Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, 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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 30
Found at i:4176305 original size:171 final size:172
Alignment explanation
Indices: 4176003--4176343 Score: 659
Period size: 170 Copynumber: 2.0 Consensus size: 172
4175993 GTATTACGAT
4176003 TTTTTGTATTATATGATGTTGATGATGATAATGAGGGTATATATACATGTATGCATTTTGTTATA
1 TTTTTGTATTATATGATGTTGATGATGATAATGAGGGTATATATACATGTATGCATTTTGTTATA
4176068 TGAAATGTTCCATGGTTTTTTTATGATTTATTGTATGAAATAATCAAGTTTTGTTAAGTATTTAA
66 TGAAATGTTCCATGGTTTTTTTATGATTTATTGTATGAAATAATCAAGTTTTGTTAAGTATTTAA
4176133 GGTTTTTATTATATAC-TT-TATGCCTCACGAAGTCAATGGA
131 GGTTTTTATTATATACTTTATATGCCTCACGAAGTCAATGGA
4176173 TTTTTGTATTATATGATGTTGATGATGATAATGAGGGTATATATACATGTATGCATTTTGTTATA
1 TTTTTGTATTATATGATGTTGATGATGATAATGAGGGTATATATACATGTATGCATTTTGTTATA
4176238 TGAAATGTTCCATGGTTTTTTTATGATATTATTGTATGAAATAATCAAGTTTTGTTAAGTATTTA
66 TGAAATGTTCCATGGTTTTTTTATGAT-TTATTGTATGAAATAATCAAGTTTTGTTAAGTATTTA
4176303 AGGTTTTTATTATATACTTTATATGCCTCACGAAGTCAATG
130 AGGTTTTTATTATATACTTTATATGCCTCACGAAGTCAATG
4176344 ACTTAGCGTT
Statistics
Matches: 168, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
170 92 0.55
171 54 0.32
172 2 0.01
173 20 0.12
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (172 bp):
TTTTTGTATTATATGATGTTGATGATGATAATGAGGGTATATATACATGTATGCATTTTGTTATA
TGAAATGTTCCATGGTTTTTTTATGATTTATTGTATGAAATAATCAAGTTTTGTTAAGTATTTAA
GGTTTTTATTATATACTTTATATGCCTCACGAAGTCAATGGA
Found at i:4179525 original size:23 final size:22
Alignment explanation
Indices: 4179491--4179623 Score: 118
Period size: 23 Copynumber: 6.2 Consensus size: 22
4179481 GAGTCGAGGG
*
4179491 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCAGTCCTTCGGGAC-A
**
4179514 TTCTACGTGGTCCTTC-GG---
1 TTCTACGCAGTCCTTCGGGACA
4179532 --CTACGCAGTCCTTCGGGACA
1 TTCTACGCAGTCCTTCGGGACA
4179552 TTTCTACGCAGTCCTTCGGGACA
1 -TTCTACGCAGTCCTTCGGGACA
*
4179575 TTTCTACACAGTCCTTCGGGACA
1 -TTCTACGCAGTCCTTCGGGACA
* ** *
4179598 -TCTATGTGGTCATTCGGGACA
1 TTCTACGCAGTCCTTCGGGACA
4179619 TTCTA
1 TTCTA
4179624 TGCGGCACTT
Statistics
Matches: 93, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.13
17 2 0.02
21 16 0.17
22 6 0.06
23 57 0.61
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (22 bp):
TTCTACGCAGTCCTTCGGGACA
Found at i:4179547 original size:39 final size:39
Alignment explanation
Indices: 4179493--4179570 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
4179483 GTCGAGGGTT
* **
4179493 CTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTCGG
1 CTACGCAGTCCTTCGGGACAATTCTACGCAGTCCTTCGG
*
4179532 CTACGCAGTCCTTCGGGACATTTCTACGCAGTCCTTCGG
1 CTACGCAGTCCTTCGGGACAATTCTACGCAGTCCTTCGG
4179571 GACATTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.14, C:0.32, G:0.26, T:0.28
Consensus pattern (39 bp):
CTACGCAGTCCTTCGGGACAATTCTACGCAGTCCTTCGG
Found at i:4179657 original size:24 final size:24
Alignment explanation
Indices: 4179625--4179673 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4179615 GACATTCTAT
*
4179625 GCGGCACTTCAGTGCAATTTTTAC
1 GCGGCACTTCAGTGCAATTTATAC
**
4179649 GCGGCACTTTGGTGCAATTTATAC
1 GCGGCACTTCAGTGCAATTTATAC
4179673 G
1 G
4179674 AGCTGTGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (24 bp):
GCGGCACTTCAGTGCAATTTATAC
Found at i:4180722 original size:57 final size:57
Alignment explanation
Indices: 4180634--4180748 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
4180624 TTTGAATACG
4180634 TAATTGTCTTATTAAGATAAATAATGTTTAGGTTGTATAATTAAATTAAAGCCTTTA
1 TAATTGTCTTATTAAGATAAATAATGTTTAGGTTGTATAATTAAATTAAAGCCTTTA
4180691 TAATTGTCTTATTAAGATAAATAATGTTTAGGTTGTATAATTAAATTAAAGCCTTTA
1 TAATTGTCTTATTAAGATAAATAATGTTTAGGTTGTATAATTAAATTAAAGCCTTTA
4180748 T
1 T
4180749 TACTGGATTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (57 bp):
TAATTGTCTTATTAAGATAAATAATGTTTAGGTTGTATAATTAAATTAAAGCCTTTA
Found at i:4180733 original size:29 final size:29
Alignment explanation
Indices: 4180644--4180734 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
4180634 TAATTGTCTT
4180644 ATTAAGATAAATAATGTTTAGGTTGTATA
1 ATTAAGATAAATAATGTTTAGGTTGTATA
*** * * *
4180673 ATTAA-ATTAAAGCCT-TTATA-ATTGTCTT
1 ATTAAGA-TAAATAATGTT-TAGGTTGTATA
4180701 ATTAAGATAAATAATGTTTAGGTTGTATA
1 ATTAAGATAAATAATGTTTAGGTTGTATA
4180730 ATTAA
1 ATTAA
4180735 ATTAAAGCCT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
28 20 0.44
29 25 0.56
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (29 bp):
ATTAAGATAAATAATGTTTAGGTTGTATA
Found at i:4183247 original size:21 final size:22
Alignment explanation
Indices: 4183223--4183274 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
4183213 TTTCTACGCA
*
4183223 GTCCTTCGGGACA-TCTATGTG
1 GTCCTTCAGGACATTCTATGTG
*
4183244 GTCCTTCAGGATATTCTATGTG
1 GTCCTTCAGGACATTCTATGTG
4183266 G-CACTTCAG
1 GTC-CTTCAG
4183275 TGCAATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (22 bp):
GTCCTTCAGGACATTCTATGTG
Found at i:4183290 original size:24 final size:24
Alignment explanation
Indices: 4183257--4183306 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
4183247 CTTCAGGATA
*
4183257 TTCTATGTGGCACTTCAGTGCAAT
1 TTCTACGTGGCACTTCAGTGCAAT
*
4183281 TTCTACGTGGCACTTCGGTGCAAT
1 TTCTACGTGGCACTTCAGTGCAAT
4183305 TT
1 TT
4183307 ATACAAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (24 bp):
TTCTACGTGGCACTTCAGTGCAAT
Found at i:4186537 original size:44 final size:44
Alignment explanation
Indices: 4186486--4186575 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
4186476 TATGTGATAT
* * *
4186486 ATGATCTATGTGAACATATGAGA-ACAAGATATGAGCTATGTGAC
1 ATGATCTATATGAACATATGA-ATACAAGATATAAGCTAGGTGAC
** *
4186530 ATGATCTATATGATTATATGAATATAAGATATAAGCTAGGTGAC
1 ATGATCTATATGAACATATGAATACAAGATATAAGCTAGGTGAC
4186574 AT
1 AT
4186576 AACCTACGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.03
44 38 0.97
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (44 bp):
ATGATCTATATGAACATATGAATACAAGATATAAGCTAGGTGAC
Found at i:4186724 original size:23 final size:22
Alignment explanation
Indices: 4186692--4186788 Score: 88
Period size: 23 Copynumber: 4.4 Consensus size: 22
4186682 GAGTCGAGGG
*
4186692 TTCTACGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGAC-A
* *
4186715 TTCTATGTGGTCATTCAGGACA
1 TTCTATGTGGTCCTTCGGGACA
* * * *
4186737 TTTCTACGCGGTCTTTTGGGACA
1 -TTCTATGTGGTCCTTCGGGACA
*
4186760 -TCTATGTGGTCCTTTGGGACA
1 TTCTATGTGGTCCTTCGGGACA
*
4186781 CTCTATGT
1 TTCTATGT
4186789 TGCACTTCGG
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
21 18 0.30
22 8 0.13
23 35 0.57
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (22 bp):
TTCTATGTGGTCCTTCGGGACA
Found at i:4190799 original size:24 final size:24
Alignment explanation
Indices: 4190744--4190820 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
4190734 CGATCTTGTT
* *
4190744 TTAGTGCATTCATACACT-TCTATA
1 TTAGTGCATTCGTGCACTCTC-ATA
* * * **
4190768 TCAATGCATTTGTGCACTCTTGTA
1 TTAGTGCATTCGTGCACTCTCATA
4190792 TTAGTGCATTCGTGCACTCTCATA
1 TTAGTGCATTCGTGCACTCTCATA
4190816 TTAGT
1 TTAGT
4190821 ATCATTGTGT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (24 bp):
TTAGTGCATTCGTGCACTCTCATA
Found at i:4196917 original size:12 final size:12
Alignment explanation
Indices: 4196902--4196947 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
4196892 CGGTTTTTTT
*
4196902 ACCGGATAAAAA
1 ACCGGTTAAAAA
4196914 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
4196929 ACCGGTTAAAAA
1 ACCGGTTAAAAA
4196941 ACCGGTT
1 ACCGGTT
4196948 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:4196929 original size:15 final size:13
Alignment explanation
Indices: 4196908--4196948 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
4196898 TTTTACCGGA
4196908 TAAAAAACCGGTT
1 TAAAAAACCGGTT
4196921 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
4196935 TAAAAAACCGGTT
1 TAAAAAACCGGTT
4196948 T
1 T
4196949 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:4199255 original size:21 final size:21
Alignment explanation
Indices: 4199231--4199270 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4199221 TTTATTTTAT
4199231 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
4199252 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
4199271 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:4199318 original size:33 final size:33
Alignment explanation
Indices: 4199265--4199363 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
4199255 TTTGTTTCAA
4199265 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4199297 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
4199330 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4199363 T
1 T
4199364 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:4199392 original size:13 final size:13
Alignment explanation
Indices: 4199349--4199403 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4199339 TTGGAAGTAT
4199349 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
4199362 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
4199376 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
4199389 TTAAGTATTTGAA
1 TTAAGTATTTCAA
4199402 TT
1 TT
4199404 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:4199785 original size:15 final size:15
Alignment explanation
Indices: 4199733--4199785 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
4199723 ATCTGGAATA
4199733 TTAAAATCGATTTTT
1 TTAAAATCGATTTTT
* *
4199748 TTATAACCGATTTTT
1 TTAAAATCGATTTTT
* *
4199763 TAAAAAAATCGGTTTTT
1 T--TAAAATCGATTTTT
4199780 TTAAAA
1 TTAAAA
4199786 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 18 0.62
17 11 0.38
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (15 bp):
TTAAAATCGATTTTT
Found at i:4199905 original size:15 final size:17
Alignment explanation
Indices: 4199879--4199910 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4199869 TTCTATGGGA
