATAAAAATATTAAAAATT
1 AATATAAAAATATTAAAAATT
11056329 AA
1 AA
11056331 AATATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATATAAAAATATTAAAAATT
Found at i:11056559 original size:19 final size:20
Alignment explanation
Indices: 11056531--11056568 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11056521 AAAAAATTTT
11056531 TTTAAGAAAAGAAAA-GTCAA
1 TTTAAGAAAA-AAAATGTCAA
11056551 TTTAA-AAAAAAAATGTCA
1 TTTAAGAAAAAAAATGTCA
11056569 TTTTCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.24
Consensus pattern (20 bp):
TTTAAGAAAAAAAATGTCAA
Found at i:11061035 original size:21 final size:22
Alignment explanation
Indices: 11060990--11061040 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 22
11060980 ACTAACTCTC
*
11060990 CTTTTTT-CCTTTTCTTTCTAT
1 CTTTTTTGGCTTTTCTTTCTAT
*
11061011 -TTTTTTGGCTTTTC-TTCTTT
1 CTTTTTTGGCTTTTCTTTCTAT
11061031 CTTTTCTTGG
1 CTTTT-TTGG
11061041 TTGTGACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 11 0.44
21 10 0.40
22 4 0.16
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.71
Consensus pattern (22 bp):
CTTTTTTGGCTTTTCTTTCTAT
Found at i:11070342 original size:40 final size:40
Alignment explanation
Indices: 11070297--11070395 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
11070287 GGTTTCAACT
*
11070297 TGCTATTTAGTTTCAGTTTTGAATTTTCTTTGTTAATTGC
1 TGCTATTTAATTTCAGTTTTGAATTTTCTTTGTTAATTGC
*
11070337 TGCTATTCAATTTCAGTTTTGAATTTTCTTTGTTAATTGC
1 TGCTATTTAATTTCAGTTTTGAATTTTCTTTGTTAATTGC
*
11070377 TGC-ATGTT-CTTTCAGTTTT
1 TGCTAT-TTAATTTCAGTTTT
11070396 CATTCTTCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
39 12 0.22
40 42 0.78
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (40 bp):
TGCTATTTAATTTCAGTTTTGAATTTTCTTTGTTAATTGC
Found at i:11070694 original size:10 final size:10
Alignment explanation
Indices: 11070679--11070718 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
11070669 GGAAGTTGAG
11070679 TAGTTAGTTA
1 TAGTTAGTTA
*
11070689 TAGTTAGTTG
1 TAGTTAGTTA
11070699 TAGTTAGTTA
1 TAGTTAGTTA
*
11070709 TAGTGAGTTA
1 TAGTTAGTTA
11070719 ATTGGTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (10 bp):
TAGTTAGTTA
Found at i:11070703 original size:20 final size:20
Alignment explanation
Indices: 11070678--11070717 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
11070668 TGGAAGTTGA
*
11070678 GTAGTTAGTTATAGTTAGTT
1 GTAGTTAGTTATAGTGAGTT
11070698 GTAGTTAGTTATAGTGAGTT
1 GTAGTTAGTTATAGTGAGTT
11070718 AATTGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (20 bp):
GTAGTTAGTTATAGTGAGTT
Found at i:11074003 original size:160 final size:160
Alignment explanation
Indices: 11073734--11074049 Score: 578
Period size: 160 Copynumber: 2.0 Consensus size: 160
11073724 GCTTTCAGAA
*
11073734 AAGATTGAATATTGTGTGAAATATAAGATTATGCTTAGGTTTAGTGAATTCTTAAGTATGAGTTT
1 AAGATTGAATATTGTGTGAAATATAAGATGATGCTTAGGTTTAGTGAATTCTTAAGTATGAGTTT
* * *
11073799 TCATTTGTGAATTGATACTTTGATCATTGAATTGCATCTTTTATCTGGTGATTGATTATGTGAGC
66 TCATTTGTGAATTGATACTTTGATCATTAAAGTGCATCTTTTATCTAGTGATTGATTATGTGAGC
11073864 ATGAGATTTTTTTTTCATTGCCCTTTAAAG
131 ATGAGATTTTTTTTTCATTGCCCTTTAAAG
*
11073894 AAGATTGAATATTGTGTGAAATATAAGATGATGCTTAGGTTTAGTGAATTCTTGAGTATGAGTTT
1 AAGATTGAATATTGTGTGAAATATAAGATGATGCTTAGGTTTAGTGAATTCTTAAGTATGAGTTT
*
11073959 TCATTTGTGAATTGATACTTTGATCATTAAAGTGCATTTTTTATCTAGTGATTGATTATGTGAGC
66 TCATTTGTGAATTGATACTTTGATCATTAAAGTGCATCTTTTATCTAGTGATTGATTATGTGAGC
11074024 ATGAGATTTTTTTTTCATTGCCCTTT
131 ATGAGATTTTTTTTTCATTGCCCTTT
11074050 GAAGTTGTGT
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 150 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (160 bp):
AAGATTGAATATTGTGTGAAATATAAGATGATGCTTAGGTTTAGTGAATTCTTAAGTATGAGTTT
TCATTTGTGAATTGATACTTTGATCATTAAAGTGCATCTTTTATCTAGTGATTGATTATGTGAGC
ATGAGATTTTTTTTTCATTGCCCTTTAAAG
Found at i:11075137 original size:184 final size:184
Alignment explanation
Indices: 11074828--11075187 Score: 605
Period size: 184 Copynumber: 2.0 Consensus size: 184
11074818 AGGATGTGGG
*
11074828 GAGGTATTGCTTGCTTATGGAACCATAGTTAGGAATGAGCTTAGCCTAGGTTGATTCTTGTATAT
1 GAGGTATTGCTTGCTTATGGAACCATAGTTAGGAATGAGCTTAGCCTAAGTTGATTCTTGTATAT
11074893 TAGCATATGTTCATGATTTTACTTTAGTTATATTCATTGATCAATCCATGAGGCATTCATGTTGA
66 TAGCATATGTTCATGATTTTACTTTAGTTATATTCATTGATCAATCCATGAGGCATTCATGTTGA
** * *
11074958 ATCAAACATTGAAATTATATGATGATTCTTGCTCAATTTTGTTTTGATATGTGA
131 ATCAAACATTGAAAGCATATGATGATTCTCGCACAATTTTGTTTTGATATGTGA
* * * *
11075012 GAGGTATTGCTT-TTTCGTGGAACCATTGTTAGGAATGCGCTTAGCCTAAGTTGATTCTTGTATA
1 GAGGTATTGCTTGCTT-ATGGAACCATAGTTAGGAATGAGCTTAGCCTAAGTTGATTCTTGTATA
11075076 TTAGCATATGTTCATGATTTTACTTTAGTTATATTCATTGATCAATCCATGAGGCATTCATGTTG
65 TTAGCATATGTTCATGATTTTACTTTAGTTATATTCATTGATCAATCCATGAGGCATTCATGTTG
* *
11075141 AATGAAACTTTGAAAGCATATGATGATTCTCGCACAATTTTGTTTTG
130 AATCAAACATTGAAAGCATATGATGATTCTCGCACAATTTTGTTTTG
11075188 CTTGAGGACA
Statistics
Matches: 164, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 2 0.01
184 162 0.99
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (184 bp):
GAGGTATTGCTTGCTTATGGAACCATAGTTAGGAATGAGCTTAGCCTAAGTTGATTCTTGTATAT
TAGCATATGTTCATGATTTTACTTTAGTTATATTCATTGATCAATCCATGAGGCATTCATGTTGA
ATCAAACATTGAAAGCATATGATGATTCTCGCACAATTTTGTTTTGATATGTGA
Found at i:11081189 original size:21 final size:21
Alignment explanation
Indices: 11081164--11081203 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11081154 GTTTGAAATG
**
11081164 GAAGAAGATTTTAAAGAATAT
1 GAAGAAGATCCTAAAGAATAT
*
11081185 GAAGAGGATCCTAAAGAAT
1 GAAGAAGATCCTAAAGAAT
11081204 TCATTTAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAGAAGATCCTAAAGAATAT
Found at i:11082972 original size:7 final size:7
Alignment explanation
Indices: 11082962--11083114 Score: 78
Period size: 7 Copynumber: 22.0 Consensus size: 7
11082952 GGTTTAGTTC
11082962 AGGTTTA
1 AGGTTTA
*
11082969 AGGTTAA
1 AGGTTTA
11082976 AGGTTTA
1 AGGTTTA
**
11082983 ATATTTA
1 AGGTTTA
*
11082990 ATGTTTA
1 AGGTTTA
*
11082997 TGGTTTA
1 AGGTTTA
*
11083004 ACGTTTA
1 AGGTTTA
* *
11083011 GGGCTT-
1 AGGTTTA
11083017 A-GTGTTA
1 AGGT-TTA
*
11083024 GGGTTT-
1 AGGTTTA
11083030 AGGTTTTA
1 AGG-TTTA
*
11083038 AGCTTTA
1 AGGTTTA
11083045 AGGTTTA
1 AGGTTTA
*
11083052 GGGTTTA
1 AGGTTTA
*
11083059 GGGTTTA
1 AGGTTTA
*
11083066 AGGTCTA
1 AGGTTTA
*
11083073 GGGTTTA
1 AGGTTTA
* *
11083080 GGGTCTA
1 AGGTTTA
* *
11083087 ATGTCTA
1 AGGTTTA
*
11083094 GGGTTTA
1 AGGTTTA
* *
11083101 GGGTCTA
1 AGGTTTA
11083108 AGGTTTA
1 AGGTTTA
11083115 GGATTTAGGA
Statistics
Matches: 109, Mismatches: 32, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
7 100 0.92
8 4 0.04
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (7 bp):
AGGTTTA
Found at i:11083122 original size:21 final size:21
Alignment explanation
Indices: 11082992--11083123 Score: 122
Period size: 21 Copynumber: 6.3 Consensus size: 21
11082982 AATATTTAAT
* * *
11082992 GTTTATGGTTTAACGTTTAGG
1 GTTTAGGGTCTAAGGTTTAGG
* * *
11083013 GCTTAGTGT-TAGGGTTTAGG
1 GTTTAGGGTCTAAGGTTTAGG
* * * *
11083033 TTTTAAGCTTTAAGGTTTAGG
1 GTTTAGGGTCTAAGGTTTAGG
* *
11083054 GTTTAGGGTTTAAGGTCTAGG
1 GTTTAGGGTCTAAGGTTTAGG
* *
11083075 GTTTAGGGTCTAATGTCTAGG
1 GTTTAGGGTCTAAGGTTTAGG
11083096 GTTTAGGGTCTAAGGTTTAGG
1 GTTTAGGGTCTAAGGTTTAGG
*
11083117 ATTTAGG
1 GTTTAGG
11083124 ATAGCGGGTT
Statistics
Matches: 90, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 13 0.14
21 77 0.86
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (21 bp):
GTTTAGGGTCTAAGGTTTAGG
Found at i:11083141 original size:7 final size:7
Alignment explanation
Indices: 11082992--11083123 Score: 95
