Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005344.1 Hibiscus syriacus cultivar Beakdansim tig00012104_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: 640787
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 3 of 3
Found at i:491020 original size:43 final size:43
Alignment explanation
Indices: 490958--491096 Score: 208
Period size: 43 Copynumber: 3.2 Consensus size: 43
490948 TTTCAAGAAA
* * *
490958 AAACGCCGCAATAGGTGTTGTTATTTAGCGGCGTTT-GATAGAC
1 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGA-AGAC
*
491001 AAATGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
1 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
* *
491044 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
491087 AAACGCCACA
1 AAACGCCACA
491097 GTAGGTTTCG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 85 0.98
44 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:491348 original size:60 final size:59
Alignment explanation
Indices: 491281--491405 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
491271 CACATACGAA
* * * *
491281 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCCTTAGCTCTTTATCATTCACATGGT
1 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
* *
491340 TTCTTATCTTGGCTTACCTAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
1 TT-TTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
491400 TTTTAT
1 TTTTAT
491406 TCATGGATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (59 bp):
TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
Found at i:492604 original size:42 final size:42
Alignment explanation
Indices: 492541--492661 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
492531 GGGTAACCAA
** *
492541 TTGCGGCGTTTTTAATTAAAAACGCAACTAAAGTACGCAT-CAT
1 TTGCGGCGTTTTT-ACGAAAAACGCAACTAAAGTACGAATAC-T
** * *
492584 TTGCGGCGTTTGTTA-GAAAAACGCTGCTAAATTACTAATACT
1 TTGCGGCGTTT-TTACGAAAAACGCAACTAAAGTACGAATACT
* *
492626 TTGCGGCGTTTCTACG-AAAACGCCACTAAAGTACGA
1 TTGCGGCGTTTTTACGAAAAACGCAACTAAAGTACGA
492662 GGCTATAGCG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
41 18 0.28
42 31 0.48
43 13 0.20
44 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (42 bp):
TTGCGGCGTTTTTACGAAAAACGCAACTAAAGTACGAATACT
Found at i:493221 original size:57 final size:57
Alignment explanation
Indices: 493002--493189 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
492992 ATTAAAACAG
493002 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
493059 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
*
493116 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
493173 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
493190 CAGTCTTCAC
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:494262 original size:39 final size:39
Alignment explanation
Indices: 494213--494362 Score: 115
Period size: 41 Copynumber: 3.7 Consensus size: 39
494203 TATATTTAAC
494213 ATTTTGCGGCGTTTTTACAAAACGCCACTATATCACA-T
1 ATTTTGCGGCGTTTTTACAAAACGCCACTATATCACACT
* * * *
494251 ATTTTTGCGGCGTTTATACAATAAGCGTCGCTATATTACACT
1 A-TTTTGCGGCGTTTTTACAA-AA-CGCCACTATATCACACT
* * * * **
494293 ATATTGCGGCATTTTTAGCTAAAACGCCGCTAAATGTCTACT
1 ATTTTGCGGCGTTTTTA-C-AAAACGCCACTATATCAC-ACT
*
494335 ATATTGCGGCG-TTTTACTATAAACGCCA
1 ATTTTGCGGCGTTTTTAC-A-AAACGCCA
494363 TTATTGTTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.01
39 18 0.20
40 5 0.05
41 47 0.52
42 18 0.20
43 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (39 bp):
ATTTTGCGGCGTTTTTACAAAACGCCACTATATCACACT
Found at i:497686 original size:2 final size:2
Alignment explanation
Indices: 497679--497707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
497669 GAAATCAATA
497679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
497708 ATGATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:497927 original size:60 final size:60
Alignment explanation
Indices: 497815--497963 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
497805 AATTGGTCTC
*** *
497815 TAAACTTTTAAACATTTCAATTTCATCGTTAAAATATGGCTATCATTTTAAATTAGTTCT
1 TAAACTTTTAAACATTTCAATTTCATCCCCAAAATATGGCTATCATTCTAAATTAGTTCT
* * * * *
497875 TAAACTTTTAAACATTTCATTTTCATCCCCAAATTGTGATCT-TCATTCTAAATTAGTCCT
1 TAAACTTTTAAACATTTCAATTTCATCCCCAAAATATG-GCTATCATTCTAAATTAGTTCT
* * * * *
497935 CAAGCTTTTTGAATATTTCAATTTTATCC
1 TAAAC-TTTTAAACATTTCAATTTCATCC
497964 TAAATTATAT
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
60 51 0.71
61 21 0.29
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (60 bp):
TAAACTTTTAAACATTTCAATTTCATCCCCAAAATATGGCTATCATTCTAAATTAGTTCT
Found at i:498185 original size:58 final size:58
Alignment explanation
Indices: 498089--498276 Score: 211
Period size: 60 Copynumber: 3.2 Consensus size: 58
498079 TTTGGATGAA
* * * *
498089 TTTGGGGATGAAATTGGAA-GATCTAAAAGTATAGGGACTAATTTAGAAT-GATTCATAG
1 TTTGGGGATAAAATTGGAATG-T-TAAAAGTTTAAGGACTAATTTAGAATAGAGTCATAG
*
498147 TTTGGGGATAAAATTGGAATGTTAAAAAATTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATAAAATTGGAATGTT-AAAAGTTTAAGGACTAATTTAGAAT-AGAGTCATAG
** **
498207 TTTAAGGATGTAATTGGAATGTTTAAAAGTTTAAGGACTAATTT-GAAATGAGAGTCATAG
1 TTTGGGGATAAAATTGGAATG-TTAAAAGTTTAAGGACTAATTTAG-AAT-AGAGTCATAG
498267 TTTGGGGATA
1 TTTGGGGATA
498277 TATGATGCAA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 41 0.37
59 2 0.02
60 65 0.59
61 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (58 bp):
TTTGGGGATAAAATTGGAATGTTAAAAGTTTAAGGACTAATTTAGAATAGAGTCATAG
Found at i:498211 original size:31 final size:30
Alignment explanation
Indices: 498176--498269 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
