Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 36 of 143
Found at i:10926253 original size:20 final size:20
Alignment explanation
Indices: 10926228--10926300 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
10926218 GTGAACGCAG
10926228 GCGTCGAGCAATGTCAAGCA
1 GCGTCGAGCAATGTCAAGCA
*
10926248 GCGTCGAGC--TGGTGCGATAGAA
1 GCGTCGAGCAAT-GT-C-A-AGCA
*
10926270 TGCGTCGAGCAACGTCAAGCA
1 -GCGTCGAGCAATGTCAAGCA
*
10926291 ACGTCGAGCA
1 GCGTCGAGCA
10926301 CTTGCAGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 19 0.45
21 4 0.10
22 4 0.10
23 10 0.24
24 2 0.05
ACGTcount: A:0.27, C:0.25, G:0.33, T:0.15
Consensus pattern (20 bp):
GCGTCGAGCAATGTCAAGCA
Found at i:10958871 original size:3 final size:3
Alignment explanation
Indices: 10958863--10958919 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
10958853 GGGCAACATA
*
10958863 TTC TTC TTC TTCC TTC -TC TTC TTT TTC TTC TTC TT- TTC TTTC TTC
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
* *
10958908 TTA TTC TGC TTC
1 TTC TTC TTC TTC
10958920 AATACCCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:10958895 original size:24 final size:24
Alignment explanation
Indices: 10958861--10958919 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
10958851 CAGGGCAACA
10958861 TATTCTTCTTC-TTCCTTCTCTTCT
1 TATTCTTCTTCTTTCCTT-TCTTCT
* *
10958885 TTTTCTTCTTCTTTTCTTTCTTCT
1 TATTCTTCTTCTTTCCTTTCTTCT
*
10958909 TATTCTGCTTC
1 TATTCTTCTTC
10958920 AATACCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTCTTCTTCTTTCCTTTCTTCT
Found at i:10958909 original size:15 final size:16
Alignment explanation
Indices: 10958863--10958914 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
10958853 GGGCAACATA
*
10958863 TTCTTCTTCTTCCTTC
1 TTCTTCTTCTTTCTTC
10958879 -TCTTCTT-TTTCTTC
1 TTCTTCTTCTTTCTTC
10958893 TTCTT-TTCTTTCTTC
1 TTCTTCTTCTTTCTTC
*
10958908 TTATTCT
1 TTCTTCT
10958915 GCTTCAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 8 0.26
15 22 0.71
16 1 0.03
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTCTTCTTTCTTC
Found at i:10966542 original size:15 final size:15
Alignment explanation
Indices: 10966519--10966551 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10966509 ATTTTAGTTA
10966519 AAAAATACACAATTC
1 AAAAATACACAATTC
*
10966534 AAAACTACACAATTC
1 AAAAATACACAATTC
10966549 AAA
1 AAA
10966552 GAATTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAATACACAATTC
Found at i:10974035 original size:40 final size:41
Alignment explanation
Indices: 10973990--10974073 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
10973980 AATTATTTAC
10973990 ATTTTTTAA-TTAA-AATTTAAACTGATTCTGAAATTGTATG
1 ATTTTTTAACTTAAGAATTTAAA-TGATTCTGAAATTGTATG
* **
10974030 A-TTTTTAACTTAAGACTTTGTATGATTCTGAAATTGTATG
1 ATTTTTTAACTTAAGAATTTAAATGATTCTGAAATTGTATG
10974070 ATTT
1 ATTT
10974074 GTAAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 7 0.18
40 24 0.63
41 7 0.18
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (41 bp):
ATTTTTTAACTTAAGAATTTAAATGATTCTGAAATTGTATG
Found at i:10974087 original size:60 final size:60
Alignment explanation
Indices: 10974023--10974141 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
10974013 GATTCTGAAA
* *
10974023 TTGTATGATTTTTAACTTAAGAC-TTTGT-ATGATTCTGAAATTGTATGATTTGTAAAAAAT
1 TTGTATGATTTTTAACTT-AGACATTTGTAATCATTAT-AAATTGTATGATTTGTAAAAAAT
* * * *
10974083 TTGTATGATTTTTAAGTTTGTCATTTTTAATCATTATAAATTGTATGATTTGTAAAAAA
1 TTGTATGATTTTTAACTTAGACATTTGTAATCATTATAAATTGTATGATTTGTAAAAAA
10974142 AATTTGCACA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.84
61 6 0.12
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (60 bp):
TTGTATGATTTTTAACTTAGACATTTGTAATCATTATAAATTGTATGATTTGTAAAAAAT
Found at i:10975440 original size:31 final size:31
Alignment explanation
Indices: 10975405--10975465 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
10975395 GGACTAGATT
* *
10975405 AAAATAGTTTTATTATTAAGTGGATCAAATC
1 AAAATAGTCTTATTATTAAGTGAATCAAATC
10975436 AAAATAGTCTTATTATTAAGTGAATCAAAT
1 AAAATAGTCTTATTATTAAGTGAATCAAAT
10975466 TAACCACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (31 bp):
AAAATAGTCTTATTATTAAGTGAATCAAATC
Found at i:10983407 original size:77 final size:77
Alignment explanation
Indices: 10983300--10983455 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 77
10983290 TTACCCTTAG
* *
10983300 ATAACAATAGTATTTTAATTATATTATTAATATCTTATATCTAAATAAATTATTTAATAAAATAT
1 ATAACAATAGTATTTTAAGTATATTATTAATATCTTAGATCTAAATAAATTATTTAATAAAATAT
10983365 AAAACTATTATC
66 AAAACTATTATC
10983377 ATAACAATAGTATTTTAAGTATATTATTAATATCTTAGATCTAAATAAATTATTTAATAAAATAT
1 ATAACAATAGTATTTTAAGTATATTATTAATATCTTAGATCTAAATAAATTATTTAATAAAATAT
10983442 AAAACTATTATC
66 AAAACTATTATC
10983454 AT
1 AT
10983456 CTTTTTAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (77 bp):
ATAACAATAGTATTTTAAGTATATTATTAATATCTTAGATCTAAATAAATTATTTAATAAAATAT
AAAACTATTATC
Found at i:10983652 original size:13 final size:13
Alignment explanation
Indices: 10983634--10983666 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10983624 CATATTTTGC
*
10983634 ATTATTTTAAAAT
1 ATTATTTAAAAAT
10983647 ATTATTTAAAAAT
1 ATTATTTAAAAAT
10983660 ATT-TTTA
1 ATTATTTA
10983667 GATATTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATTTAAAAAT
Found at i:10996813 original size:21 final size:20
Alignment explanation
Indices: 10996754--10996813 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
10996744 TGTGGACAAG
*
10996754 CCACCAGAATCGCAGATATA
1 CCACCAGAATTGCAGATATA
*
10996774 CTACCAGAACATATG--GATATA
1 CCACCAG-A-AT-TGCAGATATA
10996795 CCACCAGAATGTGCAGATA
1 CCACCAGAAT-TGCAGATA
10996814 ATTAAACTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 17 0.55
22 2 0.06
23 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
CCACCAGAATTGCAGATATA
Found at i:11011748 original size:18 final size:20
Alignment explanation
Indices: 11011711--11011749 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
11011701 TCAGTCACAT
11011711 AAAGAAAAATGAATGAGAAAA
1 AAAGAAAAA-GAATGAGAAAA
11011732 AAAGAAAAA-AA-GAGAAAA
1 AAAGAAAAAGAATGAGAAAA
11011750 GAAAAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
21 9 0.50
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (20 bp):
AAAGAAAAAGAATGAGAAAA
Found at i:11021557 original size:9 final size:9
Alignment explanation
Indices: 11021543--11021594 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
11021533 GCTCATTTGT
11021543 TTGCTTTTC
1 TTGCTTTTC
11021552 TTGCTTTGT-
1 TTGCTTT-TC
11021561 TTGCTTTTC
1 TTGCTTTTC
11021570 TTGCTTTAT-
1 TTGCTTT-TC
*
11021579 TTTCTTTTC
1 TTGCTTTTC
11021588 TTG-TTTT
1 TTGCTTTT
11021595 GTTTGCTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 6 0.16
9 29 0.78
10 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.12, T:0.71
Consensus pattern (9 bp):
TTGCTTTTC
Found at i:11021561 original size:18 final size:18
Alignment explanation
Indices: 11021538--11021602 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
11021528 CTCAAGCTCA
11021538 TTTGTTTGCTTTTCTTGC
1 TTTGTTTGCTTTTCTTGC
11021556 TTTGTTTGCTTTTCTTGC
1 TTTGTTTGCTTTTCTTGC
* * *
11021574 TTTATTTTCTTTTCTTGT
1 TTTGTTTGCTTTTCTTGC
11021592 TTTGTTTGCTT
1 TTTGTTTGCTT
11021603 GAGGACAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.02, C:0.14, G:0.14, T:0.71
Consensus pattern (18 bp):
TTTGTTTGCTTTTCTTGC
Found at i:11023927 original size:37 final size:37
Alignment explanation
Indices: 11023872--11024122 Score: 256
Period size: 37 Copynumber: 6.8 Consensus size: 37
11023862 AGTAATTCGA
* *
11023872 GCTATATGCCTAGAAGGCTTCGTGCCGGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* **
11023909 GCTATGTGTCTAGCAGGCTTCGTGCC-GAAT-TTCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
*
11023944 GCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* *
11023981 GCTATGTGTCTAGCAGGCTTCGTGCCGATG-ATTTCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTA-TTCAG
* * * **
11024018 GCTATGTGCCAAGCAGGCTTTGTGCCGGTGAAAGCAG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* * * * * * *
11024055 GCTGTGTGCCTAGTAGGATTCGTGGCGGTGAACTCGG
1 GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
* * *
11024092 GCTATATGCCTAGCAAGCCTTTGTGCCGGTG
1 GCTATGTGCCTAGC-AGGCTTCGTGCCGGTG
11024123 ATTGAAGAAC
Statistics
Matches: 175, Mismatches: 34, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
35 29 0.17
36 5 0.03
37 128 0.73
38 13 0.07
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (37 bp):
GCTATGTGCCTAGCAGGCTTCGTGCCGGTGTATTCAG
Found at i:11024077 original size:74 final size:74
Alignment explanation
Indices: 11023872--11024123 Score: 310
Period size: 74 Copynumber: 3.4 Consensus size: 74
11023862 AGTAATTCGA
* * *
11023872 GCTATATGCCTAGAAGGCTTCGTGCCGGTGTATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
1 GCTATATGCCTAGCAGGCTTTGTGCCGGTGAATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
11023937 --ATTTCAG
66 TGATTTCAG
* *
11023944 GCTATGTGCCTAGCAGGCTTTGTGCCGGTGTATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
1 GCTATATGCCTAGCAGGCTTTGTGCCGGTGAATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
11024009 TGATTTCAG
66 TGATTTCAG
* * ** * * * * * *
11024018 GCTATGTGCCAAGCAGGCTTTGTGCCGGTGAAAGCAGGCTGTGTGCCTAGTAGGATTCGTGGCGG
1 GCTATATGCCTAGCAGGCTTTGTGCCGGTGAATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
** *
11024083 TGAACTCGG
66 TGATTTCAG
*
11024092 GCTATATGCCTAGCAAGCCTTTGTGCCGGTGA
1 GCTATATGCCTAGC-AGGCTTTGTGCCGGTGA
11024124 TTGAAGAACT
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
72 62 0.39
74 80 0.51
75 16 0.10
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (74 bp):
GCTATATGCCTAGCAGGCTTTGTGCCGGTGAATTCAGGCTATGTGTCTAGCAGGCTTCGTGCCGA
TGATTTCAG
Found at i:11024449 original size:20 final size:20
Alignment explanation
Indices: 11024413--11024451 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11024403 ATCCTAGTTA
*
11024413 ATATGATGCTTGAGTTGTTT
1 ATATGATGCTGGAGTTGTTT
