Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 23 of 74
Found at i:5546065 original size:60 final size:60
Alignment explanation
Indices: 5545792--5546139 Score: 361
Period size: 59 Copynumber: 5.7 Consensus size: 60
5545782 AATAAAAATC
* *
5545792 AAAAAAAATATTTTTG-GGAAAACGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC-
1 AAAAAAAAAATTTTTGAGGAAAA-GTTGAAAGTATCAATTTTCCTTAAAAATCAAATTTCT
*** * *
5545851 -AAAAAAAGGGTTTTGAGAAAAAGTTGAAAATATCAATTTTCCTTAAAAATCAAAATTT-T
1 AAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC-AAATTTCT
* * * * *
5545910 -CAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATATTT-TTTGAAAATCAAAGTTTTTT
1 AAAAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAAT-TTTCCTTAAAAATCAAA--TTTCT
* *
5545971 CAAAAAGAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTCT
1 -AAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTTCT
* * *
5546031 AAAAAAAAAAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTCAAA
1 AAAAAAAAAA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAA--TTTC--T
*
5546096 AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
5546140 CTACACAATA
Statistics
Matches: 244, Mismatches: 26, Indels: 32
0.81 0.09 0.11
Matches are distributed among these distances:
58 44 0.18
59 55 0.23
60 49 0.20
61 4 0.02
62 6 0.02
63 42 0.17
64 3 0.01
65 40 0.16
66 1 0.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (60 bp):
AAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTTCT
Found at i:5547318 original size:14 final size:16
Alignment explanation
Indices: 5547287--5547319 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
5547277 ATGTACATTT
5547287 CATTCATACATCAAAG
1 CATTCATACATCAAAG
5547303 CATT-ATACAT-AAAG
1 CATTCATACATCAAAG
5547317 CAT
1 CAT
5547320 AGCATAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (16 bp):
CATTCATACATCAAAG
Found at i:5549828 original size:10 final size:10
Alignment explanation
Indices: 5549783--5549821 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5549773 AAAAATGAGC
5549783 AAAAAGAAAA
1 AAAAAGAAAA
* *
5549793 AAGATGATAAA
1 AAAAAGA-AAA
5549804 AAAAAGAAAA
1 AAAAAGAAAA
5549814 AAAAAGAA
1 AAAAAGAA
5549822 GGAAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:5551258 original size:44 final size:43
Alignment explanation
Indices: 5551166--5551247 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
5551156 GCCTTTGAAC
*
5551166 TCAAATGAAAAGCTTTGAATTTTTGAATGTGAATTTCCAAAAT
1 TCAAATGAAAAGCTTTGAATTTTTGAATATGAATTTCCAAAAT
* *
5551209 TCAAATGAAAAGTTTTAGACTTTTTG-ATATGAA-TTCCAA
1 TCAAATGAAAAGCTTT-GAATTTTTGAATATGAATTTCCAA
5551248 GTTTGCCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 6 0.17
43 21 0.60
44 8 0.23
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (43 bp):
TCAAATGAAAAGCTTTGAATTTTTGAATATGAATTTCCAAAAT
Found at i:5551711 original size:42 final size:41
Alignment explanation
Indices: 5551512--5551822 Score: 523
Period size: 41 Copynumber: 7.5 Consensus size: 41
5551502 ATGATTGTCA
*
5551512 AGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
5551553 AGGAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5551594 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
5551635 AAGAGTAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5551676 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5551718 AGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5551760 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5551801 AGGAGCAATTTACTTTTCAAAG
1 AGGAGCAATTTACTTTTCAAAG
5551823 AGCAATTTAC
Statistics
Matches: 253, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
41 174 0.69
42 79 0.31
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5551827 original size:19 final size:19
Alignment explanation
Indices: 5551803--5551841 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5551793 CTGTTTAGAG
5551803 GAGCAATTTACTTTTCAAA
1 GAGCAATTTACTTTTCAAA
5551822 GAGCAATTTACTTTTCAAA
1 GAGCAATTTACTTTTCAAA
5551841 G
1 G
5551842 TCGTGGTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
GAGCAATTTACTTTTCAAA
Found at i:5551856 original size:60 final size:59
Alignment explanation
Indices: 5551762--5551881 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 59
5551752 CTGTTTAGAG
*
5551762 GAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAA
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAA
*
5551822 GAGCAATTTACTTTTCAAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTACTTTCAAA
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAA
5551881 G
1 G
5551882 TTGTGGTGTC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 8 0.14
60 50 0.86
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (59 bp):
GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAA
Found at i:5551919 original size:100 final size:102
Alignment explanation
Indices: 5551720--5551922 Score: 338
Period size: 100 Copynumber: 2.0 Consensus size: 102
5551710 CTGTTTAGAG
* *
5551720 GAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
1 GAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATCTTTCAAAGTCG
*
5551785 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAA
66 TGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAA
* *
5551822 GAGCAATTTA-CTTTTCAAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTA-CTTTCAAAGTTG
1 GAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATCTTTCAAAGTCG
*
5551885 TGGTGTCTCTATTTAGAGGAGCAATTTACTTTTCAAA
66 TGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAA
5551922 G
1 G
5551923 TCGTGGTGCA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 46 0.48
101 39 0.41
102 10 0.11
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (102 bp):
GAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATCTTTCAAAGTCG
TGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAA
Found at i:5551951 original size:41 final size:41
Alignment explanation
Indices: 5551822--5552031 Score: 278
Period size: 41 Copynumber: 5.1 Consensus size: 41
5551812 ACTTTTCAAA
*
5551822 GAGCAATTTACTTTTCAAAGTCGTGGTGCTTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
* * *
5551863 GAGCAATTTAC-TTTCAAAGTTGTGGTGTCTCTATTTAGAG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
5551903 GAGCAATTTACTTTTCAAAGTCGTGGTGCATCTGTTTAAAG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
* * * *
5551944 GAACAATTTATTTTTCAAAGTTGTGATGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
* * *
5551985 GAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAGAG
5552028 GAGC
1 GAGC
5552032 TTTGATAAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
40 36 0.25
41 79 0.54
42 3 0.02
43 27 0.19
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (41 bp):
GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
Found at i:5551951 original size:141 final size:143
Alignment explanation
Indices: 5551678--5551963 Score: 459
Period size: 141 Copynumber: 2.0 Consensus size: 143
5551668 CTGTTTAGAG
*
5551678 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTC
1 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TCTTTCAAAGTC
* * * * *
5551743 GTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
65 GTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAACA
5551808 ATTTACTTTTCAAA
130 ATTTACTTTTCAAA
* *
5551822 GAGCAATTTAC-TTTTCAAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTA-CTTTCAAAGTTG
1 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATCTTTCAAAGTCG
*
5551885 TGGTGTCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAACAA
66 TGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAACAA
*
5551950 TTTATTTTTCAAA
131 TTTACTTTTCAAA
5551963 G
1 G
5551964 TTGTGATGCC
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
141 82 0.62
143 39 0.30
144 11 0.08
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (143 bp):
GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATCTTTCAAAGTCG
TGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAACAA
TTTACTTTTCAAA
Found at i:5551976 original size:182 final size:184
Alignment explanation
Indices: 5551635--5551994 Score: 589
Period size: 182 Copynumber: 2.0 Consensus size: 184
5551625 CTCTGTTTAG
*
5551635 AAGAGTAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGT
1 AAGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAGT
* * * * *
5551700 CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
65 CGTGGTGCCTCTATTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAA
*
5551765 CAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
130 CAATTTATTTTTCAAAGTCGTGATGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
* * *
5551820 AAGAGCAATTTACTTTTCAAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTT
1 AAGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
*
5551884 GTGGTGTCTCTATTTAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAAC
66 GTGGTGCCTCTATTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAAC
*
5551948 AATTTATTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTA
131 AATTTATTTTTCAAAGTCGTGATGCCTCTGTTTAGAGGAGCAATTTA
5551995 TGTTTCTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
182 76 0.47
183 36 0.22
185 51 0.31
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (184 bp):
AAGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
GTGGTGCCTCTATTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGGTGCATCTGTTTAAAGGAAC
AATTTATTTTTCAAAGTCGTGATGCCTCTGTTTAGAGGAGCAATTTACTTTTCA
Found at i:5552261 original size:17 final size:15
Alignment explanation
Indices: 5552224--5552303 Score: 94