498166 TGTTAAAAAA
498176 TTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTAAGGACTAATTT-GAATGAGAGTCATAG
* * ** * *
498207 TTTAAGGATGTAATTGGAAT--GTTTAAAAG
1 TTTAAGGA-CTAATTTGAATGAGAGTCATAG
498236 TTTAAGGACTAATTTGAAATGAGAGTCATAG
1 TTTAAGGACTAATTTG-AATGAGAGTCATAG
498267 TTT
1 TTT
498270 GGGGATATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
28 6 0.13
29 16 0.34
31 20 0.43
32 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (30 bp):
TTTAAGGACTAATTTGAATGAGAGTCATAG
Found at i:502821 original size:36 final size:36
Alignment explanation
Indices: 502754--502823 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
502744 GTGTGATTAA
* *
502754 TGGATTTGTGTGATTATGTTTCAATATCAATTTATT
1 TGGATTTGTATGATTATGTTTCAATACCAATTTATT
* *
502790 TGGATTTGTATGATT-TGATTTGAATGCCAATTTA
1 TGGATTTGTATGATTATG-TTTCAATACCAATTTA
502824 AGAATATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.50
Consensus pattern (36 bp):
TGGATTTGTATGATTATGTTTCAATACCAATTTATT
Found at i:505423 original size:17 final size:16
Alignment explanation
Indices: 505390--505432 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
505380 TCGGTGATAG
505390 ATATTA-TTTTAAATA
1 ATATTATTTTTAAATA
505405 AT-TATATTTTTACAATA
1 ATAT-TATTTTTA-AATA
505422 ATATTATTTTT
1 ATATTATTTTT
505433 TTCACCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 4 0.17
16 5 0.21
17 13 0.54
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTATTTTTAAATA
Found at i:505431 original size:16 final size:15
Alignment explanation
Indices: 505390--505431 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
505380 TCGGTGATAG
505390 ATATTATTTTAAATA
1 ATATTATTTTAAATA
505405 AT-TATATTTTTACAATA
1 ATAT-TA-TTTTA-AATA
505422 ATATTATTTT
1 ATATTATTTT
505432 TTTCACCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.17
16 9 0.39
17 8 0.35
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATTTTAAATA
Found at i:506452 original size:20 final size:20
Alignment explanation
Indices: 506415--506453 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
506405 TCGATTTTTT
*
506415 AAATTTTTTTTAGCAAAATC
1 AAATTTTTTTTAGAAAAATC
506435 AAATTTTTATTTA-AAAAAT
1 AAATTTTT-TTTAGAAAAAT
506454 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATTTTTTTTAGAAAAATC
Found at i:513106 original size:60 final size:60
Alignment explanation
Indices: 513009--513125 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
512999 ATGTGTCTCC
* *
513009 AAACTATAACTTTCATTTTAAATTGATCCTTAAACTTTAAAATATTCCAATTTCATCCCT
1 AAACTATAACTCTCATTCTAAATTGATCCTTAAACTTTAAAATATTCCAATTTCATCCCT
* * ** * *
513069 AAACTATGACTCTCATTCTAAATT-AGTCCTTACACTTTTGAATGTTCTAATTTCATC
1 AAACTATAACTCTCATTCTAAATTGA-TCCTTAAACTTTAAAATATTCCAATTTCATC
513126 TATTATTCTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
AAACTATAACTCTCATTCTAAATTGATCCTTAAACTTTAAAATATTCCAATTTCATCCCT
Found at i:513974 original size:18 final size:16
Alignment explanation
Indices: 513951--513991 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
513941 TAATAAACAA
513951 TTTTTTATATATCAATT
1 TTTTTTATATAT-AATT
513968 GTTTTTTATATATAATT
1 -TTTTTTATATATAATT
513985 TTTTTTA
1 TTTTTTA
513992 AAAACTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTTTATATATAATT
Found at i:513977 original size:16 final size:16
Alignment explanation
Indices: 513947--513991 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
513937 AATTTAATAA
*
513947 ACAATTTTTTATATAT
1 ACAATTTTTTTTATAT
513963 -CAATTGTTTTTTATAT
1 ACAATT-TTTTTTATAT
*
513979 ATAATTTTTTTTA
1 ACAATTTTTTTTA
513992 AAAACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (16 bp):
ACAATTTTTTTTATAT
Found at i:515396 original size:31 final size:32
Alignment explanation
Indices: 515323--515414 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
515313 TTAAAAATTA
* *
515323 GGTACTAAAATGAAAAAAAAAAGGTAACAGTGG
1 GGTACTAAAATG-AAAAAAAAAGTTAACAATGG
* *
515356 GGTATTAAAATGAAACAAAAAGTTAACAAT-G
1 GGTACTAAAATGAAAAAAAAAGTTAACAATGG
*
515387 GGTACTAAAAT-AAAATAAAAAGTAAACA
1 GGTACTAAAATGAAAA-AAAAAGTTAACA
515415 TTAGGTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
30 3 0.06
31 22 0.43
32 15 0.29
33 11 0.22
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.18
Consensus pattern (32 bp):
GGTACTAAAATGAAAAAAAAAGTTAACAATGG
Found at i:518120 original size:15 final size:16
Alignment explanation
Indices: 518100--518132 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
518090 TAAAATGCTA
*
518100 TTCTTTC-TTTCTTTT
1 TTCTTTCATTGCTTTT
518115 TTCTTTCATTGCTTTT
1 TTCTTTCATTGCTTTT
518131 TT
1 TT
518133 GCAAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (16 bp):
TTCTTTCATTGCTTTT
Found at i:518474 original size:15 final size:15
Alignment explanation
Indices: 518454--518484 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
518444 TATCTAGATA
518454 TGATCTTAAGCCATG
1 TGATCTTAAGCCATG
518469 TGATCTTAAGCCATG
1 TGATCTTAAGCCATG
518484 T
1 T
518485 CACGTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
TGATCTTAAGCCATG
Found at i:518861 original size:12 final size:12
Alignment explanation
Indices: 518844--518875 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
518834 ATACCTAATG
518844 TTTATTTTTGGT
1 TTTATTTTTGGT
518856 TTTATTTTTGGT
1 TTTATTTTTGGT
518868 TTTATTTT
1 TTTATTTT
518876 AGATCCCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.78
Consensus pattern (12 bp):
TTTATTTTTGGT
Found at i:518973 original size:30 final size:30
Alignment explanation
Indices: 518899--518985 Score: 113
Period size: 30 Copynumber: 2.8 Consensus size: 30
518889 TAAAATTTTA