11024433 ATATG-TGCTGGATGTTGTT
1 ATATGATGCTGGA-GTTGTT
11024452 GTTGAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (20 bp):
ATATGATGCTGGAGTTGTTT
Found at i:11031073 original size:21 final size:21
Alignment explanation
Indices: 11031056--11031102 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
11031046 AGTAGGCTTC
11031056 GTGCCAGTGTATTCAGGCTAT
1 GTGCCAGTGTATTCAGGCTAT
* *
11031077 GTGCCGGTGTATTTAGGCTAT
1 GTGCCAGTGTATTCAGGCTAT
11031098 GTGCC
1 GTGCC
11031103 TAGTAGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (21 bp):
GTGCCAGTGTATTCAGGCTAT
Found at i:11031132 original size:37 final size:37
Alignment explanation
Indices: 11031077--11031237 Score: 164
Period size: 37 Copynumber: 4.3 Consensus size: 37
11031067 TTCAGGCTAT
*
11031077 GTGCCGGTGTATTT-AGGCTATGTGCCTAGTAGACTTC
1 GTGCCGGTG-ATTTCAGGCTATGTGCCTAGTAGGCTTC
* *
11031114 GTGCCGATGATTTCAGGCTATGTGCCTAGTAGGCTTT
1 GTGCCGGTGATTTCAGGCTATGTGCCTAGTAGGCTTC
** *
11031151 GTGCCGGTGAAATC-GAGCTGTGTGCCTAGTAGGCTTC
1 GTGCCGGTGATTTCAG-GCTATGTGCCTAGTAGGCTTC
* ** * * * *
11031188 GTGTCGGTGAACTCCGGCTATATGCCTAGCAGGCCTTT
1 GTGCCGGTGATTTCAGGCTATGTGCCTAGTAGG-CTTC
11031226 GTGCCGGTGATT
1 GTGCCGGTGATT
11031238 GGAGAACTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
36 5 0.05
37 85 0.83
38 13 0.13
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (37 bp):
GTGCCGGTGATTTCAGGCTATGTGCCTAGTAGGCTTC
Found at i:11031175 original size:74 final size:75
Alignment explanation
Indices: 11031097--11031235 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
11031087 ATTTAGGCTA
** * *
11031097 TGTGCCTAGTAGACTTCGTGCCGATGATTTCAGGCTATGTGCCTAGTAGG-CTTTGTGCCGGTGA
1 TGTGCCTAGTAGACTTCGTGCCGATGAACTCAGGCTATATGCCTAGCAGGCCTTTGTGCCGGTGA
11031161 AATCGAGCTG
66 AATCGAGCTG
* * * *
11031171 TGTGCCTAGTAGGCTTCGTGTCGGTGAACTCCGGCTATATGCCTAGCAGGCCTTTGTGCCGGTGA
1 TGTGCCTAGTAGACTTCGTGCCGATGAACTCAGGCTATATGCCTAGCAGGCCTTTGTGCCGGTGA
11031236 TTGGAGAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 42 0.75
75 14 0.25
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (75 bp):
TGTGCCTAGTAGACTTCGTGCCGATGAACTCAGGCTATATGCCTAGCAGGCCTTTGTGCCGGTGA
AATCGAGCTG
Found at i:11031991 original size:60 final size:60
Alignment explanation
Indices: 11031898--11032018 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
11031888 ATGCATGTTT
11031898 ATGTTGTTTTGGTGATGTTATTATGTGAATGCAAGTATGGTAGTCGAGTAATACTTCTTA
1 ATGTTGTTTTGGTGATGTTATTATGTGAATGCAAGTATGGTAGTCGAGTAATACTTCTTA
*
11031958 ATGTTGTTTTGGTGATGTTATTATGTGAATGCAAGTATGGTAGTTGAGTAATACTTCTTA
1 ATGTTGTTTTGGTGATGTTATTATGTGAATGCAAGTATGGTAGTCGAGTAATACTTCTTA
11032018 A
1 A
11032019 CCTAGTCCAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.44
Consensus pattern (60 bp):
ATGTTGTTTTGGTGATGTTATTATGTGAATGCAAGTATGGTAGTCGAGTAATACTTCTTA
Found at i:11037973 original size:15 final size:15
Alignment explanation
Indices: 11037955--11037984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11037945 TACTGTTTAC
11037955 CAATTTACTTTCTTG
1 CAATTTACTTTCTTG
*
11037970 CAATTTATTTTCTTG
1 CAATTTACTTTCTTG
11037985 TATTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (15 bp):
CAATTTACTTTCTTG
Found at i:11038233 original size:12 final size:13
Alignment explanation
Indices: 11038172--11038235 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
11038162 TTTATTCTTT
*
11038172 ATATATATATTAA
1 ATATATATATTAC
* *
11038185 AAACATATTATT-C
1 ATATATA-TATTAC
11038198 TATATATATATATAC
1 -ATATATATAT-TAC
11038213 ATATATATATTAC
1 ATATATATATTAC
*
11038226 TTAT-TATATT
1 ATATATATATT
11038236 TTTATTCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.15
13 14 0.34
14 20 0.49
15 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATTAC
Found at i:11043391 original size:21 final size:22
Alignment explanation
Indices: 11043366--11043408 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
11043356 AATCTAGATT
11043366 AATAAG-AGTTTAATTGAAACA
1 AATAAGAAGTTTAATTGAAACA
11043387 AATAAGCAAAGTTTAATTGAAA
1 AATAAG--AAGTTTAATTGAAA
11043409 GATTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
24 13 0.68
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (22 bp):
AATAAGAAGTTTAATTGAAACA
Found at i:11045157 original size:23 final size:24
Alignment explanation
Indices: 11045129--11045176 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11045119 GATAAAAATT
* *
11045129 AAACCCT-GAAACTTAAAAACAAA
1 AAACCCTCAAAACATAAAAACAAA
*
11045152 AAACCCTCAAAACATAAACACAAA
1 AAACCCTCAAAACATAAAAACAAA
11045176 A
1 A
11045177 TTTTCCAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.62, C:0.25, G:0.02, T:0.10
Consensus pattern (24 bp):
AAACCCTCAAAACATAAAAACAAA
Found at i:11046152 original size:113 final size:113
Alignment explanation
Indices: 11045950--11046158 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 113
11045940 GACAAAACTT
** * ** *
11045950 ATGCCTATGTCGTGACGCCAAGACACCGATGTTGCAACATCGAAGACAGAAGCAAAAACAAGTTC
1 ATGCCTATGTCGCAACACCAAGACACCGATGTCACAACATCGAAGACAGAAGAAAAAACAAGTTC
11046015 TGGAGCAAAACTACCTTCGATGTCGCAACACTGTAGCTCGAATAGCTG
66 TGGAGCAAAACTACCTTCGATGTCGCAACACTGTAGCTCGAATAGCTG
* *
11046063 ATGCCTATGTCGCAACACCAAGACATCGATGTCATAACATCGAAGACAGAAGAAAAAACAAGTTC
1 ATGCCTATGTCGCAACACCAAGACACCGATGTCACAACATCGAAGACAGAAGAAAAAACAAGTTC
** * *
11046128 TGGAGTGAAACTACCTTCGGTGTCGCGACAC
66 TGGAGCAAAACTACCTTCGATGTCGCAACAC
11046159 CGCCCTACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
113 84 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (113 bp):
ATGCCTATGTCGCAACACCAAGACACCGATGTCACAACATCGAAGACAGAAGAAAAAACAAGTTC
TGGAGCAAAACTACCTTCGATGTCGCAACACTGTAGCTCGAATAGCTG
Found at i:11047526 original size:17 final size:17
Alignment explanation
Indices: 11047484--11047526 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
11047474 AGTTACCCTA
*
11047484 ATTTTCTTAGTTTTTAT
1 ATTTTTTTAGTTTTTAT
*
11047501 TTTTTTTTA-TTTTTAT
1 ATTTTTTTAGTTTTTAT
11047517 GATTTTTTTA
1 -ATTTTTTTA
11047527 ATAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (17 bp):
ATTTTTTTAGTTTTTAT
Found at i:11049460 original size:42 final size:42
Alignment explanation
Indices: 11049413--11049494 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
11049403 GCAAAAATGA
11049413 GATAAAGTAGTATGTACGGAGGTGGACCGTTTAAAGGGCCCC
1 GATAAAGTAGTATGTACGGAGGTGGACCGTTTAAAGGGCCCC
11049455 GATAAAGTAGTATGTACGGAGGTGGACCGTTTAAAGGGCC
1 GATAAAGTAGTATGTACGGAGGTGGACCGTTTAAAGGGCC
11049495 TAGGGGGGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GATAAAGTAGTATGTACGGAGGTGGACCGTTTAAAGGGCCCC
Found at i:11049662 original size:32 final size:30
Alignment explanation
Indices: 11049613--11049684 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 30
11049603 CTTTTTTTTT
*
11049613 TTTGAAAATTTAAATTAAGCTCACTTAAAATA
1 TTTGAAAATTTAAATTAAGCTCAC--AAAAAA
* *
11049645 TTTGAAAATTCT-CATTAATCTCACAAAAAA
1 TTTGAAAATT-TAAATTAAGCTCACAAAAAA
11049675 TTT-AAAATTT
1 TTTGAAAATTT
11049685 TTAATTAGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.03
29 6 0.17
30 8 0.22
32 20 0.56
33 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTGAAAATTTAAATTAAGCTCACAAAAAA
Found at i:11062423 original size:24 final size:24
Alignment explanation
Indices: 11062396--11062477 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
11062386 ATTTAGCCCA
* *
11062396 TACGAGCCCAGAATGGCTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
* *
11062420 TACGAGCTCAGAACGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
11062444 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
11062468 TATGAGCCCA
1 TACGAGCCCA
11062478 AAATAAGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:11062521 original size:27 final size:27
Alignment explanation
Indices: 11062463--11062539 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
11062453 AGAATGGTTA
* * *
11062463 GCTCTTATGAGCCCAAAATAAGAATAAC
1 GCTCTTTTGAG-CCAGAATCAGAATAAC
11062491 GCTCTTTTGAGCCAGAATCAGAATAAC
1 GCTCTTTTGAGCCAGAATCAGAATAAC
11062518 GCTCTTTTGAGCCAGAATCAGA
1 GCTCTTTTGAGCCAGAATCAGA
11062540 TTACTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 36 0.78
28 10 0.22
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (27 bp):
GCTCTTTTGAGCCAGAATCAGAATAAC
Found at i:11066126 original size:24 final size:24
Alignment explanation
Indices: 11066099--11066232 Score: 160
Period size: 24 Copynumber: 5.6 Consensus size: 24
11066089 ATTTAGCCCA
* * *
11066099 TACGAGCTCAGAGTGGTTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
* *
11066123 TACGAGCCCAGAACGGTTAGCTTT
1 TACGAGCCCAGAATGGTTAGCTCT
* * *
11066147 TACGAGGCTAGAATGGTTAGCGCT
1 TACGAGCCCAGAATGGTTAGCTCT
* * *
11066171 TATGAGCCCAAAATGGTTAGCGCT
1 TACGAGCCCAGAATGGTTAGCTCT
11066195 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
11066219 TACGAACCCAGAAT
1 TACGAGCCCAGAAT
11066233 CAGAATAATG
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 92 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:11066258 original size:27 final size:27
Alignment explanation
Indices: 11066226--11066313 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
11066216 TCTTACGAAC
* *
11066226 CCAGAATCAGAATAATGCTCTTTTGTG
1 CCAGAATCAGAATAACGCTCTTTTGAG
* *
11066253 CCAGAATCAAAATAGCGCTCTTTTGAG
1 CCAGAATCAGAATAACGCTCTTTTGAG
* *
11066280 CCAGAATCAGAAAAACGCTTTTTTGAG
1 CCAGAATCAGAATAACGCTCTTTTGAG
11066307 CCAGAAT
1 CCAGAAT
11066314 TAGATTACTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (27 bp):
CCAGAATCAGAATAACGCTCTTTTGAG
Found at i:11069001 original size:17 final size:16
Alignment explanation
Indices: 11068970--11069003 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11068960 ACAACTCAAC
*
11068970 TTTTACTTTTATTTTA
1 TTTTACTTGTATTTTA
11068986 TTTTATCTTGTATTTTA
1 TTTTA-CTTGTATTTTA
11069003 T
1 T
11069004 GCTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTACTTGTATTTTA
Found at i:11073431 original size:21 final size:22
Alignment explanation
Indices: 11073405--11073446 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
11073395 AATCAAAAGG
