Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 26
Found at i:5228827 original size:18 final size:18
Alignment explanation
Indices: 5228771--5228826 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
5228761 TTTCAAAAAT
5228771 AAAACAAAAAAAAGGCAAA
1 AAAACAAAAAAAA-GCAAA
*
5228790 AAAACAAAAAAAGGC-AA
1 AAAACAAAAAAAAGCAAA
*
5228807 AAATC-AAAAAAA-CAAA
1 AAAACAAAAAAAAGCAAA
5228823 AAAA
1 AAAA
5228827 AAGCCAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 1 0.03
16 11 0.34
17 6 0.19
18 2 0.06
19 12 0.38
ACGTcount: A:0.80, C:0.11, G:0.07, T:0.02
Consensus pattern (18 bp):
AAAACAAAAAAAAGCAAA
Found at i:5228835 original size:18 final size:18
Alignment explanation
Indices: 5228771--5228818 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
5228761 TTTCAAAAAT
5228771 AAAAC-AAAAAAAAGGCA
1 AAAACAAAAAAAAAGGCA
5228788 AAAA-AACAAAAAAAGGCA
1 AAAACAA-AAAAAAAGGCA
5228806 AAAATCAAAAAAA
1 AAAA-CAAAAAAA
5228819 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.19
18 15 0.56
19 5 0.19
20 2 0.07
ACGTcount: A:0.79, C:0.10, G:0.08, T:0.02
Consensus pattern (18 bp):
AAAACAAAAAAAAAGGCA
Found at i:5229615 original size:11 final size:11
Alignment explanation
Indices: 5229599--5229629 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5229589 TTGGTGATGG
5229599 AAACAAGATTA
1 AAACAAGATTA
5229610 AAACAAGATTA
1 AAACAAGATTA
5229621 AAACAAGAT
1 AAACAAGAT
5229630 AAATAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
AAACAAGATTA
Found at i:5229643 original size:21 final size:22
Alignment explanation
Indices: 5229599--5229640 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5229589 TTGGTGATGG
*
5229599 AAACAAGATTAAAACAAGATTA
1 AAACAAGATTAAAAAAAGATTA
5229621 AAACAAGA-TAAATAAAAGAT
1 AAACAAGATTAAA-AAAAGAT
5229641 AAAGGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
AAACAAGATTAAAAAAAGATTA
Found at i:5236396 original size:23 final size:23
Alignment explanation
Indices: 5236351--5236396 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5236341 TTATACCTAT
*
5236351 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
5236374 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
5236397 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:5240848 original size:23 final size:23
Alignment explanation
Indices: 5240803--5240848 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5240793 TTATACCTAT
*
5240803 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
5240826 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
5240849 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:5245599 original size:16 final size:15
Alignment explanation
Indices: 5245562--5245609 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
5245552 AAGATATGGT
*
5245562 AATGAAATAAGAAAA
1 AATGAAATAATAAAA
*
5245577 GATGAAATAATAAAGA
1 AATGAAATAATAAA-A
*
5245593 AATGAAATGATAAAA
1 AATGAAATAATAAAA
5245608 AA
1 AA
5245610 ATTTAAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.17
Consensus pattern (15 bp):
AATGAAATAATAAAA
Found at i:5245611 original size:16 final size:16
Alignment explanation
Indices: 5245562--5245611 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
5245552 AAGATATGGT
*
5245562 AATGAAATAA-GAAAA
1 AATGAAATAATAAAAA
* *
5245577 GATGAAATAATAAAGA
1 AATGAAATAATAAAAA
*
5245593 AATGAAATGATAAAAA
1 AATGAAATAATAAAAA
5245609 AAT
1 AAT
5245612 TTAAGATAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (16 bp):
AATGAAATAATAAAAA
Found at i:5255049 original size:19 final size:20
Alignment explanation
Indices: 5255013--5255053 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5255003 CTTGGCTTGC
*
5255013 TTTCTTTTTTTTTAATTCTT
1 TTTCTTTTCTTTTAATTCTT
5255033 TTTCTTTTCTTTT-ATTCTT
1 TTTCTTTTCTTTTAATTCTT
5255052 TT
1 TT
5255054 CTGATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTCTTTTAATTCTT
Found at i:5255050 original size:13 final size:12
Alignment explanation
Indices: 5255013--5255085 Score: 58
Period size: 13 Copynumber: 5.6 Consensus size: 12
5255003 CTTGGCTTGC
*
5255013 TTTCTTTTTTTT
1 TTTCTTTTTTCT
5255025 TAATTC-TTTTTCT
1 T--TTCTTTTTTCT
5255038 TTTCTTTTATTCT
1 TTTCTTTT-TTCT
5255051 TTTCTGATTTTTCT
1 TTTCT--TTTTTCT
*
5255065 CTTCTTTTTGTCTT
1 TTTCTTTTT-TC-T
5255079 TTTCTTT
1 TTTCTTT
5255086 CTTTTTGCAC
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.06
12 8 0.16
13 18 0.36
14 18 0.36
15 3 0.06
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:5255069 original size:19 final size:18
Alignment explanation
Indices: 5255047--5255092 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
5255037 TTTTCTTTTA
5255047 TTCTTTTCTG-ATTTTTCT
1 TTCTTTT-TGTATTTTTCT
*
5255065 CTTCTTTTTGTCTTTTTCT
1 -TTCTTTTTGTATTTTTCT
5255084 TTCTTTTTG
1 TTCTTTTTG
5255093 CACTCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.74
Consensus pattern (18 bp):
TTCTTTTTGTATTTTTCT
Found at i:5257348 original size:20 final size:21
Alignment explanation
Indices: 5257311--5257349 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5257301 GATGGTCTTG
*
5257311 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
5257332 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
5257350 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:5258783 original size:36 final size:36
Alignment explanation
Indices: 5258732--5258873 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
5258722 GATACAATCT
5258732 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
5258768 GTCAATCACCATTATCACGCCTTTATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
5258804 GTCCATCTCCATTATCACGCCTATATCGTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
5258840 TTCCACCACCATTATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5258874 ACTTATAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5259333 original size:9 final size:8
Alignment explanation
Indices: 5259319--5259362 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
5259309 TTTGGAGTTC
5259319 AAAAGAAA
1 AAAAGAAA
5259327 GAAAAGAAA
1 -AAAAGAAA
5259336 AAGAAGAATA
1 AA-AAGAA-A
5259346 AAAA-AAA
1 AAAAGAAA
5259353 AAAAGAAA
1 AAAAGAAA
5259361 AA
1 AA
5259363 GTGAAGCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 5 0.16
8 9 0.28
9 15 0.47
10 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAGAAA
Found at i:5263338 original size:36 final size:36
Alignment explanation
Indices: 5263291--5263432 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
5263281 GATACAATCT
*
5263291 GTCCATCACCATTATCACGCCTATATCATCACCGTA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
5263327 GTCCATCACCATTATCACGCCTTTATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
5263363 GTCCATCTCCATTATCACGCCTATATCGTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
5263399 TTCCACCACCATTATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5263433 ACTTATAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.27, C:0.37, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5271243 original size:29 final size:29
Alignment explanation