*
518899 GGTACTAAAATGAAACAAAAAAAGTAACAACGG
1 GGTACTAAAATGAAAC--AAAAAGT-ACAACGC
*
518932 GGTATTAAAATGAAACAAAAAGT-CAACGAC
1 GGTACTAAAATGAAACAAAAAGTACAACG-C
518962 GGTACTAAAATGAAACAAAAAGTA
1 GGTACTAAAATGAAACAAAAAGTA
518986 AACATTAGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
29 5 0.10
30 22 0.45
31 7 0.14
33 15 0.31
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.15
Consensus pattern (30 bp):
GGTACTAAAATGAAACAAAAAGTACAACGC
Found at i:526101 original size:21 final size:20
Alignment explanation
Indices: 526077--526124 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
526067 AAATATTTAT
*
526077 AATAATTATACATATATAAAA
1 AATAATTATAAAT-TATAAAA
* *
526098 AATATTTTATAAATTTTAAAA
1 AATA-ATTATAAATTATAAAA
526119 AATAAT
1 AATAAT
526125 AAAAGGAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATTATAAATTATAAAA
Found at i:526635 original size:24 final size:24
Alignment explanation
Indices: 526603--526657 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
526593 TATATTATTG
526603 TAATTTAGTTTCTAAAATCATAAA
1 TAATTTAGTTTCTAAAATCATAAA
*
526627 TAATTTAGTTTCTAAAATCATATA
1 TAATTTAGTTTCTAAAATCATAAA
526651 TAATTTA
1 TAATTTA
526658 TATGTATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (24 bp):
TAATTTAGTTTCTAAAATCATAAA
Found at i:529259 original size:23 final size:22
Alignment explanation
Indices: 529233--529344 Score: 69
Period size: 23 Copynumber: 5.2 Consensus size: 22
529223 TGTGTGATTA
529233 TGATTCCGAGTGTTATTATTGTG
1 TGATTCC-AGTGTTATTATTGTG
* * *
529256 TGATT--A-TGTT-TCAATGTAA
1 TGATTCCAGTGTTATTATTGT-G
529275 TGATTCCCAGTGTTATTATTGTG
1 TGATT-CCAGTGTTATTATTGTG
* * *
529298 TGATT--A-TGTT-TCAATGTAA
1 TGATTCCAGTGTTATTATTGT-G
529317 TGATTCCCAGTGTTATTATTGTG
1 TGATT-CCAGTGTTATTATTGTG
529340 TGATT
1 TGATT
529345 ATGTTTGAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
18 10 0.15
19 18 0.28
20 2 0.03
22 2 0.03
23 23 0.35
24 10 0.15
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (22 bp):
TGATTCCAGTGTTATTATTGTG
Found at i:529278 original size:19 final size:19
Alignment explanation
Indices: 529256--529321 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
529246 TATTATTGTG
529256 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
* * *
529275 TGATTCCCAGTGTTATTATTGT-G
1 TGATT---A-TGTT-TCAATGTAA
529298 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
529317 TGATT
1 TGATT
529322 CCCAGTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.14
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (19 bp):
TGATTATGTTTCAATGTAA
Found at i:529291 original size:42 final size:42
Alignment explanation
Indices: 529232--529356 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
529222 TTGTGTGATT
*
529232 ATGATTCCGAGTGTTATTATTGTGTGATTATGTTTCAATGTA
1 ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTCAATGTA
529274 ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTCAATGTA
1 ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTCAATGTA
*
529316 ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTGAATGT
1 ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTCAATGT
529357 CAATTTAAGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (42 bp):
ATGATTCCCAGTGTTATTATTGTGTGATTATGTTTCAATGTA
Found at i:531390 original size:64 final size:65
Alignment explanation
Indices: 531240--531400 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 65
531230 TTGTTTAAGG
* * * ** *
531240 TGCATCGATGCACATGCAGTGCATCGATGCATGACTTTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACAAGTAGTGCATCGATGCATCACCATTAAATAGAAAACATCGAATAGCATTTA
* *
531305 TGCATCGATGCATAA-TGAGTGCATCGATGCATCCCCATTAAATA-AAAACATCGAAT-GCATTT
1 TGCATCGATGCACAAGT-AGTGCATCGATGCATCACCATTAAATAGAAAACATCGAATAGCA-TT
531367 TA
64 TA
*
531369 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGTAGTGCATCGATGCAT
531401 ACCTTCATTG
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.02
64 44 0.53
65 37 0.45
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCACAAGTAGTGCATCGATGCATCACCATTAAATAGAAAACATCGAATAGCATTTA
Found at i:532105 original size:31 final size:30
Alignment explanation
Indices: 532066--532162 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
532056 GTCGAGGGTT
532066 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTTT-GAGACATATGGACAG
**
532096 TATACCTATGTTCTAAG-GAACATATGGACAG
1 T-TACCTATGTTCTTTGAG-ACATATGGACAG
* * *
532127 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 -TTACCTATGTTCTTTGAGACATATGGACAG
532158 TTACC
1 TTACC
532163 GGGGTCTGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 7 0.12
31 44 0.79
32 5 0.09
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (30 bp):
TTACCTATGTTCTTTGAGACATATGGACAG
Found at i:532206 original size:57 final size:57
Alignment explanation
Indices: 532134--532242 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
532124 CAGTTTACCT
*
532134 AGGTTCTTTGGGACCTATGGACAGTTACCGGGGTCTGTGTGACCTCTGGATATGCCG
1 AGGTTCTTTAGGACCTATGGACAGTTACCGGGGTCTGTGTGACCTCTGGATATGCCG
* * *
532191 AGGTTCTTTATGACCTCTGGATAGTTACCGGGGTCTGTGTGACCTCTGGATA
1 AGGTTCTTTAGGACCTATGGACAGTTACCGGGGTCTGTGTGACCTCTGGATA
532243 GGTCCTTCGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (57 bp):
AGGTTCTTTAGGACCTATGGACAGTTACCGGGGTCTGTGTGACCTCTGGATATGCCG
Found at i:532243 original size:29 final size:29
Alignment explanation
Indices: 532145--532243 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
532135 GGTTCTTTGG
* *
532145 GACCTATGGACAGTTACCGGGGTCTGTGT
1 GACCTCTGGATAGTTACCGGGGTCTGTGT
* * * *