Period size: 7 Copynumber: 19.0 Consensus size: 7
11082982 AATATTTAAT
*
11082992 GTTTATG
1 GTTTAGG
**
11082999 GTTTAAC
1 GTTTAGG
11083006 GTTTAGG
1 GTTTAGG
* *
11083013 GCTTAGT
1 GTTTAGG
11083020 G-TTAGG
1 GTTTAGG
11083026 GTTTAGG
1 GTTTAGG
* *
11083033 TTTTAAG
1 GTTTAGG
* *
11083040 CTTTAAG
1 GTTTAGG
11083047 GTTTAGG
1 GTTTAGG
11083054 GTTTAGG
1 GTTTAGG
*
11083061 GTTTAAG
1 GTTTAGG
*
11083068 GTCTAGG
1 GTTTAGG
11083075 GTTTAGG
1 GTTTAGG
* **
11083082 GTCTAAT
1 GTTTAGG
*
11083089 GTCTAGG
1 GTTTAGG
11083096 GTTTAGG
1 GTTTAGG
* *
11083103 GTCTAAG
1 GTTTAGG
11083110 GTTTAGG
1 GTTTAGG
*
11083117 ATTTAGG
1 GTTTAGG
11083124 ATAGCGGGTT
Statistics
Matches: 97, Mismatches: 27, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
6 5 0.05
7 92 0.95
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:11085226 original size:3 final size:3
Alignment explanation
Indices: 11085218--11085244 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11085208 CTATACTATC
11085218 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
11085245 TAGTAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11085671 original size:66 final size:66
Alignment explanation
Indices: 11085543--11085671 Score: 186
Period size: 66 Copynumber: 2.0 Consensus size: 66
11085533 GGGATAAAAT
* ** * *
11085543 CGTGAGTCAAAAAGATAAAGTGACCAAGATCAAGTTGAGGTCAAAAATGGCTGACTAGGATGGGA
1 CGTGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGGGA
11085608 C
66 C
* * *
11085609 CGTGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGTTGACCAAGATGG
1 CGTGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGG
11085672 AAACATTAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (66 bp):
CGTGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGGGA
C
Found at i:11085683 original size:66 final size:66
Alignment explanation
Indices: 11085545--11085687 Score: 178
Period size: 66 Copynumber: 2.2 Consensus size: 66
11085535 GATAAAATCG
* ** * * * *
11085545 TGAGTCAAAAAGATAAAGTGACCAAGATCAAGTTGAGGTCAAAAATGGCTGACTAGGATGGGACC
1 TGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGGAAAC
*
11085610 G
66 A
* * *
11085611 TGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGTTGACCAAGATGGAAAC
1 TGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGGAAAC
11085676 A
66 A
*
11085677 TTAGTCAAAAA
1 TGAGTCAAAAA
11085688 ATGATTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.18
Consensus pattern (66 bp):
TGAGTCAAAAAGATAAAGTGACCAAAATCAAGTCAAGGTCAAAAATGGCTGACCAAGATGGAAAC
A
Found at i:11086064 original size:120 final size:122
Alignment explanation
Indices: 11085733--11086073 Score: 280
Period size: 122 Copynumber: 2.8 Consensus size: 122
11085723 TGAAACCGCG
* * * * * ** * * * * * *
11085733 AGTCGAAAAAATATAAAGCAACTAAGACCAAGTCAAGGTCAAAGATAACTAATTGAGATGAAACC
1 AGTCAAAAAAATATAAAACCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACT
* * * *** *
11085798 ACGAGTCA-AGAAATGATCTGGACTGAGCCGAGATTGAATGATCGAGTTGAAATCGTC
66 ACAAGTCAGA-AAATGATCTGGACTAAGCCGAGATCGAATGATCGAGACAAAATCATC
** *
11085855 AGTCAAAAAAATATAAAATGACCAAGATCAAGTTGAGGTCGAATATGATTGATCGAGATGAAACT
1 AGTCAAAAAAATATAAAACCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACT
* * * *
11085920 ACAAGTTAGGAAATGATCTTGACTAAGCCGAGATCGAATGA-CGGAGACAAAATCATG
66 ACAAGTCAGAAAATGATCTGGACTAAGCCGAGATCGAATGATC-GAGACAAAATCATC
* * * * * *
11085977 AGTC-AAAAAA-ATAAAGCCACCAGGATCGAGTTGAGGTTGAATATGACTGA-CTGGGATGGAAC
1 AGTCAAAAAAATATAAAACCACCAAGATCAAGTTGAGGTCGAATATGACTGATC-GAGATGAAAC
* * *
11086039 TGCAAGTCCA-AAAATGATCTGGACTATGCTGAGAT
65 TACAAGT-CAGAAAATGATCTGGACTAAGCCGAGAT
11086074 AAAAAATGAG
Statistics
Matches: 174, Mismatches: 41, Indels: 10
0.77 0.18 0.04
Matches are distributed among these distances:
119 1 0.01
120 68 0.39
121 8 0.05
122 97 0.56
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (122 bp):
AGTCAAAAAAATATAAAACCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACT
ACAAGTCAGAAAATGATCTGGACTAAGCCGAGATCGAATGATCGAGACAAAATCATC
Found at i:11087399 original size:66 final size:66
Alignment explanation
Indices: 11087320--11087464 Score: 191
Period size: 66 Copynumber: 2.2 Consensus size: 66
11087310 GGGATAAAAT
* * ** * * * *
11087320 CGTGAGTCGAAAAGATAAAGTGACCAAGATCGAGTTGAGGTCGAAGATGGCTGACTAGGATGGGA
1 CGTGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGCTGACCAAGATGGAA
*
11087385 C
66 A
*
11087386 CGTGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGTTGACCAAGATGGAA
1 CGTGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGCTGACCAAGATGGAA
11087451 A
66 A
*
11087452 CGTTAGTCAAAAA
1 CGTGAGTCAAAAA
11087465 ATGATTTAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (66 bp):
CGTGAGTCAAAAAGATAAAGTGACCAAAATCGAGTCAAGGTCAAAGATGGCTGACCAAGATGGAA
A
Found at i:11087834 original size:120 final size:122
Alignment explanation
Indices: 11087456--11087850 Score: 327
Period size: 122 Copynumber: 3.3 Consensus size: 122
11087446 TGGAAACGTT
* * * * * * ** * * *
11087456 AGTCAAAAAATGATTTAGACTGAGCCAAGATCGAATGA-CTGCGATGAAACCACGAGTCGAAAAA
1 AGTCAGAAAATGATCTGGACTAAGCCGAGATCGAATGATC-GAGACAAAATCATGAGTCAAAAAA
* * * ** * * * * * *
11087520 ATATAAAGCAACTAAGACCAAGTCAAGGTCAAAGATAACTGATTGAGATGAAACCACG
65 ATATAAAGCCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
* * *** *
11087578 AGTCA-AGAAATGATCTGGACTGAGCCGAGATTGAATGATCGAGTTGAAATCGTGAGTCAAAAAA
1 AGTCAGA-AAATGATCTGGACTAAGCCGAGATCGAATGATCGAGACAAAATCATGAGTCAAAAAA
**
11087642 ATATAAAGTGACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
65 ATATAAAGCCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
* * *
11087700 AGTTAGGAAATGATCTCGACTAAGCCGAGATCGAATGA-CGGAGACAAAATCATGAGTC-AAAAA
1 AGTCAGAAAATGATCTGGACTAAGCCGAGATCGAATGATC-GAGACAAAATCATGAGTCAAAAAA
* * * * * *
11087763 A-ATAAAGCCACCAGGATCGAGTTGAGGTTGAATATGACTGA-CTGGGATGGAACTGCA
65 ATATAAAGCCACCAAGATCAAGTTGAGGTCGAATATGACTGATC-GAGATGAAACTACA
* *
11087820 AGTCCA-AAAATGATCTGGACTATGCTGAGAT
1 AGT-CAGAAAATGATCTGGACTAAGCCGAGAT
11087851 AAAAGATGAG
Statistics
Matches: 223, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
119 1 0.00
120 70 0.31
121 9 0.04
122 142 0.64
123 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (122 bp):
AGTCAGAAAATGATCTGGACTAAGCCGAGATCGAATGATCGAGACAAAATCATGAGTCAAAAAAA
TATAAAGCCACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
Found at i:11088770 original size:3 final size:3
Alignment explanation
Indices: 11088762--11088803 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
11088752 CTATACTATC
11088762 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11088804 TAGTAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11089215 original size:66 final size:66
Alignment explanation
Indices: 11089102--11089246 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 66
11089092 GGGATAAAAT
* ** * * * * *
11089102 CGTGAGT-AGAAAAGATAAAGTGACCAAGATTGAGTTGAGGTCGAAGATGGCTGACTAGGATGGG
1 CGTGAGTCA-AAAAGATAAAGTGACCAAGATCGAGTCAAAGTCAAAGATGGCTGACCAAGATGGA
*
11089166 AC
65 AA
*
11089168 CGTGAGTCAAAAAGATAAAGTGACC-AGAATCGAGTCAAAGTCAAAGATGGTTGACCAAGATGGA
1 CGTGAGTCAAAAAGATAAAGTGACCAAG-ATCGAGTCAAAGTCAAAGATGGCTGACCAAGATGGA
11089232 AA
65 AA
*
11089234 CGTTAGTCAAAAA
1 CGTGAGTCAAAAA
11089247 ATGATTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 63 0.95
67 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (66 bp):
CGTGAGTCAAAAAGATAAAGTGACCAAGATCGAGTCAAAGTCAAAGATGGCTGACCAAGATGGAA
A
Found at i:11089538 original size:122 final size:120
Alignment explanation
Indices: 11089238--11089632 Score: 380
Period size: 122 Copynumber: 3.3 Consensus size: 120
11089228 TGGAAACGTT