4199879 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
4199895 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
4199911 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:4200464 original size:15 final size:15
Alignment explanation
Indices: 4200446--4200498 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
4200436 CCGGTTTCGG
*
4200446 TTTTAAAAAAACCGA
1 TTTTAAAAAAATCGA
* *
4200461 TTTTTTTAAAAAATCGG
1 --TTTTAAAAAAATCGA
*
4200478 TTATAAAAAAATCGA
1 TTTTAAAAAAATCGA
4200493 TTTTAA
1 TTTTAA
4200499 TATTCCAGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 17 0.59
17 12 0.41
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (15 bp):
TTTTAAAAAAATCGA
Found at i:4200849 original size:13 final size:13
Alignment explanation
Indices: 4200828--4200882 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4200818 AAGTTCGATA
*
4200828 AATTCAAATACTT
1 AATTGAAATACTT
4200841 AATTGAAATACTT
1 AATTGAAATACTT
* *
4200854 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
4200868 AATTGAAATACTT
1 AATTGAAATACTT
4200881 AA
1 AA
4200883 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:4200964 original size:32 final size:33
Alignment explanation
Indices: 4200868--4200966 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
4200858 AACTCAACAT
* * *
4200868 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4200901 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4200934 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4200966 A
1 A
4200967 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:4200985 original size:21 final size:21
Alignment explanation
Indices: 4200961--4201000 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4200951 ACTTCAAGTT
4200961 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
4200982 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
4201001 AAAAATAAAC
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:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:4201008 original size:21 final size:21
Alignment explanation
Indices: 4200963--4201008 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4200953 TTCAAGTTCG
* **
4200963 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTTAAAA
*
4200984 ATAATTGAAATAAAGTTAAAA
1 ATAATTGAAACAAAGTTAAAA
4201005 ATAA
1 ATAA
4201009 ACTACATTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTAAAA
Found at i:4203310 original size:12 final size:12
Alignment explanation
Indices: 4203293--4203338 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
4203283 TTCGGATAAA
4203293 AACCGGTTTTTT
1 AACCGGTTTTTT
4203305 AACCGGTTTTTTT
1 AACCGG-TTTTTT
4203318 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
4203332 ATCCGGT
1 AACCGGT
4203339 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:4203323 original size:15 final size:14
Alignment explanation
Indices: 4203292--4203331 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
4203282 TTTCGGATAA
4203292 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
4203305 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
4203318 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
4203332 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:4208925 original size:39 final size:39
Alignment explanation
Indices: 4208864--4209031 Score: 169
Period size: 39 Copynumber: 4.3 Consensus size: 39
4208854 AGGGCTTACG
* * *
4208864 GTAAGGACTTATCCTTG-ACACAAAGTAGAAGAGCCTGCA
1 GTAAGGACTTA-CCTTGTGCACAAAGCAGAGGAGCCTGCA
* * * *
4208903 ATAAGAACTTACCTTGTGCACAAAGTAGAGGAGCATGCA
1 GTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCCTGCA
* * * *
4208942 GTAAGGACTTGCC-CGATGCACAAAGCAGAGGAGCCTACG
1 GTAAGGACTTACCTTG-TGCACAAAGCAGAGGAGCCTGCA
* * *
4208981 GTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCTTACA
1 GTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCCTGCA
*
4209020 GTAAGGTCTTAC
1 GTAAGGACTTAC
4209032 AAGTCATAGA
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
38 6 0.06
39 101 0.94
40 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (39 bp):
GTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCCTGCA
Found at i:4208977 original size:78 final size:78
Alignment explanation
Indices: 4208882--4209025 Score: 198
Period size: 78 Copynumber: 1.8 Consensus size: 78
4208872 TTATCCTTGA
* * * * *
4208882 CACAAAGTAGAAGAGCCTGCAATAAGAACTTACCTTGTGCACAAAGTAGAGGAGCATGCAGTAAG
1 CACAAAGCAGAAGAGCCTACAATAAGAACTTACCCTGTGCACAAAGCAGAGGAGCATACAGTAAG
4208947 GACTTGCCCGATG
66 GACTTGCCCGATG
* ** * *
4208960 CACAAAGCAGAGGAGCCTACGGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCTTACAGTAAG
1 CACAAAGCAGAAGAGCCTACAATAAGAACTTACCCTGTGCACAAAGCAGAGGAGCATACAGTAAG
4209025 G
66 G
4209026 TCTTACAAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (78 bp):
CACAAAGCAGAAGAGCCTACAATAAGAACTTACCCTGTGCACAAAGCAGAGGAGCATACAGTAAG
GACTTGCCCGATG
Found at i:4209811 original size:24 final size:24
Alignment explanation
Indices: 4209784--4209832 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4209774 GACTCGACCA
* *
4209784 ATTCAATTCAGTTGGACCGGTCTG
1 ATTCAATTAAATTGGACCGGTCTG
*
4209808 ATTCAATTAAATTGGGCCGGTCTG
1 ATTCAATTAAATTGGACCGGTCTG
4209832 A
1 A
4209833 CTGGCCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
ATTCAATTAAATTGGACCGGTCTG
Found at i:4211655 original size:54 final size:54
Alignment explanation
Indices: 4211535--4211965 Score: 596
Period size: 54 Copynumber: 8.0 Consensus size: 54
4211525 TTGCACCCGT
* * * * * ***
4211535 AGTGCCAATACAGTAATTCACAAAGTTATTATGAATTACGTGGGGTTGCACAC-C
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAAGTTGCACACAC
* *
4211589 TAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACAC
1 -AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* *
4211644 AGTGCCAATACGGAAATTCATAAACTCATTTTGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* * * *
4211698 AGTGCCAATATGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* * *
4211752 AGTGTCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* *
4211806 AGTGCCAATACGGAAATTCATAAAGTTATTATGAATTTCTTAATTTGCACACAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* * *
4211860 AGTGCCAATACAGAAATTCATAAACTTTTTATGAATTTCTTAAGTTGCAC-CAT
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
* *
4211913 AGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACA
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACA
4211966 TAGTATTGAT
Statistics
Matches: 341, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
53 50 0.15
54 257 0.75
55 34 0.10
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (54 bp):
AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
Found at i:4214644 original size:23 final size:23
Alignment explanation
Indices: 4214614--4214669 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
4214604 TAAATGCACC
4214614 GAAGTGCCATGTAGAATTGAACT
1 GAAGTGCCATGTAGAATTGAACT
** * *
4214637 GAAGTGCCGCGTATAATTGCACT
1 GAAGTGCCATGTAGAATTGAACT
*
4214660 GTAGTGCCAT
1 GAAGTGCCAT
4214670 ATAAGATTGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (23 bp):
GAAGTGCCATGTAGAATTGAACT
Found at i:4219866 original size:54 final size:54
Alignment explanation
Indices: 4219744--4220441 Score: 967
Period size: 54 Copynumber: 12.9 Consensus size: 54
4219734 ACTCGTAGCA
* * ***
4219744 CCAATAC-AATAATTCATAAACTCATTGTGAATTATGTGGGGTTGCACAC-CTAGTG
1 CCAATACGAA-AATTCATAAACTCATTATGAATT-TCTTAAGTTGCACACAC-AGTG
* *
4219799 CTAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* * * *
4219853 CCAAAACGAAAATTCATAAACTTATTATGAATTTCTTAGGCTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
*
4219907 CCAATAC-ATAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
*
4219961 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
4220015 CCAATAC-ATAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
*
4220069 CCAATAC-AGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACACACAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
*
4220123 CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* * * * *
4220177 ACAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGTACACATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* *
4220231 CTAATATGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* * ** * * *
4220285 GCAATAC-AGAAATTCATAAAGTTGTTATGAATTTCTTAAGTTGTATAAACAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* *
4220339 CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
* * * * *
4220393 TCAATACGGAAATTCATAAACTTATTTTGAATTTCTTAGGTTGCACACA
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACA
4220442 TAGTACTGAT
Statistics
Matches: 580, Mismatches: 55, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
53 3 0.01
54 546 0.94
55 30 0.05
56 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
CCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
Found at i:4221528 original size:23 final size:23
Alignment explanation
Indices: 4221510--4221570 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
4221500 CTCGTATAAA
4221510 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
4221533 TGCACCGAAGTGCCGA-GTAGAAT
1 TGCACCGAAGTGCC-ACGTAGAAT
*
4221556 TGCACCGAGGTGCCA
1 TGCACCGAAGTGCCA
4221571 TATAAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:4228594 original size:3 final size:3
Alignment explanation
Indices: 4228564--4228654 Score: 76
Period size: 3 Copynumber: 29.7 Consensus size: 3
4228554 TTCATTTAAA
* * * *
4228564 TAT TAT T-T ATAT TAT AAT TAT AAT TAT TAT TAT TAT AAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4228609 TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
4228655 CAAGCCCAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 1 0.01
3 62 0.90
4 6 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:4228632 original size:22 final size:22
Alignment explanation
Indices: 4228591--4228655 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