11073405 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
11073426 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
11073447 ACATGAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:11075316 original size:17 final size:16
Alignment explanation
Indices: 11075289--11075322 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
11075279 TCCACTCAAC
11075289 TTTTACTTTTATTTTA
1 TTTTACTTTTATTTTA
11075305 TTTTATCTTTTATTTTA
1 TTTTA-CTTTTATTTTA
11075322 T
1 T
11075323 GCTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTACTTTTATTTTA
Found at i:11079977 original size:32 final size:32
Alignment explanation
Indices: 11079941--11080003 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
11079931 AGCCGAAATT
* *
11079941 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
11079973 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
11080004 TATGTATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:11081057 original size:14 final size:14
Alignment explanation
Indices: 11081038--11081073 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11081028 AGTAAGTTCT
11081038 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
11081052 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
11081066 T-AAAAAAA
1 TGAAAAAAA
11081074 TAGAGAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Found at i:11083183 original size:21 final size:21
Alignment explanation
Indices: 11083159--11083198 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11083149 TGTTGATCAA
*
11083159 GAGAGGGAAAAAGAAAAGAGT
1 GAGAAGGAAAAAGAAAAGAGT
*
11083180 GAGAATGAAAAAGAAAAGA
1 GAGAAGGAAAAAGAAAAGA
11083199 AAATTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (21 bp):
GAGAAGGAAAAAGAAAAGAGT
Found at i:11083200 original size:11 final size:11
Alignment explanation
Indices: 11083186--11083272 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
11083176 GAGTGAGAAT
11083186 GAAAAAGAAAA
1 GAAAAAGAAAA
*
11083197 GAAAATTG-AAA
1 GAAAA-AGAAAA
*
11083208 -AAAAAGAAAG
1 GAAAAAGAAAA
*
11083218 GAAAAATG-AGA
1 GAAAAA-GAAAA
*
11083229 GAAAAAAGCAAA
1 G-AAAAAGAAAA
**
11083241 GAAAGTGAAAA
1 GAAAAAGAAAA
11083252 GAAAGAGAGAAAA
1 GAAA-A-AGAAAA
11083265 GAAAAAGA
1 GAAAAAGA
11083273 TAAAAAGGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
9 1 0.02
10 6 0.11
11 30 0.53
12 11 0.19
13 9 0.16
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.05
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:11083264 original size:29 final size:28
Alignment explanation
Indices: 11083210--11083265 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
11083200 AATTGAAAAA
*
11083210 AAAGAAAGGAAAAATGAGAGAAAAAAGC
1 AAAGAAAGGAAAAATAAGAGAAAAAAGC
*
11083238 AAAGAAAGTGAAAAGA-AAGAGAGAAAAG
1 AAAGAAAG-GAAAA-ATAAGAGAAAAAAG
11083266 AAAAAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 15 0.62
30 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.04
Consensus pattern (28 bp):
AAAGAAAGGAAAAATAAGAGAAAAAAGC
Found at i:11086557 original size:32 final size:32
Alignment explanation
Indices: 11086497--11086559 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
11086487 GGCCGAAATT
* * * *
11086497 AATTAGCTGATTAATTTGTTTTAGGTACATGC
1 AATTAGCTGATTAATATATTTCAAGTACATGC
11086529 AATTAGCTGATTAATATATTTCAAGTACATG
1 AATTAGCTGATTAATATATTTCAAGTACATG
11086560 TATGGATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAAGTACATGC
Found at i:11089355 original size:12 final size:12
Alignment explanation
Indices: 11089338--11089372 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
11089328 GGGTTTAATA
11089338 AAACTAAAAATT
1 AAACTAAAAATT
11089350 AAACTAAATAATT
1 AAACTAAA-AATT
*
11089363 TAACTAAAAA
1 AAACTAAAAA
11089373 AAGAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (12 bp):
AAACTAAAAATT
Found at i:11091294 original size:136 final size:136
Alignment explanation
Indices: 11090999--11091525 Score: 764
Period size: 137 Copynumber: 3.9 Consensus size: 136
11090989 CTCTCAAAGT
* * *** *
11090999 GAATATTAATTTTTATGACTTTTATATTTTGATTGAAATTAATTAATATAACTGCTTATATTAAT
1 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAACTGTTTATATTAAT
*
11091064 AAATTATGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC--ATATT-A-T-ATTCTT
66 AAATT-CGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAATTAATTCTT
11091124 TCCAAAA
130 TCCAAAA
*
11091131 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAATTGTTTATATTAAT
1 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAACTGTTTATATTAAT
* *
11091196 AAATAT-GTCAAATATATACAATTAATATTTT-TATGAATCAAATTCATATATTAATTAAATTAT
66 AAAT-TCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAATT-AATTCT
*
11091259 TTCTAAAA
129 TTCCAAAA
*
11091267 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAATTGTTTATATTAAT
1 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAACTGTTTATATTAAT
* * * * *
11091332 AAATTCAATCAAATATATAAAATTAATATTTT-TATGAATCAAATTCATATATCAATGATATTCT
66 AAATTC-GTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAATTA-ATTCT
11091396 TTCCAAAA
129 TTCCAAAA
* * *
11091404 GAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATAACCGTTTATATTAAT
1 GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAACTGTTTATATTAAT
11091469 AAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
66 AAATTC-GTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAAT
11091526 ATTACCTATG
Statistics
Matches: 359, Mismatches: 25, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
130 14 0.04
131 24 0.07
132 67 0.19
133 2 0.01
134 1 0.00
135 1 0.00
136 81 0.23
137 146 0.41
138 23 0.06
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (136 bp):
GAATATTAATTTTCATGTCTTTTATATTTTGACCCAAATTAATTAATATAACTGTTTATATTAAT
AAATTCGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAATTAATTCTTT
CCAAAA
Found at i:11096034 original size:24 final size:24
Alignment explanation
Indices: 11096002--11096061 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
11095992 AAGTACTCAT
11096002 ACTACCGATACTACTATGAATTGA
1 ACTACCGATACTACTATGAATTGA
11096026 ACTACCGATACTACTATGAATTGA
1 ACTACCGATACTACTATGAATTGA
11096050 ACTACCGATACT
1 ACTACCGATACT
11096062 GTAAACACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (24 bp):
ACTACCGATACTACTATGAATTGA
Found at i:11096667 original size:26 final size:25
Alignment explanation
Indices: 11096636--11096720 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
11096626 ATTTTGGTCA
* *
11096636 TACGAGCCCAAATAGAGTATCGCTCT
1 TACGAG-CCAAACAGAATATCGCTCT
* *
11096662 TTCGAGCCAAACAAAATATCGCTCT
1 TACGAGCCAAACAGAATATCGCTCT
*
11096687 TACGAGCCTAACAGAATATCGCTCT
1 TACGAGCCAAACAGAATATCGCTCT
11096712 TACGAGCCA
1 TACGAGCCA
11096721 GTGTTCAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 46 0.90
26 5 0.10
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (25 bp):
TACGAGCCAAACAGAATATCGCTCT
Found at i:11105476 original size:26 final size:26
Alignment explanation
Indices: 11105447--11105501 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
11105437 GTCTTCCAGA
*
11105447 AGTTTAGCTCGTACGAGCCCAGATAG
1 AGTTTAGCTCGTACGAGCCCAGACAG
*
11105473 AGTTTAGCTCTTACGAGCCCAGACAG
1 AGTTTAGCTCGTACGAGCCCAGACAG
11105499 AGT
1 AGT
11105502 ATCGCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (26 bp):
AGTTTAGCTCGTACGAGCCCAGACAG
Found at i:11105512 original size:26 final size:26
Alignment explanation
Indices: 11105451--11105517 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
11105441 TCCAGAAGTT
* * *
11105451 TAGCTCGTACGAGCCCAGATAGAGTT
1 TAGCTCTTACGAGCCCAGACAGAGTA
11105477 TAGCTCTTACGAGCCCAGACAGAGTA
1 TAGCTCTTACGAGCCCAGACAGAGTA
* *
11105503 TCGCTTTTACGAGCC
1 TAGCTCTTACGAGCC
11105518 AGTGTTTAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (26 bp):
TAGCTCTTACGAGCCCAGACAGAGTA
Found at i:11120854 original size:126 final size:126
Alignment explanation
Indices: 11120629--11120876 Score: 410
Period size: 126 Copynumber: 2.0 Consensus size: 126
11120619 TTTATCAAAG
*
11120629 ATGTAACCTCCCCAACCCGGCCTAGACATTATGGCCGAATCGTGGAAGCCACATGGGACACCTAA
1 ATGTAACCTCCCCAACCCAGCCTAGACATTATGGCCGAATCGTGGAAGCCACATGGGACACCTAA
* *
11120694 GTGTCGACCTTGACCTAAAATAGACAAACCTTCAAGTAATTCCTTTTTGTAAAACCACCAA
66 GTGTCGACCTTGACCCAAAAGAGACAAACCTTCAAGTAATTCCTTTTTGTAAAACCACCAA
* *
11120755 ATGTAACCTCCCCAACTCAGCCTAGACATTATGGCTGAATCGTGGAAGCCACATGGGACACCTAA
1 ATGTAACCTCCCCAACCCAGCCTAGACATTATGGCCGAATCGTGGAAGCCACATGGGACACCTAA
*
11120820 GTGTCGACCCTT-ACCCAAGAGA-ATCAAACCTTCAAGTAATTCCTTTTTGTAAAACCA
66 GTGTCGA-CCTTGACCCAAAAGAGA-CAAACCTTCAAGTAATTCCTTTTTGTAAAACCA
11120877 TAATTTTAAG
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
125 1 0.01
126 109 0.96
127 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (126 bp):
ATGTAACCTCCCCAACCCAGCCTAGACATTATGGCCGAATCGTGGAAGCCACATGGGACACCTAA
GTGTCGACCTTGACCCAAAAGAGACAAACCTTCAAGTAATTCCTTTTTGTAAAACCACCAA
Found at i:11121197 original size:16 final size:17
Alignment explanation
Indices: 11121157--11121198 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
11121147 ATGTGTGAAA
11121157 AATCCCAAAGCAAAATC
1 AATCCCAAAGCAAAATC
11121174 AATCCCAAAGCAAAA-C
1 AATCCCAAAGCAAAATC
*
11121190 AATTCCAAA
1 AATCCCAAA
11121199 CCACAGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.55, C:0.29, G:0.05, T:0.12
Consensus pattern (17 bp):
AATCCCAAAGCAAAATC
Found at i:11121649 original size:28 final size:29
Alignment explanation
Indices: 11121627--11121723 Score: 130
Period size: 28 Copynumber: 3.4 Consensus size: 29
11121617 AATAATGCAG
11121627 AAGATCTGCCAAATAACGAATAATGCGATA
1 AAGATCTGCC-AATAACGAATAATGCGATA
*
11121657 AAGATC-GCCAATATCG-ATAATGCGATA
1 AAGATCTGCCAATAACGAATAATGCGATA
* *
11121684 AAGAT-TGCCAATAACAAATAATGCAATA
1 AAGATCTGCCAATAACGAATAATGCGATA
11121712 AAGATCT-CCAAT
1 AAGATCTGCCAAT
11121724 CCCCTCTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
27 24 0.40
28 26 0.43
29 4 0.07
30 6 0.10
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGATCTGCCAATAACGAATAATGCGATA
