Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004600.1 Hibiscus syriacus cultivar Beakdansim tig00010276_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: 75519
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:225 original size:110 final size:111
Alignment explanation
Indices: 2--307 Score: 426
Period size: 110 Copynumber: 2.8 Consensus size: 111
1 A
* *
2 AGACTTGTTCCACTTACTTTGAAGGGAATATCAAATC-TGGAAAAGTGAGACATGTTATGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAA--GAGACATGTTCTGCTTAC
* * *
66 TCTGAAGGGAA-A--ATATCTGGGGGAGTTGATCCATTGAATCGGTGC
64 TCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCACTGAATCAGTGC
*
111 AGACTTGTTCCACTTACTCTGAA-GGAATATCAAATCTTGGAAAAGAGACTTGTTCTGCTTACTC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGACATGTTCTGCTTACTC
*
175 TAAAGGGAATATCAGATCTGGGGGAGTTGATCCACTGAATCAAG-GC
66 TGAAGGGAATATCAGATCTGGGGGAGTTGATCCACTGAATC-AGTGC
* * **
221 AGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTTGAAAAAGAGAGACATGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTG-GAAA-AGAGACATGTTCTGCTTAC
286 TCTGAAGGGAATATCAGATCTG
64 TCTGAAGGGAATATCAGATCTG
308 CAAATTAAAC
Statistics
Matches: 176, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
107 26 0.15
108 14 0.08
109 29 0.16
110 50 0.28
111 17 0.10
112 3 0.02
113 37 0.21
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (111 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGACATGTTCTGCTTACTC
TGAAGGGAATATCAGATCTGGGGGAGTTGATCCACTGAATCAGTGC
Found at i:2783 original size:14 final size:14
Alignment explanation
Indices: 2757--2816 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
2747 ACTTGATTTA
2757 TTTTCTCTT-TTTTC
1 TTTT-TCTTCTTTTC
*
2771 TTTTTCCTCTTTT-
1 TTTTTCTTCTTTTC
2784 TTTTTCTTCTTTTC
1 TTTTTCTTCTTTTC
* *
2798 TTCTTCTTTTTTTC
1 TTTTTCTTCTTTTC
2812 TTTTT
1 TTTTT
2817 TTGAGTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 15 0.38
14 24 0.62
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTCTTTTC
Found at i:2796 original size:22 final size:23
Alignment explanation
Indices: 2764--2818 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
2754 TTATTTTCTC
2764 TTTT-TTCTTTTTCCTCTT-TTT
1 TTTTCTTCTTTTTCCTCTTCTTT
*
2785 TTTTCTTC-TTTTCTTCTTCTTT
1 TTTTCTTCTTTTTCCTCTTCTTT
2807 TTTTCTT-TTTTT
1 TTTTCTTCTTTTT
2819 GAGTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTCTTCTTTTTCCTCTTCTTT
Found at i:8072 original size:3 final size:3
Alignment explanation
Indices: 8031--8098 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
8021 TAAAACCTGA
* * * *
8031 AAT AAT AAA AAT ATT AAT ATT AAT AGT AAT -AT GAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
8076 AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AA-T AAT A
8099 GCATTACTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:8520 original size:15 final size:15
Alignment explanation
Indices: 8500--8538 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
8490 GAAAATCAAG
8500 AATAAAGATTAAGAT
1 AATAAAGATTAAGAT
* *
8515 AATAAAGACTGAGAT
1 AATAAAGATTAAGAT
8530 AATAAAGAT
1 AATAAAGAT
8539 AAATAAGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.23
Consensus pattern (15 bp):
AATAAAGATTAAGAT
Found at i:15149 original size:3 final size:3
Alignment explanation
Indices: 15141--15171 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
15131 CTTAAACAAA
15141 TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
15172 ATTTTTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20314 original size:22 final size:23
Alignment explanation
Indices: 20287--20331 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
20277 TGCGAAGATC
* *
20287 AAATCAAAGTAA-AGAGAAAAAA
1 AAATCAAAGAAACAAAGAAAAAA
20309 AAATCAAAGAAACAAAGAAAAAA
1 AAATCAAAGAAACAAAGAAAAAA
20332 GCAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.76, C:0.07, G:0.11, T:0.07
Consensus pattern (23 bp):
AAATCAAAGAAACAAAGAAAAAA
Found at i:20331 original size:20 final size:21
Alignment explanation
Indices: 20287--20340 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
20277 TGCGAAGATC
*
20287 AAATCAAAGTAAAGAGAAAAAA
1 AAATCAAAG-AAACAGAAAAAA
*
20309 AAATCAAAGAAACA-AAGAAA
1 AAATCAAAGAAACAGAAAAAA
*
20329 AAAGCAAAGAAA
1 AAATCAAAGAAA
20341 AAATGGACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.55
21 4 0.14
22 9 0.31
ACGTcount: A:0.74, C:0.07, G:0.13, T:0.06
Consensus pattern (21 bp):
AAATCAAAGAAACAGAAAAAA
Found at i:21544 original size:38 final size:36
Alignment explanation
Indices: 21494--21571 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
21484 TTGAGGGTGT
21494 TTTTTCTCGAAACAAAGTGTCGTCTCGCTAGAGACAA
1 TTTTTCTCGAAACAAA-TGTCGTCTCGCTAGAGACAA
* * * * *
21531 TTTTTCTTTGAAACAAATTTTGTCTCGCTTGAGACAG
1 TTTTTC-TCGAAACAAATGTCGTCTCGCTAGAGACAA
21568 TTTT
1 TTTT
21572 CTCTAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (36 bp):
TTTTTCTCGAAACAAATGTCGTCTCGCTAGAGACAA
Found at i:21556 original size:37 final size:37
Alignment explanation
Indices: 21515--21641 Score: 116
Period size: 37 Copynumber: 3.4 Consensus size: 37
21505 ACAAAGTGTC
* **
21515 GTCTCGCTAGAGACAATTTTTCTTTGAAACAAATTTT
