Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008524.1 Hibiscus syriacus cultivar Beakdansim tig00111393_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: 760704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1059 original size:21 final size:21
Alignment explanation
Indices: 993--1059 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
983 GTGAATCGGG
*
993 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1013 TCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1035 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1056 CTCT
1 CTCT
1060 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1078 original size:42 final size:41
Alignment explanation
Indices: 993--1115 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
983 GTGAATCGGG
* * * *
993 CTCTTGAATGGTGGGA-GGGATCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1035 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1077 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1116 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3206 original size:32 final size:32
Alignment explanation
Indices: 3170--3234 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3160 CACGAAATGA
*
3170 AAATCGCAACGCGGAATAAAAATCGCAACGCG
1 AAATCGCAACGCGAAATAAAAATCGCAACGCG
* *
3202 AAATCGCAACGCGAAATGAAAATCGCAATGCG
1 AAATCGCAACGCGAAATAAAAATCGCAACGCG
3234 A
1 A
3235 TTTTTGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (32 bp):
AAATCGCAACGCGAAATAAAAATCGCAACGCG
Found at i:3207 original size:13 final size:13
Alignment explanation
Indices: 3189--3218 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3179 CGCGGAATAA
3189 AAATCGCAACGCG
1 AAATCGCAACGCG
3202 AAATCGCAACGCG
1 AAATCGCAACGCG
3215 AAAT
1 AAAT
3219 GAAAATCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.10
Consensus pattern (13 bp):
AAATCGCAACGCG
Found at i:3222 original size:51 final size:52
Alignment explanation
Indices: 3097--3229 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 52
3087 GTTGAAATAA
* * * ** *
3097 AAATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCGACGAG
1 AAATCGCAACGCGA-AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAG
* *
3150 AGAATCGCAACACGAAATGAAAATCGCAACGCGG-AATAAAAATCGCAACGCG
1 A-AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAG
3202 AAATCGCAACGCGAAATGAAAATCGCAA
1 AAATCGCAACGCGAAATGAAAATCGCAA
3230 TGCGATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 26 0.37
52 14 0.20
53 19 0.27
54 11 0.16
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (52 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAG
Found at i:3226 original size:19 final size:19
Alignment explanation
Indices: 3090--3234 Score: 96
Period size: 19 Copynumber: 8.1 Consensus size: 19
3080 TCTTTTGGTT
* *
3090 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3109 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
3129 GGAAATGACTATCGCGA--C
1 -GAAATGAAAATCGCAACGC
* *
3147 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
3163 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
3182 GGAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3201 -----G-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3214 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3233 GA
1 GA
3235 TTTTTGTTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
13 12 0.12
14 8 0.08
15 1 0.01
16 2 0.02
17 1 0.01
18 3 0.03
19 44 0.45
20 25 0.26
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3262 original size:18 final size:19
Alignment explanation
Indices: 3230--3273 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
3220 AAAATCGCAA
*
3230 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
3249 TGCG-TTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
3267 TGCGATT
1 TGCGATT
3274 CTCTCATTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.07, C:0.16, G:0.25, T:0.52
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3848 original size:20 final size:20
Alignment explanation
Indices: 3823--3875 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3813 GCGCTATGTA
3823 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3843 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3863 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3876 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3909 original size:20 final size:20
Alignment explanation
Indices: 3884--3937 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3874 GATTTTGTAT
3884 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3904 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3924 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3938 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3922 original size:61 final size:61
Alignment explanation
Indices: 3824--3940 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3814 CGCTATGTAA
* * * * *
3824 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
3885 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
3941 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:3956 original size:61 final size:61
Alignment explanation
Indices: 3819--3958 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
3809 AATGGCGCTA
* * * * *
3819 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
3879 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
3940 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
3959 TTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:4048 original size:21 final size:21
Alignment explanation
Indices: 4008--4048 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3998 ACTGTAGACC
**
4008 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
4029 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
4049 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:20088 original size:36 final size:34
Alignment explanation
Indices: 20048--20131 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 34
20038 GAAGTTAAAA
* *
20048 TAAATATTTTAAAAAATAATTTTGGAATGTTATGAT
1 TAAATAATTTAAAAAATAA--TTAGAATGTTATGAT
*
20084 TAAATAATTT--AAGA-AATTAGAATGTTATGAT
1 TAAATAATTTAAAAAATAATTAGAATGTTATGAT
*
20115 GAAATAATTTAAAAAAT
1 TAAATAATTTAAAAAAT
20132 TATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
31 23 0.57
33 5 0.12
34 3 0.08
36 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (34 bp):
TAAATAATTTAAAAAATAATTAGAATGTTATGAT
Found at i:20107 original size:31 final size:32
Alignment explanation
Indices: 20072--20138 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
20062 AATAATTTTG
* *
20072 GAATGTTATGATTAAATAATTTAAGAAATTA-
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
20103 GAATGTTATGATGAAATAATTTAAAAAATTAT
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
20135 GAAT
1 GAAT
20139 TTAAAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (32 bp):
GAATGTTATGATGAAATAATTTAAAAAATTAT
Found at i:23866 original size:20 final size:20
Alignment explanation
Indices: 23828--23863 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
23818 CTAAAAATTT
23828 AAAATTATAATATATTTTAA
1 AAAATTATAATATATTTTAA
23848 AAAATT-TAATAT-TTTT
1 AAAATTATAATATATTTT
23864 TTATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTATAATATATTTTAA
Found at i:29114 original size:17 final size:17
Alignment explanation
Indices: 29094--29126 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29084 TTTAGGGAAG
29094 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
29111 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
29127 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:30977 original size:13 final size:13
Alignment explanation
Indices: 30907--30981 Score: 50
Period size: 13 Copynumber: 6.0 Consensus size: 13
30897 AAATATTAAA
*
30907 AATAATTAT-TAT
1 AATATTTATATAT
*
30919 -ATATATATATAT
1 AATATTTATATAT
* *
30931 AATATTAATAAAT
1 AATATTTATATAT
* *
30944 -TTAATTTAAAT-T
1 AAT-ATTTATATAT
*
30956 AAAATTTATATAT
1 AATATTTATATAT
30969 AATATTTATATAT
1 AATATTTATATAT
30982 TTAATTTAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 9
0.67 0.19 0.13
Matches are distributed among these distances:
11 6 0.13
12 12 0.27
13 27 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATTTATATAT
Found at i:32076 original size:244 final size:244
Alignment explanation
Indices: 31647--32382 Score: 1463
Period size: 244 Copynumber: 3.0 Consensus size: 244
31637 TTTCTCCGAA
31647 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
31712 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
66 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
31777 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