Found at i:11121977 original size:43 final size:43
Alignment explanation
Indices: 11121913--11122038 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
11121903 ATCATGCTCT
* * *
11121913 CAATCAATCACATGCTATCAATATTAGGAAACAATGTTCCA-A
1 CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
* *** * *
11121955 TCATTTGTTCACATACTTTCAATAATAGGAAACAGTGTTTCACA
1 -CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
* *
11121999 CAATCAATCTCATACTTTCAATTTTAGGAAACAGTGTTCC
1 CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCC
11122039 TCTCAATGTC
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
43 64 0.98
44 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (43 bp):
CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
Found at i:11128902 original size:26 final size:26
Alignment explanation
Indices: 11128869--11128922 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
11128859 AAAATCTCTC
*
11128869 TTAA-TTTTAAATTT-TTTTAAATTG
1 TTAACTTTTTAATTTATTTTAAATTG
11128893 TTAACTTTTTAATTTATTTTAAATTG
1 TTAACTTTTTAATTTATTTTAAATTG
11128919 TTAA
1 TTAA
11128923 TATTTTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 4 0.15
25 9 0.33
26 14 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
TTAACTTTTTAATTTATTTTAAATTG
Found at i:11128928 original size:26 final size:26
Alignment explanation
Indices: 11128872--11128929 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
11128862 ATCTCTCTTA
11128872 ATTTTAAATTTTTTTAAATTGTTAACT
1 ATTTT-AATTTTTTTAAATTGTTAACT
11128899 -TTTTAATTTATTTTAAATTGTTAA-T
1 ATTTTAATTT-TTTTAAATTGTTAACT
11128924 ATTTTA
1 ATTTTA
11128930 TACTAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (26 bp):
ATTTTAATTTTTTTAAATTGTTAACT
Found at i:11131312 original size:12 final size:13
Alignment explanation
Indices: 11131291--11131325 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
11131281 AACCCAAATT
11131291 AATT-AAATTAAA
1 AATTAAAATTAAA
11131303 AA-TAAAATTAAA
1 AATTAAAATTAAA
11131315 AATTAAAATTA
1 AATTAAAATTA
11131326 TGCTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 12 0.57
13 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAATTAAA
Found at i:11132945 original size:31 final size:31
Alignment explanation
Indices: 11132909--11132971 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11132899 TAACGCGAAA
11132909 ACAATTAATGAACCTTTTTAAAACTTTTTCT
1 ACAATTAATGAACCTTTTTAAAACTTTTTCT
11132940 ACAATTAATGAACCTTTTTAAAACTTTTTCT
1 ACAATTAATGAACCTTTTTAAAACTTTTTCT
11132971 A
1 A
11132972 TGTATTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (31 bp):
ACAATTAATGAACCTTTTTAAAACTTTTTCT
Found at i:11134151 original size:22 final size:22
Alignment explanation
Indices: 11134126--11134181 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
11134116 TAAAAAATAT
*
11134126 TCAATTAAATTGGCGCAATCAA
1 TCAATTAAATTGGCGAAATCAA
* * *
11134148 TCAATTAAATTTGTGAAATTAA
1 TCAATTAAATTGGCGAAATCAA
*
11134170 TCAATTATATTG
1 TCAATTAAATTG
11134182 ATATAATACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
TCAATTAAATTGGCGAAATCAA
Found at i:11149071 original size:16 final size:16
Alignment explanation
Indices: 11149050--11149084 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11149040 TTAGTTTGTC
11149050 AAATAGAAAAATAAAT
1 AAATAGAAAAATAAAT
* *
11149066 AAATAGATAAATGAAT
1 AAATAGAAAAATAAAT
11149082 AAA
1 AAA
11149085 ATGTAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (16 bp):
AAATAGAAAAATAAAT
Found at i:11151139 original size:18 final size:18
Alignment explanation
Indices: 11151114--11151160 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
11151104 TGAAGTGAAA
* *
11151114 ATCCTGAAGTAGAGGAAG
1 ATCCTGAAGAAGAAGAAG
*
11151132 ATCTTGAAGAAGAAGAAG
1 ATCCTGAAGAAGAAGAAG
11151150 ATCCTGAAGAA
1 ATCCTGAAGAA
11151161 ATAGAGCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.28, T:0.17
Consensus pattern (18 bp):
ATCCTGAAGAAGAAGAAG
Found at i:11156739 original size:10 final size:10
Alignment explanation
Indices: 11156711--11156742 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11156701 TTTTTTATTT
11156711 AATATTAAAA
1 AATATTAAAA
11156721 AA-ATT-AAA
1 AATATTAAAA
11156729 AATATTAAAA
1 AATATTAAAA
11156739 AATA
1 AATA
11156743 CTTGTATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.25
9 6 0.30
10 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATATTAAAA
Found at i:11160013 original size:21 final size:21
Alignment explanation
Indices: 11159988--11160028 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11159978 TTAGTGTTTG
11159988 GGATTTTAGATTTCAGATTTT
1 GGATTTTAGATTTCAGATTTT
* *
11160009 GGATTTTGGATTTTAGATTT
1 GGATTTTAGATTTCAGATTT
11160029 AAGGTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (21 bp):
GGATTTTAGATTTCAGATTTT
Found at i:11160043 original size:7 final size:7
Alignment explanation
Indices: 11159989--11160042 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
11159979 TAGTGTTTGG
11159989 GATTTTA
1 GATTTTA
*
11159996 GATTTCA
1 GATTTTA
*
11160003 GATTTTG
1 GATTTTA
*
11160010 GATTTTG
1 GATTTTA
11160017 GATTTTA
1 GATTTTA
*
11160024 GATTTAA
1 GATTTTA
* *
11160031 GGTTTAA
1 GATTTTA
11160038 GATTT
1 GATTT
11160043 AGGGTTTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (7 bp):
GATTTTA
Found at i:11160075 original size:12 final size:12
Alignment explanation
Indices: 11160058--11160085 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11160048 TTGCTCTAAC
11160058 TTAAGTACTTAA
1 TTAAGTACTTAA
11160070 TTAAGTACTTAA
1 TTAAGTACTTAA
11160082 TTAA
1 TTAA
11160086 TGGATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
TTAAGTACTTAA
Found at i:11160919 original size:12 final size:12
Alignment explanation
Indices: 11160902--11160931 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11160892 GTTTGTTCCA
11160902 ACTTAAGTACTT
1 ACTTAAGTACTT
11160914 ACTTAAGTACTT
1 ACTTAAGTACTT
*
11160926 AATTAA
1 ACTTAA
11160932 TTGAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (12 bp):
ACTTAAGTACTT
Found at i:11161189 original size:35 final size:38
Alignment explanation
Indices: 11161124--11161202 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 38
11161114 AAATAAAAAA
11161124 CCTAAACTCTAATACCTTAAAAATCATAAACCATAAAC
1 CCTAAACTCTAATACCTTAAAAATCATAAACCATAAAC
* *
11161162 CCTAAACTCT-ATACC-T-AAAATCCTAAACCATGAAC
1 CCTAAACTCTAATACCTTAAAAATCATAAACCATAAAC
11161197 CCTAAA
1 CCTAAA
11161203 ACCCTAAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 23 0.59
36 1 0.03
37 5 0.13
38 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (38 bp):
CCTAAACTCTAATACCTTAAAAATCATAAACCATAAAC
Found at i:11161203 original size:22 final size:22
Alignment explanation
Indices: 11161175--11161217 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11161165 AAACTCTATA
*
11161175 CCTAAAATCCTAAACCATGAAC
1 CCTAAAACCCTAAACCATGAAC
*
11161197 CCTAAAACCCTAAACCCTGAA
1 CCTAAAACCCTAAACCATGAA
11161218 TACAAACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16
Consensus pattern (22 bp):
CCTAAAACCCTAAACCATGAAC
Found at i:11161211 original size:7 final size:7
Alignment explanation
Indices: 11161150--11161214 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
11161140 TTAAAAATCA
*
11161150 TAAACCA
1 TAAACCC
11161157 TAAACCC
1 TAAACCC
*
11161164 TAAACTC
1 TAAACCC
*
11161171 TATA-CC
1 TAAACCC
*
11161177 TAAAATCC
1 T-AAACCC
*
11161185 TAAACCA
1 TAAACCC
*
11161192 TGAACCC
1 TAAACCC
11161199 TAAAACCC
1 T-AAACCC
11161207 TAAACCC
1 TAAACCC
11161214 T
1 T
11161215 GAATACAAAC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
6 2 0.04
7 34 0.76
8 9 0.20
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:11161252 original size:26 final size:26
Alignment explanation
Indices: 11161216--11161346 Score: 147
Period size: 26 Copynumber: 5.0 Consensus size: 26
11161206 CTAAACCCTG
*
11161216 AATACAAACATCAACATAATTAATTA
1 AATACAAACATAAACATAATTAATTA
11161242 AATACAAACATAAACATAATTAATTA
1 AATACAAACATAAACATAATTAATTA
* *
11161268 AATACAAACATAAAAATTATTAATTA
1 AATACAAACATAAACATAATTAATTA
**
11161294 AATACAAATTTAAACATGAA-TAATTCCA
1 AATACAAACATAAACAT-AATTAATT--A
* ** *
11161322 AATTCATTCATAAACTTAATTAATT
1 AATACAAACATAAACATAATTAATT
11161347 CCAAATGAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
26 68 0.77
27 3 0.03
28 17 0.19
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (26 bp):
AATACAAACATAAACATAATTAATTA
Found at i:11164146 original size:20 final size:20
Alignment explanation
Indices: 11164121--11164169 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11164111 TTGTTTGAAC
*
11164121 AAAATTTG-CTTCCTTGTTAA
1 AAAATTTGTCTT-CTTCTTAA
*
11164141 AAAATTTGTCTTCTTCTTCA
1 AAAATTTGTCTTCTTCTTAA
11164161 AAAATTTGT
1 AAAATTTGT
11164170 GTTTAAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAATTTGTCTTCTTCTTAA
Found at i:11164279 original size:27 final size:27
Alignment explanation
Indices: 11164206--11164273 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
11164196 AAATAGGCAG
11164206 TGGTGCCGCCTACCCAATAGGCATCAT
1 TGGTGCCGCCTACCCAATAGGCATCAT
11164233 TGGTGCCGCCTACCCAATAGGCATCAT
1 TGGTGCCGCCTACCCAATAGGCATCAT
*
11164260 TGGTGCCACCTACC
1 TGGTGCCGCCTACC
11164274 TCATAGACAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCTACCCAATAGGCATCAT
Found at i:11165180 original size:35 final size:35
Alignment explanation
Indices: 11165133--11165298 Score: 251
Period size: 35 Copynumber: 4.7 Consensus size: 35
11165123 TATAATAGCA
*
11165133 TTACGCTCTAACCGAGATGTAAGCAGTCCATAACC
1 TTACGCTCTAACCGAGATGTAAGCAATCCATAACC
* *
11165168 TTACGCTTTAACCGAGACGTAAGCAAATCCATAACC
1 TTACGCTCTAACCGAGATGTAAGC-AATCCATAACC
* *
11165204 TTACACTCTAACCGAGATGTAAGCAATACATAACC
1 TTACGCTCTAACCGAGATGTAAGCAATCCATAACC
*
11165239 TTACGCTCTAATCGAGATGTAAGCAATCCATAACC
1 TTACGCTCTAACCGAGATGTAAGCAATCCATAACC
* *
11165274 TTACGCTCTAACAGAGACGTAAGCA
1 TTACGCTCTAACCGAGATGTAAGCA
11165299 GATCAAAGCT
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 86 0.74
36 31 0.26