Indices: 5271207--5271270 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
5271197 TAAATAAAAT
*
5271207 GGAAATGAATTAATGAAATAGTTGGTAAC
1 GGAAATGAATTAATGAAAAAGTTGGTAAC
5271236 GGAAATGAATTAATGAAAAAGTTGGTAAC
1 GGAAATGAATTAATGAAAAAGTTGGTAAC
*
5271265 GAAAAT
1 GGAAAT
5271271 AAATATGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.25
Consensus pattern (29 bp):
GGAAATGAATTAATGAAAAAGTTGGTAAC
Found at i:5274928 original size:22 final size:20
Alignment explanation
Indices: 5274903--5274942 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5274893 ATGTTTGTTT
5274903 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
5274925 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
5274943 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:5276299 original size:13 final size:13
Alignment explanation
Indices: 5276277--5276306 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5276267 ACTAAACACC
5276277 TTTC-ACATACCT
1 TTTCAACATACCT
5276289 TTTCAACATACCT
1 TTTCAACATACCT
5276302 TTTCA
1 TTTCA
5276307 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:5280487 original size:22 final size:20
Alignment explanation
Indices: 5280462--5280501 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5280452 ATGTTTGTTT
5280462 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
5280484 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
5280502 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:5285495 original size:35 final size:37
Alignment explanation
Indices: 5285432--5285504 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
5285422 ATAAGATACA
*
5285432 ATATATCCATCACCATTGTCACGCCTATATCATCACC
1 ATATATCCATCACCATTATCACGCCTATATCATCACC
*
5285469 ATAT-TCCATCACCA-TATCACGCCTATATTATCACC
1 ATATATCCATCACCATTATCACGCCTATATCATCACC
5285504 A
1 A
5285505 ACTTCTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 20 0.59
36 10 0.29
37 4 0.12
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (37 bp):
ATATATCCATCACCATTATCACGCCTATATCATCACC
Found at i:5289419 original size:35 final size:36
Alignment explanation
Indices: 5289363--5289430 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
5289353 ATACATTCTG
5289363 TCCATCACCATTATCACGCCTATATGATCACCATAT
1 TCCATCACCATTATCACGCCTATATGATCACCATAT
*
5289399 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATGATCACCA
5289431 ACTTCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATGATCACCATAT
Found at i:5311972 original size:11 final size:11
Alignment explanation
Indices: 5311956--5312008 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
5311946 ATTTCTTTTT
5311956 AAAAAAAAAAC
1 AAAAAAAAAAC
**
5311967 AAAAAAAAGGC
1 AAAAAAAAAAC
5311978 AAAAAAAAAAGC
1 AAAAAAAAAA-C
* *
5311990 CAAAAAAAAGC
1 AAAAAAAAAAC
5312001 TAAAAAAA
1 -AAAAAAA
5312009 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.81, C:0.09, G:0.08, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:5311983 original size:13 final size:13
Alignment explanation
Indices: 5311967--5311998 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5311957 AAAAAAAAAC
*
5311967 AAAAAAAAGGCAA
1 AAAAAAAAGCCAA
5311980 AAAAAAAAGCCAA
1 AAAAAAAAGCCAA
5311993 AAAAAA
1 AAAAAA
5311999 GCTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGCCAA
Found at i:5311994 original size:10 final size:10
Alignment explanation
Indices: 5311981--5312015 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5311971 AAAAGGCAAA
5311981 AAAAAAAGCC
1 AAAAAAAGCC
*
5311991 AAAAAAAAGCT
1 -AAAAAAAGCC
5312002 AAAAAAAGCC
1 AAAAAAAGCC
5312012 AAAA
1 AAAA
5312016 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.74, C:0.14, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:5320581 original size:17 final size:18
Alignment explanation
Indices: 5320554--5320589 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5320544 TAGTAATAAA
5320554 AAAATAACCTCACAAAAC
1 AAAATAACCTCACAAAAC
*
5320572 AAAA-AACCTCACAGAAC
1 AAAATAACCTCACAAAAC
5320589 A
1 A
5320590 CTCCAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.28, G:0.03, T:0.08
Consensus pattern (18 bp):
AAAATAACCTCACAAAAC
Found at i:5327151 original size:13 final size:13
Alignment explanation
Indices: 5327133--5327158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5327123 AACACCTGTC
5327133 ACATACCTTTTCA
1 ACATACCTTTTCA
5327146 ACATACCTTTTCA
1 ACATACCTTTTCA
5327159 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:5330701 original size:29 final size:29
Alignment explanation
Indices: 5330659--5330721 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
5330649 GTGTCTCCTC
5330659 CAAGCTAGCTTGAGTGTGGAGCTAGCTAG
1 CAAGCTAGCTTGAGTGTGGAGCTAGCTAG
*
5330688 CAAGCTAGCTTGAGTGTGGAGCTTGCTAG
1 CAAGCTAGCTTGAGTGTGGAGCTAGCTAG
5330717 CAAGC
1 CAAGC
5330722 ATGGGCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (29 bp):
CAAGCTAGCTTGAGTGTGGAGCTAGCTAG
Found at i:5333621 original size:2 final size:2
Alignment explanation
Indices: 5333614--5333656 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5333604 GTGCAACAAA
5333614 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
5333656 A
1 A
5333657 AAGAAGTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5333735 original size:23 final size:24
Alignment explanation
Indices: 5333707--5333760 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
5333697 AAAAACAGCA
5333707 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
5333730 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
5333754 AAGAAAA
1 AAGAAAA
5333761 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:5333765 original size:24 final size:23
Alignment explanation
Indices: 5333707--5333766 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
5333697 AAAAACAGCA
5333707 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
5333730 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
5333754 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
5333767 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:5336547 original size:11 final size:13
Alignment explanation
Indices: 5336515--5336544 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5336505 TGGCCAAAGA
5336515 TGAAAAGGTATGT
1 TGAAAAGGTATGT
5336528 TGAAAAGGTATG-
1 TGAAAAGGTATGT
5336540 TGAAA
1 TGAAA
5336545 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:5341883 original size:23 final size:24
Alignment explanation
Indices: 5341837--5341883 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5341827 AGAAAAGAAG
***
5341837 CACTCAAAAAGAAGAAATTGAAAA
1 CACTCAAAAAGAAGAAAAAAAAAA
5341861 CACTC-AAAAGAAGAAAAAAAAAA
1 CACTCAAAAAGAAGAAAAAAAAAA
5341884 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.09
Consensus pattern (24 bp):
CACTCAAAAAGAAGAAAAAAAAAA
Found at i:5343130 original size:21 final size:24
Alignment explanation
Indices: 5343083--5343133 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
5343073 TAGAAAGTTT
*
5343083 AAGAAAAAAATATGGTAATGAAAC
1 AAGAAAAAAATATGGTAAAGAAAC
*
5343107 AAGAAAAAAA-AT-G-AAAGAATC