131 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
31842 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
196 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
31891 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
31956 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
66 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
32021 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
131 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
32086 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
196 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
32135 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
32200 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
66 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
32265 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
131 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
*
32330 TATCTGGGGTTCCACTTATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
196 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
32379 CTCC
1 CTCC
32383 TAAGCAGATC
Statistics
Matches: 491, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 491 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (244 bp):
CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
Found at i:35861 original size:23 final size:25
Alignment explanation
Indices: 35817--35863 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35807 CCTATAGTTG
35817 AGATATCATTTTATAACTTTAAAAT
1 AGATATCATTTTATAACTTTAAAAT
35842 AGATA-CATTATTA-AA-TTTAAAA
1 AGATATCATT-TTATAACTTTAAAA
35864 CAATCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AGATATCATTTTATAACTTTAAAAT
Found at i:36611 original size:25 final size:25
Alignment explanation
Indices: 36571--36621 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36561 CGATGAAGCA
*
36571 CAAATCTTAAACCCACATCATCTCT
1 CAAATCTTAAACCCACACCATCTCT
** *
36596 CAAATCTTAATTCCACGCCATCTCT
1 CAAATCTTAAACCCACACCATCTCT
36621 C
1 C
36622 GTTATCGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.29
Consensus pattern (25 bp):
CAAATCTTAAACCCACACCATCTCT
Found at i:38196 original size:178 final size:179
Alignment explanation
Indices: 37911--38265 Score: 545
Period size: 178 Copynumber: 2.0 Consensus size: 179
37901 GTAAGATTTT
* * * *
37911 TTTTTTCATTAAACTAATGTGAATTACAAAGTAGTATCAATTCTAAGTAATCTAAATCATTTAAC
1 TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAATTCTAAATAATCTAAACCATTTAAC
37976 AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAATAA-T
66 AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAATAATT
* *
38040 AATATTTTTAACCGCTGAAATAAGTTGATTTATGAAATATTAAAGTAAAA
131 AAT-TTTTTAACCACCGAAATAAGTTGATTTATGAAATATTAAAGTAAAA
* * *
38090 TTTTTTCATGAAACTAATGTG-ATTACAAAGTAATATCAGTTCTAAATACTCTAAACCATTTGAC
1 TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAATTCTAAATAATCTAAACCATTTAAC
* * * *
38154 AATGAACGTTTAATCATCTTTG-TAGTTGCTGGTGTCTGAACTCATGACCTCTATAAACAATAAT
66 AATAAACGTTTAATCATCTATGCT-GTTGATGGTGTCTGAACTCATGACCTCTAGAAACAATAAT
*
38218 TACTTTTTTAACCACCGAAATAAGTTGATTTATGAAATATTAAAGTAA
130 TAATTTTTTAACCACCGAAATAAGTTGATTTATGAAATATTAAAGTAA
38266 GAACTAAATT
Statistics
Matches: 160, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
177 1 0.01
178 136 0.85
179 23 0.14
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.37
Consensus pattern (179 bp):
TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAATTCTAAATAATCTAAACCATTTAAC
AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAATAATT
AATTTTTTAACCACCGAAATAAGTTGATTTATGAAATATTAAAGTAAAA
Found at i:45845 original size:3 final size:3
Alignment explanation
Indices: 45837--45896 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
45827 GTCAAAATAC
45837 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
45885 ATT GTT ATT ATT
1 ATT ATT ATT ATT
45897 GTATTAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:48062 original size:23 final size:19
Alignment explanation
Indices: 48035--48110 Score: 84
Period size: 18 Copynumber: 3.9 Consensus size: 19
48025 CATATGAATT
48035 TGTCCCGAAGGACCACTAGGAAA
1 TGTCCCGAAGGACCACT----AA
*
48058 TGTCCCGAAAGACCACT-A
1 TGTCCCGAAGGACCACTAA
48076 TGTCCCGAAGGACCACT-A
1 TGTCCCGAAGGACCACTAA
*
48094 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
48111 GATAATCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 34 0.68
23 16 0.32
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTAA
Found at i:48080 original size:18 final size:18
Alignment explanation
Indices: 48057--48110 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
48047 CCACTAGGAA
48057 ATGTCCCGAAAGACCACT
1 ATGTCCCGAAAGACCACT
*
48075 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAAGACCACT
*
48093 ATGTCCCGAATGACCACT
1 ATGTCCCGAAAGACCACT
48111 GATAATCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACT
Found at i:49525 original size:22 final size:22
Alignment explanation
Indices: 49495--49539 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
49485 ATGTAAAATT
49495 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
*
49517 TGTCTCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
49539 T
1 T
49540 CCCTCGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:49545 original size:22 final size:22
Alignment explanation
Indices: 49500--49546 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
49490 AAATTTGTCC
**
49500 CGAAGGACCACTGTATATGTCT
1 CGAAGGACCACTGTATATCCCT
49522 CGAAGGACCACTGTATATCCCT
1 CGAAGGACCACTGTATATCCCT
49544 CGA
1 CGA
49547 CTCTTGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
CGAAGGACCACTGTATATCCCT
Found at i:51307 original size:15 final size:16
Alignment explanation
Indices: 51284--51316 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
51274 TAATTTATAC
51284 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
51299 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
51315 AT
1 AT
51317 TTTGTAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:52559 original size:29 final size:29
Alignment explanation
Indices: 52521--52583 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
52511 ATATATTTAA
* * *
52521 ATATTTTATTCTTATCTTCACGTAAAAAT
1 ATATTCTATTCTTATCTTAAAGTAAAAAT
* * *
52550 ATATTCTATTTTTATTTTAAATTAAAAAT
1 ATATTCTATTCTTATCTTAAAGTAAAAAT
52579 ATATT
1 ATATT
52584 TTATCATTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATTCTATTCTTATCTTAAAGTAAAAAT
Found at i:52759 original size:27 final size:29
Alignment explanation
Indices: 52710--52765 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
52700 GTTAAGATAA
**
52710 TAATAAAAAATATATTTTTATA-TTAAAT
1 TAATAAAAAATATATTTAAATATTTAAAT
*
52738 TAATAATAAA-ATATTTAAATATTTAAAT
1 TAATAAAAAATATATTTAAATATTTAAAT
52766 ATATTTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATAAAAAATATATTTAAATATTTAAAT
Found at i:52834 original size:15 final size:15
Alignment explanation
Indices: 52814--52843 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52804 CTGATGATAA
*
52814 AGATAAAATATATAT
1 AGATAAAATAAATAT
52829 AGATAAAATAAATAT
1 AGATAAAATAAATAT
52844 TTTAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AGATAAAATAAATAT
Found at i:52944 original size:24 final size:24
Alignment explanation
Indices: 52903--52962 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 24
52893 ACACTAAAAT
52903 AAAAATAAGTATATTTAATAAGTTAA
1 AAAAATAA--ATATTTAATAAGTTAA
52929 GAAAAA-AAATATTTAATAAGTTAA
1 -AAAAATAAATATTTAATAAGTTAA
52953 AAAAATAAAT
1 AAAAATAAAT
52963 GATAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.16
24 20 0.62
26 2 0.06
27 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (24 bp):
AAAAATAAATATTTAATAAGTTAA
Found at i:55456 original size:24 final size:24
Alignment explanation
Indices: 55429--55479 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
55419 TTCTCATTTT
*
55429 CTAATCCCT-CCTCTTTCAAAATCC
1 CTAA-CCCTGCCTCGTTCAAAATCC
*
55453 CTAACTCTGCCTCGTTCAAAATCC
1 CTAACCCTGCCTCGTTCAAAATCC
55477 CTA
1 CTA
55480 GCTGAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.25, C:0.39, G:0.04, T:0.31
Consensus pattern (24 bp):
CTAACCCTGCCTCGTTCAAAATCC
Found at i:60593 original size:24 final size:24
Alignment explanation
Indices: 60566--60616 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
60556 TTCTCATTTT
*
60566 CTAATCCCT-CCTCTTTCAAAATCC
1 CTAA-CCCTCCCTCGTTCAAAATCC
*
60590 CTAACTCTCCCTCGTTCAAAATCC
1 CTAACCCTCCCTCGTTCAAAATCC
60614 CTA
1 CTA
60617 GTTGAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.25, C:0.41, G:0.02, T:0.31
Consensus pattern (24 bp):
CTAACCCTCCCTCGTTCAAAATCC
Found at i:62057 original size:15 final size:16
Alignment explanation
