Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006419.1 Hibiscus syriacus cultivar Beakdansim tig00015486_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: 137293
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2580 original size:13 final size:14
Alignment explanation
Indices: 2557--2586 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2547 TTCCCATTAC
2557 AGACGTGCATATGA
1 AGACGTGCATATGA
2571 AGAC-TGCATATGA
1 AGACGTGCATATGA
2584 AGA
1 AGA
2587 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:3168 original size:19 final size:20
Alignment explanation
Indices: 3127--3176 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3117 TAATCAAATT
3127 AAAAATTAAAATGAAACCAA
1 AAAAATTAAAATGAAACCAA
3147 AAAAATTAAAATGAAACC-A
1 AAAAATTAAAATGAAACCAA
3166 AAAAATTAAAA
1 AAAAATTAAAA
3177 CAAACCAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (20 bp):
AAAAATTAAAATGAAACCAA
Found at i:5409 original size:22 final size:22
Alignment explanation
Indices: 5382--5426 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5372 TTGCCAATGG
*
5382 TTTTTCTGCTCGAAACGTTTTT
1 TTTTTCTGCTCGAAACGTATTT
* *
5404 TTTTTCTGTTCGAATCGTATTT
1 TTTTTCTGCTCGAAACGTATTT
5426 T
1 T
5427 CTGCTTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (22 bp):
TTTTTCTGCTCGAAACGTATTT
Found at i:6341 original size:36 final size:36
Alignment explanation
Indices: 6110--6705 Score: 448
Period size: 36 Copynumber: 15.9 Consensus size: 36
6100 GATCGATTTA
* *
6110 CTTCACTACTCTTTGGTGAATGCTTAAGATGGATTTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGA-TTG
* *
6147 CTTCACTACTCTTTGGTGAAGGATTAAGATGGATTTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGA-TTG
* *
6184 CTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGA--TTG
* * *
6222 CTTCACTACTCTTTGGTGAAGGCTTAAGATGGCTCG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
**** * * * * *
6258 GAGGACTTAATCATCATGCTCGGAAGGCTTACTGATTGATTTG
1 CTTCAC-TACTCTTC--GGT--GAAGGCTTA-AGATGGA-TTG
*
6301 CTTCACTACTCTTCGGTAAAGGCTTAAGATGGATTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
* ** *
6337 CTTCACTCCTCTTCGGTGAAGGCTTAAGATTGCCTGGGG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGA-TGGAT--TG
* *
6376 ACTT-AAT-CATCATGCTCGG-G-AGGCTTACTGATGGATTTG
1 -CTTCACTAC-TC-T--TCGGTGAAGGCTTA-AGATGGA-TTG
* * *
6415 CTTCACTACTCTTCTGTGAAGGCTTAAAATGGATTA
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
* * * *
6451 CTTCACTCCTCTTCGGTGAAGGCTTAAGATTGCTCG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
**** * *
6487 GAGGACTTAATCATCATGCTCGG-G-AGGCTTACTGATGGATTTT
1 CTTCAC-T-A-C-TC-T--TCGGTGAAGGCTTA-AGATGGA-TTG
*
6530 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
* * *
6566 CTTCACTACTCTTCGATGAAGGCTTAGGATGGATTT
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
* * * *
6602 CTTTACTACTCTTCGGTGAAGGCTTAGGATTGTTTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
*
6638 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
*
6674 CTTCACTACTCTTCGGTGAAGGCTTAGGATGG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGG
6706 CCCGGAGGAC
Statistics
Matches: 445, Mismatches: 81, Indels: 67
0.75 0.14 0.11
Matches are distributed among these distances:
36 202 0.45
37 93 0.21
38 63 0.14
39 15 0.03
40 19 0.04
41 22 0.05
42 20 0.04
43 11 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (36 bp):
CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
Found at i:6542 original size:115 final size:115
Alignment explanation
Indices: 6174--6795 Score: 782
Period size: 115 Copynumber: 5.5 Consensus size: 115
6164 GAAGGATTAA
* *
6174 GATGGATTTGCTTCACTACTCTT-TGGTGAAGGCTTAAGATTGATTTTGCTTCACTACTCTTTGG
1 GATGGATTTGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGGA--TTGCTTCACTACTCTTCGG
*
6238 TGAAGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACT
63 TGAAGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACT
* * * *
6291 GATTGATTTGCTTCACTACTCTTCGGTAAAGGCTTAAGATGGATTGCTTCACTCCTCTTCGGTGA
1 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTGA
*
6356 AGGCTTAAGATTGC-CTGG-GGACTTAATCATCATGCTCGGGAGGCTTACT
66 AGGCTTAAGATGGCTC-GGAGGACTTAATCATCATGCTCGGGAGGCTTACT
* * *
6405 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAATGGATTACTTCACTCCTCTTCGGTGA
1 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTGA
*
6470 AGGCTTAAGATTGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACT
66 AGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACT
* *
6520 GATGGATTTTCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGATGA
1 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTGA
* * ****** *
6585 AGGCTTAGGATGGATTTCTTTAC-T-A-C-TC-T--TCGGTGAAGGCTTA-G
66 AGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGG-G-AGGCTTACT
* * *
6629 GATTG-TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGA
1 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTGA
* * * * * *
6693 AGGCTTAGGATGGCCCGGAGGACTTAATTACCATGCTCAGAAGGCTTACT
66 AGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACT
* * * *
6743 GATGGATTTGCTTCACTACTCTCCAGTGAAGGCTTCAGATGGTTTGCTTCACT
1 GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACT
6796 CTCAACATGA
Statistics
Matches: 440, Mismatches: 50, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
108 74 0.17
109 6 0.01
110 9 0.02
111 2 0.00
112 2 0.00
113 9 0.02
114 112 0.25
115 188 0.43
117 38 0.09
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (115 bp):
GATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTGA
AGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACT
Found at i:6740 original size:223 final size:224
Alignment explanation
Indices: 6110--6795 Score: 878
Period size: 223 Copynumber: 3.0 Consensus size: 224
6100 GATCGATTTA
* * * * *
6110 CTTCACTACTCTTTGGTGAATGCTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGATTAAG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTT-CTTTACTACTCTTCGGTGAAGGCTTAAG
* * *
6175 ATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTTGCTTCACTACTCTTTGGTG
65 ATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TG-GTTTGCTTCACTACTCTTCGGTG
*
6240 AAGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATTGATTTGCTTC
128 AAGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTC
* *
6305 ACTACTCTTCGGTAAAGGCTTAAGATGGATTG
193 ACTACTCTTCAGTGAAGGCTTAAGATGGATTG
* **** *
6337 CTTCACTCCTCTTCGGTGAAGGCTTAAGATTGCCTGGGGAC-TTAAT-CATCATGCTCGG-G-AG
1 CTTCACTACTCTTCGGTGAAGGCTTAAGA-TG---GATTTCTTTACTAC-TC-T--TCGGTGAAG
* * * * * *
6398 GCTTACTGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAATGGATTACTTCACTCCTCT
58 GCTTA-AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTACTCT
* *
6463 TCGGTGAAGGCTTAAGATTGCTCGGAGGACTTAATCATCATGCTCGGGAGGCTTACTGATGGATT
122 TCGGTGAAGGCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATT
* *
6528 TTCTTCACTACTCTTCTGTGAAGGCTTAAGATGGATTG
187 TGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGATTG
* * *
6566 CTTCACTACTCTTCGATGAAGGCTTAGGATGGATTTCTTTACTACTCTTCGGTGAAGGCTTAGGA
1 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTTCTTTACTACTCTTCGGTGAAGGCTTAAGA
*
6631 TTG-TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGAAG
66 TGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGAAG
* * * * *
6695 GCTTAGGATGGCCCGGAGGACTTAATTACCATGCTCAGAAGGCTTACTGATGGATTTGCTTCACT
131 GCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACT
* * *
6760 ACTCTCCAGTGAAGGCTTCAGATGGTTTG
196 ACTCTTCAGTGAAGGCTTAAGATGGATTG
6789 CTTCACT
1 CTTCACT
6796 CTCAACATGA
Statistics
Matches: 393, Mismatches: 53, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
223 149 0.38
224 5 0.01
225 10 0.03
226 6 0.02
227 27 0.07
228 5 0.01
229 140 0.36
230 10 0.03
231 38 0.10
232 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (224 bp):
CTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTTCTTTACTACTCTTCGGTGAAGGCTTAAGA
TGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGAAG
GCTTAAGATGGCTCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACT
ACTCTTCAGTGAAGGCTTAAGATGGATTG
Found at i:11858 original size:21 final size:21
Alignment explanation
Indices: 11832--11875 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11822 TTGCCAATGG
*
11832 TTTTTCTGCTCGAAACGTTTT
1 TTTTTCTGCTCGAAACATTTT
* *
11853 TTTTTCTGTTCGAATCATTTT
1 TTTTTCTGCTCGAAACATTTT
11874 TT
1 TT
11876 CTGCTTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTTCTGCTCGAAACATTTT
Found at i:13186 original size:18 final size:18
Alignment explanation
Indices: 13160--13205 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
13150 TTTATATATT
* *
13160 TTAACTTAAATTCACATA