Period size: 16 Copynumber: 5.2 Consensus size: 15
5552214 GCCCAATTCA
5552224 ATTTTTATTTTGTATT
1 ATTTTTATTTT-TATT
5552240 ATTTTTATTTTGTATT
1 ATTTTTATTTT-TATT
5552256 ATTTTTATTTTT-TT
1 ATTTTTATTTTTATT
5552270 ATTTTTTATATTTTATT
1 A-TTTTTAT-TTTTATT
5552287 A--TTTATTTATTATT
1 ATTTTTATTT-TTATT
5552301 ATT
1 ATT
5552304 ATGTATTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.03
14 14 0.24
15 8 0.14
16 31 0.53
17 3 0.05
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
ATTTTTATTTTTATT
Found at i:5552267 original size:7 final size:7
Alignment explanation
Indices: 5552225--5552300 Score: 62
Period size: 7 Copynumber: 10.1 Consensus size: 7
5552215 CCCAATTCAA
5552225 TTTTTAT
1 TTTTTAT
*
5552232 TTTGTATT
1 TTTTTA-T
5552240 ATTTTTAT
1 -TTTTTAT
*
5552248 TTTGTATT
1 TTTTTA-T
5552256 ATTTTTATT
1 -TTTTTA-T
5552265 TTTTTAT
1 TTTTTAT
5552272 TTTTTAT
1 TTTTTAT
*
5552279 ATTTTAT
1 TTTTTAT
*
5552286 TATTTAT
1 TTTTTAT
*
5552293 TTATTAT
1 TTTTTAT
5552300 T
1 T
5552301 ATTATGTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
7 35 0.62
8 9 0.16
9 12 0.21
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (7 bp):
TTTTTAT
Found at i:5552310 original size:17 final size:16
Alignment explanation
Indices: 5552259--5552310 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5552249 TTGTATTATT
* * *
5552259 TTTATTTTTTTATTTT
1 TTTATTTTATTATGTA
*
5552275 TTATATTTTATTATTTA
1 TT-TATTTTATTATGTA
5552292 TTTATTATTATTATGTA
1 TTTATT-TTATTATGTA
5552309 TT
1 TT
5552311 AATATATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTATTTTATTATGTA
Found at i:5552379 original size:23 final size:23
Alignment explanation
Indices: 5552353--5552396 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5552343 CTGTTAATAT
5552353 TTATATGTATT-TTATTTATATAG
1 TTATATGTATTATTA-TTATATAG
*
5552376 TTATATTTATTATTATTATAT
1 TTATATGTATTATTATTATAT
5552397 TTTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (23 bp):
TTATATGTATTATTATTATATAG
Found at i:5552496 original size:17 final size:17
Alignment explanation
Indices: 5552460--5552519 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
5552450 TCTGTTAATT
*
5552460 TGATTTTTATTCATTTATC
1 TGATTTTT-TTTA-TTATC
5552479 TGATTTTTTTTATTATC
1 TGATTTTTTTTATTATC
* * *
5552496 TTATTATTATTATTAT-
1 TGATTTTTTTTATTATC
5552512 T-ATTTTTT
1 TGATTTTTT
5552520 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 18 0.51
18 3 0.09
19 8 0.23
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (17 bp):
TGATTTTTTTTATTATC
Found at i:5552499 original size:22 final size:19
Alignment explanation
Indices: 5552231--5552530 Score: 88
Period size: 22 Copynumber: 15.4 Consensus size: 19
5552221 TCAATTTTTA
*
5552231 TTTTGTATTATTT-TTA--
1 TTTTTTATTATTTATTATT
*
5552247 TTTTGTATTATTT-TTA-T
1 TTTTTTATTATTTATTATT
*
5552264 TTTTTTATTTTTTA-TA-T
1 TTTTTTATTATTTATTATT
*
5552281 TTTATTATTTATTTATTATT
1 TTTTTTA-TTATTTATTATT
* * *
5552301 ATTATGTATTAATATATGTA-T
1 -TTTTTTATT-ATTTAT-TATT
* *
5552322 ATCTTTATTTATTTATT-TT
1 TTTTTTA-TTATTTATTATT
* * *
5552341 TTCTGTTAATATTTA-TATG
1 TT-TTTTATTATTTATTATT
* *
5552360 TATTTTATT-TATA-TAGTT
1 TTTTTTATTATTTATTA-TT
* *
5552378 ATATTTATTA-TTATTATAT
1 TTTTTTATTATTTATTAT-T
*
5552397 TTTTTT-TTACCTTGTAATATT
1 TTTTTTATTA--TT-TATTATT
** *
5552418 TTTTGGATTTATCTTATTTTAT
1 TTTTTTA-TTAT-TTATTAT-T
* *
5552440 TTTTTTATTATCTGTTAATT
1 TTTTTTATTATTTATT-ATT
5552460 TGATTTTTATTCATTTATCTGATT
1 T--TTTTTATT-ATTTAT-T-ATT
5552484 TTTTTTATTATCTTATTATT
1 TTTTTTATTAT-TTATTATT
* * *
5552504 ATTATTATTATTTTTTATT
1 TTTTTTATTATTTATTATT
5552523 TTTTTTAT
1 TTTTTTAT
5552531 GGCTGTGATT
Statistics
Matches: 208, Mismatches: 46, Indels: 57
0.67 0.15 0.18
Matches are distributed among these distances:
16 16 0.08
17 25 0.12
18 25 0.12
19 33 0.16
20 32 0.15
21 31 0.15
22 34 0.16
23 7 0.03
24 5 0.02
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTTATTATTTATTATT
Found at i:5552527 original size:10 final size:10
Alignment explanation
Indices: 5552484--5552530 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
5552474 TTATCTGATT
5552484 TTTTTTATTA
1 TTTTTTATTA
*
5552494 TCTTATTATTA
1 T-TTTTTATTA
*
5552505 -TTATTATTA
1 TTTTTTATTA
5552514 TTTTTTATT-
1 TTTTTTATTA
5552523 TTTTTTAT
1 TTTTTTAT
5552531 GGCTGTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 17 0.52
10 8 0.24
11 8 0.24
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:5553329 original size:10 final size:11
Alignment explanation
Indices: 5553313--5553345 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
5553303 TTTCTTCTTT
5553313 AAGCCGAGCCG
1 AAGCCGAGCCG
5553324 -AGCCGAGCCG
1 AAGCCGAGCCG
5553334 ATAGCCGAGCCG
1 A-AGCCGAGCCG
5553346 TTCCAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.24, C:0.36, G:0.36, T:0.03
Consensus pattern (11 bp):
AAGCCGAGCCG
Found at i:5553444 original size:16 final size:16
Alignment explanation
Indices: 5553425--5553510 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 16
5553415 ATTTAAAATT
5553425 TTTTATCTTTATTTTA
1 TTTTATCTTTATTTTA
* *
5553441 TTTTTATTTTTGTTTTA
1 -TTTTATCTTTATTTTA
* *
5553458 CTTT-TCTTTATTTTT
1 TTTTATCTTTATTTTA
5553473 TTTTATCTTTA-TTTA
1 TTTTATCTTTATTTTA
*
5553488 TTTTCA-CTTTTATTTTG
1 TTTT-ATC-TTTATTTTA
5553505 TTTTAT
1 TTTTAT
5553511 TTTCTTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 19 0.35
16 15 0.27
17 21 0.38
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTA
Found at i:5553472 original size:10 final size:10
Alignment explanation
Indices: 5553425--5553518 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 10
5553415 ATTTAAAATT
5553425 TTTTATCTTTA
1 TTTT-TCTTTA
*
5553436 TTTTATTTTTA
1 TTTT-TCTTTA
*
5553447 TTTTTGTTTTA
1 TTTTT-CTTTA
*
5553458 CTTTTCTTTA
1 TTTTTCTTTA
*
5553468 TTTTTTTTTA
1 TTTTTCTTTA
* *
5553478 TCTTTATTTA
1 TTTTTCTTTA
*
5553488 TTTTCACTTTTA
1 TTTT-TC-TTTA
5553500 TTTTGT-TTTA
1 TTTT-TCTTTA
5553510 -TTTTCTTTA
1 TTTTTCTTTA
5553519 AATAAAAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
8 1 0.01
9 7 0.10
10 28 0.42
11 23 0.34
12 8 0.12
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:5553476 original size:20 final size:21
Alignment explanation
Indices: 5553443--5553491 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5553433 TTATTTTATT
*
5553443 TTTATTTTTGTTTTA-CTTTTC
1 TTTATTTTTGTTTTATC-TTTA
5553464 TTTATTTTT-TTTTATCTTTA
1 TTTATTTTTGTTTTATCTTTA
5553484 TTTATTTT
1 TTTATTTT
5553492 CACTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTATTTTTGTTTTATCTTTA
Found at i:5553651 original size:59 final size:60
Alignment explanation
Indices: 5553527--5553953 Score: 523
Period size: 59 Copynumber: 7.2 Consensus size: 60
5553517 TAAATAAAAA
** *
5553527 TCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAA-TT
1 TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
* *
5553585 TCAAAAAAAGGGTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT
1 TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
5553645 TCAAAAAATA--TTTTT-AGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT--AAATTT
1 TCAAAAAA-AGGTTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
* * *
5553702 TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAAGTT
1 TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
* *** * * *
5553761 TCTAAAAAACACTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTT
1 TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAA--ATTT
** *
5553823 TCAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT--AAATTT
1 TC-AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
* * *
5553882 CCAAAAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTT
1 TC---AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
5553945 TCAAAAAAA
1 TCAAAAAAA
5553954 AAAAAAACAT
Statistics
Matches: 323, Mismatches: 30, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
56 1 0.00
57 14 0.04
58 85 0.26
59 100 0.31
60 19 0.06
61 50 0.15
62 4 0.01
63 50 0.15
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (60 bp):
TCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAATTT
Found at i:5553669 original size:117 final size:119
Alignment explanation
Indices: 5553527--5553953 Score: 580
Period size: 117 Copynumber: 3.6 Consensus size: 119
5553517 TAAATAAAAA
* *
5553527 TCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-ATTTCAAA
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGTTTTCAAA
*
5553590 AAAAGGGTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT
66 AAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC-AAATTT
5553645 TC-AAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-TTTTCAA
1 TCAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGTTTTCAA
* *
5553706 AAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTT
65 AAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
* * * * *
5553761 TCTAAAAAACACTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTTTCA
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAG--TTTTC-
** * *
5553826 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTT
63 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
* * *
5553882 CCAAAAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTC
1 TC-AAAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGTTTTC
5553947 AAAAAAA
63 AAAAAAA
5553954 AAAAAAACAT
Statistics
Matches: 278, Mismatches: 20, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
116 8 0.03
117 145 0.52
118 6 0.02
121 18 0.06
122 57 0.21
124 44 0.16
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (119 bp):
TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGTTTTCAAA
AAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAATTT
Found at i:5554691 original size:3 final size:3
Alignment explanation
Indices: 5554685--5554710 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5554675 TATTAGTAGT
5554685 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5554711 TTGGGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5559295 original size:11 final size:11
Alignment explanation
Indices: 5559279--5559321 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5559269 AATCTAAAAT
5559279 ACGATATGAAA
1 ACGATATGAAA
5559290 ACGATATGAAAA
1 ACGATATG-AAA
**
5559302 AATATATGAAA
1 ACGATATGAAA
*
5559313 ATGATATGA
1 ACGATATGA
5559322 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (11 bp):
ACGATATGAAA
Found at i:5560156 original size:11 final size:11
Alignment explanation
Indices: 5560140--5560170 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5560130 TTGAACTATG
5560140 TATTTTATTTT
1 TATTTTATTTT
5560151 TATTTTATTTT
1 TATTTTATTTT
*
5560162 TATTCTATT
1 TATTTTATT
5560171 ATATGTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:5560287 original size:10 final size:10
Alignment explanation
Indices: 5560272--5560308 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5560262 TTATTTTATA
5560272 TTTTTAGTAT
1 TTTTTAGTAT
5560282 TTTTTAGTAT
1 TTTTTAGTAT
5560292 ATTTTTAGTAT
1 -TTTTTAGTAT
*
5560303 ATTTTA
1 TTTTTA
5560309 CATTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTAGTAT
Found at i:5560292 original size:21 final size:21
Alignment explanation
Indices: 5560268--5560308 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5560258 TTTTTTATTT
*
5560268 TATATTTTTAGTATTTTTTAG
1 TATATTTTTAGTATATTTTAG
5560289 TATATTTTTAGTATATTTTA
1 TATATTTTTAGTATATTTTA
5560309 CATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (21 bp):
TATATTTTTAGTATATTTTAG
Found at i:5560296 original size:11 final size:11
Alignment explanation
Indices: 5560268--5560307 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
5560258 TTTTTTATTT
5560268 TATATTTTTAG
1 TATATTTTTAG
5560279 TAT-TTTTTAG
1 TATATTTTTAG
5560289 TATATTTTTAG
1 TATATTTTTAG
5560300 TATATTTT
1 TATATTTT
5560308 ACATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (11 bp):
TATATTTTTAG
Found at i:5560393 original size:21 final size:18
Alignment explanation
Indices: 5560353--5560420 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
5560343 AGATATAGAT
5560353 ATAGATTTAATTTAATAG
1 ATAGATTTAATTTAATAG
5560371 ATAGATTTAATTTTAACATAG
1 ATAGATTTAA-TTT-A-ATAG
5560392 ATAGA--TACATTTAAT--
1 ATAGATTTA-ATTTAATAG
5560407 ATAGATTTAATTTA
1 ATAGATTTAATTTA
5560421 TTTATATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.11
16 5 0.11
17 4 0.09
18 11 0.25
19 8 0.18
20 2 0.05
21 9 0.20
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (18 bp):
ATAGATTTAATTTAATAG
Found at i:5560819 original size:13 final size:13
Alignment explanation
Indices: 5560801--5560827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5560791 CAAAAGAAGG
5560801 GAATTATGCAGTA
1 GAATTATGCAGTA
5560814 GAATTATGCAGTA
1 GAATTATGCAGTA
5560827 G
1 G
5560828 CACAGCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (13 bp):
GAATTATGCAGTA
Found at i:5561401 original size:2 final size:2
Alignment explanation
Indices: 5561394--5561436 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5561384 TCAGCGTGTC
5561394 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5561436 G
1 G
5561437 TACCTTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5569544 original size:5 final size:5
Alignment explanation
Indices: 5569536--5569607 Score: 65
Period size: 5 Copynumber: 14.0 Consensus size: 5
5569526 GATATATATT
* * * *
5569536 TTTAA TTTAT TTATAA TTAAA TTTAA TTTAA TTTAA TGTT-A TATAA ATTATA
1 TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA TTTAA T-TTAA TTTAA TTTA-A
*
5569588 TTTAA TTTAA TTTAA CTTAA
1 TTTAA TTTAA TTTAA TTTAA
5569608 AATTAATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
4 1 0.02
5 43 0.80
6 10 0.19
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:5569571 original size:31 final size:31
Alignment explanation
Indices: 5569536--5569602 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5569526 GATATATATT
*
5569536 TTTAAT-TTATTTATAATTAAATTTAATTTAA
1 TTTAATGTTATATA-AATTAAATTTAATTTAA
*
5569567 TTTAATGTTATATAAATTATATTTAATTTAA
1 TTTAATGTTATATAAATTAAATTTAATTTAA
5569598 TTTAA
1 TTTAA
5569603 CTTAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTAATGTTATATAAATTAAATTTAATTTAA
Found at i:5569608 original size:26 final size:25
Alignment explanation
Indices: 5569536--5569614 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 25
5569526 GATATATATT
*
5569536 TTTAATTTATTTATAATTAAATTTAA
1 TTTAATTTAATT-TAATTAAATTTAA
5569562 TTTAATTTAATGTT-ATATAAA-TTATA
1 TTTAATTTAAT-TTAAT-TAAATTTA-A
*
5569588 TTTAATTTAATTTAACTTAAAATTAA
1 TTTAATTTAATTTAA-TTAAATTTAA
5569614 T
1 T
5569615 AAAATATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
25 7 0.15
26 34 0.74
27 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTAATTTAATTTAATTAAATTTAA
Found at i:5569626 original size:36 final size:36
Alignment explanation
Indices: 5569555--5569626 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
5569545 TTTATAATTA
* ** *
5569555 AATTTAATTTAATTTAATGTTATATAAATTATATTT
1 AATTTAATTTAACTTAAAATTATATAAAATATATTT
5569591 AATTTAATTTAACTTAAAATTA-ATAAAATATTATTT
1 AATTTAATTTAACTTAAAATTATATAAAATA-TATTT
5569627 TTTAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
AATTTAATTTAACTTAAAATTATATAAAATATATTT
Found at i:5569659 original size:25 final size:22
Alignment explanation
Indices: 5569604--5569666 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 22
5569594 TTAATTTAAC
5569604 TTAAAATTAATAAAATATTATTTT
1 TTAAAA-T-ATAAAATATTATTTT
5569628 TTAAAATATAAAATATTATTTT
1 TTAAAATATAAAATATTATTTT
5569650 TAATATAAATATAAAAT
1 T--TA-AAATATAAAAT
5569667 TAAATAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.44
23 1 0.03
24 8 0.22
25 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATATAAAATATTATTTT
Found at i:5570221 original size:19 final size:19
Alignment explanation
Indices: 5570199--5570235 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5570189 AAGATAAGAC
*
5570199 AATATAAAAATGATATAAA
1 AATATAAAAATAATATAAA
5570218 AATATAAAAATAATATAA
1 AATATAAAAATAATATAA
5570236 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AATATAAAAATAATATAAA
Found at i:5570264 original size:19 final size:17
Alignment explanation
Indices: 5570205--5570274 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
5570195 AGACAATATA
*
5570205 AAAATGATATAAAAATAT
1 AAAATTATATAAAAAT-T
* * *
5570223 AAAAATA-ATATAATTT
1 AAAATTATATAAAAATT
5570239 AAAATTATGATAAAAATT
1 AAAATTAT-ATAAAAATT
*
5570257 AAATATTATATATAAATT
1 AAA-ATTATATAAAAATT
5570275 TGATAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
16 7 0.17
17 6 0.15
18 23 0.56
19 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATTATATAAAAATT
Found at i:5570756 original size:2 final size:2
Alignment explanation
Indices: 5570749--5570781 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5570739 CTTCTTAACA
5570749 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
5570782 AAGAAAGAAG
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:5571554 original size:33 final size:32
Alignment explanation
Indices: 5571512--5571573 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
5571502 TCGAATAAAA
* * *
5571512 ATAATATAAATATATAAATTATTAATATTTTAT
1 ATAAAATAAATAGATAAACTATT-ATATTTTAT
5571545 ATAAAATAAATAGATAAACTATTATATTT
1 ATAAAATAAATAGATAAACTATTATATTT
5571574 AAATGAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 6 0.23
33 20 0.77
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
ATAAAATAAATAGATAAACTATTATATTTTAT
Found at i:5571982 original size:23 final size:23
Alignment explanation
Indices: 5571956--5571999 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5571946 AATTTATAGA
5571956 TATTAAA-ATTAAAATTTTAAATT
1 TATTAAATATT-AAATTTTAAATT
*
5571979 TATTAAATATTATATTTTAAA
1 TATTAAATATTAAATTTTAAA
5572000 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAAATATTAAATTTTAAATT
Found at i:5572416 original size:11 final size:11
Alignment explanation
Indices: 5572400--5572443 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
5572390 AATCTCATAA
5572400 GAGATTTATTT
1 GAGATTTATTT
5572411 GAGATTTATTT
1 GAGATTTATTT
* *
5572422 AAGATTTGTTT
1 GAGATTTATTT
*
5572433 GAAATTTATTT
1 GAGATTTATTT
5572444 AAAATTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (11 bp):
GAGATTTATTT
Found at i:5572427 original size:22 final size:22
Alignment explanation
Indices: 5572401--5572452 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
5572391 ATCTCATAAG
*
5572401 AGATTTATTTGAGATTTATTTA
1 AGATTTATTTGAAATTTATTTA
*
5572423 AGATTTGTTTGAAATTTATTTA
1 AGATTTATTTGAAATTTATTTA
*
5572445 AAATTTAT
1 AGATTTAT
5572453 CAGATATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (22 bp):
AGATTTATTTGAAATTTATTTA
Found at i:5572448 original size:11 final size:11
Alignment explanation
Indices: 5572403--5572452 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
5572393 CTCATAAGAG
* *
5572403 ATTTATTTGAG
1 ATTTATTTAAA
*
5572414 ATTTATTTAAG
1 ATTTATTTAAA
* *
5572425 ATTTGTTTGAA
1 ATTTATTTAAA
5572436 ATTTATTTAAA
1 ATTTATTTAAA
5572447 ATTTAT
1 ATTTAT
5572453 CAGATATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (11 bp):
ATTTATTTAAA
Found at i:5572596 original size:51 final size:51
