Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 50 of 193
Found at i:15224924 original size:336 final size:336
Alignment explanation
Indices: 15224311--15224984 Score: 1330
Period size: 336 Copynumber: 2.0 Consensus size: 336
15224301 ATTAACTTAT
15224311 GATTGAACAAAAGTTTTTAACCACGAAACCTAACCATTCCCTAAAGAGAATGTAACAATATGTGA
1 GATTGAACAAAAGTTTTTAACCACGAAACCTAACCATTCCCTAAAGAGAATGTAACAATATGTGA
15224376 TAAATTTGAAAGAAATAATTTTTTCCATGGATGTAGTAAATTGGACTATAATAATAGTCATGAGG
66 TAAATTTGAAAGAAATAATTTTTTCCATGGATGTAGTAAATTGGACTATAATAATAGTCATGAGG
15224441 GATAGTCGTAATGAATGTTCTCACCACCAGAAGTGGAAAAATAAAGAAAGCAAAAAAGATCAAGA
131 GATAGTCGTAATGAATGTTCTCACCACCAGAAGTGGAAAAATAAAGAAAGCAAAAAAGATCAAGA
15224506 ATTTCCAAACACTCGTTAAGAAGAGAGACAACTTAAGTGTGAAAAGTCATTGGTTATATACCTGT
196 ATTTCCAAACACTCGTTAAGAAGAGAGACAACTTAAGTGTGAAAAGTCATTGGTTATATACCTGT
15224571 TGTACACTTGGAAAATAAGATTTTCTCTCAAAGATTGCTATTAATAAATTTTGGTTGGAATCAAA
261 TGTACACTTGGAAAATAAGATTTTCTCTCAAAGATTGCTATTAATAAATTTTGGTTGGAATCAAA
15224636 GTTTACTACTA
326 GTTTACTACTA
15224647 GATTGAACAAAAGTTTTTAACCACGAAACCTAACCATTCCCTAAAGAGAATGTAACAATATGTGA
1 GATTGAACAAAAGTTTTTAACCACGAAACCTAACCATTCCCTAAAGAGAATGTAACAATATGTGA
15224712 TAAATTTGAAAGAAATAATTTTTTCCATGGATGTAGTAAATTGGACTATAATAATAGTCATGAGG
66 TAAATTTGAAAGAAATAATTTTTTCCATGGATGTAGTAAATTGGACTATAATAATAGTCATGAGG
15224777 GATAGTCGTAATGAATGTTCTCACCACCAGAAGTGGAAAAATAAAGAAAGCAAAAAAGATCAAGA
131 GATAGTCGTAATGAATGTTCTCACCACCAGAAGTGGAAAAATAAAGAAAGCAAAAAAGATCAAGA
15224842 ATTTCCAAACACTCGTTAAGAAGAGAGACAACTTAAGTGTGAAAAGTCATTGGTTATATACCTGT
196 ATTTCCAAACACTCGTTAAGAAGAGAGACAACTTAAGTGTGAAAAGTCATTGGTTATATACCTGT
* *
15224907 TGTACACTTGGAAAATAAGATTTTCTCTCAAAGATTGCTATTAATATATTTTGGTTGGATTCAAA
261 TGTACACTTGGAAAATAAGATTTTCTCTCAAAGATTGCTATTAATAAATTTTGGTTGGAATCAAA
15224972 GTTTACTACTA
326 GTTTACTACTA
15224983 GA
1 GA
15224985 AGTTTAATTT
Statistics
Matches: 336, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
336 336 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (336 bp):
GATTGAACAAAAGTTTTTAACCACGAAACCTAACCATTCCCTAAAGAGAATGTAACAATATGTGA
TAAATTTGAAAGAAATAATTTTTTCCATGGATGTAGTAAATTGGACTATAATAATAGTCATGAGG
GATAGTCGTAATGAATGTTCTCACCACCAGAAGTGGAAAAATAAAGAAAGCAAAAAAGATCAAGA
ATTTCCAAACACTCGTTAAGAAGAGAGACAACTTAAGTGTGAAAAGTCATTGGTTATATACCTGT
TGTACACTTGGAAAATAAGATTTTCTCTCAAAGATTGCTATTAATAAATTTTGGTTGGAATCAAA
GTTTACTACTA
Found at i:15227922 original size:20 final size:20
Alignment explanation
Indices: 15227897--15227941 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
15227887 AACTTTAAAG
15227897 AAAAC-ACTAGCCCATAAAT-C
1 AAAACAACTA-CCCA-AAATAC
15227917 AAAACAACTACCCAAAATAC
1 AAAACAACTACCCAAAATAC
15227937 AAAAC
1 AAAAC
15227942 TAAAAGGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 15 0.65
21 4 0.17
ACGTcount: A:0.58, C:0.29, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAACAACTACCCAAAATAC
Found at i:15228022 original size:18 final size:18
Alignment explanation
Indices: 15227999--15228042 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
15227989 AAAGAAAAAC
15227999 AAAAGACTGAAAAAACTA
1 AAAAGACTGAAAAAACTA
*
15228017 AAAAGATTGAAAAAACTA
1 AAAAGACTGAAAAAACTA
15228035 AAAAGACT
1 AAAAGACT
15228043 AAACACTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAAGACTGAAAAAACTA
Found at i:15240874 original size:18 final size:17
Alignment explanation
Indices: 15240845--15240916 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
15240835 CTGTGATAGT
*
15240845 AAAATTGTGAGCTCACC
1 AAAATTGCGAGCTCACC
15240862 AAATATTGCGAGCTCTA-C
1 AAA-ATTGCGAGCTC-ACC
* *
15240880 AAGCA-TACGAGCTCACC
1 AA-AATTGCGAGCTCACC
*
15240897 AAAAGATGCGAGCTCACC
1 AAAA-TTGCGAGCTCACC
15240915 AA
1 AA
15240917 GACTGTGAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
16 2 0.05
17 14 0.32
18 27 0.61
19 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATTGCGAGCTCACC
Found at i:15246179 original size:15 final size:15
Alignment explanation
Indices: 15246155--15246196 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
15246145 AGAGAACGCA
*
15246155 ACTTTAGAATCCGTT
1 ACTTTGGAATCCGTT
* *
15246170 GCTTTGGAATCTGTT
1 ACTTTGGAATCCGTT
15246185 ACTTTGGAATCC
1 ACTTTGGAATCC
15246197 AACATTTAGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (15 bp):
ACTTTGGAATCCGTT
Found at i:15249275 original size:23 final size:23
Alignment explanation
Indices: 15249247--15249294 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
15249237 GAGTAAAATC
* *
15249247 TGTCAGTGC-AATGTAATATAAAA
1 TGTCAGAGCAAAT-TAATAAAAAA
15249270 TGTCAGAGCAAATTAATAAAAAA
1 TGTCAGAGCAAATTAATAAAAAA
15249293 TG
1 TG
15249295 GATTGATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (23 bp):
TGTCAGAGCAAATTAATAAAAAA
Found at i:15251476 original size:17 final size:17
Alignment explanation
Indices: 15251423--15251476 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
15251413 ACTACAATGC
15251423 AAATGCTAGA-ACAAATA
1 AAATGC-AGAGACAAATA
*
15251440 AAATGCAGAGACAAAAA
1 AAATGCAGAGACAAATA
*
15251457 AAATGCA-ATGACAATTA
1 AAATGCAGA-GACAAATA
15251474 AAA
1 AAA
15251477 GAAATGCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.15
Consensus pattern (17 bp):
AAATGCAGAGACAAATA
Found at i:15259990 original size:42 final size:42
Alignment explanation
Indices: 15259943--15260026 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
15259933 ACCTTCCAGT
15259943 GAATGTGACTGTAATCGCACTTCTGTGGTCAAAACAGTTAAA
1 GAATGTGACTGTAATCGCACTTCTGTGGTCAAAACAGTTAAA
15259985 GAATGTGACTGTAATCGCACTTCTGTGGTCAAAACAGTTAAA
1 GAATGTGACTGTAATCGCACTTCTGTGGTCAAAACAGTTAAA
15260027 TCCAAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
GAATGTGACTGTAATCGCACTTCTGTGGTCAAAACAGTTAAA
Found at i:15262968 original size:50 final size:49
Alignment explanation
Indices: 15262907--15263060 Score: 150
Period size: 50 Copynumber: 3.1 Consensus size: 49
15262897 AAAAAATATA
* * * *
15262907 AAATAAATATTTATGTTTATGTAAAATACCAGATCTAAACAAACTAATTT
1 AAATAAATATTTATATTTATATAAAACACCAGATATAAACAAAC-AATTT
* * ** * *
15262957 AAATAAATATTTATATTTATTTGAAACATTATATAT-GA-AAACAATTT
1 AAATAAATATTTATATTTATATAAAACACCAGATATAAACAAACAATTT
* * *
15263004 AAATAAATATTTATTTTTATATAAAACACCAGATTTAAGCAAAACAATTT
1 AAATAAATATTTATATTTATATAAAACACCAGATATAAAC-AAACAATTT
*
15263054 AGATAAA
1 AAATAAA
15263061 CAAGATCTCA
Statistics
Matches: 82, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
47 34 0.41
48 4 0.05
49 1 0.01
50 43 0.52
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (49 bp):
AAATAAATATTTATATTTATATAAAACACCAGATATAAACAAACAATTT
Found at i:15265787 original size:25 final size:24
Alignment explanation
Indices: 15265714--15265860 Score: 164
Period size: 22 Copynumber: 6.2 Consensus size: 24
15265704 CAAAGGAACA
15265714 GAGAGCACCAAA-GTGCTAAT--CG
1 GAGAGCA-CAAATGTGCTAATAACG
15265736 GAGAGCACAAATGTGCT-A-AACG
1 GAGAGCACAAATGTGCTAATAACG
*
15265758 GAGAGCACTACATGTGCTAATAACG
1 GAGAGCAC-AAATGTGCTAATAACG
15265783 GAGAGCACAAATGTGCT-A-AACG
1 GAGAGCACAAATGTGCTAATAACG
*
15265805 GAGAGCACTACATGTGCTAATAACG
1 GAGAGCAC-AAATGTGCTAATAACG
*
15265830 GAGAGCACAATACGTGCTAAGTAACG
1 GAGAGCACAA-ATGTGCTAA-TAACG
*
15265856 AAGAG
1 GAGAG
15265861 TGCACTAGGG
Statistics
Matches: 108, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.05
22 34 0.31
23 17 0.16
24 11 0.10
25 32 0.30
26 9 0.08
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (24 bp):
GAGAGCACAAATGTGCTAATAACG
Found at i:15265788 original size:47 final size:47
Alignment explanation
Indices: 15265726--15265849 Score: 216
Period size: 47 Copynumber: 2.7 Consensus size: 47
15265716 GAGCACCAAA
15265726 GTGCTAAT--CGGAGAGCACAAATGTGCTAAACGGAGAGCACTACAT
1 GTGCTAATAACGGAGAGCACAAATGTGCTAAACGGAGAGCACTACAT
15265771 GTGCTAATAACGGAGAGCACAAATGTGCTAAACGGAGAGCACTACAT
1 GTGCTAATAACGGAGAGCACAAATGTGCTAAACGGAGAGCACTACAT
*
15265818 GTGCTAATAACGGAGAGCACAATACGTGCTAA
1 GTGCTAATAACGGAGAGCACAA-ATGTGCTAA
15265850 GTAACGAAGA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
45 8 0.11
47 59 0.79
48 8 0.11
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (47 bp):
GTGCTAATAACGGAGAGCACAAATGTGCTAAACGGAGAGCACTACAT
Found at i:15266071 original size:2 final size:2
Alignment explanation
Indices: 15266064--15266100 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15266054 TGTTCAATAC
15266064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15266101 ATAAATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15268402 original size:82 final size:82
Alignment explanation
Indices: 15268283--15268729 Score: 430
Period size: 82 Copynumber: 5.5 Consensus size: 82
15268273 CAAAATCGAT
* * * * * *
15268283 TCTGTTGAACGGCAGGAATAAATC-CTGAAATAGAATTATTTAATTAATTATTGTTTGGAAACAA
1 TCTGTTGAACGACAGGAATAAATCTC-GAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAA
*
15268347 AATCAAAATGGAATAAAA
65 AATCAAAATAGAATAAAA
** * * * *
15268365 TCTGTTGAACGGTA-TAAGTAAATCTCGAAACAAAATTATTTAATTAATCCTTGTTTG------G
1 TCTGTTGAACGACAGGAA-TAAATCTCGAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAA
15268423 AATCAAAATAGAATAAAA
65 AATCAAAATAGAATAAAA
* ** * * * * *
15268441 TCTATTGAACGATGGGAATAAATCTCGAAATAGAATTATTCAATTAATTCTTGTTTGAAAATAGA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAAA
* *
15268506 ATAAAAATAGAACAAAA
66 ATCAAAATAGAATAAAA
* * * * * * *
15268523 TCTGTTAAACAACAGGAATAAATCCCAAAATAAAATTATTCAATTAATCCTTATTTGCAAACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAAA
15268588 ATCAAAATAGAATAAAA
66 ATCAAAATAGAATAAAA
* * * *
15268605 TCTGTTGAACGGCAGGAAT-AATC-CGAAACATAATTATTCAATTAATTCTTGTTTACATACAAA
1 TCTGTTGAACGACAGGAATAAATCTCGAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAAA
* *
15268668 ATAAAAATAAAATAAAA
66 ATCAAAATAGAATAAAA
* * * *
15268685 TTTGTTGAACGACAAGAATAAATC-CTGAAACATATTTATTCAATT
1 TCTGTTGAACGACAGGAATAAATCTC-GAAACAAAATTATTCAATT
15268730 TTAATTTTTT
Statistics
Matches: 305, Mismatches: 49, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