1 GTCTCACTAGAGACAATTTTTCTTAAAAACAAATTTT
* * *
21552 GTCTCGCTTGAGAC-AGTTTTCTCTAAAAATCAAATTTT
1 GTCTCACTAGAGACAATTTTTCT-TAAAAA-CAAATTTT
* *
21590 GTCTCACTTA-AGGCAATTTTTAC-TCAAAACAAATTTT
1 GTCTCAC-TAGAGACAATTTTT-CTTAAAAACAAATTTT
*
21627 GTCTCACTTGAGACA
1 GTCTCACTAGAGACA
21642 GTTTCCCTCG
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
36 8 0.11
37 36 0.49
38 22 0.30
39 6 0.08
40 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (37 bp):
GTCTCACTAGAGACAATTTTTCTTAAAAACAAATTTT
Found at i:21854 original size:65 final size:64
Alignment explanation
Indices: 21773--22046 Score: 379
Period size: 65 Copynumber: 4.2 Consensus size: 64
21763 TTGGAAATTG
*
21773 TTTCACTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATAAGTTTTGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATAA-TTTTGTCTCCCTTGAGACAA
* * * *
21838 TTTCTCTTGAATCATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGA-AA
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAA-TAATTTTGTCTCCCTTGAGACAA
* *
21902 GTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAGTTTTGTCTCCCTTGAGACA
1 -TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAA-TAATTTTGTCTCCCTTGAGACA
*
21967 G
64 A
* * * *
21968 TTTCTTTTGAAAAATCATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAAT-AATTTTGTCTCCCTTGAGACAA
*
22033 GTTCTCTTGAAACA
1 TTTCTCTTGAAACA
22047 AATCCCTAAA
Statistics
Matches: 187, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
64 2 0.01
65 182 0.97
66 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (64 bp):
TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATAATTTTGTCTCCCTTGAGACAA
Found at i:21912 original size:36 final size:36
Alignment explanation
Indices: 21858--22045 Score: 117
Period size: 36 Copynumber: 5.6 Consensus size: 36
21848 ATCATCATCT
21858 TTGAGATCA-TTTCCCTTGAAACGAATTTTGTCTCTC
1 TTGAGA-CAGTTTCCCTTGAAACGAATTTTGTCTCTC
* *
21894 TTGAGAAAGTTTCTCTTGAAAC--A-----TCATCT-
1 TTGAGACAGTTTCCCTTGAAACGAATTTTGTC-TCTC
* *
21923 TTGAGATC-GTTTCCCTTGAAACGAGTTTTGTCTCCC
1 TTGAGA-CAGTTTCCCTTGAAACGAATTTTGTCTCTC
**
21959 TTGAGACAGTTTCTTTTGAAA--AA-----TCATCT-
1 TTGAGACAGTTTCCCTTGAAACGAATTTTGTC-TCTC
*
21988 TTGAGATC-GTTTCCCTTGAAATGAATTTTGTCTCTC
1 TTGAGA-CAGTTTCCCTTGAAACGAATTTTGTCTCTC
* *
22024 TTGAGACAGGTTCTCTTGAAAC
1 TTGAGACAGTTTCCCTTGAAAC
22046 AAATCCCTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 46
0.65 0.09 0.26
Matches are distributed among these distances:
29 40 0.35
30 6 0.05
31 2 0.02
34 2 0.02
35 8 0.07
36 56 0.49
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACGAATTTTGTCTCTC
Found at i:21930 original size:130 final size:130
Alignment explanation
Indices: 21772--22046 Score: 451
Period size: 130 Copynumber: 2.1 Consensus size: 130
21762 TTTGGAAATT
* *
21772 GTTTCACTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAATAAGTTTTGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
**
21837 ATTTCTCTTGAATCATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGAAA
66 ATTTCTCTTGAAAAATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGAAA
*
21902 GTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAGTTTTGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
* * * * *
21967 GTTTCTTTTGAAAAATCATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACA
66 ATTTCTCTTGAAAAATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGAAA
*
22032 GGTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
22047 AATCCCTAAA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 134 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (130 bp):
GTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
ATTTCTCTTGAAAAATCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGAAA
Found at i:21934 original size:29 final size:29
Alignment explanation
Indices: 21902--22008 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 29
21892 TCTTGAGAAA
*
21902 GTTTCTCTTGAAACATCATCTTTGAGATC
1 GTTTCCCTTGAAACATCATCTTTGAGATC
**
21931 GTTTCCCTTGAAACGAGTTTTGTCTCCCTTGAGA-C
1 GTTTCCCTTGAAAC-A---TCATCT---TTGAGATC
** *
21966 AGTTTCTTTTGAAAAATCATCTTTGAGATC
1 -GTTTCCCTTGAAACATCATCTTTGAGATC
21996 GTTTCCCTTGAAA
1 GTTTCCCTTGAAA
22009 TGAATTTTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
29 30 0.51
30 2 0.03
32 4 0.07
33 4 0.07
35 2 0.03
36 17 0.29
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (29 bp):
GTTTCCCTTGAAACATCATCTTTGAGATC
Found at i:22389 original size:133 final size:131
Alignment explanation
Indices: 22048--22390 Score: 420
Period size: 131 Copynumber: 2.6 Consensus size: 131
22038 CTTGAAACAA
**** * * *
22048 ATCCCTAAAGATGGCCAATTGTCCTCATCGCGTAGAAATTGTTTCATCCACTGACCAGATCTCCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
* * * *
22113 CATCACGTAGGAGTCGCGTCAACCTTAGATAACCAACTGTCCTCATCACGTAAGAATCGTGTTAT
66 CATCACGTAAGAGCCGCGTCAACCTTAGATAACCAACCGTCCTCATCACGTAAGAACCGTGTTAT
22178 C
131 C
* * * *
22179 ATCCCTAAAGATGGCCAGCCATCCTTATCACGTAGGAATTATGTCATCC-CCAGACCAGATCTCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACC-GACCAGATCTCC
* ** *
22243 TCATCACGTAAGAGCCGCGTCAACCTTAGATAACCAGCCGTCCTCATTGCGTAGGAACCGTGTTA