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (35 bp):
TTACGCTCTAACCGAGATGTAAGCAATCCATAACC
Found at i:11165255 original size:71 final size:70
Alignment explanation
Indices: 11165133--11165298 Score: 251
Period size: 71 Copynumber: 2.4 Consensus size: 70
11165123 TATAATAGCA
* * *
11165133 TTACGCTCTAACCGAGATGTAAGCAGTCCATAACCTTACGCTTTAACCGAGACGTAAGCAAATCC
1 TTACGCTCTAACCGAGATGTAAGCAATACATAACCTTACGCTCTAACCGAGACGTAAGC-AATCC
11165198 ATAACC
65 ATAACC
* * *
11165204 TTACACTCTAACCGAGATGTAAGCAATACATAACCTTACGCTCTAATCGAGATGTAAGCAATCCA
1 TTACGCTCTAACCGAGATGTAAGCAATACATAACCTTACGCTCTAACCGAGACGTAAGCAATCCA
11165269 TAACC
66 TAACC
* *
11165274 TTACGCTCTAACAGAGACGTAAGCA
1 TTACGCTCTAACCGAGATGTAAGCA
11165299 GATCAAAGCT
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 33 0.38
71 53 0.62
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (70 bp):
TTACGCTCTAACCGAGATGTAAGCAATACATAACCTTACGCTCTAACCGAGACGTAAGCAATCCA
TAACC
Found at i:11167926 original size:2 final size:2
Alignment explanation
Indices: 11167919--11167964 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11167909 GACAATTATT
11167919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11167961 TA TA
1 TA TA
11167965 AATTACCATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11169874 original size:43 final size:43
Alignment explanation
Indices: 11169760--11169937 Score: 277
Period size: 43 Copynumber: 4.2 Consensus size: 43
11169750 CCTTTAGCAA
*
11169760 CCGCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCACAAGCG
1 CCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
* *
11169803 CCGCTAAAGG-CATGTTTTTTAGCGGCGCTTTCTCCACAAGTG
1 CCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
*
11169845 CCGCTAAAGCCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
1 CCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
* * * *
11169888 CCACTAAAGGCCATGTTCTTTAGTGACGCTTTCTCCAAAAGCG
1 CCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
11169931 CCGCTAA
1 CCGCTAA
11169938 TATAACAGAT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 38 0.31
43 84 0.69
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCACAAGCG
Found at i:11170245 original size:21 final size:21
Alignment explanation
Indices: 11170220--11170272 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
11170210 CTTGTAGCCT
* *
11170220 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
11170241 CTGCTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
* *
11170262 CTTCTACCTCC
1 CTGCTGCCTCC
11170273 ACTTTAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.47, G:0.17, T:0.34
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Found at i:11170344 original size:65 final size:66
Alignment explanation
Indices: 11170268--11170414 Score: 242
Period size: 66 Copynumber: 2.2 Consensus size: 66
11170258 CTCGCTTCTA
* *
11170268 CCTCCACTTTAAGTTGTAGATGGAGTTCTTCATA-TTTTTTTGAGACTCTGCTTCTCTCACTGCA
1 CCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCA
11170332 G
66 G
* * *
11170333 CCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCA
1 CCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCA
11170398 G
66 G
11170399 CCTCCTCTTTAAGTTG
1 CCTCCTCTTTAAGTTG
11170415 AGCAATTTGC
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 31 0.41
66 44 0.59
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43
Consensus pattern (66 bp):
CCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCA
G
Found at i:11176023 original size:112 final size:108
Alignment explanation
Indices: 11175900--11176748 Score: 987
Period size: 112 Copynumber: 7.7 Consensus size: 108
11175890 TTGTTTTCAT
***
11175900 TAATTAAATAA-TTATATATAATTATTTACGAAAATATTTTAAATTAAATATTTAATTAAATATA
1 TAATTAAATAATTTA-ATATAATTATTTACTTTAATA---TAAATTAAATATTTAATTAAAT-TA
**
11175964 ATTAAATAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
61 ATTATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* *
11176012 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAATAATTAAATCTTTTAATTAA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAAT-ATTTAA---TTAAATTAA
* *
11176077 ATATTTAATTAATTGATACTGTTTACAATTAAGTACATAATTAAACA
62 TTATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* * *
11176124 TAATTAATTGATTTAATATAATTATTTACTTTAATAT-AATTAAATAATTAAATATTTTAAATTA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAAT-ATT---TA-ATTAAATTA
* *
11176188 ATTATTTAATTAATTGATACGGTTTATAATTAAATACATAATTAAACA
61 ATTATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
*
11176236 TAATTAAATAATTTAATATAATTATTTAGTTTAATAT-AATTAAATA-TT--TTAAATTAATTAT
1 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAATATTTAATTAAATTAATTAT
* * *
11176297 TTAATTAATTGGTACTGTTTATAATTTAATACATAATTAAACA
66 TTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* *
11176340 TAATTAAATAATTTAATATAATTATTTACTTTAATATAACTTAAATAATTAAATCTTTTAAATTA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAAT-ATTTAA----TTAAATTA
*
11176405 AATATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
61 ATTATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* * *
11176453 TAATTAATTGATTTAATATAATTATTTACTTTAATATAAATTAAATAATTAAATCTTTTAAATTA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAAT-ATTTAA----TTAAATTA
*
11176518 AATATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
61 ATTATTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* * * * * * *
11176566 TAATTAATTGATTTAATATAATTATTTAGTTTAATATTTAATTAAAT-CTT--TCAAATTAAATA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATA-TAAATTAAATATTTAATTAAATTAATTA
* * * * *
11176628 TTTAATTAACTAATAATGTTTATAATTAAATATATAATTAAACA
65 TTTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
* * * *
11176672 TAATTAAATAATTAAATATAATTATTTAATTAAATATTTCAAAATAAATATTTAATTAAATATAA
1 TAATTAAATAATTTAATATAATTATTTACTTTAATA--T-AAATTAAATATTTAATTAAAT-TAA
**
11176737 TTAAATAATTAA
62 TTATTTAATTAA
11176749 ATTTTTCAAA
Statistics
Matches: 656, Mismatches: 56, Indels: 50
0.86 0.07 0.07
Matches are distributed among these distances:
104 89 0.14
105 7 0.01
106 82 0.12
107 4 0.01
108 7 0.01
109 12 0.02
110 6 0.01
111 18 0.03
112 216 0.33
113 205 0.31
114 10 0.02
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (108 bp):
TAATTAAATAATTTAATATAATTATTTACTTTAATATAAATTAAATATTTAATTAAATTAATTAT
TTAATTAATTGATACTGTTTACAATTAAATACATAATTAAACA
Found at i:11176024 original size:18 final size:18
Alignment explanation
Indices: 11176001--11176393 Score: 101
Period size: 18 Copynumber: 21.6 Consensus size: 18
11175991 AATTAAATAC
*
11176001 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
* *
11176019 ATAATTTAATATAATTAT
1 ATAATTAAATATAATTAA
* * *
11176037 TTACTTTAATATAAATTAA
1 ATAATTAAATAT-AATTAA
*
11176056 ATAATTAAATCTTTTAATTAA
1 ATAATTAAA---TATAATTAA
*
11176077 AT-ATTTAAT-TAATTGATA
1 ATAATTAAATATAATT-A-A
* ** * *
11176095 CTGTTTACAAT-TAAGTAC
1 ATAATTA-AATATAATTAA
*
11176113 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
* * * *
11176131 TTGATTTAATATAATTAT
1 ATAATTAAATATAATTAA
* * *
11176149 TTACTTTAATATAATTAA
1 ATAATTAAATATAATTAA
*
11176167 ATAATTAAATAT-TTTAA
1 ATAATTAAATATAATTAA
*
11176184 ATTAATTATTTAAT-TAATT-G
1 A-TAATTA---AATATAATTAA
* * *
11176204 ATACGGTTTATAAT-TAAATAC
1 ATA---ATTA-AATATAATTAA
*
11176225 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
* *
11176243 ATAATTTAATATAATTAT
1 ATAATTAAATATAATTAA
* * *
11176261 TTAGTTTAATATAATTAA
1 ATAATTAAATATAATTAA
* *
11176279 ATATTTTAAAT-TAATTAT
1 ATA-ATTAAATATAATTAA
* **
11176297 TTAATT-AAT-T-GGT-A
1 ATAATTAAATATAATTAA
* ** * *
11176311 CTGTTTATAATTTAA-TAC
1 ATAATTA-AATATAATTAA
*
11176329 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
* *
11176347 ATAATTTAATATAATTAT
1 ATAATTAAATATAATTAA
* * *
11176365 TTACTTTAATATAACTTAA
1 ATAATTAAATATAA-TTAA
11176384 ATAATTAAAT
1 ATAATTAAAT
11176394 CTTTTAAATT
Statistics
Matches: 270, Mismatches: 78, Indels: 53
0.67 0.19 0.13
Matches are distributed among these distances:
14 3 0.01
15 1 0.00
16 12 0.04
17 20 0.07
18 160 0.59
19 31 0.11
20 22 0.08
21 16 0.06
22 5 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:11176073 original size:13 final size:12
Alignment explanation
Indices: 11175899--11176088 Score: 74
Period size: 12 Copynumber: 15.7 Consensus size: 12
11175889 GTTGTTTTCA
*
11175899 TTAATTAAATAA
1 TTAATTAAATAT
*
11175911 TTATATATAATTAT
1 TTA-AT-TAAATAT
***
11175925 TTACGAAAATATT
1 TTAATTAAATA-T
11175938 TTAAATTAAATAT
1 TT-AATTAAATAT
11175951 TTAATTAAATA-
1 TTAATTAAATAT
*
11175962 -TAATTAAATAA
1 TTAATTAAATAT
* *
11175973 TTAATTGATACTGT
1 TTAATT-A-AATAT
*
11175987 TTACAATTAAATAC
1 TT--AATTAAATAT
* *
11176001 ATAATTAAACA-
1 TTAATTAAATAT
11176012 -TAATTAAATAAT
1 TTAATTAAAT-AT
*
11176024 TTAATATAATTAT
1 TTAAT-TAAATAT
* *
11176037 TTACTTTAATA-
1 TTAATTAAATAT
*
11176048 TAAATT-AA-A-
1 TTAATTAAATAT
*
11176057 -TAATTAAATCTT
1 TTAATTAAAT-AT
11176069 TTAATTAAATAT
1 TTAATTAAATAT
11176081 TTAATTAA
1 TTAATTAA
11176089 TTGATACTGT
Statistics
Matches: 132, Mismatches: 27, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
8 4 0.03
9 3 0.02
10 20 0.15
11 5 0.04
12 42 0.32
13 28 0.21
14 25 0.19
15 1 0.01
16 4 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAATTAAATAT
Found at i:11176360 original size:10 final size:10
Alignment explanation
Indices: 11176316--11176389 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
11176306 TGGTACTGTT
11176316 TATAATTTAA
1 TATAATTTAA
*
11176326 TACATAATTAAA
1 T--ATAATTTAA
*
11176338 CATAA-TTAA
1 TATAATTTAA
11176347 -ATAATTTAA
1 TATAATTTAA
11176356 TATAA-TT-A
1 TATAATTTAA
* *
11176364 TTTACTTTAA
1 TATAATTTAA
*
11176374 TATAACTTAA
1 TATAATTTAA
11176384 -ATAATT
1 TATAATT
11176390 AAATCTTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
8 8 0.16
9 16 0.33
10 17 0.35
12 8 0.16
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (10 bp):
TATAATTTAA
Found at i:11176399 original size:113 final size:112
Alignment explanation
Indices: 11176266--11176708 Score: 646