1 AAGAAAAAAATATGGTAAAGAAAC
5343128 AAGAAA
1 AAGAAA
5343134 TGAAATAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 2 0.08
24 10 0.40
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.12
Consensus pattern (24 bp):
AAGAAAAAAATATGGTAAAGAAAC
Found at i:5343827 original size:35 final size:36
Alignment explanation
Indices: 5343780--5343888 Score: 157
Period size: 36 Copynumber: 3.0 Consensus size: 36
5343770 ACTTATAAGT
*
5343780 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
** *
5343815 TGGTGATGATATAGGCGTGATAATCTTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
5343851 TAGTGATGATATAGGCGTGATAATGGTGATGGACATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA-ATA
5343888 T
1 T
5343889 TGTATCTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 20 0.31
36 41 0.64
37 3 0.05
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:5345025 original size:21 final size:23
Alignment explanation
Indices: 5344992--5345033 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5344982 ATATGCTTGA
5344992 ATATCAATCAATG-ATGCAAACC
1 ATATCAATCAATGAATGCAAACC
*
5345014 ATAT-AATGAATGAATGCAAA
1 ATATCAATCAATGAATGCAAA
5345034 TGTTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (23 bp):
ATATCAATCAATGAATGCAAACC
Found at i:5350763 original size:4 final size:5
Alignment explanation
Indices: 5350735--5350760 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5350725 ACTCAAAAAG
5350735 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
5350761 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5353371 original size:20 final size:22
Alignment explanation
Indices: 5353336--5353375 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5353326 CATGCTTAAT
5353336 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
5353358 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
5353376 GGTCTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:5354840 original size:11 final size:12
Alignment explanation
Indices: 5354811--5354845 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5354801 TTTGGTGTTG
5354811 GAAACAAGATAA
1 GAAACAAGATAA
*
5354823 GAAACAAGATTA
1 GAAACAAGATAA
5354835 -AAACAAGATAA
1 GAAACAAGATAA
5354846 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:5359183 original size:20 final size:20
Alignment explanation
Indices: 5359160--5359197 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5359150 CTTTTTGTTT
5359160 TTTTGTGTGTTTTTTTTGCC
1 TTTTGTGTGTTTTTTTTGCC
* *
5359180 TTTTTTGTTTTTTTTTTG
1 TTTTGTGTGTTTTTTTTG
5359198 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (20 bp):
TTTTGTGTGTTTTTTTTGCC
Found at i:5359554 original size:11 final size:12
Alignment explanation
Indices: 5359524--5359559 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5359514 TTTAGGTGCT
5359524 AGAAACAAGATA
1 AGAAACAAGATA
*
5359536 AGAAACAAGATT
1 AGAAACAAGATA
5359548 A-AAACAAGATA
1 AGAAACAAGATA
5359559 A
1 A
5359560 ATAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.67, C:0.08, G:0.14, T:0.11
Consensus pattern (12 bp):
AGAAACAAGATA
Found at i:5364145 original size:13 final size:13
Alignment explanation
Indices: 5364123--5364152 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5364113 ACTAAACACC
5364123 TTTC-ACATACCT
1 TTTCAACATACCT
5364135 TTTCAACATACCT
1 TTTCAACATACCT
5364148 TTTCA
1 TTTCA
5364153 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:5368198 original size:25 final size:25
Alignment explanation
Indices: 5368139--5368199 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5368129 TTTCTTTGTT
* *
5368139 TTTCTTCTTCTTTTTGAGTGCTGGAA
1 TTTCTT-TTCTTTTGGAGTGCTGCAA
*
5368165 TTT-TCTTTCTTTTGGAGTGCTTCAA
1 TTTCT-TTTCTTTTGGAGTGCTGCAA
5368190 TTTCTTTTCT
1 TTTCTTTTCT
5368200 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.10, C:0.16, G:0.15, T:0.59
Consensus pattern (25 bp):
TTTCTTTTCTTTTGGAGTGCTGCAA
Found at i:5371870 original size:26 final size:26
Alignment explanation
Indices: 5371834--5371888 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5371824 CATAGTATAT
5371834 AATCTATTGTTTGGGATGCATTTTTA
1 AATCTATTGTTTGGGATGCATTTTTA
5371860 AATCTATTGTTTGGGATGCATTTTTA
1 AATCTATTGTTTGGGATGCATTTTTA
5371886 AAT
1 AAT
5371889 GATTCAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (26 bp):
AATCTATTGTTTGGGATGCATTTTTA
Found at i:5375554 original size:20 final size:21
Alignment explanation
Indices: 5375531--5375574 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
5375521 TTCTTTTCTT
*
5375531 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
5375551 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
5375570 TGCTT
1 TGCTT
5375575 CTTTTCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:5380631 original size:35 final size:36
Alignment explanation
Indices: 5380555--5380631 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
5380545 ACCTAAACAT
* * *
5380555 CACCATCTTCCATCACCATTTTCACGCCTATATCAT
1 CACCATCTTCCATCACCATTTTCACGCCTAAATAAC
* *
5380591 TACCATCTTCTATCACCA-TTTCACGCCTAAATAAC
1 CACCATCTTCCATCACCATTTTCACGCCTAAATAAC
5380626 CACCAT
1 CACCAT
5380632 TCCCTTATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.29, C:0.38, G:0.03, T:0.31
Consensus pattern (36 bp):
CACCATCTTCCATCACCATTTTCACGCCTAAATAAC
Found at i:5381011 original size:24 final size:23
Alignment explanation
Indices: 5380984--5381046 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
5380974 CAAGTGTTGC
* *
5380984 AAGAAAAGAAACAAAAAAGAGAAA
1 AAGAAAAGAAA-AAAAAACAAAAA
5381008 AAGAAAGAAGAAAAAAAAACAAAAA
1 AAG-AA-AAGAAAAAAAAACAAAAA
*
5381033 AAGGGAAAGAAAAA
1 AA-GAAAAGAAAAA
5381047 GACTCCTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 11 0.33
25 15 0.45
26 7 0.21
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.00
Consensus pattern (23 bp):
AAGAAAAGAAAAAAAAACAAAAA
Found at i:5381031 original size:23 final size:23
Alignment explanation
Indices: 5380988--5381032 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5380978 TGTTGCAAGA
* *
5380988 AAAGAAACAAAAAAGAGAAAAAG
1 AAAGAAACAAAAAAAACAAAAAG
5381011 AAAGAAGA-AAAAAAAACAAAAA
1 AAAGAA-ACAAAAAAAACAAAAA
5381033 AAGGGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAGAAACAAAAAAAACAAAAAG
Found at i:5381272 original size:16 final size:16
Alignment explanation
Indices: 5381233--5381291 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
5381223 GAGTTGTAAG
5381233 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
5381250 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
* * *
5381266 TTCTTTCATTTTTTTC
1 TTATTTCATTTCTTTA
5381282 TTATTTCATT
1 TTATTTCATT
5381292 ACCATATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 4 0.11
16 28 0.80
17 3 0.09
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:5392351 original size:15 final size:15
Alignment explanation
Indices: 5392331--5392366 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5392321 TTGATAACAT
5392331 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
* *
5392346 TTCTTTGCATTTCAT