* * * * * *
11089238 AGTCAAAAAATGATTTAGACTGAGCCAAGATCGAATGACTGCGATGAAACCGCGAGTCGAAAAAA
1 AGTCAAAAAATGATCTGGACTAAGCCGAGATCGAATGAC-GAGATGAAACCGTGAGTC-AAAAAA
* * ** * * * * * * *
11089303 TATAAAGCAACTAAGACCAAGTCAAGGTCAAAGATAATTGATTGAGATGAAACCACG
64 TATAAAGCAACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
* * * *
11089360 AGTCAAAAAATGACCTGGACTAAGCCGAGATTGAATGATCGAGTTGAAATCGTGAGTCAAAAAAA
1 AGTCAAAAAATGATCTGGACTAAGCCGAGATCGAATGA-CGAGATGAAACCGTGAGTC-AAAAAA
**
11089425 TATAAAGTGACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
64 TATAAAGCAACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
* ** ** *
11089482 AGTTAGGAAATGATCTGGACTAAGCCGAGATCGAATGACGGAGACAAAACCATGAGTCAAAAAA-
1 AGTCAAAAAATGATCTGGACTAAGCCGAGATCGAATGAC-GAGATGAAACCGTGAGTCAAAAAAT
* * * * * * *
11089546 ATAAAGCCACCAGGATCGAGTTGAGGTTGAATATGACTGA-CTGGGATGGAACTGCA
65 ATAAAGCAACCAAGATCAAGTTGAGGTCGAATATGACTGATC-GAGATGAAACTACA
* *
11089602 AGTCAAAAAATGATCTGGACTATGCTGAGAT
1 AGTCAAAAAATGATCTGGACTAAGCCGAGAT
11089633 AAAAAGTGAG
Statistics
Matches: 223, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
119 1 0.00
120 72 0.32
121 7 0.03
122 142 0.64
123 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (120 bp):
AGTCAAAAAATGATCTGGACTAAGCCGAGATCGAATGACGAGATGAAACCGTGAGTCAAAAAATA
TAAAGCAACCAAGATCAAGTTGAGGTCGAATATGACTGATCGAGATGAAACTACA
Found at i:11090412 original size:18 final size:18
Alignment explanation
Indices: 11090391--11090439 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
11090381 AAGTCTTTTT
11090391 TTTTCCTCTTT-TTTCTCA
1 TTTTCCT-TTTGTTTCTCA
*
11090409 TTTTTCTTTTGTTTCTCA
1 TTTTCCTTTTGTTTCTCA
*
11090427 TTTT-TTTTTGTTT
1 TTTTCCTTTTGTTT
11090440 TTTTTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCCTTTTGTTTCTCA
Found at i:11090435 original size:17 final size:18
Alignment explanation
Indices: 11090402--11090439 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
11090392 TTTCCTCTTT
11090402 TTTCTCATTTTTCTTTTG
1 TTTCTCATTTTTCTTTTG
11090420 TTTCTCATTTTT-TTTTG
1 TTTCTCATTTTTCTTTTG
11090437 TTT
1 TTT
11090440 TTTTTTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTCTCATTTTTCTTTTG
Found at i:11094669 original size:18 final size:17
Alignment explanation
Indices: 11094627--11094672 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
11094617 AGAAGAGATT
11094627 TAAAAAAACAA-T-AAAA
1 TAAAAAAA-AACTGAAAA
*
11094643 TTAAAAAAAACTGAAAA
1 TAAAAAAAAACTGAAAA
11094660 TAAAATAAAAACT
1 TAAAA-AAAAACT
11094673 TAAGATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 8 0.32
17 8 0.32
18 7 0.28
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (17 bp):
TAAAAAAAAACTGAAAA
Found at i:11095568 original size:3 final size:3
Alignment explanation
Indices: 11095554--11095595 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
11095544 GAGAAAAATA
*
11095554 AAT AAC AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11095596 TAGTGAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11095583 original size:17 final size:17
Alignment explanation
Indices: 11095561--11095597 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
11095551 ATAAATAACA
11095561 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
11095578 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
11095595 ATA
1 ATA
11095598 GTGAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:11095586 original size:23 final size:23
Alignment explanation
Indices: 11095550--11095621 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
11095540 AGGAGAGAAA
*
11095550 AATAA-ATAACAATAATAATAAT
1 AATAATATAATAATAATAATAAT
11095572 AATAATATAATAATAATAATAAT
1 AATAATATAATAATAATAATAAT
11095595 ATAGTGAAGTATAAT-ATAAT-ATAAT
1 A-A-T-AA-TATAATAATAATAATAAT
11095620 AA
1 AA
11095622 AATCGACTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 5 0.11
23 17 0.39
24 2 0.05
25 7 0.16
26 7 0.16
27 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (23 bp):
AATAATATAATAATAATAATAAT
Found at i:11105161 original size:24 final size:25
Alignment explanation
Indices: 11105128--11105192 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
11105118 AGGAACACCT
*
11105128 TAAATAATCCTTTTAT-AAAAAAAA
1 TAAATGATCCTTTTATAAAAAAAAA
**
11105152 TAAATGATCCATAATATAAAAAAAAA
1 TAAATGATCC-TTTTATAAAAAAAAA
11105178 TAAAATGAT-CTTTTA
1 T-AAATGATCCTTTTA
11105193 AGGCATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 9 0.27
25 7 0.21
26 10 0.30
27 7 0.21
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (25 bp):
TAAATGATCCTTTTATAAAAAAAAA
Found at i:11105501 original size:99 final size:103
Alignment explanation
Indices: 11105264--11105501 Score: 263
Period size: 99 Copynumber: 2.3 Consensus size: 103
11105254 TAATTTATTT
* * * *
11105264 ATAAAAGGATTATTTAAGGCATTTTCTGTACAG-AAACACCTTAAATAATCCTTTTATAAATAAA
1 ATAAAAGGATTATTTAAGGCTTTTTTTGTAAAGAAAACACCTTAAATAATCATTTTAT-AATAAA
* * ** *
11105328 TTAAAGCATCATTTTAAATTTTTTTCATAATATAAAAAA
65 TTAAAGCATAATTTTAAATATGATCCATAATATAAAAAA
* * *
11105367 ATTAAAGGATCATTTAAGG-TGTTTTTTGTATAGAAAACACCTTAAATAAT-ATTTT-T-ATAAA
1 ATAAAAGGATTATTTAAGGCT-TTTTTTGTAAAGAAAACACCTTAAATAATCATTTTATAATAAA
* * *
11105428 TTAAAGGATAATTTT-TATATGATCCATAATGTAAAAAA
65 TTAAAGCATAATTTTAAATATGATCCATAATATAAAAAA
* *
11105466 ATAAAATGATTATTTAAGGCTTTTTTTATAAAGAAA
1 ATAAAAGGATTATTTAAGGCTTTTTTTGTAAAGAAA
11105502 TGCCTTAAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
99 46 0.41
100 19 0.17
102 1 0.01
103 31 0.27
104 16 0.14
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (103 bp):
ATAAAAGGATTATTTAAGGCTTTTTTTGTAAAGAAAACACCTTAAATAATCATTTTATAATAAAT
TAAAGCATAATTTTAAATATGATCCATAATATAAAAAA
Found at i:11105679 original size:164 final size:162
Alignment explanation
Indices: 11105370--11105686 Score: 390
Period size: 165 Copynumber: 1.9 Consensus size: 162
11105360 TAAAAAAATT
* ** *
11105370 AAAGGATCATTTAAGGTGTTTTTTGTATAGAAAACACCTTAAATAATATTTTTATAAATTAAAGG
1 AAAGGATCATTTAAAGTCATTTTTGTATAGAAAACACCTTAAATAATATTTTTATAAATAAAAGG
* * * * *
11105435 ATAATTTTTATATGATCCATAATGTAAAAAAATAAAATGATTATTTAAGGCTTTTTTTATAAAGA
66 ATAATTTTTATATGATCCATAATATAAAAAAACAAAAGGATCATTTAAGGCTTTTTGTATAAAGA
11105500 AATGCCTTAAATGATCCTTTTATTTTTTTATA
131 AATGCCTTAAATGATCCTTTTATTTTTTTATA
* *
11105532 AAAGGATCATTTAAAG-CATTTTTGTATAG-AAACACCTTAAATTATCTTTTTATAACAAAATAA
1 AAAGGATCATTTAAAGTCATTTTTGTATAGAAAACACCTTAAATAATATTTTTAT----AAATAA
* * ** * *
11105595 AAGGATCATTTTTTATTTTTTTCATGATATAAAAAAACAAAAGGATCATTTAAGGCATTTTTGTA
62 AAGGAT-AATTTTTATATGATCCATAATATAAAAAAACAAAAGGATCATTTAAGGC-TTTTTGTA
*
11105660 -CAA-AAATGCCTTAAATGATCCTTTTAT
125 TAAAGAAATGCCTTAAATGATCCTTTTAT
11105687 AAAATAATAA
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
160 22 0.17
161 11 0.08
162 15 0.11
164 35 0.27
165 41 0.31
166 7 0.05
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (162 bp):
AAAGGATCATTTAAAGTCATTTTTGTATAGAAAACACCTTAAATAATATTTTTATAAATAAAAGG
ATAATTTTTATATGATCCATAATATAAAAAAACAAAAGGATCATTTAAGGCTTTTTGTATAAAGA
AATGCCTTAAATGATCCTTTTATTTTTTTATA
Found at i:11111351 original size:7 final size:7
Alignment explanation
Indices: 11111339--11111364 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11111329 TGGGTTAGGT
11111339 AAAAATA
1 AAAAATA
11111346 AAAAATA
1 AAAAATA
11111353 AAAAATA
1 AAAAATA
11111360 AAAAA
1 AAAAA
11111365 GAGATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:11117363 original size:17 final size:18
Alignment explanation
Indices: 11117341--11117379 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
11117331 AATTAGAACT
* *
11117341 AATATATTTGTATTTA-A
1 AATATATATATATTTATA