76 63 0.21
77 2 0.01
80 64 0.21
81 11 0.04
82 164 0.54
83 1 0.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.31
Consensus pattern (82 bp):
TCTGTTGAACGACAGGAATAAATCTCGAAACAAAATTATTCAATTAATTCTTGTTTGCAAACAAA
ATCAAAATAGAATAAAA
Found at i:15268478 original size:158 final size:158
Alignment explanation
Indices: 15268287--15268729 Score: 471
Period size: 158 Copynumber: 2.8 Consensus size: 158
15268277 ATCGATTCTG
* * * * *
15268287 TTGAACGGCAGGAATAAATCCTGAAATAGAATTATTTAATTAATTATTGTTTGGAAACAAAATCA
1 TTGAACGACAGGAATAAATCC-GAAATAGAATTATTCAATTAATTCTTGTTTGAAAACAAAATAA
* ** * * * *
15268352 AAATGGAATAAAATCTGTTGAACGGTA-TAAGTAAATCTCGAAACAAAATTATTTAATTAATCCT
65 AAATAGAATAAAATCTGTTGAACGACAGGAA-TAAATCCCAAAACAAAATTATTCAATTAATCCT
* *
15268416 TGTTTG-GAATCAAAATAGAATAAAATCTA
129 TATTTGAAAATCAAAATAGAATAAAATCTA
** * *
15268445 TTGAACGATGGGAATAAATCTCGAAATAGAATTATTCAATTAATTCTTGTTTGAAAATAGAATAA
1 TTGAACGACAGGAATAAATC-CGAAATAGAATTATTCAATTAATTCTTGTTTGAAAACAAAATAA
* * * *
15268510 AAATAGAACAAAATCTGTTAAACAACAGGAATAAATCCCAAAATAAAATTATTCAATTAATCCTT
65 AAATAGAATAAAATCTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTCAATTAATCCTT
*
15268575 ATTTGCAAACAAAATCAAAATAGAATAAAATCTG
130 ATTTG-----AAAATCAAAATAGAATAAAATCTA
* * * *
15268609 TTGAACGGCAGGAAT-AATCCGAAACATAATTATTCAATTAATTCTTGTTT-ACATACAAAATAA
1 TTGAACGACAGGAATAAATCCGAAATAGAATTATTCAATTAATTCTTGTTTGA-AAACAAAATAA
* * * ** * *
15268672 AAATAAAATAAAATTTGTTGAACGACAAGAATAAATCCTGAAACATATTTATTCAATT
65 AAATAGAATAAAATCTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTCAATT
15268730 TTAATTTTTT
Statistics
Matches: 234, Mismatches: 42, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
158 109 0.47
159 3 0.01
161 1 0.00
162 84 0.36
163 4 0.02
164 33 0.14
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (158 bp):
TTGAACGACAGGAATAAATCCGAAATAGAATTATTCAATTAATTCTTGTTTGAAAACAAAATAAA
AATAGAATAAAATCTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTCAATTAATCCTTA
TTTGAAAATCAAAATAGAATAAAATCTA
Found at i:15269256 original size:51 final size:50
Alignment explanation
Indices: 15269193--15269377 Score: 198
Period size: 50 Copynumber: 3.7 Consensus size: 50
15269183 TAAATATAAA
* *
15269193 ATATTTATGTAAAATA-CAAGATCTGAACAAAACAATATAAAATAAATATTT
1 ATATTTATGTAAAACATC-AGATCTAAACAAAACAAT-TAAAATAAATATTT
* * *
15269244 ATGTTTATGTAAAACATCATATCTAAACAAAACAATTTAAATAAATATTT
1 ATATTTATGTAAAACATCAGATCTAAACAAAACAATTAAAATAAATATTT
* * * * *
15269294 ATATTTATTTAAAACATCATATCT--A-AAAATAATTTAAACAAATATTT
1 ATATTTATGTAAAACATCAGATCTAAACAAAACAATTAAAATAAATATTT
* * * *
15269341 ATTTTTATATAAAACACCATATCTAAACAAAACAATT
1 ATATTTATGTAAAACATCAGATCTAAACAAAACAATT
15269378 TAGATAAACA
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
47 41 0.35
48 1 0.01
49 1 0.01
50 43 0.37
51 30 0.26
52 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (50 bp):
ATATTTATGTAAAACATCAGATCTAAACAAAACAATTAAAATAAATATTT
Found at i:15269307 original size:50 final size:50
Alignment explanation
Indices: 15269213--15269385 Score: 226
Period size: 50 Copynumber: 3.5 Consensus size: 50
15269203 AAAATACAAG
* * * *
15269213 ATCTGAACAAAACAATATAAAATAAATATTTATGTTTATGTAAAACATCAT
1 ATCTAAACAAAACAAT-TTAAATAAATATTTATATTTATATAAAACATCAT
*
15269264 ATCTAAACAAAACAATTTAAATAAATATTTATATTTATTTAAAACATCAT
1 ATCTAAACAAAACAATTTAAATAAATATTTATATTTATATAAAACATCAT
* * * *
15269314 ATCT--A-AAAATAATTTAAACAAATATTTATTTTTATATAAAACACCAT
1 ATCTAAACAAAACAATTTAAATAAATATTTATATTTATATAAAACATCAT
*
15269361 ATCTAAACAAAACAATTTAGATAAA
1 ATCTAAACAAAACAATTTAAATAAA
15269386 CAAGATTTGA
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
47 41 0.38
48 1 0.01
49 1 0.01
50 49 0.46
51 15 0.14
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (50 bp):
ATCTAAACAAAACAATTTAAATAAATATTTATATTTATATAAAACATCAT
Found at i:15269348 original size:47 final size:47
Alignment explanation
Indices: 15269221--15269367 Score: 177
Period size: 47 Copynumber: 3.0 Consensus size: 47
15269211 AGATCTGAAC
* * * *
15269221 AAAACAATATAAAATAAATATTTATGTTTATGTAAAACATCATATCTAAA
1 AAAACAAT-TTAAACAAATATTTATATTTATATAAAACATCATATCT--A
* *
15269271 CAAAACAATTTAAATAAATATTTATATTTATTTAAAACATCATATCTA
1 -AAAACAATTTAAACAAATATTTATATTTATATAAAACATCATATCTA
* * *
15269319 AAAATAATTTAAACAAATATTTATTTTTATATAAAACACCATATCTA
1 AAAACAATTTAAACAAATATTTATATTTATATAAAACATCATATCTA
15269366 AA
1 AA
15269368 CAAAACAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 44 0.50
48 1 0.01
50 35 0.40
51 8 0.09
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (47 bp):
AAAACAATTTAAACAAATATTTATATTTATATAAAACATCATATCTA
Found at i:15270071 original size:107 final size:107
Alignment explanation
Indices: 15269885--15270088 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 107
15269875 GACTAAAAAT
* *
15269885 TCCCCAAGCCTGATCGGTTCAGACATTTCACGTCGCCCACATCGCGCAGGTGCACCCCCAATCCT
1 TCCCCAAGCCTGATCGATTCAGACATTTCACGTCGCCCACATCACGCAGGTGCACCCCCAATCCT
*
15269950 AAAGGATTTGGATTTGCACCCCTTGCATGCAAATGGTGCAAA
66 AAAGGATTTGGATTTGCACCCCTTGCACGCAAATGGTGCAAA
* * *
15269992 TCCCCATGCCTGATCGATTCAGACATTTCGCGTCGCCCACATCATGCAGGTGCACCCCCAATCCT
1 TCCCCAAGCCTGATCGATTCAGACATTTCACGTCGCCCACATCACGCAGGTGCACCCCCAATCCT
15270057 AAAGGATTTGGATTTGCACCCCTTGCACGCAA
66 AAAGGATTTGGATTTGCACCCCTTGCACGCAA
15270089 GGCAAGGCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 91 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.23
Consensus pattern (107 bp):
TCCCCAAGCCTGATCGATTCAGACATTTCACGTCGCCCACATCACGCAGGTGCACCCCCAATCCT
AAAGGATTTGGATTTGCACCCCTTGCACGCAAATGGTGCAAA
Found at i:15271350 original size:20 final size:20
Alignment explanation
Indices: 15271325--15271379 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
15271315 AAAAATATAA
15271325 ATTTTAAAATTTTTATAAA-T
1 ATTTTAAAATTTTTA-AAATT
15271345 ATTTTAAAA-TTTTAAAATT
1 ATTTTAAAATTTTTAAAATT
*
15271364 ATTTT-TAATTTTTAAA
1 ATTTTAAAATTTTTAAA
15271380 TTTTTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAAAATTTTTAAAATT
Found at i:15271358 original size:28 final size:27
Alignment explanation
Indices: 15271323--15271384 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
15271313 TAAAAAATAT
15271323 AAATTTTAAAATT-TTTATAAATATTTTA
1 AAATTTTAAAATTATTT-TAAAT-TTTTA
*
15271351 AAATTTTAAAATTATTTTTAATTTTTA
1 AAATTTTAAAATTATTTTAAATTTTTA
*
15271378 AATTTTT
1 AAATTTT
15271385 GTAATTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 11 0.35
28 17 0.55
29 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AAATTTTAAAATTATTTTAAATTTTTA
Found at i:15271380 original size:18 final size:18
Alignment explanation
Indices: 15271332--15271392 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
15271322 TAAATTTTAA
* *
15271332 AATTTTTATAAATATTTTAA
1 AATTTTTA-AATTATTTT-T
*
15271352 AATTTTAAAATTATTTTT
1 AATTTTTAAATTATTTTT
*
15271370 AATTTTTAAATT-TTTGT
1 AATTTTTAAATTATTTTT
15271387 AATTTT
1 AATTTT
15271393 GTTGAGAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 10 0.28
18 11 0.31
19 8 0.22
20 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
AATTTTTAAATTATTTTT
Found at i:15276605 original size:20 final size:19
Alignment explanation
Indices: 15276566--15276605 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
15276556 AAATAGTGAG
*
15276566 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
*
15276585 AATTCTATTTTCTAGGAATA
1 AATT-TATTTTCTAAGAATA
15276605 A
1 A
15276606 CAATTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:15278684 original size:53 final size:53
Alignment explanation
Indices: 15278600--15278899 Score: 381
Period size: 53 Copynumber: 5.7 Consensus size: 53
15278590 TGTGTCAAGT
* * * *
15278600 ATTAAAGGTCCGATAACTCTGTGTCACCGTGAGTTATATGAATCTTATCATGG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGG
* * *
15278653 ATTTAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGG
* *
15278706 ATTAAAGGTCCGATGACT-TTTCGTCATCGTGAGTTATACGAATCCTATCACGG
1 ATTAAAGGTCCGATGACTCTGT-GTCATCGTGAGTTATATGAATCCTATCACGG
* * * * *
15278759 ATTAAAAGTCCGATGACTCTGTATCATCATGAGTTATATGAACCCTATTACGG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGG
* * * * * *
15278812 ATTAAGGGTTCGATGACTTTGTGTCATCGTGAGTTACACGAATCC-ATCATGG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGG
*
15278864 ATTAAAGGT-CGATGACTCCGTGTCATCGTGAGTTAT
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
15278900 CAAATGCGAA
Statistics
Matches: 211, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
51 24 0.11
52 15 0.07
53 170 0.81
54 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (53 bp):
ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGG
Found at i:15282231 original size:22 final size:24
Alignment explanation
Indices: 15282189--15282238 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
15282179 TATATGTTGT
*
15282189 ATTTTTATGCTATTCTTTTATTTC
1 ATTTTTATGCTATTCTTTTATTTA
*
15282213 ATTTTT-TGC-ATTTTTTTATTTA
1 ATTTTTATGCTATTCTTTTATTTA
15282235 ATTT
1 ATTT
15282239 ATGCCCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 3 0.12
24 6 0.25
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (24 bp):
ATTTTTATGCTATTCTTTTATTTA
Found at i:15291682 original size:17 final size:17
Alignment explanation
Indices: 15291662--15291709 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
15291652 CACATTCCCT
*
15291662 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* * *
15291679 TTGTCACTGCATCTGCA
1 TTGTCATTGCATTTGAA
*
15291696 TTGTCATTGTATTT
1 TTGTCATTGCATTT
15291710 CCACGTGTCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:15308194 original size:23 final size:20
Alignment explanation
Indices: 15308168--15308223 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 20
15308158 AATTAATAAT
*
15308168 AAAATAAATTAACTAAACTTCCA
1 AAAATAAATTAA--AAA-GTCCA
15308191 AAAATAAAATATAAAAAGTCCA
1 AAAAT-AAAT-TAAAAAGTCCA
15308213 AAAATAAATTA
1 AAAATAAATTA