1 TTAAATTAAAATCACATA
*
13178 TTAAATTAAAATCACATC
1 TTAAATTAAAATCACATA
13196 TTAACATTAA
1 TTAA-ATTAA
13206 TTTTCTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAATTAAAATCACATA
Found at i:13284 original size:29 final size:30
Alignment explanation
Indices: 13214--13284 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
13204 AATTTTCTTG
* * *
13214 TTTTTATTTTAAATTATTAAATCTATTTTA
1 TTTTTATTTTAAACTATAAAATATATTTTA
* * * *
13244 TTCTTGTCTTAACCTA-AAAATATATTTTA
1 TTTTTATTTTAAACTATAAAATATATTTTA
13273 TTTTTATTTTAA
1 TTTTTATTTTAA
13285 TCTTATCTTA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTTTATTTTAAACTATAAAATATATTTTA
Found at i:23260 original size:2 final size:2
Alignment explanation
Indices: 23253--23282 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23243 TTGTTAATGA
23253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23283 TAAGCGTAAA
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):
AT
Found at i:24074 original size:23 final size:23
Alignment explanation
Indices: 24043--24096 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
24033 GTTCATGTTC
* *
24043 GTTCATTTAATGTTCACGAACGT
1 GTTCGTTTAATGTTCACGAACAT
*
24066 GTTCGTTTAATGTTCATGAACAT
1 GTTCGTTTAATGTTCACGAACAT
*
24089 GTTTGTTT
1 GTTCGTTT
24097 GGCGTTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (23 bp):
GTTCGTTTAATGTTCACGAACAT
Found at i:24095 original size:27 final size:27
Alignment explanation
Indices: 24036--24095 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 27
24026 TGAACGTGTT
*
24036 CATGTTCGTTCATTTAATGTTCACGAA
1 CATGTTTGTTCATTTAATGTTCACGAA
* *
24063 C--G--TGTTCGTTTAATGTTCATGAA
1 CATGTTTGTTCATTTAATGTTCACGAA
24086 CATGTTTGTT
1 CATGTTTGTT
24096 TGGCGTTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
23 19 0.73
25 2 0.08
27 5 0.19
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (27 bp):
CATGTTTGTTCATTTAATGTTCACGAA
Found at i:24138 original size:34 final size:34
Alignment explanation
Indices: 24065--24150 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
24055 TTCACGAACG
* * ** **
24065 TGTTCGTTTAATGTTCATGAACATGTTTGTTTGG
1 TGTTCGTTTAACGTTCATGAACATATTCATTTAA
*
24099 CGTTCGTTTAACGTTCATGAACATATTCATTTAA
1 TGTTCGTTTAACGTTCATGAACATATTCATTTAA
*
24133 TGTTCGTTTAGCGTTCAT
1 TGTTCGTTTAACGTTCAT
24151 TTAACATCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (34 bp):
TGTTCGTTTAACGTTCATGAACATATTCATTTAA
Found at i:25845 original size:18 final size:19
Alignment explanation
Indices: 25822--25857 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25812 TGTATTGGAG
*
25822 CTCTT-AAACTTGCTTCTT
1 CTCTTAAAACTTCCTTCTT
25840 CTCTTAAAACTTCCTTCT
1 CTCTTAAAACTTCCTTCT
25858 GTGTTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (19 bp):
CTCTTAAAACTTCCTTCTT
Found at i:30145 original size:35 final size:35
Alignment explanation
Indices: 30106--30188 Score: 166
Period size: 35 Copynumber: 2.4 Consensus size: 35
30096 TGTTAATATA
30106 TTTGTATTTCAGTTTGAGATGTTCTGTTTTTATTT
1 TTTGTATTTCAGTTTGAGATGTTCTGTTTTTATTT
30141 TTTGTATTTCAGTTTGAGATGTTCTGTTTTTATTT
1 TTTGTATTTCAGTTTGAGATGTTCTGTTTTTATTT
30176 TTTGTATTTCAGT
1 TTTGTATTTCAGT
30189 CACATTTGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (35 bp):
TTTGTATTTCAGTTTGAGATGTTCTGTTTTTATTT
Found at i:33048 original size:3 final size:3
Alignment explanation
Indices: 33040--33098 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
33030 GATTCATAGG
* *
33040 AGA AGA AGA AGA TGA AGA AGA AGA AGA TGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
33088 AGA AGA AGA AG
1 AGA AGA AGA AG
33099 GTTTTGCTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:44138 original size:21 final size:21
Alignment explanation
Indices: 44113--44166 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
44103 CAATCCACTC
44113 GAAATCCCTAACTCATCCAGA
1 GAAATCCCTAACTCATCCAGA
44134 GAAATCCCTAACTCATCCAGA
1 GAAATCCCTAACTCATCCAGA
44155 GAAATCCCTAAC
1 GAAATCCCTAAC
44167 ATTTCCCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (21 bp):
GAAATCCCTAACTCATCCAGA
Found at i:49868 original size:40 final size:42
Alignment explanation
Indices: 49813--49891 Score: 135
Period size: 40 Copynumber: 1.9 Consensus size: 42
49803 GAGAATAAAA
49813 AACTAAAATTAACAAAGAAATAG-A-GGGGAAAAAAGAGTAT
1 AACTAAAATTAACAAAGAAATAGAACGGGGAAAAAAGAGTAT