4228581 TTATAATTAT
*
4228591 TATTATTATAATTATAATTACTAA
1 TATTATTAT--TTATTATTACTAA
* *
4228615 TATTATTATTTATTATTAATAT
1 TATTATTATTTATTATTACTAA
**
4228637 TATTATTAAATATTATTAC
1 TATTATTATTTATTATTAC
4228656 AAGCCCAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 26 0.74
24 9 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATTATTTATTATTACTAA
Found at i:4230812 original size:19 final size:18
Alignment explanation
Indices: 4230790--4230840 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
4230780 TATTTTTTTA
4230790 TATTATTTATATTTCATTT
1 TATTATTTAT-TTTCATTT
**
4230809 TATTGCAAGTATTTT-ATTT
1 TATT--ATTTATTTTCATTT
4230828 TATTATTTATTTT
1 TATTATTTATTTT
4230841 TCTGTCAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.27
19 12 0.46
20 3 0.12
21 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTATTTATTTTCATTT
Found at i:4241479 original size:10 final size:10
Alignment explanation
Indices: 4241455--4241541 Score: 101
Period size: 10 Copynumber: 8.8 Consensus size: 10
4241445 ATTATGCTTG
4241455 AAGAAAAAAA
1 AAGAAAAAAA
4241465 GAA-AAAAGAAA
1 -AAGAAAA-AAA
4241476 AA-AAAGAAAA
1 AAGAAA-AAAA
4241486 AAGAAAAAAA
1 AAGAAAAAAA
4241496 AAG-AAAAAA
1 AAGAAAAAAA
4241505 AA-AAAAAAA
1 AAGAAAAAAA
4241514 AAGAAAAAAA
1 AAGAAAAAAA
* *
4241524 GAGAAAAAAG
1 AAGAAAAAAA
4241534 AAGAAAAA
1 AAGAAAAA
4241542 GGGGGGGTCA
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
9 16 0.24
10 43 0.63
11 9 0.13
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:4241541 original size:1 final size:1
Alignment explanation
Indices: 4241458--4241523 Score: 78
Period size: 1 Copynumber: 66.0 Consensus size: 1
4241448 ATGCTTGAAG
* * * * * *
4241458 AAAAAAAGAAAAAAGAAAAAAAAGAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4241523 A
1 A
4241524 GAGAAAAAAG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:4241542 original size:9 final size:9
Alignment explanation
Indices: 4241458--4241541 Score: 111
Period size: 9 Copynumber: 9.4 Consensus size: 9
4241448 ATGCTTGAAG
4241458 AAAAAAAG-
1 AAAAAAAGA
4241466 -AAAAAAGA
1 AAAAAAAGA
4241474 AAAAAAAGA
1 AAAAAAAGA
*
4241483 AAAAAGA-A
1 AAAAAAAGA
4241491 AAAAAAAGA
1 AAAAAAAGA
*
4241500 AAAAAAAAA
1 AAAAAAAGA
4241509 AAAAAAAGA
1 AAAAAAAGA
4241518 AAAAAAGAGA
1 AAAAAA-AGA
4241528 AAAAAGAAGA
1 AAAAA-AAGA
4241538 AAAA
1 AAAA
4241542 GGGGGGGTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
7 7 0.10
8 7 0.10
9 37 0.55
10 15 0.22
11 1 0.01
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:4242789 original size:83 final size:83
Alignment explanation
Indices: 4242687--4243864 Score: 2122
Period size: 83 Copynumber: 14.2 Consensus size: 83
4242677 ACTGGAACAA
*
4242687 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4242752 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
* *
4242770 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* * *
4242835 AATCATTGAAATTGAAGG
66 AGTCATTGAATTTGAAAG
4242853 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4242918 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
4242936 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243001 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
4243019 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243084 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
4243102 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* *
4243167 AATCATTGAATTTCAAAG
66 AGTCATTGAATTTGAAAG
4243185 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243250 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
4243268 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243333 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
*
4243351 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243416 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
* *
4243434 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* * *
4243499 AATCATTGAAATTGAAGG
66 AGTCATTGAATTTGAAAG
* * *
4243517 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACT
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* * *
4243582 AATCATTGAAATTGAAGG
66 AGTCATTGAATTTGAAAG
4243600 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* *
4243665 AATCATTAAATTTGAAAG
66 AGTCATTGAATTTGAAAG
*
4243683 ATGAATGTGCTCATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
4243748 AGTCATTGAATTTGAAAG
66 AGTCATTGAATTTGAAAG
4243766 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* *
4243831 AATCATTGAATTTAAAAG
66 AGTCATTGAATTTGAAAG
*
4243849 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
4243865 TAGAAATAAG
Statistics
Matches: 1059, Mismatches: 36, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 1059 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
AGTCATTGAATTTGAAAG
Found at i:4244981 original size:113 final size:113
Alignment explanation
Indices: 4244657--4245420 Score: 1032
Period size: 113 Copynumber: 6.8 Consensus size: 113
4244647 GCAAAGATTT
* * ***
4244657 AAATCCATCA-TTCAATGGATCAACTTTTCCAGTTCAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
4244721 GAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
4244770 AAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAA--CG-AG----CATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
4244828 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCCC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
4244876 AAATCCATCACTTGATGGATTAGCTTTTCTAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
4244941 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
4244989 AAATACATCACTTGATGGATCCGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
4245054 AAGGATGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
4245102 AAATCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
4245167 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * * *
4245215 GAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCCTAATGAGAAGAACTCATCATCT
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCT
*
4245279 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
4245331 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---G
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
4245393 AA-GAAGAAGAAGTTCATAATGAGAAGAA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAA
4245421 CTAATCTGAA
Statistics
Matches: 573, Mismatches: 65, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
106 95 0.17
108 1 0.00
109 28 0.05
110 5 0.01
111 1 0.00
112 1 0.00
113 339 0.59
114 3 0.01
115 1 0.00
116 98 0.17
117 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:4245413 original size:36 final size:36
Alignment explanation
Indices: 4245366--4245444 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
4245356 TTTCCAGAGA
* *
4245366 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
4245402 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
4245438 AAGTTCA
1 AAGTTCA
4245445 CCATGAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
Found at i:4245710 original size:3 final size:3
Alignment explanation
Indices: 4245695--4245791 Score: 106
Period size: 3 Copynumber: 31.7 Consensus size: 3
4245685 TTCATTTAAA
*
4245695 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
4245740 TAT AAT TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT
4245787 TAT TA
1 TAT TA
4245792 CAAGCCCAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.01
3 72 0.91
4 6 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:4249223 original size:39 final size:39
Alignment explanation
Indices: 4249161--4249277 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
4249151 TAAGGGCATG
* * *
4249161 TGGTAAGGACTTACCCTGGGCACAAAGAAGAGGAGTCTA
1 TGGTAAGGACTTACCTTGTGCACAAAGAAGAGGAGCCTA
* *
4249200 TGGTAAGGACTTACCTTGTGCACAATGCAGAGGAGCCTA
1 TGGTAAGGACTTACCTTGTGCACAAAGAAGAGGAGCCTA
* * * * *
4249239 CGATAAGAACTT-CCTTTGTGAACAAAGAAGAAGAGCCTA
1 TGGTAAGGACTTACC-TTGTGCACAAAGAAGAGGAGCCTA
4249278 CAGTAAGGTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 2 0.03
39 63 0.97
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (39 bp):
TGGTAAGGACTTACCTTGTGCACAAAGAAGAGGAGCCTA
Found at i:4250643 original size:34 final size:32
Alignment explanation
Indices: 4250590--4250659 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
4250580 CCTTACAAAC
*
4250590 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
4250622 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
4250656 TCCC
1 TCCC
4250660 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:4250898 original size:20 final size:21
Alignment explanation
Indices: 4250873--4250911 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4250863 AGTCGTATAT
4250873 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGGGATGATTTTGG
4250893 AGCCGTTGGGGATGATTTT
1 AGCCGTTGGGGATGATTTT
4250912 TATACTCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.13, C:0.10, G:0.41, T:0.36
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTGG
Found at i:4251048 original size:29 final size:31
Alignment explanation
Indices: 4251016--4251075 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4251006 AAATTTTGAA
*
4251016 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
4251045 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
4251076 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:4251570 original size:22 final size:21
Alignment explanation
Indices: 4251545--4251599 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
4251535 ATACTAACTT
*
4251545 ATTAAATATATTTTATTATTAA
1 ATTAAATATATTTTAAT-TTAA
4251567 ATT-AAT-TATTTTAATTTAA
1 ATTAAATATATTTTAATTTAA
*
4251586 ATTTAAAAATATTT
1 A-TTAAATATATTT
4251600 ATTTTATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 5 0.18
20 10 0.36
21 5 0.18
22 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAAATATATTTTAATTTAA
Found at i:4256081 original size:60 final size:59
Alignment explanation
Indices: 4256016--4256186 Score: 202