15308224 TATTTACAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 9 0.30
23 8 0.27
24 4 0.13
25 3 0.10
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAATTAAAAAGTCCA
Found at i:15308291 original size:3 final size:3
Alignment explanation
Indices: 15308275--15308333 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
15308265 AAAATTCCAA
* *
15308275 AAT AAT -AT AGT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15308322 AAAT AAT AAT AA
1 -AAT AAT AAT AA
15308334 CCAAAATGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15309389 original size:13 final size:13
Alignment explanation
Indices: 15309371--15309395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15309361 TTTCTCGAAA
15309371 AAAGTCAACGGTT
1 AAAGTCAACGGTT
15309384 AAAGTCAACGGT
1 AAAGTCAACGGT
15309396 CAACGATCAA
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:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (13 bp):
AAAGTCAACGGTT
Found at i:15309399 original size:20 final size:20
Alignment explanation
Indices: 15309374--15309419 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
15309364 CTCGAAAAAA
* *
15309374 GTCAACGGTTAAAGTCAACG
1 GTCAACGATCAAAGTCAACG
*
15309394 GTCAACGATCAAAGTCAATG
1 GTCAACGATCAAAGTCAACG
15309414 GTCAAC
1 GTCAAC
15309420 AGTCGCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
GTCAACGATCAAAGTCAACG
Found at i:15323647 original size:68 final size:68
Alignment explanation
Indices: 15323538--15323674 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
15323528 CTAGAAGAAG
*
15323538 TCCATGAGGGTGTTTGTGGGACATATGCCAATAGTTTTACAATGGCCAGGCAGATCATGAGATTC
1 TCCATGAGGGTGTTTGTGGGACACATGCCAATAGTTTTACAATGGCCAGGCAGATCATGAGATTC
15323603 GGA
66 GGA
15323606 TCCATGAGGGTGTTTGTGGGACACATGCCAATAGTTTTACAATGGCCAGGCAGATCATGAGATTC
1 TCCATGAGGGTGTTTGTGGGACACATGCCAATAGTTTTACAATGGCCAGGCAGATCATGAGATTC
15323671 GGA
66 GGA
15323674 T
1 T
15323675 ATTATTAGTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (68 bp):
TCCATGAGGGTGTTTGTGGGACACATGCCAATAGTTTTACAATGGCCAGGCAGATCATGAGATTC
GGA
Found at i:15324728 original size:5 final size:5
Alignment explanation
Indices: 15324718--15324742 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15324708 AAACTAGCAA
15324718 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
15324743 GGAGGGGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:15325778 original size:48 final size:48
Alignment explanation
Indices: 15325705--15326155 Score: 365
Period size: 48 Copynumber: 9.2 Consensus size: 48
15325695 TGTAGTGGAA
* * *
15325705 TAGAGTGAAGCTACCACATCTAATCTTATACCCCTAAATCTAGAGGGG
1 TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * *
15325753 TGGATTGAAGATACCACATCCAATCTTATACCCCTAAATCCAAAGGGG
1 TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * * * * * *
15325801 CATACTGAAGCTACCACATCCAATCTTATACCCTTAAATCTAAAGAGA
1 TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* *
15325849 CAGATTGAATCTACCACATCC-ATCTTATACCCCTAAATCCAGAGGGG
1 TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* *** * * *
15325896 TAGATTCAAAAGGGATAGATTGAAGCTACCACAATCTTATACCCTTAAATCCAGAGAGG
1 TAGATT-------GA-AGCTACCA-C-ATC-CAATCTTATACCCCTAAATCCAGAGGGG
* * * * *
15325955 T-GAATTGAAGCTACAACATCTAATCTTTTACCCTTAAATCTAGAGGGG
1 TAG-ATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* *
15326003 AAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAAAGGGG
1 TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * *
15326051 CT-GATTAAAGCTACAACATCCAATCTTATACTCCTAAATCCAGAGGGG
1 -TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * * * **
15326099 TAAATTAAAGCCA-CACA--GAACTCCTATACCTTTAAATCCAGAGGGG
1 TAGATTGAAGCTACCACATCCAA-TCTTATACCCCTAAATCCAGAGGGG
*
15326145 CAGATTGAAGC
1 TAGATTGAAGC
15326156 CACACATAAC
Statistics
Matches: 323, Mismatches: 63, Indels: 36
0.77 0.15 0.09
Matches are distributed among these distances:
45 2 0.01
46 29 0.09
47 30 0.09
48 213 0.66
49 3 0.01
50 1 0.00
51 5 0.02
52 2 0.01
54 2 0.01
55 3 0.01
56 1 0.00
57 2 0.01
58 2 0.01
59 28 0.09
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (48 bp):
TAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
Found at i:15326072 original size:202 final size:203
Alignment explanation
Indices: 15325726--15326100 Score: 536
Period size: 202 Copynumber: 1.9 Consensus size: 203
15325716 TACCACATCT
* * * *
15325726 AATCTTATACCCCTAAATCTAGAGGGGTGGATTGAAGATACCACATCCAATCTTATACCCCTAAA
1 AATCTTATACCCCTAAATCCAGAGAGGTGAATTGAAGATACAACATCCAATCTTATACCCCTAAA
* * * * *
15325791 TCCAAAGGGGCATACTGAAGCTACCACATCCAATCTTATACCCTTAAATCTAAAGAGACAGATTG
66 TCCAAAGGGGAAGACTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAAAGAGACAGATTA
* *
15325856 AATCTACCACATCC-ATCTTATACCCCTAAATCCAGAGGGGTAGATTCAAAAGGGATAGATTGAA
131 AAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGGGGTAGATTCAAAAGGGATAGATTGAA
15325920 GCTACCAC
196 GCTACCAC
* * * * *
15325928 AATCTTATACCCTTAAATCCAGAGAGGTGAATTGAAGCTACAACATCTAATCTTTTACCCTTAAA
1 AATCTTATACCCCTAAATCCAGAGAGGTGAATTGAAGATACAACATCCAATCTTATACCCCTAAA
* * * * * *
15325993 TCTAGAGGGGAAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAAAGGGGCTGATTA
66 TCCAAAGGGGAAGACTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAAAGAGACAGATTA
*
15326058 AAGCTACAACATCCAATCTTATACTCCTAAATCCAGAGGGGTA
131 AAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGGGGTA
15326101 AATTAAAGCC
Statistics
Matches: 149, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
202 122 0.82
203 27 0.18
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (203 bp):
AATCTTATACCCCTAAATCCAGAGAGGTGAATTGAAGATACAACATCCAATCTTATACCCCTAAA
TCCAAAGGGGAAGACTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAAAGAGACAGATTA
AAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGGGGTAGATTCAAAAGGGATAGATTGAA
GCTACCAC
Found at i:15326144 original size:46 final size:46
Alignment explanation
Indices: 15326085--15326180 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
15326075 CTTATACTCC
*
15326085 TAAATCCAGAGGGGTAAATTAAAGCCACACAGAACTCCTATACCTT
1 TAAATCCAGAGGGGCAAATTAAAGCCACACAGAACTCCTATACCTT
* * * *
15326131 TAAATCCAGAGGGGCAGATTGAAGCCACACATAACTTCTATACCTT
1 TAAATCCAGAGGGGCAAATTAAAGCCACACAGAACTCCTATACCTT
15326177 TAAA
1 TAAA
15326181 ATTACAGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (46 bp):
TAAATCCAGAGGGGCAAATTAAAGCCACACAGAACTCCTATACCTT
Found at i:15339362 original size:49 final size:48
Alignment explanation
Indices: 15339263--15339493 Score: 306
Period size: 48 Copynumber: 4.8 Consensus size: 48
15339253 TGGAATGGAG
* *
15339263 TGAAGCTACCACATCTAATCTTATACCCCTAAATCTAGAGGGGCAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCTAGAGGGACAGAT
* *
15339311 TGAAGCTACCACATCCAATCTTATACCTCCTAAATTTAGAGGGACGGAT
1 TGAAGCTACCACATCCAATCTTATACC-CCTAAATCTAGAGGGACAGAT
* * *
15339360 TGAAGCTACCACATCCAATCTTATACCCCTAAATTCAAAAGGG-CACAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAA-TCTAGAGGGACAGAT
* * * *
15339408 TAAAGCTACCACGTCCAATCTTACACCCTTAAATCTAGAGGG-CAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCTAGAGGGACAGAT
* *
15339455 TGAATCTACCACATCC-ATCTTATACCCCTAAATCCAGAG
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCTAGAG
15339494 AGGTAGATTC
Statistics
Matches: 159, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
46 20 0.13
47 24 0.15
48 64 0.40
49 51 0.32
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TGAAGCTACCACATCCAATCTTATACCCCTAAATCTAGAGGGACAGAT
Found at i:15339429 original size:97 final size:96
Alignment explanation
Indices: 15339263--15339487 Score: 312
Period size: 97 Copynumber: 2.4 Consensus size: 96
15339253 TGGAATGGAG
* * * * *
15339263 TGAAGCTACCACATCTAATCTTATACCCCTAAA-TCTAGAGGGGCAGATTGAAGCTACCACATCC
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATTCTAAAAGGGCACATTAAAGCTACCACATCC
* * *
15339327 AATCTTATACCTCCTAAATTTAGAGGGACGGAT
66 AATCTTACACC-CCTAAATCTAGAGGG-CAGAT
*
15339360 TGAAGCTACCACATCCAATCTTATACCCCTAAATTC-AAAAGGGCACATTAAAGCTACCACGTCC
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATTCTAAAAGGGCACATTAAAGCTACCACATCC
*
15339424 AATCTTACACCCTTAAATCTAGAGGGCAGAT
66 AATCTTACACCCCTAAATCTAGAGGGCAGAT
*
15339455 TGAATCTACCACATCC-ATCTTATACCCCTAAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAAT
15339488 CCAGAGAGGT
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
94 17 0.15
95 19 0.16
96 13 0.11
97 65 0.56
98 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (96 bp):
TGAAGCTACCACATCCAATCTTATACCCCTAAATTCTAAAAGGGCACATTAAAGCTACCACATCC
AATCTTACACCCCTAAATCTAGAGGGCAGAT
Found at i:15339599 original size:48 final size:48
Alignment explanation
Indices: 15339513--15339927 Score: 370
Period size: 48 Copynumber: 8.8 Consensus size: 48
15339503 CAAGAGGGAT
* * * ** *
15339513 AGATTGAAGCTACCAAATTCAAATCTTATACCGC-TAAATCCAAAGCAGT
1 AGATTGAAGCTACCACA-TCCAATCTTATACC-CTTAAATCCAGAGGGGC
*
15339562 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCTAGAGGGGC
1 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
* * * **
15339610 ATATTGAAGCTACAACATCTAATCTTATA-CCTTAAATTTAGAGGGGC
1 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
* * * *
15339657 AAATTGAAGCTACTACATCTAATCTTATACCCTTAAATCCAGAGGGGA
1 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
* *
15339705 AGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGAGGC
1 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
* * * * ** *
15339753 AGATTAAAGTTACAACATCCAATCTTATACCCCTATTTCCAGAGGGGA
1 AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
* * * *
15339801 AGATTGAAGCCA-TACA--CAA-CTTCTATACCCTTAAATCCAGAGAGGT
1 AGATTGAAGCTACCACATCCAATC-T-TATACCCTTAAATCCAGAGGGGC
* * *
15339847 AGATTGAAGCCA-CACAT--AACTCCTATACCCTTAAA-CTCAGAGGGGA
1 AGATTGAAGCTACCACATCCAA-TCTTATACCCTTAAATC-CAGAGGGGC
* *
15339893 AAATTGAAGCCA-CACA--CAACTCTTATACCCTTAAA
1 AGATTGAAGCTACCACATCCAA-TCTTATACCCTTAAA
15339928 ATTACAGAAA
