Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008493.1 Hibiscus syriacus cultivar Beakdansim tig00111336_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: 691020
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:416384 original size:39 final size:38
Alignment explanation
Indices: 416330--416424 Score: 163
Period size: 39 Copynumber: 2.5 Consensus size: 38
416320 TATATTATAC
416330 ATGTTTTCAAAACTATATATTATATACATTTTCAAAAAA
1 ATGTTTTCAAAACTATATATTATATACATTTTC-AAAAA
*
416369 ATGTTTTCAAAACTATATATTATATATATTTTCAAAAA
1 ATGTTTTCAAAACTATATATTATATACATTTTCAAAAA
*
416407 ATATTTTCAAAACTATAT
1 ATGTTTTCAAAACTATAT
416425 TATATTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 22 0.41
39 32 0.59
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (38 bp):
ATGTTTTCAAAACTATATATTATATACATTTTCAAAAA
Found at i:416412 original size:13 final size:13
Alignment explanation
Indices: 416394--416418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
416384 TATATTATAT
416394 ATATTTTCAAAAA
1 ATATTTTCAAAAA
416407 ATATTTTCAAAA
1 ATATTTTCAAAA
416419 CTATATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTTCAAAAA
Found at i:417232 original size:72 final size:72
Alignment explanation
Indices: 417079--417278 Score: 267
Period size: 72 Copynumber: 2.8 Consensus size: 72
417069 ATTGAGCACA
* * * * * * * *
417079 ATATCCTTCGTCGTGAAGTTGAAATCGTGGGTAACTTCTTCATC-TAAAGTTGTGTCGATCTCTT
1 ATATCCTTCGTCATGAAGTTGAAATCGTGGGTGACTTCTTCGTCATGAAGTTGAGTTGATATCTC
*
417143 GGGCGTG
66 GGGCGGG
* * ** *
417150 ATATCCTTCGTCATGAAATTGAAATCGTGGGTGGCCCCTTCGTCATGAAGTTAAGTTGATATCTC
1 ATATCCTTCGTCATGAAGTTGAAATCGTGGGTGACTTCTTCGTCATGAAGTTGAGTTGATATCTC
417215 GGGCGGG
66 GGGCGGG
417222 ATATCCTTCGTCATGAAGTTGAAATCGTGGGTGACTTCTTCGTCATGAAGTTGAGTT
1 ATATCCTTCGTCATGAAGTTGAAATCGTGGGTGACTTCTTCGTCATGAAGTTGAGTT
417279 CAAATTTGTT
Statistics
Matches: 109, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
71 37 0.34
72 72 0.66
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (72 bp):
ATATCCTTCGTCATGAAGTTGAAATCGTGGGTGACTTCTTCGTCATGAAGTTGAGTTGATATCTC
GGGCGGG
Found at i:424646 original size:12 final size:12
Alignment explanation
Indices: 424626--424659 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
424616 AGTTAGTAAG
424626 ATAAAAATAATA
1 ATAAAAATAATA
*
424638 ATCAAAATAATA
1 ATAAAAATAATA
424650 ATAAAAATAA
1 ATAAAAATAA
424660 AAAGTGATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:425716 original size:22 final size:21
Alignment explanation
Indices: 425691--425738 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
425681 AGGGTTAGAA
425691 TAAAACAAATAAAAATTTAAAT
1 TAAAACAAATAAAAA-TTAAAT
***
425713 TAAATTGAATAAAAATTAAAT
1 TAAAACAAATAAAAATTAAAT
*
425734 CAAAA
1 TAAAA
425739 AGAAAATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAACAAATAAAAATTAAAT
Found at i:427076 original size:15 final size:16
Alignment explanation
Indices: 427056--427090 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
427046 TATGAATATA
427056 TTTCAAAAA-ATATGT
1 TTTCAAAAACATATGT
427071 TTTCAAAAACTATATGT
1 TTTCAAAAAC-ATATGT
427088 TTT
1 TTT
427091 TTTTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (16 bp):
TTTCAAAAACATATGT
Found at i:427099 original size:20 final size:20
Alignment explanation
Indices: 427070--427121 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 20
427060 AAAAAATATG
427070 TTTTCAAAAACTATATGTTTT
1 TTTTCAAAAACTATATG-TTT
427091 TTTTCAAAAACTATATGTTT
1 TTTTCAAAAACTATATGTTT
427111 TTTTCAAAAAC
1 TTTTCAAAAAC
427122 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCAAAAACTATATGTTT
Found at i:427184 original size:36 final size:35
Alignment explanation
Indices: 427133--427201 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
427123 TTTTTTTAAA
* *
427133 AAACTATATATTATATATTTTCAAAAACTATTTTAT
1 AAACTATATAATATATACTTTCAAAAA-TATTTTAT
* *
427169 AAACTATATAATATATGCTTTCAAATATATTTT
1 AAACTATATAATATATACTTTCAAAAATATTTT
427202 TTTTAAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.46
Consensus pattern (35 bp):
AAACTATATAATATATACTTTCAAAAATATTTTAT
Found at i:428003 original size:13 final size:13
Alignment explanation
Indices: 428000--428070 Score: 115
Period size: 13 Copynumber: 5.5 Consensus size: 13
427990 CCGTTTACCC
*
428000 GACCCGACCTGTT
1 GACCCGACCCGTT
*
428013 TACCCGACCCGTT
1 GACCCGACCCGTT
428026 GACCCGACCCGTT
1 GACCCGACCCGTT
428039 GACCCGACCCGTT
1 GACCCGACCCGTT
*
428052 GACTCGACCCGTT
1 GACCCGACCCGTT
428065 GACCCG
1 GACCCG
428071 TTGACCGTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.15, C:0.44, G:0.23, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:428048 original size:18 final size:18
Alignment explanation
Indices: 427979--428023 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
427969 ACCGGTCACA
427979 ACCCGA-CCGACCCGTTT
1 ACCCGACCCGACCCGTTT
*
427996 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTT
428014 ACCCGACCCG
1 ACCCGACCCG
428024 TTGACCCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.18, C:0.49, G:0.18, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:428084 original size:10 final size:8
Alignment explanation
Indices: 428018--428096 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
428008 CTGTTTACCC
428018 GACCCGTT
1 GACCCGTT
428026 GACCC---
1 GACCCGTT
428031 GACCCGTT
1 GACCCGTT
428039 GACCC---
1 GACCCGTT
428044 GACCCGTT
1 GACCCGTT
*
428052 GA--C-TC
1 GACCCGTT
428057 GACCCGTT
1 GACCCGTT
428065 GACCCGTT
1 GACCCGTT
428073 GACCGTCGTT
1 GACC--CGTT
428083 GACCACTGTT
1 GACC-C-GTT
428093 GACC
1 GACC
428097 AAAACTTTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 22
0.69 0.04 0.27
Matches are distributed among these distances:
5 13 0.23
6 1 0.02
7 1 0.02
8 25 0.45
9 1 0.02
10 15 0.27
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:429389 original size:18 final size:18
Alignment explanation
Indices: 429363--429397 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
429353 TCGAAAGGAC
*
429363 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
429381 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
429398 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:431913 original size:37 final size:37
Alignment explanation
Indices: 431811--432021 Score: 220
Period size: 37 Copynumber: 5.8 Consensus size: 37
431801 CAAAAATACA
**
431811 TTTTCAAAAACTATAT-TATATATATGTTTTCAAAAAT-
1 TTTTC-AAAACTATATAT-TATATATCATTTCAAAAATG
* * * *
431848 ATTTAAAAACTATATATTATACAT--TTTCAATAATG
1 TTTTCAAAACTATATATTATATATCATTTCAAAAATG
*
431883 TTTTCAAAACTATATATTATATATGATTTCAAAAATG
1 TTTTCAAAACTATATATTATATATCATTTCAAAAATG
** * * *
431920 TTTTTTAAACTATATATTATATACCTTTTAAAAAATG
1 TTTTCAAAACTATATATTATATATCATTTCAAAAATG
431957 TTTTCAAAACTATATATTATATA-CATTTTCAAAAAATG
1 TTTTCAAAACTATATATTATATATCA-TTTC-AAAAATG
431995 TTTTCAAAAC--TATATTATATTATCATT
1 TTTTCAAAACTATATATTATA-TATCATT
432022 ATATATATAC
Statistics
Matches: 148, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
34 9 0.06
35 21 0.14
36 26 0.18
37 73 0.49
38 19 0.13
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATATCATTTCAAAAATG
Found at i:432700 original size:2 final size:2
Alignment explanation
Indices: 432693--432748 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
432683 ATCCTAACCT
432693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
432735 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
432749 GGGTTAGGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:433969 original size:21 final size:21
Alignment explanation
Indices: 433943--434002 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
433933 CAGAATAAGT
433943 AGTATCGGTACTCCTTCAATG
1 AGTATCGGTACTCCTTCAATG
*
433964 AGTATCAGTACTCCTTCAATG
1 AGTATCGGTACTCCTTCAATG
433985 AGTATCGGTACTACCTTC
1 AGTATCGGTACT-CCTTC
434003 GTAATATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 31 0.86
22 5 0.14
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTATCGGTACTCCTTCAATG
Found at i:434166 original size:20 final size:20
Alignment explanation
Indices: 434141--434215 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
434131 GTATCAATAC
434141 TACTATTCATACAATATCGA
1 TACTATTCATACAATATCGA
** *
434161 TACTATTCATTTAGTATC-A
1 TACTATTCATACAATATCGA
* *
434180 GTATTATTCATACAGTA-CGA
1 -TACTATTCATACAATATCGA
434200 TACTATTCATA-AATAT
1 TACTATTCATACAATAT
434216 TTTGTGATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 3 0.07
19 12 0.27
20 29 0.66
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:436885 original size:20 final size:20
Alignment explanation
Indices: 436836--436905 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
436826 GTATTGATAC
*
436836 TACTATTCACACAGTATCAA
1 TACTATTCATACAGTATCAA
* **
436856 TACTATTCATACAGTGTCGG
1 TACTATTCATACAGTATCAA
* *
436876 TACTATTCATATAGTA-CGA
1 TACTATTCATACAGTATCAA
*
436895 TAATATTCATA
1 TACTATTCATA
436906 AAAATGTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:438848 original size:12 final size:13
Alignment explanation
Indices: 438792--438867 Score: 50
Period size: 15 Copynumber: 5.6 Consensus size: 13
438782 TTTGAACCTA
438792 AATAAATATAACAT
1 AATAAATAT-ACAT
*
438806 AAT-ATTA-ACAAT
1 AATAAATATAC-AT
* *
438818 CATATAATATAATAT
1 AATA-AATAT-ACAT
438833 AATAAATATA-AT
1 AATAAATATACAT
438845 AATAAATAATACTAT
1 AATAAAT-ATAC-AT
438860 AATAAATA
1 AATAAATA
438868 ATATGTACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
11 2 0.04
12 13 0.27
13 7 0.14
14 12 0.24
15 14 0.29
16 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAATATACAT
Found at i:438855 original size:15 final size:15
Alignment explanation
Indices: 438821--438871 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
438811 TAACAATCAT
438821 ATAATATAAT-AT-A
1 ATAATATAATAATAA
438834 ATAAATATAATAATAA
1 AT-AATATAATAATAA
438850 ATAATACT-ATAATAA
1 ATAATA-TAATAATAA
438865 ATAATAT
1 ATAATAT
438872 GTACACTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 19 0.56
16 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATATAATAATAA
Found at i:438949 original size:16 final size:17
Alignment explanation
Indices: 438928--438961 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
438918 TGAAAACTAT
*
438928 ATAATATTTTTTC-AAA
1 ATAATATGTTTTCTAAA
438944 ATAATATGTTTTCTAAA
1 ATAATATGTTTTCTAAA
438961 A
1 A
438962 CTATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAATATGTTTTCTAAA
Found at i:439057 original size:24 final size:22
Alignment explanation
Indices: 438993--439131 Score: 132
Period size: 22 Copynumber: 6.5 Consensus size: 22
438983 AAACCGTTTT
438993 AAAACTATATTATATGTTTTCA
1 AAAACTATATTATATGTTTTCA
439015 AAAACTATATTATATGTTTTCA
1 AAAACTATATTATATGTTTTCA
439037 AAAACTATATTATATATGTTTT-A
1 AAAACTATA-T-TATATGTTTTCA
* **
439060 AAGAAC-----CAT-T-TTTAAA
1 AA-AACTATATTATATGTTTTCA
*
439076 AAAGCTATATATAATATGTTTTCA
1 AAAACTATAT-T-ATATGTTTTCA
*
439100 AAAACTATATTATATATTTTCA
1 AAAACTATATTATATGTTTTCA
439122 AAAACTATAT
1 AAAACTATAT
439132 ATTATATATA
Statistics
Matches: 96, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 2 0.02
22 53 0.55
23 6 0.06
24 26 0.27
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAACTATATTATATGTTTTCA
Found at i:439132 original size:24 final size:24
Alignment explanation
Indices: 439069--439140 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 24