65 TCATCACGTAAGAGCCGCGTCAACCTTAGATAACCAACCGTCCTCATCACGTAAGAACCGTG-T-
22308 TCATC
128 T-ATC
* * * *
22313 ATCCCTAAAGAT-GTCAGCCATCCTCATCGCATAGGAATCGTGTCATCCACCGACTAGATCTCCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
*
22377 CATTACGTAAGAGC
66 CATCACGTAAGAGC
22391 TGTGCCACCC
Statistics
Matches: 179, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 105 0.59
132 1 0.01
133 55 0.31
134 17 0.09
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
CATCACGTAAGAGCCGCGTCAACCTTAGATAACCAACCGTCCTCATCACGTAAGAACCGTGTTAT
C
Found at i:22403 original size:133 final size:131
Alignment explanation
Indices: 22048--22442 Score: 418
Period size: 131 Copynumber: 3.0 Consensus size: 131
22038 CTTGAAACAA
**** * * *
22048 ATCCCTAAAGATGGCCAATTGTCCTCATCGCGTAGAAATTGTTTCATCCACTGACCAGATCTCCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
* * * *
22113 CATCACGTAGGAG-TCGCGTCAACCTTAGATAACCAACTGTCCTCATCACGTAAGAATCGTGTTA
66 CATCACGTAAGAGCT-GCGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAAGAACCGTGTTA
22177 TC
130 TC
* * * *
22179 ATCCCTAAAGATGGCCAGCCATCCTTATCACGTAGGAATTATGTCATCC-CCAGACCAGATCTCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACC-GACCAGATCTCC
* ** *
22243 TCATCACGTAAGAGCCGCGTCAACCTTAGATAACCAGCCGTCCTCATTGCGTAGGAACCGTGTTA
65 TCATCACGTAAGAGCTGCGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAAGAACCGTG-T-
22308 TCATC
128 T-ATC
* * * *
22313 ATCCCTAAAGAT-GTCAGCCATCCTCATCGCATAGGAATCGTGTCATCCACCGACTAGATCTCCT
1 ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
* * * * * * * * * * *
22377 CATTACGTAAGAGCTGTGCCACCCTTAGATAGCCAGACTTCCTTATCACATAGGAACCGTGCTAT
66 CATCACGTAAGAGCTGCGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAAGAACCGTGTTAT
22442 C
131 C
22443 TCCAAATTTA
Statistics
Matches: 218, Mismatches: 40, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.02
131 105 0.48
132 1 0.00
133 91 0.42
134 17 0.08
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAGCCATCCTCATCGCGTAGGAATTGTGTCATCCACCGACCAGATCTCCT
CATCACGTAAGAGCTGCGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAAGAACCGTGTTAT
C
Found at i:22655 original size:3 final size:3
Alignment explanation
Indices: 22647--22678 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
22637 GGTCTTAAAA
22647 ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
22679 ATTACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:22674 original size:10 final size:10
Alignment explanation
Indices: 22650--22682 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
22640 CTTAAAAATT
22650 ATTATTATT-
1 ATTATTATTA
22659 ATTATTATTA
1 ATTATTATTA
22669 ATTATTATTA
1 ATTATTATTA
22679 ATTA
1 ATTA
22683 CATTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTATTATTA
Found at i:22925 original size:28 final size:28
Alignment explanation
Indices: 22885--22938 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
22875 GACTCTTCAG
22885 CCATCTCCTCGCGCGCGTGAGTTATCAC
1 CCATCTCCTCGCGCGCGTGAGTTATCAC
22913 CCATCTCCTCGCGCGCGTGAGTTATC
1 CCATCTCCTCGCGCGCGTGAGTTATC
22939 GCCAAGCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.13, C:0.39, G:0.22, T:0.26
Consensus pattern (28 bp):
CCATCTCCTCGCGCGCGTGAGTTATCAC
Found at i:27365 original size:21 final size:21
Alignment explanation
Indices: 27313--27359 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
27303 GTTTCCAGAT
27313 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
27334 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
27355 TCGCA
1 TCGCA
27360 TTGCGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:27380 original size:20 final size:20
Alignment explanation
Indices: 27355--27406 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
27345 ACTTCGACTA
27355 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
27375 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
27395 TCGCATTGCGAT
1 TCGCATTGCGAT
27407 AGTCCAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:27476 original size:42 final size:42
Alignment explanation
Indices: 27400--27621 Score: 349
Period size: 42 Copynumber: 5.3 Consensus size: 42
27390 CATATTCGCA
27400 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
27440 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
27482 TTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
27524 TTGTGATAGTCCAAGTTCGCATTGCGATTTATTACAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
27566 TTGCGCTATTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
27608 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
27622 AATCGCAACG
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 27 0.16
41 2 0.01
42 137 0.83
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:27628 original size:84 final size:84
Alignment explanation
Indices: 27374--27621 Score: 353
Period size: 84 Copynumber: 3.0 Consensus size: 84
27364 GATTTACATA
*
27374 TTCGCATTGCGA--T-TTACATATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCA
1 TTCGCATTGCGATTTATTACAAATTCG--TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCA
27434 AATTCGTTGCGATAGTCCAAG
64 AATTCGTTGCGATAGTCCAAG
* * * *