Statistics
Matches: 313, Mismatches: 44, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
44 1 0.00
45 5 0.02
46 86 0.27
47 48 0.15
48 157 0.50
49 16 0.05
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (48 bp):
AGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAGGGGC
Found at i:15339675 original size:95 final size:96
Alignment explanation
Indices: 15339508--15339927 Score: 366
Period size: 95 Copynumber: 4.4 Consensus size: 96
15339498 AGATTCAAGA
* * * * *
15339508 GGGATAGATTGAAGCTACCAA-ATTCAAATCTTATACCGCTAAATCCAAAGCA-GTAGATTGAAG
1 GGGA-AGATTGAAGCTA-CAACA-TCCAATCTTATACCCCTAAATCCAGAG-AGGCAAATTGAAG
* *
15339571 CTACCACATCCAATCTTATACCCTTAAATCTAGAG
62 CTACAACATCCAATCTTATACCCTTAAATCCAGAG
* * * * ** *
15339606 GGGCATATTGAAGCTACAACATCTAATCTTATA-CCTTAAATTTAGAGGGGCAAATTGAAGCTAC
1 GGGAAGATTGAAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGAGGCAAATTGAAGCTAC
* *
15339670 TACATCTAATCTTATACCCTTAAATCCAGAG
66 AACATCCAATCTTATACCCTTAAATCCAGAG
* * * *
15339701 GGGAAGATTGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGAGGCAGATTAAAGTTAC
1 GGGAAGATTGAAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGAGGCAAATTGAAGCTAC
* **
15339766 AACATCCAATCTTATACCCCTATTTCCAGAG
66 AACATCCAATCTTATACCCTTAAATCCAGAG
* * *
15339797 GGGAAGATTGAAGC--CATACA--CAA-CTTCTATACCCTTAAATCCAGAGAGGTAGATTGAAGC
1 GGGAAGATTGAAGCTACA-ACATCCAATC-T-TATACCCCTAAATCCAGAGAGGCAAATTGAAGC
* *
15339857 CAC-ACAT--AACTCCTATACCCTTAAA-CTCAGAG
63 TACAACATCCAA-TCTTATACCCTTAAATC-CAGAG
* * *
15339889 GGGAAAATTGAAGCCAC-ACA--CAACTCTTATACCCTTAAA
1 GGGAAGATTGAAGCTACAACATCCAA-TCTTATACCCCTAAA
15339928 ATTACAGAAA
Statistics
Matches: 269, Mismatches: 41, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
91 3 0.01
92 48 0.18
93 9 0.03
94 34 0.13
95 82 0.30
96 78 0.29
97 12 0.04
98 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (96 bp):
GGGAAGATTGAAGCTACAACATCCAATCTTATACCCCTAAATCCAGAGAGGCAAATTGAAGCTAC
AACATCCAATCTTATACCCTTAAATCCAGAG
Found at i:15339717 original size:143 final size:143
Alignment explanation
Indices: 15339508--15339927 Score: 431
Period size: 143 Copynumber: 2.9 Consensus size: 143
15339498 AGATTCAAGA
* * *
15339508 GGGATAGATTGAAGCTACCAAATTCAAATCTTATACCGC-TAAATCCAAAGCA-GTAGATTGAAG
1 GGGA-AGATTGAAGCTACTACA-TC-AATCTTATACC-CTTAAATCCAGAG-AGGTAGATTGAAG
*
15339571 CTACCACATCCAATCTTATACCCTTAAATCTAGAGGGGCATATTGAAGCTACAACATCTAATCTT
61 CTACCACATCCAATCTTATACCCTTAAATCTAGAGGGGCAAATTGAAGCTACAACATC-AATCTT
15339636 ATA-CCTTAAATTT-AGAG
125 ATACCCTTAAATTTCAGAG
* *
15339653 GGGCAA-ATTGAAGCTACTACATCTAATCTTATACCCTTAAATCCAGAGGGGAAGATTGAAGCTA
1 GGG-AAGATTGAAGCTACTACATC-AATCTTATACCCTTAAATCCAGAGAGGTAGATTGAAGCTA
* * * * * *
15339717 CCACATCCAATCTTATACCCCTAAATCCAGAGAGGCAGATTAAAGTTACAACATCCAATCTTATA
64 CCACATCCAATCTTATACCCTTAAATCTAGAGGGGCAAATTGAAGCTACAACAT-CAATCTTATA
*
15339782 CCCCT--ATTTCCAGAG
128 CCCTTAAATTT-CAGAG
* *
15339797 GGGAAGATTGAAGCCA-TACA-CAA-CTTCTATACCCTTAAATCCAGAGAGGTAGATTGAAGCCA
1 GGGAAGATTGAAGCTACTACATCAATC-T-TATACCCTTAAATCCAGAGAGGTAGATTGAAGCTA
* * *
15339859 -CACAT--AACTCCTATACCCTTAAA-CTCAGAGGGGAAAATTGAAGCCAC-ACA-CAACTCTTA
64 CCACATCCAA-TCTTATACCCTTAAATCT-AGAGGGGCAAATTGAAGCTACAACATCAA-TCTTA
15339918 TACCCTTAAA
126 TACCCTTAAA
15339928 ATTACAGAAA
Statistics
Matches: 233, Mismatches: 27, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
137 3 0.01
138 11 0.05
139 6 0.03
140 30 0.13
141 8 0.03
142 38 0.16
143 99 0.42
144 33 0.14
145 4 0.02
146 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (143 bp):
GGGAAGATTGAAGCTACTACATCAATCTTATACCCTTAAATCCAGAGAGGTAGATTGAAGCTACC
ACATCCAATCTTATACCCTTAAATCTAGAGGGGCAAATTGAAGCTACAACATCAATCTTATACCC
TTAAATTTCAGAG
Found at i:15346800 original size:81 final size:81
Alignment explanation
Indices: 15346711--15346873 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
15346701 CTGAACGTAA
* * *
15346711 ACACTTCAATTTCAAGTGAGTTGAAACTAGATTTGTAGCTAATGAAATCAGATTGGAAATTAAAA
1 ACACTTCAATTCCAAGTGAGTCGAAACTAGATTTGTACCTAATGAAATCAGATTGGAAATTAAAA
15346776 ATAACTTTTATCCATT
66 ATAACTTTTATCCATT
*
15346792 ACACTTCAATTCCAGGTGAGTCGAAACTAGATTTGTACCTAATGAAATCAGATTGGAAATTAAAA
1 ACACTTCAATTCCAAGTGAGTCGAAACTAGATTTGTACCTAATGAAATCAGATTGGAAATTAAAA
*
15346857 ATCACTTTTATCCATT
66 ATAACTTTTATCCATT
15346873 A
1 A
15346874 GAAGAAATTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (81 bp):
ACACTTCAATTCCAAGTGAGTCGAAACTAGATTTGTACCTAATGAAATCAGATTGGAAATTAAAA
ATAACTTTTATCCATT
Found at i:15348366 original size:27 final size:27
Alignment explanation
Indices: 15348331--15348382 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
15348321 TAATAGAATG
* *
15348331 GACATGTAACTAATAAAAAAAATAAGT
1 GACAAGTAAATAATAAAAAAAATAAGT
*
15348358 GACAAGTAAATAATAAATAAAATAA
1 GACAAGTAAATAATAAAAAAAATAA
15348383 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (27 bp):
GACAAGTAAATAATAAAAAAAATAAGT
Found at i:15348447 original size:31 final size:31
Alignment explanation
Indices: 15348369--15348453 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 31
15348359 ACAAGTAAAT
*
15348369 AATAAATAAAATAATTAATTAAATCATGCCAATTA
1 AATAAAT-AAATAA-TAA--AAATCATGCAAATTA
* *
15348404 AACAAA-ACAATAATAAAAATCATGCAAATTC
1 AATAAATA-AATAATAAAAATCATGCAAATTA
15348435 AATAAATAAATAAATAAAA
1 AATAAATAAAT-AATAAAA
15348454 CCCTATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
31 21 0.49
32 8 0.19
33 4 0.09
34 5 0.12
35 5 0.12
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (31 bp):
AATAAATAAATAATAAAAATCATGCAAATTA
Found at i:15349660 original size:12 final size:13
Alignment explanation
Indices: 15349638--15349682 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
15349628 TTATATTTAA
15349638 AACAT-AATAAAT
1 AACATAAATAAAT
15349650 AA-ATAAATAAAT
1 AACATAAATAAAT
15349662 AACAT-AATAATAAT
1 AACATAAAT-A-AAT
15349676 AACATAA
1 AACATAA
15349683 TTGGATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 14 0.50
13 3 0.11
14 8 0.29
15 1 0.04
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
AACATAAATAAAT
Found at i:15350142 original size:50 final size:50
Alignment explanation
Indices: 15350088--15350197 Score: 114
Period size: 50 Copynumber: 2.2 Consensus size: 50
15350078 TTATATCTTT
* *
15350088 AGGGAGATAGGACTTGCTAATGTAGCCTCAATC-CAATCCACTACAACTTC
1 AGGGAGATAAGACTTGATAATGTAGCCTC-ATCTCAATCCACTACAACTTC
* * * * * * * *
15350138 AGGGATATAAGATTTGATATTGTAGCTTCATCTTACTCCACTGCAGCTTC
1 AGGGAGATAAGACTTGATAATGTAGCCTCATCTCAATCCACTACAACTTC
15350188 AGGGAGATAA
1 AGGGAGATAA
15350198 AGATTTTCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 3 0.06
50 45 0.94
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (50 bp):
AGGGAGATAAGACTTGATAATGTAGCCTCATCTCAATCCACTACAACTTC
Found at i:15350488 original size:50 final size:50
Alignment explanation
Indices: 15350445--15350604 Score: 212
Period size: 50 Copynumber: 3.2 Consensus size: 50
15350435 AGCTTCAAGA
* * *
15350445 GTATAAGATTCACCCTTGCAGCTTCAATATGCCCCTCTACAGCTTTAGGT
1 GTATAAGATTCACCATTGCGGCTTCAATATGCTCCTCTACAGCTTTAGGT
* * * **
15350495 GTATGAGATTCACCATTGCGGCCTCAATCTATTCCTCTACAGCTTTAGGT
1 GTATAAGATTCACCATTGCGGCTTCAATATGCTCCTCTACAGCTTTAGGT
* * * *
15350545 GTATGAGATTCGCCATTGTGGCTTCAATTTGCTCCTCTACAGCTTTAGGT
1 GTATAAGATTCACCATTGCGGCTTCAATATGCTCCTCTACAGCTTTAGGT
15350595 GTATAAGATT
1 GTATAAGATT
15350605 TGTTGTTTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (50 bp):
GTATAAGATTCACCATTGCGGCTTCAATATGCTCCTCTACAGCTTTAGGT
Found at i:15358963 original size:41 final size:41
Alignment explanation
Indices: 15358874--15359006 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 41
15358864 AGGTAAAGGC
* *
15358874 GGGTTTAATTTAAGG-TTTCTTT-AGGATGGAAAAATTGAT-TTT
1 GGGTTTAATTTAAGGATTTTTTTAAGAAT---AAAATT-ATATTT
*
15358916 GAGTTTAATTTAAGGATTTTTTTAAGAATAAAATTATATTT
1 GGGTTTAATTTAAGGATTTTTTTAAGAATAAAATTATATTT
* * * *
15358957 GGGTTTAGTTTATGAATATTTTTTAAGAATGAAATTATATTT
1 GGGTTTAATTTAAGGAT-TTTTTTAAGAATAAAATTATATTT
*
15358999 GTGTTTAA
1 GGGTTTAA
15359007 AAATATTTGG
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.03
41 22 0.29
42 43 0.56
43 6 0.08
44 4 0.05
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (41 bp):
GGGTTTAATTTAAGGATTTTTTTAAGAATAAAATTATATTT
Found at i:15365652 original size:16 final size:17
Alignment explanation
Indices: 15365631--15365663 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15365621 TTTATATTTA
*
15365631 AAAATAATAAAT-AAAT
1 AAAATAAAAAATGAAAT
15365647 AAAATAAAAAATGAAAT
1 AAAATAAAAAATGAAAT
15365664 TAGGTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATAAAAAATGAAAT
Found at i:15373459 original size:38 final size:38
Alignment explanation
Indices: 15373385--15373467 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
15373375 TTGTATTATT
* **
15373385 GAAAACGAAATCGCTTTCCAGAGGGATGTGACTTAAAA
1 GAAAAGGAAATCGCTTTCCAGAGGGATGCCACTTAAAA
* * * *
15373423 GAAAAGGAAATGGCTTTGCTGAGGGATGCCATTTAAAA
1 GAAAAGGAAATCGCTTTCCAGAGGGATGCCACTTAAAA
*
15373461 GAGAAGG
1 GAAAAGG
15373468 GGAATGGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (38 bp):
GAAAAGGAAATCGCTTTCCAGAGGGATGCCACTTAAAA
Found at i:15378963 original size:26 final size:26
Alignment explanation
Indices: 15378892--15379043 Score: 78
Period size: 27 Copynumber: 5.7 Consensus size: 26
15378882 CGACTTATAC
*
15378892 TTGGTGAA-CCCTAGTTCGCCAAACCAA
1 TTGG-GAACCCCTAGTTTGCC-AACCAA
* **
15378919 TTGACGAACCCC-AACTTGCCAACCAA
1 TTG-GGAACCCCTAGTTTGCCAACCAA
** ***
15378945 TTGGGGCCCCCTAGTTTGCTCAACTGG
1 TTGGGAACCCCTAGTTTGC-CAACCAA
* * *
15378972 TTGGCAAACCCTAGTTCGCCAAACCAA
1 TTGGGAACCCCTAGTTTGCC-AACCAA
* *
15378999 TTGACGAACCCC-AGCTTGCCAACCAA
1 TTG-GGAACCCCTAGTTTGCCAACCAA
*
15379025 TTGGG-GCCCCTTAGTTTGC
1 TTGGGAACCCC-TAGTTTGC
15379044 TAAACTGGTT
Statistics
Matches: 89, Mismatches: 28, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
24 4 0.04
25 6 0.07
26 30 0.34
27 41 0.46
28 8 0.09