11117358 AATATATATATATTTATA
1 AATATATATATATTTATA
11117376 AATA
1 AATA
11117380 AATGTGCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATATATATATATTTATA
Found at i:11121462 original size:29 final size:28
Alignment explanation
Indices: 11121430--11121489 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
11121420 AATATAGTAT
11121430 TTTTATTAA-ATTAAGATATTAAAT-AATAA
1 TTTTATTAACA-TAA-A-ATTAAATAAATAA
11121459 TTTTATTAACATAAAATTAAATAAATAA
1 TTTTATTAACATAAAATTAAATAAATAA
11121487 TTT
1 TTT
11121490 AAAATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 7 0.24
28 9 0.31
29 12 0.41
30 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTTATTAACATAAAATTAAATAAATAA
Found at i:11122623 original size:15 final size:16
Alignment explanation
Indices: 11122596--11122627 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11122586 AAAACAAAGA
11122596 AAATAATATATAAAAT
1 AAATAATATATAAAAT
11122612 AAATAA-ATATAAAAT
1 AAATAATATATAAAAT
11122627 A
1 A
11122628 CAAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATATATAAAAT
Found at i:11123507 original size:18 final size:19
Alignment explanation
Indices: 11123484--11123542 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
11123474 CAAAGGTTTG
11123484 CAAAAGATTTAAA-ATTCA
1 CAAAAGATTTAAAGATTCA
*
11123502 CAAAAGATTCAAAGATTCA
1 CAAAAGATTTAAAGATTCA
* *
11123521 CAAGA-ATTTAAAGATTTA
1 CAAAAGATTTAAAGATTCA
11123539 CAAA
1 CAAA
11123543 TTTCAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (19 bp):
CAAAAGATTTAAAGATTCA
Found at i:11123571 original size:37 final size:37
Alignment explanation
Indices: 11123525--11123617 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
11123515 GATTCACAAG
* * *
11123525 AATTT-AAAGATTTACAAATT-TCAAATATTTGCAACT
1 AATTTCAAAGATTCACAAATTATAAAAT-TTTGCAAAT
*
11123561 AATTTCAAAGATTCGC-AATTATAAAATTTTGCAAAT
1 AATTTCAAAGATTCACAAATTATAAAATTTTGCAAAT
*
11123597 ATTTTGCAAAGATTCACAAAT
1 AATTT-CAAAGATTCACAAAT
11123618 GAAATTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 21 0.45
37 23 0.49
38 3 0.06
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (37 bp):
AATTTCAAAGATTCACAAATTATAAAATTTTGCAAAT
Found at i:11123578 original size:20 final size:20
Alignment explanation
Indices: 11123541--11123578 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11123531 AAGATTTACA
* *
11123541 AATTTCAAATATTTGCAACT
1 AATTTCAAAGATTCGCAACT
11123561 AATTTCAAAGATTCGCAA
1 AATTTCAAAGATTCGCAA
11123579 TTATAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (20 bp):
AATTTCAAAGATTCGCAACT
Found at i:11123720 original size:23 final size:23
Alignment explanation
Indices: 11123647--11123738 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
11123637 ACTGAGATTC
*
11123647 AAAGATTCACATTCAAAATAATTTT
1 AAAGATTCACATTCAAAA-AA-TTA
** * * *
11123672 TGAGATTCACA-TCCAAAATTTC
1 AAAGATTCACATTCAAAAAATTA
11123694 AAAGATTCACATTCAAAAAATTA
1 AAAGATTCACATTCAAAAAATTA
* *
11123717 AAAGATTCTCATTAAAAAAATT
1 AAAGATTCACATTCAAAAAATT
11123739 TTAGAGATTA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 11 0.20
23 29 0.54
24 5 0.09
25 9 0.17
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (23 bp):
AAAGATTCACATTCAAAAAATTA
Found at i:11123746 original size:24 final size:24
Alignment explanation
Indices: 11123647--11123758 Score: 77
Period size: 23 Copynumber: 4.7 Consensus size: 24
11123637 ACTGAGATTC
* *
11123647 AAAGATTCACATTCAAAATAATTTT
1 AAAGATTCACATT-AAAAAAATTTA
** ** *
11123672 TGAGATTCACA-T-CCAAAATTTC
1 AAAGATTCACATTAAAAAAATTTA
*
11123694 AAAGATTCACATTCAAAAAA-TTA
1 AAAGATTCACATTAAAAAAATTTA
* *
11123717 AAAGATTCTCATTAAAAAAATTTT
1 AAAGATTCACATTAAAAAAATTTA
* *
11123741 AGAGATTAACATATAAAA
1 AAAGATTCACAT-TAAAA
11123759 TTCTAAGATT
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
22 15 0.23
23 21 0.32
24 16 0.24
25 14 0.21
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAGATTCACATTAAAAAAATTTA
Found at i:11123884 original size:21 final size:22
Alignment explanation
Indices: 11123834--11123904 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
11123824 ATTCAAGTAT
*
11123834 AAATTTCAAAGATTCACATTCGACA
1 AAATTTCAAGGATTCACATT---CA
* *
11123859 AAATTT-AGGGATTCACATTTA
1 AAATTTCAAGGATTCACATTCA
*
11123880 AAATTTCAAGGATTCTCATTCA
1 AAATTTCAAGGATTCACATTCA
11123902 AAA
1 AAA
11123905 AATTTTGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 7 0.18
22 15 0.38
24 11 0.28
25 6 0.15
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (22 bp):
AAATTTCAAGGATTCACATTCA
Found at i:11123887 original size:46 final size:46
Alignment explanation
Indices: 11123834--11123945 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 46
11123824 ATTCAAGTAT
* * * **
11123834 AAATTTCAAAGATTCACATTCGACAAAATTTAGG-GATTCACATTTA
1 AAATTTCAAAGATTCTCATTC-AAAAAATTTAGGAGAATCACATCCA
* *
11123880 AAATTTCAAGGATTCTCATTCAAAAAATTTTGGAGAATCACATCCA
1 AAATTTCAAAGATTCTCATTCAAAAAATTTAGGAGAATCACATCCA
* *
11123926 AGATTTTAAAGATTCTCATT
1 AAATTTCAAAGATTCTCATT
11123946 TGAAAGGTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 10 0.18
46 45 0.82
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (46 bp):
AAATTTCAAAGATTCTCATTCAAAAAATTTAGGAGAATCACATCCA
Found at i:11125129 original size:18 final size:18
Alignment explanation
Indices: 11125079--11125130 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
11125069 TTTCCTCTTT
* **
11125079 TTTTTCTTTTTTTTTTCA
1 TTTTTCTTTCTTTTCACA
*
11125097 TTTTTCATATC-TTTCACA
1 TTTTTC-TTTCTTTTCACA
11125115 TTTTTCTTTCTTTTCA
1 TTTTTCTTTCTTTTCA
11125131 TTTCATTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 22 0.81
19 2 0.07
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTCTTTTCACA
Found at i:11131722 original size:29 final size:29
Alignment explanation
Indices: 11131690--11131780 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
11131680 GGATTTTGGA
*
11131690 TTTTAGGGTTCGAGGTTTTAGTTTTAGGG
1 TTTTAGGGTTTGAGGTTTTAGTTTTAGGG
* * * *
11131719 TTTTGAGGGTTTGGGGTTTCAATTTCAGGG
1 TTTT-AGGGTTTGAGGTTTTAGTTTTAGGG
* *
11131749 -TTTAGAGGTTTTAGGATTTAGTTTTAGGG
1 TTTTAG-GGTTTGAGGTTTTAGTTTTAGGG
11131778 TTT
1 TTT
11131781 GGAGGGCTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.04
29 24 0.50
30 22 0.46
ACGTcount: A:0.15, C:0.03, G:0.33, T:0.48
Consensus pattern (29 bp):
TTTTAGGGTTTGAGGTTTTAGTTTTAGGG
Found at i:11131726 original size:22 final size:23
Alignment explanation
Indices: 11131661--11131726 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
11131651 GATTTTAAAG
*
11131661 TTTTTGATTTTAGGGTTT-AGGA
1 TTTTAGATTTTAGGGTTTGAGGA
* *
11131683 TTTTGGATTTTAGGGTTCGAGG-
1 TTTTAGATTTTAGGGTTTGAGGA
11131705 TTTTAG-TTTTAGGGTTTTGAGG
1 TTTTAGATTTTAGGG-TTTGAGG
11131727 GTTTGGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.21
22 27 0.71
23 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.32, T:0.52
Consensus pattern (23 bp):
TTTTAGATTTTAGGGTTTGAGGA
Found at i:11131728 original size:30 final size:30
Alignment explanation
Indices: 11131690--11131786 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
11131680 GGATTTTGGA
*
11131690 TTTT-AGGGTTCGAGGTTTTAGTTTTAGGG
1 TTTTGAGGGTTTGAGGTTTTAGTTTTAGGG
* * * *
11131719 TTTTGAGGGTTTGGGGTTTCAATTTCAGGG
1 TTTTGAGGGTTTGAGGTTTTAGTTTTAGGG
* * *
11131749 TTTAGA-GGTTTTAGGATTTAGTTTTAGGG
1 TTTTGAGGGTTTGAGGTTTTAGTTTTAGGG
*
11131778 TTTGGAGGG
1 TTTTGAGGG
11131787 CTTAGGGTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 26 0.49
30 27 0.51
ACGTcount: A:0.15, C:0.03, G:0.36, T:0.45
Consensus pattern (30 bp):
TTTTGAGGGTTTGAGGTTTTAGTTTTAGGG
Found at i:11131729 original size:9 final size:8
Alignment explanation