532174 GACCTCTGGATA--TGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCG-GGGTCTGTGT
532202 GACCTCTGGATAGTTACCGGGGTCTGTGT
1 GACCTCTGGATAGTTACCGGGGTCTGTGT
532231 GACCTCTGGATAG
1 GACCTCTGGATAG
532244 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 4 0.07
28 19 0.33
29 30 0.53
30 4 0.07
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.30
Consensus pattern (29 bp):
GACCTCTGGATAGTTACCGGGGTCTGTGT
Found at i:534004 original size:21 final size:23
Alignment explanation
Indices: 533980--534022 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
533970 AATTAAGTAT
533980 ATTA-AGTTT-AGTAAAAAAAAA
1 ATTATAGTTTCAGTAAAAAAAAA
* *
534001 ATTATATTTTCAGTAAATAAAA
1 ATTATAGTTTCAGTAAAAAAAA
534023 TAAGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (23 bp):
ATTATAGTTTCAGTAAAAAAAAA
Found at i:539130 original size:19 final size:21
Alignment explanation
Indices: 539088--539135 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
539078 TTTGAATTTT
539088 AAAAAATCAGAAAAAATACAA
1 AAAAAATCAGAAAAAATACAA
* *
539109 AAAAAAT-AGAATAATTACAA
1 AAAAAATCAGAAAAAATACAA
539129 AAAAAAT
1 AAAAAAT
539136 TAGTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (21 bp):
AAAAAATCAGAAAAAATACAA
Found at i:539218 original size:11 final size:11
Alignment explanation
Indices: 539202--539238 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
539192 ATTTGAATTT
539202 AAAAAATACAA
1 AAAAAATACAA
539213 AAAAAAT-CAGA
1 AAAAAATACA-A
539224 AAAAAATACAA
1 AAAAAATACAA
539235 AAAA
1 AAAA
539239 TCAGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08
Consensus pattern (11 bp):
AAAAAATACAA
Found at i:539258 original size:20 final size:21
Alignment explanation
Indices: 539202--539246 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 21
539192 ATTTGAATTT
539202 AAAAAATACAAAAAAAATCAGA
1 AAAAAATAC-AAAAAAATCAGA
539224 AAAAAATAC-AAAAAATCAGA
1 AAAAAATACAAAAAAATCAGA
539244 AAA
1 AAA
539247 TTTACAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.61
22 9 0.39
ACGTcount: A:0.78, C:0.09, G:0.04, T:0.09
Consensus pattern (21 bp):
AAAAAATACAAAAAAATCAGA
Found at i:539313 original size:124 final size:123
Alignment explanation
Indices: 539088--539328 Score: 308
Period size: 124 Copynumber: 1.9 Consensus size: 123
539078 TTTGAATTTT
* *
539088 AAAAAATCAGAAAAAATACAAAAAAAATAGAATAATTACAAAAAAAATTAGTATGTTTATTTATC
1 AAAAAATCAGAAAAAATAC-AAAAAAATAGAATAATTACAAAAAAAATTAATATGTTTATATATC
**
539153 TAATTACCCCATATTTTTATATATCTTGCAAATTAATCTATTTGAATTTAAAAAATACAA
65 TAATTACAACATATTTTTATATATCTTGCAAATTAATCTATTTGAA-TTAAAAAATACAA
539213 AAAAAATCAGAAAAAAATAC-AAAAAATCAGAA-AATTTACAAAAAAAA-TAATATGTTTATATA
1 AAAAAATCAG-AAAAAATACAAAAAAAT-AGAATAA-TTACAAAAAAAATTAATATGTTTATATA
** ** * ** *
539275 TCTAATTTTAATGTATTTTTATCTATCTTTTAATTTAATCTATTTGAATTAAAA
63 TCTAATTACAACATATTTTTATATATCTTGCAAATTAATCTATTTGAATTAAAA
539329 GAAATTGTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
123 6 0.06
124 60 0.59
125 26 0.26
126 9 0.09
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (123 bp):
AAAAAATCAGAAAAAATACAAAAAAATAGAATAATTACAAAAAAAATTAATATGTTTATATATCT
AATTACAACATATTTTTATATATCTTGCAAATTAATCTATTTGAATTAAAAAATACAA
Found at i:540463 original size:17 final size:17
Alignment explanation
Indices: 540436--540474 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
540426 AATTTACAAT
540436 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
540452 TAATTATAAATAATATC
1 TAATTATAAATAATATC
540469 TAATTA
1 TAATTA
540475 ATCTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:541532 original size:43 final size:43
Alignment explanation
Indices: 541469--541560 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
541459 GTCAACTATA
* *
541469 TATATATATATAATACGAATTTAAGAAATTATATTCAAATTAT
1 TATATATATATAATACGAATTTAAAAAATTATATTAAAATTAT
** *
541512 TATATATATATAATGTGAATTTAAAAAATTATATTAAAATTGT
1 TATATATATATAATACGAATTTAAAAAATTATATTAAAATTAT
541555 TA-ATAT
1 TATATAT
541561 TTAAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (43 bp):
TATATATATATAATACGAATTTAAAAAATTATATTAAAATTAT
Found at i:547286 original size:21 final size:21
Alignment explanation
Indices: 547260--547299 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
547250 GCAACACAGG
547260 TTCCAAAATCGCAACGCGATT
1 TTCCAAAATCGCAACGCGATT
*
547281 TTCCAAATTCGCAACGCGA
1 TTCCAAAATCGCAACGCGA
547300 ATAGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCCAAAATCGCAACGCGATT
Found at i:547314 original size:20 final size:20
Alignment explanation
Indices: 547289--547334 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
547279 TTTTCCAAAT
*
547289 TCGCAACGCGAATAGT-TAAA
1 TCGCAACGAGAATA-TATAAA
*
547309 TCGCAACGATAATATATAAA
1 TCGCAACGAGAATATATAAA
547329 TCGCAA
1 TCGCAA
547335 AACGAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (20 bp):
TCGCAACGAGAATATATAAA
Found at i:547688 original size:40 final size:40
Alignment explanation
Indices: 547640--547735 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
547630 AATTTGGAGA
* *
547640 ATTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
*
547680 ATTCGCGTTGAGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
547720 ATTCGCGTTGCGAATT
1 ATTCGCGTTGCGAATT
547736 TGACTTTCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (40 bp):
ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
Found at i:547744 original size:20 final size:21
Alignment explanation
Indices: 547626--547757 Score: 100
Period size: 20 Copynumber: 6.5 Consensus size: 21
547616 AAATTCAAGA
**
547626 TGCGAATTTGGAGAATTCGCGT
1 TGCGAATTT-GACTATTCGCGT
**
547648 TGCG-ATTT-ACATATTATCGT