439059 AAAGAACCAT
* * *
439069 TTTTAAAAAAGCTATATATAATATG
1 TTTTCAAAAA-CTATATATTATATA
439094 TTTTCAAAAAC--TATATTATATA
1 TTTTCAAAAACTATATATTATATA
439116 TTTTCAAAAACTATATATTATATA
1 TTTTCAAAAACTATATATTATATA
439140 T
1 T
439141 ATTTTTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 20 0.48
24 13 0.31
25 9 0.21
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (24 bp):
TTTTCAAAAACTATATATTATATA
Found at i:439967 original size:50 final size:51
Alignment explanation
Indices: 439877--439972 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 51
439867 TGAGTCTAGA
** **
439877 TTGAATGTTCTTCTAAGTTGGATATCCTTCGTTGTAAAGTTGAAATCCAAC
1 TTGAATGTTCTTCTAAGTTCAATATCCTTCAATGTAAAGTTGAAATCCAAC
* * *
439928 TTGAATGTTCTTC-GAGTTCAATATCCTTTAATGTGAAGTTGAAAT
1 TTGAATGTTCTTCTAAGTTCAATATCCTTCAATGTAAAGTTGAAAT
439973 TGACTCTGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 25 0.66
51 13 0.34
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.41
Consensus pattern (51 bp):
TTGAATGTTCTTCTAAGTTCAATATCCTTCAATGTAAAGTTGAAATCCAAC
Found at i:444106 original size:2 final size:2
Alignment explanation
Indices: 444099--444130 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
444089 AAAGAGGGGA
444099 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
444131 GTAAGAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449041 original size:21 final size:20
Alignment explanation
Indices: 448988--449042 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
448978 AACAATGATC
*
448988 TTGAAAGTAAAATAAAAGAA
1 TTGAAAATAAAATAAAAGAA
* * *
449008 TTGTAAATCAAAATAGAAGAT
1 TTGAAAAT-AAAATAAAAGAA
449029 TTAGAAAATAAAAT
1 TT-GAAAATAAAAT
449043 TTCTGATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
22 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.25
Consensus pattern (20 bp):
TTGAAAATAAAATAAAAGAA
Found at i:452497 original size:21 final size:20
Alignment explanation
Indices: 452445--452502 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
452435 ACATTTTTGG
*
452445 TCACTAGGTATCGATACCTG
1 TCACTAGGTATCGATACCTC
* *
452465 TCACCCATGTATCGATACCCTC
1 TCA-CTAGGTATCGATA-CCTC
*
452487 TTACTAGGTATCGATA
1 TCACTAGGTATCGATA
452503 TTGATTCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.10
21 22 0.73
22 5 0.17
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (20 bp):
TCACTAGGTATCGATACCTC
Found at i:456039 original size:246 final size:247
Alignment explanation
Indices: 455605--456097 Score: 970
Period size: 246 Copynumber: 2.0 Consensus size: 247
455595 TCAAGTTTGA
455605 GCAATTCAAGACAAATTCCTTTCAATATTCATTTTACTTTCAAGAACCCAAATTGTGCTTAATTG
1 GCAATTCAAGACAAATTCCTTTCAATATTCATTTTACTTTCAAGAACCCAAATTGTGCTTAATTG
*
455670 TATTTATCTTTAAGTGTTTTTTCCTTGTTCTAGAATTGTGCAAACATTCTACCTTGTGAGGTTTT
66 TATTTATCTTTAAGTGTTTTTTCCTTGTTCTAGAATTGTGCAAAAATTCTACCTTGTGAGGTTTT
455735 TCTATAAGTTTGCAAAATTTGTAAGTTTCTCTTTGGGAGAGAGTGTTATTGAGAATTTGGGGTAT
131 TCTATAAGTTTGCAAAATTTGTAAGTTTCTCTTTGGGAGAGAGTGTTATTGAGAATTTGGGGTAT
455800 AATTCTTGAGGGAGTTGTAAGGTTACTCTTTGTCCTC-AAAGAAAGACAAGT
196 AATTCTTGAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGACAAGT
455851 GCAATTCAAGACAAATTCCTTTCAATATTCATTTTACTTTCAAGAACCCAAATTGTGCTTAATTG
1 GCAATTCAAGACAAATTCCTTTCAATATTCATTTTACTTTCAAGAACCCAAATTGTGCTTAATTG
455916 TATTTATCTTTAAGTGTTTTTTCCTTGTTCTAGAATTGTGCAAAAATTCTACCTTGTGAGGTTTT
66 TATTTATCTTTAAGTGTTTTTTCCTTGTTCTAGAATTGTGCAAAAATTCTACCTTGTGAGGTTTT
455981 TCTATAAGTTTGCAAAATTTGTAAGTTTCTCTTTGGGAGAGAGTGTTATTGAGAATTTGGGGTAT
131 TCTATAAGTTTGCAAAATTTGTAAGTTTCTCTTTGGGAGAGAGTGTTATTGAGAATTTGGGGTAT
456046 AATTCTTGAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGACAAGT
196 AATTCTTGAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGACAAGT
456098 TAGTAAATTT
Statistics
Matches: 245, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
246 231 0.94
247 14 0.06
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (247 bp):
GCAATTCAAGACAAATTCCTTTCAATATTCATTTTACTTTCAAGAACCCAAATTGTGCTTAATTG
TATTTATCTTTAAGTGTTTTTTCCTTGTTCTAGAATTGTGCAAAAATTCTACCTTGTGAGGTTTT
TCTATAAGTTTGCAAAATTTGTAAGTTTCTCTTTGGGAGAGAGTGTTATTGAGAATTTGGGGTAT
AATTCTTGAGGGAGTTGTAAGGTTACTCTTTGTCCTCAAAAGAAAGACAAGT
Found at i:460767 original size:31 final size:32
Alignment explanation
Indices: 460726--460791 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
460716 CAAATTGAAG
*
460726 TTAAATAAAATAAA-A-TAAA-AAGGTATTAAAT
1 TTAAAGAAAATAAATATTAAAGAAGG-ATT-AAT
460757 TTAAAGAAAATAAATATTAAAGAAGGATTAAT
1 TTAAAGAAAATAAATATTAAAGAAGGATTAAT
460789 TTA
1 TTA
460792 GAAAGAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 13 0.42
32 7 0.23
33 7 0.23
34 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (32 bp):
TTAAAGAAAATAAATATTAAAGAAGGATTAAT
Found at i:461828 original size:15 final size:14
Alignment explanation
Indices: 461790--461843 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 14
461780 AAATATTATT
461790 AATAATCATATAATA
1 AATAAT-ATATAATA
461805 TAATAAATATAATAATA
1 -AAT-AATAT-ATAATA
461822 AATAATATTATAATA
1 AATAATA-TATAATA
461837 AATAATA
1 AATAATA
461844 CGTACACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 17 0.49
16 9 0.26
17 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATATATAATA
Found at i:461881 original size:27 final size:29
Alignment explanation
Indices: 461851--461904 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
461841 ATACGTACAC
461851 TATA-TCTA-TTTTAAAAACTATATAACA
1 TATATTCTATTTTTAAAAACTATATAACA
* *
461878 TATATTTTATTTTTTAAAACTATATAA
1 TATATTCTATTTTTAAAAACTATATAA
461905 TATGTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 3 0.13
29 16 0.70
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (29 bp):
TATATTCTATTTTTAAAAACTATATAACA
Found at i:461922 original size:16 final size:16
Alignment explanation
Indices: 461901--461933 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
461891 TTAAAACTAT
*
461901 ATAATATGTTTTCAAA
1 ATAATATGCTTTCAAA
461917 ATAATATGCTTTCAAA
1 ATAATATGCTTTCAAA
461933 A
1 A
461934 ACTATATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (16 bp):
ATAATATGCTTTCAAA
Found at i:461997 original size:14 final size:14
Alignment explanation
Indices: 461978--462006 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
461968 AAACTATATT
461978 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
461992 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
462006 A
1 A
462007 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:462015 original size:36 final size:36
Alignment explanation
Indices: 461893--462022 Score: 149
Period size: 36 Copynumber: 3.6 Consensus size: 36
461883 TTTATTTTTT
* *
461893 AAAACTATATAATATGTTTTCAAAATAATATGCTTTCA
1 AAAACTATATTATATGTTTTC-AAA-AATATGTTTTCA
* *
461931 AAAACTATATGATA-GATGTTTCAAAAA-ACCGTTTT-A
1 AAAACTATATTATATG-T-TTTCAAAAATA-TGTTTTCA
461967 AAAACTATATTATATGTTTTCAAAAATATGTTTTCA
1 AAAACTATATTATATGTTTTCAAAAATATGTTTTCA
*
462003 AAAACTATATTATATATTTT
1 AAAACTATATTATATGTTTT
462023 TGAAATTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
35 14 0.17
36 37 0.46
37 8 0.10
38 17 0.21
39 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (36 bp):
AAAACTATATTATATGTTTTCAAAAATATGTTTTCA
Found at i:469807 original size:15 final size:16
Alignment explanation
Indices: 469779--469808 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
469769 TTTTAGTCAC
469779 TAAAATTCATAATTTG
1 TAAAATTCATAATTTG
469795 TAAAATT-ATAATTT
1 TAAAATTCATAATTT
469809 AGTCACTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAATTCATAATTTG
Found at i:469869 original size:20 final size:21
Alignment explanation
Indices: 469840--469885 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
469830 AAACCCTATT
*
469840 AAAATTATA-TTTAATATTCA
1 AAAATCATATTTTAATATTCA
*
469860 AAAATCATATTTTAATATTTA
1 AAAATCATATTTTAATATTCA
469881 AAAAT
1 AAAAT
469886 ATTTTCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATCATATTTTAATATTCA
Found at i:469889 original size:18 final size:18
Alignment explanation
Indices: 469838--469890 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
469828 CTAAACCCTA
*
469838 TTAAAATTATATTTAATAT
1 TTAAAAATAT-TTTAATAT
*
469857 TCAAAAATCATATTTTAATAT
1 T-TAAAA--ATATTTTAATAT
469878 TTAAAAATATTTT
1 TTAAAAATATTTT
469891 CCATAGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.25
19 1 0.04
20 8 0.29
21 9 0.32
22 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAAATATTTTAATAT
Found at i:474267 original size:33 final size:33
Alignment explanation
Indices: 474225--474290 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
474215 CAGTTAGATG
*
474225 AAAGGTTAAATACCTTTGAGTAAAATATTAATT
1 AAAGGTTAAATACCTTTGAGTAAAAGATTAATT
474258 AAAGGTTAAATACCTTTGAGTAAAAGATTAATT
1 AAAGGTTAAATACCTTTGAGTAAAAGATTAATT
474291 GCCTAGTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (33 bp):
AAAGGTTAAATACCTTTGAGTAAAAGATTAATT
Found at i:474355 original size:81 final size:81
Alignment explanation
Indices: 474258--474526 Score: 351
Period size: 81 Copynumber: 3.3 Consensus size: 81
474248 AATATTAATT
* * *
474258 AAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAA
1 AAAGGCTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474323 TTATGCCAGTTAGATG
66 TCATGCCAGTTAGATG
* * * * *
474339 AAAGGTTAAATACCTTTGAGTAAAATATTAATTACCTAACTGTGCATTTGGCAGAAAGGTGTCAG
1 AAAGGCTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474404 TCATGCCCGTTAGATG
66 TCATGCCAGTTAGATG
* * * * * *
474420 AAAGGCTAAATGCTTTTGAGTTAAAGATTAAATGCTTGGCTGTGCATTTGGCAG-AAGGTGTCAA
1 AAAGGCTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474484 TCATGCAAGTTAGATG
66 TCATGCCAGTTAGATG
* * *
474500 AAACGCTAAATGCCTTTGGGTAAAAGA
1 AAAGGCTAAATACCTTTGAGTAAAAGA
474527 CTAAATGCAT
Statistics
Matches: 163, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 46 0.28
81 117 0.72
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (81 bp):
AAAGGCTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
TCATGCCAGTTAGATG
Found at i:474364 original size:114 final size:114
Alignment explanation
Indices: 474164--474372 Score: 373
Period size: 114 Copynumber: 1.8 Consensus size: 114
474154 CTGTTTTAAA
* *
474164 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGAGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGAGCCAATTATGCCAGTTAGATGAAAG
474229 GTTAAATACCTTTGAGTAAAATATTAATTAAAGGTTAAATACCTTTGAG
66 GTTAAATACCTTTGAGTAAAATATTAATTAAAGGTTAAATACCTTTGAG
* * *
474278 TAAAAGATTAATTGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGAGCCAATTATGCCAGTTAGATGAAAG
474343 GTTAAATACCTTTGAGTAAAATATTAATTA
66 GTTAAATACCTTTGAGTAAAATATTAATTA
474373 CCTAACTGTG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 90 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (114 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGAGCCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAGTAAAATATTAATTAAAGGTTAAATACCTTTGAG
Found at i:474511 original size:80 final size:81
Alignment explanation
Indices: 474258--474561 Score: 349
Period size: 81 Copynumber: 3.7 Consensus size: 81
474248 AATATTAATT
* * * * *
474258 AAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAA
1 AAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474323 TTATGCCAGTTAGATG
66 TCATGCCAGTTAGATG
* * * * * * *
474339 AAAGGTTAAATACCTTTGAGTAAAATATTAATTACCTAACTGTGCATTTGGCAGAAAGGTGTCAG