Indices: 11131668--11131826 Score: 51
Period size: 8 Copynumber: 21.4 Consensus size: 8
11131658 AAGTTTTTGA
11131668 TTTTAGGG
1 TTTTAGGG
*
11131676 -TTTAGGA
1 TTTTAGGG
*
11131683 TTTT-GGA
1 TTTTAGGG
11131690 TTTTAGGG
1 TTTTAGGG
**
11131698 TTCGA-GG
1 TTTTAGGG
11131705 TTTTA--G
1 TTTTAGGG
11131711 TTTTAGGG
1 TTTTAGGG
11131719 TTTTGAGGG
1 TTTT-AGGG
*
11131728 -TTTGGGG
1 TTTTAGGG
* *
11131735 TTTCA--A
1 TTTTAGGG
*
11131741 TTTCAGGG
1 TTTTAGGG
11131749 -TTTAGAGG
1 TTTTAG-GG
11131757 TTTTA-GG
1 TTTTAGGG
*
11131764 ATTTA--G
1 TTTTAGGG
11131770 TTTTAGGG
1 TTTTAGGG
*
11131778 TTTGGAGGG
1 TTT-TAGGG
*
11131787 -CTTAGGG
1 TTTTAGGG
* *
11131794 TTTCA--A
1 TTTTAGGG
*
11131800 TTTCAGGG
1 TTTTAGGG
*
11131808 TTTAAGGG
1 TTTTAGGG
11131816 TTTTAGGG
1 TTTTAGGG
11131824 TTT
1 TTT
11131827 GGACGGTTGA
Statistics
Matches: 112, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
6 21 0.19
7 35 0.31
8 44 0.39
9 12 0.11
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (8 bp):
TTTTAGGG
Found at i:11131773 original size:59 final size:59
Alignment explanation
Indices: 11131706--11131822 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
11131696 GGTTCGAGGT
* * *
11131706 TTTAGTTTTAGGGTTTTGAGGGTTTGGGGTTTCAATTTCAGGGTTT-AGAGGTTTTAGGA
1 TTTAGTTTTAGGGTTTGGAGGGCTTAGGGTTTCAATTTCAGGGTTTAAG-GGTTTTAGGA
11131765 TTTAGTTTTAGGGTTTGGAGGGCTTAGGGTTTCAATTTCAGGGTTTAAGGGTTTTAGG
1 TTTAGTTTTAGGGTTTGGAGGGCTTAGGGTTTCAATTTCAGGGTTTAAGGGTTTTAGG
11131823 GTTTGGACGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 52 0.96
60 2 0.04
ACGTcount: A:0.17, C:0.04, G:0.34, T:0.44
Consensus pattern (59 bp):
TTTAGTTTTAGGGTTTGGAGGGCTTAGGGTTTCAATTTCAGGGTTTAAGGGTTTTAGGA
Found at i:11131810 original size:30 final size:30
Alignment explanation
Indices: 11131715--11131826 Score: 129
Period size: 30 Copynumber: 3.8 Consensus size: 30
11131705 TTTTAGTTTT
* *
11131715 AGGGTTTTGAGGGTTTGGGGTTTCAATTTC
1 AGGGTTTAGAGGGTTTAGGGTTTCAATTTC
* * * *
11131745 AGGGTTTAGAGGTTTTAGGATTT-AGTTTT
1 AGGGTTTAGAGGGTTTAGGGTTTCAATTTC
* *
11131774 AGGGTTTGGAGGGCTTAGGGTTTCAATTTC
1 AGGGTTTAGAGGGTTTAGGGTTTCAATTTC
11131804 AGGGTTTA-AGGGTTTTAGGGTTT
1 AGGGTTTAGAGGG-TTTAGGGTTT
11131827 GGACGGTTGA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
29 27 0.41
30 39 0.59
ACGTcount: A:0.17, C:0.04, G:0.36, T:0.43
Consensus pattern (30 bp):
AGGGTTTAGAGGGTTTAGGGTTTCAATTTC
Found at i:11131823 original size:46 final size:47
Alignment explanation
Indices: 11131769--11131869 Score: 145
Period size: 46 Copynumber: 2.2 Consensus size: 47
11131759 TTAGGATTTA
*
11131769 GTTTTAGGGTTTGGAGGGCTT-AGGGTTTCAATTTC-AGGGTTTA-AGG
1 GTTTTAGGGTTTGGACGG-TTGAGGGTTTCAATTTCGA-GGTTTAGAGG
*
11131815 GTTTTAGGGTTTGGACGGTTGAGGGTTTCAATTTCGAGGTTTAGAGT
1 GTTTTAGGGTTTGGACGGTTGAGGGTTTCAATTTCGAGGTTTAGAGG
11131862 GTTTTAGG
1 GTTTTAGG
11131870 ATTTAGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
45 2 0.04
46 37 0.74
47 11 0.22
ACGTcount: A:0.17, C:0.06, G:0.37, T:0.41
Consensus pattern (47 bp):
GTTTTAGGGTTTGGACGGTTGAGGGTTTCAATTTCGAGGTTTAGAGG
Found at i:11131904 original size:106 final size:106
Alignment explanation
Indices: 11131710--11131933 Score: 289
Period size: 106 Copynumber: 2.1 Consensus size: 106
11131700 CGAGGTTTTA
* *
11131710 GTTTTAGGGTTTTGAGGGTTTGGGGTTTCAATTTCAGGGTTTAGAGGTTTTAGGATTTAGTTTTA
1 GTTTTAGGGTTTGGACGGTTTGGGGTTTCAATTTCAGGGTTTAGAGGTTTTAGGATTTAGTTTTA
** * *
11131775 GGGTTTGGAGGGCTTAGGGTTTCAATTTC-AGGGTTTA-AGG
66 AAGTTTGGAGGGCTTAGGGTTTCAACTTCGA-GATTTAGAGG
11131815 GTTTTAGGGTTTGGACGG-TTGAGGGTTTCAATTTC-GAGGTTTAGAGTGTTTTAGGATTTAGTT
1 GTTTTAGGGTTTGGACGGTTTG-GGGTTTCAATTTCAG-GGTTTAGAG-GTTTTAGGATTTAGTT
*
11131878 TTAAAGTTCT-GAGGG-TCTAGGGTTTCAACTTCGAGATTTAGAGT
63 TTAAAGTT-TGGAGGGCT-TAGGGTTTCAACTTCGAGATTTAGAGG
11131922 GTTTTAGGGTTT
1 GTTTTAGGGTTT
11131934 AGGGTTTTGG
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
104 4 0.04
105 39 0.37
106 46 0.44
107 16 0.15
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.43
Consensus pattern (106 bp):
GTTTTAGGGTTTGGACGGTTTGGGGTTTCAATTTCAGGGTTTAGAGGTTTTAGGATTTAGTTTTA
AAGTTTGGAGGGCTTAGGGTTTCAACTTCGAGATTTAGAGG
Found at i:11132410 original size:26 final size:25
Alignment explanation
Indices: 11132380--11132436 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
11132370 ATGAACTATT
11132380 AAAAAATAAAACTAAAAATAATAAT-
1 AAAAAATAAAACTAAAAA-AATAATA
* * *
11132405 ATAAAA-AAAATTAGAAAAATAATA
1 AAAAAATAAAACTAAAAAAATAATA
11132429 AAAAAATA
1 AAAAAATA
11132437 GAAAATACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.23
24 14 0.54
25 6 0.23
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (25 bp):
AAAAAATAAAACTAAAAAAATAATA
Found at i:11132433 original size:19 final size:18
Alignment explanation
Indices: 11132381--11132441 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
11132371 TGAACTATTA
11132381 AAAAATAAAACTAAAAATA-
1 AAAAATAAAA--AAAAATAG
* *
11132400 ATAATATAAAAAAAATTAG
1 A-AAAATAAAAAAAAATAG
11132419 AAAAATAATAAAAAAATAG
1 AAAAATAA-AAAAAAATAG
11132438 AAAA
1 AAAA
11132442 TACTTGAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 12 0.34
19 15 0.43
20 8 0.23
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAATAAAAAAAAATAG
Found at i:11133839 original size:3 final size:3
Alignment explanation
Indices: 11133831--11133889 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
11133821 AATAATGTTT
11133831 TAA TAA TAA TAA 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 TAA TAA TAA TAA
11133879 TAA TAAA TAA T
1 TAA T-AA TAA T
11133890 TTTATCTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11134145 original size:12 final size:12
Alignment explanation
Indices: 11134130--11134172 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
11134120 AACCCTAACC
11134130 TAAAACCTAAAA
1 TAAAACCTAAAA
*
11134142 TAAAACCCTAAAT
1 TAAAA-CCTAAAA
*
11134155 TAAAACGTAAAA
1 TAAAACCTAAAA
11134167 TAAAAC
1 TAAAAC
11134173 TTTAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.19
Consensus pattern (12 bp):
TAAAACCTAAAA
Found at i:11134151 original size:13 final size:13
Alignment explanation
Indices: 11134119--11134172 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 13
11134109 CCTTATAATG
**
11134119 AAACCCTAACCTA
1 AAACCCTAAAATA
11134132 AAA-CCTAAAATA
1 AAACCCTAAAATA
*
11134144 AAACCCTAAATTA
1 AAACCCTAAAATA
*
11134157 AAA-CGTAAAATA
1 AAACCCTAAAATA
11134169 AAAC
1 AAAC
11134173 TTTAAATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
12 20 0.59
13 14 0.41
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (13 bp):
AAACCCTAAAATA
Found at i:11134179 original size:12 final size:12
Alignment explanation
Indices: 11134139--11134190 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
11134129 CTAAAACCTA
**
11134139 AAATAAAACCCT
1 AAATAAAACTTT
* *
11134151 AAATTAAAACGTA
1 AAA-TAAAACTTT
11134164 AAATAAAACTTT
1 AAATAAAACTTT
*
11134176 AAATGAAACTTT
1 AAATAAAACTTT
11134188 AAA
1 AAA
11134191 CCCTAGGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.60, C:0.12, G:0.04, T:0.25
Consensus pattern (12 bp):
AAATAAAACTTT
Found at i:11134179 original size:25 final size:25
Alignment explanation
Indices: 11134119--11134172 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
11134109 CCTTATAATG
**
11134119 AAACCCTAACCTAAAACCTAAAATA
1 AAACCCTAAATTAAAACCTAAAATA
*
11134144 AAACCCTAAATTAAAACGTAAAATA
1 AAACCCTAAATTAAAACCTAAAATA
11134169 AAAC
1 AAAC
11134173 TTTAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (25 bp):
AAACCCTAAATTAAAACCTAAAATA
Found at i:11136449 original size:19 final size:19