Indices: 62037--62076 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
62027 GATGATTAGA
62037 AAAATATATCAAA-TT
1 AAAATATATCAAATTT
62052 AAAATATA--AAATTT
1 AAAATATATCAAATTT
62066 ACAAATATATC
1 A-AAATATATC
62077 CCATTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 15 0.71
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATATCAAATTT
Found at i:62957 original size:2 final size:2
Alignment explanation
Indices: 62952--62979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62942 GGTCCCCCCC
62952 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
62980 TCTATTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:72442 original size:18 final size:19
Alignment explanation
Indices: 72407--72443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
72397 CACGGAATGT
72407 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
72427 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
72444 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:81431 original size:18 final size:16
Alignment explanation
Indices: 81391--81438 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
81381 CAAAAACTAA
*
81391 ATAATTATATTTATTT
1 ATAATTATTTTTATTT
81407 AT-A-TATTTTTATTAAT
1 ATAATTATTTTTATT--T
81423 ATAATTATTTTTATTT
1 ATAATTATTTTTATTT
81439 GCAATGTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 6 0.22
17 1 0.04
18 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATAATTATTTTTATTT
Found at i:87261 original size:23 final size:23
Alignment explanation
Indices: 87235--87326 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
87225 CACCACAGCT
*
87235 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
87258 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
87281 CGTA-AAATTGCATCAAAGTGCCG
1 CGTAGAAA-TGCACCGAAGTGCCA
*
87304 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
87327 TATAAAATGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 2 0.04
23 53 0.93
24 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:88889 original size:20 final size:22
Alignment explanation
Indices: 88864--88921 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
88854 TTCCCCTTGA
88864 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
88884 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
88907 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
88922 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:88996 original size:64 final size:63
Alignment explanation
Indices: 88909--89069 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
88899 TCTTTAACAT
* * * *
88909 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGGG
1 GTGCATCAATGCACTTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
** * * * *
88972 GATGCATTGATGCAC-TCTTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAAGGG
1 G-TGCATCAATGCACTTC-CTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
*
89036 GTGCATCAATGCACTTCCTGTGCATCGATACACA
1 GTGCATCAATGCACTTCCTATGCATCGATACACA
89070 CTGAACAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 26 0.32
64 55 0.68
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCAATGCACTTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGG
Found at i:92416 original size:23 final size:23
Alignment explanation
Indices: 92398--92458 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
92388 CTCGTATAAA
92398 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
92421 TGCACCGAAATACCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
92444 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
92459 TATAAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:94046 original size:20 final size:23
Alignment explanation
Indices: 94021--94073 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
94011 CTTGAAGTTT
94021 ATCGATGCATTC-T-ACA-GTGC
1 ATCGATGCATTCTTAACATGTGC
94041 ATCGATGCATTCTTTAACATGTGC
1 ATCGATGCATTC-TTAACATGTGC
94065 ATCGATGCA
1 ATCGATGCA
94074 CTACCCATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.41
22 1 0.03
23 3 0.10
24 13 0.45
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (23 bp):
ATCGATGCATTCTTAACATGTGC
Found at i:94137 original size:64 final size:62
Alignment explanation
Indices: 94061--94221 Score: 223
Period size: 64 Copynumber: 2.5 Consensus size: 62
94051 TCTTTAACAT
* * *
94061 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGAG
* * * *
94124 GATGCATTGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAAGAG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGAG
94188 GTGCATCGATGCACTTCCTATGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
94222 CTGAACAATT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 29 0.34
64 56 0.66
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGAG
Found at i:99257 original size:2 final size:2
Alignment explanation
Indices: 99250--99278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
99240 TCCTAACTTT
99250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99279 TGTTAATATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113837 original size:21 final size:20
Alignment explanation
Indices: 113813--113936 Score: 62
Period size: 21 Copynumber: 6.3 Consensus size: 20
113803 CAACGCGATT
113813 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
** *
113834 TTGCGATTTTCCAA-AT---
1 TTGCGATAGTCCAAGTTCCG
* * *
113850 TTACGTTAGTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCCG
*
113869 TTGCAATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTC-CG
** *
113890 TTGTAATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
** *
113911 TTGCGATTTTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCCG
113930 TTGCGAT
1 TTGCGAT
113937 CGCAACGACT
Statistics
Matches: 77, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
16 10 0.13
17 1 0.01
19 22 0.29
20 1 0.01
21 43 0.56
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCCG
Found at i:114362 original size:19 final size:20
Alignment explanation
Indices: 114337--114427 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 20
114327 CTTATTTTGG
114337 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
*
114357 -TTTTTCACTATCGTAATAACAC
1 ATTTTTCACTATCG---CAACAC
* *
114379 GTTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
* *
114401 A-TTTTAACTATCGTAACAC
1 ATTTTTCACTATCGCAACAC
114420 ATTTTTCA
1 ATTTTTCA
114428 AAATCGCGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
19 25 0.45
20 5 0.09
21 4 0.07
22 10 0.18
23 6 0.11
25 6 0.11
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:131098 original size:17 final size:19
Alignment explanation
Indices: 131076--131119 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
131066 TTAAGGAGCG
131076 AAAATATAAATACATA-C-
1 AAAATATAAATACATATCT
* *
131093 AAAATATATATATATATCT
1 AAAATATAAATACATATCT
131112 AAAATATA
1 AAAATATA
131120 TTTTAAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 14 0.61
18 1 0.04
19 8 0.35
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATATAAATACATATCT
Found at i:131661 original size:82 final size:82
Alignment explanation
Indices: 131568--131724 Score: 296
Period size: 82 Copynumber: 1.9 Consensus size: 82
131558 AATTTAAAAA
*
131568 TAATTCCCTAAACCTAATACTTAAATTCCTAACATTAATCTTAAATTTATTATTCTCATCCTAAA
1 TAATTCCCTAAACCTAATACTTAAATTCCTAACATTAATCCTAAATTTATTATTCTCATCCTAAA
131633 TTAACTTTAATTAAACT
66 TTAACTTTAATTAAACT
*
131650 TAATTCTCTAAACCTAATACTTAAATTCCTAACATTAATCCTAAATTTATTATTCTCATCCTAAA
1 TAATTCCCTAAACCTAATACTTAAATTCCTAACATTAATCCTAAATTTATTATTCTCATCCTAAA
131715 TTAACTTTAA
66 TTAACTTTAA
131725 AGATCTACAG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (82 bp):
TAATTCCCTAAACCTAATACTTAAATTCCTAACATTAATCCTAAATTTATTATTCTCATCCTAAA
TTAACTTTAATTAAACT
Found at i:131810 original size:51 final size:51
Alignment explanation
Indices: 131734--131839 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
131724 AAGATCTACA
131734 GAGATAATGAAGAGGGGTATTGAATACAACTGGAGAGGAAGAAAACTTTTT
1 GAGATAATGAAGAGGGGTATTGAATACAACTGGAGAGGAAGAAAACTTTTT
131785 GAGATAATGAAGAGGGGTATTGAATACAACTGGAGAGGAAGAAAACTTTTT
1 GAGATAATGAAGAGGGGTATTGAATACAACTGGAGAGGAAGAAAACTTTTT
131836 GAGA
1 GAGA
131840 AGGCGAGGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.23
Consensus pattern (51 bp):
GAGATAATGAAGAGGGGTATTGAATACAACTGGAGAGGAAGAAAACTTTTT
Found at i:133971 original size:15 final size:16
Alignment explanation
Indices: 133933--134009 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 16
133923 CAATCATTTT
*
133933 ATAATTTTTAATAATTA
1 ATAATATTTAATAA-TA
133950 A-AATATTTAATAA-A
1 ATAATATTTAATAATA
*
133964 ATAATATTTTATAATA
1 ATAATATTTAATAATA
* * *
133980 A-AA-AATTAAT-TTT
1 ATAATATTTAATAATA
*
133993 ATAATTTTTAATAATA