1 TGCGAATTTGAC-TATTCGCGT
547668 TGCG-ATTT-ACCTATTCGCGT
1 TGCGAATTTGA-CTATTCGCGT
* **
547688 TGAGAA-TT-ACATATTATCGT
1 TGCGAATTTGAC-TATTCGCGT
*
547708 TGCG-ATTTAACTATTCGCGT
1 TGCGAATTTGACTATTCGCGT
547728 TGCGAATTTGACT-TTCGCGT
1 TGCGAATTTGACTATTCGCGT
547748 TGCGAATTTG
1 TGCGAATTTG
547758 GAAAATCGCA
Statistics
Matches: 90, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.03
20 68 0.76
21 15 0.17
22 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (21 bp):
TGCGAATTTGACTATTCGCGT
Found at i:548933 original size:21 final size:20
Alignment explanation
Indices: 548901--548952 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
548891 TGGTAATTTT
*
548901 AAAAAAACATTTAAAATTAA
1 AAAAAAAAATTTAAAATTAA
* *
548921 AAAAAATAAATTTATATTTAA
1 AAAAAA-AAATTTAAAATTAA
*
548942 AAACAAAAATT
1 AAAAAAAAATT
548953 CTGAAATACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAAAAATTTAAAATTAA
Found at i:551910 original size:37 final size:37
Alignment explanation
Indices: 551869--551944 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
551859 AAAAATACGT
551869 TTCAGCACTCAAGTATTCTGAGTTTCATGACAAAACC
1 TTCAGCACTCAAGTATTCTGAGTTTCATGACAAAACC
** * *
551906 TTCAGCACTTGAGTATTCTGTGTTTCATGTCAAAACC
1 TTCAGCACTCAAGTATTCTGAGTTTCATGACAAAACC
551943 TT
1 TT
551945 GAATTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (37 bp):
TTCAGCACTCAAGTATTCTGAGTTTCATGACAAAACC
Found at i:553873 original size:24 final size:24
Alignment explanation
Indices: 553839--553888 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
553829 GCGATCGAAA
* *
553839 TCAATCTGTCCTGCAACATGTTCT
1 TCAATCCGTCCAGCAACATGTTCT
*
553863 TCAATCCGTCCAGTAACATGTTCT
1 TCAATCCGTCCAGCAACATGTTCT
553887 TC
1 TC
553889 GCATTGCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (24 bp):
TCAATCCGTCCAGCAACATGTTCT
Found at i:554763 original size:18 final size:18
Alignment explanation
Indices: 554742--554781 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
554732 AGCTCCTCTC
* *
554742 CCACGGCCCCTGCCTCGT
1 CCACGGCCCCTCCCTCGG
*
554760 CCACGGCCTCTCCCTCGG
1 CCACGGCCCCTCCCTCGG
554778 CCAC
1 CCAC
554782 TGGTGCCAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.57, G:0.20, T:0.15
Consensus pattern (18 bp):
CCACGGCCCCTCCCTCGG
Found at i:559403 original size:20 final size:20
Alignment explanation
Indices: 559378--559430 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
559368 TGACCCTAAG
559378 GTATCGATACTACAAGCAGA
1 GTATCGATACTACAAGCAGA
559398 GTATCGATACTACAAGCAGA
1 GTATCGATACTACAAGCAGA
559418 GTATCGATACTAC
1 GTATCGATACTAC
559431 TCACTTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
GTATCGATACTACAAGCAGA
Found at i:561044 original size:12 final size:12
Alignment explanation
Indices: 561029--561054 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
561019 TAACCCTAAT
561029 CCTAGTCCCAGC
1 CCTAGTCCCAGC
561041 CCTAGTCCCAGC
1 CCTAGTCCCAGC
561053 CC
1 CC
561055 GTCTATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15
Consensus pattern (12 bp):
CCTAGTCCCAGC
Found at i:563596 original size:23 final size:23
Alignment explanation
Indices: 563561--563606 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
563551 AAATACATGA
* *
563561 GAAAATGTGTCATAAAGGTAGAT
1 GAAAACGTCTCATAAAGGTAGAT
*
563584 GAAAACGTCTCATACAGGTAGAT
1 GAAAACGTCTCATAAAGGTAGAT
563607 TTATTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (23 bp):
GAAAACGTCTCATAAAGGTAGAT
Found at i:564486 original size:92 final size:91
Alignment explanation
Indices: 564356--564531 Score: 343
Period size: 92 Copynumber: 1.9 Consensus size: 91
564346 TTAGCTTTCA
564356 ATTCAAGTCATTTTGTTTGTACCTTACTTGCCAAGATTAATGTTAAAATACCTTTTTTAAAGAAA
1 ATTCAAGTCATTTTGTTTGTACCTTACTTGCCAAGATTAATGTTAAAATACCTTTTTTAAAGAAA
564421 TTCCTATTTATTGTTAGAAAGAAGCC
66 TTCCTATTTATTGTTAGAAAGAAGCC
564447 ATTCAAGTCATTCTTGTTTGTACCTTACTTGCCAAGATTAATGTTAAAATACCTTTTTTAAAGAA
1 ATTCAAGTCATT-TTGTTTGTACCTTACTTGCCAAGATTAATGTTAAAATACCTTTTTTAAAGAA
564512 ATTCCTATTTATTGTTAGAA
65 ATTCCTATTTATTGTTAGAA
564532 CAAGAAGTCA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 12 0.14
92 72 0.86
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (91 bp):
ATTCAAGTCATTTTGTTTGTACCTTACTTGCCAAGATTAATGTTAAAATACCTTTTTTAAAGAAA
TTCCTATTTATTGTTAGAAAGAAGCC
Found at i:566869 original size:23 final size:23
Alignment explanation
Indices: 566843--566911 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
566833 TGTGTGATTA
566843 TGTTTCAATGTAATGATTCCCAG
1 TGTTTCAATGTAATGATTCCCAG
* * *
566866 TGTTATTATTGT-GTGATT---A-
1 TGTT-TCAATGTAATGATTCCCAG
566885 TGTTTCAATGTAATGATTCCCAG
1 TGTTTCAATGTAATGATTCCCAG
566908 TGTT
1 TGTT
566912 ATTATTGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 1 0.03
22 1 0.03
23 13 0.38
24 5 0.15
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (23 bp):
TGTTTCAATGTAATGATTCCCAG
Found at i:566891 original size:42 final size:42
Alignment explanation
Indices: 566832--566937 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
566822 ATTAATGGAT
566832 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
1 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
566874 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
1 TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
*
566916 TTGTGTGATTATGTTTGAATGT
1 TTGTGTGATTATGTTTCAATGT
566938 CAATTTAAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (42 bp):
TTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATTA
Found at i:566901 original size:19 final size:19
Alignment explanation
Indices: 566837--566902 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