Alignment explanation
Indices: 5572477--5572632 Score: 134
Period size: 51 Copynumber: 3.0 Consensus size: 51
5572467 TCGACAAGAA
* * * * *
5572477 GACTTACAAAAAAAAAATTTTAAGA-GAAAAAATATTTTTAATAGGTAAATTT
1 GACTTACAAGAAAAGAATTCTAAAAGGAAAAAA-A-TTTTAATAGGTAAGTTT
* *
5572529 AACTTGCAAGAAAAGAATTCTAAAAGGAAAAAAATTTTAATAGGTAAGTTT
1 GACTTACAAGAAAAGAATTCTAAAAGGAAAAAAATTTTAATAGGTAAGTTT
* * * * * * * * *
5572580 GATTTATAAGAGAAGAATTTTAAGAGGAAAGAGATTCTTGATAGGCAAGTTT
1 GACTTACAAGAAAAGAATTCTAAAAGGAAAAAAATT-TTAATAGGTAAGTTT
5572632 G
1 G
5572633 TATGGTTATA
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
51 43 0.51
52 34 0.40
53 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (51 bp):
GACTTACAAGAAAAGAATTCTAAAAGGAAAAAAATTTTAATAGGTAAGTTT
Found at i:5572781 original size:24 final size:24
Alignment explanation
Indices: 5572749--5572799 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5572739 TTACGTCTTA
5572749 TGGGTGTGTATATTTGTTTGTGAG
1 TGGGTGTGTATATTTGTTTGTGAG
5572773 TGGGTGTGTATATTTGTTTGTGAG
1 TGGGTGTGTATATTTGTTTGTGAG
5572797 TGG
1 TGG
5572800 ATTAAAGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (24 bp):
TGGGTGTGTATATTTGTTTGTGAG
Found at i:5572888 original size:51 final size:51
Alignment explanation
Indices: 5572828--5572927 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
5572818 TTCACATAGA
* *
5572828 TATGATGTATGGGAGAGTATTGGGACTCTACGTCTTATGGGTGTGTATGGG
1 TATGATGTATGAGAGAGTATTGGGACTCTACGTCTTATGAGTGTGTATGGG
* * *
5572879 TATGATGTATGAGAGAGTGTTGGGATTCTACGTCTTATTAGTGTGTATG
1 TATGATGTATGAGAGAGTATTGGGACTCTACGTCTTATGAGTGTGTATG
5572928 TTTGTTTGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.38
Consensus pattern (51 bp):
TATGATGTATGAGAGAGTATTGGGACTCTACGTCTTATGAGTGTGTATGGG
Found at i:5573228 original size:12 final size:12
Alignment explanation
Indices: 5573211--5573242 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5573201 TTCTTGTGTG
5573211 TTTGATTTATTA
1 TTTGATTTATTA
*
5573223 TTTGATTTATTG
1 TTTGATTTATTA
5573235 TTTGATTT
1 TTTGATTT
5573243 TACTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (12 bp):
TTTGATTTATTA
Found at i:5573387 original size:22 final size:23
Alignment explanation
Indices: 5573350--5573393 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5573340 ATAAATTATT
5573350 AATAATAAAATTTAAAGTTTACA
1 AATAATAAAATTTAAAGTTTACA
* *
5573373 AATAA-AATATTTAAATTTTAC
1 AATAATAAAATTTAAAGTTTAC
5573394 TAACTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
AATAATAAAATTTAAAGTTTACA
Found at i:5574268 original size:6 final size:6
Alignment explanation
Indices: 5574257--5574297 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
5574247 AATTAATTAA
**
5574257 ATATTT ATATTT ATATTT AT-TAA AT-TTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT A
5574298 AAAAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 6 0.20
6 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:5574288 original size:22 final size:23
Alignment explanation
Indices: 5574252--5574317 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
5574242 TAATTAATTA
5574252 ATTAAATATTTATATTTATATTT
1 ATTAAATATTTATATTTATATTT
5574275 ATTAAAT-TTTATATTTATATTT
1 ATTAAATATTTATATTTATATTT
* *
5574297 A--AAAAATATAT-TTTATATTT
1 ATTAAATATTTATATTTATATTT
5574317 A
1 A
5574318 AATAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.32
21 4 0.10
22 16 0.40
23 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTAAATATTTATATTTATATTT
Found at i:5574330 original size:21 final size:20
Alignment explanation
Indices: 5574284--5574333 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5574274 TATTAAATTT
5574284 TATA-TTTATATTTAAAAAA
1 TATATTTTATATTTAAAAAA
*
5574303 TATATTTTATATTTAAATAA
1 TATATTTTATATTTAAAAAA
5574323 TAATATTTTAT
1 T-ATATTTTAT
5574334 TAATTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 4 0.14
20 15 0.54
21 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTTATATTTAAAAAA
Found at i:5584296 original size:12 final size:12
Alignment explanation
Indices: 5584281--5584312 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5584271 TAGTTTTTAT
5584281 TAAAAAAATAAA
1 TAAAAAAATAAA
*
5584293 TAAACAAATAAA
1 TAAAAAAATAAA
5584305 TAAAAAAA
1 TAAAAAAA
5584313 ATACCCACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:5584937 original size:65 final size:64
Alignment explanation
Indices: 5584863--5584996 Score: 180
Period size: 65 Copynumber: 2.1 Consensus size: 64
5584853 CAAGGCCAAG
* * * *
5584863 AATGAGTGATCAAAATTGAACCATAAGTCAAAACAATAAATGATCTAGATTGAGCC-GAGATTGA
1 AATGAGTGATCAAAATTGAACCACAAATCAAAAAAATAAATGA-CTAGATTGAGCCAAAG-TTGA
5584927 A
64 A
* * *
5584928 AATGAGTGATCGAGATTGAACCACAAATCAAAAAAATAAATGACTGGATTGAGCCAAAGTTGAA
1 AATGAGTGATCAAAATTGAACCACAAATCAAAAAAATAAATGACTAGATTGAGCCAAAGTTGAA
5584992 AATGA
1 AATGA
5584997 CTAGACTAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 21 0.34
65 40 0.66
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (64 bp):
AATGAGTGATCAAAATTGAACCACAAATCAAAAAAATAAATGACTAGATTGAGCCAAAGTTGAA
Found at i:5595342 original size:29 final size:29
Alignment explanation
Indices: 5595300--5595358 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5595290 TTAGGCAAGG
*
5595300 TAGAGATACAACCATATGGTATATAATCT
1 TAGAGATACAACCATATGATATATAATCT
5595329 TAGAGATACAACCATATGATATATAATCT
1 TAGAGATACAACCATATGATATATAATCT
5595358 T
1 T
5595359 TCTCTTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (29 bp):
TAGAGATACAACCATATGATATATAATCT
Found at i:5597079 original size:18 final size:18
Alignment explanation
Indices: 5597056--5597093 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5597046 ACTTCTATGC
*
5597056 CAAAACGGCATCGTTTAG
1 CAAAACAGCATCGTTTAG
5597074 CAAAACAGCATCGTTTAG
1 CAAAACAGCATCGTTTAG
5597092 CA
1 CA
5597094 CTACTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (18 bp):
CAAAACAGCATCGTTTAG
Found at i:5599119 original size:58 final size:57
Alignment explanation
Indices: 5598960--5599301 Score: 250
Period size: 58 Copynumber: 5.8 Consensus size: 57
5598950 AAAGATACGT
* * * * **
5598960 TTTTTGAAATTTTCATTTTTAAGAAAAAATTAATACTTTCAACTTTTTCTCAAAAACAC
1 TTTTTAAAATTTTTATTTTCAA-AGAAAATTAATACTTTCAACTTTTTCTC-AAAATTC
*
5599019 ATTTTTTGAGAATTTTTATTTTC-AAGAAAAATTAATACTTTCAACTTTTTCTCAAAATTGC
1 --TTTTT-AAAATTTTTATTTTCAAAG-AAAATTAATACTTTCAACTTTTTCTCAAAATT-C
* * * *
5599080 TTTTTAAAATTTTTATTTTCAAAGAAAATTGACACTTTCAACATTTCCTCAAAAATTC
1 TTTTTAAAATTTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTC-AAAATTC
* * * * *
5599138 TTTTTGAAGTTTTTATTTTCAAAGAAAATTGATATTTTTAA-TTTTTCCTTCAAAAATATC
1 TTTTTAAAATTTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTT-C-TC-AAAAT-TC
* * * *
5599198 TTTTGAAAA-TTTTATCTTTC--AGAAAACTTAATA-TATTTAACTTTTCCTCAAAAAACATC
1 TTTTTAAAATTTTTAT-TTTCAAAGAAAA-TTAATACT-TTCAACTTTTTCTC--AAAA-TTC
* * *
5599257 TTTTGAAAA-TTTTATTTT-TAAGAAAAATTGATACTTTCAACTTTT
1 TTTTTAAAATTTTTATTTTCAAAG-AAAATTAATACTTTCAACTTTT
5599302 CTTTAAAACA
Statistics
Matches: 236, Mismatches: 27, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
57 3 0.01
58 86 0.36
59 77 0.33
60 26 0.11
61 33 0.14
62 11 0.05
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (57 bp):
TTTTTAAAATTTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAATTC
Found at i:5599281 original size:59 final size:56
Alignment explanation
Indices: 5598916--5599302 Score: 276
Period size: 59 Copynumber: 6.6 Consensus size: 56
5598906 TCAAAAATAT
* * * * * * *
5598916 TTTTTAAAAAAATTGATACTTTTAACTTTTCTTTAAAGATACGTTTTTTG-AAATTTTCA
1 TTTTTAAGAAAATTAATACTTTCAACTTTTCCTCAAA-A-A-ATCTTTTGAAAATTTT-A
* * *
5598975 TTTTTAAGAAAAAATTAATACTTTCAACTTTTTCTCAAAAACACATTTTTTGAGAATTTTTA
1 TTTTTAAG--AAAATTAATACTTTCAACTTTTCCTC-AAAA-A-ATCTTTTGA-AAATTTTA
* * * *
5599037 TTTTCAAGAAAAATTAATACTTTCAACTTTTTCTC-AAAATTGCTTTTTAAAATTTTTA
1 TTTTTAAG-AAAATTAATACTTTCAACTTTTCCTCAAAAAAT-CTTTTGAAAA-TTTTA
* * * * * **
5599095 TTTTCAAAGAAAATTGACACTTTCAACATTTCCTCAAAAATTCTTTTTGAAGTTTTTA
1 TTTT-TAAGAAAATTAATACTTTCAACTTTTCCTCAAAAAATC-TTTTGAAAATTTTA
* * * * *
5599153 TTTTCAAAGAAAATTGATATTTTTAATTTTTCCTTCAAAAATATCTTTTGAAAATTTTA
1 TTTT-TAAGAAAATTAATACTTTCAACTTTTCC-TCAAAAA-ATCTTTTGAAAATTTTA
* * *
5599212 TCTTTCAGAAAACTTAATA-TATTTAACTTTTCCTCAAAAAACATCTTTTGAAAATTTTA
1 TTTTTAAGAAAA-TTAATACT-TTCAACTTTTCCTC-AAAAA-ATCTTTTGAAAATTTTA
*
5599271 TTTTTAAGAAAAATTGATACTTTCAACTTTTC
1 TTTTTAAG-AAAATTAATACTTTCAACTTTTC
5599303 TTTAAAACAT
Statistics
Matches: 271, Mismatches: 40, Indels: 34
0.79 0.12 0.10
Matches are distributed among these distances:
57 3 0.01
58 80 0.30
59 106 0.39
60 7 0.03
61 58 0.21
62 11 0.04
63 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (56 bp):
TTTTTAAGAAAATTAATACTTTCAACTTTTCCTCAAAAAATCTTTTGAAAATTTTA
Found at i:5601195 original size:85 final size:85
Alignment explanation
Indices: 5601048--5601616 Score: 633
Period size: 85 Copynumber: 6.7 Consensus size: 85
5601038 GAATGACCCG
* * * * * * * * *
5601048 AAGATGGATCTAGCATAGGTCGAAATCC-AAA-ATAATGACATGGATGAAATCGAAGTCTGAGAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
* * *
5601111 ACTTAACTTGGACTGAACCC
66 AATTAACTTGGACTAAACCA
* * * * * *
5601131 AAGAAGGATCTGACATAGGCCAAAATCCAAAACAAAATTACCTGGATGGAATCGAAGTCTGAGAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
*
5601196 AGTTAACTTGGACTAAACCA
66 AATTAACTTGGACTAAACCA
* * * * *
5601216 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATAACCTGGATGGAATCAAAGTATGAGAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
* *
5601281 AATTAACTTAGACTAAATCA
66 AATTAACTTGGACTAAACCA
* * * *