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (26 bp):
TTGGGAACCCCTAGTTTGCCAACCAA
Found at i:15379008 original size:27 final size:25
Alignment explanation
Indices: 15378897--15379027 Score: 82
Period size: 27 Copynumber: 4.9 Consensus size: 25
15378887 TATACTTGGT
15378897 GAACCCTAGTTCGCCAAACCAATTGAC
1 GAACCCTAGTT-GCC-AACCAATTGAC
* * **
15378924 GAACCCCAACTTGCCAACCAATTGGG
1 GAA-CCCTAGTTGCCAACCAATTGAC
** *** *
15378950 GCCCCCTAGTTTGCTCAACTGGTTGGC
1 GAACCCTAG-TTGC-CAACCAATTGAC
*
15378977 AAACCCTAGTTCGCCAAACCAATTGAC
1 GAACCCTAGTT-GCC-AACCAATTGAC
*
15379004 GAACCCCAGCTTGCCAACCAATTG
1 GAACCCTAG-TTGCCAACCAATTG
15379028 GGGCCCCTTA
Statistics
Matches: 77, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
25 4 0.05
26 26 0.34
27 39 0.51
28 8 0.10
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (25 bp):
GAACCCTAGTTGCCAACCAATTGAC
Found at i:15379076 original size:80 final size:80
Alignment explanation
Indices: 15378898--15379068 Score: 315
Period size: 80 Copynumber: 2.1 Consensus size: 80
15378888 ATACTTGGTG
15378898 AACCCTAGTTCGCCAAACCAATTGACGAACCCCAACTTGCCAACCAATTGGGGCCCCCTAGTTTG
1 AACCCTAGTTCGCCAAACCAATTGACGAACCCCAACTTGCCAACCAATTGGGGCCCCCTAGTTTG
*
15378963 CTCAACTGGTTGGCA
66 CTAAACTGGTTGGCA
* *
15378978 AACCCTAGTTCGCCAAACCAATTGACGAACCCCAGCTTGCCAACCAATTGGGGCCCCTTAGTTTG
1 AACCCTAGTTCGCCAAACCAATTGACGAACCCCAACTTGCCAACCAATTGGGGCCCCCTAGTTTG
15379043 CTAAACTGGTTGGCA
66 CTAAACTGGTTGGCA
15379058 AACCCTAGTTC
1 AACCCTAGTTC
15379069 ACGAAACCTG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 88 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (80 bp):
AACCCTAGTTCGCCAAACCAATTGACGAACCCCAACTTGCCAACCAATTGGGGCCCCCTAGTTTG
CTAAACTGGTTGGCA
Found at i:15384838 original size:54 final size:54
Alignment explanation
Indices: 15384773--15384875 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
15384763 TTGTAAATCG
*
15384773 AAGACCATATAGTGTAAGACCTAGTCATGGTAGCTATGGCATCATATGGGGAAA
1 AAGACCATATAGTGTAAAACCTAGTCATGGTAGCTATGGCATCATATGGGGAAA
* * *
15384827 AAGACCGTATAGTGTAAAACCTAGTCATGGTTGCTATGGTATCATATGG
1 AAGACCATATAGTGTAAAACCTAGTCATGGTAGCTATGGCATCATATGG
15384876 AATAAGATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (54 bp):
AAGACCATATAGTGTAAAACCTAGTCATGGTAGCTATGGCATCATATGGGGAAA
Found at i:15385057 original size:29 final size:28
Alignment explanation
Indices: 15384984--15385061 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
15384974 CCATAAAAGG
* * * *
15384984 AAGCCTTTTTGGCTGATTCTATTAAAAG
1 AAGCCTTTGTGGTTGATTCTGTTAAAAA
*
15385012 AAGTCTTTGTGGTTGATTCTGTTAAAATA
1 AAGCCTTTGTGGTTGATTCTGTTAAAA-A
15385041 AAGCCTTTGTGGTTGATTCTG
1 AAGCCTTTGTGGTTGATTCTG
15385062 ATAATGAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 23 0.53
29 20 0.47
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (28 bp):
AAGCCTTTGTGGTTGATTCTGTTAAAAA
Found at i:15385228 original size:28 final size:28
Alignment explanation
Indices: 15385186--15385291 Score: 97
Period size: 28 Copynumber: 3.8 Consensus size: 28
15385176 TCCTCTATGG
**
15385186 CTATCTTTG-TGTAAGGACGTCATTGTGA
1 CTATCTTTGCT-TAAGGACACCATTGTGA
* *
15385214 CTATCTTTGCTTAAGGACACCTTTGTGG
1 CTATCTTTGCTTAAGGACACCATTGTGA
* * *
15385242 CTATCTTTACTTAAGGACACCTTTGTGG
1 CTATCTTTGCTTAAGGACACCATTGTGA
* **
15385270 CTATGTTTTTTTCAAGGACACC
1 CTATCTTTGCTT-AAGGACACC
15385292 TCTGTGGCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 58 0.85
29 10 0.15
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (28 bp):
CTATCTTTGCTTAAGGACACCATTGTGA
Found at i:15385245 original size:56 final size:57
Alignment explanation
Indices: 15385177--15385302 Score: 139
Period size: 56 Copynumber: 2.2 Consensus size: 57
15385167 GATTGAAAAT
* * **
15385177 CCTCTATGGCTATCTTT-GTGTAAGGACGTCATTGTGACTATCTTTGCTT-AAGGACA
1 CCTCTGTGGCTATCTTTACT-TAAGGACACCATTGTGACTATCTTTGCTTCAAGGACA
* * * * **
15385233 CCTTTGTGGCTATCTTTACTTAAGGACACCTTTGTGGCTATGTTTTTTTCAAGGACA
1 CCTCTGTGGCTATCTTTACTTAAGGACACCATTGTGACTATCTTTGCTTCAAGGACA
15385290 CCTCTGTGGCTAT
1 CCTCTGTGGCTAT
15385303 TTATGTCGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
56 37 0.65
57 20 0.35
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (57 bp):
CCTCTGTGGCTATCTTTACTTAAGGACACCATTGTGACTATCTTTGCTTCAAGGACA
Found at i:15385297 original size:29 final size:28
Alignment explanation
Indices: 15385208--15385302 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
15385198 AAGGACGTCA
* *
15385208 TTGTGACTATCTTTGCTTAAGGACACCT
1 TTGTGGCTATCTTTACTTAAGGACACCT
15385236 TTGTGGCTATCTTTACTTAAGGACACCT
1 TTGTGGCTATCTTTACTTAAGGACACCT
* **
15385264 TTGTGGCTATGTTTTTTTCAAGGACACCT
1 TTGTGGCTATCTTTACTT-AAGGACACCT
*
15385293 CTGTGGCTAT
1 TTGTGGCTAT
15385303 TTATGTCGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 41 0.68
29 19 0.32
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (28 bp):
TTGTGGCTATCTTTACTTAAGGACACCT
Found at i:15386567 original size:46 final size:46
Alignment explanation
Indices: 15386484--15386650 Score: 115
Period size: 46 Copynumber: 3.6 Consensus size: 46
15386474 AGTTCCCAGC
* ** * * *
15386484 TCTTGCATTTGTTACGGACTGGTGAATATGGATTTAGGGTCGCATT
1 TCTTGCATTTGTTACAGACTGGTGAATATAAAATTAGGGTCCCAAT
* *
15386530 TCTTGCATTTGTTACAGATTGGTGAAT-TCAAAATTAGGTTCCCAAT
1 TCTTGCATTTGTTACAGACTGGTGAATAT-AAAATTAGGGTCCCAAT
** * * * * *
15386576 TCTTGCATACGTTAC-GAACAGGTGAATACT-GATTTAGGTTCCCAGT
1 TCTTGCATTTGTTACAG-ACTGGTGAATA-TAAAATTAGGGTCCCAAT
* * * *
15386622 TCTCGCATTTGTTGCAAACTGGAGAATAT
1 TCTTGCATTTGTTACAGACTGGTGAATAT
15386651 GGAATAATAA
Statistics
Matches: 94, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
45 3 0.03
46 90 0.96
48 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (46 bp):
TCTTGCATTTGTTACAGACTGGTGAATATAAAATTAGGGTCCCAAT
Found at i:15389072 original size:28 final size:28
Alignment explanation
Indices: 15389041--15389101 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
15389031 TCTTTCCAAG
*
15389041 CCAGAAACAG-ATGAATGCTCTACTCGAA
1 CCAGAAACAGAAT-AATGCTATACTCGAA
** *
15389069 CCAGAATTAGAATAATGCTATACTCGAG
1 CCAGAAACAGAATAATGCTATACTCGAA
15389097 CCAGA
1 CCAGA
15389102 TTCAAAGTAA
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:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (28 bp):
CCAGAAACAGAATAATGCTATACTCGAA
Found at i:15389177 original size:28 final size:28
Alignment explanation
Indices: 15389133--15389208 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
15389123 ACCCAGAATT
*
15389133 AGAAT-TCACTCTATCCGAGCTAGAAA-C
1 AGAATATCGCTCTATCCGAGCTA-AAATC
*
15389160 AGAATATTGCTCTATCCGAGCTAAAATC
1 AGAATATCGCTCTATCCGAGCTAAAATC
15389188 AGAATATCGCTCTATCCGAGC
1 AGAATATCGCTCTATCCGAGC
15389209 CTTCCACTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.18
28 36 0.82
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (28 bp):
AGAATATCGCTCTATCCGAGCTAAAATC
Found at i:15403055 original size:20 final size:19
Alignment explanation
Indices: 15403030--15403068 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
15403020 TCTCGTTAGA
*
15403030 TTTTAATACAAATATTTTAT
1 TTTTAAAACAAA-ATTTTAT
*
15403050 TTTTAAAATAAAATTTTAT
1 TTTTAAAACAAAATTTTAT
15403069 AAATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAACAAAATTTTAT
Found at i:15405536 original size:18 final size:19
Alignment explanation
Indices: 15405508--15405547 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
15405498 GAGAAATCAG
15405508 TTTTATTA-TTTTTAATATA
1 TTTTATTATTTTTTAAT-TA
15405527 TTTT-TTATTTTTTAATTA
1 TTTTATTATTTTTTAATTA
15405545 TTT
1 TTT
15405548 ATGTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTATTATTTTTTAATTA
Found at i:15408187 original size:17 final size:17
Alignment explanation
Indices: 15408165--15408198 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15408155 CTTCCGAGAT
15408165 CCTCTATCTCTTTAGCA
1 CCTCTATCTCTTTAGCA
15408182 CCTCTATCTCTTTAGCA
1 CCTCTATCTCTTTAGCA
15408199 TATCGGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.06, T:0.41
Consensus pattern (17 bp):
CCTCTATCTCTTTAGCA
Found at i:15418928 original size:29 final size:29
Alignment explanation
Indices: 15418895--15418962 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
15418885 CTACATTTGG
15418895 AAATGTAAGAAAT-TCATTTGCATTAAACA
1 AAATGTAAGAAATCT-ATTTGCATTAAACA
* *
15418924 AAATGTAAGAAATCTATTTGTATTTAACA
1 AAATGTAAGAAATCTATTTGCATTAAACA
15418953 AAATGTAAGA
1 AAATGTAAGA
15418963 GCACATGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATGTAAGAAATCTATTTGCATTAAACA
Found at i:15423521 original size:16 final size:18
Alignment explanation
Indices: 15423485--15423521 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
15423475 GCTCACCTAC
*
15423485 GAGCTCATTCAGAGTTGT
1 GAGCTCATTCAAAGTTGT
15423503 GAGCTCA-TCAAAG-TGT
1 GAGCTCATTCAAAGTTGT
15423519 GAG
1 GAG
15423522 ATGCTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (18 bp):
GAGCTCATTCAAAGTTGT
Found at i:15441796 original size:58 final size:59
Alignment explanation
Indices: 15441717--15441884 Score: 186
Period size: 58 Copynumber: 2.9 Consensus size: 59
15441707 AATTGAATCT
* **
15441717 AAAAAAAGCTTAGGTACCAAATTAG-GAAAAATGTCAAGTT-TGGATACCAAATTGGGTC
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAG-TACCAAATTGGGTC
* * *
15441775 AAAAAAAGTTTAGGTATCAAATTAGAAAAAAATGTCAAGTTCAAGTATCAAATTGGGTC
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
* * *
15441834 -AAAAAA--TTTGGATACCAAATTA-AAAAAAAGTGTCAAATTCAAGTACTAAAT
1 AAAAAAAGCTTAGG-TACCAAATTAGAAAAAAA-TGTCAAGTTCAAGTACCAAAT
15441885 ATTATATTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
56 11 0.12
57 27 0.28
58 29 0.31
59 27 0.28
60 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (59 bp):
AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
Found at i:15441855 original size:57 final size:59
Alignment explanation
Indices: 15441717--15441884 Score: 195
Period size: 57 Copynumber: 2.9 Consensus size: 59