Period size: 60 Copynumber: 2.8 Consensus size: 59
4256006 ATAGTCTCCG
* * * *
4256016 ACTATATGATATTGTTTTATT-AGGTCCCTTGATTATT-AAAGTTACAAAAATGGCCCCTCA
1 ACTATATGA-ATTGCTTTATTGA-GTCCCTCGACTATTAAAAGTTAC-AAAATGACCCCTCA
* *
4256076 ACTATATGGAGTTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGACCCCTCA
1 ACTATAT-GAATTGCTTTATTGAGTCCCTCGACTATTAAAAGTTACAAAATGACCCCTCA
* * *
4256136 ACTATATGGAGTTGCTTTGTTGAGTCACTCGACTATTAAAAGTTACAAAAT
1 ACTATAT-GAATTGCTTTATTGAGTCCCTCGACTATTAAAAGTTACAAAAT
4256187 TATCACTTGA
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
60 90 0.89
61 11 0.11
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (59 bp):
ACTATATGAATTGCTTTATTGAGTCCCTCGACTATTAAAAGTTACAAAATGACCCCTCA
Found at i:4256111 original size:31 final size:31
Alignment explanation
Indices: 4256070--4256171 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 31
4256060 CAAAAATGGC
4256070 CCCTCAACTATATGGAGTTGCTTTGTTGAGT
1 CCCTCAACTATATGGAGTTGCTTTGTTGAGT
* ** * **** *
4256101 CCCTCGACTAT-TAAAAGTTAC-AAAATGA-C
1 CCCTCAACTATAT-GGAGTTGCTTTGTTGAGT
4256130 CCCTCAACTATATGGAGTTGCTTTGTTGAGT
1 CCCTCAACTATATGGAGTTGCTTTGTTGAGT
* *
4256161 CACTCGACTAT
1 CCCTCAACTAT
4256172 TAAAAGTTAC
Statistics
Matches: 47, Mismatches: 20, Indels: 8
0.63 0.27 0.11
Matches are distributed among these distances:
29 15 0.32
30 8 0.17
31 24 0.51
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (31 bp):
CCCTCAACTATATGGAGTTGCTTTGTTGAGT
Found at i:4256200 original size:60 final size:60
Alignment explanation
Indices: 4256049--4256186 Score: 224
Period size: 60 Copynumber: 2.3 Consensus size: 60
4256039 GTCCCTTGAT
* * *
4256049 TATT-AAAGTTACAAAAATGGCCCCTCAACTATATGGAGTTGCTTTGTTGAGTCCCTCGAC
1 TATTAAAAGTTAC-AAAATGACCACTCAACTATATGGAGTTGCTTTGTTGAGTCACTCGAC
*
4256109 TATTAAAAGTTACAAAATGACCCCTCAACTATATGGAGTTGCTTTGTTGAGTCACTCGAC
1 TATTAAAAGTTACAAAATGACCACTCAACTATATGGAGTTGCTTTGTTGAGTCACTCGAC
4256169 TATTAAAAGTTACAAAAT
1 TATTAAAAGTTACAAAAT
4256187 TATCACTTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
60 67 0.89
61 8 0.11
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (60 bp):
TATTAAAAGTTACAAAATGACCACTCAACTATATGGAGTTGCTTTGTTGAGTCACTCGAC
Found at i:4256537 original size:59 final size:61
Alignment explanation
Indices: 4256388--4256537 Score: 159
Period size: 59 Copynumber: 2.5 Consensus size: 61
4256378 TTGGAACATA
* *
4256388 ATGA-ATAGTCAAGAGACCATTTTGTAACTTTTAATAGTTAAGGGACTCAACAAAGTAACT
1 ATGATATAGTCAAGGGACCATTTTGTAACTTTTAATAGTTAAGGGACTCAACAAAGCAACT
** * * *
4256448 -TCCTATAGTC-GGAGGACCATTTTGTAACTTTTAATAGTT-AGGGACTTAATAAAGCAA-T
1 ATGATATAGTCAAG-GGACCATTTTGTAACTTTTAATAGTTAAGGGACTCAACAAAGCAACT
* *
4256506 ATGATATAGTCATGGGACAATTTATGT-ACTTT
1 ATGATATAGTCAAGGGACCATTT-TGTAACTTT
4256538 ACCCTATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
58 1 0.01
59 38 0.51
60 35 0.47
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (61 bp):
ATGATATAGTCAAGGGACCATTTTGTAACTTTTAATAGTTAAGGGACTCAACAAAGCAACT
Found at i:4257715 original size:83 final size:83
Alignment explanation
Indices: 4257571--4257732 Score: 261
Period size: 83 Copynumber: 2.0 Consensus size: 83
4257561 AAATTTCGAT
* * * *
4257571 AGAGTTTTACTCCATCTAAATCTCTTTTAGTATCTAAATTTAAAAAGATAATAATATCTTTTAAA
1 AGAGATTTACTCCAACCAAATCTCTTTTAATATCTAAATTTAAAAAGATAATAATATCTTTTAAA
*
4257636 TTTAAAATATTAAATATG
66 TATAAAATATTAAATATG
* *
4257654 AGAGATTTACTCCAACCAAATGTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
1 AGAGATTTACTCCAACCAAATCTCTTTTAATATCTAAATTTAAAAAGATAATAATATCTTTTAAA
4257719 TATAAAATATTAAA
66 TATAAAATATTAAA
4257733 CAGGTATACA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (83 bp):
AGAGATTTACTCCAACCAAATCTCTTTTAATATCTAAATTTAAAAAGATAATAATATCTTTTAAA
TATAAAATATTAAATATG
Found at i:4262789 original size:6 final size:6
Alignment explanation
Indices: 4262780--4262811 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4262770 TAAAGATGTT
4262780 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
4262812 GATGACCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:4263106 original size:15 final size:16
Alignment explanation
Indices: 4263086--4263118 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4263076 GATAACTTCT
*
4263086 AACTCTT-TTGATTTA
1 AACTCTTATTCATTTA
4263101 AACTCTTATTCATTTA
1 AACTCTTATTCATTTA
4263117 AA
1 AA
4263119 GAGTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (16 bp):
AACTCTTATTCATTTA
Found at i:4268313 original size:22 final size:21
Alignment explanation
Indices: 4268288--4268335 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
4268278 TTCCAGAATG
4268288 CTACAGGGGTA-TCGATACCCTA
1 CTACA-GGGTACT-GATACCCTA
*
4268310 CTACAGTGTACTGATACCCTA
1 CTACAGGGTACTGATACCCTA
4268331 CTACA
1 CTACA
4268336 TTAATTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
CTACAGGGTACTGATACCCTA
Found at i:4275493 original size:229 final size:227
Alignment explanation
Indices: 4275088--4275536 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
4275078 GTAAATTATC
* * *
4275088 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
4275153 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
4275218 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
4275283 GAAACATAAA-TACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
4275316 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
4275381 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
4275446 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
4275511 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
4275537 GCAGTTATAA
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 58 0.28
229 152 0.72
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:4275625 original size:20 final size:19
Alignment explanation
Indices: 4275602--4275647 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
4275592 CGATATACCA
4275602 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
4275622 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
4275642 GGTAAA
1 GGTAAA
4275648 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:4275792 original size:20 final size:19
Alignment explanation
Indices: 4275769--4275815 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4275759 CGATATAACA
4275769 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
4275789 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
4275809 GGTAAAA
1 GGTAAAA
4275816 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:4275817 original size:17 final size:19
Alignment explanation
Indices: 4275778--4275820 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4275768 AGGTAAAAAT
4275778 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
4275798 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
4275815 ATGATA
1 ATGATA
4275821 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:4278094 original size:21 final size:21
Alignment explanation
Indices: 4278047--4278111 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
4278037 AAGACAATCA
* * *
4278047 AGAGTTGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
4278069 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
4278089 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
4278110 AG
1 AG
4278112 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:4278187 original size:33 final size:33
Alignment explanation
Indices: 4278145--4278210 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4278135 AAATAGATTG
*
4278145 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
4278178 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
4278211 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:4279231 original size:197 final size:197
Alignment explanation
Indices: 4278634--4279694 Score: 2041
Period size: 197 Copynumber: 5.4 Consensus size: 197
4278624 ATATTCCAAG
4278634 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4278699 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
66 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
*
4278764 AAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
131 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
4278829 AC
196 AC
*
4278831 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTACTATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
4278896 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
66 GTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
4278961 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
130 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
4279026 AAC
195 AAC
4279029 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4279094 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
66 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
*
4279159 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGTAATATGTAATTTTTCAATCTA
131 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
4279224 AC
196 AC
4279226 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4279291 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
66 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
*
4279356 AAAAAGTGTCGATCCCAAAATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTA
131 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
4279421 AC
196 AC
4279423 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
* *
4279488 GTGTCGATATTTTTTTTCCATAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
66 GTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
4279553 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
130 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
4279618 AAC
195 AAC
4279621 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4279686 GTGTCGATA
66 GTGTCGATA
4279695 CTAATTTAAA
Statistics
Matches: 851, Mismatches: 11, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
197 463 0.54
198 388 0.46
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
AC