5601301 AAGAAAGATCTGGCATAGATCAAAATCTAAAACAAAATGACATGGATGGAACCAAAGTCTGAAAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
* *
5601366 AAATAACTTAGACTAAACCA
66 AATTAACTTGGACTAAACCA
* * * *
5601386 AAGAGGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACTTGGATGGAACCGAAGTCTGAAAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
* *
5601451 AATTAACTTGGATTGAACCA
66 AATTAACTTGGACTAAACCA
* * * * *
5601471 AAGAGGGATCTAGCATAGGTCAAAATTCAAAACAAAATGACCTGGATAGAACCAAAGTATGAAAT
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
*
5601536 AATTAACTTGGACTAAACTGA
66 AATTAACTTGGACTAAAC-CA
* * * * * * * *
5601557 AAGAA-GATATGGTATAAGTCGAAAT-CAAAACAAAATGACTTAGATTGAACCGAAGTCTGA
1 AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGA
5601617 CTTTACAACA
Statistics
Matches: 419, Mismatches: 64, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
83 23 0.05
84 33 0.08
85 358 0.85
86 5 0.01
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (85 bp):
AAGAAGGATCTGGCATAGGTCAAAATCCAAAACAAAATGACCTGGATGGAACCAAAGTCTGAAAT
AATTAACTTGGACTAAACCA
Found at i:5601349 original size:170 final size:170
Alignment explanation
Indices: 5601048--5601616 Score: 698
Period size: 170 Copynumber: 3.4 Consensus size: 170
5601038 GAATGACCCG
* * * *
5601048 AAGATGGATCTAGCATAGGTCGAAATCC-AAA-ATAATGACATGGATGAAATCGAAGTCTGAGAT
1 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACATGGATGGAATCGAAGTCTGAGAT
* * * * * *
5601111 ACTTAACTTGGACTGAACCCAAGAAGGATCTGACATAGGCCAAAATCCAAAACAAAATTACCTGG
66 AATTAACTTGGACTGAACCAAAGAAGGATCTGGCATAGGTCAAAATCTAAAACAAAATGACCTGG
* * * *
5601176 ATGGAATCGAAGTCTGAGATAGTTAACTTGGACTAAACCA
131 ATGGAACCAAAGTCTGAAATAATTAACTTGGACTAAACCA
* * * *
5601216 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATAACCTGGATGGAATCAAAGTATGAGAT
1 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACATGGATGGAATCGAAGTCTGAGAT
* * * * * *
5601281 AATTAACTTAGACTAAATCAAAGAAAGATCTGGCATAGATCAAAATCTAAAACAAAATGACATGG
66 AATTAACTTGGACTGAACCAAAGAAGGATCTGGCATAGGTCAAAATCTAAAACAAAATGACCTGG
* *
5601346 ATGGAACCAAAGTCTGAAATAAATAACTTAGACTAAACCA
131 ATGGAACCAAAGTCTGAAATAATTAACTTGGACTAAACCA
* * * *
5601386 AAGAGGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACTTGGATGGAACCGAAGTCTGAAAT
1 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACATGGATGGAATCGAAGTCTGAGAT
* * *
5601451 AATTAACTTGGATTGAACCAAAGAGGGATCTAGCATAGGTCAAAAT-TCAAAACAAAATGACCTG
66 AATTAACTTGGACTGAACCAAAGAAGGATCTGGCATAGGTCAAAATCT-AAAACAAAATGACCTG
* * *
5601515 GATAGAACCAAAGTATGAAATAATTAACTTGGACTAAACTGA
130 GATGGAACCAAAGTCTGAAATAATTAACTTGGACTAAAC-CA
* * * * * * *
5601557 AAGAA-GATATGGTATAAGTCGAAAT-CAAAACAAAATGACTTAGATTGAACCGAAGTCTGA
1 AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACATGGATGGAATCGAAGTCTGA
5601617 CTTTACAACA
Statistics
Matches: 344, Mismatches: 53, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
168 26 0.08
169 37 0.11
170 276 0.80
171 5 0.01
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (170 bp):
AAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATGACATGGATGGAATCGAAGTCTGAGAT
AATTAACTTGGACTGAACCAAAGAAGGATCTGGCATAGGTCAAAATCTAAAACAAAATGACCTGG
ATGGAACCAAAGTCTGAAATAATTAACTTGGACTAAACCA
Found at i:5601532 original size:255 final size:254
Alignment explanation
Indices: 5601081--5601616 Score: 707
Period size: 255 Copynumber: 2.1 Consensus size: 254
5601071 AATCCAAAAT
* * * ** * * *
5601081 AATGACATGGATGAAATCGAAGTCTGAGATACTTAACTTGGACTGAACCCAAGAAGGATCTGACA
1 AATGACATGGATGGAACCGAAGTCTGAAATAAATAACTTAGACTAAACCAAAGAAGGATCTGACA
* * * *
5601146 TAGGCCAAAATCCAAAACAAAATTACCTGGATGGAATCGAAGTCTGAGATAGTTAACTTGGACTA
66 TAGGCCAAAATCCAAAACAAAATGACCTGGATGGAACCGAAGTCTGAAATAATTAACTTGGACTA
* * * *
5601211 AACCAAAGAAGGATCTGGCATAGGTCGAAATCCAAAACAAAATAACCTGGATGGAATCAAAGTAT
131 AACCAAAGAAGGATCTAGCATAGGTCAAAATCCAAAACAAAATAACCTGGATAGAACCAAAGTAT
* *
5601276 GAGATAATTAACTTAGACTAAA-TCAAAGAAAGATCTGGCAT-AGATCAAAATCTAAAACAA
196 GAAATAATTAACTTAGACTAAACTCAAAG-AAGATATGGCATAAG-TCAAAATC-AAAACAA
* * *
5601336 AATGACATGGATGGAACCAAAGTCTGAAATAAATAACTTAGACTAAACCAAAGAGGGATCTGGCA
1 AATGACATGGATGGAACCGAAGTCTGAAATAAATAACTTAGACTAAACCAAAGAAGGATCTGACA
* * * * *
5601401 TAGGTCGAAATCCAAAACAAAATGACTTGGATGGAACCGAAGTCTGAAATAATTAACTTGGATTG
66 TAGGCCAAAATCCAAAACAAAATGACCTGGATGGAACCGAAGTCTGAAATAATTAACTTGGACTA
* * *
5601466 AACCAAAGAGGGATCTAGCATAGGTCAAAATTCAAAACAAAATGACCTGGATAGAACCAAAGTAT
131 AACCAAAGAAGGATCTAGCATAGGTCAAAATCCAAAACAAAATAACCTGGATAGAACCAAAGTAT
* * * *
5601531 GAAATAATTAACTTGGACTAAACTGAAAGAAGATATGGTATAAGTCGAAATCAAAACAA
196 GAAATAATTAACTTAGACTAAACTCAAAGAAGATATGGCATAAGTCAAAATCAAAACAA
* * *
5601590 AATGACTTAGATTGAACCGAAGTCTGA
1 AATGACATGGATGGAACCGAAGTCTGA
5601617 CTTTACAACA
Statistics
Matches: 242, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
254 30 0.12
255 205 0.85
256 7 0.03
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (254 bp):
AATGACATGGATGGAACCGAAGTCTGAAATAAATAACTTAGACTAAACCAAAGAAGGATCTGACA
TAGGCCAAAATCCAAAACAAAATGACCTGGATGGAACCGAAGTCTGAAATAATTAACTTGGACTA
AACCAAAGAAGGATCTAGCATAGGTCAAAATCCAAAACAAAATAACCTGGATAGAACCAAAGTAT
GAAATAATTAACTTAGACTAAACTCAAAGAAGATATGGCATAAGTCAAAATCAAAACAA
Found at i:5601834 original size:17 final size:17
Alignment explanation
Indices: 5601812--5601884 Score: 101
Period size: 17 Copynumber: 4.3 Consensus size: 17
5601802 GTAAGAAAAC
*
5601812 AGATTCGCAAGAATTGG
1 AGATTCGCAAGAATTGA
*
5601829 AGATTCGTAAGAATTGA
1 AGATTCGCAAGAATTGA
*
5601846 AGATTCGCAAGAATTAA
1 AGATTCGCAAGAATTGA
* *
5601863 AGATTCGCAATAATTAA
1 AGATTCGCAAGAATTGA
5601880 AGATT
1 AGATT
5601885 TACGAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (17 bp):
AGATTCGCAAGAATTGA
Found at i:5601852 original size:34 final size:34
Alignment explanation
Indices: 5601812--5601924 Score: 111
Period size: 34 Copynumber: 3.4 Consensus size: 34
5601802 GTAAGAAAAC
* *
5601812 AGATTCGCAAGAATTGGAGATTCGTAAGAATTGA
1 AGATTCACAAGAATTAGAGATTCGTAAGAATTGA
* * * * *
5601846 AGATTCGCAAGAATTAAAGATTCGCAATAATTAA
1 AGATTCACAAGAATTAGAGATTCGTAAGAATTGA
* * * *
5601880 AGATTTACGA-AATTAGAGATTTGTAAGATTTGA
1 AGATTCACAAGAATTAGAGATTCGTAAGAATTGA
*
5601913 AAATTCACAAGA
1 AGATTCACAAGA
5601925 CTTTCATATT
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
33 24 0.39
34 37 0.61
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.28
Consensus pattern (34 bp):
AGATTCACAAGAATTAGAGATTCGTAAGAATTGA
Found at i:5601964 original size:56 final size:56
Alignment explanation
Indices: 5601904--5602019 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 56
5601894 AGAGATTTGT
*
5601904 AAGATTTGAAAATTCACAAGACTTTCATATTCACAA-AAATTGAATTGGAGATTCAC
1 AAGATTTGAAAATTCACAAGACTTTCAGATTCACAAGAAA-TGAATTGGAGATTCAC
* * ** * * *
5601960 AAGATTTGGAGATTCGTAAGACTTTTAGATTCACAAGAAATGGATTGGAGATTCGC
1 AAGATTTGAAAATTCACAAGACTTTCAGATTCACAAGAAATGAATTGGAGATTCAC
5602016 AAGA
1 AAGA
5602020 ATTTCTAGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 48 0.94
57 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (56 bp):
AAGATTTGAAAATTCACAAGACTTTCAGATTCACAAGAAATGAATTGGAGATTCAC
Found at i:5601970 original size:17 final size:18
Alignment explanation
Indices: 5601948--5601997 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
5601938 AAAAATTGAA
5601948 TTGGAGATTCACAAGA-T
1 TTGGAGATTCACAAGACT
**
5601965 TTGGAGATTCGTAAGACT
1 TTGGAGATTCACAAGACT
*
5601983 TT-TAGATTCACAAGA
1 TTGGAGATTCACAAGA
5601998 AATGGATTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 24 0.89
18 3 0.11
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (18 bp):
TTGGAGATTCACAAGACT
Found at i:5602042 original size:56 final size:56
Alignment explanation
Indices: 5601932--5602046 Score: 135
Period size: 56 Copynumber: 2.1 Consensus size: 56
5601922 AGACTTTCAT
* * * *
5601932 ATTCACAAAAATTGAATTGGAGATTCACAAGATTTGGAGATTCGTAAGACTTTTAG
1 ATTCACAAAAATTGAATTGGAGATTCACAAGATTTCGAGATTCATAAAAATTTTAG
* * *
5601988 ATTCACAAGAAA-TGGATTGGAGATTCGCAAGAATTTCTAG-TTCATAAAAATTTTAG
1 ATTCACAA-AAATTGAATTGGAGATTCACAAG-ATTTCGAGATTCATAAAAATTTTAG
5602044 ATT
1 ATT
5602047 TGTAAGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 41 0.82
57 9 0.18
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (56 bp):
ATTCACAAAAATTGAATTGGAGATTCACAAGATTTCGAGATTCATAAAAATTTTAG
Found at i:5602208 original size:21 final size:21
Alignment explanation
Indices: 5602184--5602237 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5602174 AAAAAATTTC
*
5602184 AAGATTTTCATTAAAAACTCA
1 AAGATTCTCATTAAAAACTCA
* **
5602205 AAGATCCTCATTTGAAACTCA
1 AAGATTCTCATTAAAAACTCA
*
5602226 AATATTCTCATT
1 AAGATTCTCATT
5602238 TGAAAATTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (21 bp):
AAGATTCTCATTAAAAACTCA
Found at i:5602238 original size:21 final size:21
Alignment explanation
Indices: 5602198--5602242 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5602188 TTTTCATTAA
5602198 AAACTCAAAGATCCTCATTTG
1 AAACTCAAAGATCCTCATTTG
* *
5602219 AAACTCAAATATTCTCATTTG
1 AAACTCAAAGATCCTCATTTG
5602240 AAA
1 AAA
5602243 ATTCTTAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (21 bp):
AAACTCAAAGATCCTCATTTG
Found at i:5603358 original size:25 final size:24
Alignment explanation
Indices: 5603330--5603386 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
5603320 TGAGTCTTTC
* **
5603330 TTTTCTTTTTTTTTTTTTTCACCTT
1 TTTTATTTTTTTGCTTTTTCA-CTT
5603355 TTTTATTTTTTTGCTTTTTCACTT
1 TTTTATTTTTTTGCTTTTTCACTT
*
5603379 TTTCATTT
1 TTTTATTT
5603387 CATCCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTATTTTTTTGCTTTTTCACTT
Found at i:5607430 original size:42 final size:42