1 TTCTTTCCATTTCAA
5392361 TTCTTT
1 TTCTTT
5392367 AATTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.03, T:0.61
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:5412257 original size:19 final size:20
Alignment explanation
Indices: 5412233--5412283 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5412223 CGGCCAAGAG
5412233 CATGTATCTTT-ATT-AAAAT
1 CATGTAT-TTTCATTAAAAAT
5412252 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
5412272 CATGTATTTTCA
1 CATGTATTTTCA
5412284 AAGGTGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 17 0.57
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:5418486 original size:22 final size:22
Alignment explanation
Indices: 5418458--5418504 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5418448 TTTTTTTTTC
5418458 AAAAAAA-CAAAAAAAAAAGCCA
1 AAAAAAAGC-AAAAAAAAAGCCA
* *
5418480 AAAAAAAGCCAACAAAAAGCCA
1 AAAAAAAGCAAAAAAAAAGCCA
5418502 AAA
1 AAA
5418505 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAAGCAAAAAAAAAGCCA
Found at i:5418487 original size:11 final size:11
Alignment explanation
Indices: 5418468--5418504 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
5418458 AAAAAAACAA
5418468 AAAAAAAAGCC
1 AAAAAAAAGCC
5418479 AAAAAAAAGCC
1 AAAAAAAAGCC
*
5418490 AACAAAAAGCC
1 AAAAAAAAGCC
5418501 AAAA
1 AAAA
5418505 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.73, C:0.19, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCC
Found at i:5427251 original size:35 final size:37
Alignment explanation
Indices: 5427211--5427283 Score: 123
Period size: 35 Copynumber: 2.0 Consensus size: 37
5427201 ATTTATAAGT
5427211 TGGTGATAATATAGGCGTGAT-ATGGTGATGGA-ATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACATA
*
5427246 TGGTGATGATATAGGCGTGATAATGGTGATGGACATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACATA
5427283 T
1 T
5427284 TGTATCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 20 0.57
36 11 0.31
37 4 0.11
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (37 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGACATA
Found at i:5429105 original size:19 final size:21
Alignment explanation
Indices: 5429064--5429112 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
5429054 AACCCCTTTC
5429064 AAAATACATGACTTTTAAATG
1 AAAATACATGACTTTTAAATG
5429085 AAAATACATGA-TTTT-AATG
1 AAAATACATGACTTTTAAATG
*
5429104 AATATACAT
1 AAAATACAT
5429113 ACTCTTGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
AAAATACATGACTTTTAAATG
Found at i:5432311 original size:25 final size:23
Alignment explanation
Indices: 5432260--5432319 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 23
5432250 TTTGAAATTC
5432260 TTCTTTTTTTTTCTTTTCTTCTA
1 TTCTTTTTTTTTCTTTTCTTCTA
*
5432283 TTCTGGTTTTTTTTCTTTT-TGTCTT
1 TTCT--TTTTTTTTCTTTTCT-TCTA
5432308 TTCTTTTTTTTT
1 TTCTTTTTTTTT
5432320 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 12 0.36
24 1 0.03
25 20 0.61
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (23 bp):
TTCTTTTTTTTTCTTTTCTTCTA
Found at i:5433058 original size:19 final size:21
Alignment explanation
Indices: 5433015--5433066 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5433005 GAAACCCCTT
5433015 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5433036 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5433055 TGAAGATACATG
1 TGAAAATACATG
5433067 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5443161 original size:24 final size:22
Alignment explanation
Indices: 5443117--5443163 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
5443107 ATTTATAAGT
5443117 TGGTGATAATATAGGTGTGATA
1 TGGTGATAATATAGGTGTGATA
5443139 TGGTGATGGAATAT-GGTGATGATA
1 TGGTGAT--AATATAGGTG-TGATA
5443163 T
1 T
5443164 AGACGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (22 bp):
TGGTGATAATATAGGTGTGATA
Found at i:5443164 original size:35 final size:36
Alignment explanation
Indices: 5443117--5443184 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
5443107 ATTTATAAGT
**
5443117 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGACGTGATAATGGTGATGGAATA
*
5443152 TGGTGATGATATAGACGTGATAATGGTGATGGA
1 TGGTGATAATATAGACGTGATAATGGTGATGGA
5443185 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.31, C:0.01, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGACGTGATAATGGTGATGGAATA
Found at i:5447324 original size:19 final size:19
Alignment explanation
Indices: 5447298--5447344 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5447288 CAACAAAACC
*
5447298 AAAA-AAAAAAGAGAAAAAG
1 AAAAGAAAAAA-ACAAAAAG
5447317 -AAAGAAAAAAACAAAAAG
1 AAAAGAAAAAAACAAAAAG
5447335 AAAAGAAAAA
1 AAAAGAAAAA
5447345 GACTCCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAACAAAAAG
Found at i:5447338 original size:23 final size:23
Alignment explanation
Indices: 5447298--5447342 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5447288 CAACAAAACC
*
5447298 AAAAAAAAAAGAGAAAAAGAAAG
1 AAAAAAAAAAAAGAAAAAGAAAG
5447321 AAAAAAACAAAAAG-AAAAGAAA
1 AAAAAAA-AAAAAGAAAAAGAAA
5447343 AAGACTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAGAAAAAGAAAG
Found at i:5449259 original size:24 final size:24
Alignment explanation
Indices: 5449205--5449259 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
5449195 AAAAAATCAG
*
5449205 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
5449228 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
5449252 AAAAGAAA
1 AAAAGAAA
5449260 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:5450938 original size:19 final size:21
Alignment explanation
Indices: 5450908--5450959 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5450898 CGGCCAAGAG
*
5450908 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
5450927 CGTGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5450948 CATGTATTTTCA
1 CATGTATTTTCA
5450960 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5451687 original size:17 final size:17
Alignment explanation
Indices: 5451665--5451723 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
5451655 AAATTGGAGT
5451665 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
5451682 ACAAAAAGAAA-AAAA-
1 ACAAAAAGAAAGAAAAG
* *
5451697 TCAGAAA-AAAGAAAAG
1 ACAAAAAGAAAGAAAAG
5451713 A-AGAAAAGAAA
1 ACA-AAAAGAAA
5451724 ATGAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 7 0.21
17 14 0.41
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:5451696 original size:8 final size:8
Alignment explanation
Indices: 5451667--5451719 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
5451657 ATTGGAGTAC
5451667 AAAAAGAA
1 AAAAAGAA
*
5451675 AGAAAAGAC
1 A-AAAAGAA
5451684 AAAAAGAA
1 AAAAAGAA
*
5451692 AAAAATCAGA
1 AAAAA-GA-A
5451702 AAAAAGAA
1 AAAAAGAA
*
5451710 AAGAAGAA
1 AAAAAGAA
5451718 AA
1 AA
5451720 GAAAATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 22 0.59
9 9 0.24
10 6 0.16
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5454807 original size:19 final size:21
Alignment explanation