1 ATAATATTTAATAATA
134009 A
1 A
134010 AAAACCCAAC
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
13 2 0.04
14 9 0.20
15 18 0.40
16 15 0.33
17 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATTTAATAATA
Found at i:133980 original size:18 final size:19
Alignment explanation
Indices: 133957--133997 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
133947 TTAAAATATT
133957 TAATAAAATAA-T-ATTTTA
1 TAATAAAA-AATTAATTTTA
133975 TAATAAAAAATTAATTTTA
1 TAATAAAAAATTAATTTTA
133994 TAAT
1 TAAT
133998 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAAAAATTAATTTTA
Found at i:133997 original size:29 final size:29
Alignment explanation
Indices: 133928--134013 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
133918 TCGAACAATC
*
133928 ATTTTATAATTTTTAATAATTAAAATATTTA
1 ATTTTATAATTTTTAATAA-TAAAA-AATTA
***
133959 ATAAAATAATATTTT-ATAATAAAAAATTA
1 ATTTTATAAT-TTTTAATAATAAAAAATTA
133988 ATTTTATAATTTTTAATAATAAAAAA
1 ATTTTATAATTTTTAATAATAAAAAA
134014 CCCAACAACA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.09
29 22 0.48
30 5 0.11
31 11 0.24
32 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTTATAATTTTTAATAATAAAAAATTA
Found at i:135554 original size:15 final size:15
Alignment explanation
Indices: 135530--135602 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
135520 TTGGTTTTTC
135530 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
135545 GGAATTTGAATTACT
1 GGAAAATGAATTACT
135560 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
135575 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
135589 GGAAAATGAATTAC
1 GGAAAATGAATTAC
135603 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:135600 original size:29 final size:30
Alignment explanation
Indices: 135530--135602 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
135520 TTGGTTTTTC
135530 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
135560 GGAAAATGAATTACTGGAATTTGAATT-CT
1 GGAAAATGAATTACTGGAATTTGAATTACT
135589 GGAAAATGAATTAC
1 GGAAAATGAATTAC
135603 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:135608 original size:20 final size:20
Alignment explanation
Indices: 135585--135634 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
135575 GGAATTTGAA
*
135585 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
135605 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
135625 TTCTGGAAAA
1 TTCTGGAAAA
135635 CATCTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:136004 original size:19 final size:21
Alignment explanation
Indices: 135956--136004 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
135946 ATATCTTTAC
135956 TAAA-ATATTATTTAAATATA
1 TAAATATATTATTTAAATATA
*
135976 TAAATAATATTATTT-ATTAT-
1 TAAAT-ATATTATTTAAATATA
135996 TAAATATAT
1 TAAATATAT
136005 AAAAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 4 0.15
22 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATATATTATTTAAATATA
Found at i:136011 original size:30 final size:30
Alignment explanation
Indices: 135961--136061 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 30
135951 TTTACTAAAA
135961 TATTATTTAAATATAT--AAATAATATTATT
1 TATTA-TTAAATATATAAAAATAATATTATT
* *
135990 TATTATTAAATATATAAAAATATTATTATA
1 TATTATTAAATATATAAAAATAATATTATT
136020 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-ATAATA--TTAT-T
136052 TATTA-TAAAT
1 TATTATTAAAT
136062 TGATTATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
28 14 0.23
29 13 0.21
30 21 0.34
31 8 0.13
32 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTATTAAATATATAAAAATAATATTATT
Found at i:136013 original size:20 final size:21
Alignment explanation
Indices: 135990--136032 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
135980 TAATATTATT
135990 TATTATTAAATA-TATAAAAA
1 TATTATTAAATATTATAAAAA
* *
136010 TATTATTATATATTATTAAAA
1 TATTATTAAATATTATAAAAA
136031 TA
1 TA
136033 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTATTAAATATTATAAAAA
Found at i:136113 original size:27 final size:25
Alignment explanation
Indices: 135960--136118 Score: 85
Period size: 27 Copynumber: 6.0 Consensus size: 25
135950 CTTTACTAAA
135960 ATATTATT-TAAATATATAAATAATATT
1 ATATTATTAT-AATAT-TAAA-AATATT
135987 AT-TTATTATTAAATATATAAAAATATT
1 ATATTATTA-T-AATAT-TAAAAATATT
* *
136014 ATTATATATTATTAA-AATAAAAATATA
1 A-TAT-TATTA-TAATATTAAAAATATT
* * *
136041 ATA-TCTTATATTATTATAAATTGATT
1 ATATTATTATAATATTA-AAAAT-ATT
**
136067 ATATTATTA-AACTAAAAATATAATATT
1 ATATTATTATAA-TATTAA-A-AATATT
136094 ATATTATTATAATATTAATAAATAT
1 ATATTATTATAATATTAA-AAATAT
136119 ATTTTAAATA
Statistics
Matches: 105, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
23 2 0.02
24 7 0.07
25 4 0.04
26 19 0.18
27 45 0.43
28 18 0.17
29 3 0.03
30 7 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATTATTATAATATTAAAAATATT
Found at i:136365 original size:42 final size:42
Alignment explanation
Indices: 136306--136424 Score: 220
Period size: 42 Copynumber: 2.8 Consensus size: 42
136296 ATGAATTACG
136306 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
136348 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
* *
136390 TTTCGGAAAACGAATTACATGAAACAAACACGGGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGA
136425 TTTCGGGGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
Found at i:136782 original size:6 final size:6
Alignment explanation
Indices: 136773--136803 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
136763 TATATATATA
136773 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
136804 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:138307 original size:28 final size:28
Alignment explanation
Indices: 138275--138402 Score: 229
Period size: 28 Copynumber: 4.5 Consensus size: 28
138265 AAAAATATCA
*
138275 CAACTGAAGAAACCTGAAAGCTTTCTTC
1 CAACTCAAGAAACCTGAAAGCTTTCTTC
138303 CAACTCAAGAAACCTGAAAGCTTTCTTC
1 CAACTCAAGAAACCTGAAAGCTTTCTTC
138331 CAACTCAAGAAACCTGAAAGCTTTCTTC
1 CAACTCAAGAAACCTGAAAGCTTTCTTC
138359 CAACTCAAGAAACCTAGGAAAGCTTTCTTC
1 CAACTCAAGAAACCT--GAAAGCTTTCTTC
138389 CAACTCAAGAAACC
1 CAACTCAAGAAACC
138403 ATTTGATGTT
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
28 70 0.72
30 27 0.28
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (28 bp):
CAACTCAAGAAACCTGAAAGCTTTCTTC
Found at i:148474 original size:41 final size:42
Alignment explanation
Indices: 148428--148513 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 42
148418 GGGCTTGGCC
* *
148428 TATTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAAAAG-CT
1 TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGTCT
**
148469 TATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAAGTCT
1 TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGTCT
148511 TAT
1 TAT
148514 AAGCCTGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 35 0.88
42 5 0.12
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (42 bp):
TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGTCT
Found at i:149753 original size:11 final size:12
Alignment explanation
Indices: 149728--149761 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
149718 ATCGCGGTAG
149728 GAGCAATTCATC
1 GAGCAATTCATC
149740 GAGCAATT-ATC
1 GAGCAATTCATC
149751 GAGCAATTCAT
1 GAGCAATTCAT
149762 GTTGTTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (12 bp):
GAGCAATTCATC
Found at i:155771 original size:30 final size:30
Alignment explanation
Indices: 155737--155796 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
155727 TTAAAAGTTG
155737 AAACAATTTATATCCCTCAGAAAGACTAGC
1 AAACAATTTATATCCCTCAGAAAGACTAGC
155767 AAACAATTTATATCCCTCAGAAAGACTAGC
1 AAACAATTTATATCCCTCAGAAAGACTAGC
155797 CACATTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (30 bp):
AAACAATTTATATCCCTCAGAAAGACTAGC
Found at i:161654 original size:25 final size:23
Alignment explanation
Indices: 161620--161672 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
161610 GTATGATTTT
*
161620 ATAAATTTATAAAATATTAAGAGAG
1 ATAAACTTATAAAATATTAA-A-AG
*
161645 ATAAACTTATAAAATTTTAAAAG
1 ATAAACTTATAAAATATTAAAAG
161668 ATAAA
1 ATAAA
161673 AACAAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 1 0.04
25 18 0.69
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (23 bp):
ATAAACTTATAAAATATTAAAAG
Found at i:162478 original size:18 final size:20
Alignment explanation
Indices: 162444--162480 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
162434 GCAATATAAC
162444 TAAATTATATATATATTTTT
1 TAAATTATATATATATTTTT
162464 TAAATTATA-AT-TATTTT
1 TAAATTATATATATATTTT
162481 ATGAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAATTATATATATATTTTT
Found at i:163366 original size:3 final size:3
Alignment explanation