15441707 AATTGAATCT
* * **
15441717 AAAAAAAGCTTAGGTACCAAATTAG-GAAAAATGTCAAGTT-TGGATACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAG-TACCAAATTGGGTC
* *
15441775 AAAAAAAGTTTAGGTATCAAATTAGAAAAAAATGTCAAGTTCAAGTATCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
* *
15441834 -AAAAAA-TTT-GGATACCAAATTA-AAAAAAAGTGTCAAATTCAAGTACTAAAT
1 AAAAAAAGTTTAGG-TACCAAATTAGAAAAAAA-TGTCAAGTTCAAGTACCAAAT
15441885 ATTATATTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
56 9 0.09
57 30 0.31
58 29 0.30
59 27 0.28
60 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
Found at i:15443616 original size:15 final size:15
Alignment explanation
Indices: 15443577--15443614 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
15443567 TAGATTTTAG
15443577 AATTA-TTTTATTTT
1 AATTATTTTTATTTT
*
15443591 TATTATTTTTATTTT
1 AATTATTTTTATTTT
15443606 AA-TATTTTT
1 AATTATTTTT
15443615 TAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
AATTATTTTTATTTT
Found at i:15444065 original size:26 final size:27
Alignment explanation
Indices: 15444017--15444069 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
15444007 TCAAAATATA
* * *
15444017 TTATTTTTATTAAATGTTTTTATTAAT
1 TTATCTTTATTAAATATTATTATTAAT
15444044 TTATCTTT-TTAAATATTATTATTAAT
1 TTATCTTTATTAAATATTATTATTAAT
15444070 AACAATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATCTTTATTAAATATTATTATTAAT
Found at i:15454326 original size:19 final size:21
Alignment explanation
Indices: 15454285--15454329 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
15454275 AAATTATAAT
*
15454285 TTAAATTTAATATTAAATCTTA
1 TTAAATTTAATA-TAAATATTA
15454307 TTAAA-TTAATA-AAATATTA
1 TTAAATTTAATATAAATATTA
15454326 TTAA
1 TTAA
15454330 GATAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
21 6 0.27
22 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAATTTAATATAAATATTA
Found at i:15454332 original size:58 final size:57
Alignment explanation
Indices: 15454247--15454374 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 57
15454237 TCACTTTAAA
* *
15454247 ATTAAATTAATATAATACTTATCAAGATAA-ATTATAATTTAAATTTAATATTAAATCTT
1 ATTAAATTAATAAAATACTTATCAAGATAAGATTA-AATTT-AATTTAATATTAAAT-AT
*
15454306 ATTAAATTAATAAAATA-TTATTAAGATAAGTATTAAATTTAATTTAATATTAAATAT
1 ATTAAATTAATAAAATACTTATCAAGATAAG-ATTAAATTTAATTTAATATTAAATAT
*
15454363 ATTAAAATAATA
1 ATTAAATTAATA
15454375 TTATTTTTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
57 12 0.19
58 26 0.41
59 21 0.33
60 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (57 bp):
ATTAAATTAATAAAATACTTATCAAGATAAGATTAAATTTAATTTAATATTAAATAT
Found at i:15454365 original size:26 final size:27
Alignment explanation
Indices: 15454273--15454368 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 27
15454263 ACTTATCAAG
15454273 ATAA-ATTATAATTTAAATTTAATATTAA
1 ATAATATTA-AATTT-AATTTAATATTAA
** ** *
15454301 ATCTTATTAAATTAATAAAATATTATTAA
1 ATAATATTAAATT--TAATTTAATATTAA
15454330 GATAAGTATTAAATTTAATTTAATATTAA
1 -ATAA-TATTAAATTTAATTTAATATTAA
15454359 AT-ATATTAAA
1 ATAATATTAAA
15454369 ATAATATTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
26 7 0.13
27 1 0.02
28 8 0.15
29 25 0.47
30 3 0.06
31 9 0.17
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (27 bp):
ATAATATTAAATTTAATTTAATATTAA
Found at i:15466909 original size:19 final size:19
Alignment explanation
Indices: 15466885--15466927 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
15466875 AAAACATTTG
15466885 ATATTAACATCAATTTCAC
1 ATATTAACATCAATTTCAC
*
15466904 ATATTAATATCAATTTCAC
1 ATATTAACATCAATTTCAC
15466923 ATATT
1 ATATT
15466928 TTTCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATTAACATCAATTTCAC
Found at i:15475139 original size:6 final size:6
Alignment explanation
Indices: 15475128--15475175 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
15475118 GGAAAGTGTC
15475128 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG
1 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG
15475176 GCACTTCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
TCCCTG
Found at i:15475645 original size:17 final size:18
Alignment explanation
Indices: 15475614--15475647 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15475604 AATTTAACTT
15475614 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
15475632 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
15475648 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:15475694 original size:20 final size:19
Alignment explanation
Indices: 15475669--15475713 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15475659 TATATTTTCT
*
15475669 TTTTTTACAAAATTTAATCA
1 TTTTTTACAAAAGTTAAT-A
*
15475689 TTTTTT-CATAAGTTAATA
1 TTTTTTACAAAAGTTAATA
15475707 TTTTTTA
1 TTTTTTA
15475714 TTTTTGTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTTACAAAAGTTAATA
Found at i:15475881 original size:6 final size:6
Alignment explanation
Indices: 15475862--15475907 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
15475852 AAAATTTAAC
*
15475862 GTTTAG GATTTAG GTTTAG GTTTGG GTTTAGG GTTTTAG GTTTAG G
1 GTTTAG G-TTTAG GTTTAG GTTTAG GTTTA-G G-TTTAG GTTTAG G
15475908 ATTCAAGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 21 0.60
7 10 0.29
8 4 0.11
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (6 bp):
GTTTAG
Found at i:15476863 original size:16 final size:16
Alignment explanation
Indices: 15476842--15476872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15476832 AAAACTAAAT
15476842 TTTAATCTTATATTTA
1 TTTAATCTTATATTTA
*
15476858 TTTAATTTTATATTT
1 TTTAATCTTATATTT
15476873 TAATATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATCTTATATTTA
Found at i:15479557 original size:29 final size:29
Alignment explanation
Indices: 15479525--15479583 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
15479515 TAAGTGTATC
*
15479525 TTTTTATGAGAT-ATCATATCATAAAAATA
1 TTTTAATGAGATAATC-TATCATAAAAATA
* *
15479554 TTTTAATGAGATAATCTTTCATAAAGATA
1 TTTTAATGAGATAATCTATCATAAAAATA
15479583 T
1 T
15479584 ATATTCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTTAATGAGATAATCTATCATAAAAATA
Found at i:15479792 original size:22 final size:23
Alignment explanation
Indices: 15479758--15479818 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 23
15479748 TTAAAATGAT
* * *
15479758 AAAATTTTGATTTAATCTGT-TA
1 AAAATTATAATTTAATCTATATA
*
15479780 AAAATTATAATTTTA-CTATAATA
1 AAAATTATAATTTAATCTAT-ATA
*
15479803 AAAATTACAATTTAAT
1 AAAATTATAATTTAAT
15479819 TTCAGCCCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.10
22 12 0.40
23 15 0.50
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
AAAATTATAATTTAATCTATATA
Found at i:15480612 original size:2 final size:2
Alignment explanation
Indices: 15480605--15480637 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15480595 GCCAAGTAAG
15480605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15480638 AACATGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15480901 original size:3 final size:3
Alignment explanation
Indices: 15480893--15480928 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15480883 TATTTACTAA
15480893 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15480929 TTAACGACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:15482281 original size:23 final size:24
Alignment explanation
Indices: 15482248--15482293 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
15482238 CATACATTTC
15482248 ATTATGTATTGTATGTTATTTTTT
1 ATTATGTATTGTATGTTATTTTTT
15482272 ATTAT-TATTGTATGTTATTTTT
1 ATTATGTATTGTATGTTATTTTT
15482294 AAATACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (24 bp):
ATTATGTATTGTATGTTATTTTTT
Found at i:15483098 original size:24 final size:24
Alignment explanation
Indices: 15483063--15483112 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15483053 CTAATTTAAT
* *
15483063 TTACAAATATATATTTTTTAAAAA
1 TTACAAAAATATATTATTTAAAAA
* *
15483087 TTACAAAAATATCTTATTTAATAA
1 TTACAAAAATATATTATTTAAAAA
15483111 TT
1 TT
15483113 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTACAAAAATATATTATTTAAAAA
Found at i:15485077 original size:19 final size:18
Alignment explanation
Indices: 15485041--15485083 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
15485031 ATACGGTATC
15485041 ATTTT-AAATTTATTGAT
1 ATTTTAAAATTTATTGAT
*
15485058 ATTTTAAAATATTTTTGAT
1 ATTTTAAAAT-TTATTGAT
15485077 ATATTTA
1 AT-TTTA
15485084 TAGAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 9 0.41
20 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTTAAAATTTATTGAT
Found at i:15489348 original size:17 final size:17
Alignment explanation
Indices: 15489316--15489373 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 17
15489306 ATATTTGGTA
*
15489316 TTTAAATTTGATATTTT
1 TTTAAATTTGACATTTT
*
15489333 TTTAAATTTGGCA----
1 TTTAAATTTGACATTTT
15489346 TTTAAATTTGACACTTTT
1 TTTAAATTTGACA-TTTT
*
15489364 TTTTAATTTG
1 TTTAAATTTG
15489374 GTACTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
13 12 0.38
17 11 0.34
18 9 0.28
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (17 bp):
TTTAAATTTGACATTTT
Found at i:15489372 original size:31 final size:31
Alignment explanation
Indices: 15489308--15489415 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 31
15489298 TTAATATAAT
* *
15489308 ATTTGGTATTTAAATTTGATA-TTTTTTTAA
1 ATTTGGTATTTAAATTTGACACTTTTTTTTA
*
15489338 ATTTGGCATTTAAATTTGACACTTTTTTTTA
1 ATTTGGTATTTAAATTTGACACTTTTTTTTA
* *
15489369 ATTTGGTACTTAAATTTGTCACTTTTTTGTTA
1 ATTTGGTATTTAAATTTGACACTTTTTT-TTA
* * *
15489401 AGTTGATACTTAAAT
1 ATTTGGTATTTAAAT
15489416 ATTTTAGGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.28
31 33 0.49
32 16 0.24
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (31 bp):
ATTTGGTATTTAAATTTGACACTTTTTTTTA
Found at i:15489709 original size:13 final size:13
Alignment explanation