*
49853 AACTAAAATTAACAAAGAAGTAGAACGGGGAAAAAAGAG
1 AACTAAAATTAACAAAGAAATAGAACGGGGAAAAAAGAG
49892 AAAAGGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 22 0.61
41 1 0.03
42 13 0.36
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.13
Consensus pattern (42 bp):
AACTAAAATTAACAAAGAAATAGAACGGGGAAAAAAGAGTAT
Found at i:51262 original size:60 final size:60
Alignment explanation
Indices: 51217--51352 Score: 213
Period size: 60 Copynumber: 2.3 Consensus size: 60
51207 TGGGTCGCTT
* *
51217 TGGTTATAACCAGGGTTTGGAATACAATAAAAACATAATATTTTT-CAGCTGGTTATAACC
1 TGGTTATAACCAGGGTTTGGAATACAATAAAAACAGAATATTTTTCCAGATGG-TATAACC
*
51277 TGGTTATAACCAGGGTTTGGAATACAATAAAAACAGAATATTTTT-CAGCTGGTTATAACC
1 TGGTTATAACCAGGGTTTGGAATACAATAAAAACAGAATATTTTTCCAGATGG-TATAACC
51337 TGGTTATAACCAGGGT
1 TGGTTATAACCAGGGT
51353 CTTGTATACC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (60 bp):
TGGTTATAACCAGGGTTTGGAATACAATAAAAACAGAATATTTTTCCAGATGGTATAACC
Found at i:55065 original size:15 final size:15
Alignment explanation
Indices: 55038--55089 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
55028 ATATTTAGCT
* *
55038 GGGCGGGCGGATGTG
1 GGGCGGGCAGATGCG
*
55053 GGGTGGGCAGATGCG
1 GGGCGGGCAGATGCG
55068 GGGCGGGCAGATGCG
1 GGGCGGGCAGATGCG
55083 GGGCGGG
1 GGGCGGG
55090 TAATGTCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.10, C:0.15, G:0.65, T:0.10
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:57500 original size:26 final size:26
Alignment explanation
Indices: 57447--57524 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
57437 AATGACTTAA
57447 AAAAATAAATAAAAAAGATAAAACAAAC
1 AAAAA-AAATAAAAAAGAT-AAACAAAC
*
57475 AAAAAAAATAAAATAAGAT-AATAAAC
1 AAAAAAAATAAAA-AAGATAAACAAAC
* *
57501 AAATAAAATAAACAA-ATAAACAAA
1 AAAAAAAATAAAAAAGATAAACAAA
57525 TTAGAAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.05
25 7 0.16
26 17 0.39
27 8 0.18
28 10 0.23
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.13
Consensus pattern (26 bp):
AAAAAAAATAAAAAAGATAAACAAAC
Found at i:57510 original size:13 final size:13
Alignment explanation
Indices: 57444--57520 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
57434 ATAAATGACT
*
57444 TAAAAAAAT-AAA
1 TAAACAAATAAAA
*
57456 TAAAAAAGATAAAA
1 TAAACAA-ATAAAA
* *
57470 CAAACAAAAAAAA
1 TAAACAAATAAAA
* *
57483 TAAA-ATAAGATAA
1 TAAACA-AATAAAA
57496 TAAACAAATAAAA
1 TAAACAAATAAAA
57509 TAAACAAATAAA
1 TAAACAAATAAA
57521 CAAATTAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
12 8 0.15
13 36 0.68
14 9 0.17
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (13 bp):
TAAACAAATAAAA
Found at i:57521 original size:21 final size:21
Alignment explanation
Indices: 57444--57525 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
57434 ATAAATGACT
* *
57444 TAAAA-AAATAAATAAAAAAGA
1 TAAAATAAACAAATAAACAA-A
*
57465 TAAAACAAAC-AA-AAA-AAA
1 TAAAATAAACAAATAAACAAA
*
57483 TAAAATAAGA-TAATAAACAAA
1 TAAAATAA-ACAAATAAACAAA
57504 TAAAATAAACAAATAAACAAA
1 TAAAATAAACAAATAAACAAA
57525 T
1 T
57526 TAGAAAAACC
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 8 0.15
19 5 0.10
20 7 0.13
21 29 0.56
22 3 0.06
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (21 bp):
TAAAATAAACAAATAAACAAA
Found at i:57534 original size:21 final size:22
Alignment explanation
Indices: 57494--57539 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
57484 AAAATAAGAT
57494 AATAAACAAATAAAATAAA-CA
1 AATAAACAAATAAAATAAACCA
*
57515 AATAAACAAATTAGAA-AAACCA
1 AATAAACAAA-TAAAATAAACCA
57537 AAT
1 AAT
57540 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AATAAACAAATAAAATAAACCA
Found at i:58008 original size:18 final size:18
Alignment explanation
Indices: 57978--58042 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
57968 TACATACATA
*
57978 AATAAAAAAAATAGTAAT
1 AATAAAAATAATAGTAAT
* *
57996 AATAGAAATAATAAG-GAT
1 AATAAAAATAAT-AGTAAT
* * *
58014 AATATAAAGAATAATAAT
1 AATAAAAATAATAGTAAT
58032 AATAAAAATAA
1 AATAAAAATAA
58043 AAATGGTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 1 0.03
18 33 0.92
19 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AATAAAAATAATAGTAAT
Found at i:58104 original size:3 final size:3
Alignment explanation
Indices: 58096--58138 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
58086 ATATATACAT