Indices: 163358--163387 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
163348 AATCACTCCC
163358 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
163388 GCTCTTTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:164215 original size:18 final size:18
Alignment explanation
Indices: 164192--164230 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
164182 CAAATAATTT
*
164192 TTTTTAA-AATAATTATAA
1 TTTTTAATAA-AAATATAA
164210 TTTTTAATAAAAATATAA
1 TTTTTAATAAAAATATAA
164228 TTT
1 TTT
164231 AATCATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTAATAAAAATATAA
Found at i:165115 original size:101 final size:100
Alignment explanation
Indices: 164939--165140 Score: 350
Period size: 101 Copynumber: 2.0 Consensus size: 100
164929 GCAGCGCATC
* * *
164939 CTGGTTTTAATACAGATGGAAAACGCGGGGGAAACTTTCATTTCCTTTACAGATCAAGACAATTG
1 CTGGTTTTAATACAGATAGAAAACGCGGGGGAAACGTTCATTTCCTTTACAGATCAAGACAAGTG
165004 ACGATCGGAAAAAAATGGAGATGCGGGGTATCGATG
66 ACGATCGG-AAAAAATGGAGATGCGGGGTATCGATG
165040 CTGGTTTTAATACAGATAGAAAACGCGGGGGAAACGTTCATTTCCTTTACAGATCAAGACAAGTG
1 CTGGTTTTAATACAGATAGAAAACGCGGGGGAAACGTTCATTTCCTTTACAGATCAAGACAAGTG
* *
165105 ACGATTGGAAAATATGGAGATGCGGGGTATCGATG
66 ACGATCGGAAAAAATGGAGATGCGGGGTATCGATG
165140 C
1 C
165141 CCTTACCTCT
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 27 0.28
101 69 0.72
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (100 bp):
CTGGTTTTAATACAGATAGAAAACGCGGGGGAAACGTTCATTTCCTTTACAGATCAAGACAAGTG
ACGATCGGAAAAAATGGAGATGCGGGGTATCGATG
Found at i:172507 original size:2 final size:2
Alignment explanation
Indices: 172500--172540 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
172490 GGTTTATGAA
172500 AT AT AT AT 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 AT AT AT AT A
172541 AGTTTAAACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:175849 original size:20 final size:20
Alignment explanation
Indices: 175824--175875 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
175814 AATTAAATCC
*
175824 TTTTAAAGGTTTTAATAAAA
1 TTTTAAAAGTTTTAATAAAA
* *
175844 TTTTAAAATTTTTATTAAAA
1 TTTTAAAAGTTTTAATAAAA
*
175864 ATTTAAAA-TTTT
1 TTTTAAAAGTTTT
175876 GAAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTAAAAGTTTTAATAAAA
Found at i:176157 original size:24 final size:23
Alignment explanation
Indices: 176104--176171 Score: 55
Period size: 24 Copynumber: 2.8 Consensus size: 23
176094 TCTAAATTAT
* * *
176104 TAATTTTATTTTTATTTTAATACT
1 TAATTTT-TATTTATTTTAAAACA
176128 TAAATTTTTATTTATTTTAAAATCA
1 T-AATTTTTATTTATTTTAAAA-CA
**
176153 TAATTAATATTTACTTTTA
1 TAATTTTTATTTA-TTTTA
176172 TTTCATTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATTTTTATTTATTTTAAAACA
Found at i:176172 original size:60 final size:60
Alignment explanation
Indices: 176107--176245 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 60
176097 AAATTATTAA
* * *
176107 TTTTATTTTTATTTTAATA-CTTAAATTTTTATTTATTTTAAAATCATA-ATTAA-TATTTAC
1 TTTTATTTTTATTTTAATATC-AAAACTTTTATTTATTTTAAAATAATACA-TAACT-TTTAC
* * *
176167 TTTTA-TTTCATTTTGATATCAAAACTTTTATTTGTTTTAAAATAATACATAACTTTTAC
1 TTTTATTTTTATTTTAATATCAAAACTTTTATTTATTTTAAAATAATACATAACTTTTAC
*
176226 TTTT-TATTTTGTTTTAATAT
1 TTTTAT-TTTTATTTTAATAT
176246 TTCTTCGTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
59 46 0.71
60 19 0.29
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.59
Consensus pattern (60 bp):
TTTTATTTTTATTTTAATATCAAAACTTTTATTTATTTTAAAATAATACATAACTTTTAC
Found at i:177018 original size:26 final size:24
Alignment explanation
Indices: 176988--177035 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
176978 AATTTATGAT
176988 GAATTTATAAAATTTTAAAGAATAAC
1 GAATTTATAAAA-TTTAAA-AATAAC
177014 GAATTTATAAAATTTAAAAATA
1 GAATTTATAAAATTTAAAAATA
177036 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 12 0.55
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
GAATTTATAAAATTTAAAAATAAC
Found at i:177048 original size:14 final size:13
Alignment explanation
Indices: 177029--177058 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
177019 TATAAAATTT
177029 AAAAATATTAATAA
1 AAAAATATTAA-AA
177043 AAAAATATTAAAA
1 AAAAATATTAAAA
177056 AAA
1 AAA
177059 TTAAAGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATATTAAAA
Found at i:178251 original size:23 final size:22
Alignment explanation
Indices: 178223--178266 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
178213 TAACAAATTT
*
178223 TTATTTTTCATATTTTCATATTA
1 TTATTTTTAATATTTT-ATATTA
178246 TTATTTTTAATATTTTATATT
1 TTATTTTTAATATTTTATATT
178267 TTACATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTTTAATATTTTATATTA
Found at i:178274 original size:16 final size:16
Alignment explanation
Indices: 178227--178274 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
178217 AAATTTTTAT
178227 TTTTCATATTTT-CATA
1 TTTT-ATATTTTACATA
178243 TTATTAT-TTTTA-ATA
1 TT-TTATATTTTACATA
178258 TTTTATATTTTACATA
1 TTTTATATTTTACATA
178274 T
1 T
178275 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 8 0.29
17 2 0.07
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTTACATA
Found at i:183380 original size:8 final size:9
Alignment explanation
Indices: 183364--183407 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
183354 TTGTTTTAGT
183364 AAGAAAATA
1 AAGAAAATA
183373 AA-AAAATAA
1 AAGAAAAT-A
183382 AATGAAAAT-
1 AA-GAAAATA
183391 AAGAAAATA
1 AAGAAAATA
183400 AAGAAAAT
1 AAGAAAAT
183408 GATAACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 11 0.35
9 15 0.48
11 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (9 bp):
AAGAAAATA
Found at i:193949 original size:27 final size:27
Alignment explanation
Indices: 193897--193964 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
193887 TGTGTAATAT
*
193897 ATATTTAATTTTTTAATGGTATAATTAA
1 ATATTTAATTTTTTAA-GGTACAATTAA
* *
193925 ATATTTAATTTTTTCAA-GTGCAATTAG
1 ATATTTAATTTTTT-AAGGTACAATTAA
*
193952 ATATTTACTTTTT
1 ATATTTAATTTTT
193965 ATACAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.54
28 14 0.40
29 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (27 bp):
ATATTTAATTTTTTAAGGTACAATTAA
Found at i:194401 original size:20 final size:21
Alignment explanation
Indices: 194367--194432 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
194357 AGCTAACGAC
194367 ATTAAAATATAAATATAAATA
1 ATTAAAATATAAATATAAATA
*
194388 ATTAAAAT-TAAATATATATA
1 ATTAAAATATAAATATAAATA
* *
194408 ATTTAAAATATTAAT-TACATA
1 A-TTAAAATATAAATATAAATA
194429 ATTA
1 ATTA
194433 TATCAACGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 15 0.38
21 21 0.52
22 4 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAATATAAATATAAATA
Found at i:195801 original size:18 final size:19
Alignment explanation
Indices: 195758--195803 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
195748 CACATTATCC
195758 ATCTCTACAATAATAATAA
1 ATCTCTACAATAATAATAA
** *
195777 AAGTCTACAA-AATAATCA
1 ATCTCTACAATAATAATAA
195795 ATCTCTACA
1 ATCTCTACA
195804 CCATTTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (19 bp):
ATCTCTACAATAATAATAA
Found at i:219935 original size:24 final size:24
Alignment explanation
Indices: 219891--219936 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
219881 TATATATTTG
*
219891 ATAAAATTTAATTATTTAAAAGAT
1 ATAAAATTTAATTATTGAAAAGAT
*
219915 ATAAAATTTGACTT-TTGAAAAG
1 ATAAAATTT-AATTATTGAAAAG
219937 TTAATAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (24 bp):
ATAAAATTTAATTATTGAAAAGAT
Found at i:220318 original size:18 final size:18
Alignment explanation
Indices: 220292--220329 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
220282 TAACTGGAAT
220292 TTGACTATATAAAAA-TAA
1 TTGACTATA-AAAAATTAA
*
220310 TTGATTATAAAAAATTAA
1 TTGACTATAAAAAATTAA
220328 TT
1 TT
220330 TTAATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
TTGACTATAAAAAATTAA
Found at i:221279 original size:20 final size:19
Alignment explanation
Indices: 221256--221320 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
221246 TTGAATGAGT
221256 TATTTTATAAAAATTTAATA
1 TATTTTAT-AAAATTTAATA
* ** *
221276 TATTTCATGATTATTTTATA
1 TATTTTAT-AAAATTTAATA
221296 -ATTTT-TAAAATTTAATTA
1 TATTTTATAAAATTTAA-TA
221314 TATTTTA
1 TATTTTA
221321 ACATAATTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 9 0.27
20 15 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTTATAAAATTTAATA
Found at i:231447 original size:30 final size:31
Alignment explanation
Indices: 231383--231457 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
231373 ATAACTTTTA
*
231383 ATAGTTGAGGGACTCAATAGAGCGGTGCCTT
1 ATAGTCGAGGGACTCAATAGAGCGGTGCCTT
*
231414 ATAGTCGAGGGACTCAATAGAGTGGTG-CTT