1 AAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474404 TCATGCCCGTTAGATG
66 TCATGCCAGTTAGATG
* * * *
474420 AAAGGCTAAATGCTTTTGAGTTAAAGATTAAATGCTTGGCTGTGCATTTGGCAG-AAGGTGTCAA
1 AAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
*
474484 TCATGCAAGTTAGATG
66 TCATGCCAGTTAGATG
* * * * * *
474500 AAACGCTAAATGCCTTTGGGTAAAAGACTAAATGCATAACGGTGCATTATAGGCATGAAAGG
1 AAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGCTGTGCATT-T-GGCA-GAAAGG
474562 ATGCCACTAA
Statistics
Matches: 189, Mismatches: 30, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
80 62 0.33
81 118 0.62
82 4 0.02
83 1 0.01
84 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (81 bp):
AAAGGCTAAATGCCTTTGAGTAAAAGATTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAA
TCATGCCAGTTAGATG
Found at i:476010 original size:36 final size:36
Alignment explanation
Indices: 475970--476041 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
475960 TGCTACAAAG
*
475970 TTGTCAAGCCTTCTTATTAAATTATTTGGATAATTA
1 TTGTCAAGCCTTCTTATTAAATGATTTGGATAATTA
*
476006 TTGTCAAGTCTTCTTATTAAATGATTTGGATAATTA
1 TTGTCAAGCCTTCTTATTAAATGATTTGGATAATTA
476042 GACTTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (36 bp):
TTGTCAAGCCTTCTTATTAAATGATTTGGATAATTA
Found at i:480179 original size:81 final size:81
Alignment explanation
Indices: 479842--480171 Score: 392
Period size: 81 Copynumber: 4.1 Consensus size: 81
479832 CTGTTTTAAA
** *
479842 TAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATG-AAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
479906 GTTAAATACCTTTGAG
66 GCTAAATACCTTTGAG
* * * * *
479922 TAAAAGATTAATTGCCTAGTTGTGCATTTGGCAAAAAGGTGTCAATTATTCCTGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
479987 GTTAAATACCTTTGAG
66 GCTAAATACCTTTGAG
* * * * * * * *
480003 TAAAAGATTAATTGCATAGTTGTGCATTTGGCTGAAAAGTTTCGATCTTGCCACTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
480068 GCTAAATGCCTTTGAG
66 GCTAAATACCTTTGAG
* * * * * * * *
480084 TTAAAGATTAAATGCCTAGCTGTGCATTTAGCAGAAAGGTATTAAGCATGCAAGTTAGATGAAAC
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
* *
480149 GCTAAATGCCTTTGGG
66 GCTAAATACCTTTGAG
480165 TAAAAGA
1 TAAAAGA
480172 CTAAATGCAT
Statistics
Matches: 213, Mismatches: 36, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
80 55 0.26
81 158 0.74
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GCTAAATACCTTTGAG
Found at i:480266 original size:45 final size:45
Alignment explanation
Indices: 480174--480266 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
480164 GTAAAAGACT
** * * *
480174 AAATGCATAACGATGCATTATCGGCATGAAATGATGTCATAATTG
1 AAATGCATAACGATGCATTATAAGCATGAAACGATGCCACAATTG
*
480219 AAATGCATAACGGTGCATTATAAGCATGAAACGATGCCACCAA-TG
1 AAATGCATAACGATGCATTATAAGCATGAAACGATGCCA-CAATTG
480264 AAA
1 AAA
480267 ATACATAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (45 bp):
AAATGCATAACGATGCATTATAAGCATGAAACGATGCCACAATTG
Found at i:485019 original size:40 final size:40
Alignment explanation
Indices: 484973--485050 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
484963 ATTGAATCAA
* *
484973 AACTTGATTTGTTTCACTACTCTTTAGGAATACCAAATCG
1 AACTTGATTTGCTTCACTACTCTTCAGGAATACCAAATCG
* *
485013 AACTTGATTTGCTTCACTGCTCTTCAGGAATATCAAAT
1 AACTTGATTTGCTTCACTACTCTTCAGGAATACCAAAT
485051 ATGAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (40 bp):
AACTTGATTTGCTTCACTACTCTTCAGGAATACCAAATCG
Found at i:486393 original size:15 final size:13
Alignment explanation
Indices: 486360--486411 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
486350 TTCTTTTCCC
*
486360 CTTTTTTCTTCTT
1 CTTTTTTCTTTTT
486373 CTTTTTTTCTTGGTTT
1 C-TTTTTTCTT--TTT
* *
486389 GTTTTCTCTTTTT
1 CTTTTTTCTTTTT
486402 CTTTTTTCTT
1 CTTTTTTCTT
486412 CAAGTAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 12 0.39
14 9 0.29
15 8 0.26
16 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:493565 original size:19 final size:19
Alignment explanation
Indices: 493538--493579 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
493528 GAATGAATAG
* *
493538 AATGTAATACGAAAATTAA
1 AATGCAATACGAAAAGTAA
*
493557 AATGCAATATGAAAAGTAA
1 AATGCAATACGAAAAGTAA
493576 AATG
1 AATG
493580 TAGATGCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (19 bp):
AATGCAATACGAAAAGTAA
Found at i:510029 original size:40 final size:40
Alignment explanation
Indices: 509928--510029 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 40
509918 CTCACTTCGT
** *
509928 TACTCTTCAGGGAAGATTGAATCAAACTTTATTTGCTTCAC
1 TACTCTTCA-GGAAGATCAAATCAAACTTGATTTGCTTCAC
* ** * * * *
509969 TACTCTTTATAAATACCAAATCGAACTTGATTTGCTTTAC
1 TACTCTTCAGGAAGATCAAATCAAACTTGATTTGCTTCAC
*
510009 TGCTCTTCAGGAAGATCAAAT
1 TACTCTTCAGGAAGATCAAAT
510030 ATGAAAATTA
Statistics
Matches: 45, Mismatches: 16, Indels: 1
0.73 0.26 0.02
Matches are distributed among these distances:
40 37 0.82
41 8 0.18
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (40 bp):
TACTCTTCAGGAAGATCAAATCAAACTTGATTTGCTTCAC
Found at i:518967 original size:19 final size:18
Alignment explanation
Indices: 518915--518967 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
518905 AAATGAATAT
518915 AATGTAATGCGAAAAGTAA
1 AATGTAATGC-AAAAGTAA
** *
518934 AATACAATGTGAAAAGTAA
1 AATGTAATG-CAAAAGTAA
518953 AATGTAGATGCAAAA
1 AATGTA-ATGCAAAA
518968 TACAAGGTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.21
Consensus pattern (18 bp):
AATGTAATGCAAAAGTAA
Found at i:521851 original size:13 final size:14
Alignment explanation
Indices: 521827--521856 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
521817 AAAGCGAAAA
521827 ACACACACACAATC
1 ACACACACACAATC
521841 ACACA-ACACAATC
1 ACACACACACAATC
521854 ACA
1 ACA
521857 TTAGCCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (14 bp):
ACACACACACAATC
Found at i:528342 original size:17 final size:16
Alignment explanation
Indices: 528322--528364 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
528312 TAACTATGTG
*
528322 AATTAAACAAATGGATA
1 AATTAAACAAAT-GAAA
*
528339 AATTGAAATAAATGAAA
1 AATT-AAACAAATGAAA
528356 AATTAAACA
1 AATTAAACA
528365 TGCAATTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.63, C:0.05, G:0.09, T:0.23
Consensus pattern (16 bp):
AATTAAACAAATGAAA
Found at i:534130 original size:18 final size:18
Alignment explanation
Indices: 534107--534142 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
534097 AAGCTATTTG
534107 ATACTCAACTTGAAAAGC
1 ATACTCAACTTGAAAAGC
534125 ATACTCAACTTGAAAAGC
1 ATACTCAACTTGAAAAGC
534143 TCGCGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ATACTCAACTTGAAAAGC
Found at i:540942 original size:54 final size:54
Alignment explanation
Indices: 540858--541403 Score: 415
Period size: 54 Copynumber: 10.1 Consensus size: 54
540848 TTTGTACTTA
* *
540858 TAGTGCCGAAAC-GATTATTCATCAATATATGATGAATTTCGTCCTTTGCGCACT
1 TAGTGCCGAAACAG-TTATTCATCAATATATGATGAATTTCGTACTTTGCACACT
* *
540912 TCGTGCCGAAACAGTTATTTC-TCAATATATGATGAATTAT-GTACTTTGTACACT
1 TAGTGCCGAAACAGTTA-TTCATCAATATATGATGAATT-TCGTACTTTGCACACT
* * *
540966 TAGTGTCGAAACAGTTATTCATCAATATATGATGAATTCCGTACTTTTCACACT
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTCGTACTTTGCACACT
* ** * * * *
541020 TAGTGTCGAAATGGTTATTCATCAACATATAACGAATTAT-GTGA-TTTACACACT
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATT-TCGT-ACTTTGCACACT
* * * * * *
541074 TAATGCCAAAACTGTTATTCA-CAACATATGATGAATTTCATGA-TTTGCACACC
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTCGT-ACTTTGCACACT
* ** * *
541127 TAGGGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTGA-TTTGCACACT
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTCGT-ACTTTGCACACT
*** * * *
541181 TAGTTTTGAAAC-GATTGTTCATCAACATATGATGAATTAT-TTGA-TTTGCACACT
1 TAGTGCCGAAACAG-TTATTCATCAATATATGATGAATT-TCGT-ACTTTGCACACT
* * * *
541235 TAGTGTCGAAACGGTTATTCATCAACATATGATGAA-TTCAGTGAC-TTGCAAACT
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTC-GT-ACTTTGCACACT
* * *
541289 TAGTG-C-TAACATGGTTATTCATCAATATATGATGAATTCCATGA-TTTGCACACT
1 TAGTGCCGAAACA--GTTATTCATCAATATATGATGAATTTCGT-ACTTTGCACACT
* * ** * * * *
541343 TAGTGTCAAAATGGTTATTTATCAACATATGATGAATTCCATGA-TTTGCACACT
1 TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTCGT-ACTTTGCACACT
541397 TAGTGCC
1 TAGTGCC
541404 TATTTGGTAA
Statistics
Matches: 412, Mismatches: 59, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
52 5 0.01
53 47 0.11
54 348 0.84
55 10 0.02
56 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (54 bp):
TAGTGCCGAAACAGTTATTCATCAATATATGATGAATTTCGTACTTTGCACACT
Found at i:541020 original size:108 final size:107
Alignment explanation
Indices: 540858--541403 Score: 564
Period size: 108 Copynumber: 5.1 Consensus size: 107
540848 TTTGTACTTA
* * ** * * *
540858 TAGTGCCGAAACGATTATTCATCAATATATGATGAATTTCGTCCTTTGCGCACTTCGTGCCGAAA
1 TAGTGCCGAAACG-TTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCGAAA
** * *
540923 CAGTTATTTC-TCAATATATGATGAATTATGT-ACTTTGTACACT
65 TGGTTA-TTCATCAACATATGATGAATTATGTGA-TTTGCACACT
* * *
540966 TAGTGTCGAAACAGTTATTCATCAATATATGATGAATTCCGT-ACTTTTCACACTTAGTGTCGAA
1 TAGTGCCGAAAC-GTTATTCATCAATATATGATGAATTCCATGA-TTTGCACACTTAGTGTCGAA
* * *
541030 ATGGTTATTCATCAACATATAACGAATTATGTGATTTACACACT
64 ATGGTTATTCATCAACATATGATGAATTATGTGATTTGCACACT
* * * * * * *
541074 TAATGCCAAAACTGTTATTCA-CAACATATGATGAATTTCATGATTTGCACACCTAGGGCCGAAA
1 TAGTGCCGAAAC-GTTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCGAAA
**
541138 TGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACT
65 TGGTTATTCATCAACATATGATGAATTATGTGATTTGCACACT
*** * * ***
541181 TAGTTTTGAAACGATTGTTCATCAACATATGATGAATTATTTGATTTGCACACTTAGTGTCGAAA
1 TAGTGCCGAAACG-TTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCGAAA
* * *
541246 CGGTTATTCATCAACATATGATGAATTCA-GTGACTTGCAAACT
65 TGGTTATTCATCAACATATGATGAATT-ATGTGATTTGCACACT
* * *
541289 TAGTG-CTAACATGGTTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCAAA
1 TAGTGCCGAA-A-CGTTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCGAA
* ***
541353 ATGGTTATTTATCAACATATGATGAATTCCATGATTTGCACACT
64 ATGGTTATTCATCAACATATGATGAATTATGTGATTTGCACACT
541397 TAGTGCC
1 TAGTGCC
541404 TATTTGGTAA
Statistics
Matches: 364, Mismatches: 62, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
106 1 0.00
107 90 0.25
108 269 0.74
109 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (107 bp):
TAGTGCCGAAACGTTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCGAAAT
GGTTATTCATCAACATATGATGAATTATGTGATTTGCACACT
Found at i:541146 original size:161 final size:162
Alignment explanation
Indices: 540979--541372 Score: 526
Period size: 161 Copynumber: 2.4 Consensus size: 162
540969 TGTCGAAACA
*
540979 GTTATTCATCAATATATGATGAATTCCGT-ACTTTTCACACTTAGTGTCGAAATGGTTATTCATC
1 GTTATTCATCAATATATGATGAATTCCGTGA-TTTGCACACTTAGTGTCGAAATGGTTATTCATC
*
541043 AACATATAACGAATTATGTGATTTACACACTTAATGCCAAAACTGTTATTCA-CAACATATGATG
65 AACATATAACGAATTATGTGATTTACACACTTAATGCCAAAACGGTTATTCATCAACATATGATG
* *
541107 AATTTCA-TGATTTGCACACCTAGGGCCGAA-ATG
130 AA-TTCAGTGACTTGCAAACCTAGGG-CGAACATG
* * * * * *
541140 GTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTTTTGAAACGATTGTTCATCA
1 GTTATTCATCAATATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAATGGTTATTCATCA
* * * * * * *
541205 ACATATGATGAATTATTTGATTTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGA
66 ACATATAACGAATTATGTGATTTACACACTTAATGCCAAAACGGTTATTCATCAACATATGATGA
* * *
541270 ATTCAGTGACTTGCAAACTTAGTGCTAACATG
131 ATTCAGTGACTTGCAAACCTAGGGCGAACATG
* * *
541302 GTTATTCATCAATATATGATGAATTCCATGATTTGCACACTTAGTGTCAAAATGGTTATTTATCA
1 GTTATTCATCAATATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAATGGTTATTCATCA
541367 ACATAT
66 ACATAT
541373 GATGAATTCC
Statistics
Matches: 200, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
161 106 0.53
162 94 0.47
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (162 bp):
GTTATTCATCAATATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAATGGTTATTCATCA
ACATATAACGAATTATGTGATTTACACACTTAATGCCAAAACGGTTATTCATCAACATATGATGA
ATTCAGTGACTTGCAAACCTAGGGCGAACATG
Found at i:541267 original size:269 final size:270
Alignment explanation
Indices: 540862--541395 Score: 677
Period size: 269 Copynumber: 2.0 Consensus size: 270
540852 TACTTATAGT
* * * * *
540862 GCCGAAACGATTATTCATCAATATATGATGAATTTCGTCCTTTGCGCACTTCGTGCCGAAACAGT
1 GCCGAAACGATTATTCATCAACATATGATGAATTCCGTCATTTGCACACTTAGTGCCGAAACAGT
* * * *
540927 TATTTCTCAATATATGATGAATTATGTACTTTGTACACTTAGTGTCGAAACAGTTATTCATCAAT
66 TAGTTCTCAACATATGATGAATTATGTACTTTGCACACTTAGTGTCGAAACAGTTATTCATCAAC
* * *
540992 ATATGATGAATTCCGT-ACTTTTCACACTTAGTGTCGAA-ATGGTTATTCATCAACATATAACGA
131 ATATGATGAATTCAGTGAC-TTGCAAACTTAGTG-CGAACATGGTTATTCATCAACATATAACGA
** *
541055 ATTATGTGATTTACACACTTAATGCCAAAACT-GTTATTCA-CAACATATGATGAATTTCATGAT
194 ATTACATGATTTACACACTTAATGCCAAAA-TGGTTATTCATCAACATATGATGAATTCCATGAT
541118 TTGCACACCTAGG
258 TTGCACACCTAGG
* * * ***
541131 GCCGAAATGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTTTTGAAAC-GA
1 GCCGAAACGATTATTCATCAACATATGATGAATTCCGTCATTTGCACACTTAGTGCCGAAACAG-
* *
541195 TT-GTTCATCAACATATGATGAATTATTTGA-TTTGCACACTTAGTGTCGAAACGGTTATTCATC
65 TTAGTTC-TCAACATATGATGAATTATGT-ACTTTGCACACTTAGTGTCGAAACAGTTATTCATC
* * * *
541258 AACATATGATGAATTCAGTGACTTGCAAACTTAGTGCTAACATGGTTATTCATCAATATATGATG
128 AACATATGATGAATTCAGTGACTTGCAAACTTAGTGCGAACATGGTTATTCATCAACATATAACG
* * * * *
541323 AATTCCATGATTTGCACACTTAGTGTCAAAATGGTTATTTATCAACATATGATGAATTCCATGAT
193 AATTACATGATTTACACACTTAATGCCAAAATGGTTATTCATCAACATATGATGAATTCCATGAT
541388 TTGCACAC
258 TTGCACAC
541396 TTAGTGCCTA
Statistics
Matches: 226, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
268 8 0.04
269 185 0.82
270 33 0.15
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (270 bp):
GCCGAAACGATTATTCATCAACATATGATGAATTCCGTCATTTGCACACTTAGTGCCGAAACAGT
TAGTTCTCAACATATGATGAATTATGTACTTTGCACACTTAGTGTCGAAACAGTTATTCATCAAC
ATATGATGAATTCAGTGACTTGCAAACTTAGTGCGAACATGGTTATTCATCAACATATAACGAAT
TACATGATTTACACACTTAATGCCAAAATGGTTATTCATCAACATATGATGAATTCCATGATTTG
CACACCTAGG
Found at i:541478 original size:15 final size:15
Alignment explanation
Indices: 541458--541486 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
541448 GACTAGTATA
541458 ACATATAGTTACACT
1 ACATATAGTTACACT
541473 ACATATAGTTACAC
1 ACATATAGTTACAC
541487 AATTAAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
ACATATAGTTACACT
Found at i:547928 original size:54 final size:54
Alignment explanation
Indices: 547869--548413 Score: 559
Period size: 54 Copynumber: 10.1 Consensus size: 54
547859 AATGCAACCG
* * * * * * *
547869 TAGTGCCCATACGGTCATTCATAAACATATTATGAATTTCGTGTTTTGCACACA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * * * * * *
547923 TAGTGCTGAAATGATTATACAT-AACCTATGATGAATTCCGT-ACTTTCCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCACACT
* * * *
547976 TAGTGCTGAAATGATTATTCATCAACATATGATGAATTTCGT-ACTTTGCGCACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCACACT
* *
548030 TCA-TGCCGAAACAGTTATTCATCAACATATGATGAATTAT-GT-ACTTTGTACACT
1 T-AGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTGA-TTTGCACACT
** * *
548084 TAGTGCCGAAACAATTATTCATCAACATATGATGAATTCCGT-ACTTTTCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCACACT
* * * * *
548138 TAGTGCTGAAACGGTTATCCATCAATATATGATGAATTAT-ATGATTTACACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTGATTTGCACACT
* * * * *
548192 TAATTCCAAAACTGTTATTCA-CAACATGTGATGAATTTCGTGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * *
548245 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGTACACA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * *
548299 TAGTGTCAAAACGATTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * * *
548353 TAGTGTCGAAATGGTTGTTCATCAACATATGATTAATTTCGTGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
*
548407 TAATGCC
1 TAGTGCC
548414 TATTTGGTAA
Statistics
Matches: 414, Mismatches: 67, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.00
53 89 0.21
54 321 0.78
55 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (54 bp):
TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
Found at i:548254 original size:215 final size:216
Alignment explanation
Indices: 547885--548410 Score: 588
Period size: 215 Copynumber: 2.4 Consensus size: 216
547875 CCATACGGTC
* * * * * * * *
547885 ATTCATAAACATATTATGAATTTCGTGTTTTGCACACATAGTG-CTGAAATGATTATACAT-AAC
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTC-GAAACGGTTATCCATCAAC
* * * * * * **
547948 CTATGATGAATTCCGT-ACTTTCCACACTTAGTGCTGAAA-TGATTATTCATCAACATATGATGA
65 ATATGATGAATTTCATGA-TTTACACACTTAATTCCAAAACTG-TTATTCATCAACATATGATGA
* *
548011 ATTTCGTACTTTGCGCACTTCATGCCGAAACAGTTATTCATCAACATATGATGAATTATGT-ACT
128 ATTTCGTACTTTGCACACTTCATGCCGAAACAGTTATTCATCAACATATGATGAATTACGTGA-T
* *
548075 TTGTACACTTAGTGCCGAAACAATT
192 TTGTACACATAGTGCCAAAACAATT
*
548100 ATTCATCAACATATGATGAATTCCGT-ACTTTTCACACTTAGTG-CTGAAACGGTTATCCATCAA
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGTC-GAAACGGTTATCCATCAA
* *
548163 TATATGATGAATTAT-ATGATTTACACACTTAATTCCAAAACTGTTATTCA-CAACATGTGATGA
64 CATATGATGAATT-TCATGATTTACACACTTAATTCCAAAACTGTTATTCATCAACATATGATGA
* *
548226 ATTTCGTGA-TTTGCACACTT-AGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGA
128 ATTTCGT-ACTTTGCACACTTCA-TGCCGAAACAGTTATTCATCAACATATGATGAATTACGTGA
* *
548289 TTTGTACACATAGTGTCAAAACGATT
191 TTTGTACACATAGTGCCAAAACAATT
* * * *
548315 ATTCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTGTCGAAATGGTTGTTCATCAACA
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATCCATCAACA
* * *
548380 TATGATTAATTTCGTGATTTGCACACTTAAT
66 TATGATGAATTTCATGATTTACACACTTAAT
548411 GCCTATTTGG
Statistics
Matches: 264, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
214 2 0.01
215 218 0.83
216 41 0.16
217 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (216 bp):
ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATCCATCAACA
TATGATGAATTTCATGATTTACACACTTAATTCCAAAACTGTTATTCATCAACATATGATGAATT
TCGTACTTTGCACACTTCATGCCGAAACAGTTATTCATCAACATATGATGAATTACGTGATTTGT
ACACATAGTGCCAAAACAATT
Found at i:548487 original size:15 final size:15
Alignment explanation
Indices: 548467--548495 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
548457 TGACTAGTGT
548467 AACATATAGTTACAC
1 AACATATAGTTACAC
548482 AACATATAGTTACA
1 AACATATAGTTACA
548496 TAATTGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:553773 original size:16 final size:17
Alignment explanation
Indices: 553752--553786 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
553742 CACTTCTTTG
*
553752 CATTTTTCCTTTTT-TT
1 CATTTTTACTTTTTCTT
553768 CATTTTTACTTTTTCTT
1 CATTTTTACTTTTTCTT
553785 CA
1 CA
553787 CTTGGAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (17 bp):
CATTTTTACTTTTTCTT
Found at i:554096 original size:2 final size:2
Alignment explanation
Indices: 554089--554166 Score: 147
Period size: 2 Copynumber: 38.5 Consensus size: 2
554079 TATGGCAGCG
554089 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
554131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
554167 GTGATATTTA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 73 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:557599 original size:47 final size:47
Alignment explanation
Indices: 557530--557624 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
557520 ATGTTTAAAG
557530 GAAATGATGAAGTATGGTAATGGAAGTAGAATAAAGGTTATGGAAAT
1 GAAATGATGAAGTATGGTAATGGAAGTAGAATAAAGGTTATGGAAAT
*
557577 GAAATGATGAAGTATGGTAATGGAAGTATAATAAAGGTTATGGAAAT
1 GAAATGATGAAGTATGGTAATGGAAGTAGAATAAAGGTTATGGAAAT
557624 G
1 G
557625 TAGATGAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (47 bp):
GAAATGATGAAGTATGGTAATGGAAGTAGAATAAAGGTTATGGAAAT
Found at i:557624 original size:26 final size:26
Alignment explanation
Indices: 557542--557624 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
557532 AATGATGAAG
* *
557542 TATGGTAATGGAAGTAGAATAAAGGT
1 TATGGAAATGGAAGTATAATAAAGGT
* *
557568 TATGGAAAT-GAA--ATGATGAA-G-
1 TATGGAAATGGAAGTATAATAAAGGT
*
557589 TATGGTAATGGAAGTATAATAAAGGT
1 TATGGAAATGGAAGTATAATAAAGGT
557615 TATGGAAATG
1 TATGGAAATG
557625 TAGATGAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
21 8 0.18
22 4 0.09
23 5 0.11
24 6 0.14
25 4 0.09
26 17 0.39
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.28
Consensus pattern (26 bp):
TATGGAAATGGAAGTATAATAAAGGT
Found at i:558777 original size:13 final size:13
Alignment explanation
Indices: 558754--558787 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
558744 TATATTATAT
558754 ATATAAATGACAGC
1 ATAT-AATGACAGC
558768 ATATAATGACAGC
1 ATATAATGACAGC
558781 ATATAAT
1 ATATAAT
558788 ATTCAACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (13 bp):
ATATAATGACAGC
Found at i:563718 original size:21 final size:20
Alignment explanation
Indices: 563694--563735 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
563684 ATTAAACCCT
* *
563694 AAATAATATTTATTAAACTAA
1 AAATAAAATATATTAAA-TAA
563715 AAATAAAATATATTAAATAA
1 AAATAAAATATATTAAATAA
563735 A
1 A
563736 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAAATATATTAAATAA
Found at i:563727 original size:25 final size:26
Alignment explanation
Indices: 563694--563742 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
563684 ATTAAACCCT
* * *
563694 AAATAATATTTATTAAACTAAAAATA
1 AAATAATATTAAATAAACAAAAAATA
563720 AAAT-ATATTAAATAAACAAAAAA
1 AAATAATATTAAATAAACAAAAAA
563743 AATAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATAATATTAAATAAACAAAAAATA
Found at i:563743 original size:21 final size:21
Alignment explanation
Indices: 563704--563743 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
563694 AAATAATATT
*
563704 TATTAAACTAAAAATAAAATA
1 TATTAAACTAAAAAAAAAATA
563725 TATTAAA-TAAACAAAAAAA
1 TATTAAACTAAA-AAAAAAA
563744 ATAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
TATTAAACTAAAAAAAAAATA
Found at i:564399 original size:27 final size:26
Alignment explanation
Indices: 564353--564412 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
564343 GTGGGTAAGG
**
564353 TTTTTTTCTCTTTCTTTTCTTAACTA
1 TTTTTTTCTCTTTCACTTCTTAACTA
**
564379 TTTTGTTTCTCTTTCACTTCTTCTCTA
1 TTTT-TTTCTCTTTCACTTCTTAACTA
564406 TTTTTTT
1 TTTTTTT
564413 TTGCAAGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTTTCTCTTTCACTTCTTAACTA
Found at i:571083 original size:97 final size:97
Alignment explanation
Indices: 570917--571108 Score: 384
Period size: 97 Copynumber: 2.0 Consensus size: 97
570907 TTTTAGACGA
570917 ATAATGTTCTTACAGTATCGATACCTCATGAATCGTACCGATATTGTTCATTTGGTATCGATACC