Alignment explanation
Indices: 11136425--11136473 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
11136415 TTCGCTTAAA
* **
11136425 GTTTAGGGTTTTATTTAGG
1 GTTTAGGGTTTCACCTAGG
* *
11136444 GTTTAGAGTTTCACCTAGT
1 GTTTAGGGTTTCACCTAGG
11136463 GTTTAGGGTTT
1 GTTTAGGGTTT
11136474 ACACATATGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.49
Consensus pattern (19 bp):
GTTTAGGGTTTCACCTAGG
Found at i:11136535 original size:19 final size:19
Alignment explanation
Indices: 11136496--11136563 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
11136486 TTATCATCTC
*
11136496 ACTTAGGG-TTTAGGTTCTT
1 ACTTAGGGTTTTAGGAT-TT
*
11136515 ACTTAGGGTTTTAGGGTTT
1 ACTTAGGGTTTTAGGATTT
* * * *
11136534 ACCTAAGGTTTAAGGATTC
1 ACTTAGGGTTTTAGGATTT
*
11136553 ATTTAGGGTTT
1 ACTTAGGGTTT
11136564 CGTTTAGAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 32 0.82
20 7 0.18
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (19 bp):
ACTTAGGGTTTTAGGATTT
Found at i:11138592 original size:37 final size:36
Alignment explanation
Indices: 11138551--11138658 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 36
11138541 CAAACCCATT
11138551 TTTTAAATAATTAATTTTTATTTTTTTGTTATTATTA
1 TTTT-AATAATTAATTTTTATTTTTTTGTTATTATTA
* * **
11138588 TTTTAATAATT--TTTATATTTTATTACTATTATTA
1 TTTTAATAATTAATTTTTATTTTTTTGTTATTATTA
* ** * *
11138622 TTATCTTAA-TAATTTTTATTTTTATGTTATCATTA
1 TTTTAATAATTAATTTTTATTTTTTTGTTATTATTA
11138657 TT
1 TT
11138659 ATATTATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
33 1 0.02
34 25 0.45
35 19 0.34
36 7 0.12
37 4 0.07
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (36 bp):
TTTTAATAATTAATTTTTATTTTTTTGTTATTATTA
Found at i:11140020 original size:16 final size:17
Alignment explanation
Indices: 11140000--11140038 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
11139990 TTCATTTATT
11140000 CAAGTTTGAATTTCTCA
1 CAAGTTTGAATTTCTCA
*
11140017 -AAGTTTGGATTTCTCA
1 CAAGTTTGAATTTCTCA
11140033 CAAGTT
1 CAAGTT
11140039 ACATAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
CAAGTTTGAATTTCTCA
Found at i:11144218 original size:131 final size:129
Alignment explanation
Indices: 11143870--11144517 Score: 453
Period size: 131 Copynumber: 5.0 Consensus size: 129
11143860 TTTGTAATTC
* * * * * *
11143870 TTTTTATCATTATAAATATGAT-AAATATTTTCGTAAC-AATTTTTTTTGTCCTTGTCTAAAATA
1 TTTTTATCATTACAAATATAATAAAAT-TTTTTGTAACTAA--ATTTTTGTCATTGTATAAAATA
* * ** ** * * **
11143933 TTAAAAATTTAAATTAAGCAACAACAATAAAAAATT-ATTACAAATAAAACGAGTTTGAACAACA
63 TTAAAAA-ATAACTTAAGCAATGAC-ATTGAAAATTCATTACAAATATAACAAGTTTTTACAACA
11143997 A-TAA
126 ACT-A
* * * * *
11144001 TTTTTATCAATACAAATATGATAAAA-GTTTTGTAAC-AAATTTTTTATCATTGTGTAAAATATT
1 TTTTTATCATTACAAATATAATAAAATTTTTTGTAACTAAA-TTTTTGTCATTGTATAAAATATT
* * *
11144064 AAAAAAATAA-TTAAGCAACGACATTGAAAATTCATTACAAATATAATAAGTTTTTGCAACAA-T
65 -AAAAAATAACTTAAGCAATGACATTGAAAATTCATTACAAATATAACAAGTTTTTACAACAACT
11144127 AA
129 -A
* *
11144129 GTTTTTATCGTTACAAATATAATAAAATTTTTTGTAACTACAATTTTTATCATTGTATAAAATAT
1 -TTTTTATCATTACAAATATAATAAAATTTTTTGTAACTA-AATTTTTGTCATTGTATAAAATAT
* ** ** *
11144194 TAAAAAATAACTTAAGCAATGACATTGAAAAATGGTTGTAAAT-TAAACAAGTTTTATGCAACAA
64 TAAAAAATAACTTAAGCAATGACATTGAAAATTCATTACAAATAT-AACAAGTTTT-TACAACAA
*
11144258 CTTT
127 C-TA
* ** * * ** *
11144262 TTTTTGTTGTTACAAATATTATAAAATTTTTTGTAA-TAACTTCGTTTGTCGCTGTGTAAAATAT
1 TTTTTATCATTACAAATATAATAAAATTTTTTGTAACTAAATT--TTTGTCATTGTATAAAATAT
* * * ** * * *
11144326 TAAAACATAATTTAAGCAATGACTTTGAAAATTTGTTGCAAATCA-AAAAAGTATTTACAACAAC
64 TAAAAAATAACTTAAGCAATGACATTGAAAATTCATTACAAAT-ATAACAAGTTTTTACAACAAC
11144390 T-
128 TA
* ** * * *
11144391 TCTTATGT-TCATTACAAATATAATACAATTTTTCATAAC-AACTTTTTTGTCATTGCATAAAAG
1 T-TT-T-TATCATTACAAATATAATAAAATTTTTTGTAACTAA-ATTTTTGTCATTGTATAAAAT
* * * * * *
11144454 ATTTAAAAATAACTTAAGTAATGACA-TGAAAAATCATTACAAATAAAACAAGGTTTCACAACAA
62 ATTAAAAAATAACTTAAGCAATGACATTGAAAATTCATTACAAATATAACAAGTTTTTACAACAA
11144518 TTTTGTTGTT
Statistics
Matches: 421, Mismatches: 73, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
127 8 0.02
128 38 0.09
129 75 0.18
130 74 0.18
131 115 0.27
132 110 0.26
134 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (129 bp):
TTTTTATCATTACAAATATAATAAAATTTTTTGTAACTAAATTTTTGTCATTGTATAAAATATTA
AAAAATAACTTAAGCAATGACATTGAAAATTCATTACAAATATAACAAGTTTTTACAACAACTA
Found at i:11144295 original size:132 final size:131
Alignment explanation
Indices: 11144011--11144501 Score: 432
Period size: 132 Copynumber: 3.8 Consensus size: 131
11144001 TTTTTATCAA
* * *
11144011 TACAAATATGATAAAA-GTTTTGTAAC-AAATTTTTTATCATTGTGTAAAATATTAAAAAAATAA
1 TACAAATATAATAAAATTTTTTGTAACTAAA-TTTTTATCATTGTATAAAATATT-AAAAAATAA
* * * * * **
11144074 -TTAAGCAACGACATTGAAAATTCATTACAAA-TATAATAAGTTTT-TGCAACAA-TAAGTTTTT
64 CTTAAGCAATGACATTGAAAAATCGTTGCAAATTA-AAAAAGTTTTATGCAACAACT-TTTTTTT
* *
11144135 ATCGT
127 GTTGT
11144140 TACAAATATAATAAAATTTTTTGTAACTACAATTTTTATCATTGTATAAAATATTAAAAAATAAC
1 TACAAATATAATAAAATTTTTTGTAACTA-AATTTTTATCATTGTATAAAATATTAAAAAATAAC
* * *
11144205 TTAAGCAATGACATTGAAAAATGGTTGTAAATTAAACAAGTTTTATGCAACAACTTTTTTTTGTT
65 TTAAGCAATGACATTGAAAAATCGTTGCAAATTAAAAAAGTTTTATGCAACAACTTTTTTTTGTT
11144270 GT
130 GT
* * * ** * *
11144272 TACAAATATTATAAAATTTTTTGTAA-TAACTTCGTTTGTCGCTGTGTAAAATATTAAAACATAA
1 TACAAATATAATAAAATTTTTTGTAACTAAATT--TTTATCATTGTATAAAATATTAAAAAATAA
* * * * * * *
11144336 TTTAAGCAATGACTTTGAAAATTTGTTGCAAATCAAAAAAGTATTTA--CAACAAC-TTCTTATG
64 CTTAAGCAATGACATTGAAAAATCGTTGCAAATTAAAAAAGT-TTTATGCAACAACTTTTTTTTG
*
11144398 TTCAT
128 TT-GT
* ** * * * * *
11144403 TACAAATATAATACAATTTTTCATAAC-AACTTTTTTGTCATTGCATAAAAGATTTAAAAATAAC
1 TACAAATATAATAAAATTTTTTGTAACTAA-ATTTTTATCATTGTATAAAATATTAAAAAATAAC
* * *
11144467 TTAAGTAATGACA-TGAAAAATCATTACAAA-TAAAA
65 TTAAGCAATGACATTGAAAAATCGTTGCAAATTAAAA
11144502 CAAGGTTTCA
Statistics
Matches: 298, Mismatches: 51, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
128 4 0.01
129 28 0.09
130 63 0.21
131 91 0.31
132 107 0.36
133 5 0.02
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (131 bp):
TACAAATATAATAAAATTTTTTGTAACTAAATTTTTATCATTGTATAAAATATTAAAAAATAACT
TAAGCAATGACATTGAAAAATCGTTGCAAATTAAAAAAGTTTTATGCAACAACTTTTTTTTGTTG
T
Found at i:11147050 original size:3 final size:3
Alignment explanation
Indices: 11147038--11147084 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
11147028 TAGTAATAAC
*
11147038 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11147085 TCATAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11147130 original size:28 final size:28
Alignment explanation
Indices: 11147090--11147150 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
11147080 TAATATCATA
* * *
11147090 AAAAATAACAACACAAAAGAAATAAAAT
1 AAAAATAACAACAAAAAAGAAAAAAAAG
*
11147118 AAAAATCAA-AACAAAAAATAAAAAAAAG
1 AAAAAT-AACAACAAAAAAGAAAAAAAAG
11147146 AAAAA
1 AAAAA
11147151 ACTTGCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.80, C:0.08, G:0.03, T:0.08
Consensus pattern (28 bp):
AAAAATAACAACAAAAAAGAAAAAAAAG
Found at i:11147520 original size:11 final size:11
Alignment explanation
Indices: 11147498--11147538 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
11147488 TTTGGTGACC
11147498 CAAAAAAT-TT
1 CAAAAAATCTT
11147508 CAAAAAATCTT
1 CAAAAAATCTT
*
11147519 CAAAAATTCTT
1 CAAAAAATCTT
11147530 -AAAACAATC
1 CAAAA-AATC
11147539 ATTTTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 12 0.44
11 15 0.56
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (11 bp):
CAAAAAATCTT
Found at i:11148385 original size:43 final size:43
Alignment explanation