1 ATAGTCGAGGGACTCAATAGAGCGGTGCCTT
*
231444 ATAGTGGAGGGACT
1 ATAGTCGAGGGACT
231458 ATTTTATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 16 0.39
31 25 0.61
ACGTcount: A:0.27, C:0.13, G:0.35, T:0.25
Consensus pattern (31 bp):
ATAGTCGAGGGACTCAATAGAGCGGTGCCTT
Found at i:238070 original size:27 final size:29
Alignment explanation
Indices: 238032--238088 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
238022 ATGAGAGAAG
238032 GAGGAGAACC-TTGTAA-GTCGGATATAT
1 GAGGAGAACCTTTGTAATGTCGGATATAT
238059 GAGGAGAACCTTTTGTAATGTCGGATATAT
1 GAGGAGAACC-TTTGTAATGTCGGATATAT
238089 CTTTAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 10 0.37
29 6 0.22
30 11 0.41
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (29 bp):
GAGGAGAACCTTTGTAATGTCGGATATAT
Found at i:239134 original size:6 final size:6
Alignment explanation
Indices: 239125--239203 Score: 78
Period size: 6 Copynumber: 13.5 Consensus size: 6
239115 GTGCGTGTAA
239125 GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GT---T GTGCAT GGTGCA-
1 GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT -GTGCAT
* *
239170 -TGCAT GTGCATGT GTGCAT GTGTAT GTGTAT GTG
1 GTGCAT GTGCA--T GTGCAT GTGCAT GTGCAT GTG
239204 TACATATACA
Statistics
Matches: 64, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
3 3 0.05
4 4 0.06
6 46 0.72
7 5 0.08
8 6 0.09
ACGTcount: A:0.15, C:0.13, G:0.35, T:0.37
Consensus pattern (6 bp):
GTGCAT
Found at i:242464 original size:19 final size:19
Alignment explanation
Indices: 242425--242466 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
242415 AGACTAACAC
***
242425 AATAAGGAAATGATGGTAT
1 AATAAGGAAATGATAAAAT
242444 AATAAGGAAATGATAAAAT
1 AATAAGGAAATGATAAAAT
242463 AATA
1 AATA
242467 TTTCAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (19 bp):
AATAAGGAAATGATAAAAT
Found at i:245732 original size:6 final size:6
Alignment explanation
Indices: 245650--245730 Score: 144
Period size: 6 Copynumber: 13.5 Consensus size: 6
245640 GTGCGTGTAA
245650 GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT
1 GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT
* *
245698 GTGCAT GTGCAT GTGCAT GTGTAT GTGTAT GTG
1 GTGCAT GTGCAT GTGCAT GTGCAT GTGCAT GTG
245731 TACATATACA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.36
Consensus pattern (6 bp):
GTGCAT
Found at i:247502 original size:40 final size:37
Alignment explanation
Indices: 247418--247503 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 37
247408 CTCAACTTCG
*
247418 TATG-ATATATGTATATCGTATATGAAAAATTGTGAA
1 TATGTATATATGTATATCATATATGAAAAATTGTGAA
** *
247454 TAAATATATATGTATATCATAGTTATTG-AAAATTGTTATA
1 TATGTATATATGTATATCATA--TA-TGAAAAATTGTGA-A
247494 TATGTATATA
1 TATGTATATA
247504 CAATTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
36 2 0.05
37 15 0.38
39 11 0.28
40 11 0.28
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (37 bp):
TATGTATATATGTATATCATATATGAAAAATTGTGAA
Found at i:248641 original size:2 final size:2
Alignment explanation
Indices: 248593--248624 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
248583 CTTAAATTAA
248593 AT AT A- 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
248625 AATTTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:249498 original size:2 final size:2
Alignment explanation
Indices: 249491--249520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
249481 GATTACAAAC
249491 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
249521 ATGAGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:251934 original size:149 final size:149
Alignment explanation
Indices: 251745--252059 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
251735 GGGTAGAGGG
*
251745 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
251810 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
251875 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
251894 TCTACGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
251959 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
252024 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
252043 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
252060 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:252071 original size:23 final size:23
Alignment explanation
Indices: 252027--252071 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
252017 ATCATTATAT
*
252027 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
252050 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
252072 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:258970 original size:149 final size:149
Alignment explanation
Indices: 258782--259096 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
258772 GGGTAGAGGG
* *
258782 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
*
258847 ACTTGATCCCTAGTATATGTATATGATTC-TTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACTTGATCCCTAGTATATGTATATGA-TCATTAAGGAATTATATGTGGTCCTTATGGACATCATT
*
258911 ATATGGCACTACGGTGTAAT
130 ATATGGCACTACGGTGCAAT
*
258931 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
258996 ACTTGATCCCTAGTATATGTATATGATCATTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCATTAAGGAATTATATGTGGTCCTTATGGACATCATTA
259061 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
259080 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
259097 TGCATTTATA
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 3 0.02
149 156 0.98
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCATTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:259108 original size:23 final size:23
Alignment explanation
Indices: 259064--259108 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
259054 ATCATTATAT
*
259064 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
259087 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
259109 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:259780 original size:31 final size:32
Alignment explanation
Indices: 259739--259811 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
259729 TAAAACTTAT
* * *
259739 AATATAATCCCCT-AATATTTAGTTCGTTTGC
1 AATATGATCCCCTCAAAATTTAGTCCGTTTGC
259770 AATATGAT-CCCTCAAAATTTAGTCCGTTTGC
1 AATATGATCCCCTCAAAATTTAGTCCGTTTGC
*
259801 AATATGGTCCC
1 AATATGATCCC
259812 TTACATAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 4 0.11
31 30 0.83
32 2 0.06
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (32 bp):
AATATGATCCCCTCAAAATTTAGTCCGTTTGC
Found at i:260521 original size:8 final size:7
Alignment explanation
Indices: 260490--260524 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
260480 CCAAAACTCC
*
260490 TAAATCC
1 TAAATCT
260497 TAAATCT
1 TAAATCT
260504 TAAATCT
1 TAAATCT
260511 TAAATTCT
1 TAAA-TCT
260519 TAAATC
1 TAAATC
260525 CCAATACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATCT
Found at i:261955 original size:18 final size:17
Alignment explanation
Indices: 261922--261955 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
261912 GAATAATTAA
261922 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
261939 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
261956 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:275288 original size:79 final size:79
Alignment explanation
Indices: 275157--275302 Score: 229
Period size: 79 Copynumber: 1.8 Consensus size: 79
275147 TGTGCTTAAC
* * *
275157 ATGAACCAAGGAAGTAATGACTTGCAATTGGATGTCTTTGTCCAAATGAATTTGTAAGAGGTTTC
1 ATGAACCAAGGAAGTAATAACTCGCAATTGAATGTCTTTGTCCAAATGAATTTGTAAGAGGTTTC
275222 ATGAAATAATTATT
66 ATGAAATAATTATT
* * * *
275236 ATGAACTAAGGAATTAATAACTCGCAATTGAATGTTTTTGTCCAAATGAATTTGTAAGTGGTTTC
1 ATGAACCAAGGAAGTAATAACTCGCAATTGAATGTCTTTGTCCAAATGAATTTGTAAGAGGTTTC
275301 AT
66 AT
275303 CCTCTTTGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 60 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (79 bp):
ATGAACCAAGGAAGTAATAACTCGCAATTGAATGTCTTTGTCCAAATGAATTTGTAAGAGGTTTC
ATGAAATAATTATT
Found at i:277227 original size:6 final size:6
Alignment explanation
Indices: 277216--277263 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
277206 TTCCTACCTA
*
277216 GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGAA GGGGAG
1 GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG
277264 TTTCGTCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
GGGGAG
Found at i:283782 original size:33 final size:33
Alignment explanation
Indices: 283745--283812 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
283735 AATTTTATAA
283745 CTGTATTATGACATGGTTCAATTAAATGATTTT
1 CTGTATTATGACATGGTTCAATTAAATGATTTT
*
283778 CTGTATTATGACGTGGTTCAATTAAATGATTTT
1 CTGTATTATGACATGGTTCAATTAAATGATTTT
283811 CT
1 CT