Indices: 5454777--5454828 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5454767 CGGCCAAGAG
*
5454777 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
5454796 CGTGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5454817 CATGTATTTTCA
1 CATGTATTTTCA
5454829 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5455566 original size:17 final size:18
Alignment explanation
Indices: 5455534--5455580 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
5455524 AAATTGGAGT
* *
5455534 ACAAAAAGAAAGAAAA-G
1 ACAAAAAGAAAAAAAATC
5455551 ACAAAAAGAAAAAAAATC
1 ACAAAAAGAAAAAAAATC
*
5455569 AGAAAAAGAAAA
1 ACAAAAAGAAAA
5455581 GAAGAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAAAAAAATC
Found at i:5455580 original size:14 final size:13
Alignment explanation
Indices: 5455543--5455594 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
5455533 TACAAAAAGA
5455543 AAGAAAAGACAAA-
1 AAGAAAAGA-AAAT
5455556 AAGAAAA-AAAAT
1 AAGAAAAGAAAAT
* *
5455568 CAGAAAAAGAAAAG
1 AAG-AAAAGAAAAT
5455582 AAGAAAAGAAAAT
1 AAGAAAAGAAAAT
5455595 GAAATTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 3 0.09
12 3 0.09
13 20 0.62
14 6 0.19
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (13 bp):
AAGAAAAGAAAAT
Found at i:5455606 original size:31 final size:30
Alignment explanation
Indices: 5455542--5455610 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 30
5455532 GTACAAAAAG
5455542 AAAGAAAAGACAAAAAGAAAAAAAATCAGAA
1 AAAGAAAAGACAAAAAGAAAAAAAATCA-AA
*
5455573 AAAGAAAAGA-AGAAAAGAAAATGAAATTC-AA
1 AAAGAAAAGACA-AAAAGAAAA--AAAATCAAA
5455604 AAAGAAA
1 AAAGAAA
5455611 GCAAGCTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 1 0.03
31 28 0.82
33 5 0.15
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.06
Consensus pattern (30 bp):
AAAGAAAAGACAAAAAGAAAAAAAATCAAA
Found at i:5458676 original size:19 final size:21
Alignment explanation
Indices: 5458646--5458697 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5458636 CGGCCAAGAG
*
5458646 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
5458665 CGTGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5458686 CATGTATTTTCA
1 CATGTATTTTCA
5458698 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5459425 original size:17 final size:17
Alignment explanation
Indices: 5459403--5459467 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
5459393 AAATTGGAGT
*
5459403 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAA
5459420 ACAAAAAGAAA-AAAAA
1 ACAAAAAGAAAGAAAAA
*
5459436 TCAGAAAAAGAAAAGAAGAAA
1 --ACAAAAAG-AAAGAA-AAA
*
5459457 AGAAAAAGAAA
1 ACAAAAAGAAA
5459468 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.10
17 11 0.27
18 10 0.24
19 11 0.27
20 2 0.05
21 3 0.07
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAA
Found at i:5459443 original size:18 final size:19
Alignment explanation
Indices: 5459406--5459467 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
5459396 TTGGAGTACA
5459406 AAAAGAAAGAAAAGACAAAAAG
1 AAAAG-AAGAAAAG--AAAAAG
*
5459428 AAAA-AA-AATCAGAAAAAG
1 AAAAGAAGAA-AAGAAAAAG
5459446 AAAAGAAGAAAAGAAAAAG
1 AAAAGAAGAAAAGAAAAAG
5459465 AAA
1 AAA
5459468 TTCAAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 10 0.29
19 15 0.43
20 6 0.17
22 4 0.11
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAAAGAAAAAG
Found at i:5459449 original size:14 final size:13
Alignment explanation
Indices: 5459406--5459462 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
5459396 TTGGAGTACA
5459406 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
5459420 ACAAA-AAGAAAA-
1 A-AAAGAAGAAAAG
**
5459432 AAAATCAGAAAAAG
1 AAAAGAAG-AAAAG
5459446 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
5459459 AAAA
1 AAAA
5459463 AGAAATTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 20 0.56
14 7 0.19
15 3 0.08
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:5459475 original size:31 final size:30
Alignment explanation
Indices: 5459411--5459479 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 30
5459401 GTACAAAAAG
5459411 AAAGAAAAGACAAAAAGAAAAAAAATCAGAA
1 AAAGAAAAGACAAAAAGAAAAAAAATCA-AA
5459442 AAAGAAAAGA-AGAAAAGAAAAAGAAATTC-AA
1 AAAGAAAAGACA-AAAAGAAAAA-AAA-TCAAA
5459473 AAAGAAA
1 AAAGAAA
5459480 GCAAGCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 1 0.03
31 29 0.83
32 3 0.09
33 2 0.06
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.04
Consensus pattern (30 bp):
AAAGAAAAGACAAAAAGAAAAAAAATCAAA
Found at i:5462546 original size:19 final size:21
Alignment explanation
Indices: 5462516--5462567 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5462506 CGGCCAAGAG
*
5462516 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
5462535 CGTGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5462556 CATGTATTTTCA
1 CATGTATTTTCA
5462568 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5463295 original size:17 final size:17
Alignment explanation
Indices: 5463273--5463337 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
5463263 AAATTGGAGT
*
5463273 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAA
5463290 ACAAAAAGAAA-AAAAA
1 ACAAAAAGAAAGAAAAA
*
5463306 TCAGAAAAAGAAAAGAAGAAA
1 --ACAAAAAG-AAAGAA-AAA
*
5463327 AGAAAAAGAAA
1 ACAAAAAGAAA
5463338 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.10
17 11 0.27
18 10 0.24
19 11 0.27
20 2 0.05
21 3 0.07
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAA
Found at i:5463313 original size:18 final size:19
Alignment explanation
Indices: 5463276--5463337 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
5463266 TTGGAGTACA
5463276 AAAAGAAAGAAAAGACAAAAAG
1 AAAAG-AAGAAAAG--AAAAAG
*
5463298 AAAA-AA-AATCAGAAAAAG
1 AAAAGAAGAA-AAGAAAAAG
5463316 AAAAGAAGAAAAGAAAAAG
1 AAAAGAAGAAAAGAAAAAG
5463335 AAA
1 AAA
5463338 TTCAAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 10 0.29
19 15 0.43
20 6 0.17
22 4 0.11
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAAAGAAAAAG
Found at i:5463319 original size:14 final size:13
Alignment explanation
Indices: 5463276--5463332 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
5463266 TTGGAGTACA
5463276 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
5463290 ACAAA-AAGAAAA-
1 A-AAAGAAGAAAAG
**
5463302 AAAATCAGAAAAAG
1 AAAAGAAG-AAAAG
5463316 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
5463329 AAAA
1 AAAA
5463333 AGAAATTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 20 0.56
14 7 0.19
15 3 0.08
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:5463345 original size:31 final size:30
Alignment explanation
Indices: 5463281--5463349 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 30
5463271 GTACAAAAAG
5463281 AAAGAAAAGACAAAAAGAAAAAAAATCAGAA
1 AAAGAAAAGACAAAAAGAAAAAAAATCA-AA
5463312 AAAGAAAAGA-AGAAAAGAAAAAGAAATTC-AA
1 AAAGAAAAGACA-AAAAGAAAAA-AAA-TCAAA
5463343 AAAGAAA
1 AAAGAAA
5463350 GCAAGCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 1 0.03
31 29 0.83
32 3 0.09
33 2 0.06
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.04