1 ATAATGTTCTTACAGTATCGATACCTCATGAATCGTACCGATATTGTTCATTTGGTATCGATACC
570982 AAAGGTAGCGGAAGTATTGATACTCATTAGCG
66 AAAGGTAGCGGAAGTATTGATACTCATTAGCG
571014 ATAATGTTCTTACAGTATCGATACCTCATGAATCGTACCGATATTGTTCATTTGGTATCGATACC
1 ATAATGTTCTTACAGTATCGATACCTCATGAATCGTACCGATATTGTTCATTTGGTATCGATACC
571079 AAAGGTAGCGGAAGTATTGATACTCATTAG
66 AAAGGTAGCGGAAGTATTGATACTCATTAG
571109 GTAGTATTGA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (97 bp):
ATAATGTTCTTACAGTATCGATACCTCATGAATCGTACCGATATTGTTCATTTGGTATCGATACC
AAAGGTAGCGGAAGTATTGATACTCATTAGCG
Found at i:571509 original size:22 final size:22
Alignment explanation
Indices: 571483--571529 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
571473 CTTTCTCTTA
571483 TAAATATTTTGTACTTGTAAGC
1 TAAATATTTTGTACTTGTAAGC
* *
571505 T-AA-ATTTTGTTCTTGTGAGC
1 TAAATATTTTGTACTTGTAAGC
571525 TAAAT
1 TAAAT
571530 TTTGTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 16 0.76
21 4 0.19
22 1 0.05
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (22 bp):
TAAATATTTTGTACTTGTAAGC
Found at i:571513 original size:20 final size:20
Alignment explanation
Indices: 571488--571535 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
571478 TCTTATAAAT
571488 ATTTTGTACTTGTAAGCTAA
1 ATTTTGTACTTGTAAGCTAA
* *
571508 ATTTTGTTCTTGTGAGCTAA
1 ATTTTGTACTTGTAAGCTAA
571528 ATTTTGTA
1 ATTTTGTA
571536 AACACCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (20 bp):
ATTTTGTACTTGTAAGCTAA
Found at i:576211 original size:2 final size:2
Alignment explanation
Indices: 576206--576602 Score: 220
Period size: 2 Copynumber: 205.0 Consensus size: 2
576196 AAAAAATACT
* *
576206 TA TA TA GA TA TA TA -A TA TA TA TA TA TA TA TA TA TT TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
576247 TA TA TA TA T- TA GA TA -A TA AA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
576285 TA TA TA T- TT TT TA TA TA -A TA CT- TA TA -A AA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
576323 TA TA TA TT TA TG TA TA TA TA CT- TA TA TA T- TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
576362 TA TA TA TA T- TA TA T- TA TA TA TA T- TA TA CT- TA TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * * *
576402 T- TA TA CTT TA TA T- TA TGC TA TA TG TT TA T- TC TT TA TA -A T-
1 TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * *
576441 TA TA CTT TA TA TG TA TA TA TA CT- TA TA CTT TA TA T- TA T- TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * *
576481 GTA TA TA TC TT TA TA CTA AA CTT TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
576524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
576566 TA TA TA TA TA CA TA CT- TA TA CTT TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
576603 ATTTTATACT
Statistics
Matches: 306, Mismatches: 46, Indels: 86
0.70 0.11 0.20
Matches are distributed among these distances:
1 28 0.09
2 262 0.86
3 16 0.05
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:576756 original size:23 final size:24
Alignment explanation
Indices: 576725--576845 Score: 69
Period size: 23 Copynumber: 5.2 Consensus size: 24
576715 GTTTATATAC
576725 ATATATATACATACTTA-AACTTT
1 ATATATATACATACTTATAACTTT
* * *
576748 ATATGTATATATACTTATATCTTT
1 ATATATATACATACTTATAACTTT
* * *
576772 AT-TCT-T-TATAATTAT-ACTTT
1 ATATATATACATACTTATAACTTT
* *
576792 ATAT-TATTATATATGTATATATACTTT
1 ATATATA-TACATA-CT-TATA-ACTTT
576819 ATATATAT--ATACTTATATACTTT
1 ATATATATACATACTTATA-ACTTT
576842 ATAT
1 ATAT
576846 TTAAACTATA
Statistics
Matches: 80, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
20 7 0.09
21 9 0.11
22 2 0.03
23 35 0.44
24 9 0.11
25 6 0.08
27 10 0.12
28 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATATATACATACTTATAACTTT
Found at i:576844 original size:15 final size:14
Alignment explanation
Indices: 576316--576844 Score: 97
Period size: 14 Copynumber: 37.9 Consensus size: 14
576306 TTATAAAATA
* *
576316 TTATATATATATAT
1 TTATATATTTATAC
* *
576330 TTATGTATATATAC
1 TTATATATTTATAC
*
576344 TTATATATTATTATAT
1 TTATATA-T-TTATAC
576360 TATATATATATTATA-
1 T-TATATAT-TTATAC
576375 TTATATATATTATAC
1 TTATATAT-TTATAC
576390 TTATACTTTATATTATAC
1 TTATA---TAT-TTATAC
*
576408 TT-TATA-TTATGC
1 TTATATATTTATAC
* *
576420 -TATATGTTTATTC
1 TTATATATTTATAC
*
576433 TT-TATAATTATAC
1 TTATATATTTATAC
*
576446 TT-TATA--TGTA-
1 TTATATATTTATAC
*
576456 -TATATACTTATAC
1 TTATATATTTATAC
*
576469 TT-TATA-TTATTAG
1 TTATATATTTA-TAC
*
576482 TATATATCTTTATAC
1 T-TATATATTTATAC
576497 -TA-A-ACTTTATA-
1 TTATATA-TTTATAC
*
576508 -TATATATATATA-
1 TTATATATTTATAC
*
576520 TATATATATATATA-
1 T-TATATATTTATAC
*
576534 TATATATATATATA-
1 T-TATATATTTATAC
*
576548 TATATATATATATAC
1 T-TATATATTTATAC
* *
576563 ATATATATATATAC
1 TTATATATTTATAC
* *
576577 ATACTTATACTTTATATG
1 TTA--TATA-TTTATA-C
576595 TATATATAATTTTATAC
1 T-TATAT-A-TTTATAC
* *
576612 TT-TAGTCTTTATAA
1 TTATA-TATTTATAC
*
576626 TTAT-TCTTTATA-
1 TTATATATTTATAC
*
576638 -TATATA-ATATAC
1 TTATATATTTATAC
*
576650 TTATA-CTTTATA-
1 TTATATATTTATAC
* *
576662 TTAT-TATATAT-G
1 TTATATATTTATAC
*
576674 TATATATACTTTATAG
1 T-TATATA-TTTATAC
*
576690 TT-TATATATATAC
1 TTATATATTTATAC
*
576703 TT-T-TACTTTATAGT
1 TTATATA-TTTATA-C
**
576717 TTATATACATATA-
1 TTATATATTTATAC
* * *
576730 TATACATACTTAAAC
1 T-TATATATTTATAC
*
576745 TTTATATGTATATATAC
1 -TTATA--TATTTATAC
* *
576762 TTATATCTTTATTC
1 TTATATATTTATAC
*
576776 TT-TATAATTATAC
1 TTATATATTTATAC
576789 TT-TATA-TTATTA-
1 TTATATATTTA-TAC
* *
576801 TATATGTATATATAC
1 T-TATATATTTATAC
*
576816 TTTATATATATATAC
1 -TTATATATTTATAC
576831 TTATATACTTTATA
1 TTATATA-TTTATA
576845 TTTAAACTAT
Statistics
Matches: 400, Mismatches: 56, Indels: 117
0.70 0.10 0.20
Matches are distributed among these distances:
9 1 0.00
10 4 0.01
11 13 0.03
12 43 0.11
13 79 0.20
14 137 0.34
15 47 0.12
16 32 0.08
17 23 0.06
18 19 0.05
19 2 0.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (14 bp):
TTATATATTTATAC
Found at i:579895 original size:22 final size:22
Alignment explanation
Indices: 579867--579908 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
579857 AGGGGGTTAC
579867 ATAAACTATATAATTTATATTA
1 ATAAACTATATAATTTATATTA
**
579889 ATAAACTATATTGTTTATAT
1 ATAAACTATATAATTTATAT
579909 ATAGTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAAACTATATAATTTATATTA
Found at i:580059 original size:2 final size:2
Alignment explanation
Indices: 579963--580041 Score: 54
Period size: 2 Copynumber: 39.0 Consensus size: 2
579953 ATATATTGTT
* * *
579963 TA TA CA TA TA TT TA TA TA TA TT TA TA TA GTA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
580004 TA AA TA TA AA TA TA AA CTA TA GTT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA
580042 CCTTATTTAC
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
1 2 0.03
2 52 0.90
3 4 0.07
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:580107 original size:21 final size:20
Alignment explanation
Indices: 580062--580191 Score: 82
Period size: 19 Copynumber: 6.7 Consensus size: 20
580052 ACTATATAGT
*
580062 TTATA-TTATATATACATAC
1 TTATACTTATATATATATAC
*
580081 TTATACGTT-TATGTATATAC
1 TTATAC-TTATATATATATAC
580101 TTTATACTTATATATATATA-
1 -TTATACTTATATATATATAC
* *
580121 TTATA-TATATGTTTATATAC
1 TTATACT-TATATATATATAC
*
580141 TTA-ATCTT-TATA-ATTATAA
1 TTATA-CTTATATATA-TATAC
*
580160 TT-TA-TATATAGATATATAC
1 TTATACT-TATATATATATAC
580179 TTATACTT-TATAT
1 TTATACTTATATAT
580192 TATTATATGT
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
17 1 0.01
18 3 0.04
19 43 0.51
20 19 0.22
21 19 0.22
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (20 bp):
TTATACTTATATATATATAC
Found at i:580166 original size:38 final size:39
Alignment explanation
Indices: 580094--580206 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 39
580084 TACGTTTATG
*
580094 TATATACTTTATAC-TTATATATATATATTATATATAT-GTT
1 TATATAC-TTATACTTTATAT-TATATATTATATATATAG-A
580134 TATATACTTA-ATCTTTATAATTATA-ATT-TATATATAGA
1 TATATACTTATA-CTTTAT-ATTATATATTATATATATAGA
580172 TATATACTTATACTTTATATTATTATATGTATATA
1 TATATACTTATACTTTATATTA-TATAT-TATATA
580207 CTTTATACTA
Statistics
Matches: 63, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
37 4 0.06
38 26 0.41
39 11 0.17
40 16 0.25
41 6 0.10
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (39 bp):
TATATACTTATACTTTATATTATATATTATATATATAGA
Found at i:580306 original size:25 final size:26
Alignment explanation
Indices: 580273--580460 Score: 88
Period size: 25 Copynumber: 7.4 Consensus size: 26
580263 GTGTGTACTT
580273 TATAGTTTATATATATATATAC-ATAC
1 TATA-TTTATATATATATATACTATAC
*
580299 TATATTTATATGTATATATACTTTATAC
1 TATATTTATATATATATATAC--TATAC
580327 TCATATATT-TATATATATATTA-TATAC
1 T-ATAT-TTATATATATATA-TACTATAC
*
580354 TTTAGTCTT-TA-A-AT-TATACT-T--
1 TATA-T-TTATATATATATATACTATAC
*
580375 TATA-TTA-ATATACT-TATACTTTA-
1 TATATTTATATATA-TATATACTATAC
*
580398 TATATTATATATATATACTTTA-TATA-
1 TATATT-TATATATATA-TATACTATAC
*
580424 TATATTTAGTTTATATATATACT-TA-
1 TATATTTA-TATATATATATACTATAC
580449 TATACTTTATAT
1 TATA-TTTATAT
580461 TTAAACTATA
Statistics
Matches: 130, Mismatches: 10, Indels: 45
0.70 0.05 0.24
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 1 0.01
21 10 0.08
22 1 0.01
23 7 0.05
24 4 0.03
25 34 0.26
26 33 0.25
27 14 0.11
28 5 0.04
29 13 0.10
30 4 0.03
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (26 bp):
TATATTTATATATATATATACTATAC
Found at i:580323 original size:17 final size:16
Alignment explanation
Indices: 580268--580444 Score: 90
Period size: 17 Copynumber: 11.0 Consensus size: 16
580258 TATGTGTGTG
580268 TACTTTATAGTT-TATA
1 TACTTTATA-TTATATA
* *
580284 TA-TATATATACATACTA
1 TACTTTATAT-TATA-TA
580301 TA-TTTATATGTATATA
1 TACTTTATAT-TATATA
*
580317 TACTTTATACTCATATA
1 TACTTTATA-TTATATA
580334 T--TTATATATATATTATA
1 TACTT-TATAT-TA-TATA
* *
580351 TACTTTAGTCTTTAAATTA
1 TACTTTA-T-ATTATA-TA
580370 TACTTTATATTA-ATA
1 TACTTTATATTATATA
580385 TAC-TTATACTT-TATA
1 TACTTTATA-TTATATA
580400 TA--TTATA-TATATA
1 TACTTTATATTATATA
*
580413 TACTTTATATATATATT
1 TACTTTATAT-TATATA
*
580430 TAGTTTATA-TATATA
1 TACTTTATATTATATA
580445 CTTATATACT
Statistics
Matches: 128, Mismatches: 13, Indels: 41
0.70 0.07 0.23
Matches are distributed among these distances:
12 1 0.01
13 6 0.05
14 11 0.09
15 30 0.23
16 14 0.11
17 46 0.36
18 5 0.04
19 14 0.11
20 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (16 bp):
TACTTTATATTATATA
Found at i:580391 original size:21 final size:20
Alignment explanation
Indices: 580330--580499 Score: 94
Period size: 19 Copynumber: 8.6 Consensus size: 20
580320 TTTATACTCA
*
580330 TATA-TTTATA-TATATATT
1 TATACTTTATATTATATACT
* *
580348 ATATACTTTAGTCTT-TA-AAT
1 -TATACTTTA-TATTATATACT
580368 TATACTTTATATTAATATACT
1 TATACTTTATATT-ATATACT
580389 TATACTTTATATATTATATA-T
1 TATAC-TT-TATATTATATACT
580410 ATATACTTTATA-TATATA-T
1 -TATACTTTATATTATATACT
*
580429 T-TAGTTTATA-TATATACTT
1 TATACTTTATATTATATAC-T
*
580448 ATATACTTTATATT-TAAACT
1 -TATACTTTATATTATATACT
* *
580468 ATATA-ATTATATTAATAAAC-
1 -TATACTTTATATT-ATATACT
*
580488 TATAGTTTATAT
1 TATACTTTATAT
580500 ATAGTTCAAT
Statistics
Matches: 125, Mismatches: 9, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
17 14 0.11
18 4 0.03
19 32 0.26
20 25 0.20
21 30 0.24
22 14 0.11
23 6 0.05