283813 AAATTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (33 bp):
CTGTATTATGACATGGTTCAATTAAATGATTTT
Found at i:285535 original size:14 final size:14
Alignment explanation
Indices: 285516--285561 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
285506 GCTGGGCATC
*
285516 CGAGGCCATCCGAT
1 CGAGGCCATCCGAA
*
285530 CGAGGCCATCCGAC
1 CGAGGCCATCCGAA
*
285544 CGAGACCATCCGAA
1 CGAGGCCATCCGAA
285558 CGAG
1 CGAG
285562 CTATGCGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (14 bp):
CGAGGCCATCCGAA
Found at i:285595 original size:33 final size:33
Alignment explanation
Indices: 285553--285627 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
285543 CCGAGACCAT
* * *
285553 CCGAACGAGCTATGCGAGGGCATCCGAGGGCAA-
1 CCGAGCGAGCTATGCGAGGGAATCCGA-GGAAAG
285586 CCGAGCGAGCTATGCGAGGGAATCCGAGGAAAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGAAAG
285619 CCGAGCGAG
1 CCGAGCGAG
285628 GGTAGGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.28, C:0.25, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGAAAG
Found at i:285703 original size:12 final size:12
Alignment explanation
Indices: 285686--285710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
285676 TGCTATGCAA
285686 CACGTTCATTCT
1 CACGTTCATTCT
285698 CACGTTCATTCT
1 CACGTTCATTCT
285710 C
1 C
285711 TTTGTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:286003 original size:56 final size:56
Alignment explanation
Indices: 285888--286012 Score: 175
Period size: 56 Copynumber: 2.2 Consensus size: 56
285878 TAGAGGCTTT
* * *
285888 AAATAAAATATATTTATCAATTATTGCTATTAATAAATATAAAAATAGAGATATTG
1 AAATTAAATATATTTATCAATTATTGCTATTAATAAAAATAAAAATAGAGATATCG
*
285944 AAATTAAATATATTTATCAATTATTGTTATTAATAAAAATAAAAATATGAG-T-TCCG
1 AAATTAAATATATTTATCAATTATTGCTATTAATAAAAATAAAAATA-GAGATAT-CG
286000 AAATTAAAT-TATT
1 AAATTAAATATATT
286013 GATATTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
55 5 0.08
56 55 0.87
57 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.39
Consensus pattern (56 bp):
AAATTAAATATATTTATCAATTATTGCTATTAATAAAAATAAAAATAGAGATATCG
Found at i:294533 original size:20 final size:20
Alignment explanation
Indices: 294508--294548 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
294498 TTTCACTAGA
* *
294508 AAATTGATTGTTGGTAAAAT
1 AAATTGAGTGTTGATAAAAT
294528 AAATTGAGTGTTGATAAAAT
1 AAATTGAGTGTTGATAAAAT
294548 A
1 A
294549 TTATCTCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.37
Consensus pattern (20 bp):
AAATTGAGTGTTGATAAAAT
Found at i:314534 original size:9 final size:10
Alignment explanation
Indices: 314505--314532 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
314495 ACCGTGCAAA
314505 AAGAAAAAAC
1 AAGAAAAAAC
314515 AAGAAAAAAC
1 AAGAAAAAAC
314525 AAGAAAAA
1 AAGAAAAA
314533 CAGTCCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAC
Found at i:318376 original size:2 final size:2
Alignment explanation
Indices: 318367--318397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
318357 TGTCAAAAAA
318367 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318398 TACGGATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:322124 original size:20 final size:20
Alignment explanation
Indices: 322057--322126 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
322047 TCCCTCTATA
322057 TATTA-TTTTTTAATTAAAT-
1 TATTATTTTTTTAA-TAAATG
322076 TCA-TATTTTTATTGAATACAA-G
1 T-ATTATTTTT-TT-AATA-AATG
*
322098 TAATATTTTTTTAATAAATG
1 TATTATTTTTTTAATAAATG
322118 TATTATTTT
1 TATTATTTT
322127 AGATCAGATC
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
19 5 0.12
20 18 0.43
21 7 0.17
22 12 0.29
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTATTTTTTTAATAAATG
Found at i:322621 original size:20 final size:21
Alignment explanation
Indices: 322591--322629 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
322581 ATTACATGTA
322591 CAAATATGACAAAACCGGTCC
1 CAAATATGACAAAACCGGTCC
322612 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
322630 AAAACGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCC
Found at i:323010 original size:183 final size:181
Alignment explanation
Indices: 322577--323903 Score: 1371
Period size: 183 Copynumber: 7.4 Consensus size: 181
322567 CGCTCCATAG
* * * * * *
322577 CAATATTACATGTACAAATATGACAAAACCGGTC-CCAAAATGACAAAACCGGTAAAACGCTACC
1 CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG-AAAACGCTACC
* * *
322641 GGATATATGTCG--AGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAATAGAA
65 GGATATAT-T-GAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAA
* * * *
322704 GAAGTTATAGCGCCTATAAAGTGTCAATACTTTAAAAAAAATATCGATCCACAA
128 GAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAAATATATCGATCCACAA
* *
322758 CAATATAACAAGTAAAAATATGATAAAACTA-GTCTCAAAAATGACAAAACCGGAAAAAGTTACC
1 CAATATAACAAGTAAAAATATGATAAAAC-AGGTCTCAAAAATGACAAAACCGGAAAACGCTACC
*
322822 GGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAAAAGA
65 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGA
* * * * ** *
322887 AGTTATAGCGCCTAAAAAAATGTCGACACTTTACGAAAATGTATTGATCCTTAC
130 AGTTATAGCGCCT-AAAAAGTGTCGACACTTTA-AAAAATATATCGATCCACAA
* * * *
322941 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTATCG
1 CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAACGCTACCG
* *
323006 GATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAA-A
66 GATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA-AAAGA
* * * * * *
323070 AATTATTGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAA
130 AGTTATAGCGCCTAAAAAGTGTCGACACTTTA-AAAAATATATCGATCCACAA
* * * * *
323123 CAATATAACATGTAAAAATATAATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACT
1 CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAACGCTACC
* * * *
323188 GAATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAATA
65 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGA
* * *
323253 AGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATATATCGATCAACAA
130 AGTTATAGCGCCTAAAAAGTGTCGACACTTT-AAAAAATATATCGATCCACAA
* ** * * * *
323306 CAATATAACAAGTAAAAATATGATAAAACAGGTCCCAAATTTGACAAAATCAGTAAAACGATATC
1 CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAA-CCGGAAAACGCTACC
* * **
323371 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTATGAAATT-AAACTAAA-A
65 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGA
* * * * * * * *
323434 AG-TGT--CG-----ACACT-T---TA--TGAAAATATATCGATCCAT-AACAA
130 AGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAAATAT--ATCGATCCACAA
* * * ** * * * *
323473 -TATAA--CAGGTAAAAATATGATAAAATTGTTCTCAAAAATGACAAAATCGGAAAAAGTTACCG
1 CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAACGCTACCG
* * *
323535 GATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACATTTTCTGAATTTAAAAGAGAAGAA
66 GATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGAA
* * * * *** *
323600 GTTATAGTGCTTAAAAAGTGTCGACACTTTATTAAAATGTATCGATCTTTAC
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTA-AAAAATATATCGATCCACAA
* * *
323652 CAATATAACATA-TAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGAAAAAAGTTACC
1 CAATATAACA-AGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAACGCTACC
* * *
323716 GGATATGTTGAAAGTGTCGAAAATTTAATATAAGTATCGACACTTTATGAATTTAAAAGAAAAGA
65 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGA
* * * * *
323781 AGTTATAGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCAATCCAGAA
130 AGTTATAGCGCCTAAAAAGTGTCGACACTTTA-AAAAATATATCGATCCACAA
* * * *
323834 CAATATAGCAGGTAAAAATATGATAAAATC-GATCTC-AAAATGACAAAACCGGTAAATA-GATA
1 CAATATAACAAGTAAAAATATGATAAAA-CAGGTCTCAAAAATGACAAAACCGG-AAA-ACGCTA
323896 CCGGATAT
63 CCGGATAT
323904 GTTAATCCAG
Statistics
Matches: 965, Mismatches: 141, Indels: 79
0.81 0.12 0.07
Matches are distributed among these distances:
163 59 0.06
164 39 0.04
165 3 0.00
166 13 0.01
167 6 0.01
168 6 0.01
169 2 0.00
172 1 0.00
173 6 0.01
174 1 0.00
177 1 0.00
178 7 0.01
179 4 0.00
180 11 0.01
181 125 0.13
182 321 0.33
183 355 0.37
184 5 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (181 bp):
CAATATAACAAGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAACGCTACCG
GATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAAAAGAA
GTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAAATATATCGATCCACAA
Found at i:323743 original size:182 final size:181
Alignment explanation
Indices: 323429--323906 Score: 688
Period size: 182 Copynumber: 2.6 Consensus size: 181
323419 GAAATTAAAC
*
323429 TAAAAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * * * * *
323494 AAAATTGTTCTCAAAAATGACAAAATCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATT
66 AAAA-CGATCTCAAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGAAAATT
* * * * *
323559 TAATATTAGTATCGACATTTTCTGAATTTAAAAGAGAAGAAGTTATAGTGCT
130 TAATATAAGTATCGACACTTTATGAATTTAAAAGAAAAGAAGTTATAGCGCT
* ** * **
323611 TAAAAAGTGTCGACACTTTATTAAAATGTATCGATCTTTACCAATATAACATATAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
*
323676 AAAACAGGTCTCAAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGAAAATT
66 AAAAC-GATCTCAAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGAAAATT
323741 TAATATAAGTATCGACACTTTATGAATTTAAAAGAAAAGAAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTATGAATTTAAAAGAAAAGAAGTTATAGCGCT
* * *
323793 TAAAAAGTGTCGACACTTTATGAAAATGTATCAATCCAGAACAATATAGCAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * *
323858 AAAATCGATCTC-AAAATGACAAAACCGGTAAATAGATACCGGATATGTT
66 AAAA-CGATCTCAAAAATGACAAAACC-GAAAAAAGTTACCGGATATGTT
323907 AATCCAGAAT
Statistics
Matches: 262, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
181 14 0.05
182 247 0.94
183 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (181 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
AAAACGATCTCAAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGAAAATTT
AATATAAGTATCGACACTTTATGAATTTAAAAGAAAAGAAGTTATAGCGCT
Found at i:324342 original size:15 final size:15
Alignment explanation
Indices: 324322--324379 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
324312 TTTCTCAAAT
324322 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
324337 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
324352 CTCTTCTCAACCACAAC
1 CTCTTCTCAACC-C-AC
324369 CTCCTTCTCAA
1 CT-CTTCTCAA
324380 ACAATCGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 24 0.67
16 1 0.03
17 3 0.08
18 8 0.22
ACGTcount: A:0.22, C:0.50, G:0.02, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:326972 original size:21 final size:21
Alignment explanation
Indices: 326948--326993 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
326938 ACAAAATGTA
326948 TCGACACTA-ATAAAACAAGTG
1 TCGACA-TATATAAAACAAGTG
* *
326969 TCGATATATTTAAAACAAGTG
1 TCGACATATATAAAACAAGTG
326990 TCGA
1 TCGA
326994 TCCCAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (21 bp):
TCGACATATATAAAACAAGTG
Found at i:327506 original size:199 final size:199
Alignment explanation
Indices: 326964--327821 Score: 1151
Period size: 199 Copynumber: 4.3 Consensus size: 199
326954 CTAATAAAAC
* * * *
326964 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCAAAAAACATAATTGTAATGTAA
1 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
* * * *
327029 TAGGTAAATTATTC-ATGTAAAAGGTCTAAATATACTGGTTTTTGAGAAAACATGTGTACAAAAA
66 TAGGTAAATTA-TCAATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAA
*
327093 GTATCGACACAAATCTAACAAGTGTCGATACTTTT-TCTCAGAACTGTATTTCAAAACCAAGTGC
130 GTATCGACACAAATATAACAAGTGTCGATACTTTTGTC-CAGAACTGTATTTCAAAACCAAGTGC
327157 ACTAAA
194 ACTAAA
* * *
327163 AAGTGTCGATACATATATAACAAGTGTCGATTCCAAAAAACATCGAAAACCATAATTATAATGTA
1 AAGTGTCGATACATTTATAACAAGTGTCGA-TCCCAAAAACATCGAAAAACATAATTATAATGTA
* * * * * * *
327228 ATAGGCAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACA
65 ATAGGTAAATTATCAATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAA
* *
327293 GTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAA-TGTATTTCAGAACCAAGTGC
130 GTATCGACACAAATATAACAAGTGTCGATACTTTT-GTCCAGAACTGTATTTCAAAACCAAGTGC
327357 AC-ATAA
194 ACTA-AA
* * * *
327363 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCGAAAACATTGAAAAACATAATTATAATGTAA
1 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
327428 TAGGTAAATTATTC-ATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAA
66 TAGGTAAATTA-TCAATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAA
* *
327492 GTATCGACACAAATATAACAAGTATCGATACTTTTTCTCCAGAA-TGTATTTCAAAACCAAGTGC
130 GTATCGACACAAATATAACAAGTGTCGATAC-TTTTGTCCAGAACTGTATTTCAAAACCAAGTGC
327556 ACTAAA
194 ACTAAA
327562 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCG-AAAACTATAATTATAATGTA
1 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAAC-ATAATTATAATGTA
* * * * **
327626 ATAGGTAAATTAACAATG-GAACTGGTCTAAATGTACCGGTTTATGAGAAAACAAGTATACATGA
65 ATAGGTAAATTATCAATGTAAAC-GGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAA
* * * * * * *
327690 AGTATCGACATAAATACATCAAGTTTTGATACATTTTGTCCA-AACTATATTTTAAAAACCAAGT
129 AGTATCGACACAAATATAACAAGTGTCGATAC-TTTTGTCCAGAACTGTA-TTTCAAAACCAAGT
327754 GCAC-AATA
192 GCACTAA-A
* * *
327762 AAGTTTCGATACATTTATAACAATTGTCGATCCCCAAAACATCGAAAAACATAATTATAA
1 AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAA
327822 CCAAATGTCT
Statistics
Matches: 586, Mismatches: 58, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
198 11 0.02
199 320 0.55
200 243 0.41
201 10 0.02
202 2 0.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (199 bp):
AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
TAGGTAAATTATCAATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAAG
TATCGACACAAATATAACAAGTGTCGATACTTTTGTCCAGAACTGTATTTCAAAACCAAGTGCAC
TAAA
Found at i:327752 original size:399 final size:399
Alignment explanation
Indices: 326964--327821 Score: 1296
Period size: 399 Copynumber: 2.2 Consensus size: 399
326954 CTAATAAAAC
* *
326964 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCAAAAAACATAATTGTAATGTAA
1 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
* * *
327029 TAGGTAAATTATTCATGTAAAAGGTCTAAATATACTGGTTTTTGAGAAAACATGTGTACAAAAAG
66 TAGGTAAATTATTCATGTAAAAGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAAG
* *
327094 TATCGACACAAATCTAACAAGTGTCGATACTTTTTCTCAGAACTGTATTTCAAAACCAAGTGCAC
131 TATCGACACAAATATAACAAGTATCGATACTTTTTCTCAGAACTGTATTTCAAAACCAAGTGCAC
327159 TAAAAAGTGTCGATACATATATAACAAGTGTCGATTCCAAAAAACATCGAAAACCATAATTATAA
196 TAAAAAGTGTCGATACATATATAACAAGTGTCGATTCCAAAAAACATCGAAAACCATAATTATAA
* * * * *
327224 TGTAATAGGCAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACA
261 TGTAATAGGCAAATTAACAATAGAACCGGTCTAAATATACCGGTTTATGAGAAAACAAGTATACA
* * * *
327289 AACAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGAACCAAG
326 AACAGTATCGACACAAATACAACAAGTGTCGATACTTTTGGTCCAGAATATATTTAAAAACCAAG
327354 TGCAC-ATAA
391 TGCACAAT-A
* *
327363 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCGAAAACATTGAAAAACATAATTATAATGTAA
1 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
*
327428 TAGGTAAATTATTCATGTAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAAG
66 TAGGTAAATTATTCATGTAAAAGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAAG
327493 TATCGACACAAATATAACAAGTATCGATACTTTTTCTCCAGAA-TGTATTTCAAAACCAAGTGCA
131 TATCGACACAAATATAACAAGTATCGATACTTTTTCT-CAGAACTGTATTTCAAAACCAAGTGCA
* * *
327557 CTAAAAAGTGTCGATACATTTATAACAAGTGTCGA-TCCCAAAAACATCGAAAACTATAATTATA
195 CTAAAAAGTGTCGATACATATATAACAAGTGTCGATTCCAAAAAACATCGAAAACCATAATTATA
* * * *
327621 ATGTAATAGGTAAATTAACAATGGAACTGGTCTAAATGTACCGGTTTATGAGAAAACAAGTATAC
260 ATGTAATAGGCAAATTAACAATAGAACCGGTCTAAATATACCGGTTTATGAGAAAACAAGTATAC
* * * * *
327686 ATGA-AGTATCGACATAAATACATCAAGTTTTGATACATTTT-GTCCA-AACTATATTTTAAAAA
325 A-AACAGTATCGACACAAATACAACAAGTGTCGATAC-TTTTGGTCCAGAA-TATA-TTTAAAAA
327748 CCAAGTGCACAATA
386 CCAAGTGCACAATA
* * * * *
327762 AAGTTTCGATACATTTATAACAATTGTCGATCCCCAAAACATCGAAAAACATAATTATAA
1 AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAA
327822 CCAAATGTCT
Statistics
Matches: 416, Mismatches: 37, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
397 2 0.00
398 119 0.29
399 288 0.69
400 7 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (399 bp):
AAGTGTCGATATATTTAAAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAA
TAGGTAAATTATTCATGTAAAAGGTCTAAATATACCGGTTTTTGAGAAAACAAGTATACAAAAAG
TATCGACACAAATATAACAAGTATCGATACTTTTTCTCAGAACTGTATTTCAAAACCAAGTGCAC
TAAAAAGTGTCGATACATATATAACAAGTGTCGATTCCAAAAAACATCGAAAACCATAATTATAA
TGTAATAGGCAAATTAACAATAGAACCGGTCTAAATATACCGGTTTATGAGAAAACAAGTATACA
AACAGTATCGACACAAATACAACAAGTGTCGATACTTTTGGTCCAGAATATATTTAAAAACCAAG
TGCACAATA
Found at i:328468 original size:18 final size:18
Alignment explanation
Indices: 328445--328480 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
328435 AAATGTCCTA
328445 TTTCAATGTTGTTGCCTC
1 TTTCAATGTTGTTGCCTC
328463 TTTCAATGTTGTTGCCTC
1 TTTCAATGTTGTTGCCTC
328481 ATCGATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTCAATGTTGTTGCCTC
Found at i:329984 original size:23 final size:23
Alignment explanation
Indices: 329934--329978 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
329924 TGCCTATTTT
* *
329934 ATTATATAAACGCTACTTATTAC
1 ATTATATAAACGCTACCTAATAC
*
329957 ATTATATAAGCGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
329979 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Done.