Found at i:4279515 original size:395 final size:395
Alignment explanation
Indices: 4278634--4279694 Score: 2043
Period size: 395 Copynumber: 2.7 Consensus size: 395
4278624 ATATTCCAAG
4278634 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4278699 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
66 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
*
4278764 AAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
131 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
*
4278829 ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTACTATAGT
196 ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
*
4278894 TTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATA
261 TTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATA
4278959 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
326 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
4279024 CTAAC
391 CTAAC
4279029 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
4279094 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
66 GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
*
4279159 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGTAATATGTAATTTTTCAATCTA
131 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
4279224 ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
196 ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
4279289 TTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATA
261 TTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATA
*
4279353 TATAAAAAGTGTCGATCCCAAAATCATCGAACCTAAAAGTATAATGTAATATGTAATTTTTCAAT
326 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
4279418 CTAAC
391 CTAAC
4279423 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
1 CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
* *
4279488 GTGTCGATATTTTTTTTCCATAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
66 GTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATA
4279553 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
130 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT
4279618 AACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAG
195 AACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAG
4279683 TTTGTGTCGATA
260 TTTGTGTCGATA
4279695 CTAATTTAAA
Statistics
Matches: 657, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
394 195 0.30
395 462 0.70
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (395 bp):
CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATATAT
AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
ACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
TTGTGTCGATATTTTATTTCCAGAATGAATGGAAAACAGGGTGCACCATAAAGTGTCGATCCATA
TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
CTAAC
Found at i:4281174 original size:18 final size:18
Alignment explanation
Indices: 4281153--4281214 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
4281143 AGCGGTCGTA
4281153 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
4281171 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
4281189 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
4281207 GAAGATGA
1 GAAGATGA
4281215 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:4281177 original size:6 final size:6
Alignment explanation
Indices: 4281153--4281238 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
4281143 AGCGGTCGTA
* * * * * *
4281153 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
4281201 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
4281239 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:4281188 original size:3 final size:3
Alignment explanation
Indices: 4281168--4281242 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
4281158 TGAAGCTGAC
* * * * * ** *
4281168 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
4281216 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
4281243 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:4281207 original size:36 final size:36
Alignment explanation
Indices: 4281156--4281234 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
4281146 GGTCGTAGAA
*
4281156 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
4281192 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
4281228 GATGAAG
1 GATGAAG
4281235 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:4281242 original size:12 final size:12
Alignment explanation
Indices: 4281156--4281238 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
4281146 GGTCGTAGAA
*
4281156 GATGAAGCTGAC
1 GATGAAGATGAC
4281168 GATGAAGATGAC
1 GATGAAGATGAC
*
4281180 GATGATGATGAC
1 GATGAAGATGAC
* *
4281192 GATGAAGCTGGC
1 GATGAAGATGAC
*
4281204 GATGAAGATGAT
1 GATGAAGATGAC
* * *
4281216 GACGATGATGAT
1 GATGAAGATGAC
4281228 GATGAAGATGA
1 GATGAAGATGA
4281239 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:4283019 original size:183 final size:183
Alignment explanation
Indices: 4282711--4283478 Score: 1432
Period size: 183 Copynumber: 4.2 Consensus size: 183
4282701 CTTTCAACAT
** * * * * * *
4282711 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
4282776 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
4282841 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
4282894 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTTTAT-ACGCGAAT
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGA-GCGAAT
4282958 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAA
65 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAA
4283023 AAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
130 AAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
4283077 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
4283142 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
4283207 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
4283259 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
4283324 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
4283389 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
4283442 ATTATAATGTAATAGATAATTTTGTAATATAACAGGT
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGT
4283479 GAACAGAAGA
Statistics
Matches: 574, Mismatches: 8, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
182 182 0.32
183 391 0.68
184 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:4283382 original size:365 final size:366
Alignment explanation
Indices: 4282711--4283478 Score: 1432
Period size: 365 Copynumber: 2.1 Consensus size: 366
4282701 CTTTCAACAT
** * * * * * *
4282711 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
4282776 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
4282841 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
*
4282906 TAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTTTATACGCGAATAGGTCTACAACCT
196 TAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATACGCGAATAGGTCTACAACCT
4282971 ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
261 ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
4283036 CGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
326 CGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
4283077 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
4283142 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
4283207 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
4283271 TAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGA-GCGAATAGGTCTACAACC
196 TAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTAT-ACGCGAATAGGTCTACAACC
4283335 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
260 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
4283400 ACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
325 ACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
4283442 ATTATAATGTAATAGATAATTTTGTAATATAACAGGT
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGT
4283479 GAACAGAAGA
Statistics
Matches: 392, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
365 251 0.64
366 141 0.36
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (366 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
TAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATACGCGAATAGGTCTACAACCT
ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
CGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:4283819 original size:28 final size:23
Alignment explanation
Indices: 4283763--4283816 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
4283753 TAACTACAAG
*
4283763 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCGTT
*
4283786 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGTT
4283809 TATATAAT
1 TATATAAT
4283817 ATATTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGTT
Found at i:4284269 original size:18 final size:18
Alignment explanation
Indices: 4284248--4284284 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4284238 GTAATTGGAG
4284248 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
4284266 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
4284284 T
1 T
4284285 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:4284292 original size:24 final size:24
Alignment explanation
Indices: 4284240--4284286 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4284230 TTTCATATGT
* *
4284240 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
4284264 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
4284287 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:4284584 original size:39 final size:39
Alignment explanation
Indices: 4284541--4284627 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
4284531 TCCGATGCTC
*
4284541 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
4284580 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
4284619 ATCAAAATC
1 ATCAAAATC
4284628 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:4285081 original size:23 final size:23
Alignment explanation
Indices: 4285050--4285122 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