Period size: 113 Copynumber: 4.0 Consensus size: 112
11176256 ATTATTTAGT
* * * * *
11176266 TTAATATAATTAAATATTTTAAATTAATTATTTAATTAATTGGTACTGTTTATAATTTAATACAT
1 TTAA-ATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACAT
11176331 AATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAA
65 AATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAA
11176379 CTTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACAT
1 -TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACAT
* *
11176444 AATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAAA
65 AATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATAT-AA
11176493 TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
1 TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
* * *
11176558 ATTAAACATAATTAATTGATTTAATATAATTATTTAGTTT-A-AT-A
66 ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAA
* * * * * *
11176602 TT---TAATTAAATCTTTCAAATTAAATATTTAATTAACTAATAATGTTTATAATTAAATATATA
1 TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
* * *
11176664 ATTAAACATAATTAAATAATTAAATATAATTATTTAATTAAATAT
66 ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATAT
11176709 TTCAAAATAA
Statistics
Matches: 307, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
106 89 0.29
107 1 0.00
108 2 0.01
109 3 0.01
111 2 0.01
112 1 0.00
113 203 0.66
114 6 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (112 bp):
TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
ATTAAACATAATTAAATAATTTAATATAATTATTTACTTTAATATAA
Found at i:11176475 original size:18 final size:19
Alignment explanation
Indices: 11176452--11176496 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
11176442 ATAATTAAAC
11176452 ATAATTAATTGA-TTTAAT
1 ATAATTAATTGACTTTAAT
*
11176470 ATAATT-ATTTACTTTAAT
1 ATAATTAATTGACTTTAAT
11176488 ATAAATTAA
1 AT-AATTAA
11176497 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 4 0.17
20 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATAATTAATTGACTTTAAT
Found at i:11176588 original size:18 final size:18
Alignment explanation
Indices: 11176565--11176602 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11176555 ATAATTAAAC
11176565 ATAATTAATTGA-TTTAAT
1 ATAATT-ATTGAGTTTAAT
*
11176583 ATAATTATTTAGTTTAAT
1 ATAATTATTGAGTTTAAT
11176601 AT
1 AT
11176603 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATAATTATTGAGTTTAAT
Found at i:11176592 original size:13 final size:12
Alignment explanation
Indices: 11176566--11176636 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 12
11176556 TAATTAAACA
11176566 TAATTAATTGATT
1 TAATTAATT-ATT
11176579 TAATATAATTATT
1 TAAT-TAATTATT
*
11176592 TAGTTTAA-TATT
1 TA-ATTAATTATT
* *
11176604 TAATTAAATCTT
1 TAATTAATTATT
*
11176616 TCAAATTAAATATT
1 T--AATTAATTATT
11176630 TAATTAA
1 TAATTAA
11176637 CTAATAATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.08
12 16 0.33
13 12 0.24
14 17 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
TAATTAATTATT
Found at i:11176674 original size:10 final size:9
Alignment explanation
Indices: 11176661--11176749 Score: 53
Period size: 8 Copynumber: 10.0 Consensus size: 9
11176651 AATTAAATAT
11176661 ATAATTAAA
1 ATAATTAAA
11176670 CATAATT-AA
1 -ATAATTAAA
11176679 ATAATTAAA
1 ATAATTAAA
*
11176688 TATAATT-AT
1 -ATAATTAAA
*
11176697 TTAATT-AA
1 ATAATTAAA
*
11176705 ATATTTCAAA
1 ATAATT-AAA
* *
11176715 ATAAAT-AT
1 ATAATTAAA
*
11176723 TTAATTAAA
1 ATAATTAAA
11176732 TATAATT-AA
1 -ATAATTAAA
11176741 ATAATTAAA
1 ATAATTAAA
11176750 TTTTTCAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
8 27 0.45
9 10 0.17
10 23 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAATTAAA
Found at i:11176686 original size:62 final size:61
Alignment explanation
Indices: 11176619--11176750 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 61
11176609 AAATCTTTCA
* *
11176619 AATTAAATAT-TTAATTAACT-AATAATGTTTATAATTAAATATATAATTAAACATAATTAAAT
1 AATTAAATATATTAATTAACTAAAT-AT-TTCA-AAATAAATATATAATTAAACATAATTAAAT
* * * *
11176681 AATTAAATATAATTATTTAATTAAATATTTCAAAATAAATATTTAATTAAATATAATTAAAT
1 AATTAAATAT-ATTAATTAACTAAATATTTCAAAATAAATATATAATTAAACATAATTAAAT
11176743 AATTAAAT
1 AATTAAAT
11176751 TTTTCAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 45 0.74
63 3 0.05
64 10 0.16
65 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (61 bp):
AATTAAATATATTAATTAACTAAATATTTCAAAATAAATATATAATTAAACATAATTAAAT
Found at i:11176706 original size:18 final size:18
Alignment explanation
Indices: 11176661--11176750 Score: 74
Period size: 18 Copynumber: 5.6 Consensus size: 18
11176651 AATTAAATAT
*
11176661 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
*
11176679 ATAATTAAATATAATTAT
1 ATAATTAAATATAATTAA
* *
11176697 TTAATTAAATAT--TTCA
1 ATAATTAAATATAATTAA
11176713 A-AA-T-AA-AT-ATT--
1 ATAATTAAATATAATTAA
11176724 -TAATTAAATATAATTAA
1 ATAATTAAATATAATTAA
11176741 ATAATTAAAT
1 ATAATTAAAT
11176751 TTTTCAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
11 2 0.04
12 3 0.05
13 6 0.11
14 3 0.05
15 5 0.09
16 2 0.04
18 36 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:11176706 original size:26 final size:26
Alignment explanation
Indices: 11176672--11176771 Score: 96
Period size: 26 Copynumber: 3.7 Consensus size: 26
11176662 TAATTAAACA
*
11176672 TAATTAAATAATTAAATATAATTATT
1 TAATTAAATAATTAAATATAAATATT
*
11176698 TAATTAAATATTTCAAA-ATAAATATT
1 TAATTAAATAATT-AAATATAAATATT
*
11176724 TAATTAAATATAATTAAATAATTAAATTTT
1 TAATT-AA-ATAATTAAAT-A-TAAATATT
11176754 TCAAATTAAAT-ATTAAAT
1 T--AATTAAATAATTAAAT
11176772 TGACTAATAC
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
26 25 0.40
27 8 0.13
28 5 0.08
29 8 0.13
30 10 0.16
31 2 0.03
32 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATTAAATAATTAAATATAAATATT
Found at i:11176735 original size:44 final size:44
Alignment explanation
Indices: 11176600--11176772 Score: 168
Period size: 44 Copynumber: 3.8 Consensus size: 44
11176590 TTTAGTTTAA
* * *
11176600 TATTTAATTAAATCTTTCAAATTAAATATTTAATTAACTAATAAT
1 TATTTAATTAAATATTTCAAAATAAATATTTAATTAAAT-ATAAT
* * **
11176645 GT-TTATAATTAAATATATAATTAAACATAATTAAATAATTAAATATAAT
1 -TATT-TAATTAAATAT-T--TCAAA-ATAAATATTTAATTAAATATAAT
11176694 TATTTAATTAAATATTTCAAAATAAATATTTAATTAAATATAAT
1 TATTTAATTAAATATTTCAAAATAAATATTTAATTAAATATAAT
** * * *
11176738 TAAATAATTAAATTTTTCAAATTAAATATTAAATT
1 TATTTAATTAAATATTTCAAAATAAATATTTAATT
11176773 GACTAATACT
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
44 50 0.48
45 6 0.06
46 11 0.10
47 2 0.02
48 12 0.11
49 11 0.10
50 13 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (44 bp):
TATTTAATTAAATATTTCAAAATAAATATTTAATTAAATATAAT
Found at i:11176803 original size:330 final size:329
Alignment explanation
Indices: 11175970--11176819 Score: 1121
Period size: 330 Copynumber: 2.6 Consensus size: 329
11175960 TATAATTAAA
* * * * *
11175970 TAATTAATTGATACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAATATAATT
1 TAATTAACTAATAATGTTTATAATTAAATACATAATTAAACATAATTAAATAATTAAATATAATT
* * * * *
11176035 ATTTACTTTAATATAAATTAAATAATTAAATC-TTTTAATTAAATATTTAATTAATTGATACTGT
66 ATTTACATTAATATAACTTAAATAATTAAATCATTTAAATTAAATATTTAAATAATTGATAATGT
* * *
11176099 TTACAATTAAGTACATAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAAT
131 TTACAATTAAATACATAATTAAACATAATTAATTAATTAAATATAATTATTTACTTTAATATAAT
* *
11176164 TAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGATACGGTTTATAATTAAATACATAA
196 TAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACGGTTTACAATTAAATACATAA
* *
11176229 TTAAACATAATTAAATAATTTAATATAATTATTTAGTTTAATATAATTAAATATTTTAAATTAAT
261 TTAAACATAATTAAATAATTTAATATAATTATTTAGTTTAATATAATTAAATATTTCAAATTAAA
11176294 TATT
326 TATT
* ** * * *
11176298 TAATTAATTGGTACTGTTTATAATTTAATACATAATTAAACATAATTAAATAATTTAATATAATT
1 TAATTAACTAATAATGTTTATAATTAAATACATAATTAAACATAATTAAATAATTAAATATAATT
* * * *
11176363 ATTTACTTTAATATAACTTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGT
66 ATTTACATTAATATAACTTAAATAATTAAATCATTTAAATTAAATATTTAAATAATTGATAATGT
* *
11176428 TTACAATTAAATACATAATTAAACATAATTAATTGATTTAATATAATTATTTACTTTAATATAAA
131 TTACAATTAAATACATAATTAAACATAATTAATTAATTAAATATAATTATTTACTTTAATAT-AA
* *
11176493 TTAAATAATTAAATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTAAATACATA
195 TTAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACGGTTTACAATTAAATACATA
* * *
11176558 ATTAAACATAATTAATTGATTTAATATAATTATTTAGTTTAATATTTAATTAAATCTTTCAAATT
260 ATTAAACATAATTAAATAATTTAATATAATTATTTAGTTTAATA--TAATTAAATATTTCAAATT
11176623 AAATATT
323 AAATATT
*
11176630 TAATTAACTAATAATGTTTATAATTAAATATATAATTAAACATAATTAAATAATTAAATATAATT
1 TAATTAACTAATAATGTTTATAATTAAATACATAATTAAACATAATTAAATAATTAAATATAATT
* *
11176695 ATTTA-ATTAA-AT-ATTTCAA-AA-TAAAT-ATTT-AATTAAATATAATTAAATAATT-A-AAT
66 ATTTACATTAATATAACTTAAATAATTAAATCATTTAAATTAAATAT--TTAAATAATTGATAAT
* * * * **
11176751 -TTTTCAAATTAAATA-TTAAATTGACTAATACTGATTGTTTAAATTAAATATAATTATTTACTT
129 GTTTAC-AATTAAATACAT-AATT-A--AACA-TAATTAATT-AATTAAATATAATTATTTACTT
11176814 TAATAT
187 TAATAT
11176820 TTTAATTTTA
Statistics
Matches: 473, Mismatches: 36, Indels: 24
0.89 0.07 0.05
Matches are distributed among these distances:
324 5 0.01
325 25 0.05
326 5 0.01
327 14 0.03
328 98 0.21
329 103 0.22
330 133 0.28
331 4 0.01
332 86 0.18
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (329 bp):
TAATTAACTAATAATGTTTATAATTAAATACATAATTAAACATAATTAAATAATTAAATATAATT
ATTTACATTAATATAACTTAAATAATTAAATCATTTAAATTAAATATTTAAATAATTGATAATGT
TTACAATTAAATACATAATTAAACATAATTAATTAATTAAATATAATTATTTACTTTAATATAAT
TAAATAATTAAATATTTTAAATTAAATATTTAATTAATTGATACGGTTTACAATTAAATACATAA
TTAAACATAATTAAATAATTTAATATAATTATTTAGTTTAATATAATTAAATATTTCAAATTAAA
TATT
Found at i:11177059 original size:18 final size:18
Alignment explanation
Indices: 11177038--11177087 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
11177028 TAAATTAAAC
11177038 ATAATTAAATAATTTAAT
1 ATAATTAAATAATTTAAT
** *
11177056 ATAATTATTTACTTTAAT