27455 TTCGCGTTGCGATTTATTCCAAATTTGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAA
* *
27520 TTTGTTGTGATAGTCCAAG
66 TTCGTTGCGATAGTCCAAG
* * *
27539 TTCGCATTGCGATTTATTACAAATTCGTTGCGCTATTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAA
27604 TTCGTTGCGATAGTCCAA
66 TTCGTTGCGATAGTCCAA
27622 AATCGCAACG
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
81 11 0.08
82 26 0.18
83 3 0.02
84 106 0.73
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (84 bp):
TTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAA
TTCGTTGCGATAGTCCAAG
Found at i:27781 original size:21 final size:20
Alignment explanation
Indices: 27748--27999 Score: 230
Period size: 21 Copynumber: 12.2 Consensus size: 20
27738 CGTTGCGATT
*
27748 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
27767 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
27790 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
27809 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
27832 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
* *
27853 TTGGACTATCGCAA-TGAAT
1 TTGGACTATCGCAAGCGAAC
*
27872 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
27895 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
27914 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
*
27935 TTGGAC-ATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
27953 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
27976 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
27995 TTGGA
1 TTGGA
28000 AAATCGCATT
Statistics
Matches: 194, Mismatches: 20, Indels: 38
0.77 0.08 0.15
Matches are distributed among these distances:
18 9 0.05
19 52 0.27
20 7 0.04
21 88 0.45
23 38 0.20
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:27845 original size:63 final size:61
Alignment explanation
Indices: 27776--28007 Score: 276
Period size: 63 Copynumber: 3.8 Consensus size: 61
27766 TTTGGAATAA
* *
27776 ATCGCAATGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGG-A-AAATCGCAACGCGAACTTGGACT
* * *
27839 ATCGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGG-A-AAATCGCAACGCGAACTTGGACT
* * *
27902 ATCGCAA--CGAACTTGGACTATCGCAACGCGAACTTGG-ACATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACTATCGCAA--CGAACTTGGAAAATCGCAACGCGAACTTGGACT
*
27960 AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCA
1 --ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAAAATCGCA
28008 TTGCGATAGT
Statistics
Matches: 149, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
58 9 0.06
60 23 0.15
61 26 0.17
62 19 0.13
63 72 0.48
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAAAATCGCAACGCGAACTTGGACT
Found at i:27864 original size:42 final size:40
Alignment explanation
Indices: 27748--27999 Score: 262
Period size: 42 Copynumber: 6.1 Consensus size: 40
27738 CGTTGCGATT
* *
27748 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
* *
27790 TTCGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
* *
27832 TTGGACTATCGCAACGCGAACTTGGACTATCGCAATGAAT
1 TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
* *
27872 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACT--ATCGCAACGCGAACTTGGACTATCGCAACGAAC
*
27914 TTGGACTATCGCAACGCGAACTTGGAC-ATCGCAACGAAT
1 TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
* *
27953 TTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAT
1 TTGGACT--ATCGCAACGCGAACTTGGACTATCGCAACGAAC
27995 TTGGA
1 TTGGA
28000 AAATCGCATT
Statistics
Matches: 188, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 17 0.09
40 28 0.15
41 20 0.11
42 112 0.60
44 11 0.06
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAAC
Found at i:27973 original size:81 final size:82
Alignment explanation
Indices: 27818--27999 Score: 312
Period size: 81 Copynumber: 2.2 Consensus size: 82
27808 CTTGGAATAA
*
27818 ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAAAT
1 ATCGCAA--CGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAAT
27883 CGCAACGCGAACTTCGACT
64 CGCAACGCGAACTTCGACT
27902 ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGAC-ATCGCAACGAATTTGGAATAAATCG
1 ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
*
27966 CAACGCGAACTTGGACT
66 CAACGCGAACTTCGACT
*
27983 ATCGCAACGAATTTGGA
1 ATCGCAACGAACTTGGA
28000 AAATCGCATT
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
81 56 0.59
82 32 0.34
84 7 0.07
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (82 bp):
ATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
CAACGCGAACTTCGACT
Found at i:28000 original size:42 final size:42
Alignment explanation
Indices: 27839--28007 Score: 267
Period size: 42 Copynumber: 4.1 Consensus size: 42
27829 AACTTGGACT
*
27839 ATCGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* * *
27881 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACT--
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
27921 ATCGCAACGCGAACTTGGAC-ATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
27962 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
28002 ATCGCA
1 ATCGCA
28008 TTGCGATAGT
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
39 17 0.15
40 27 0.23
41 21 0.18