4285040 ATAGGTAAAA
*
4285050 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
4285073 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
4285096 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
4285119 ATAT
1 ATAT
4285123 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4285515 original size:23 final size:23
Alignment explanation
Indices: 4285484--4285556 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
4285474 ATAGGTAAAA
*
4285484 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
4285507 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
4285530 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
4285553 ATAT
1 ATAT
4285557 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4285646 original size:434 final size:433
Alignment explanation
Indices: 4284837--4285898 Score: 2015
Period size: 434 Copynumber: 2.5 Consensus size: 433
4284827 TTATCTTTGG
4284837 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
4284902 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAA
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAAA
* *
4284967 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGATACTT
130 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
4285032 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
195 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
4285097 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
260 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
*
4285162 TTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
325 TTTTCACCGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
4285227 AATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
390 AATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
4285271 TTTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTT
1 -TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTT
*
4285336 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAACCATGAAACACTATTAAAAAAAA
65 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
*
4285401 TTGAAACACAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
130 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
4285466 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
195 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
4285531 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
260 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
4285596 TTTTCACCGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
325 TTTTCACCGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
4285661 AATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
390 AATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
*
4285705 TT-A--TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
*
4285767 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-CAAAAAAT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
4285831 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
131 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
4285896 CAA
196 CAA
4285899 CATATTATAA
Statistics
Matches: 618, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
429 74 0.12
430 113 0.18
432 1 0.00
433 2 0.00
434 308 0.50
435 120 0.19
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (433 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTAT
ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
TTTCACCGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTA
ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
Found at i:4288736 original size:17 final size:17
Alignment explanation
Indices: 4288714--4288755 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
4288704 TTAGCACAAA
4288714 ACCTTTGTTTAAACATG
1 ACCTTTGTTTAAACATG
4288731 ACCTTTGTTTAAACATG
1 ACCTTTGTTTAAACATG
4288748 ACCTTTGT
1 ACCTTTGT
4288756 CGTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (17 bp):
ACCTTTGTTTAAACATG
Found at i:4291819 original size:49 final size:48
Alignment explanation
Indices: 4291756--4291899 Score: 191
Period size: 49 Copynumber: 3.0 Consensus size: 48
4291746 GGTAAGCTTT
4291756 GTTTACTCGGTTTCTGTTTAGCTGTTCTATTGGTAAATTTAAATGTTTC
1 GTTTACTCGGTTTCTGTTT-GCTGTTCTATTGGTAAATTTAAATGTTTC
* ** *
4291805 GTTTACTCGGTTTCTGCTTCGCTGTTCTATAAGTAAATTTAAGTGTTTC
1 GTTTACTCGGTTTCTG-TTTGCTGTTCTATTGGTAAATTTAAATGTTTC
* * *
4291854 ATTTACTCTGTTTCTGCTTTGCTGTTCTATTGATAAATTT-AATGTT
1 GTTTACTCGGTTTCTG-TTTGCTGTTCTATTGGTAAATTTAAATGTT
4291900 CTATTGATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
48 5 0.06
49 76 0.92
50 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.51
Consensus pattern (48 bp):
GTTTACTCGGTTTCTGTTTGCTGTTCTATTGGTAAATTTAAATGTTTC
Found at i:4294666 original size:21 final size:21
Alignment explanation
Indices: 4294642--4294687 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4294632 ACTCTGATAA
4294642 TATAAGATTTTAAAATGTTAT
1 TATAAGATTTTAAAATGTTAT
**
4294663 TATAAGATTTTGGAATGTTAT
1 TATAAGATTTTAAAATGTTAT
4294684 TATA
1 TATA
4294688 TTGTTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (21 bp):
TATAAGATTTTAAAATGTTAT
Found at i:4295295 original size:19 final size:17
Alignment explanation
Indices: 4295273--4295319 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
4295263 TTTTTCCATA
4295273 TTTTAAATATTACATTAATT
1 TTTTAAAT-TTA-ATT-ATT
4295293 TTTTATAATTTAATTA-T
1 TTTTA-AATTTAATTATT
4295310 TTTTAAATTT
1 TTTTAAATTT
4295320 TTTATTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 1 0.04
19 3 0.12
20 8 0.31
21 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTAATTATT
Found at i:4296016 original size:21 final size:21
Alignment explanation
Indices: 4295990--4296040 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4295980 GCCGCAAAAG
* * *
4295990 GCGACGAAATGGATGCTTTTA
1 GCGACGAAATGAATACTATTA
*
4296011 GCGACGAAGTGAATACTATTA
1 GCGACGAAATGAATACTATTA
4296032 GCGACGAAA
1 GCGACGAAA
4296041 CTCGTCTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
GCGACGAAATGAATACTATTA
Found at i:4296943 original size:25 final size:25
Alignment explanation
Indices: 4296902--4296949 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4296892 AGATACTAGG
4296902 GATGTGAGCCTTCAATGTCAAAAGT
1 GATGTGAGCCTTCAATGTCAAAAGT
* *
4296927 GATGTGAGTCTTTAATGTCAAAA
1 GATGTGAGCCTTCAATGTCAAAA
4296950 TGTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (25 bp):
GATGTGAGCCTTCAATGTCAAAAGT
Found at i:4297848 original size:2 final size:2
Alignment explanation
Indices: 4297841--4297886 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4297831 AAAAATGTGA
4297841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4297883 AT AT
1 AT AT
4297887 GAGTTGAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4298208 original size:2 final size:2
Alignment explanation
Indices: 4298199--4298239 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4298189 TATTTTTTTC
4298199 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4298240 CTTTAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4299169 original size:23 final size:25
Alignment explanation
Indices: 4299138--4299195 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
4299128 AACATGAATC
* *
4299138 TTAAATATATTTTG-ATT-AATAAT
1 TTAATTATATATTGTATTGAATAAT
*
4299161 TTAATTATATATTGTATTGATTAAT
1 TTAATTATATATTGTATTGAATAAT
4299186 TATAATTATA
1 T-TAATTATA
4299196 ATTATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.41
24 3 0.10
25 6 0.21
26 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (25 bp):
TTAATTATATATTGTATTGAATAAT
Found at i:4300316 original size:24 final size:24
Alignment explanation
Indices: 4300261--4300317 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
4300251 ACTTTATTCG
**
4300261 AATTTAATTACTTTTAATTTTTAA
1 AATTTAATTACTTTTAATTAATAA
* * *
4300285 AATATAATTATTTTTAATTAATAC
1 AATTTAATTACTTTTAATTAATAA
4300309 AATTTAATT
1 AATTTAATT
4300318 TATTCAGTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTAATTACTTTTAATTAATAA
Found at i:4303143 original size:17 final size:18
Alignment explanation
Indices: 4303118--4303162 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
4303108 ATGAAATTGA
*
4303118 ATTCCAATTCC-TAACAG
1 ATTCAAATTCCATAACAG
*
4303135 ATTCAAATTCCATCACAG
1 ATTCAAATTCCATAACAG
4303153 ATTCAAATTC
1 ATTCAAATTC
4303163 TCTCATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (18 bp):
ATTCAAATTCCATAACAG
Found at i:4303817 original size:2 final size:2
Alignment explanation
Indices: 4303812--4303865 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
4303802 TTCTTGATCG
4303812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4303854 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4303866 TAGACTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4305357 original size:21 final size:21
Alignment explanation
Indices: 4305331--4305381 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4305321 GCCGTAAAAG
* * *
4305331 GCGACGAAATGGATGCTTTTA
1 GCGACGAAATGAATACTATTA
4305352 GCGACGAAATGAATACTATTA
1 GCGACGAAATGAATACTATTA
4305373 GCGACGAAA
1 GCGACGAAA
4305382 CTCGTCTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (21 bp):
GCGACGAAATGAATACTATTA
Found at i:4307408 original size:21 final size:21
Alignment explanation
Indices: 4307384--4307428 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4307374 AAACGACCGG
4307384 AAACATGCCA-AAAGACATAGA
1 AAACATGCCATAAA-ACATAGA
*
4307405 AAACATGCCATAAAACATATA
1 AAACATGCCATAAAACATAGA
4307426 AAA
1 AAA
4307429 ACATTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.60, C:0.18, G:0.09, T:0.13
Consensus pattern (21 bp):
AAACATGCCATAAAACATAGA
Found at i:4311331 original size:20 final size:21
Alignment explanation
Indices: 4311298--4311337 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4311288 GAATTTGTTC
*
4311298 AAGCCCTCGAGTATCGATACT
1 AAGCCCTCGAGTATCAATACT
4311319 AAGCCCT-GAGTATCAATAC
1 AAGCCCTCGAGTATCAATAC