1 ATAATTAAATAATTTAAT
11177074 ATAATTAAATAATT
1 ATAATTAAATAATT
11177088 AAATCTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAATTAAATAATTTAAT
Found at i:11177154 original size:76 final size:76
Alignment explanation
Indices: 11177074--11177588 Score: 478
Period size: 76 Copynumber: 7.2 Consensus size: 76
11177064 TTACTTTAAT
11177074 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
11177139 TTTAATTAAAC
66 TTTAATTAAAC
*
11177150 ATAATTAAATAATTAAATCTTTTAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
11177215 TTTAATTAAAC
66 TTTAATTAAAC
* *
11177226 ATAATTAAATAATTAAATCTTTTAAATTAAATATTAAA-TAACTAATACAGTTTATAATTAAATA
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
*
11177290 TATAATTAAAC
66 TTTAATTAAAC
* * * ** * *
11177301 ATAGTTAAATAATTAAA--TAT--AATT--AT-TTACATTAA-T-ATTTTAATTT-T-ATT-CAT
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACT-GTTTATAATTAAAT
*
11177354 -TTAAATAT----
65 ATTTAAT-TAAAC
* *
11177362 --AATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAATTAAATA
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
*
11177425 TATAATTAAAC
66 TTTAATTAAAC
* * ** ** * *
11177436 ATAGTTAAATAATTAAA--TAT--AATT--AT-TTACTTTAA-T-ATTTTAATTT-T-ATT-CAT
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACT-GTTTATAATTAAAT
*
11177489 -TTAAATAT----
65 ATTTAAT-TAAAC
* * *
11177497 --AATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTATTTATAATTAAATA
1 ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
11177560 TTTAATTAAAC
66 TTTAATTAAAC
11177571 ATAATTAAATAATTAAAT
1 ATAATTAAATAATTAAAT
11177589 ATAATTAAAT
Statistics
Matches: 353, Mismatches: 43, Indels: 86
0.73 0.09 0.18
Matches are distributed among these distances:
59 28 0.08
61 4 0.01
63 8 0.02
64 8 0.02
65 10 0.03
66 19 0.05
67 16 0.05
68 20 0.06
69 17 0.05
70 8 0.02
71 13 0.04
72 4 0.01
73 2 0.01
74 2 0.01
75 51 0.14
76 143 0.41
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (76 bp):
ATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAATTAAATA
TTTAATTAAAC
Found at i:11177444 original size:135 final size:135
Alignment explanation
Indices: 11177220--11177595 Score: 664
Period size: 135 Copynumber: 2.8 Consensus size: 135
11177210 AAATATTTAA
* * * * *
11177220 TTAAACATAATTAAATAATTAAATCTTTTAAATTAAATA-TTAAATAACTAATACAGTTTATAAT
1 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAAT
11177284 TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTATTTACATTAATATTTTAATTTTA
66 TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTATTTACATTAATATTTTAATTTTA
11177349 TTCAT
131 TTCAT
11177354 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAAT
1 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAAT
*
11177419 TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTATTTACTTTAATATTTTAATTTTA
66 TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTATTTACATTAATATTTTAATTTTA
11177484 TTCAT
131 TTCAT
*
11177489 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTATTTATAAT
1 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAAT
* *
11177554 TAAATATTTAATTAAACATAATTAAATAATTAAATATAATTA
66 TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTA
11177596 AATAATTAAA
Statistics
Matches: 232, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
134 37 0.16
135 195 0.84
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (135 bp):
TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTGTTTATAAT
TAAATATATAATTAAACATAGTTAAATAATTAAATATAATTATTTACATTAATATTTTAATTTTA
TTCAT
Found at i:11177582 original size:8 final size:8
Alignment explanation
Indices: 11177549--11177606 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
11177539 GATACTATTT
11177549 ATAATTAA
1 ATAATTAA
*
11177557 ATATTTAA
1 ATAATTAA
* *
11177565 TTAA--AC
1 ATAATTAA
11177571 ATAATTAA
1 ATAATTAA
11177579 ATAATTAAA
1 ATAATT-AA
11177588 TATAATTAA
1 -ATAATTAA
11177597 ATAATTAA
1 ATAATTAA
11177605 AT
1 AT
11177607 CTTTCAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
6 4 0.10
8 26 0.65
9 4 0.10
10 6 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATTAA
Found at i:11177587 original size:94 final size:94
Alignment explanation
Indices: 11177489--11177689 Score: 366
Period size: 94 Copynumber: 2.1 Consensus size: 94
11177479 TTTTATTCAT
* *
11177489 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACTGATACTATTTATAAT
1 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTATTTATAAT
*
11177554 TAAATATTTAATTAAACATAATTAAATAA
66 TAAATATATAATTAAACATAATTAAATAA
*
11177583 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTGTTTATAAT
1 TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTATTTATAAT
11177648 TAAATATATAATTAAACATAATTAAATAA
66 TAAATATATAATTAAACATAATTAAATAA
11177677 TTAAATATAATTA
1 TTAAATATAATTA
11177690 TTTACTTTAA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 103 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (94 bp):
TTAAATATAATTAAATAATTAAATCTTTCAAATTAAATATTAAATTAACTAATACTATTTATAAT
TAAATATATAATTAAACATAATTAAATAA
Found at i:11177649 original size:32 final size:31
Alignment explanation
Indices: 11177519--11177684 Score: 105
Period size: 32 Copynumber: 5.3 Consensus size: 31
11177509 AAATCTTTCA
* * *
11177519 AATTAAATATTTAATTAACTGATACTATTTAT
1 AATTAAATATTAAATTAACTAATAAT-TTTAT
* **
11177551 AATTAAATATTTAATTAA--ACATAATTAAAT
1 AATTAAATATTAAATTAACTA-ATAATTTTAT
*
11177581 AATTAAATA-T-AATTAAATAATTAAATCTTTCA-
1 AATTAAATATTAAATTAACTAA-T-AAT-TTT-AT
*
11177613 AATTAAATATTAAATTAACTAATACTGTTTAT
1 AATTAAATATTAAATTAACTAATAAT-TTTAT
**
11177645 AATTAAATA-TATAATTAA--ACATAATTAAAT
1 AATTAAATATTA-AATTAACTA-ATAATTTTAT
11177675 AATTAAATAT
1 AATTAAATAT
11177685 AATTATTTAC
Statistics
Matches: 109, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
28 6 0.06
29 2 0.02
30 27 0.25
31 14 0.13
32 48 0.44
33 3 0.03
34 9 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (31 bp):
AATTAAATATTAAATTAACTAATAATTTTAT
Found at i:11180221 original size:13 final size:13
Alignment explanation
Indices: 11180205--11180230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11180195 TTTTCCTCAG
11180205 ATTTTGGCTGATT
1 ATTTTGGCTGATT
11180218 ATTTTGGCTGATT
1 ATTTTGGCTGATT
11180231 TTGGTACGTA
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:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
ATTTTGGCTGATT
Found at i:11180402 original size:15 final size:17
Alignment explanation
Indices: 11180370--11180402 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11180360 TTATTTGTTT
11180370 TTTTCTTTTAAATCTAA
1 TTTTCTTTTAAATCTAA
11180387 TTTT-TTTTAAAT-TAA
1 TTTTCTTTTAAATCTAA
11180402 T
1 T
11180403 CAAACTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTTTTAAATCTAA
Found at i:11181575 original size:42 final size:42
Alignment explanation
Indices: 11181503--11181702 Score: 239
Period size: 41 Copynumber: 4.9 Consensus size: 42
11181493 GCTTATGGGA
* * *
11181503 AAGCGCCGCTAAT-TC-ACACCTTTAGTGGCGCTTTTCTAAT
1 AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCTAAT
* ** *
11181543 AAGCGCCGCTAAAGACCTGACCTTTAGCGGCGCTTATTATAA-
1 AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTT-TTCTAAT
* *
11181585 AAGCGCCGCTAATGACAAAACCTTTAGCGGCGCTTTT-TTAT
1 AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCTAAT
*
11181626 AAACGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCT-AT
1 AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCTAAT
** *
11181667 AAGCGCCGCTAATGACCCGACCTTTAGCGGTGCTTT
1 AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTT
11181703 GTGGAAAGCG
Statistics
Matches: 138, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
40 14 0.10
41 72 0.52
42 47 0.34
43 5 0.04
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (42 bp):
AAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCTAAT
Found at i:11182385 original size:36 final size:36
Alignment explanation
Indices: 11182312--11182544 Score: 344
Period size: 36 Copynumber: 6.5 Consensus size: 36
11182302 TATAATAGCT
* * *
11182312 GCTCTAATCGAGACGTAA-TAAGTCCATAACCTTAC
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
*
11182347 GCTCTAACCGAGACGTAAGCAAATCCATAACCTGAC
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
*
11182383 GCTCTAATCGAGACGTAAGCAAATCCATAACCTTAC
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
* **
11182419 ACTCTAACCGAGACGTAAGCAAATCCATAACCTTGT
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
*
11182455 GCTCTAACCGAGACGTAAACAAATCCATAACCTTAC
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
* *
11182491 ACTCTAACCGAAACGTAAGC-AATCCATAACCTTAC
1 GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
*
11182526 GCTCTAACCGAGACCTAAG
1 GCTCTAACCGAGACGTAAG
11182545 GAGGGTCCAA
Statistics
Matches: 177, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 48 0.27
36 129 0.73
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (36 bp):
GCTCTAACCGAGACGTAAGCAAATCCATAACCTTAC
Found at i:11185689 original size:35 final size:35
Alignment explanation
Indices: 11185568--11185771 Score: 254
Period size: 35 Copynumber: 5.9 Consensus size: 35
11185558 CGAGAAGTAG
11185568 TCCATAACCTTACGCTCTAACCGAGACGTAAGCAAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAAGC-AA
* *
11185604 TCCGTAACCTTACACTCTAACCGAGACGTAAGCAAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAAGC-AA
* ** *
11185640 TCCAT----TTACTCTCTAACTAATACGTAAGCAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAAGCAA
* * *
11185671 TCCAAAACCTTACTCTCTAACCGAGACATAAGCAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAAGCAA
*
11185706 TCCATAACCTTACGCTCTAACCGAGACATAAGCAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAAGCAA
* *
11185741 TCCATAACCTTACACCCTAACCGAGACGTAA
1 TCCATAACCTTACGCTCTAACCGAGACGTAA
11185772 ACAGATCAAA
Statistics
Matches: 147, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
31 6 0.04
32 20 0.14
35 83 0.56
36 38 0.26
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.22
Consensus pattern (35 bp):