Alignment explanation
Indices: 5607333--5607430 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
5607323 TTGAAATTTT
*
5607333 TATTTTTTTAAAAAATTGATACTTCCAACTTTTCTTAAAAAG
1 TATTTTTTTGAAAAATTGATACTTCCAACTTTTCTTAAAAAG
* * * *
5607375 TATATTTTAGAAAAATTGATACTTTCAACTTTTCTTAAATA-
1 TATTTTTTTGAAAAATTGATACTTCCAACTTTTCTTAAAAAG
5607416 TATTTTTTTTGAAAA
1 TA-TTTTTTTGAAAA
5607431 TTTCATTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (42 bp):
TATTTTTTTGAAAAATTGATACTTCCAACTTTTCTTAAAAAG
Found at i:5607450 original size:59 final size:57
Alignment explanation
Indices: 5607383--5607842 Score: 447
Period size: 59 Copynumber: 7.8 Consensus size: 57
5607373 AGTATATTTT
* * *
5607383 AGAAAAATTGATACTTTCAACTTTTCTTAAATATATTTTTTTTGAAAATTTCATTTTCA
1 AGAAAAATTGATACTTTCAACTTTTCTTAAA-A-ATATTTTTTGAAATTTTTATTTTCA
* * ** *
5607442 AGAAAAATTGATACTTTCAACTTTTTTTAAAAAATACATTTTCAAAAATTTTATTTTCA
1 AGAAAAATTGATACTTTCAACTTTTCTT-AAAAATA-TTTTTTGAAATTTTTATTTTCA
** * * *
5607501 AGGGAAGTTGATATTTTCAACTTTTTTTCAAAAATACCTTTTTTGAGAATTTTTATTTTCA
1 AGAAAAATTGATACTTTCAACTTTTCTT-AAAAATA--TTTTTTGA-AATTTTTATTTTCA
* * * * *
5607562 ATAAAAATTAATACTTTCAACATTTTCTCAAAAATATTTTTTGAAGTTTTTATTTTTA
1 AGAAAAATTGATACTTTCAAC-TTTTCTTAAAAATATTTTTTGAAATTTTTATTTTCA
* *
5607620 A-AGAAAATTGATACTTTCAACTTTTCCTTAAAAAATATCTTTTGAAATTTTTATTTTTA
1 AGA-AAAATTGATACTTTCAACTTTT-CTT-AAAAATATTTTTTGAAATTTTTATTTTCA
* * * * * * *
5607679 AGAAAAATTTATACATTCAACTTTTTCTCAAAAACATCTTTTGAAAATTTTATCTTCA
1 AGAAAAATTGATACTTTCAAC-TTTTCTTAAAAATATTTTTTGAAATTTTTATTTTCA
* ** * *
5607737 AGGAAAATTGATACTTTCAACTTTTTCTTAAAGAGCATTTTTTGAAGTTTTTATTTTTA
1 AGAAAAATTGATACTTTCAAC-TTTTCTTAAA-AATATTTTTTGAAATTTTTATTTTCA
*
5607796 AGAAAAATTGATACTTTCAATTTTTTCTTAAAACAT-TTATTTTGAAA
1 AGAAAAATTGATACTTTCAA-CTTTTCTTAAAA-ATATT-TTTTGAAA
5607843 CATATTTTGA
Statistics
Matches: 336, Mismatches: 51, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
57 5 0.01
58 90 0.27
59 187 0.56
60 14 0.04
61 35 0.10
62 5 0.01
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (57 bp):
AGAAAAATTGATACTTTCAACTTTTCTTAAAAATATTTTTTGAAATTTTTATTTTCA
Found at i:5607706 original size:117 final size:116
Alignment explanation
Indices: 5607386--5607842 Score: 511
Period size: 117 Copynumber: 3.9 Consensus size: 116
5607376 ATATTTTAGA
* * * *
5607386 AAAATTGATACTTTCAACTTTTCTTAAATATATTTTTTTTGAAAATTTCATTTTCAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCTTAAA-AAATATTTTTTGAAATTTTTATTTTCAAGAAAAATT
* * * **
5607451 GATACTTTCAACTTTTTTTAAAAAATACATTTTCAAAAATTTTATTTTCAAGG
65 GATACTTTCAACTTTTTCTCAAAAATA-TTTTTTGAAAATTTTATTTTCAAGG
* * * * * *
5607504 GAAGTTGATATTTTCAACTTTTTTTCAAAAATACCTTTTTTGAGAATTTTTATTTTCAATAAAAA
1 AAAATTGATACTTTCAACTTTTCTTAAAAAATA--TTTTTTGA-AATTTTTATTTTCAAGAAAAA
* * ** * *
5607569 TTAATACTTTCAACATTTTCTCAAAAATATTTTTTGAAGTTTTTATTTTTAAAG
63 TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTTATTTTCAAGG
* *
5607623 AAAATTGATACTTTCAACTTTTCCTTAAAAAATATCTTTTGAAATTTTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTT-CTTAAAAAATATTTTTTGAAATTTTTATTTTCAAGAAAAATT
* * * * *
5607688 TATACATTCAACTTTTTCTCAAAAACATCTTTTGAAAATTTTATCTTCAAGG
65 GATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTTATTTTCAAGG
* ** * *
5607740 AAAATTGATACTTTCAACTTTTTCTTAAAGAGCATTTTTTGAAGTTTTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAAC-TTTTCTTAAAAAATATTTTTTGAAATTTTTATTTTCAAGAAAAATT
* *
5607805 GATACTTTCAATTTTTTCTTAAAACAT-TTATTTTGAAA
65 GATACTTTCAACTTTTTCTCAAAA-ATATT-TTTTGAAA
5607843 CATATTTTGA
Statistics
Matches: 282, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
117 142 0.50
118 43 0.15
119 45 0.16
120 52 0.18
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCTTAAAAAATATTTTTTGAAATTTTTATTTTCAAGAAAAATTG
ATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTTATTTTCAAGG
Found at i:5608716 original size:19 final size:20
Alignment explanation
Indices: 5608675--5608718 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5608665 TTCTTTCACA
5608675 TTTTTGTTTCTGACTTTCTT
1 TTTTTGTTTCTGACTTTCTT
5608695 TTTTTGTTTCTGA-TTCTCTT
1 TTTTTGTTTCTGACTT-TCTT
5608715 TTTT
1 TTTT
5608719 ATAGGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.05, C:0.14, G:0.09, T:0.73
Consensus pattern (20 bp):
TTTTTGTTTCTGACTTTCTT
Found at i:5609295 original size:37 final size:36
Alignment explanation
Indices: 5609245--5609316 Score: 135
Period size: 37 Copynumber: 2.0 Consensus size: 36
5609235 CTGCCAATGG
5609245 ATTAAATAATGGTGATGAGGATAGGATGCTCAGTTTT
1 ATTAAATAATGGTGATGAGGATAGGAT-CTCAGTTTT
5609282 ATTAAATAATGGTGATGAGGATAGGATCTCAGTTT
1 ATTAAATAATGGTGATGAGGATAGGATCTCAGTTT
5609317 AAAACTGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (36 bp):
ATTAAATAATGGTGATGAGGATAGGATCTCAGTTTT
Found at i:5609444 original size:25 final size:26
Alignment explanation
Indices: 5609397--5609445 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5609387 TTATCACCTG
* **
5609397 TTTTATCTTTTCTATTTTTTTTTATA
1 TTTTATCCTTTCTATTTACTTTTATA
5609423 TTTTATCCTTT-TATTTACTTTTA
1 TTTTATCCTTTCTATTTACTTTTA
5609446 GGGTAGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATCCTTTCTATTTACTTTTATA
Found at i:5609635 original size:2 final size:2
Alignment explanation
Indices: 5609628--5609655 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5609618 AAGTGAATCT
5609628 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
5609656 AGATAAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5609766 original size:21 final size:20
Alignment explanation
Indices: 5609700--5609766 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
5609690 GCATTTTTTG
*
5609700 TTTTTTTAATTTACTTTT-CC
1 TTTTTTTAATTT-CTTTTACA
*
5609720 TTTTTTTAATTTATATTTA-A
1 TTTTTTTAATTTCT-TTTACA
*
5609740 TGTTTTTTTATTTGCTTTTACA
1 T-TTTTTTAATTT-CTTTTACA
5609762 TTTTT
1 TTTTT
5609767 AATTTGTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.42
21 18 0.47
22 3 0.08
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTTAATTTCTTTTACA
Found at i:5610601 original size:29 final size:28
Alignment explanation
Indices: 5610569--5610654 Score: 73
Period size: 32 Copynumber: 2.9 Consensus size: 28
5610559 ATTAATTATT
* *
5610569 TAATTTTATATTTATATATATTATATTAA
1 TAATATTATATTTATATATATT-TAATAA
* *
5610598 TAATGTTATTATTTAGTATTTTAATTTAATAA
1 TAATATTA-TATTTA-TA-TAT-ATTTAATAA
* *
5610630 CAATATTATATTTATATATAATTAA
1 TAATATTATATTTATATATATTTAA
5610655 GATGTAATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 5 0.11
29 9 0.20
30 8 0.17
31 8 0.17
32 13 0.28
33 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (28 bp):
TAATATTATATTTATATATATTTAATAA
Found at i:5611013 original size:22 final size:20
Alignment explanation
Indices: 5610981--5611025 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5610971 TTTTTTTTCT
*
5610981 TTTTTTGTTTTTATTTTTTA
1 TTTTTTGTTTTGATTTTTTA
*
5611001 TTTTTTGCTTTTTGCTTTTTTA
1 TTTTTTG--TTTTGATTTTTTA
5611023 TTT
1 TTT
5611026 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.82
Consensus pattern (20 bp):
TTTTTTGTTTTGATTTTTTA
Found at i:5611034 original size:22 final size:22
Alignment explanation
Indices: 5610994--5611035 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5610984 TTTGTTTTTA
* **
5610994 TTTTTTATTTTTTGCTTTTTGC
1 TTTTTTATTTATTAATTTTTGC
5611016 TTTTTTATTTATTAATTTTT
1 TTTTTTATTTATTAATTTTT
5611036 AAATTAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTTTTATTTATTAATTTTTGC
Found at i:5611234 original size:59 final size:59
Alignment explanation
Indices: 5611116--5611263 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 59
5611106 CCTTTCAAAA
* * **
5611116 TTTTTATGTATTTTAATTTGATAAATTTTACAACAAAATGAGTTAATTGATAGGATTTT
1 TTTTTATGTTTTTTAATTAGATAAATTTTACAACAAAATGAGCCAATTGATAGGATTTT
* * **
5611175 TTTTTATGTTTTTTAATTAGGTAAATTTTACAACAAAATGAGCCATTTG-T-GTTTTTTT
1 TTTTTATGTTTTTTAATTAGATAAATTTTACAACAAAATGAGCCAATTGATAG-GATTTT
*
5611233 TTTTTTTGTATTTTTTAATTAGATAAATTTT
1 TTTTTATG--TTTTTTAATTAGATAAATTTT
5611264 TTGTGTTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.01
58 12 0.16
59 43 0.57
60 20 0.26
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (59 bp):
TTTTTATGTTTTTTAATTAGATAAATTTTACAACAAAATGAGCCAATTGATAGGATTTT
Found at i:5612533 original size:2 final size:2
Alignment explanation
Indices: 5612526--5612569 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5612516 AATTCTCTTC
* *
5612526 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5612568 AT
1 AT
5612570 TAATTAAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5612547 original size:14 final size:14
Alignment explanation
Indices: 5612528--5612568 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
5612518 TTCTCTTCAT
5612528 ATATATATATATAA
1 ATATATATATATAA
5612542 ATATATATATATAA
1 ATATATATATATAA
5612556 ATATATATATATA
1 ATATATATATATA
5612569 TTAATTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:5618787 original size:24 final size:24
Alignment explanation
Indices: 5618742--5618810 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 24
5618732 TTTATATTTA
* * *
5618742 ATACATTATTAGTATATAAGATAC
1 ATACATTATCAATAAATAAGATAC
*
5618766 ATACATTATCAATAAATCAGATA-
1 ATACATTATCAATAAATAAGATAC
*
5618789 ATGACAAGTTATTAATAAATAA
1 AT-AC-A-TTATCAATAAATAA
5618811 ATATTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 2 0.06
24 21 0.58
25 1 0.03
26 12 0.33
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (24 bp):
ATACATTATCAATAAATAAGATAC
Found at i:5623305 original size:24 final size:24
Alignment explanation
Indices: 5623278--5623328 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5623268 TCATTATCGA