Consensus pattern (30 bp):
AAAGAAAAGACAAAAAGAAAAAAAATCAAA
Found at i:5466409 original size:19 final size:21
Alignment explanation
Indices: 5466385--5466436 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5466375 CGGCCAAGAG
*
5466385 CATGTATCTTCA-CT-AAAAT
1 CATGTATTTTCATCTAAAAAT
*
5466404 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATCTAAAAAT
5466425 CATGTATTTTCA
1 CATGTATTTTCA
5466437 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 17 0.59
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATCTAAAAAT
Found at i:5474269 original size:246 final size:246
Alignment explanation
Indices: 5473824--5474321 Score: 883
Period size: 246 Copynumber: 2.0 Consensus size: 246
5473814 TCATCAACAT
**
5473824 CATC-CATCTCTTCCATCTCTTCCGCAACCATCTCTATCATTTATTTATTTCATTTCATTCTTAT
1 CATCACATCTCTTCCATCAATTCCGCAACCATCTCTATCATTTATTTATTTCATTTCATTCTTAT
5473888 TATTTATTTTCATTACTTATATTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTAT
66 TATTTATTTTCATTACTTATATTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTAT
* *
5473953 TATCTTATTTTGCAGCCCAAACTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGGG
131 TATCTTATTTTGCAACCCAAACTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGCG
*
5474018 ACACAATAAGGCTAACTACTCTCTTCTC-CCAAAGCGTGTAGATTCGCCTTA
196 ACACAATAAGGCTAACTACCCTCTTC-CACCAAAGCGTGTAGATTCGCCTTA
* *
5474069 CATCACATCTCTTCCATCAATTCCGCAGCCATCTCTATCCTTTATTTATTTCATTTCATTCTTAT
1 CATCACATCTCTTCCATCAATTCCGCAACCATCTCTATCATTTATTTATTTCATTTCATTCTTAT
*
5474134 TATTTATTTTCATTACTTATATTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTCT
66 TATTTATTTTCATTACTTATATTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTAT
5474199 TATCTTATTTTGCAACCCAAACTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGCG
131 TATCTTATTTTGCAACCCAAACTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGCG
* *
5474264 ACACAATAAGGCTATCTACCCTCTTCCATCAAAGCGTGTAGATTCGCCTTA
196 ACACAATAAGGCTAACTACCCTCTTCCACCAAAGCGTGTAGATTCGCCTTA
5474315 CATCACA
1 CATCACA
5474322 AAGTCAAGAG
Statistics
Matches: 241, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
245 5 0.02
246 236 0.98
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (246 bp):
CATCACATCTCTTCCATCAATTCCGCAACCATCTCTATCATTTATTTATTTCATTTCATTCTTAT
TATTTATTTTCATTACTTATATTATTATCCCCTTTATTAAATTCCATTATTAATCATTATTTTAT
TATCTTATTTTGCAACCCAAACTTATAAATTCAAGGACATCAGTACTTGTCAATCCTAGATCGCG
ACACAATAAGGCTAACTACCCTCTTCCACCAAAGCGTGTAGATTCGCCTTA
Found at i:5479264 original size:20 final size:20
Alignment explanation
Indices: 5479239--5479283 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
5479229 CAACAAAACC
*
5479239 AAAAAAAGAGAAAAA-TAAAG
1 AAAAAAA-AGAAAAAGAAAAG
5479259 AAAAAAAAGAAAAAGAAAAG
1 AAAAAAAAGAAAAAGAAAAG
5479279 AAAAA
1 AAAAA
5479284 GACTCCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGAAAAAGAAAAG
Found at i:5479285 original size:11 final size:10
Alignment explanation
Indices: 5479239--5479283 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
5479229 CAACAAAACC
*
5479239 AAAAAAAGAG
1 AAAAAAAAAG
*
5479249 AAAAATAAAG
1 AAAAAAAAAG
5479259 -AAAAAAAAG
1 AAAAAAAAAG
5479268 AAAAAGAAAAG
1 AAAAA-AAAAG
5479279 AAAAA
1 AAAAA
5479284 GACTCCTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.27
10 12 0.40
11 10 0.33
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5479326 original size:14 final size:14
Alignment explanation
Indices: 5479310--5479365 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
5479300 TTTGGAGTGC
5479310 AAAAGAAAGAAAACA
1 AAAAG-AAGAAAACA
5479325 AAAAGAAGAAAATTCA
1 AAAAGAAGAAAA--CA
*
5479341 AAGAAAAAGAAAA-A
1 AA-AAGAAGAAAACA
*
5479355 AAATGAAGAAA
1 AAAAGAAGAAA
5479366 GTTGCAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.20
14 10 0.29
15 5 0.14
16 4 0.11
17 9 0.26
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAGAAGAAAACA
Found at i:5479365 original size:30 final size:32
Alignment explanation
Indices: 5479307--5479374 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
5479297 AAATTTGGAG
*
5479307 TGCAAA-AGAAAGAAAACAAAAAGAAGAAAAT
1 TGCAAAGAAAAAGAAAACAAAAAGAAGAAAAT
* *
5479338 T-CAAAGAAAAAGAAAA-AAAATGAAGAAAGT
1 TGCAAAGAAAAAGAAAACAAAAAGAAGAAAAT
5479368 TGCAAAG
1 TGCAAAG
5479375 TACACTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.68, C:0.06, G:0.18, T:0.09
Consensus pattern (32 bp):
TGCAAAGAAAAAGAAAACAAAAAGAAGAAAAT
Found at i:5479537 original size:16 final size:16
Alignment explanation
Indices: 5479486--5479540 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
5479476 GTAAGTTATC
5479486 TTCATTTTTCTTACTAT
1 TTCATTTTTCTTA-TAT
*
5479503 TTCA-TTTTCTTATGCT
1 TTCATTTTTCTTAT-AT
5479519 TTCATCTTTTCTTAT-T
1 TTCAT-TTTTCTTATAT
5479535 TTCATT
1 TTCATT
5479541 ACTTTATCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 19 0.56
17 4 0.12
18 9 0.26
ACGTcount: A:0.15, C:0.18, G:0.02, T:0.65
Consensus pattern (16 bp):
TTCATTTTTCTTATAT
Found at i:5483851 original size:29 final size:29
Alignment explanation
Indices: 5483817--5483878 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
5483807 TTGGAGTGCA
5483817 AAAGAAAGAA-AACAAAATGAAGAAAATT-C
1 AAAGAAA-AAGAA-AAAATGAAGAAAATTGC
* *
5483846 AAAGAAAAAGAAAAAGTGAAGAAAGTTGC
1 AAAGAAAAAGAAAAAATGAAGAAAATTGC
5483875 AAAG
1 AAAG
5483879 TACACTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.66, C:0.05, G:0.19, T:0.10
Consensus pattern (29 bp):
AAAGAAAAAGAAAAAATGAAGAAAATTGC
Found at i:5495036 original size:15 final size:17
Alignment explanation
Indices: 5495016--5495052 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5495006 AATATGAAAG
5495016 AAGAAAA-GAAA-TGAT
1 AAGAAAAGGAAATTGAT
5495031 AAGAAAAGGAAATTGAT
1 AAGAAAAGGAAATTGAT
5495048 -AGAAA
1 AAGAAA
5495053 TGTTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (17 bp):
AAGAAAAGGAAATTGAT
Found at i:5499037 original size:16 final size:17
Alignment explanation
Indices: 5499005--5499053 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
5498995 AAAGTAATGA
5499005 AATAAGAAAAGATGAAAG
1 AATAAGAAAA-ATGAAAG
*
5499023 AATAAG-AAAATGAAAT
1 AATAAGAAAAATGAAAG
*
5499039 AGTAAGAAAAATGAA
1 AATAAGAAAAATGAA
5499054 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 11 0.39
18 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (17 bp):
AATAAGAAAAATGAAAG
Found at i:5499266 original size:6 final size:6
Alignment explanation
Indices: 5499255--5499298 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
5499245 GATGTAGGAG
*
5499255 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
5499299 TTTGGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:5499278 original size:12 final size:12
Alignment explanation
Indices: 5499255--5499298 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
5499245 GATGTAGGAG
5499255 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
5499266 TCTTTTTGTTTT
1 TCTTTTTCTTTT
5499278 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
5499291 TCTCTTTT
1 TCT-TTTT