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
TATACTTTATATTATATACT
Found at i:580402 original size:60 final size:60
Alignment explanation
Indices: 580268--580460 Score: 163
Period size: 60 Copynumber: 3.3 Consensus size: 60
580258 TATGTGTGTG
* * * * * * *
580268 TACTT-TATAGTTTATATA-TATATATACATAC--TATATTTATATGTA-TATATACTTTA
1 TACTTATATACTTTATATATTATATATATATACTTTATATATAAATTTACTTTATA-TATA
* * *
580324 TACTCATATA-TTTATATA-TATAT-TATATACTTTAGTCTTTAAATTATACTTTATATTAATA
1 TACTTATATACTTTATATATTATATATATATACTTTA-TATATAAATT-TACTTTATA-T-ATA
* *
580385 TAC-T-TATACTTTATATATTATATATATATACTTTATATATATATTTAGTTTATATATA
1 TACTTATATACTTTATATATTATATATATATACTTTATATATAAATTTACTTTATATATA
580443 TACTTATATACTTTATAT
1 TACTTATATACTTTATAT
580461 TTAAACTATA
Statistics
Matches: 112, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
55 6 0.05
56 17 0.15
57 6 0.05
58 13 0.12
59 8 0.07
60 34 0.30
61 17 0.15
62 11 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (60 bp):
TACTTATATACTTTATATATTATATATATATACTTTATATATAAATTTACTTTATATATA
Found at i:580412 original size:13 final size:14
Alignment explanation
Indices: 580282--580452 Score: 91
Period size: 13 Copynumber: 12.4 Consensus size: 14
580272 TTATAGTTTA
580282 TATATATATATAC-
1 TATATATATATACT
*
580295 -ATACTATATTTA--
1 TATA-TATATATACT
*
580307 TATGTATATATACT
1 TATATATATATACT
580321 T-TATACTCATATA-T
1 TATATA-T-ATATACT
580335 T-TATATATATA-T
1 TATATATATATACT
*
580347 TATATACTTTAGT-CT
1 TATATA-TATA-TACT
*
580362 T-TAAAT-TATACT
1 TATATATATATACT
580374 T-TATATTAATATACT
1 TATATA-T-ATATACT
*
580389 TATACTTTATATA-T
1 TATA-TATATATACT
580403 TATATATATATACT
1 TATATATATATACT
*
580417 T-TATATATATATT
1 TATATATATATACT
580430 TAGTTTATATATATACT
1 TA---TATATATATACT
580447 TATATA
1 TATATA
580453 CTTTATATTT
Statistics
Matches: 126, Mismatches: 11, Indels: 41
0.71 0.06 0.23
Matches are distributed among these distances:
11 1 0.01
12 25 0.20
13 38 0.30
14 25 0.20
15 20 0.16
16 3 0.02
17 14 0.11
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATATATATACT
Found at i:580452 original size:2 final size:2
Alignment explanation
Indices: 580280--580444 Score: 63
Period size: 2 Copynumber: 80.0 Consensus size: 2
580270 CTTTATAGTT
* * * *
580280 TA TA TA TA TA TA TA CA TA CTA TA TT TA TA TG TA TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
580324 TA CTCA TA TA TT TA TA TA TA TA T- TA TA TA CTT TA GTC TT TA AA
1 TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA
* *
580367 T- TA TA CTT TA TA T- TA -A TA TA CT- TA TA CTT TA TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * *
580405 TA TA TA TA TA CTT TA TA TA TA TA TT TA GTT TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
580445 CTTATATACT
Statistics
Matches: 119, Mismatches: 27, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
1 6 0.05
2 100 0.84
3 12 0.10
4 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:580564 original size:2 final size:2
Alignment explanation
Indices: 580552--580825 Score: 69
Period size: 2 Copynumber: 138.5 Consensus size: 2
580542 GTATGTAGTT
* * *
580552 TA TA CA TA TA TA TA TA TA -A TA TA TA GTT TA CA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
580595 -A AA T- TA -A TA TA AA CTA TA GTT TA TA TA TA TA TA TA TA CTT
1 TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
580635 TA TA TA CA CTA TA TA -A T- TA TA TA T- TG TT TA TA T- TA -A TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
580673 AA CTA TA TA GTT TA TA CA TA GTT TA TA TG TA -A TA TA TA TA AA
1 TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
580715 CTA TA TA TG CA CTA TA TA GTT TT TA -A TA TA AA T- TA TA TT TA
1 -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
580756 TG TT TA TA CA TA -A TA TA TA TA TA GT- TCA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA
*
580797 -A TA TA TA TA TA TA TA -A TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
580826 TATTTTTTTC
Statistics
Matches: 195, Mismatches: 46, Indels: 62
0.64 0.15 0.20
Matches are distributed among these distances:
1 17 0.09
2 163 0.84
3 15 0.08
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:580575 original size:11 final size:11
Alignment explanation
Indices: 580559--580818 Score: 62
Period size: 11 Copynumber: 23.6 Consensus size: 11
580549 GTTTATACAT
580559 ATATATATATA
1 ATATATATATA
*
580570 ATATATAGTTTA
1 ATATATA-TATA
580582 CATATAGTATATA
1 -ATATA-TATATA
*
580595 AAAT-TAATATA
1 ATATAT-ATATA
*
580606 A-ACTATAGT-TT
1 ATA-TATA-TATA
580617 ATATATATAT-
1 ATATATATATA
*
580627 ATATACTTTAT-
1 ATATA-TATATA
*
580638 ATACACTATATA
1 ATATA-TATATA
*
580650 AT-TATATATT
1 ATATATATATA
* *
580660 GTTTATAT-TA
1 ATATATATATA
*
580670 ATAAACTATATA
1 ATATA-TATATA
* * *
580682 GTTTATACATA
1 ATATATATATA
* * *
580693 GTTTATATGTA
1 ATATATATATA
580704 ATATATATA-A
1 ATATATATATA
**
580714 ACTATATATGCA
1 A-TATATATATA
* *
580726 CTATATAGT-TT
1 ATATATA-TATA
*
580737 TTA-ATATA-A
1 ATATATATATA
*
580746 AT-TATATTTA
1 ATATATATATA
* * *
580756 TGTTTATACATA
1 -ATATATATATA
580768 ATATATATATA
1 ATATATATATA
* *
580779 GT-TCATATATT
1 ATAT-ATATATA
580790 ATATATA-ATA
1 ATATATATATA
580800 TATATATATATA
1 -ATATATATATA
580812 ATATATA
1 ATATATA
580819 CATATATTAT
Statistics
Matches: 182, Mismatches: 41, Indels: 52
0.66 0.15 0.19
Matches are distributed among these distances:
9 6 0.03
10 26 0.14
11 113 0.62
12 27 0.15
13 8 0.04
14 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (11 bp):
ATATATATATA
Found at i:580697 original size:33 final size:33
Alignment explanation
Indices: 580642--580706 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
580632 CTTTATATAC
* *
580642 ACTATATAATTATATATTGTTTATAT-TAATAA
1 ACTATATAATTATACATAGTTTATATGTAATAA
*
580674 ACTATATAGTTTATACATAGTTTATATGTAATA
1 ACTATATA-ATTATACATAGTTTATATGTAATA
580707 TATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 15 0.54
34 5 0.18
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (33 bp):
ACTATATAATTATACATAGTTTATATGTAATAA
Found at i:580809 original size:15 final size:15
Alignment explanation
Indices: 580760--580825 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
580750 TATTTATGTT
*
580760 TATACATAATATATA
1 TATATATAATATATA
*
580775 TATAGT-TCATATAT-
1 TATA-TATAATATATA
580789 TATATATAATATATA
1 TATATATAATATATA
580804 TATATATAATATATA
1 TATATATAATATATA
*
580819 CATATAT
1 TATATAT
580826 TATTTTTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.02
14 11 0.25
15 32 0.73
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (15 bp):
TATATATAATATATA
Found at i:580815 original size:29 final size:29
Alignment explanation
Indices: 580759--580817 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
580749 ATATTTATGT
*
580759 TTATACATAATATATATATAGTTCATATA
1 TTATACATAATATATATATAGTTAATATA
*
580788 TTATATATAATATATATATA-TATAATATA
1 TTATACATAATATATATATAGT-TAATATA
580817 T
1 T
580818 ACATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (29 bp):
TTATACATAATATATATATAGTTAATATA
Found at i:583947 original size:153 final size:153
Alignment explanation
Indices: 583677--584247 Score: 900
Period size: 153 Copynumber: 3.7 Consensus size: 153
583667 CGTTCTTGAA
*
583677 GTTCAGCATCCGAACTCAACATCGTT-TCGGCCAACTGTTAATGATGAAGCAATGAACAATGAAG
1 GTTCAGCATCCGAACTCAACATCGTTCT-GGCCAACTGTTAATGATGGAGCAATGAACAATGAAG
* * * * *
583741 CTTCGTTGATGACAGCTGGTAATAACAGTAATTTCGTATTTGAAGGT-AGTAACTCGGTCACGAC
65 CTTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCA-TAACTTGGTCGCGAC
*
583805 TCAGCCGAATAACAATGTTCTCCAT
129 TCAGCCGAATAACAATGTTCTCAAT
* * *
583830 GTTCAGCATCCCAACTCAACAACGTTTTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAGC
1 GTTCAGCATCCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAGC
*
583895 TTCGTTGATGGCAGCTGGTAATGACAGTAATGTCATATTTGAAGGTCATAACTTGGTCGCGACTC
66 TTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCATAACTTGGTCGCGACTC
*
583960 AGCTGAATAACAATGTTCTCAAT
131 AGCCGAATAACAATGTTCTCAAT
* * *
583983 GTTCAGCAAT-GGAACTC-ACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGACCATTGAAG
1 GTTCAGC-ATCCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAG
* *
584046 CTT-GATTGATGGCAGATGGTAATAACAGTAATGTCATATTTGAAGGTCGTAACTTGGTCGCGAC
65 CTTCG-TTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCATAACTTGGTCGCGAC
*
584110 TCAGCCGAATAACAATGTTCTCGAT
129 TCAGCCGAATAACAATGTTCTCAAT
*
584135 GTTCAGCAACCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAGC
1 GTTCAGCATCCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAGC
584200 TTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCA
66 TTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCA
584248 ACATCCATGA
Statistics
Matches: 383, Mismatches: 28, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
151 2 0.01
152 137 0.36
153 239 0.62
154 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (153 bp):
GTTCAGCATCCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCAATGAACAATGAAGC
TTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCATAACTTGGTCGCGACTC
AGCCGAATAACAATGTTCTCAAT
Found at i:584246 original size:305 final size:306
Alignment explanation
Indices: 583688--584247 Score: 937
Period size: 305 Copynumber: 1.8 Consensus size: 306
583678 TTCAGCATCC
583688 GAACTCAACATCGTTTCGGCCAACTGTTAATGATGAAGCAATGAACAATGAAGCTTCGTTGATGA
1 GAACTCAACATCGTTTCGGCCAACTGTTAATGATGAAGCAATGAACAATGAAGCTTCGTTGATGA
* * *
583753 CAGCTGGTAATAACAGTAATTTCGTATTTGAAGGTAGTAACTCGGTCACGACTCAGCCGAATAAC
66 CAGATGGTAATAACAGTAATGTCATATTTGAAGGTAGTAACTCGGTCACGACTCAGCCGAATAAC
* *
583818 AATGTTCTCCATGTTCAGCATCCCAACTCAACAACGTTTTGGCCAACTGTTAATGATGGAGCAAT
131 AATGTTCTCCATGTTCAGCAACCCAACTCAACAACGTTCTGGCCAACTGTTAATGATGGAGCAAT
*
583883 GAACAATGAAGCTTCGTTGATGGCAGCTGGTAATGACAGTAATGTCATATTTGAAGGTCATAACT
196 GAACAATGAAGCTTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCATAACT
583948 TGGTCGCGACTCAGCTGAATAACAATGTTCTCAATGTTCAGCAATG
261 TGGTCGCGACTCAGCTGAATAACAATGTTCTCAATGTTCAGCAATG
* * *
583994 GAACTC-ACATCG-TTCTGGCCAACTGTTAATGATGGAGCAATGACCATTGAAGCTT-GATTGAT
1 GAACTCAACATCGTTTC-GGCCAACTGTTAATGATGAAGCAATGAACAATGAAGCTTCG-TTGAT
* * * *
584056 GGCAGATGGTAATAACAGTAATGTCATATTTGAAGGTCGTAACTTGGTCGCGACTCAGCCGAATA
64 GACAGATGGTAATAACAGTAATGTCATATTTGAAGGTAGTAACTCGGTCACGACTCAGCCGAATA
* * *
584121 ACAATGTTCTCGATGTTCAGCAACCGAACTCAACATCGTTCTGGCCAACTGTTAATGATGGAGCA
129 ACAATGTTCTCCATGTTCAGCAACCCAACTCAACAACGTTCTGGCCAACTGTTAATGATGGAGCA
584186 ATGAACAATGAAGCTTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCA
194 ATGAACAATGAAGCTTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCA
584248 ACATCCATGA
Statistics
Matches: 236, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
304 4 0.02
305 226 0.96
306 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (306 bp):
GAACTCAACATCGTTTCGGCCAACTGTTAATGATGAAGCAATGAACAATGAAGCTTCGTTGATGA
CAGATGGTAATAACAGTAATGTCATATTTGAAGGTAGTAACTCGGTCACGACTCAGCCGAATAAC
AATGTTCTCCATGTTCAGCAACCCAACTCAACAACGTTCTGGCCAACTGTTAATGATGGAGCAAT
GAACAATGAAGCTTCGTTGATGGCAGCTGGTAATAACAGTAATGTCATATTTGAAGGTCATAACT
TGGTCGCGACTCAGCTGAATAACAATGTTCTCAATGTTCAGCAATG
Found at i:585904 original size:20 final size:19
Alignment explanation
Indices: 585881--585939 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
585871 AAAAAATTAA
585881 AAATTCTAAATTATATCCTT
1 AAATTCTAAATTATATCC-T
* * * *