5623278 ATTTTGTTATAATAGTTCAAATTC
1 ATTTTGTTATAATAGTTCAAATTC
*
5623302 ATTTTGTTATAGTAGTTCAAATTC
1 ATTTTGTTATAATAGTTCAAATTC
5623326 ATT
1 ATT
5623329 GAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (24 bp):
ATTTTGTTATAATAGTTCAAATTC
Found at i:5628167 original size:6 final size:6
Alignment explanation
Indices: 5628156--5628221 Score: 66
Period size: 6 Copynumber: 10.8 Consensus size: 6
5628146 TTTTTATCTT
*
5628156 TTTATA TTTATA TTTATA TTTATA TTGATA TTTATCA -TTAT- TATTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT-A TTTATA T-TTATA
5628204 TTTTATTA TTT-TA TTTAT
1 -TTTA-TA TTTATA TTTAT
5628222 TTTCTTGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 5 0.10
6 36 0.71
7 7 0.14
8 3 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:5629392 original size:4 final size:4
Alignment explanation
Indices: 5629383--5629408 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5629373 TTTTTATCTG
5629383 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
5629409 GTGAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:5629507 original size:42 final size:41
Alignment explanation
Indices: 5629437--5629534 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 41
5629427 TAATAAAGAT
* * *
5629437 ATTTTAGACAAATGAAACTTACTAACATATTGGAAA-GTTTAAA
1 ATTTTA-AAAAATAAAACTTACCAACATATT-GAAATGTTT-AA
*
5629480 ATTTTAAAAAATAAAATTTACCAACATATTGAAATGTTTAA
1 ATTTTAAAAAATAAAACTTACCAACATATTGAAATGTTTAA
5629521 ATTTCTAAATAAAT
1 ATTT-TAAA-AAAT
5629535 TTTTGAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 10 0.21
42 28 0.58
43 10 0.21
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (41 bp):
ATTTTAAAAAATAAAACTTACCAACATATTGAAATGTTTAA
Found at i:5630433 original size:13 final size:13
Alignment explanation
Indices: 5630415--5630453 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5630405 TTCGATTCAA
*
5630415 ATTAAATTTGGAT
1 ATTAAATGTGGAT
**
5630428 ATTAAATGTATAT
1 ATTAAATGTGGAT
5630441 ATTAAATGTGGAT
1 ATTAAATGTGGAT
5630454 CATATTTCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
ATTAAATGTGGAT
Found at i:5630531 original size:19 final size:18
Alignment explanation
Indices: 5630505--5630548 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
5630495 AACCAAACTG
*
5630505 AATTATATATATATTTT-
1 AATTTTATATATATTTTA
5630522 AATTTTATATATATTTTA
1 AATTTTATATATATTTTA
5630540 AATTTTATA
1 AATTTTATA
5630549 AAATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTATATATATTTTA
Found at i:5633428 original size:3 final size:3
Alignment explanation
Indices: 5633420--5633469 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5633410 ATTCATAAGC
5633420 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5633468 TT
1 TT
5633470 TATAAAAGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5633783 original size:29 final size:29
Alignment explanation
Indices: 5633746--5633805 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
5633736 AGGCGGAGAC
5633746 TTAGACAAAGACAGGTTCAAAGTTTCTTT
1 TTAGACAAAGACAGGTTCAAAGTTTCTTT
*
5633775 TTAGGCAAAGACAGGTTCAAAGTTTCTTT
1 TTAGACAAAGACAGGTTCAAAGTTTCTTT
5633804 TT
1 TT
5633806 GAATATTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (29 bp):
TTAGACAAAGACAGGTTCAAAGTTTCTTT
Found at i:5634726 original size:17 final size:18
Alignment explanation
Indices: 5634693--5634729 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5634683 TCATATTTAT
5634693 ATTTAAATTATTCATATC
1 ATTTAAATTATTCATATC
*
5634711 ATTTAAA-TATTTATATC
1 ATTTAAATTATTCATATC
5634728 AT
1 AT
5634730 ATTTATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAATTATTCATATC
Found at i:5638187 original size:21 final size:21
Alignment explanation
Indices: 5638149--5638188 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5638139 GCTACAATAC
5638149 TTTTGACTCTTGTATACCATA
1 TTTTGACTCTTGTATACCATA
*
5638170 TTTT-ACTCTATGTTTACCA
1 TTTTGACTCT-TGTATACCA
5638189 CCAATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTGACTCTTGTATACCATA
Found at i:5645370 original size:16 final size:17
Alignment explanation
Indices: 5645349--5645380 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5645339 ACATCATGTT
5645349 AAAAAAT-TTAAAAGAA
1 AAAAAATCTTAAAAGAA
5645365 AAAAAATCTTAAAAGA
1 AAAAAATCTTAAAAGA
5645381 TTATATGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (17 bp):
AAAAAATCTTAAAAGAA
Found at i:5648134 original size:2 final size:2
Alignment explanation
Indices: 5648127--5648154 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5648117 ATTTGCAATG
5648127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5648155 CATTGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5648903 original size:3 final size:3
Alignment explanation
Indices: 5648897--5648941 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5648887 TCTAAAACCC
5648897 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5648942 CCTCCTCCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5650453 original size:3 final size:3
Alignment explanation
Indices: 5650445--5650504 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5650435 CTTGTTTCTC
5650445 ATT ATT ATT ATT 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 ATT ATT ATT ATT
5650493 ATT ATT ATT ATT
1 ATT ATT ATT ATT
5650505 TAAAGGAGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5659768 original size:22 final size:22
Alignment explanation
Indices: 5659728--5659774 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5659718 GAAAAAAATT
*
5659728 AAAAAAAAACAAGACAAAGTAA
1 AAAAAAAAACAAGACAAAGGAA
*
5659750 AAAAAAAAAGAAGTA-AAAGGAA
1 AAAAAAAAACAAG-ACAAAGGAA
5659772 AAA
1 AAA
5659775 TGAATGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (22 bp):
AAAAAAAAACAAGACAAAGGAA
Found at i:5660139 original size:17 final size:17
Alignment explanation
Indices: 5660119--5660182 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
5660109 AAAATGAAGG
*
5660119 AAAAAATAAAAAAATGA
1 AAAAAAGAAAAAAATGA
**
5660136 AAAAAAGAAATGAATGA
1 AAAAAAGAAAAAAATGA
5660153 AAATAAA-AAATAAAAT-A
1 AAA-AAAGAAA-AAAATGA
5660170 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
5660183 TAAAAGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.15
17 27 0.69
18 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAGAAAAAAATGA
Found at i:5660147 original size:33 final size:34
Alignment explanation
Indices: 5660110--5660179 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
5660100 ACAAATGGAA
*
5660110 AAATGAAGGAAAA-AATAAA-AAAATGAAAAAAAG
1 AAATGAAGGAAAATAAAAAATAAAAT-AAAAAAAG
*
5660143 AAATGAATGAAAATAAAAAATAAAATAAAAAAAG
1 AAATGAAGGAAAATAAAAAATAAAATAAAAAAAG
5660177 AAA
1 AAA
5660180 AAATAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 12 0.36
34 16 0.48
35 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (34 bp):
AAATGAAGGAAAATAAAAAATAAAATAAAAAAAG
Found at i:5660192 original size:11 final size:11
Alignment explanation
Indices: 5660158--5660200 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
5660148 AATGAAAATA
*
5660158 AAAAATAAAAT
1 AAAAATAAAAG
*
5660169 AAAAA-AAGA-
1 AAAAATAAAAG
5660178 AAAAATAAAAG
1 AAAAATAAAAG
5660189 AAAAATAAAAG
1 AAAAATAAAAG
5660200 A
1 A
5660201 GATAAAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 5 0.18
10 6 0.21
11 17 0.61
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:5660205 original size:20 final size:18
Alignment explanation
Indices: 5660152--5660208 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
5660142 GAAATGAATG
*
5660152 AAAATAAAAAATAAAATAAA
1 AAAATAAAAAAT-AAA-AGA
*
5660172 AAAAGAAAAAATAAAAGA
1 AAAATAAAAAATAAAAGA
5660190 AAAATAAAAGAGATAAAAG
1 AAAATAAAA-A-ATAAAAG
5660209 GAATACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 10 0.31
19 4 0.12
20 18 0.56
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAATAAAAAATAAAAGA
Found at i:5660207 original size:26 final size:27
Alignment explanation
Indices: 5660118--5660198 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
5660108 AAAAATGAAG
*
5660118 GAAAAAATAAAAAAATGAAAA-AAAGAAAT
1 GAAAAAAT-AAAAAAT-AAAATAAA-AAAA
5660147 GAATGAAAATAAAAAATAAAATAAAAAAA
1 GAA--AAAATAAAAAATAAAATAAAAAAA
*
5660176 GAAAAAATAAAAGA-AAAATAAAA
1 GAAAAAATAAAAAATAAAATAAAA
5660199 GAGATAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
26 9 0.19
27 10 0.21
29 13 0.28
30 10 0.21
31 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (27 bp):
GAAAAAATAAAAAATAAAATAAAAAAA
Found at i:5661628 original size:107 final size:107
Alignment explanation
Indices: 5661429--5661631 Score: 282
Period size: 107 Copynumber: 1.9 Consensus size: 107
5661419 GTTTTAAACT
* * * *
5661429 TTTTGGATGTGAATCCTAGATTTGTCGAATGTGAACCTTTAAATTTAGATGTGAAACTCTAAGAT
1 TTTTCGATGTGAATCCTAAATTTGTCGAATGAGAACCTTTAAACTTAGATGTGAAACTCTAAGAT
*
5661494 TTATTGGATGTGAATCTTCGAACTCAAATGATAAGCTTTAAC
66 TTATTGAATGTGAATCTTCGAACTCAAATGATAAGCTTTAAC
* * * *
5661536 TTTTCGATGTGAATCTTTAAATTT-TTGAATGAGAACCTTTGAACTTAGATGTGAAACTCTAATA
1 TTTTCGATGTGAATC-CTAAATTTGTCGAATGAGAACCTTTAAACTTAGATGTGAAACTCTAAGA
* * *
5661600 TTTATTGAATGTGAATTTTTGAATTCAAATGA
65 TTTATTGAATGTGAATCTTCGAACTCAAATGA
5661632 GGAGTTTTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 77 0.93
108 6 0.07
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (107 bp):
TTTTCGATGTGAATCCTAAATTTGTCGAATGAGAACCTTTAAACTTAGATGTGAAACTCTAAGAT
TTATTGAATGTGAATCTTCGAACTCAAATGATAAGCTTTAAC
Found at i:5662145 original size:43 final size:43
Alignment explanation
Indices: 5662067--5662440 Score: 283
Period size: 43 Copynumber: 8.6 Consensus size: 43