4311338 CACCTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGCCCTCGAGTATCAATACT
Found at i:4314141 original size:210 final size:212
Alignment explanation
Indices: 4313779--4314201 Score: 823
Period size: 210 Copynumber: 2.0 Consensus size: 212
4313769 CTTCTCCCAC
4313779 CATATTCGCCTTGCCTAGGTGATAATCGATCACACAATCATAATCCTTAAGAAATTCCACCCAAC
1 CATATTCGCCTTGCCTAGGTGATAATCGATCACACAATCATAATCCTTAAGAAATTCCACCCAAC
4313844 GTCCCTGCCTTAGATTCAACTCTTTTTACATGAGTAAATACTTCAAATTCTTGTGGTCGATGAAG
66 GTCCCTGCCTTAGATTCAACTCTTTTTACATGAGTAAATACTTCAAATTCTTGTGGTCGATGAAG
4313909 ATCTAACATTTCTCTCCAAAGA-GTAGTGCCTCCAAATCTTCAAGGCAAAGACCACGACCG-AGT
131 ATCTAACATTTCTCTCCAAAGAGGTAGTGCCTCCAAATCTTCAAGGCAAAGACCACGACCGCAGT
4313972 TCCAAATCGTGAGTGGG
196 TCCAAATCGTGAGTGGG
4313989 CATATTCGCCTTGCCTAGGTGATAATCGATCACACAATCATAATCCTTAAGAAATTCCACCCAAC
1 CATATTCGCCTTGCCTAGGTGATAATCGATCACACAATCATAATCCTTAAGAAATTCCACCCAAC
4314054 GTCCCTGCCTTAGATTCAACTCTTTTTACATGAGTAAATACTTCAAATTCTTGTGGTCGATGAAG
66 GTCCCTGCCTTAGATTCAACTCTTTTTACATGAGTAAATACTTCAAATTCTTGTGGTCGATGAAG
4314119 ATCTAACATTTCTCTCCAAAGAGGTAGTGCCTCCAAATCTTCAAGGCAAAGACCACGACCGCTAG
131 ATCTAACATTTCTCTCCAAAGAGGTAGTGCCTCCAAATCTTCAAGGCAAAGACCACGACCGC-AG
4314184 TTCCAAATCGTGAGTGGG
195 TTCCAAATCGTGAGTGGG
4314202 GTAGTTACGA
Statistics
Matches: 210, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
210 152 0.72
211 38 0.18
213 20 0.10
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (212 bp):
CATATTCGCCTTGCCTAGGTGATAATCGATCACACAATCATAATCCTTAAGAAATTCCACCCAAC
GTCCCTGCCTTAGATTCAACTCTTTTTACATGAGTAAATACTTCAAATTCTTGTGGTCGATGAAG
ATCTAACATTTCTCTCCAAAGAGGTAGTGCCTCCAAATCTTCAAGGCAAAGACCACGACCGCAGT
TCCAAATCGTGAGTGGG
Found at i:4325108 original size:23 final size:23
Alignment explanation
Indices: 4325040--4325100 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
4325030 CATTATTATA
4325040 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
* *
4325063 CGACACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
4325086 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
4325101 TTTATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:4327227 original size:23 final size:24
Alignment explanation
Indices: 4327167--4327228 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 24
4327157 TCAGAGATGA
* *
4327167 GTATAAATGATAAGAAAAGAGTAT
1 GTATATATTATAAGAAAAGAGTAT
*
4327191 GTGTATATTA-AAGAAAAGA-TAT
1 GTATATATTATAAGAAAAGAGTAT
*
4327213 G-ATATGTGTATAAGAA
1 GTATATAT-TATAAGAA
4327229 GATTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.13
22 6 0.19
23 14 0.45
24 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (24 bp):
GTATATATTATAAGAAAAGAGTAT
Found at i:4329576 original size:23 final size:23
Alignment explanation
Indices: 4329516--4329568 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
4329506 CATTATTATA
4329516 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
4329539 CGGCACTGCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
4329562 TGGCACT
1 TGGCACT
4329569 TCTGTGCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:4337915 original size:135 final size:137
Alignment explanation
Indices: 4337751--4338012 Score: 492
Period size: 135 Copynumber: 1.9 Consensus size: 137
4337741 AATCTAATAA
4337751 ATACTTACGTTAATTTGTTGTACTGAGATTATAAAATTAACTTGACTTGAAGTTAGAAAATTTT-
1 ATACTTACGTTAATTTGTTGTACTGAGATTATAAAATTAACTTGACTTGAAGTTAGAAAATTTTA
4337815 A-ATATATATATATATTAATTAATTTGGGTAAATACAAGGCAATATATGTTTATAGATAATTTAA
66 ATATATATATATATATTAATTAATTTGGGTAAATACAAGGCAATATATGTTTATAGATAATTTAA
4337879 TATATAT
131 TATATAT
*
4337886 ATACTTACGTTAATTTGTTGTACTGAGATTATAAAATTAACTTGACTTGAAGTTATAAAATTTTA
1 ATACTTACGTTAATTTGTTGTACTGAGATTATAAAATTAACTTGACTTGAAGTTAGAAAATTTTA
*
4337951 ATATATATATATATATTGATTAATTTGGGTAAATACAAGGCAATATATGTTTATAGATAATT
66 ATATATATATATATATTAATTAATTTGGGTAAATACAAGGCAATATATGTTTATAGATAATT
4338013 CTAAATTATT
Statistics
Matches: 123, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
135 63 0.51
136 1 0.01
137 59 0.48
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (137 bp):
ATACTTACGTTAATTTGTTGTACTGAGATTATAAAATTAACTTGACTTGAAGTTAGAAAATTTTA
ATATATATATATATATTAATTAATTTGGGTAAATACAAGGCAATATATGTTTATAGATAATTTAA
TATATAT
Found at i:4339695 original size:31 final size:32
Alignment explanation
Indices: 4339641--4339700 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
4339631 CGGGGTGATC
4339641 ACATCTTAATTAAATAAAAAACGAAAGTGACT
1 ACATCTTAATTAAATAAAAAACGAAAGTGACT
4339673 ACATCTTAATTAAAT-AAAAACGAAAGTG
1 ACATCTTAATTAAATAAAAAACGAAAGTG
4339701 GTCATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (32 bp):
ACATCTTAATTAAATAAAAAACGAAAGTGACT
Found at i:4342352 original size:3 final size:3
Alignment explanation
Indices: 4342344--4342376 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
4342334 TTTTCTTTCT
4342344 TTC TTC TTC TTC TTC TTC TTC TTC TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TT
4342377 TCTGTTTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:4346119 original size:42 final size:37
Alignment explanation
Indices: 4346051--4346171 Score: 190
Period size: 42 Copynumber: 3.2 Consensus size: 37
4346041 ATTCGGATTC
4346051 GAATGTAAGTGTTGGGTTCGG-TTCGAATACGAATAT
1 GAATGTAAGTGTTGGGTTCGGATTCGAATACGAATAT
4346087 GAATGTAAGTGTTGGGTTCGGTTTGGATTCGAATACGAATAT
1 GAATGTAAGTGTTGGGTTC-----GGATTCGAATACGAATAT
4346129 GAATGTAAGTGTTGGGTTCGGATTCGAATACGAATAT
1 GAATGTAAGTGTTGGGTTCGGATTCGAATACGAATAT
4346166 GAATGT
1 GAATGT
4346172 CGTGTTCGGG
Statistics
Matches: 79, Mismatches: 0, Indels: 11
0.88 0.00 0.12
Matches are distributed among these distances:
36 19 0.24
37 24 0.30
41 2 0.03
42 34 0.43
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (37 bp):
GAATGTAAGTGTTGGGTTCGGATTCGAATACGAATAT
Found at i:4346918 original size:21 final size:21
Alignment explanation
Indices: 4346801--4346938 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
4346791 ACGCGAAATA
**
4346801 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
4346821 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
4346841 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
4346862 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
4346883 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
4346904 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
4346924 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4346939 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:4347000 original size:20 final size:20
Alignment explanation
Indices: 4346906--4347274 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
4346896 GATTTTCCAT
* ** *
4346906 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
4346926 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
4346946 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4346966 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
4346986 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
4347006 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4347026 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
4347046 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
4347066 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
4347086 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4347106 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
4347126 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4347146 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
4347166 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
4347186 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4347206 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4347226 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
4347246 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
4347266 AATCACAAC
1 AATCGCAAC
4347275 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:4348194 original size:12 final size:12
Alignment explanation
Indices: 4348177--4348201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4348167 ATATAATCCT
4348177 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4348189 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4348201 G
1 G
4348202 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4350507 original size:19 final size:19
Alignment explanation
Indices: 4350485--4350791 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
4350475 CGGAAAATAC
*
4350485 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4350504 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
4350518 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
4350538 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4350552 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350571 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4350590 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4350604 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350623 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4350642 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
4350656 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
4350675 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350694 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350713 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350732 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
4350746 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350765 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4350784 AATCGCAA
1 AATCGCAA
4350792 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4350600 original size:52 final size:52
Alignment explanation
Indices: 4350513--4350791 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
4350503 AAATCCCAAC
4350513 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4350566 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4350618 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