5499299 TTTGGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:5506278 original size:14 final size:12
Alignment explanation
Indices: 5506256--5506318 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
5506246 TTGGCTCTTA
5506256 TTTTGTTTTTTT
1 TTTTGTTTTTTT
***
5506268 TTGCCTTTTTTT
1 TTTTGTTTTTTT
5506280 TTTTGCCTTTTTTT
1 TTTTG--TTTTTTT
5506294 GTTTT-TTTTTTT
1 -TTTTGTTTTTTT
5506306 TTTTGTTTTTTT
1 TTTTGTTTTTTT
5506318 T
1 T
5506319 GGAAAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 4 0.10
12 26 0.63
14 7 0.17
15 4 0.10
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:5506281 original size:15 final size:14
Alignment explanation
Indices: 5506261--5506318 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
5506251 TCTTATTTTG
5506261 TTTTTTTTTGCCTT
1 TTTTTTTTTGCCTT
5506275 TTTTTTTTTGCCTT
1 TTTTTTTTTGCCTT
5506289 TTTTTGTTTT---TT
1 TTTTT-TTTTGCCTT
5506301 TTTTTTTTTG--TT
1 TTTTTTTTTGCCTT
5506313 TTTTTT
1 TTTTTT
5506319 GGAAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.10
12 15 0.36
14 19 0.45
15 4 0.10
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTGCCTT
Found at i:5506283 original size:24 final size:24
Alignment explanation
Indices: 5506256--5506319 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
5506246 TTGGCTCTTA
5506256 TTTTGTTTTTTTTTGCCTTTTTTT
1 TTTTGTTTTTTTTTGCCTTTTTTT
** **
5506280 TTTTGCCTTTTTTTGTTTTTTTTT
1 TTTTGTTTTTTTTTGCCTTTTTTT
*
5506304 TTTTTTGTTTTTTTTG
1 TTTTGT-TTTTTTTTG
5506320 GAAAAAATAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (24 bp):
TTTTGTTTTTTTTTGCCTTTTTTT
Found at i:5509551 original size:10 final size:10
Alignment explanation
Indices: 5509536--5509574 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
5509526 CCGGGTTAGT
*
5509536 AAAAAAATAA
1 AAAAAAACAA
5509546 AAAAAAACAAA
1 AAAAAAAC-AA
5509557 AAAAAAACAA
1 AAAAAAACAA
5509567 AAGAAAAA
1 AA-AAAAA
5509575 AAGTTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.90, C:0.05, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:5509552 original size:11 final size:11
Alignment explanation
Indices: 5509544--5509575 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
5509534 GTAAAAAAAT
5509544 AAAAAAAAACA
1 AAAAAAAAACA
5509555 AAAAAAAAACA
1 AAAAAAAAACA
5509566 AAAGAAAAAA
1 AAA-AAAAAA
5509576 AGTTTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:5523862 original size:12 final size:11
Alignment explanation
Indices: 5523837--5523880 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
5523827 GATACAACAA
5523837 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
5523850 AAAGAAGAAAAG
1 AAA-AAGAAAAG
5523862 AAAAGAGAAAAG
1 AAAA-AGAAAAG
5523874 AAAAAGA
1 AAAAAGA
5523881 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:5530588 original size:12 final size:12
Alignment explanation
Indices: 5530550--5530585 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
5530540 GATGTAGTAG
5530550 TCTTTT-TCTTT
1 TCTTTTCTCTTT
5530561 TCTTTTCTCTTT
1 TCTTTTCTCTTT
5530573 TCTTTTCTTCTTT
1 TCTTTTC-TCTTT
5530586 CTTGTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.26
12 12 0.52
13 5 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTTTCTCTTT
Found at i:5532691 original size:35 final size:36
Alignment explanation
Indices: 5532634--5532701 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
5532624 ATACACTCTG
5532634 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
5532670 TCCATCACCA-TATCACTCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
5532702 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.31, C:0.37, G:0.01, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:5536417 original size:14 final size:12
Alignment explanation
Indices: 5536389--5536426 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
5536379 ACCATTCAAT
5536389 AAAAAGAAAATC
1 AAAAAGAAAATC
5536401 AAAAAGAGAAATGC
1 AAAAAGA-AAAT-C
5536415 AAAAA-AAAATC
1 AAAAAGAAAATC
5536426 A
1 A
5536427 GCAAGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 11 0.46
13 5 0.21
14 6 0.25
ACGTcount: A:0.74, C:0.08, G:0.11, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATC
Found at i:5536492 original size:13 final size:14
Alignment explanation
Indices: 5536469--5536498 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5536459 AAGTGAAGAA
5536469 AAACAAAAGAAAGG
1 AAACAAAAGAAAGG
5536483 AAAC-AAAGAAAGG
1 AAACAAAAGAAAGG
5536496 AAA
1 AAA
5536499 ATGCAAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (14 bp):
AAACAAAAGAAAGG
Found at i:5547491 original size:15 final size:17
Alignment explanation
Indices: 5547466--5547497 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5547456 CTTTCTTCTT
5547466 TCATATTCTAT-TTTAA
1 TCATATTCTATCTTTAA
5547482 TCAT-TTCTATCTTTAA
1 TCATATTCTATCTTTAA
5547498 ATTTTGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (17 bp):
TCATATTCTATCTTTAA
Found at i:5551457 original size:19 final size:20
Alignment explanation
Indices: 5551411--5551459 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5551401 TAATAAAGGG
5551411 AATAATAAT-ATAAGAAATGA
1 AATAA-AATAATAAGAAATGA
5551431 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGAAATGA
5551450 AATAAAATAA
1 AATAAAATAA
5551460 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
AATAAAATAATAAGAAATGA
Found at i:5551915 original size:19 final size:21
Alignment explanation
Indices: 5551872--5551923 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5551862 GAAACCCCTT
5551872 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
5551893 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
5551912 TGAATATACATG
1 TGAAAATACATG
5551924 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5553509 original size:24 final size:23
Alignment explanation
Indices: 5553476--5553526 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
5553466 GAACAATCAT
*
5553476 GTCCCCAAAAGTTATGTTCCTTG
1 GTCCCCAAAAGTCATGTTCCTTG
5553499 GTCCCTCAAAAGTCATGTTCCTTG
1 GTCCC-CAAAAGTCATGTTCCTTG
5553523 GTCC
1 GTCC
5553527 TTAGAATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (23 bp):
GTCCCCAAAAGTCATGTTCCTTG
Found at i:5555580 original size:19 final size:20
Alignment explanation
Indices: 5555534--5555582 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5555524 TAATAAAGGG
5555534 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
5555554 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
5555573 AATAAAATAA
1 AATAAAATAA
5555583 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:5557245 original size:11 final size:11
Alignment explanation
Indices: 5557231--5557264 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
5557221 CAAAATAGGC
5557231 AAAAAAACACA
1 AAAAAAACACA
5557242 AAAAAAACA-A
1 AAAAAAACACA
5557252 AAAAAAA-ACA
1 AAAAAAACACA
5557262 AAA
1 AAA
5557265 TTTCAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 12 0.55
11 9 0.41
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACACA
Found at i:5557264 original size:9 final size:9
Alignment explanation