42 52 0.44
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:28032 original size:21 final size:21
Alignment explanation
Indices: 28003--28055 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
27993 ATTTGGAAAA
*
28003 TCGCATTGCGATAGTCGA-AGT
1 TCGCGTTGCGATAGTCGATA-T
28024 TCGCGTTGCGATAGTCGATAT
1 TCGCGTTGCGATAGTCGATAT
*
28045 TCACGTTGCGA
1 TCGCGTTGCGA
28056 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGATAT
Found at i:34555 original size:2 final size:2
Alignment explanation
Indices: 34548--34579 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34538 TTTTTAAAAG
34548 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
34580 AATAAAATTT
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):
TA
Found at i:35348 original size:24 final size:24
Alignment explanation
Indices: 35303--35348 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
35293 TTTCGTCTTT
* * * *
35303 TTAAATTTTTTAAGTTCGTCTCTC
1 TTAAATTTTATAAATCCATCTCTC
35327 TTAAATTTTATAAATCCATCTC
1 TTAAATTTTATAAATCCATCTC
35349 CTAACATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (24 bp):
TTAAATTTTATAAATCCATCTCTC
Found at i:36696 original size:20 final size:21
Alignment explanation
Indices: 36671--36722 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36661 TTTTACTTAT
*
36671 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
36691 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
36712 TCGCAATGCGA
1 TCGCAATGCGA
36723 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:37392 original size:20 final size:19
Alignment explanation
Indices: 37346--37429 Score: 123
Period size: 19 Copynumber: 4.4 Consensus size: 19
37336 GAGAATCGCA
*
37346 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
37365 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
37384 TGCGATTTTTATTTCGCGGT
1 TGCGATTTTTATTTCGC-GT
* *
37404 TGCGATTTTCATTTCGCAT
1 TGCGATTTTTATTTCGCGT
37423 TGCGATT
1 TGCGATT
37430 GTCTGGTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 41 0.69
20 18 0.31
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:37418 original size:39 final size:38
Alignment explanation
Indices: 37341--37429 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 38
37331 AACGAGAGAA
* * *
37341 TCGCA-TGCGATTTTTGTTTCGCGTTGCGTTTTTTATT
1 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
*
37378 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCATTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
37417 TCGCATTGCGATT
1 TCGCATTGCGATT
37430 GTCTGGTCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
37 4 0.09
38 16 0.36
39 25 0.56
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.49
Consensus pattern (38 bp):
TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:37470 original size:14 final size:14
Alignment explanation
Indices: 37453--37479 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37443 AGTCATTTCG
37453 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37467 CGTTGCGATTCTC
1 CGTTGCGATTCTC
37480 ATTATCTCGT
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:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37475 original size:33 final size:33
Alignment explanation
Indices: 37402--37496 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
37392 TTATTTCGCG
* * * *
37402 GTTGCGATTTTCATTTCGCATTGCGATTGTCTG
1 GTTGCGATTCTCATTTCGCGTTGCGATTCTCTC
* **
37435 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTCTCATTTCGCGTTGCGATTCTCTC
*
37468 GTTGCGATTCTCATTATCTCGTTGCGATT
1 GTTGCGATTCTCATT-TCGCGTTGCGATT
37497 TTCATTTCAA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 39 0.76
34 12 0.24
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.42
Consensus pattern (33 bp):
GTTGCGATTCTCATTTCGCGTTGCGATTCTCTC
Found at i:37489 original size:20 final size:20
Alignment explanation
Indices: 37464--37502 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
37454 GTTGCGATTC
37464 TCTCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
37484 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
37503 TCAACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:39232 original size:14 final size:14
Alignment explanation
Indices: 39213--39248 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39203 GATTGTTAAT
39213 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
39227 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
39241 TGATTTGT
1 TGATTTGT
39249 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:39472 original size:33 final size:32
Alignment explanation
Indices: 39430--39556 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
39420 ATTAAATTCG
39430 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
39463 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
39496 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
39529 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
39557 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:39520 original size:66 final size:66
Alignment explanation
Indices: 39423--39555 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
39413 ACGCGAAATT
*