TCCATAACCTTACGCTCTAACCGAGACGTAAGCAA
Found at i:11186217 original size:17 final size:17
Alignment explanation
Indices: 11186195--11186227 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11186185 ACATCATTTC
11186195 AAATGAATACACTCATA
1 AAATGAATACACTCATA
11186212 AAATGAATACACTCAT
1 AAATGAATACACTCAT
11186228 CAGTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATGAATACACTCATA
Found at i:11186468 original size:35 final size:35
Alignment explanation
Indices: 11186396--11186559 Score: 211
Period size: 35 Copynumber: 4.7 Consensus size: 35
11186386 TAAGCATTAC
*
11186396 ACGCTCTAACCAAGACGTAAGCAAATCCATAATCTT
1 ACGCTCTAACCAAGACGTAAGCAAA-CCATAACCTT
* *
11186432 ACTCTTTAACCAAGACGTAAGCAAACCATAACCTT
1 ACGCTCTAACCAAGACGTAAGCAAACCATAACCTT
* * * *
11186467 ACGCTCTAACCTAGACATAAACAATCCATAACCTT
1 ACGCTCTAACCAAGACGTAAGCAAACCATAACCTT
* * *
11186502 ACGCTCTAACCGAGATGTAAGCAATCCATAACCTT
1 ACGCTCTAACCAAGACGTAAGCAAACCATAACCTT
* *
11186537 ACGCTCTAACCGAGACATAAGCA
1 ACGCTCTAACCAAGACGTAAGCA
11186560 GATCAAAGCT
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
35 90 0.80
36 23 0.20
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.21
Consensus pattern (35 bp):
ACGCTCTAACCAAGACGTAAGCAAACCATAACCTT
Found at i:11187190 original size:20 final size:22
Alignment explanation
Indices: 11187155--11187210 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
11187145 AAAAAAATAT
* *
11187155 CACCAAAACAGCAAAAA-A-AG
1 CACCAAAACAACAAAAACACAA
*
11187175 CACCAAAACAATAAAAACACAA
1 CACCAAAACAACAAAAACACAA
11187197 CACCAAAACAACAA
1 CACCAAAACAACAA
11187211 CCAAAACAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.66, C:0.29, G:0.04, T:0.02
Consensus pattern (22 bp):
CACCAAAACAACAAAAACACAA
Found at i:11187215 original size:12 final size:12
Alignment explanation
Indices: 11187176--11187222 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
11187166 CAAAAAAAGC
*
11187176 ACCAAAACAATA
1 ACCAAAACAACA
11187188 A--AAACACAAC-
1 ACCAAA-ACAACA
11187198 ACCAAAACAACA
1 ACCAAAACAACA
11187210 ACCAAAACAACA
1 ACCAAAACAACA
11187222 A
1 A
11187223 AAAAATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 4 0.13
11 9 0.30
12 17 0.57
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.02
Consensus pattern (12 bp):
ACCAAAACAACA
Found at i:11189907 original size:20 final size:20
Alignment explanation
Indices: 11189884--11189930 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11189874 TGTCAAACTG
*
11189884 GGGCACCAAAGTGCAAATGA
1 GGGCACCAAAGTACAAATGA
* *
11189904 GGGCATCGAAGTACAAATGA
1 GGGCACCAAAGTACAAATGA
11189924 GGGCACC
1 GGGCACC
11189931 GTAGAGCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGCACCAAAGTACAAATGA
Found at i:11189940 original size:20 final size:21
Alignment explanation
Indices: 11189884--11189940 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
11189874 TGTCAAACTG
*
11189884 GGGCACCAAAGT-GCAAATGA
1 GGGCACCGAAGTAGCAAATGA
*
11189904 GGGCATCGAAGTA-CAAATGA
1 GGGCACCGAAGTAGCAAATGA
*
11189924 GGGCACCGTAG-AGCAAA
1 GGGCACCGAAGTAGCAAA
11189941 CAAGGGTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.11
Consensus pattern (21 bp):
GGGCACCGAAGTAGCAAATGA
Found at i:11192608 original size:59 final size:57
Alignment explanation
Indices: 11192472--11192614 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 57
11192462 TAAATTTAGG
* * * **
11192472 TACCAAATTGAATTTAAAAAAAA-TTAGGTACCACATTAGGAAAAATATCAAGTTCATG
1 TACCAAATT-AA-GTAAAAAAAATTTAGGTACCAAATTAGAAAAAATATCAAGTTCAAA
*
11192530 TACCAAATTAAGTCCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATATCAAGTTCAAA
1 TACCAAATTAAGT--AAAAAAAATTTAGGTACCAAATT-AGAAAAAATATCAAGTTCAAA
* *
11192590 TACTAAATTGAGTAAAAAAAATTTA
1 TACCAAATTAAGTAAAAAAAATTTA
11192615 AATATTAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.01
57 2 0.03
58 27 0.38
59 13 0.18
60 29 0.40
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (57 bp):
TACCAAATTAAGTAAAAAAAATTTAGGTACCAAATTAGAAAAAATATCAAGTTCAAA
Found at i:11192628 original size:20 final size:19
Alignment explanation
Indices: 11192604--11192644 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
11192594 AAATTGAGTA
11192604 AAAAAAATTTAAATATTAAAT
1 AAAAAAA-TTAAAT-TTAAAT
11192625 AAAAAAATTAAATTTAAAT
1 AAAAAAATTAAATTTAAAT
11192644 A
1 A
11192645 CTTAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 6 0.30
21 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAAATTAAATTTAAAT
Found at i:11196142 original size:108 final size:108
Alignment explanation
Indices: 11195945--11196164 Score: 305
Period size: 108 Copynumber: 2.0 Consensus size: 108
11195935 CGCGAAAGAA
* * * *
11195945 ATTGCGCCTAGCGCTAGTCAGATATATCGACGAAAGTGTGTCCAACACTAGTAAGATAAACTGAT
1 ATTGCGCCTAGCGCTAGTCAGATAAACCGACGAAAGTGTGCCCAACACTAGTAAGATAAACTGAC
* * * *
11196010 GTTATTATTAATGAGCATAGCTCTAGTTGGATAAACCAACAAT
66 GATATTATTAATGAGCACAACTCTAGTTGGATAAACCAACAAG
* * ** * *
11196053 ATTGCGCCTAGCTCTAGTCAGATAAACCTACGAAAGTGTGCCCAGGACTTGTAAGATAAATTGAC
1 ATTGCGCCTAGCGCTAGTCAGATAAACCGACGAAAGTGTGCCCAACACTAGTAAGATAAACTGAC
*
11196118 GATATTATTAATGAGCCCAACTCTAGTTGGATAAACCAACAAG
66 GATATTATTAATGAGCACAACTCTAGTTGGATAAACCAACAAG
11196161 ATTG
1 ATTG
11196165 TGCACAACAC
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (108 bp):
ATTGCGCCTAGCGCTAGTCAGATAAACCGACGAAAGTGTGCCCAACACTAGTAAGATAAACTGAC
GATATTATTAATGAGCACAACTCTAGTTGGATAAACCAACAAG
Found at i:11196183 original size:34 final size:32
Alignment explanation
Indices: 11196135--11196197 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
11196125 TTAATGAGCC
*
11196135 CAACTCTAGTTGGATAAACCAACAAGATTGTGCA
1 CAACACTAGTTGGAT-AACCAACAA-ATTGTGCA
*
11196169 CAACACTAGTTGGATAACCGACAAATTGT
1 CAACACTAGTTGGATAACCAACAAATTGT
11196198 AGATATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 5 0.19
33 8 0.30
34 14 0.52
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (32 bp):
CAACACTAGTTGGATAACCAACAAATTGTGCA
Found at i:11197711 original size:20 final size:18
Alignment explanation
Indices: 11197674--11197726 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
11197664 CTTTCAAATA
11197674 AAAATATTTAATTATATT
1 AAAATATTTAATTATATT
*
11197692 AAAATATTATGATATATATT
1 AAAATATT-TAAT-TATATT
11197712 AAACAT-TTTAATTAT
1 AAA-ATATTTAATTAT
11197727 TAGACTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 11 0.37
19 6 0.20
20 11 0.37
21 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AAAATATTTAATTATATT
Found at i:11198844 original size:24 final size:21
Alignment explanation
Indices: 11198800--11198845 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 21
11198790 AGTAAAATAT
*
11198800 AAATAATATTTATTTAATAGA
1 AAATAATATTTATCTAATAGA
11198821 AAATAATATTTTAATCTAAGTAGA
1 AAATAATA-TTT-ATCTAA-TAGA
11198845 A
1 A
11198846 TGGGGTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 5 0.24
24 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATAATATTTATCTAATAGA
Found at i:11200643 original size:21 final size:21
Alignment explanation
Indices: 11200617--11200657 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11200607 GGCAAACTCT
* *
11200617 AATATGAACATAAGATAATCC
1 AATATGAACACAAGAGAATCC
11200638 AATATGAACACAAGAGAATC
1 AATATGAACACAAGAGAATC
11200658 AAGGTCCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (21 bp):
AATATGAACACAAGAGAATCC
Found at i:11201692 original size:20 final size:20
Alignment explanation
Indices: 11201626--11201715 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
11201616 GCCTGGAGCT
* *
11201626 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGGTT-AAAATC
** *
11201647 ATTTTGAAGT-GTTAAAATG
1 ATTTTGACTTGGTTAAAATC
* *
11201666 A-TTTGACTTGGTTCAAATT
1 ATTTTGACTTGGTTAAAATC
*
11201685 ATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
11201705 ATTTTAACTTG
1 ATTTTGACTTG
11201716 ATTTTAAAGT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
18 6 0.11
19 13 0.24
20 27 0.50
21 8 0.15
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:11208107 original size:13 final size:13
Alignment explanation
Indices: 11208089--11208113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11208079 CCCATTTTAT
11208089 CATTTTTAGCATG
1 CATTTTTAGCATG
11208102 CATTTTTAGCAT
1 CATTTTTAGCAT
11208114 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:11223758 original size:19 final size:19
Alignment explanation
Indices: 11223734--11223776 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
11223724 AAACATAAAT
11223734 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
11223753 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
11223772 TAAAT
1 TAAAT
11223777 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:11225805 original size:45 final size:45
Alignment explanation
Indices: 11225754--11225841 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
11225744 GGAAAGGTCA
11225754 CCCTAACAAGATATCGAAAGATCCAGGAGTTTTATCCTCTTCTCG
1 CCCTAACAAGATATCGAAAGATCCAGGAGTTTTATCCTCTTCTCG
*
11225799 CCCTAACAAGATATCGGAAGATCCAGGAGTTTTATCCTCTTCT
1 CCCTAACAAGATATCGAAAGATCCAGGAGTTTTATCCTCTTCT
11225842 ATCTTTACCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (45 bp):
CCCTAACAAGATATCGAAAGATCCAGGAGTTTTATCCTCTTCTCG
Found at i:11228984 original size:19 final size:19
Alignment explanation
Indices: 11228960--11229002 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
11228950 AAACATAAAT
11228960 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
11228979 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
11228998 TAAAT
1 TAAAT
11229003 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:11233584 original size:18 final size:18
Alignment explanation
Indices: 11233544--11233585 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11233534 GCATTTGAAC
*
11233544 CTGTGGCTGCATCTGAGT
1 CTGTGACTGCATCTGAGT
*
11233562 ATGTGACTGCATCTG-GTT
1 CTGTGACTGCATCTGAG-T
11233580 CTGTGA
1 CTGTGA
11233586 TCGCATTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (18 bp):
CTGTGACTGCATCTGAGT
Done.