5662057 TGTCAAAGAG
* * * *
5662067 ATTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGATAAACATT
1 ATTTATTTTTC-AAAGTTGTTGAGCCTTTATTTAGAGAAACTTT
* * *
5662111 ATTTATTTTTCAAAGTTGTTGATCCTTTATTTAGAGGAGACATT
1 ATTTATTTTTCAAAGTTGTTGAGCCTTTATTTAGA-GAAACTTT
* * * *
5662155 ATTTATTTTTTCAAAGTTGTTGAGCCTTTGTTCAGAGGAGCTTT
1 ATTTA-TTTTTCAAAGTTGTTGAGCCTTTATTTAGAGAAACTTT
* * * * * * *
5662199 ATTTATTTTTCAAAATTATTGAACCTTTGATTAAAAG-AGCCTT
1 ATTTATTTTTCAAAGTTGTTGAGCCTTT-ATTTAGAGAAACTTT
* * * * *
5662242 GTTTATTTTTCAAA-TTCATTGAACCTCTATTTAGA-AGAGCTTT
1 ATTTATTTTTCAAAGTT-GTTGAGCCTTTATTTAGAGA-AACTTT
* * * * * *
5662285 GTTTATTTTTCAAAGTTGTTGAGTCTCTAATTAAAGGAACTTT
1 ATTTATTTTTCAAAGTTGTTGAGCCTTTATTTAGAGAAACTTT
* * *
5662328 ATTTATTTTTCAAAGTTGTTAAGCCTTTGA-TTAGAGGAACCTT
1 ATTTATTTTTCAAAGTTGTTGAGCCTTT-ATTTAGAGAAACTTT
* * * * *
5662371 ATTTATTTTTCAAAGTTATTGAGCCTCTGA-TTAGAGGAGCCTT
1 ATTTATTTTTCAAAGTTGTTGAGCCT-TTATTTAGAGAAACTTT
5662414 ATTTATTTTTTCAAAAGTTG-TGAGCCT
1 ATTTA-TTTTTC-AAAGTTGTTGAGCCT
5662441 CTACTTATGG
Statistics
Matches: 276, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
42 7 0.03
43 183 0.66
44 53 0.19
45 33 0.12
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (43 bp):
ATTTATTTTTCAAAGTTGTTGAGCCTTTATTTAGAGAAACTTT
Found at i:5662290 original size:86 final size:86
Alignment explanation
Indices: 5662067--5662428 Score: 313
Period size: 86 Copynumber: 4.2 Consensus size: 86
5662057 TGTCAAAGAG
* * * * * *
5662067 ATTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGATA-AACATTATTTATTTTTCAAAGTTGTT
1 ATTTATTTTTC-AAAGTTATTAAGCCTCTGATTAGA-AGAGCTTTATTTATTTTTCAAAGTTATT
* * * *
5662131 GATCCT-TTATTTAGAGGAGACATT
64 GAGCCTCTGA-TTAAAGGAG-CCTT
* * * * *
5662155 ATTTATTTTTTCAAAGTTGTTGAGCCTTTG-TTCAGAGGAGCTTTATTTATTTTTCAAAATTATT
1 ATTTA-TTTTTCAAAGTTATTAAGCCTCTGATT-AGAAGAGCTTTATTTATTTTTCAAAGTTATT
* * *
5662219 GAACCTTTGATTAAAAGAGCCTT
64 GAGCCTCTGATTAAAGGAGCCTT
* * *
5662242 GTTTATTTTTCAAA-TTCATTGAA-CCTCT-ATTTAGAAGAGCTTTGTTTATTTTTCAAAGTTGT
1 ATTTATTTTTCAAAGTT-ATT-AAGCCTCTGA-TTAGAAGAGCTTTATTTATTTTTCAAAGTTAT
* * * *
5662304 TGAGTCTCTAATTAAAGGAACTTT
63 TGAGCCTCTGATTAAAGGAGCCTT
* * * * *
5662328 ATTTATTTTTCAAAGTTGTTAAGCCTTTGATTAGAGGAACCTTATTTATTTTTCAAAGTTATTGA
1 ATTTATTTTTCAAAGTTATTAAGCCTCTGATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
*
5662393 GCCTCTGATTAGAGGAGCCTT
66 GCCTCTGATTAAAGGAGCCTT
5662414 ATTTATTTTTTCAAA
1 ATTTA-TTTTTCAAA
5662429 AGTTGTGAGC
Statistics
Matches: 222, Mismatches: 40, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
85 4 0.02
86 128 0.58
87 24 0.11
88 58 0.26
89 8 0.04
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (86 bp):
ATTTATTTTTCAAAGTTATTAAGCCTCTGATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
GCCTCTGATTAAAGGAGCCTT
Found at i:5662328 original size:129 final size:131
Alignment explanation
Indices: 5662067--5662443 Score: 410
Period size: 129 Copynumber: 2.9 Consensus size: 131
5662057 TGTCAAAGAG
* * * * * * *
5662067 ATTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGATA-AACATTATTTATTTTTCAAAGTTGTT
1 ATTTATTTTTCAAAA-TTATTAAGCCTTTGATTA-AAAGAACCTTATTTATTTTTCAAAGTTATT
* * ** * *
5662131 GATCCTTTATTTAGAGGAGACATTATTTATTTTTTCAAAGTTGTTGAGCCT-TTGTTCAGAGGAG
64 GAACCTCTATTTAGAGGAG-CATTATTTATTTTTTCAAAGTTGTTGAGCCTCTAATTCAAAGGAA
5662195 CTTT
128 CTTT
* *
5662199 ATTTATTTTTCAAAATTATTGAA-CCTTTGATTAAAAGAGCCTTGTTTATTTTTCAAA-TTCATT
1 ATTTATTTTTCAAAATTATT-AAGCCTTTGATTAAAAGAACCTTATTTATTTTTCAAAGTT-ATT
* * * *
5662262 GAACCTCTATTTAGAAGAGCTTTGTTTA-TTTTTCAAAGTTGTTGAGTCTCTAATT-AAAGGAAC
64 GAACCTCTATTTAGAGGAGCATTATTTATTTTTTCAAAGTTGTTGAGCCTCTAATTCAAAGGAAC
5662325 TTT
129 TTT
* * * *
5662328 ATTTATTTTTCAAAGTTGTTAAGCCTTTGATTAGAGGAACCTTATTTATTTTTCAAAGTTATTGA
1 ATTTATTTTTCAAAATTATTAAGCCTTTGATTAAAAGAACCTTATTTATTTTTCAAAGTTATTGA
* *
5662393 GCCTCTGA-TTAGAGGAGCCTTATTTATTTTTTCAAAAGTTG-TGAGCCTCTA
66 ACCTCT-ATTTAGAGGAGCATTATTTATTTTTTC-AAAGTTGTTGAGCCTCTA
5662444 CTTATGGGAG
Statistics
Matches: 206, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
128 2 0.01
129 102 0.50
130 32 0.16
131 54 0.26
132 16 0.08
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (131 bp):
ATTTATTTTTCAAAATTATTAAGCCTTTGATTAAAAGAACCTTATTTATTTTTCAAAGTTATTGA
ACCTCTATTTAGAGGAGCATTATTTATTTTTTCAAAGTTGTTGAGCCTCTAATTCAAAGGAACTT
T
Found at i:5662510 original size:15 final size:15
Alignment explanation
Indices: 5662490--5662519 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5662480 GTCTGATTAT
5662490 GCAAAAAAAAAAAAA
1 GCAAAAAAAAAAAAA
5662505 GCAAAAAAAAAAAAA
1 GCAAAAAAAAAAAAA
5662520 AAACAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (15 bp):
GCAAAAAAAAAAAAA
Found at i:5662779 original size:20 final size:20
Alignment explanation
Indices: 5662728--5662781 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5662718 TATTCTACAA
5662728 TTTTTTTGGTTTTATTTATC
1 TTTTTTTGGTTTTATTTATC
** *
5662748 CATTTTT-ATTTTATATTA-C
1 TTTTTTTGGTTTTAT-TTATC
5662767 TTTTTTTGGTTTTAT
1 TTTTTTTGGTTTTAT
5662782 CTTTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTTTTGGTTTTATTTATC
Found at i:5664853 original size:2 final size:2
Alignment explanation
Indices: 5664846--5664886 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5664836 TAATTTTTGC
* * *
5664846 TA TA TA TA TA TA TA TA TA TA TA GA TA TA CA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5664887 CAATAGTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5665950 original size:10 final size:10
Alignment explanation
Indices: 5665935--5665960 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5665925 TAATAAAATC
5665935 TTAAAATTTA
1 TTAAAATTTA
5665945 TTAAAATTTA
1 TTAAAATTTA
5665955 TTAAAA
1 TTAAAA
5665961 AAATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:5667114 original size:11 final size:11
Alignment explanation
Indices: 5667097--5667192 Score: 55
Period size: 10 Copynumber: 9.1 Consensus size: 11
5667087 ATTTTGGAAC
5667097 ATAAAAAAATA
1 ATAAAAAAATA
*
5667108 CT-AAAAAATA
1 ATAAAAAAATA
5667118 AT--AAAAAT-
1 ATAAAAAAATA
*
5667126 ATAAAAAAGTAA
1 ATAAAAAAAT-A
*
5667138 ATAAAAAATTCA
1 ATAAAAAAAT-A
5667150 A-AAATACAAA-A
1 ATAAA-A-AAATA
*
5667161 ATACAAAAA-A
1 ATAAAAAAATA
*
5667171 ATATAAAAAT-
1 ATAAAAAAATA
5667181 ATAAAAAAATA
1 ATAAAAAAATA
5667192 A
1 A
5667193 ACTAGATTGG
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.03
9 6 0.09
10 35 0.52
11 8 0.12
12 14 0.21
13 2 0.03
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:5667115 original size:10 final size:9
Alignment explanation
Indices: 5667100--5667193 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
5667090 TTGGAACATA
5667100 AAAAAATACT
1 AAAAAATA-T
5667110 AAAAAATA-
1 AAAAAATAT
5667118 ATAAAAATAT
1 A-AAAAATAT
5667128 AAAAAAGTAAAT
1 AAAAAA-T--AT
5667140 AAAAAAT-T
1 AAAAAATAT
*
5667148 CAAAAATA-
1 AAAAAATAT
* *
5667156 CAAAAATAC
1 AAAAAATAT
5667165 AAAAAA-AT
1 AAAAAATAT
5667173 ATAAAAATAT
1 A-AAAAATAT
5667183 AAAAAA-AT
1 AAAAAATAT
5667191 AAA
1 AAA
5667194 CTAGATTGGT
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
8 23 0.32
9 27 0.38
10 13 0.18
11 1 0.01
12 8 0.11
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (9 bp):
AAAAAATAT
Found at i:5667118 original size:18 final size:17
Alignment explanation
Indices: 5667097--5667193 Score: 86
Period size: 18 Copynumber: 5.3 Consensus size: 17
5667087 ATTTTGGAAC
5667097 ATAAAAAAATACTAAAAA
1 ATAAAAAAATA-TAAAAA
5667115 ATAATAAAAATATAAAAA
1 ATAA-AAAAATATAAAAA
* *
5667133 AGTAAATAAAAAATTCAAAA
1 A-TAAA-AAAATA-TAAAAA
* *
5667153 ATACAAAAATACAAAAAA
1 ATAAAAAAATA-TAAAAA
*
5667171 ATATAAAAATATAAAAAA
1 ATAAAAAAATAT-AAAAA
5667189 ATAAA
1 ATAAA
5667194 CTAGATTGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
18 40 0.62
19 18 0.28
20 6 0.09
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (17 bp):
ATAAAAAAATATAAAAA
Found at i:5667129 original size:8 final size:8
Alignment explanation
Indices: 5667101--5667193 Score: 61
Period size: 8 Copynumber: 11.4 Consensus size: 8
5667091 TGGAACATAA
5667101 AAAAATACT
1 AAAAATA-T
5667110 AAAAAATAAT
1 -AAAAAT-AT
5667120 AAAAATAT
1 AAAAATAT
5667128 AAAAA-AGT
1 AAAAATA-T
5667136 --AAATA-
1 AAAAATAT
5667141 AAAAAT-T
1 AAAAATAT
*
5667148 CAAAAATAC
1 -AAAAATAT
*
5667157 AAAAATACAA
1 AAAAAT--AT
5667167 AAAAATAT
1 AAAAATAT
5667175 AAAAATAT
1 AAAAATAT
*
5667183 AAAAAAAT
1 AAAAATAT
5667191 AAA
1 AAA
5667194 CTAGATTGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
6 3 0.04
7 6 0.09
8 39 0.57
9 6 0.09
10 14 0.20
11 1 0.01
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (8 bp):
AAAAATAT
Found at i:5668280 original size:18 final size:18
Alignment explanation
Indices: 5668254--5668288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5668244 ATTAGCTAAT
*
5668254 TATTGTTATTTTTATTTG
1 TATTGTTATATTTATTTG
*
5668272 TATTTTTATATTTATTT
1 TATTGTTATATTTATTT
5668289 TGTAATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TATTGTTATATTTATTTG
Found at i:5668930 original size:40 final size:40
Alignment explanation
Indices: 5668864--5668948 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
5668854 TAAAATTCAA
*
5668864 GAAAAATGATATTTTTAAGATAAAAAACACAATCTTTATT
1 GAAAAATGATATTTCTAAGATAAAAAACACAATCTTTATT
* *
5668904 GAAAAGATGATATTTCTAAGAT-AAAAACATATTCTTTATT
1 GAAAA-ATGATATTTCTAAGATAAAAAACACAATCTTTATT
5668944 -AAAAA
1 GAAAAA
5668949 CATGAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.10
40 21 0.51
41 15 0.37
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (40 bp):
GAAAAATGATATTTCTAAGATAAAAAACACAATCTTTATT
Done.