566827 TGGATTTGTG
566837 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
* * *
566856 TGATTCCCAGTGTTATTATTGT-G
1 TGATT---A-TGTT-TCAATGTAA
566879 TGATTATGTTTCAATGTAA
1 TGATTATGTTTCAATGTAA
566898 TGATT
1 TGATT
566903 CCCAGTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.14
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (19 bp):
TGATTATGTTTCAATGTAA
Found at i:566924 original size:23 final size:23
Alignment explanation
Indices: 566856--566925 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
566846 TTCAATGTAA
566856 TGATTCCCAGTGTTATTATTGTG
1 TGATTCCCAGTGTTATTATTGTG
* * *
566879 TGATT---A-TGTT-TCAATGTAA
1 TGATTCCCAGTGTTATTATTGT-G
566898 TGATTCCCAGTGTTATTATTGTG
1 TGATTCCCAGTGTTATTATTGTG
566921 TGATT
1 TGATT
566926 ATGTTTGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
19 9 0.26
20 1 0.03
22 1 0.03
23 14 0.40
24 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (23 bp):
TGATTCCCAGTGTTATTATTGTG
Found at i:567216 original size:30 final size:31
Alignment explanation
Indices: 567177--567253 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
567167 AAACCGTACC
* *
567177 TTTATGTACCCAAACTATCAAATTTACTC-CT
1 TTTA-GTACCTAAACTATCAAATTTACTCAAT
567208 TTTAGTACCTAAACTATCAAATTTACTCAAT
1 TTTAGTACCTAAACTATCAAATTTACTCAAT
567239 TTTAGTACCTAAACT
1 TTTAGTACCTAAACT
567254 TTTAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 23 0.53
31 20 0.47
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAAATTTACTCAAT
Found at i:568260 original size:36 final size:35
Alignment explanation
Indices: 568219--568286 Score: 127
Period size: 36 Copynumber: 1.9 Consensus size: 35
568209 TTATGCCTTT
568219 ATGCTGCATGAGATTTGAGGATAAAATCCCAATGGC
1 ATGCTGCATGAGATTTGAGGAT-AAATCCCAATGGC
568255 ATGCTGCATGAGATTTGAGGATAAATCCCAAT
1 ATGCTGCATGAGATTTGAGGATAAATCCCAAT
568287 TTCCTTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (35 bp):
ATGCTGCATGAGATTTGAGGATAAATCCCAATGGC
Found at i:569390 original size:38 final size:38
Alignment explanation
Indices: 569343--569416 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
569333 GAATCGAAAT
* * * *
569343 ATATTAAAGTCGATTGTTAATTCATTTGTGAGATAAAC
1 ATATCAAAGTCGATTGTCAATTCATTTATGAAATAAAC
* *
569381 ATATCAAAGTTGATTGTCATTTCATTTATGAAATAA
1 ATATCAAAGTCGATTGTCAATTCATTTATGAAATAA
569417 CTCAATAACG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (38 bp):
ATATCAAAGTCGATTGTCAATTCATTTATGAAATAAAC
Found at i:572969 original size:42 final size:42
Alignment explanation
Indices: 572912--573052 Score: 189
Period size: 42 Copynumber: 3.4 Consensus size: 42
572902 TCCATAGTCG
*
572912 AATCGAAATCCTAAAATAATGATCGTAACAAACACGGATAGT
1 AATCGAAATCATAAAATAATGATCGTAACAAACACGGATAGT
* * *
572954 AATCAAAATCATAAAATAATGTTCGTGACAAACACGGATAGT
1 AATCGAAATCATAAAATAATGATCGTAACAAACACGGATAGT
*
572996 CGAATCGAAATCATAAAATAA-GATAGTAACAAACACGGATAG-
1 --AATCGAAATCATAAAATAATGATCGTAACAAACACGGATAGT
*
573038 AATC-AAATTATAAAA
1 AATCGAAATCATAAAA
573053 CCGAGATCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
39 10 0.11
40 4 0.05
42 38 0.43
43 18 0.20
44 18 0.20
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.21
Consensus pattern (42 bp):
AATCGAAATCATAAAATAATGATCGTAACAAACACGGATAGT
Found at i:575564 original size:134 final size:130
Alignment explanation
Indices: 575283--575564 Score: 474
Period size: 134 Copynumber: 2.1 Consensus size: 130
575273 AAATTAGAAT
* *
575283 ATTTAAAAGTTTAAAAATCAATTCAAAATGAAGATTATAGTTTGGGAACTATGATTCAATTAACT
1 ATTTATAATTTTAAAAATCAATTCAAAATGAAGATTATAGTTTGGGAACTATGATTCAATTAACT
575348 CACTCTATATACATATGGTTAATTTCAACAAACATGTCAAGTTATATAGCCCTAAACTTTAACTG
66 CACTCTATATACATATGGTTAATTTCAACAAACATGTCAAGTTATATAGCCCTAAACTTTAACTG
575413 ATTTATAATTTTGTTTAAAAATCAATTCAAAATGAAGATTATAGTTTGGGAACATATGATTCAAT
1 ATTTATAA---T-TTTAAAAATCAATTCAAAATGAAGATTATAGTTTGGGAAC-TATGATTCAAT
575478 TAACTCACTCTATATAACATATGGTTAATTTCAACAAACATGTCCAAGTTATATAGCCCTAAACT
61 TAACTCACTCTATAT-ACATATGGTTAATTTCAACAAACATGT-CAAGTTATATAGCCCTAAACT
575543 TTAACTTG
124 TTAAC-TG
575551 ATTTATAATTTTAA
1 ATTTATAATTTTAA
575565 GATCGTATTA
Statistics
Matches: 142, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
130 7 0.05
134 45 0.32
135 27 0.19
136 27 0.19
137 26 0.18
138 10 0.07
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (130 bp):
ATTTATAATTTTAAAAATCAATTCAAAATGAAGATTATAGTTTGGGAACTATGATTCAATTAACT
CACTCTATATACATATGGTTAATTTCAACAAACATGTCAAGTTATATAGCCCTAAACTTTAACTG
Found at i:576109 original size:19 final size:19
Alignment explanation
Indices: 576067--576114 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
576057 GTATTAATTA
576067 ATTAATTTTATTATTTTAAC
1 ATTAA-TTTATTATTTTAAC
*
576087 ATTAATTTA-TATTTTAAAT
1 ATTAATTTATTATTTT-AAC
576106 ATTAATTTA
1 ATTAATTTA
576115 AGTATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 15 0.58
20 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTAATTTATTATTTTAAC
Found at i:578979 original size:185 final size:185
Alignment explanation
Indices: 578646--579028 Score: 651
Period size: 185 Copynumber: 2.1 Consensus size: 185
578636 ATAAAATTTT
*
578646 AAATTTTAAATATATTATATCTAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATA-CTAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAA
578711 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
65 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
* *
578776 TTATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTG-TTTTTTTGAATTAAA
*
578833 AAATATTAAATATATTATA-TAACATATGGGCTCAGCCCAAACCATTTAAAATCTAATTAATAAT
1 AAATATTAAATATATTATACTAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAAT
* * **
578897 TTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAATTTTTT
66 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTT
*
578962 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTATA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
*
579017 AAATATTTAATA
1 AAATATTAAATA
579029 AAAGAAAATT
Statistics
Matches: 186, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
184 25 0.13
185 143 0.77
187 18 0.10
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATACTAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAAT
TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
Found at i:585188 original size:26 final size:27
Alignment explanation
Indices: 585128--585210 Score: 97
Period size: 26 Copynumber: 3.3 Consensus size: 27
585118 TATATTATAG
*
585128 ATATT-AATTTTAATATTAATTTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
585154 A-A-TAAATTA-AATATTAATTTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
*
585178 ATATTATATTATAGATATTAA--TTTTA
1 ATATTAAATTATA-ATATTAATTTTTTA
585204 ATATTAA
1 ATATTAA
585211 TTTTTAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 17 0.35
25 6 0.12
26 18 0.37
27 1 0.02
28 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATATTAAATTATAATATTAATTTTTTA
Found at i:585213 original size:40 final size:36
Alignment explanation
Indices: 585163--585245 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 36
585153 AAATAAATTA
*
585163 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAA-TTTTTAA-A-TAAATTA-A-ATATTAATTTTT
585203 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
1 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
585239 AATATTA
1 AATATTA
585246 TATTATAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 7 0.17
36 12 0.29
37 6 0.15
38 1 0.02
39 7 0.17
40 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AATATTAATTTTTAAATAAATTAAATATTAATTTTT
Found at i:585262 original size:63 final size:64
Alignment explanation
Indices: 585110--585266 Score: 282
Period size: 64 Copynumber: 2.5 Consensus size: 64
585100 AGGTTTTATA
*
585110 TTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
585174 TTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAA-TT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
585236 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA
585267 TATCATATAA
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
62 23 0.25
63 32 0.35
64 36 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
Found at i:585494 original size:8 final size:8
Alignment explanation
Indices: 585481--585505 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
585471 TAAATTATGT
585481 TTTTAAAA
1 TTTTAAAA
585489 TTTTAAAA
1 TTTTAAAA
585497 TTTTAAAA
1 TTTTAAAA
585505 T
1 T
585506 ATGATCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:585980 original size:31 final size:31
Alignment explanation
Indices: 585943--586002 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
585933 TAGTTGTATG
* * *
585943 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCACTATTGCAAAACTAA
585974 AATTATTTAAATCTCACTATTGCAAAACT
1 AATTATTTAAATCTCACTATTGCAAAACT
586003 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCACTATTGCAAAACTAA
Found at i:586261 original size:39 final size:37
Alignment explanation
Indices: 586218--586303 Score: 86
Period size: 39 Copynumber: 2.2 Consensus size: 37
586208 AAATTATACA
*
586218 TAAAATTTATTTA-TTTTATTTCATTTTAGTACCCAACTT
1 TAAAATTTA-TTAGTTTTATCTCATTTTAGTACCC--CTT
**
586257 TAAAA-ACATTAGTTTTTATCTCATTTTAGTACCCCTT
1 TAAAATTTATTAG-TTTTATCTCATTTTAGTACCCCTT
586294 TCAAAATTTA
1 T-AAAATTTA
586304 ACATTAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
37 7 0.18
38 5 0.13
39 26 0.68
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (37 bp):
TAAAATTTATTAGTTTTATCTCATTTTAGTACCCCTT
Found at i:586760 original size:3 final size:3
Alignment explanation
Indices: 586752--586830 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
586742 TTACCCTATC
586752 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
586800 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
586831 GTTTAATACC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:587718 original size:3 final size:3
Alignment explanation
Indices: 587665--587702 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
587655 GTATTAAAGC
587665 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
587703 CCGACAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:589345 original size:2 final size:2
Alignment explanation
Indices: 589338--589373 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
589328 CATCATTTTA
589338 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
589374 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:590848 original size:24 final size:24
Alignment explanation
Indices: 590820--590875 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
590810 ATACAATAGG
590820 GAAGCGAATGAGAAAAAAATAGAT
1 GAAGCGAATGAGAAAAAAATAGAT
590844 GAAGCGAATGAGAAAAAAATAGAT
1 GAAGCGAATGAGAAAAAAATAGAT
*
590868 GAAACGAA
1 GAAGCGAA
590876 CAAGTCACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.59, C:0.05, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAGCGAATGAGAAAAAAATAGAT
Found at i:595898 original size:21 final size:21
Alignment explanation
Indices: 595856--595899 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
595846 ACTAAACCCT
* *
595856 ATAACCTAATTTTGAAAGAAA
1 ATAACCTAACTTTGAAAAAAA
595877 ATAACCTATACTTT-AAAAAAA
1 ATAACCTA-ACTTTGAAAAAAA