39423 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
39488 G
66 G
* *
39489 AAATTAGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
39554 G
66 G
39555 A
1 A
39556 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:42086 original size:22 final size:23
Alignment explanation
Indices: 42049--42092 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
42039 ATCATCAAAA
* *
42049 TCCGTGTATTGACCAATATCAAG
1 TCCGGGTATTGACCAAGATCAAG
42072 TCCGGGTA-TGACCAAGATCAA
1 TCCGGGTATTGACCAAGATCAA
42093 ATTTCGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (23 bp):
TCCGGGTATTGACCAAGATCAAG
Found at i:43176 original size:20 final size:20
Alignment explanation
Indices: 43151--43228 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
43141 ATTCATTTGA
43151 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
43171 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
43191 CTATCGCAACGCGAAAATGA
1 CTATCGCAACGCGAAAATGG
*
43211 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
43229 CGCAATGCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:43271 original size:14 final size:14
Alignment explanation
Indices: 43252--43305 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
43242 GAAAATCGCA
43252 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
43266 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
43283 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
43299 TTGCGAT
1 TTGCGAT
43306 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:43271 original size:33 final size:33
Alignment explanation
Indices: 43234--43304 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
43224 AAAATCGCAA
43234 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
43267 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
43300 TGCGA
1 TGCGA
43305 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:43305 original size:33 final size:33
Alignment explanation
Indices: 43247--43324 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
43237 GAAATGAAAA
***
43247 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
43280 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
43313 TCGCGTTGCGAT
1 TCGCATTGCGAT
43325 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:43431 original size:14 final size:14
Alignment explanation
Indices: 43412--43448 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
43402 CATCAATTAA
43412 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
43426 ACAAATCATCTTTT
1 ACAAATCAACATTT
43440 ACAAATCAA
1 ACAAATCAA
43449 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:45345 original size:20 final size:19
Alignment explanation
Indices: 45310--45376 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
45300 GAAACTTAAA
45310 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
45329 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
45349 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
45368 ATCGCAACG
1 ATCGCAACG
45377 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:45455 original size:32 final size:33
Alignment explanation
Indices: 45405--45498 Score: 145
Period size: 32 Copynumber: 2.9 Consensus size: 33
45395 ACACAAATCG
* *
45405 CTTTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CTTTGCGATTTTCATTTCGCATTGCGATATTGT
*
45438 CTTTGCGA-TTTCATTTCGCATTGCGAAATTGT
1 CTTTGCGATTTTCATTTCGCATTGCGATATTGT
*
45470 CGTTGCGATTTTCATTTCGCATTGCGATA
1 CTTTGCGATTTTCATTTCGCATTGCGATA
45499 GCCATTTCCG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 28 0.51
33 27 0.49
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (33 bp):
CTTTGCGATTTTCATTTCGCATTGCGATATTGT
Found at i:45516 original size:20 final size:19
Alignment explanation
Indices: 45482--45536 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
45472 TTGCGATTTT
*
45482 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
45501 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
45521 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
45537 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:46044 original size:18 final size:18
Alignment explanation
Indices: 46018--46062 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
46008 GTCGATCAGA
*
46018 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
46036 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
46054 TGATGGCTC
1 TGATGGCTC
46063 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:47403 original size:20 final size:20
Alignment explanation
Indices: 47378--47420 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
47368 AATAGTTTCT
47378 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
47398 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
47418 GAA
1 GAA
47421 TTCGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:47726 original size:22 final size:22
Alignment explanation
Indices: 47699--47742 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47689 GATGGAGATA
47699 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
47721 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