4350670 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
4350727 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
4350779 ATGAAAATCGCAA
1 ATGAAAATCGCAA
4350792 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4350636 original size:71 final size:71
Alignment explanation
Indices: 4350552--4350791 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
4350542 GCAACGAGAG
*
4350552 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
4350617 AATGAA
66 AATGAA
* *
4350623 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
4350683 TGCGAAATGAA
61 TGCGAAATGAA
4350694 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
4350759 AATGAA
66 AATGAA
4350765 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
4350792 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:4350737 original size:142 final size:138
Alignment explanation
Indices: 4350485--4350829 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
4350475 CGGAAAATAC
* * *
4350485 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
4350548 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
4350612 TGCGAAATGAA
128 TGCGAAATGAA
4350623 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
4350688 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
4350753 ATGCGAAATGAA
127 ATGCGAAATGAA
*
4350765 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
4350829 A
63 A
4350830 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:4350792 original size:52 final size:55
Alignment explanation
Indices: 4350485--4350813 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
4350475 CGGAAAATAC
* *
4350485 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
4350538 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
4350590 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
4350642 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
4350694 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
4350746 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
4350798 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
4350814 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:4350929 original size:19 final size:19
Alignment explanation
Indices: 4350820--4350921 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4350810 AAATTATAAA
4350820 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4350839 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
4350859 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
4350875 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4350892 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4350911 CGCATTGCGAT
1 CGCATTGCGAT
4350922 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:4351047 original size:14 final size:14
Alignment explanation
Indices: 4351028--4351064 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4351018 CATCAATTAC
4351028 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4351042 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4351056 ACAAATCAA
1 ACAAATCAA
4351065 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4353064 original size:14 final size:14
Alignment explanation
Indices: 4353045--4353101 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4353035 GCGAAATTAA
*
4353045 AATCGCAACGACAG
1 AATCGCAACGAAAG
4353059 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
4353076 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4353092 AATCGCAACG
1 AATCGCAACG
4353102 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:4353072 original size:33 final size:33
Alignment explanation
Indices: 4353026--4353118 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
4353016 GCGAAACCAA
* *
4353026 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
4353059 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4353092 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4353119 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:4353083 original size:19 final size:19
Alignment explanation
Indices: 4352989--4353123 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
4352979 TAGTTTACTT
* *
4352989 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4353009 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
4353028 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
4353047 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
4353061 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
4353080 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
4353094 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4353113 TCGCAATGCGA
1 TCGCAACGCGA
4353124 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4353141 original size:19 final size:19
Alignment explanation
Indices: 4353119--4353247 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4353109 AAAATCGCAA
4353119 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4353138 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
4353152 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4353171 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4353185 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4353204 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4353223 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4353243 TGCGA
1 TGCGA
4353248 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4353161 original size:33 final size:33
Alignment explanation
Indices: 4353119--4353210 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4353109 AAAATCGCAA
4353119 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
4353152 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
4353185 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
4353211 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:4353450 original size:93 final size:93
Alignment explanation
Indices: 4353291--4353854 Score: 1089
Period size: 93 Copynumber: 6.1 Consensus size: 93
4353281 TTGAATGGAT
4353291 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353356 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4353384 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353449 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4353477 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353542 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
4353570 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TATTTCATAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353633 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4353661 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353725 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4353753 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
4353818 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4353846 AAATTTACT
1 AAATTTACT
4353855 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 3, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
91 86 0.18
92 99 0.21
93 281 0.60
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:4353790 original size:276 final size:279
Alignment explanation
Indices: 4353291--4353854 Score: 1089
Period size: 276 Copynumber: 2.0 Consensus size: 279
4353281 TTGAATGGAT
4353291 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353356 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
4353421 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
4353486 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
196 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
4353551 GAATTGGCAGCAACCGAAC
261 GAATTGGCAGCAACCGAAC
*
4353570 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATA-TATTTCATAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4353633 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
4353698 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
4353762 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
196 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
4353827 GAATTGGCAGCAACCGAAT
261 GAATTGGCAGCAACCGAAC
4353846 AAATTTACT
1 AAATTTACT
4353855 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
276 154 0.54
277 91 0.32
278 4 0.01
279 34 0.12
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAAC
Found at i:4355579 original size:14 final size:14
Alignment explanation
Indices: 4355560--4355649 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
4355550 TTGAAATGAA
4355560 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4355574 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
4355591 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
4355607 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4355626 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4355640 AATCGCAACG
1 AATCGCAACG
4355650 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4355597 original size:33 final size:33
Alignment explanation
Indices: 4355552--4355666 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
4355542 TCTTTTGGTT
4355552 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
4355585 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4355618 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4355651 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4355667 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4355598 original size:19 final size:18
Alignment explanation
Indices: 4355559--4355671 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
4355549 GTTGAAATGA
4355559 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
4355574 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
4355591 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
4355607 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
4355624 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
4355640 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
4355657 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
4355672 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Done.