595898 AT
1 AT
595900 TACAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAACCTAACTTTGAAAAAAA
Found at i:615375 original size:13 final size:13
Alignment explanation
Indices: 615357--615418 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
615347 ATGGCTAAGA
*
615357 AATAAAATAAAAC
1 AATAAAATAAAAT
*
615370 AATAAAAGAAAAT
1 AATAAAATAAAAT
615383 AAGGTAAAAT-AAAT
1 AA--TAAAATAAAAT
*
615397 AA-ATAAACAAAAT
1 AATA-AAATAAAAT
615410 AATAAAATA
1 AATAAAATA
615419 TATAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 23 0.59
14 7 0.18
15 5 0.13
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:615423 original size:9 final size:9
Alignment explanation
Indices: 615356--615425 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
615346 AATGGCTAAG
615356 AAATAAAAT
1 AAATAAAAT
*
615365 AAA-ACAAT
1 AAATAAAAT
*
615373 AAAAGAAAAT
1 -AAATAAAAT
*
615383 AAGGTAAAAT
1 AA-ATAAAAT
615393 AAAT-AAAT
1 AAATAAAAT
*
615401 AAACAAAAT
1 AAATAAAAT
615410 -AATAAAAT
1 AAATAAAAT
*
615418 ATATAAAA
1 AAATAAAA
615426 ATAACAAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 18 0.38
9 19 0.40
10 11 0.23
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:615891 original size:2 final size:2
Alignment explanation
Indices: 615886--615918 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
615876 AAAAAAGAGA
615886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
615919 AGTGTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:619675 original size:19 final size:19
Alignment explanation
Indices: 619651--619690 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
619641 AAAGCAGCGG
*
619651 TAGACGTGGGTTTAGGAGT
1 TAGACGTGGGTTTAAGAGT
619670 TAGACGTGGGTTTAAGAGT
1 TAGACGTGGGTTTAAGAGT
619689 TA
1 TA
619691 AAAGGAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.33
Consensus pattern (19 bp):
TAGACGTGGGTTTAAGAGT
Found at i:619795 original size:18 final size:18
Alignment explanation
Indices: 619742--619795 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
619732 TGTGTTTTCT
619742 TTTTTTAAAAGTATATATAA
1 TTTTTTAAAA-TAT-TATAA
** *
619762 TTTTTTTTAATTTTATAA
1 TTTTTTAAAATATTATAA
*
619780 TTTTTTAAAAAATTAT
1 TTTTTTAAAATATTAT
619796 CAGGTTATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 17 0.63
19 2 0.07
20 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTTTAAAATATTATAA
Found at i:627589 original size:14 final size:14
Alignment explanation
Indices: 627565--627591 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
627555 ATATAATATA
627565 TAATATTAATTAAT
1 TAATATTAATTAAT
627579 TAATATTAATTAA
1 TAATATTAATTAA
627592 ATAGTCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATTAATTAAT
Found at i:629156 original size:39 final size:39
Alignment explanation
Indices: 629102--629180 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
629092 ATCAACATAG
629102 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATTT
1 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATTT
* * *
629141 CCAAATTTTATGAATGAAACTCCATTTCCATTTCCATTT
1 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATTT
629180 C
1 C
629181 TATCTTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (39 bp):
CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATTT
Found at i:630593 original size:80 final size:82
Alignment explanation
Indices: 630453--630639 Score: 297
Period size: 80 Copynumber: 2.3 Consensus size: 82
630443 TTCAAAATGG
*
630453 TGATCTTTGTGTAATTTTTGTTCTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAA
1 TGATCTTTGTGTAA-TTTTGGT-TCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAA
*
630518 -ATTTTCGGTTTGAAGGAC
64 TATTTTCGGTTCGAAGGAC
* * *
630536 TGATCTTTGTGTAA-TTTGGTTCTCAGGAGCTAGGTTTAGTTCTTAAACCGGTTGAGGTTGAATT
1 TGATCTTTGTGTAATTTTGGTTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAATA
630600 TTTTCGGTTCGAAGGAC
66 TTTTCGGTTCGAAGGAC
630617 TGATCTTTGTGTAATTTTGGTTC
1 TGATCTTTGTGTAATTTTGGTTC
630640 ACATTGGTGC
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
80 40 0.41
81 35 0.36
82 8 0.08
83 14 0.14
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.42
Consensus pattern (82 bp):
TGATCTTTGTGTAATTTTGGTTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAATA
TTTTCGGTTCGAAGGAC
Found at i:631102 original size:42 final size:42
Alignment explanation
Indices: 630953--631082 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
630943 AACGAATCAC
* * *
630953 CACCGATGGCTGCACGTGGTGATCAAGGACAGAAACCGGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
* *
630995 CAACAATGGCTGCACATGGTAATCAAGGACAGAAACCAGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
*
631037 CACCAATGGCTGAACATGGTAATCAAGGACAGAAACCGGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
631079 CACC
1 CACC
631083 GGTGGATGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.25, T:0.14
Consensus pattern (42 bp):
CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
Found at i:638374 original size:42 final size:41
Alignment explanation
Indices: 638327--638422 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
638317 TTTTTTTCTC
* * *
638327 TGTTTGATAGTTGAAAAATAATTCTT-GGAAAATATTTTCGGG
1 TGTTTGATAGTTG--AAATAAGTCTTACGAAAATATTTTCGAG
* * **
638369 TGTTTGATAGCTGTAATTGGTCTTACGAAAATATTTTCGAG
1 TGTTTGATAGTTGAAATAAGTCTTACGAAAATATTTTCGAG
638410 TGTTTGATAGTTG
1 TGTTTGATAGTTG
638423 GAATCCATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
40 7 0.16
41 26 0.58
42 12 0.27
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (41 bp):
TGTTTGATAGTTGAAATAAGTCTTACGAAAATATTTTCGAG
Done.