Indices: 11148304--11148386 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
11148294 CATAGGTTTG
* * **
11148304 ACAATTTTTCAAAATTTAAAAGGCTCCTTTGAGTAAAGGCTCA
1 ACAATTTTTCAAAATTTAAAAGACTACTTTGACCAAAGGCTCA
* *
11148347 ACAATTTTTGAAAATTTAAAAGACTATTTTGACCAAAGGC
1 ACAATTTTTCAAAATTTAAAAGACTACTTTGACCAAAGGC
11148387 AATGAAACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (43 bp):
ACAATTTTTCAAAATTTAAAAGACTACTTTGACCAAAGGCTCA
Found at i:11148832 original size:40 final size:39
Alignment explanation
Indices: 11148766--11148881 Score: 125
Period size: 34 Copynumber: 3.1 Consensus size: 39
11148756 TTTTAAAATT
* *
11148766 AAAGCTCCTCTAACCAGAGGCTATGAAACTTTGAATTTAA
1 AAAGCTCCTCTAACCAAAGGCAATGAAACTTT-AATTTAA
* *
11148806 AAGGCTCCTCTAACCAAAAGCAATGAAA---T--TTTAA
1 AAAGCTCCTCTAACCAAAGGCAATGAAACTTTAATTTAA
* * *
11148840 AAAGCTCCTCTGACCAAAGGTAATGAAACTTTAAATTAA
1 AAAGCTCCTCTAACCAAAGGCAATGAAACTTTAATTTAA
11148879 AAA
1 AAA
11148882 TCTAATAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
34 29 0.47
37 2 0.03
39 7 0.11
40 24 0.39
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (39 bp):
AAAGCTCCTCTAACCAAAGGCAATGAAACTTTAATTTAA
Found at i:11153065 original size:11 final size:11
Alignment explanation
Indices: 11153049--11153078 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11153039 CACAAAAGTC
11153049 ATCTTCTTCAT
1 ATCTTCTTCAT
11153060 ATCTTCTTCAT
1 ATCTTCTTCAT
11153071 ATCTTCTT
1 ATCTTCTT
11153079 TTGTCATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (11 bp):
ATCTTCTTCAT
Found at i:11158074 original size:21 final size:21
Alignment explanation
Indices: 11158033--11158075 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11158023 TCTTTCTTAC
* *
11158033 TCTTTAATTTATTTCATGCAA
1 TCTTTAATTTACTTCAAGCAA
11158054 TCTTT-ATTTACTTCAAAGCAA
1 TCTTTAATTTACTTC-AAGCAA
11158075 T
1 T
11158076 TCAGCATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (21 bp):
TCTTTAATTTACTTCAAGCAA
Found at i:11160897 original size:19 final size:18
Alignment explanation
Indices: 11160854--11160897 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
11160844 AGTATTTATT
11160854 TTAATCTATTTTAAATAAA
1 TTAAT-TATTTTAAATAAA
* *
11160873 TAAATTATTTATAATTAAA
1 TTAATTATTT-TAAATAAA
11160892 TTAATT
1 TTAATT
11160898 TAAGTATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTATTTTAAATAAA
Found at i:11161294 original size:16 final size:16
Alignment explanation
Indices: 11161265--11161298 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11161255 TTTCAATTAA
*
11161265 AATTTCATATTTTTTT
1 AATTTCATAATTTTTT
*
11161281 AATTTGATAATTTTTT
1 AATTTCATAATTTTTT
11161297 AA
1 AA
11161299 CGATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
AATTTCATAATTTTTT
Found at i:11161904 original size:32 final size:32
Alignment explanation
Indices: 11161858--11161918 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
11161848 TTTTTTACTT
*
11161858 TTTTTAATTAATAAA-AATATAATTACTTTTTA
1 TTTTAAATTAATAAAGAA-ATAATTACTTTTTA
*
11161890 TTTTAAATTAATAAAGAAATAATTGCTTT
1 TTTTAAATTAATAAAGAAATAATTACTTT
11161919 CTACCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTAAATTAATAAAGAAATAATTACTTTTTA
Found at i:11162113 original size:12 final size:12
Alignment explanation
Indices: 11162096--11162131 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
11162086 TTGTATATTC
11162096 TTTTATATTAAT
1 TTTTATATTAAT
11162108 TTTTATATTAAT
1 TTTTATATTAAT
*
11162120 TATTTTTATTAA
1 T-TTTATATTAA
11162132 AATAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTATATTAAT
Found at i:11165862 original size:12 final size:12
Alignment explanation
Indices: 11165845--11165869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11165835 TTTTGTATAT
11165845 TTATTATTATCA
1 TTATTATTATCA
11165857 TTATTATTATCA
1 TTATTATTATCA
11165869 T
1 T
11165870 ATATGCATAT
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:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTATCA
Found at i:11167260 original size:18 final size:18
Alignment explanation
Indices: 11167237--11167271 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11167227 ATTAATTTTG
*
11167237 ATAAAATTAAAAATAATA
1 ATAAAAGTAAAAATAATA
*
11167255 ATAAAAGTAAAATTAAT
1 ATAAAAGTAAAAATAAT
11167272 TTTTATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAAGTAAAAATAATA
Found at i:11172032 original size:22 final size:22
Alignment explanation
Indices: 11171994--11172041 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11171984 TTTGTTGGAT
* *
11171994 AAAA-AATTGATTGATTAATGA
1 AAAATAATTGATTAATTAATAA
*
11172015 AAAATAATTTATTAATTAATAA
1 AAAATAATTGATTAATTAATAA
11172037 AAAAT
1 AAAAT
11172042 GAGATCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAATAATTGATTAATTAATAA
Found at i:11172199 original size:18 final size:16
Alignment explanation
Indices: 11172176--11172380 Score: 114
Period size: 18 Copynumber: 12.9 Consensus size: 16
11172166 TACATTAATA
11172176 AATAAATAATATTACATT
1 AATAAATAATATT--ATT
11172194 AATAAATAATATTATGT
1 AATAAATAATATTAT-T
11172211 --T--ATAATA-TATT
1 AATAAATAATATTATT
11172222 AATAAATAATATTATAT
1 AATAAATAATATTAT-T
11172239 GAATAAATAATA-TATT
1 -AATAAATAATATTATT
* *
11172255 AATAAATATTATTATA
1 AATAAATAATATTATT
* **
11172271 AATAAATATTA-TGCT
1 AATAAATAATATTATT
* * *
11172286 AATATAT-TTA-TAAT
1 AATAAATAATATTATT
11172300 AATAAATAATATTATATT
1 AATAAATAATA-T-TATT
*
11172318 AATAAACAAATAGTCTATT
1 AATAAA-TAATA-T-TATT
*
11172337 -ATTAATAATCATATATT
1 AATAAATAAT-AT-TATT
11172354 AAT--A-AATATTA-T
1 AATAAATAATATTATT
11172366 AATAAATAATATTAT
1 AATAAATAATATTAT
11172381 AACATATTAA
Statistics
Matches: 150, Mismatches: 17, Indels: 42
0.72 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 7 0.05
13 9 0.06
14 14 0.09
15 36 0.24
16 21 0.14
17 13 0.09
18 40 0.27
19 9 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AATAAATAATATTATT
Found at i:11172234 original size:46 final size:43
Alignment explanation
Indices: 11172176--11172281 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 43
11172166 TACATTAATA
* *
11172176 AATAAATAATATTACATTAATAAATAATATTATGTTATAATATATT
1 AATAAATAATATTACATGAATAAATAATA-TAT-TAATAA-ATATT
*
11172222 AATAAATAATATTATATGAATAAATAATATATTAATAAATATT
1 AATAAATAATATTACATGAATAAATAATATATTAATAAATATT
11172265 ATTATAAATAAATATTA
1 A--ATAAAT-AATATTA
11172282 TGCTAATATA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
43 6 0.11
44 5 0.09
45 9 0.17
46 34 0.63
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (43 bp):
AATAAATAATATTACATGAATAAATAATATATTAATAAATATT
Found at i:11172271 original size:12 final size:14
Alignment explanation
Indices: 11172215--11172379 Score: 78
Period size: 14 Copynumber: 11.6 Consensus size: 14
11172205 TTATGTTATA
11172215 ATATATTAATAAAT
1 ATATATTAATAAAT
11172229 AATATTATATGAATAAAT
1 -ATA-TAT-T-AATAAAT
11172247 AATATATTAATAAAT
1 -ATATATTAATAAAT
*
11172262 ATTATTATAAATAAAT
1 A-TA-TATTAATAAAT
*
11172278 AT-TATGCTAATATAT
1 ATATAT--TAATAAAT
* *
11172293 TTATAATAATAAAT
1 ATATATTAATAAAT
*
11172307 A-ATATTATATTAAT
1 ATATATTA-ATAAAT
** *
11172321 A-A-ACAAAT-AGT
1 ATATATTAATAAAT
*
11172332 CTATTATTAAT-AAT
1 ATA-TATTAATAAAT
11172346 CATATATTAATAAAT
1 -ATATATTAATAAAT
11172361 AT-TA-TAATAAAT
1 ATATATTAATAAAT
11172373 A-ATATTA
1 ATATATTA
11172380 TAACATATTA
Statistics
Matches: 117, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
11 2 0.02
12 14 0.12
13 14 0.12
14 30 0.26
15 25 0.21
16 17 0.15
17 4 0.03
18 11 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
ATATATTAATAAAT
Found at i:11172378 original size:15 final size:15
Alignment explanation