Indices: 15489691--15489715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15489681 AAATTAAAAA
15489691 AAATATCAAATTC
1 AAATATCAAATTC
15489704 AAATATCAAATT
1 AAATATCAAATT
15489716 GAATCATAAA
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAAATTC
Found at i:15489727 original size:57 final size:57
Alignment explanation
Indices: 15489612--15489768 Score: 199
Period size: 57 Copynumber: 2.7 Consensus size: 57
15489602 AATATTTAAT
* * * * * * *
15489612 AAATTTAAGTACCACATT-AAAAAAATACCAAGTTTAGATACCAAATTGGATCAAAA
1 AAATTTAAGTACCAAATTAAAAAAAATATCAAATTCAAATATCAAATTGAATCAAAA
* *
15489668 AAATTTAAGTATCAAATTAAAAAAAATATCAAATTCAAATATCAAATTGAATCATAA
1 AAATTTAAGTACCAAATTAAAAAAAATATCAAATTCAAATATCAAATTGAATCAAAA
*
15489725 AAATTTAAATACCAAATTAAAAAAAATTATCAAATATCAAATAT
1 AAATTTAAGTACCAAATTAAAAAAAA-TATCAAAT-TCAAATAT
15489769 TGCCTTAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
56 16 0.18
57 55 0.63
58 8 0.09
59 8 0.09
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (57 bp):
AAATTTAAGTACCAAATTAAAAAAAATATCAAATTCAAATATCAAATTGAATCAAAA
Found at i:15492508 original size:24 final size:22
Alignment explanation
Indices: 15492472--15492530 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
15492462 CCTTATTATT
*
15492472 TTTAAAAAGTTTTAAATATATATA
1 TTTAATAA-TTTTAAATATA-ATA
* *
15492496 TTTATATTATTTT-AATTTAATA
1 TTTA-ATAATTTTAAATATAATA
15492518 TTTAATAATTTTA
1 TTTAATAATTTTA
15492531 TCTATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 7 0.24
22 7 0.24
23 5 0.17
24 8 0.28
25 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATAATTTTAAATATAATA
Found at i:15495054 original size:39 final size:38
Alignment explanation
Indices: 15495007--15495095 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 38
15494997 GTCAATAATT
*
15495007 TCAATATCCAACAAGGTTAAAACATAATAATTTCAATA
1 TCAATATCCAACAAGCTTAAAACATAATAATTTCAATA
15495045 TCTAATATCCAACAAGCTTAAAACATAATAATTTCAATA
1 TC-AATATCCAACAAGCTTAAAACATAATAATTTCAATA
15495084 TCAATATCCAAC
1 TCAATATCCAAC
15495096 CAACATTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.29
Consensus pattern (38 bp):
TCAATATCCAACAAGCTTAAAACATAATAATTTCAATA
Found at i:15499033 original size:25 final size:26
Alignment explanation
Indices: 15498960--15499034 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
15498950 TATCATCCTT
* *
15498960 ATTTTACCC-CTAGTAAAATTTTAACG
1 ATTTTACCCTCGA-TAAAATTTTGACG
*
15498986 ATTTTACCCTCGATAAAAGTTTGACG
1 ATTTTACCCTCGATAAAATTTTGACG
* *
15499012 ATTTTA-CCTGGTTAAAATTTTGA
1 ATTTTACCCTCGATAAAATTTTGA
15499035 GAAAATATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.33
26 26 0.62
27 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (26 bp):
ATTTTACCCTCGATAAAATTTTGACG
Found at i:15499190 original size:6 final size:6
Alignment explanation
Indices: 15499179--15499213 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
15499169 GCAAATTAAT
* *
15499179 CATTTC CATTTC CATTTA CATTCC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
15499214 TGGAAACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (6 bp):
CATTTC
Found at i:15499205 original size:18 final size:18
Alignment explanation
Indices: 15499179--15499213 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15499169 GCAAATTAAT
*
15499179 CATTTCCATTTCCATTTA
1 CATTCCCATTTCCATTTA
15499197 CATTCCCATTTCCATTT
1 CATTCCCATTTCCATTT
15499214 TGGAAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (18 bp):
CATTCCCATTTCCATTTA
Found at i:15502974 original size:53 final size:53
Alignment explanation
Indices: 15502912--15503017 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
15502902 AGAAATGACA
*
15502912 AAGTTAGATAAATAAGTTAGATTCAGAAATGAATGTGGTTTCCCACTTAGTAT
1 AAGTTAGATAAATAAGTTACATTCAGAAATGAATGTGGTTTCCCACTTAGTAT
*
15502965 AAGTTAGATAAATAAGTTACATTCGGAAATGAATGTGGTTTCCCACTTAGTAT
1 AAGTTAGATAAATAAGTTACATTCAGAAATGAATGTGGTTTCCCACTTAGTAT
15503018 GAAAATGACC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (53 bp):
AAGTTAGATAAATAAGTTACATTCAGAAATGAATGTGGTTTCCCACTTAGTAT
Found at i:15503225 original size:16 final size:18
Alignment explanation
Indices: 15503198--15503233 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
15503188 TTAGAATTAG
15503198 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
15503215 ATTGA-AAAATTAATTTA
1 ATTGAGAAAATTAATTTA
15503232 AT
1 AT
15503234 AAATAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:15504317 original size:34 final size:35
Alignment explanation
Indices: 15504274--15504345 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
15504264 GCTTTCCACC
*
15504274 ACTAAGGA-TTTTCCCAAATTCACTAATTTGCTTA
1 ACTAAGGATTTTTCCCAAATTAACTAATTTGCTTA
* *
15504308 ACTAAGGATTTTTTTCCAAATTAATTAATTTGCTTA
1 ACTAAGGA-TTTTTCCCAAATTAACTAATTTGCTTA
15504344 AC
1 AC
15504346 CTTTGAGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 8 0.24
36 25 0.76
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (35 bp):
ACTAAGGATTTTTCCCAAATTAACTAATTTGCTTA
Found at i:15519935 original size:18 final size:18
Alignment explanation
Indices: 15519888--15519935 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
15519878 GCTTGTCCTC
*
15519888 AAGCAAACAAAACAAGAA
1 AAGCAAACAAAGCAAGAA
*
15519906 AAGCAAATAAAGCAAGAA
1 AAGCAAACAAAGCAAGAA
15519924 AAGCAAACAAAG
1 AAGCAAACAAAG
15519936 GAGCTTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.02
Consensus pattern (18 bp):
AAGCAAACAAAGCAAGAA
Found at i:15527633 original size:74 final size:74
Alignment explanation
Indices: 15527491--15527638 Score: 244
Period size: 74 Copynumber: 2.0 Consensus size: 74
15527481 ATCTTTCATT
* *
15527491 CCACAATCAAAAGATTACAATCATAAAGTCAAATGGTTGATTCAAGTGAGAGTGCTGCTAACCTT
1 CCACAATCAAAAGATTACAATCATAAAGTCAAATGGCTGATTCAAGTGAGAGTGCTACTAACCTT
15527556 ATTCTTGAA
66 ATTCTTGAA
**
15527565 CCACAATCAAAAGATTACAATCATAAAGTCAAATGGCTGATTCAAGTGAGAGTTTTACTAAACC-
1 CCACAATCAAAAGATTACAATCATAAAGTCAAATGGCTGATTCAAGTGAGAGTGCTACT-AACCT
15527629 TATTCTTGAA
65 TATTCTTGAA
15527639 TTCCCAAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 65 0.94
75 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (74 bp):
CCACAATCAAAAGATTACAATCATAAAGTCAAATGGCTGATTCAAGTGAGAGTGCTACTAACCTT
ATTCTTGAA
Found at i:15529697 original size:25 final size:23
Alignment explanation
Indices: 15529661--15529706 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
15529651 TGAAAGAAGC
15529661 AGAAATAAAGGG-AGAGATGGAAT
1 AGAAATAAAGGGAAGA-ATGGAAT
15529684 AGAATATAACAGGGAAGAATGGA
1 AGAA-ATAA-AGGGAAGAATGGA
15529707 GAATAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 9 0.45
26 3 0.15
ACGTcount: A:0.52, C:0.02, G:0.33, T:0.13
Consensus pattern (23 bp):
AGAAATAAAGGGAAGAATGGAAT
Found at i:15531988 original size:33 final size:33
Alignment explanation
Indices: 15531934--15531997 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
15531924 ATCTTTATGC
*
15531934 CTTAAATTGAAAATAATTTTTA-TATAGGGGGTG
1 CTTAAATTCAAAATAATTTTTATTA-AGGGGGTG
*
15531967 CTTAAATTCAAAAT-GTCTTTTATTAAGGGGG
1 CTTAAATTCAAAATAAT-TTTTATTAAGGGGG
15531998 AGCAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 24 0.89
34 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39
Consensus pattern (33 bp):
CTTAAATTCAAAATAATTTTTATTAAGGGGGTG
Found at i:15532210 original size:31 final size:31
Alignment explanation
Indices: 15532172--15532233 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
15532162 ATCTTTATGT
*
15532172 CTTAAATTGAAAATGAT-TTTTA-TATAGGGGG
1 CTTAAATTCAAAATG-TCTTTTATTA-AGGGGG
15532203 CTTAAATTCAAAATGTCTTTTATTAAGGGGG
1 CTTAAATTCAAAATGTCTTTTATTAAGGGGG
15532234 AGCAATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.89
32 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (31 bp):
CTTAAATTCAAAATGTCTTTTATTAAGGGGG
Found at i:15532266 original size:236 final size:236
Alignment explanation
Indices: 15531800--15532282 Score: 844
Period size: 238 Copynumber: 2.0 Consensus size: 236
15531790 TTATTTTTTA
* *
15531800 TATAACAAAAAGAGGGAGAAGAGAAAGGTAAATTTTATGGTTGATTGATTGCTTATATTAGTGAG
1 TATATCAAAAAGAGGGAGAAGAGAAAGGTAAATTTTATGGTTGATTGATTGCTTATATTAGTGAC
* *
15531865 CAATTTTTTGAAAGAAAAATGAATGACAAATTTGAGCTTATTGAAAATTTATGCTCCAAATCTTT
66 CAATTTTTTCAAAGAAAAATGAATGACAAATTTGACCTTATTGAAAATTTATGCTCCAAATCTTT
15531930 ATGCCTTAAATTGAAAATAATTTTTATATAGGGGGTGCTTAAATTCAAAATGTCTTTTATTAAGG
131 ATGCCTTAAATTGAAAATAATTTTTATATAGGGGGTGCTTAAATTCAAAATGTCTTTTATTAAGG
15531995 GGGAGCAATATATTCAAAAACAAATTTACAAAATGTTTTGT
196 GGGAGCAATATATTCAAAAACAAATTTACAAAATGTTTTGT
*
15532036 TATATCAAAAAGTGGGAGATAAGAGAAAGGTAAATTTTATGGTTGATTGATTGCTTATATTAGTG
1 TATATCAAAAAGAGGGAG--AAGAGAAAGGTAAATTTTATGGTTGATTGATTGCTTATATTAGTG
* *
15532101 ACCAATTTTTTCAAAGAAAAATGAATGTCAAATTTGACCTTATTGAAAATTTATGCTTCAAATCT
64 ACCAATTTTTTCAAAGAAAAATGAATGACAAATTTGACCTTATTGAAAATTTATGCTCCAAATCT
* *
15532166 TTATGTCTTAAATTGAAAATGATTTTTATATA-GGGG-GCTTAAATTCAAAATGTCTTTTATTAA
129 TTATGCCTTAAATTGAAAATAATTTTTATATAGGGGGTGCTTAAATTCAAAATGTCTTTTATTAA
*
15532229 GGGGGAGCAATCTATTCAAAAACAAATTTACAAAATGTTTTGT
194 GGGGGAGCAATATATTCAAAAACAAATTTACAAAATGTTTTGT
15532272 TATATCAAAAA
1 TATATCAAAAA
15532283 CAGAGAGATT
Statistics
Matches: 235, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
236 96 0.41
237 4 0.02
238 135 0.57
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (236 bp):
TATATCAAAAAGAGGGAGAAGAGAAAGGTAAATTTTATGGTTGATTGATTGCTTATATTAGTGAC
CAATTTTTTCAAAGAAAAATGAATGACAAATTTGACCTTATTGAAAATTTATGCTCCAAATCTTT
ATGCCTTAAATTGAAAATAATTTTTATATAGGGGGTGCTTAAATTCAAAATGTCTTTTATTAAGG
GGGAGCAATATATTCAAAAACAAATTTACAAAATGTTTTGT
Found at i:15532606 original size:21 final size:21
Alignment explanation
Indices: 15532576--15532617 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15532566 CAAACAATGA
*
15532576 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCAATACCTTTT
*
15532597 CAAAATGTATCAATACCTTTT
1 CAAAAAGTATCAATACCTTTT