47743 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:47956 original size:20 final size:20
Alignment explanation
Indices: 47930--48002 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
47920 GATTATGTAT
47930 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
47950 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
47970 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
47990 TATCTCGTTGCGA
1 TATCGCGTTGCGA
48003 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:48057 original size:20 final size:20
Alignment explanation
Indices: 48013--48105 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
48003 TTTTGTATTA
* **
48013 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
48034 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
48054 TCGCATTGTGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
48075 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
48095 TCGCATTGCGA
1 TCGCATTGCGA
48106 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:48058 original size:41 final size:41
Alignment explanation
Indices: 48013--48105 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
48003 TTTTGTATTA
48013 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
48054 TCGCATTGTGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
48095 TCGCATTGCGA
1 TCGCATTGCGA
48106 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:51857 original size:55 final size:54
Alignment explanation
Indices: 51754--52283 Score: 414
Period size: 55 Copynumber: 9.6 Consensus size: 54
51744 AAGACGGGTT
* * * * * * *
51754 CGCTCCCTCTTCTTTTAGGAAATATATGACTCGAA-ACTTCTTCAGAAAATGGGTC
1 CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACA-ATCTTCGGAAAAT-GGTC
* * * * *
51809 CCCT-CTATATTCTTTCAGGGAGTATAGGACTTGAACAATATTCGGAAAACAT-GTT
1 CGCTCCT-TCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGG-AAA-ATGGTC
* * *
51864 TGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAA-ACATCTTCAGAAAATGGGTC
1 CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACA-ATCTTCGGAAAAT-GGTC
* * * *
51919 CTCTCCTTATTCTTTCAAGGAGTATAGCACTCGAACAATCTTCGGCAAACAT-GTC
1 CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGG-AAA-ATGGTC
** *
51974 TTCTTCCTT-TTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGAAAAATGGGTC
1 CGC-TCCTTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGAAAAT-GGTC
* * * * *
52029 TGCTCCTTCTTCTTTCAAGGAGTATAGGACTCAAACAATCTTCGGTAAACGTGTC
1 CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGAAAATG-GTC
* * * * * *
52084 CGCTCCCTATTCTTTTAGGGAGTATTATGACTCAAACAATCTTTGGCAAACAT-GTC
1 CGCTCCTTCTTCTTTCAGGGAGTA-TAGGACTCGAACAATCTTCGG-AAA-ATGGTC
* * *
52140 CGTTCCTTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACAT-GTA
1 CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGG-AAA-ATGGTC
* ** *
52195 TGCT-CTCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTAGCAAATAGGTC
1 CGCTCCT-TCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGAAAAT-GGTC
* * **
52250 AGCTCCTTCTTTTTTCAAAGAGTATCA-GACTCGA
1 CGCTCCTTCTTCTTTCAGGGAGTAT-AGGACTCGA
52284 GATTGATTTT
Statistics
Matches: 384, Mismatches: 67, Indels: 48
0.77 0.13 0.10
Matches are distributed among these distances:
53 6 0.02
54 18 0.05
55 295 0.77
56 58 0.15
57 6 0.02
58 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (54 bp):
CGCTCCTTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGAAAATGGTC
Found at i:51906 original size:110 final size:112
Alignment explanation
Indices: 51755--52283 Score: 573
Period size: 110 Copynumber: 4.8 Consensus size: 112
51745 AGACGGGTTC
* * * * * *
51755 GCTCCCTCTTCTTTTAGGAAATATATGACTCGAAAC-TTCTTCAG-AAAATGGGTCCCCT-CTAT
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAACAATCTTCAGAAAAATGGGTCCGCTCCT-T
* * * *
51817 ATTCTTTCAGGGAGTATAGGACTTGAACAATATTCGGAAAACATGTTT
65 ATTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGTTT
*
51865 GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAAC-ATCTTCAG-AAAATGGGTCCTCTCCTTA
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAACAATCTTCAGAAAAATGGGTCCGCTCCTTA
* *
51928 TTCTTTCAAGGAGTATAGCACTCGAACAATCTTCGGCAAACATGTCTT
66 TTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGT-TT
* * * *
51976 -CTTCCTTTTCTTTCAGGGAGTATAGGACTCG-AACAATCTTC-GAAAAATGGGTCTGCTCCTTC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAACAATCTTCAGAAAAATGGGTCCGCTCCTTA
* * **
52038 TTCTTTCAAGGAGTATAGGACTCAAACAATCTTCGGTAAACGTGTCC
66 TTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGTTT
* * * ** * *
52085 GCTCCCTATTCTTTTAGGGAGTATTATGACTC-AAACAATCTTTGGCAAACAT--GTCCGTTCCT
1 GCTCCCTCTTCTTTCAGGGAGTA-TAGGACTCGAAACAATCTTCAG-AAAAATGGGTCCGCTCCT
* *
52147 TCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGTAT
64 TATTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGTTT
* * * * * *
52196 GCTCTCTCTTCTTTCAGGGAGTATAGGACTCG-AACAATCTTTAG-CAAATAGGTCAGCTCCTTC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAACAATCTTCAGAAAAATGGGTCCGCTCCTTA
* *
52259 TTTTTTCAAAGAGTATCA-GACTCGA
66 TTCTTTCAAGGAGTAT-AGGACTCGA
52284 GATTGATTTT
Statistics
Matches: 361, Mismatches: 45, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
108 3 0.01