Indices: 11172176--11172382 Score: 95
Period size: 15 Copynumber: 13.1 Consensus size: 15
11172166 TACATTAATA
11172176 AATAAATAATATTACATT
1 AATAAATAATATT--A-T
11172194 AATAAATAATATTAT
1 AATAAATAATATTAT
* *
11172209 -GT-TATAATA-TATT
1 AATAAATAATATTA-T
11172222 AATAAATAATATTATAT
1 AATAAATAATA-T-TAT
11172239 GAATAAATAATA-TATT
1 -AATAAATAATATTA-T
*
11172255 AATAAATATTATTAT
1 AATAAATAATATTAT
* **
11172270 AAATAAATATTATGCT
1 -AATAAATAATATTAT
* * *
11172286 AATATAT-TTATAAT
1 AATAAATAATATTAT
11172300 AATAAATAATATTATATT
1 AATAAATAATA-T-TA-T
*
11172318 AATAAACAAATAGTCTAT
1 AATAAA-TAATA-T-TAT
* *
11172336 TATTAATAATCA-TAT
1 AATAAATAAT-ATTAT
*
11172351 -ATTAATAAATATTAT
1 AATAAAT-AATATTAT
11172366 AATAAATAATATTAT
1 AATAAATAATATTAT
11172381 AA
1 AA
11172383 CATATTAATA
Statistics
Matches: 150, Mismatches: 20, Indels: 41
0.71 0.09 0.19
Matches are distributed among these distances:
12 2 0.01
13 7 0.05
14 20 0.13
15 47 0.31
16 23 0.15
17 5 0.03
18 39 0.26
19 7 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATAAATAATATTAT
Found at i:11172398 original size:99 final size:95
Alignment explanation
Indices: 11172171--11172410 Score: 247
Period size: 99 Copynumber: 2.5 Consensus size: 95
11172161 AACATTACAT
* * ** * *
11172171 TAATAAATAAATAATATTAC-ATTAATAAATAATATTATGTTATAATATATTAATAAATAATATT
1 TAATAAATAAATATTA-TACTATTAATAAATAATAATAAATAATAATATATTAATAAAAAATATT
11172235 ATATGAATAAATAATATATTAATAAATATTA
65 ATATGAATAAATAATATATTAATAAATATTA
* * * ** *
11172266 TTATAAATAAATATTATGCTAATATATTTATAATAATAAATAATATTATATTAATAAACAAATAG
1 TAATAAATAAATATTATACTATTA-ATAAATAATAATAAATAATAATATATTAATAAA-AAATA-
* *
11172331 TCTATTATTAAT-AATCATATATTAATAAATATTA
63 T-TA-TATGAATAAATAATATATTAATAAATATTA
11172365 TAATAAAT-AATATTATAACATATTAATAAATAAT-ATAAA-AATAATA
1 TAATAAATAAATATTAT-AC-TATTAATAAATAATAATAAATAATAATA
11172411 AACAGTTTTA
Statistics
Matches: 117, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
94 2 0.02
95 17 0.15
96 26 0.22
97 10 0.09
98 14 0.12
99 38 0.32
100 10 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (95 bp):
TAATAAATAAATATTATACTATTAATAAATAATAATAAATAATAATATATTAATAAAAAATATTA
TATGAATAAATAATATATTAATAAATATTA
Found at i:11172411 original size:9 final size:10
Alignment explanation
Indices: 11172339--11172412 Score: 53
Period size: 12 Copynumber: 7.0 Consensus size: 10
11172329 AGTCTATTAT
*
11172339 TAATAATCATA
1 TAATAAT-AAA
*
11172350 TATTAATAAA
1 TAATAATAAA
11172360 TATTATAATAAA
1 TA--ATAATAAA
11172372 TAATATTATAACA
1 TAATA--ATAA-A
*
11172385 TATTAATAAA
1 TAATAATAAA
11172395 TAAT-ATAAA
1 TAATAATAAA
11172404 -AATAATAAA
1 TAATAATAAA
11172413 CAGTTTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.06
9 10 0.19
10 11 0.21
11 10 0.19
12 13 0.25
13 5 0.10
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATAATAAA
Found at i:11172469 original size:16 final size:15
Alignment explanation
Indices: 11172443--11172553 Score: 84
Period size: 17 Copynumber: 7.1 Consensus size: 15
11172433 TTTATATTAA
11172443 TAAATA-TTTAATAT
1 TAAATATTTTAATAT
*
11172457 TAAATATTATTAAAAT
1 TAAATATT-TTAATAT
*
11172473 ATAATTATTTTAAATAT
1 -TAAATATTTT-AATAT
* *
11172490 T-AATAATTTAATAA
1 TAAATATTTTAATAT
11172504 TAAATAATTTTAAATAT
1 TAAAT-ATTTT-AATAT
*
11172521 T-AATAATTTTAATAA
1 TAAAT-ATTTTAATAT
11172536 TAAATTATTTTTAATAT
1 TAAA-TA-TTTTAATAT
11172553 T
1 T
11172554 TTAATAATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
14 11 0.14
15 15 0.19
16 25 0.32
17 26 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATTTTAATAT
Found at i:11172517 original size:31 final size:31
Alignment explanation
Indices: 11172440--11172571 Score: 128
Period size: 31 Copynumber: 4.2 Consensus size: 31
11172430 TTTTTTATAT
*
11172440 TAATAAAT-A-TTT-AATATTAAATATTATTAA
1 TAATAAATAATTTTAAATATT-AATAAT-TTAA
*
11172470 -AATATAATTATTTTAAATATTAATAATTTAA
1 TAATA-AATAATTTTAAATATTAATAATTTAA
11172501 TAATAAATAATTTTAAATATTAATAATTTTAA
1 TAATAAATAATTTTAAATATTAATAA-TTTAA
* * *
11172533 TAATAAATTATTTTTAATATTTTAATAATTATAT
1 TAATAAA-TAATTTTAA-ATATTAATAATT-TAA
11172567 TAATA
1 TAATA
11172572 TTATTTTTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
29 4 0.05
30 3 0.03
31 25 0.28
32 24 0.27
33 16 0.18
34 16 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATAAATAATTTTAAATATTAATAATTTAA
Found at i:11172575 original size:32 final size:31
Alignment explanation
Indices: 11172473--11172582 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 31
11172463 TTATTAAAAT
11172473 ATAATTA-TTTTAAATATTAATAATTTAATA
1 ATAATTATTTTTAAATATTAATAATTTAATA
* *
11172503 ATAAATAATTTTAAATATTAATAATTTTAATA
1 ATAATTATTTTTAAATATTAATAA-TTTAATA
* *
11172535 ATAAATTATTTTTAATATTTTAATAATTATATTA
1 AT-AATTATTTTTAA-ATATTAATAATT-TAATA
11172569 AT-ATTATTTTTAAA
1 ATAATTATTTTTAAA
11172583 AATAGATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.09
31 17 0.24
32 20 0.29
33 12 0.17
34 15 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
ATAATTATTTTTAAATATTAATAATTTAATA
Found at i:11175972 original size:32 final size:32
Alignment explanation
Indices: 11175936--11175996 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
11175926 ATCATGCAAG
*
11175936 AATAA-ATAAAACAAACTCAAAATAAAAAAAAT
1 AATAATATAAAAAAAACTCAAAA-AAAAAAAAT
*
11175968 AATAATATAAAAAAAATTCAAAAAAAAAA
1 AATAATATAAAAAAAACTCAAAAAAAAAA
11175997 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (32 bp):
AATAATATAAAAAAAACTCAAAAAAAAAAAAT
Found at i:11177070 original size:3 final size:3
Alignment explanation
Indices: 11177035--11177061 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11177025 ATGTATATAC
11177035 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
11177062 AAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11177280 original size:22 final size:22
Alignment explanation
Indices: 11177255--11177327 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
11177245 TAGTAAATCA
* * *
11177255 AAATTATGCTCGGAGGTCTTAG
1 AAATCATGCTCGAAGGTCTTAC
11177277 AAATCATG-TCCGAAGGTCTTAC
1 AAATCATGCT-CGAAGGTCTTAC
*
11177299 AGAATCATGCTTGAAGGTCTTAC
1 A-AATCATGCTCGAAGGTCTTAC
11177322 AGAATC
1 A-AATC
11177328 GATCGGGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 1 0.02
22 18 0.41
23 24 0.55
24 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (22 bp):
AAATCATGCTCGAAGGTCTTAC
Found at i:11177462 original size:88 final size:88
Alignment explanation
Indices: 11177313--11177496 Score: 251
Period size: 88 Copynumber: 2.1 Consensus size: 88
11177303 TCATGCTTGA
*
11177313 AGGTCTTACAGAATCGATCGGGATAACACCACAAGTCGAAAGATAAAGAATTGATCAGGATAACA
1 AGGTCTTACAGAATCGATCGGGATAACACCACAAGTCGAAAGATAAAGAATCGATCAGGATAACA
** * *
11177378 CTGTGAATTAAAATTATGCCTGG
66 CCATGAATCAAAATTATGCCCGG
* * ** * * *
11177401 AGGTCTTACAGAATCGATTGGGATAACATCTTAAGTTGAAAGATAAGGAATCGATCGGGATAACA
1 AGGTCTTACAGAATCGATCGGGATAACACCACAAGTCGAAAGATAAAGAATCGATCAGGATAACA
*
11177466 CCATGAATCGAAATTATGCCCGG
66 CCATGAATCAAAATTATGCCCGG
11177489 AGGTCTTA
1 AGGTCTTA
11177497 GAAATCATGC
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (88 bp):
AGGTCTTACAGAATCGATCGGGATAACACCACAAGTCGAAAGATAAAGAATCGATCAGGATAACA
CCATGAATCAAAATTATGCCCGG
Found at i:11177506 original size:22 final size:22
Alignment explanation
Indices: 11177475--11177518 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11177465 ACCATGAATC
*
11177475 GAAATTATGCCCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
*
11177497 GAAATCATGCTCGGAGGTCTTA
1 GAAATCATGCCCGGAGGTCTTA
11177519 CAGAATTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (22 bp):
GAAATCATGCCCGGAGGTCTTA
Done.