15532618 ATCAGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (21 bp):
CAAAAAGTATCAATACCTTTT
Found at i:15535160 original size:55 final size:55
Alignment explanation
Indices: 15535086--15535195 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
15535076 GTTTAGGTCT
* ** *
15535086 AGTAGACACACGGGCGGGCACATGGGCTGACACACGATAGTGTGACCCTATTTCA
1 AGTAGACACACAGGCGGGCACACAGGCTGACACACGACAGTGTGACCCTATTTCA
* * * * * *
15535141 AGTATACACACAGGTGGGCACACAGGCTGGCACACGACCGTGTGCCCCTGTTTCA
1 AGTAGACACACAGGCGGGCACACAGGCTGACACACGACAGTGTGACCCTATTTCA
15535196 TAAATTTTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (55 bp):
AGTAGACACACAGGCGGGCACACAGGCTGACACACGACAGTGTGACCCTATTTCA
Found at i:15541230 original size:26 final size:26
Alignment explanation
Indices: 15541201--15541251 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15541191 GGGTTTTATT
*
15541201 CTTGTAGACTAAGAAACTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
* *
15541227 CTTGTAGAATAAGAACCTATAATTA
1 CTTGTAGAATAAGAAACTAAAATTA
15541252 GGGTAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:15552134 original size:84 final size:84
Alignment explanation
Indices: 15551993--15552162 Score: 295
Period size: 84 Copynumber: 2.0 Consensus size: 84
15551983 TCCTTTCCTT
* * *
15551993 TGTTAGCATTTCGCTTTCGTTCTTCAATTTCTTTCATAAATAATAAATACTCATTAACACATAAT
1 TGTTAGCATTTCGCTTTCCTTCTTCAATTTCTTTCATAAACAACAAATACTCATTAACACATAAT
*
15552058 CAATAAATAGCCATTAATA
66 CAATAAACAGCCATTAATA
15552077 TGTTAGCATTTCGCTTTCCTTCTTCAATTTCTTTCATAAACAACAAATACTCATTAACACATAAT
1 TGTTAGCATTTCGCTTTCCTTCTTCAATTTCTTTCATAAACAACAAATACTCATTAACACATAAT
*
15552142 TAATAAACAGCCATTAATA
66 CAATAAACAGCCATTAATA
15552161 TG
1 TG
15552163 GCTCAACAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (84 bp):
TGTTAGCATTTCGCTTTCCTTCTTCAATTTCTTTCATAAACAACAAATACTCATTAACACATAAT
CAATAAACAGCCATTAATA
Found at i:15552525 original size:15 final size:15
Alignment explanation
Indices: 15552505--15552534 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15552495 ACAATAATGG
*
15552505 ATTCTCTCTCCGAAA
1 ATTCTCTCTACGAAA
15552520 ATTCTCTCTACGAAA
1 ATTCTCTCTACGAAA
15552535 GTCCTCGATC
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:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (15 bp):
ATTCTCTCTACGAAA
Found at i:15567049 original size:37 final size:38
Alignment explanation
Indices: 15566952--15567049 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
15566942 ATTTCCAGAA
* * *
15566952 TGCACCCAAGAATGTCACTGCTTAAATATTCTTCAAAT
1 TGCACCCAAGAATGTCGCTACATAAATATTCTTCAAAT
* * * *
15566990 TGCATCC-AGAACTATTGCTACATAAGTATTCTTC-AAT
1 TGCACCCAAGAA-TGTCGCTACATAAATATTCTTCAAAT
*
15567027 TGCACCCAAGAATGTCGTTACAT
1 TGCACCCAAGAATGTCGCTACAT
15567050 GAACATGTAC
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 21 0.45
38 26 0.55
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (38 bp):
TGCACCCAAGAATGTCGCTACATAAATATTCTTCAAAT
Found at i:15567917 original size:16 final size:16
Alignment explanation
Indices: 15567896--15567926 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15567886 TTGTGGATTC
15567896 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
15567912 CATTTTATCTTTATT
1 CATTTTACCTTTATT
15567927 TTGACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:15571476 original size:12 final size:12
Alignment explanation
Indices: 15571459--15571500 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
15571449 CAAGTGGAAG
15571459 AAGAAGAAAGAA
1 AAGAAGAAAGAA
15571471 AAGAAG-AAGAAA
1 AAGAAGAAAG-AA
* *
15571483 AAGAGGAAGGAA
1 AAGAAGAAAGAA
15571495 AAGAAG
1 AAGAAG
15571501 TCAAGGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.80
13 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAGAA
Found at i:15571948 original size:34 final size:34
Alignment explanation
Indices: 15571905--15571974 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
15571895 CATGTAGTAA
*
15571905 TTTAATTGTCACCACATTCCCTTTGTCATTGCAT
1 TTTAATTGTCACCACATTCCCATTGTCATTGCAT
** **
15571939 TTTAATTGTCACTGCATTTGCATTGTCATTGCAT
1 TTTAATTGTCACCACATTCCCATTGTCATTGCAT
15571973 TT
1 TT
15571975 CCATTTTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.47
Consensus pattern (34 bp):
TTTAATTGTCACCACATTCCCATTGTCATTGCAT
Found at i:15571979 original size:17 final size:17
Alignment explanation
Indices: 15571927--15571979 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
15571917 CACATTCCCT
**
15571927 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTCCA
* *
15571944 TTGTCACTGCATTTGCA
1 TTGTCATTGCATTTCCA
15571961 TTGTCATTGCATTTCCA
1 TTGTCATTGCATTTCCA
15571978 TT
1 TT
15571980 TTTCATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (17 bp):
TTGTCATTGCATTTCCA
Found at i:15572483 original size:21 final size:21
Alignment explanation
Indices: 15572457--15572496 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15572447 TGTGTCGACA
15572457 CAATTACATACTCCCTGGGCG
1 CAATTACATACTCCCTGGGCG
*
15572478 CAATTACATACTCCTTGGG
1 CAATTACATACTCCCTGGG
15572497 GGTTTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (21 bp):
CAATTACATACTCCCTGGGCG
Found at i:15588088 original size:24 final size:24
Alignment explanation
Indices: 15588061--15588111 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
15588051 TTTCTTGTAA
15588061 TTTAGG-TTTAATTATTTTCATTTC
1 TTTAGGTTTTAATTATTTTCA-TTC
*
15588085 TTTAGGTTTTAGTTATTTTCATTC
1 TTTAGGTTTTAATTATTTTCATTC
15588109 TTT
1 TTT
15588112 TTTAATGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.65
Consensus pattern (24 bp):
TTTAGGTTTTAATTATTTTCATTC
Found at i:15590933 original size:21 final size:22
Alignment explanation
Indices: 15590893--15590935 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15590883 TTTTGGTCTT
* *
15590893 TTTAAATTGGAACTCTAGTCCG
1 TTTAAATTGCAACACTAGTCCG
15590915 TTTAAATTGCAA-ACTAGTCCG
1 TTTAAATTGCAACACTAGTCCG
15590936 GTAACTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (22 bp):
TTTAAATTGCAACACTAGTCCG
Found at i:15597912 original size:197 final size:193
Alignment explanation
Indices: 15597470--15597912 Score: 482
Period size: 197 Copynumber: 2.3 Consensus size: 193
15597460 AGTACTCGAT
* ** * *
15597470 ACTGCTCACACGAGCTGTCGAGGAGTCGCAATGTATGCGTACCCCAGCCATCGATACGGTGCCTG
1 ACTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGTACCTCAGCCATCGATACGGTACCTG
* * **
15597535 TCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAGTATGTGTAAAGCA
66 -CTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGACTAAAGCA
* ** *
15597600 TAGTCCGAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGGGTCACGAT
130 TAATCCGAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCACGAC
* * * * *
15597664 ACTACTCACACGAGTTGCCAAGGACTCGCAACATATGCAGTACCTCAGCCATCGATACGGTATCT
1 ACTGCTCACACGAGCTGTCGAGGACTCGCAACATATGC-GTACCTCAGCCATCGATACGGTACCT
* * *
15597729 G-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCGAGAATATGCACTTATGC
65 GCTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATG-ACTAAAGC
* * * * *
15597791 ATAAATCTC-AGCCATCGTAGGGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATTTC-CTGAC
129 AT-AATC-CGAGCCATCGTA--GGGCCTATAATCCATT-TAGGATCCATATCTC-TTTCTC-GAC
15597854 TCACGAC
187 TCACGAC
* * **
15597861 GCTGCTCACACGAGCTATCGAGGACTCATAACATATGCGGTACCTCAGCCAT
1 ACTGCTCACACGAGCTGTCGAGGACTCGCAACATATGC-GTACCTCAGCCAT
15597913 TACGTCAGTT
Statistics
Matches: 205, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
191 43 0.21
192 9 0.04
193 16 0.08
194 32 0.16
195 39 0.19
196 12 0.06
197 54 0.26
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (193 bp):
ACTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGTACCTCAGCCATCGATACGGTACCTG
CTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGACTAAAGCAT
AATCCGAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCACGAC
Found at i:15611833 original size:93 final size:93
Alignment explanation
Indices: 15611674--15611858 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 93
15611664 TTACATCCAG
*
15611674 TCCGACCTCATTATCCTCTGCTTTCACAAACTAAACCATAGGCGCAAGCATATGGTTTTTAATCA
1 TCCGACCTCATTATCCTCTGCTTTCACAAACTAAACCATAAGCGCAAGCATATGGTTTTTAATCA
* *
15611739 GAGTACCAAATTTATACCATGAGTTCAA
66 GAATACCAAATTTATACCACGAGTTCAA
*
15611767 TCCGACCTCATTATCCTCTGCTTTCACAAACTAAACCATAAGTGCAAGCATATGGTTTTTAATCA
1 TCCGACCTCATTATCCTCTGCTTTCACAAACTAAACCATAAGCGCAAGCATATGGTTTTTAATCA
*
15611832 GAATACCAAATTTCTACCACGAGTTCA
66 GAATACCAAATTTATACCACGAGTTCA
15611859 CCAAAATGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (93 bp):
TCCGACCTCATTATCCTCTGCTTTCACAAACTAAACCATAAGCGCAAGCATATGGTTTTTAATCA
GAATACCAAATTTATACCACGAGTTCAA
Found at i:15620600 original size:13 final size:13
Alignment explanation
Indices: 15620582--15620607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15620572 CAGCAGTTCT
15620582 AAATTCTATAAGG
1 AAATTCTATAAGG
15620595 AAATTCTATAAGG
1 AAATTCTATAAGG
15620608 TTAAATAAAA
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAATTCTATAAGG
Found at i:15625862 original size:16 final size:16
Alignment explanation
Indices: 15625841--15625897 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
15625831 TATTAAAATT
15625841 ATTTTTTAAAATATAA
1 ATTTTTTAAAATATAA
*
15625857 ATTTTTTTAAATTATAA
1 A-TTTTTTAAAATATAA
* *
15625874 AATTATTAAAAT-T-A
1 ATTTTTTAAAATATAA
*
15625888 TTTTTTTAAA
1 ATTTTTTAAA
15625898 TAATAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
16 9 0.27
17 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTTTAAAATATAA
Found at i:15625864 original size:17 final size:17
Alignment explanation
Indices: 15625842--15625874 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15625832 ATTAAAATTA
15625842 TTTTTTAAAATATAAAT
1 TTTTTTAAAATATAAAT
*
15625859 TTTTTTAAATTATAAA
1 TTTTTTAAAATATAAA
15625875 ATTATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTAAAATATAAAT
Done.