109 4 0.01
110 254 0.70
111 94 0.26
112 1 0.00
113 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (112 bp):
GCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAAACAATCTTCAGAAAAATGGGTCCGCTCCTTA
TTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGTAAACATGTTT
Found at i:52215 original size:221 final size:219
Alignment explanation
Indices: 51818--52274 Score: 582
Period size: 221 Copynumber: 2.1 Consensus size: 219
51808 CCCCTCTATA
* ** ** *
51818 TTCTTTCAGGGAGTATAGGACTTGAACAATATTCGGAAAACATGTTTGCTCCCTCTTCTTTCAGG
1 TTCTTTCAAGGAGTATAGGACTCAAACAATATTCGGAAAACATGTCCGCTCCCTATTCTTTCAGG
51883 GAGTATAGGACTCGAAACATCTTCAGAAAATGGGTCCTCTCCTTATTCTTTCAAGGAGTATAGCA
66 GAGTATAGGACTCGAAACATCTTCAGAAAAT-GGTCCTCTCCTTATTCTTTCAAGGAGTATAGCA
* * *
51948 CTCGAACAATCTTCGGCAAACATGTCTTCTTCCTTTTCTTTCAGGGAGTATAGGACTCGAACAAT
130 CTCGAACAATCTTCGGCAAACATGTATGCTTCCTCTTCTTTCAGGGAGTATAGGACTCGAACAAT
* *
52013 CTTCGA-AAAATGGGTCTGCTCCTTC
195 CTT-GAGAAAATAGGTCAGCTCCTTC
* * * *
52038 TTCTTTCAAGGAGTATAGGACTCAAACAATCTTCGGTAAACGTGTCCGCTCCCTATTCTTTTAGG
1 TTCTTTCAAGGAGTATAGGACTCAAACAATATTCGGAAAACATGTCCGCTCCCTATTCTTTCAGG
* ** *
52103 GAGTATTATGACTC-AAACAATCTTTGGCAAACAT-GTCCGT-TCCTTCTTCTTTCAAGGAGTAT
66 GAGTA-TAGGACTCGAAAC-ATCTTCAG-AAA-ATGGTCC-TCTCCTTATTCTTTCAAGGAGTAT
* *
52165 AGGACTCGAACAATCTTCGGTAAACATGTATGC-TCTCTCTTCTTTCAGGGAGTATAGGACTCGA
126 AGCACTCGAACAATCTTCGGCAAACATGTATGCTTC-CTCTTCTTTCAGGGAGTATAGGACTCGA
* *
52229 ACAATCTTTAGCAAATAGGTCAGCTCCTTC
190 ACAATCTTGAGAAAATAGGTCAGCTCCTTC
* *
52259 TTTTTTCAAAGAGTAT
1 TTCTTTCAAGGAGTAT
52275 CAGACTCGAG
Statistics
Matches: 205, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
220 67 0.33
221 132 0.64
222 4 0.02
223 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (219 bp):
TTCTTTCAAGGAGTATAGGACTCAAACAATATTCGGAAAACATGTCCGCTCCCTATTCTTTCAGG
GAGTATAGGACTCGAAACATCTTCAGAAAATGGTCCTCTCCTTATTCTTTCAAGGAGTATAGCAC
TCGAACAATCTTCGGCAAACATGTATGCTTCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATC
TTGAGAAAATAGGTCAGCTCCTTC
Found at i:52324 original size:37 final size:37
Alignment explanation
Indices: 52283--52408 Score: 157
Period size: 37 Copynumber: 3.4 Consensus size: 37
52273 ATCAGACTCG
* *
52283 AGATTGATTTTCTTCGCTACTC-TTCCTCGAAGGCTTA
1 AGATTGATTTTCTTCACTACTCTTTCGT-GAAGGCTTA
*
52320 AGATTGACTTGT-TTCACTACTCTTTCGTGAAGGCTTA
1 AGATTGA-TTTTCTTCACTACTCTTTCGTGAAGGCTTA
* * *
52357 AGATTGATTTGCTTCAATAATCTTTCGTGAAGGCTTA
1 AGATTGATTTTCTTCACTACTCTTTCGTGAAGGCTTA
*
52394 ATATTGATTTTCTTC
1 AGATTGATTTTCTTC
52409 GAAGGTCGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
36 2 0.03
37 68 0.88
38 7 0.09
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (37 bp):
AGATTGATTTTCTTCACTACTCTTTCGTGAAGGCTTA
Found at i:53671 original size:16 final size:18
Alignment explanation
Indices: 53645--53677 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53635 TTAAACCCCC
53645 TTTTATTCTTTT-TTTTA
1 TTTTATTCTTTTCTTTTA
53662 TTTT-TTCTTTTCTTTT
1 TTTTATTCTTTTCTTTT
53678 TGGGTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTCTTTTCTTTTA
Found at i:58669 original size:22 final size:22
Alignment explanation
Indices: 58636--58734 Score: 162
Period size: 22 Copynumber: 4.5 Consensus size: 22
58626 TCAATATTTA
58636 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
**
58658 TCCATAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
*
58680 TCCCGAAGAACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
58702 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
*
58724 TCCTGAAGGAC
1 TCCCGAAGGAC
58735 TAATATACCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.15
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACG
Found at i:67095 original size:24 final size:23
Alignment explanation
Indices: 67068--67148 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
67058 ACACTTAACA
67068 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CCTTTGAAT
* *
67092 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATGCATCCT-TTGAAT
*
67114 -TGCACCGATGCATGCC-TTGAAT
1 GTGCATCGATGCAT-CCTTTGAAT
67136 GTGCATCGATGCA
1 GTGCATCGATGCA
67149 CAGGGTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 1 0.02
23 14 0.30
24 16 0.35
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTTGAAT
Found at i:67664 original size:13 final size:13
Alignment explanation
Indices: 67646--67684 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
67636 AAAACTATAC
67646 ATATTATTTTCAA
1 ATATTATTTTCAA
67659 ATATTATTTTCAA
1 ATATTATTTTCAA
*
67672 ATAGT-TTTTCAA
1 ATATTATTTTCAA
67684 A
1 A
67685 ACCTTGCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (13 bp):
ATATTATTTTCAA
Found at i:68738 original size:21 final size:21
Alignment explanation
Indices: 68696--68747 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
68686 ACTCCGGGAG
* * *
68696 CTAGTTCCTCACGGGCTGCTC
1 CTAGCTCCTCTCGGGCTCCTC
*
68717 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGGGCTCCTC
*
68738 CT-CCTCCTCT
1 CTAGCTCCTCT
68748 GGCTCCAGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.06, C:0.46, G:0.15, T:0.33
Consensus pattern (21 bp):
CTAGCTCCTCTCGGGCTCCTC
Done.