Indices: 5557213--5557257 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
5557203 ATTCTTTTAG
5557213 AAAAAAAAC
1 AAAAAAAAC
* **
5557222 AAAATAGGC
1 AAAAAAAAC
5557231 AAAAAAACAC
1 AAAAAAA-AC
5557241 AAAAAAAAC
1 AAAAAAAAC
5557250 AAAAAAAA
1 AAAAAAAA
5557258 AACAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.82, C:0.11, G:0.04, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:5561401 original size:50 final size:50
Alignment explanation
Indices: 5561296--5561402 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
5561286 TCACACTCCA
* * * * *
5561296 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATCATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
* *
5561346 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
5561396 ATTTTCC
1 ATTTTCC
5561403 ACATATCCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
49 3 0.06
50 39 0.83
51 5 0.11
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:5561985 original size:19 final size:21
Alignment explanation
Indices: 5561942--5561993 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5561932 AAAACCCCTT
5561942 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
5561963 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
5561982 TGAATATACATG
1 TGAAAATACATG
5561994 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5563378 original size:12 final size:12
Alignment explanation
Indices: 5563349--5563385 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5563339 AAAGTGGACT
5563349 AGAGTAGCT-GG
1 AGAGTAGCTGGG
5563360 A-AGTAGCTGGG
1 AGAGTAGCTGGG
5563371 AGAGTAGCTGAGG
1 AGAGTAGCTG-GG
5563384 AG
1 AG
5563386 TTGAGAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.30
11 4 0.17
12 8 0.35
13 4 0.17
ACGTcount: A:0.30, C:0.08, G:0.46, T:0.16
Consensus pattern (12 bp):
AGAGTAGCTGGG
Found at i:5564567 original size:22 final size:24
Alignment explanation
Indices: 5564535--5564591 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
5564525 AAAATCCAGC
5564535 AAAGAAAAAA-TCAAAGCACTC-A
1 AAAGAAAAAATTCAAAGCACTCGA
* *
5564557 AAAGAATAAATTGAAAGCACTCGA
1 AAAGAAAAAATTCAAAGCACTCGA
5564581 AAAGAAGAAAA
1 AAAGAA-AAAA
5564592 AGAAATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.31
23 10 0.34
24 7 0.24
25 3 0.10
ACGTcount: A:0.63, C:0.12, G:0.14, T:0.11
Consensus pattern (24 bp):
AAAGAAAAAATTCAAAGCACTCGA
Found at i:5564596 original size:24 final size:23
Alignment explanation
Indices: 5564547--5564596 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
5564537 AGAAAAAATC
* **
5564547 AAAGCACTCAAAAGAATAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
5564570 AAAGCACTCGAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
5564594 AAA
1 AAA
5564597 TAAAGAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.10
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:5567533 original size:90 final size:91
Alignment explanation
Indices: 5567380--5567559 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
5567370 GAAATGATGC
*
5567380 TTGGCCGAATAGGGAGAAAGCTCTTCATCTTGGCGCCTAAATAAACCATATGCAAGGCATATGGG
1 TTGGCCGAATAAGGAGAAAGCTCTTCATCTTGGCGCCTAAATAAACCATATGCAAGGCATATGGG
*
5567445 G-CTGTTCACATGCAAAGCACATGGA
66 GTCTGGTCACATGCAAAGCACATGGA
*
5567470 TTGGCCGAATAAGGAGAGAA-CTCTTCATCTTGGCGCCTAAATAATCC-TCATGCAAGGCATATG
1 TTGGCCGAATAAGGAGA-AAGCTCTTCATCTTGGCGCCTAAATAAACCAT-ATGCAAGGCATATG
* *
5567533 GGGTCTGGTCATATGCAAGGCACATGG
64 GGGTCTGGTCACATGCAAAGCACATGG
5567560 GTGTTCTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
89 1 0.01
90 59 0.72
91 22 0.27
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.23
Consensus pattern (91 bp):
TTGGCCGAATAAGGAGAAAGCTCTTCATCTTGGCGCCTAAATAAACCATATGCAAGGCATATGGG
GTCTGGTCACATGCAAAGCACATGGA
Found at i:5585712 original size:12 final size:12
Alignment explanation
Indices: 5585695--5585755 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
5585685 TTTTTTTTTC
5585695 AAAAAACAAAAA
1 AAAAAACAAAAA
*
5585707 AAAAAACAAAAG
1 AAAAAACAAAAA
**
5585719 AAAAGGCAAAAA
1 AAAAAACAAAAA
**
5585731 AAAAGGCAAAAAA
1 AAAAAAC-AAAAA
5585744 AACAAAACAAAA
1 AA-AAAACAAAA
5585756 GCCAAAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 27 0.66
13 11 0.27
14 3 0.07
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:5585743 original size:21 final size:21
Alignment explanation
Indices: 5585719--5585771 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5585709 AAAACAAAAG
* *
5585719 AAAAGGCAAAAAAAAAGGCAA
1 AAAAGACAAAAAAAAAGCCAA
* *
5585740 AAAAAACAAAACAAAAGCCAA
1 AAAAGACAAAAAAAAAGCCAA
*
5585761 AAAAGCCAAAA
1 AAAAGACAAAA
5585772 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAGACAAAAAAAAAGCCAA
Found at i:5585761 original size:12 final size:11
Alignment explanation
Indices: 5585703--5585764 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
5585693 TCAAAAAACA
**
5585703 AAAAAAAAAAC
1 AAAAAAAAGGC
5585714 AAAAGAAAAGGC
1 AAAA-AAAAGGC
5585726 AAAAAAAAAGGC
1 -AAAAAAAAGGC
5585738 AAAAAAAA--C
1 AAAAAAAAGGC
*
5585747 AAAACAAAAGCC
1 AAAA-AAAAGGC
5585759 AAAAAA
1 AAAAAA
5585765 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 5 0.11
10 4 0.09
11 14 0.32
12 17 0.39
13 4 0.09
ACGTcount: A:0.79, C:0.11, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGC
Found at i:5594531 original size:30 final size:31
Alignment explanation
Indices: 5594492--5594551 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5594482 ACGTGCTGCC
**
5594492 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
5594523 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
5594552 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:5598878 original size:22 final size:23
Alignment explanation
Indices: 5598832--5598890 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
5598822 CACTGTTCAG
*
5598832 CATTCACTGTTCATGGGAATTGTT
1 CATT-ACTGTTCATCGGAATTGTT
*
5598856 CATTACTGTTCA-CGGTATTGTT
1 CATTACTGTTCATCGGAATTGTT
* *
5598878 CATCACTATTCAT
1 CATTACTGTTCAT
5598891 AAAAAATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 18 0.60
23 8 0.27
24 4 0.13
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.42
Consensus pattern (23 bp):
CATTACTGTTCATCGGAATTGTT
Found at i:5609421 original size:24 final size:22
Alignment explanation
Indices: 5609362--5609421 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
5609352 AAAATCAGCA
5609362 AAGAAAATAAAAGCACTCAAAAG
1 AAGAAAA-AAAAGCACTCAAAAG
* *
5609385 AATAAATTAAAAGCACTCGAAAAG
1 AAGAAA-AAAAAGCACTC-AAAAG
5609409 AAGAAAAAGAAAG
1 AAGAAAAA-AAAG
5609422 AAAGAAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.65, C:0.10, G:0.15, T:0.10
Consensus pattern (22 bp):
AAGAAAAAAAAGCACTCAAAAG
Found at i:5610758 original size:24 final size:21
Alignment explanation
Indices: 5610724--5610766 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
5610714 TCCACAAGAC
*
5610724 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
5610746 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
5610767 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Done.