585901 AAATTTTAAATCCAAAACCT
1 AAATTCTAAAT-TATATCCT
585921 AAATTCTCAAATTATATCC
1 AAATTCT-AAATTATATCC
585940 CAAACCCTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTCTAAATTATATCCT
Found at i:585944 original size:26 final size:26
Alignment explanation
Indices: 585910--585960 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
585900 TAAATTTTAA
*
585910 ATCCAAAA-CCTAAATTCTCAAATTAT
1 ATCCAAAACCCTAAA-CCTCAAATTAT
*
585936 ATCCCAAACCCTAAACCTCAAATTA
1 ATCCAAAACCCTAAACCTCAAATTA
585961 CAATCACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (26 bp):
ATCCAAAACCCTAAACCTCAAATTAT
Found at i:586151 original size:3 final size:3
Alignment explanation
Indices: 586143--586193 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
586133 ATGTTCCAAC
586143 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
586191 AAG
1 AAG
586194 TGTTGTGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:587764 original size:7 final size:7
Alignment explanation
Indices: 587754--587783 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
587744 TATTTTCATA
587754 ATTATTT
1 ATTATTT
587761 ATTATTT
1 ATTATTT
587768 ATTATTT
1 ATTATTT
587775 ATTTATTT
1 A-TTATTT
587783 A
1 A
587784 ATATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:587769 original size:4 final size:4
Alignment explanation
Indices: 587755--587801 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
587745 ATTTTCATAA
*
587755 TTAT TTA- TTAT TTA- TTAT TTAT TTAT TTAAT ATAAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT -TTAT TTAT TTAT TTA
587802 AATTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 6 0.16
4 26 0.70
5 4 0.11
6 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:587776 original size:18 final size:18
Alignment explanation
Indices: 587734--587802 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
587724 TGATCTATTG
* *
587734 ATATAATTTATAT-TTTC
1 ATATAATTTATTTATTTA
*
587751 ATAATTATTTA-TTATTT-
1 AT-ATAATTTATTTATTTA
587768 AT-T-ATTTATTTATTTA
1 ATATAATTTATTTATTTA
587784 ATATAATTTATTTATTTA
1 ATATAATTTATTTATTTA
587802 A
1 A
587803 ATTATTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
14 5 0.11
15 7 0.16
16 2 0.05
17 6 0.14
18 24 0.55
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATAATTTATTTATTTA
Found at i:588116 original size:73 final size:72
Alignment explanation
Indices: 588016--588189 Score: 208
Period size: 73 Copynumber: 2.4 Consensus size: 72
588006 TTTAATGAAT
* * * ** * * *
588016 AAATAATTCTTA-ATT-TTTATTATCTATAACTTACAATAGTTTATATATTTTTATTTTTTGTTA
1 AAATAATTCTTATTTTATTTATTAACTATAACTTACAAAAAATTACATATTTTTATTTTTTATCA
*
588079 ATGGAAG
66 ATGAAAG
* * *
588086 AAATGATTTTTATTTCTATTTATTAACTATAATTTACAAAAAATTACATATTTTTATTTTTTATC
1 AAATAATTCTTATTT-TATTTATTAACTATAACTTACAAAAAATTACATATTTTTATTTTTTATC
588151 AATGAAAG
65 AATGAAAG
*
588159 AAATAATTCTTATTTTATTTATTAATTATAA
1 AAATAATTCTTATTTTATTTATTAACTATAA
588190 TTTAATAATT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
70 10 0.12
71 1 0.01
72 16 0.19
73 59 0.69
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (72 bp):
AAATAATTCTTATTTTATTTATTAACTATAACTTACAAAAAATTACATATTTTTATTTTTTATCA
ATGAAAG
Found at i:590065 original size:34 final size:35
Alignment explanation
Indices: 590012--590083 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
590002 AATTAAGATT
*
590012 TAGTTTAATAAATGAACTAA-TTTGA-TGAATGAAC
1 TAGTTTAATAAATGAACTAACTTT-ATTCAATGAAC
*
590046 TAGTTTAATTAATTG-ACTAACTTTATTCAATGAAC
1 TAGTTTAA-TAAATGAACTAACTTTATTCAATGAAC
590081 TAG
1 TAG
590084 ATTCATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAACTTTATTCAATGAAC
Found at i:590967 original size:17 final size:17
Alignment explanation
Indices: 590904--590967 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
590894 AAAAATTTAT
*
590904 TTTAAAT-TAATCATATA
1 TTTAAATATAATTATA-A
* *
590921 TTAAAATTTAATTATAA
1 TTTAAATATAATTATAA
* *
590938 TTTTAATAGAATTATAA
1 TTTAAATATAATTATAA
590955 -TTAAATCATAATT
1 TTTAAAT-ATAATT
590968 TTTATTAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 5 0.14
17 25 0.68
18 7 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAATATAATTATAA
Found at i:592715 original size:11 final size:11
Alignment explanation
Indices: 592699--592729 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
592689 ATCCTAAAAA
592699 ATTATAATTTT
1 ATTATAATTTT
592710 ATTATAATTTT
1 ATTATAATTTT
*
592721 ATTAAAATT
1 ATTATAATT
592730 ATAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATAATTTT
Found at i:600181 original size:153 final size:153
Alignment explanation
Indices: 599941--600269 Score: 532
Period size: 153 Copynumber: 2.2 Consensus size: 153
599931 CATCGTTTCG
* *
599941 GCCAACTGTCAATGATGGAGCAATGAACAATGAAGCTTCGTTGATAGCAGCTGGTAATAACAGTA
1 GCCAACTGTTAATGATGGAGCAATGAACAATGAAGCTTCGTTGATAGCAGATGGTAATAACAGTA
600006 ATGTCATATTTGAAGGTCCTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCACGTTCAG
66 ATGTCATATTTGAAGGTCCTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCACGTTCAG
* * *
600071 CAACCAAGTGCAACGTTGTCTAC
131 CAACCAACTGCAACGTTGTCAAA
** * * * *
600094 GCCAACTGTTAATGATGGAGCAATGGCCATTGAAGCTTGGTTGATGGCAGATGGTAATAACAGTG
1 GCCAACTGTTAATGATGGAGCAATGAACAATGAAGCTTCGTTGATAGCAGATGGTAATAACAGTA
*
600159 ATGTCATATTTGAAGGTCCTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCATGTTCAG
66 ATGTCATATTTGAAGGTCCTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCACGTTCAG
*
600224 CAACCGACTGCAACGTTGTCAAA
131 CAACCAACTGCAACGTTGTCAAA
*
600247 GCCAACTGTTAACGATGGAGCAA
1 GCCAACTGTTAATGATGGAGCAA
600270 AGACACTGCA
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 162 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (153 bp):
GCCAACTGTTAATGATGGAGCAATGAACAATGAAGCTTCGTTGATAGCAGATGGTAATAACAGTA
ATGTCATATTTGAAGGTCCTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCACGTTCAG
CAACCAACTGCAACGTTGTCAAA
Found at i:603270 original size:14 final size:15
Alignment explanation
Indices: 603251--603283 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
603241 AGTTCGAACG
603251 AAAG-AAATAGGATA
1 AAAGAAAATAGGATA
603265 AAAGAAAAATAGGATA
1 AAAG-AAAATAGGATA
603281 AAA
1 AAA
603284 TCCTCTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
16 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (15 bp):
AAAGAAAATAGGATA
Found at i:604252 original size:17 final size:17
Alignment explanation
Indices: 604230--604265 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
604220 GTTAAACAAG
604230 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
604247 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
604264 TT
1 TT
604266 TCCACTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:604418 original size:98 final size:99
Alignment explanation
Indices: 604247--604463 Score: 337
Period size: 98 Copynumber: 2.2 Consensus size: 99
604237 CATTATGAAC
* * *
604247 TTCTTCTCATTATGAACTTTCCACTGAAAATGTTGATCCCTCGAGTGAGATGTTGCTGATTCAAC
1 TTCTTCTCATTATGAAC-TTCCACTGAAAATATTAATCCCTCGAGTGAGATATTGCTGATTCAAC
*
604312 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAG
65 TCCATATGCGATGAATCGAGCTAAGCTTGAACAAG
** * * *
604347 TTCTTCTCATTATGAA-TTCTTCTGGAAATATTAATCCCTCGTGTGAGGTATTGCTGATTCAACT
1 TTCTTCTCATTATGAACTTCCACTGAAAATATTAATCCCTCGAGTGAGATATTGCTGATTCAACT
604411 CCATATGCGATGAATCGAGCTAAGCTTGAACAAG
66 CCATATGCGATGAATCGAGCTAAGCTTGAACAAG
604445 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
604464 TTTCTCCCTT
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
98 89 0.83
99 2 0.02
100 16 0.15
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (99 bp):
TTCTTCTCATTATGAACTTCCACTGAAAATATTAATCCCTCGAGTGAGATATTGCTGATTCAACT
CCATATGCGATGAATCGAGCTAAGCTTGAACAAG
Found at i:604542 original size:138 final size:138
Alignment explanation
Indices: 604345--605056 Score: 1059
Period size: 138 Copynumber: 5.2 Consensus size: 138
604335 AGGTTGAACA
* * * *
604345 AGTTCTTCTCATTATGAATTCTTCTGGAAATATTAATCCCTCGTGTGAGGTATTGCTGATTCAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* *
604410 TCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTTT
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTT
* *
604475 TTCAGATG
131 GTCGGATG
* * ** *
604483 AGTTCTTCTCATTATGAACTATTCTGGAAATGTTGATCCCTTAAGTGAGGTGTTACTGATTCAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
*
604548 TCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTT
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTT
604613 GTCGGATG
131 GTCGGATG
* * * * *
604621 GGTTCTTCTCATTATGAACTCTTATGGAAATATTGATCCCTCGAGTAAGGTGTTACTGATTAAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* * *
604686 TCCATATGTGATGAATCGGGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTT
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTT
*
604751 ATCGGATG
131 GTCGGATG
* *** *
604759 AGTTCTTCTCATTATAAACTCTTCTGGAAATATTGATCCCTCGAAAAAAGGTGTTGTTGATTCAA
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCG-AGTGAGGTGTTGCTGATTCAA
*
604824 CTCCATATGCGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTCCCTT
65 CTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTT
*
604889 AGTCGGATG
130 TGTCGGATG
* * *
604898 AGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTAATTCAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* * * *
604963 TCTATATGCGATGAATCAAGCTAAGGTTGAACAAGTGCTTCTCATTATGAACTTCTTCTCCCTCA
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-T
605028 T-T-GGATG
130 TGTCGGATG
605035 AGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTCT
605057 CCACTAGAAA
Statistics
Matches: 519, Mismatches: 53, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
137 27 0.05
138 368 0.71
139 124 0.24
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (138 bp):
AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTT
GTCGGATG
Found at i:604936 original size:277 final size:275
Alignment explanation
Indices: 604345--605056 Score: 1073
Period size: 277 Copynumber: 2.6 Consensus size: 275
604335 AGGTTGAACA
* * * *
604345 AGTTCTTCTCATTATGAATTCTTCTGGAAATATTAATCCCTCGTGTGAGGTATTGCTGATTCAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* *
604410 TCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTTT
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTTT
* * * * * ***
604475 TTCAGATGAGTTCTTCTCATTATGAACTATTCTGGAAATGTTGATCCCTTAAGTGAGGTGTTACT
130 ATCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTGAAAAAAGGTGTTACT
604540 GATTCAACTCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTT
195 GATTCAACTCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTT
*
604605 CTCCCTTTGTCGGATG
260 CTCCCTTAGTCGGATG
* * * * *
604621 GGTTCTTCTCATTATGAACTCTTATGGAAATATTGATCCCTCGAGTAAGGTGTTACTGATTAAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* *
604686 TCCATATGTGATGAATCGGGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTT
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-CTTT
* **
604751 ATCGGATGAGTTCTTCTCATTATAAACTCTTCTGGAAATATTGATCCCTCGAAAAAAGGTGTTGT
130 ATCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCT-GAAAAAAGGTGTTAC
* *
604816 TGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCT
194 TGATTCAACTCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCT
604881 TCTCCCTTAGTCGGATG
259 TCTCCCTTAGTCGGATG
* * *
604898 AGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTAATTCAAC
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
* * * * *
604963 TCTATATGCGATGAATCAAGCTAAGGTTGAACAAGTGCTTCTCATTATGAACTTCTTCTCCCTCA
66 TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTA
*
605028 TTGGATGAGTTCTTCTCATTATGAACTCT
131 TCGGATGAGTTCTTCTCATTATGAACTCT
605057 CCACTAGAAA
Statistics
Matches: 390, Mismatches: 44, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
275 1 0.00
276 189 0.48
277 200 0.51
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (275 bp):
AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAAC
TCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTA
TCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGATCCCTGAAAAAAGGTGTTACTG
ATTCAACTCCATATGCGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTC
TCCCTTAGTCGGATG
Found at i:605996 original size:15 final size:15
Alignment explanation
Indices: 605969--606009 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
605959 AAATATTGTT
*
605969 TCAAGGGAAACTGTC
1 TCAAGGGAGACTGTC
*
605984 TCAAGTGAGACTGTC
1 TCAAGGGAGACTGTC
605999 TCAAGGGAGAC
1 TCAAGGGAGAC
606010 AAAATTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (15 bp):
TCAAGGGAGACTGTC
Found at i:606054 original size:36 final size:36
Alignment explanation
Indices: 605984--606056 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
605974 GGAAACTGTC
* * **
605984 TCAAGTGAGACTGTCTCAAGGGAGACAAAATTGGTT
1 TCAAGGGAAACTGTCTCAAGCAAGACAAAATTGGTT
* *
606020 TCAAGGGAAACTGTCTCAAGCAAGACGAAGTTGGTT
1 TCAAGGGAAACTGTCTCAAGCAAGACAAAATTGGTT
606056 T
1 T
606057 TAAGAAACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGCAAGACAAAATTGGTT
Found at i:606232 original size:77 final size:75
Alignment explanation
Indices: 606058--606232 Score: 176
Period size: 75 Copynumber: 2.3 Consensus size: 75
606048 AGTTGGTTTT
* * * ** **
606058 AAGAAACACAATATTGAGTAAAACGAATATTCTTGTTTTGGGTAAAACTAGCTCAAGCGAGATGA
1 AAGAAAAACAATATTGAGTGAAACGAATATTCTTGTTTTGAGTAAAAAAAGCTCAAGCGAGACAA
*
606123 ATCTTATTTT
66 ATCTTATTTG
* * *
606133 AAGAAAAATAATCTAT-AGTGAAACGAA-ATGTCTTGTTTTGAGTAAAAAAATGTCTCAAGTGAG
1 AAGAAAAACAATAT-TGAGTGAAACGAATAT-TCTTGTTTTGAGTAAAAAAA-G-CTCAAGCGAG
606196 ACAAAGTC-TATTTG
62 ACAAA-TCTTATTTG
*
606210 AAGAAAAACAATATTGAATGAAA
1 AAGAAAAACAATATTGAGTGAAA
606233 TGTATTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
74 2 0.03
75 38 0.47
76 3 0.04
77 35 0.44
78 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (75 bp):
AAGAAAAACAATATTGAGTGAAACGAATATTCTTGTTTTGAGTAAAAAAAGCTCAAGCGAGACAA
ATCTTATTTG
Found at i:606374 original size:65 final size:65
Alignment explanation
Indices: 606305--606430 Score: 200
Period size: 65 Copynumber: 1.9 Consensus size: 65
606295 TATTTTGTTC
* * * *
606305 CAAGAGAAATTGTCTCAA-GAGAGATAAAATTTGTTTCAAGGGAAACATTCTCAAAGTTTATTTT
1 CAAGAGAAACTGTCTCAATG-GAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATTTT
606369 A
65 A
606370 CAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTAT
1 CAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTAT
606431 CAATTTTGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 55 0.98
66 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (65 bp):
CAAGAGAAACTGTCTCAATGGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATTTTA
Found at i:608015 original size:7 final size:7
Alignment explanation
Indices: 608005--608114 Score: 220
Period size: 7 Copynumber: 15.7 Consensus size: 7
607995 TTTCTTCTTT
608005 TTTTTCA
1 TTTTTCA
608012 TTTTTCA
1 TTTTTCA
608019 TTTTTCA
1 TTTTTCA
608026 TTTTTCA
1 TTTTTCA
608033 TTTTTCA
1 TTTTTCA
608040 TTTTTCA
1 TTTTTCA
608047 TTTTTCA
1 TTTTTCA
608054 TTTTTCA
1 TTTTTCA
608061 TTTTTCA
1 TTTTTCA
608068 TTTTTCA
1 TTTTTCA
608075 TTTTTCA
1 TTTTTCA
608082 TTTTTCA
1 TTTTTCA
608089 TTTTTCA
1 TTTTTCA
608096 TTTTTCA
1 TTTTTCA
608103 TTTTTCA
1 TTTTTCA
608110 TTTTT
1 TTTTT
608115 ATCTTCTTTT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 103 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:608147 original size:25 final size:24
Alignment explanation
Indices: 608103--608182 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
608093 TCATTTTTCA
*
608103 TTTTTCATTTTTATCT-TCTTTTGT
1 TTTTTC-TTTTTTTCTATCTTTTGT
608127 TTTTTCTTTCTTTTCTATCTTTTG-
1 TTTTTCTTT-TTTTCTATCTTTTGT
* * *
608151 TATGTCTTTTTTTCTATATATTTGT
1 TTTTTCTTTTTTTCTATCT-TTTGT
608176 TTCTTTC
1 TT-TTTC
608183 CTCTTTGTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 12 0.27
24 22 0.49
25 8 0.18
26 3 0.07
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTTCTTTTTTTCTATCTTTTGT
Found at i:608164 original size:28 final size:26
Alignment explanation
Indices: 608103--608165 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
608093 TCATTTTTCA
*
608103 TTTTTCATTTTTATCTTCTTTTGTTTT
1 TTTTTC-TTTTTATCTTCTTTTGTCTT
608130 TTCTTTCTTTTCTATCTT-TTGTATGTCTT
1 TT-TTTCTTTT-TATCTTCTT-T-TGTCTT
608159 TTTTTCT
1 TTTTTCT
608166 ATATATTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 8 0.26
28 16 0.52
29 7 0.23
ACGTcount: A:0.06, C:0.14, G:0.05, T:0.75
Consensus pattern (26 bp):
TTTTTCTTTTTATCTTCTTTTGTCTT
Found at i:612475 original size:177 final size:177
Alignment explanation
Indices: 612179--612529 Score: 693
Period size: 177 Copynumber: 2.0 Consensus size: 177
612169 TCTTCCTCAC
*
612179 TCCAAACGGTGTTGCACGCCGAAACCAAGATAAAGCTCGGCCACCACACGCCGGTGGTGACCCTC
1 TCCAAACGGTGTTGCACGCCGAAACCAAGACAAAGCTCGGCCACCACACGCCGGTGGTGACCCTC
612244 TTACGCTGGTGTTATTCACAAAAGACTAAATTAAAATAATGTAAAATCATCCATTCAATTCTCAA
66 TTACGCTGGTGTTATTCACAAAAGACTAAATTAAAATAATGTAAAATCATCCATTCAATTCTCAA
612309 ATCCTTGAAAATAAACAGAAATGGGGACCAAAATGCAAAAGATGCTA
131 ATCCTTGAAAATAAACAGAAATGGGGACCAAAATGCAAAAGATGCTA
612356 TCCAAACGGTGTTGCACGCCGAAACCAAGACAAAGCTCGGCCACCACACGCCGGTGGTGACCCTC
1 TCCAAACGGTGTTGCACGCCGAAACCAAGACAAAGCTCGGCCACCACACGCCGGTGGTGACCCTC
612421 TTACGCTGGTGTTATTCACAAAAGACTAAATTAAAATAATGTAAAATCATCCATTCAATTCTCAA
66 TTACGCTGGTGTTATTCACAAAAGACTAAATTAAAATAATGTAAAATCATCCATTCAATTCTCAA
612486 ATCCTTGAAAATAAACAGAAATGGGGACCAAAATGCAAAAGATG
131 ATCCTTGAAAATAAACAGAAATGGGGACCAAAATGCAAAAGATG
612530 AAACTTAAGG
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 173 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (177 bp):
TCCAAACGGTGTTGCACGCCGAAACCAAGACAAAGCTCGGCCACCACACGCCGGTGGTGACCCTC
TTACGCTGGTGTTATTCACAAAAGACTAAATTAAAATAATGTAAAATCATCCATTCAATTCTCAA
ATCCTTGAAAATAAACAGAAATGGGGACCAAAATGCAAAAGATGCTA
Found at i:615088 original size:29 final size:27
Alignment explanation
Indices: 615024--615123 Score: 89
Period size: 26 Copynumber: 3.7 Consensus size: 27
615014 AAAATCATAG
* * *
615024 TTATTGTAATTTGT-AAAATA-ATGTCA
1 TTATTGTAATTTATAAAAATATAT-ACT
* *
615050 TTATTTTAATTTATAAAAAGTTTTATACT
1 TTATTGTAATTTATAAAAA--TATATACT
*
615079 TTATTGTAATTTA-AAGAATATATACT
1 TTATTGTAATTTATAAAAATATATACT
*
615105 TTATTGTAATTTTTAAAAA
1 TTATTGTAATTTATAAAAA
615124 AATTGTCCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
26 31 0.53
27 8 0.14
28 4 0.07
29 14 0.24
30 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (27 bp):
TTATTGTAATTTATAAAAATATATACT
Found at i:615189 original size:29 final size:29
Alignment explanation
Indices: 615126--615227 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 29
615116 TTTAAAAAAA
* * * *
615126 TTGTCCTTAATTGTAAA-TTCACAACGTT
1 TTGTCCTTTATTATAAATTTCAAAACGAT
*
615154 TTGTCCTTTATTATAAATTTCAAAACGCT
1 TTGTCCTTTATTATAAATTTCAAAACGAT
* ** * *
615183 TTATCCTTTATTGGAAATTCCAAAACAAT
1 TTGTCCTTTATTATAAATTTCAAAACGAT
615212 TTGTCCTTTATTATAA
1 TTGTCCTTTATTATAA
615228 TTCTATGATT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 15 0.25
29 45 0.75
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (29 bp):
TTGTCCTTTATTATAAATTTCAAAACGAT
Found at i:615840 original size:153 final size:153
Alignment explanation
Indices: 615562--615857 Score: 520
Period size: 153 Copynumber: 1.9 Consensus size: 153
615552 ATGTTCAGCA
* *
615562 AACTGTTAATGATGGAGCAAAGACCAATGACGCTCCGTTGATGGCAGCTGGTAATAACAGTAATG
1 AACTGTTAATGATGGAGCAAAGACCAAAGAAGCTCCGTTGATGGCAGCTGGTAATAACAGTAATG
* *
615627 TCATATTTGATGGTCGTAACTCGGTCGCGAATCAGCGGAATAACAATGTTCTCCGTGTTCAGCAA
66 TCATATTTGATGGTCGTAACTCGGTCGCGAATCAGCCGAATAACAATGTTCTCCATGTTCAGCAA
615692 CCGAGTGCAACGTTGTGTAAGCC
131 CCGAGTGCAACGTTGTGTAAGCC
* * *
615715 AACTGTTAATGATGGAGGAAAGACCAAAGAAGCTTCGTTGATGGCAGCTGGTAATAACAGTAATT
1 AACTGTTAATGATGGAGCAAAGACCAAAGAAGCTCCGTTGATGGCAGCTGGTAATAACAGTAATG
*
615780 TCATATTTGATGGTCGTAACTCGGTCGCGACTCAGCCGAATAACAATGTTCTCCATGTTCAGCAA
66 TCATATTTGATGGTCGTAACTCGGTCGCGAATCAGCCGAATAACAATGTTCTCCATGTTCAGCAA
615845 CCGAGTGCAACGT
131 CCGAGTGCAACGT
615858 AGCCAACTTC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 135 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (153 bp):
AACTGTTAATGATGGAGCAAAGACCAAAGAAGCTCCGTTGATGGCAGCTGGTAATAACAGTAATG
TCATATTTGATGGTCGTAACTCGGTCGCGAATCAGCCGAATAACAATGTTCTCCATGTTCAGCAA
CCGAGTGCAACGTTGTGTAAGCC
Found at i:621940 original size:49 final size:50
Alignment explanation
Indices: 621850--621944 Score: 158
Period size: 49 Copynumber: 1.9 Consensus size: 50
621840 TTAAAAAAAC
*
621850 TATATTAGCATAGTATCTGTGAGTGGTGATGAGAACTTAGAATTTTTGTT
1 TATATTAGCATAGTATCTGTGAATGGTGATGAGAACTTAGAATTTTTGTT
621900 TATATTAGCATAGTAATCTGTGAAT-G-GATGAGAACTTAGAATTTT
1 TATATTAGCATAGT-ATCTGTGAATGGTGATGAGAACTTAGAATTTT
621945 GGCATGTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
49 19 0.44
50 15 0.35
51 9 0.21
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (50 bp):
TATATTAGCATAGTATCTGTGAATGGTGATGAGAACTTAGAATTTTTGTT
Found at i:622289 original size:241 final size:239
Alignment explanation
Indices: 621860--622341 Score: 866
Period size: 241 Copynumber: 2.0 Consensus size: 239
621850 TATATTAGCA
621860 TAGTATCTGTGAGTGGTGATGAGAACTTAGAATTTTTGTTTATATTAGCATAGTAATCTGTGAAT
1 TAGTATCTGTGAGTGGTGATGAGAACTTAGAATTTTTGTTTATATTAGCATAGTAATCTGTGAAT
621925 GGATGAGAACTTAGAATTTTGGCATGTTGTTAGGTCATATGAAATGCAACCTGAGATATTCATTT
66 GGATGAGAACTTAGAATTTTGGCATGTTGTTAGGTCATATGAAATGCAACCTGAGATATTCATTT
621990 ATGAGAATTGTCGATGCACTTTTTTGTCTTTTGAATGACTTATTCATTAGGAAACTTGCTTGATT
131 ATGAGAATTGTCGATGCACTTTTTTGTCTTTTGAATGACTTATTCATTAGGAAACTTGCTTGATT
622055 CAGGTAGCTAGAATGTATCAACACAAATC-TCGGAAATGTTAGCCT
196 CAGGTAGCTAGAATGTATCAACACAAATCGT--GAAATGTTAGCCT
622100 TAGTAATCTGTGAGTGGTGATGAGAACTTAGAA-TTTTGTTTATATTAGCATAGTAATCTGTGAA
1 TAGT-ATCTGTGAGTGGTGATGAGAACTTAGAATTTTTGTTTATATTAGCATAGTAATCTGTGAA
622164 TGGTGATGAGAACTTAGAA-TTTGGCATGTTGTTAGGTCATATGAAATGCAACCTGAGATATTCA
65 T-G-GATGAGAACTTAGAATTTTGGCATGTTGTTAGGTCATATGAAATGCAACCTGAGATATTCA
622228 TTTATGAGAATTGTCGATGCACTTTTTTGTCTTTTGAATGTGACTTATT-ATTAGG-AACTTGCT
128 TTTATGAGAATTGTCGATGCACTTTTTTGTCTTTTGAA--TGACTTATTCATTAGGAAACTTGCT
622291 TGATTCAGGTAGCTAGAATGTATCAACACAAATCGTGAAATGTTAGCCT
191 TGATTCAGGTAGCTAGAATGTATCAACACAAATCGTGAAATGTTAGCCT
622340 TA
1 TA
622342 ATGAATTTTT
Statistics
Matches: 236, Mismatches: 0, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
240 51 0.22
241 154 0.65
242 22 0.09
243 9 0.04
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (239 bp):
TAGTATCTGTGAGTGGTGATGAGAACTTAGAATTTTTGTTTATATTAGCATAGTAATCTGTGAAT
GGATGAGAACTTAGAATTTTGGCATGTTGTTAGGTCATATGAAATGCAACCTGAGATATTCATTT
ATGAGAATTGTCGATGCACTTTTTTGTCTTTTGAATGACTTATTCATTAGGAAACTTGCTTGATT
CAGGTAGCTAGAATGTATCAACACAAATCGTGAAATGTTAGCCT
Done.