*
58096 ATA ATA ATA ATA ATA ACA ATA ATA ATA TATA TATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA A
58139 AACGTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:58135 original size:18 final size:17
Alignment explanation
Indices: 58075--58152 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 17
58065 GAAATAAGTA
58075 AATATATACAT-ATATAT
1 AATATATA-ATAATATAT
58092 ACATATAATAATAATA-AT
1 A-ATAT-ATAATAATATAT
*
58110 AACA-ATAATAATATAT
1 AATATATAATAATATAT
* **
58126 ATATATATAATAAAACGT
1 A-ATATATAATAATATAT
58144 AATATATAA
1 AATATATAA
58153 AAAAAAGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 13 0.26
18 19 0.38
19 6 0.12
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (17 bp):
AATATATAATAATATAT
Found at i:59195 original size:15 final size:15
Alignment explanation
Indices: 59175--59204 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59165 ATAATTGTAC
*
59175 AATATATATATATAT
1 AATATAAATATATAT
59190 AATATAAATATATAT
1 AATATAAATATATAT
59205 GTTTATTTCA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAAATATATAT
Found at i:60064 original size:105 final size:105
Alignment explanation
Indices: 59644--60412 Score: 1322
Period size: 106 Copynumber: 7.3 Consensus size: 105
59634 CTATCTTGAG
* * * *
59644 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCC
59709 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * *
59750 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCC
*
59815 CTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * * * *
59856 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTATTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCC
59921 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
59962 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
60027 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
60067 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
60132 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
60172 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCC
*
60237 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
60278 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
*
60343 TTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
60383 TCCTTCGTTATGAAGTTGAAATTGGCTCTG
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTG
60413 GGTAAAACCT
Statistics
Matches: 640, Mismatches: 22, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
105 296 0.46
106 344 0.54
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
Found at i:60222 original size:316 final size:317
Alignment explanation
Indices: 59644--60412 Score: 1369
Period size: 316 Copynumber: 2.4 Consensus size: 317
59634 CTATCTTGAG
* * *
59644 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCC
*
59709 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* *
59774 GCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCG
130 GCTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCG
* *
59839 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTATTTG
195 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTG
*
59904 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
260 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
59962 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
60027 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
* *
60092 CTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGT
* *
60156 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGT
196 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGT
60221 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
261 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
60278 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
* *
60343 TTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
60408 CTCTG
131 CTCTG
60413 GGTAAAACCT
Statistics
Matches: 433, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
316 294 0.68
317 101 0.23
318 38 0.09
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (317 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
CTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGT
TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGT
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
Found at i:71699 original size:21 final size:21
Alignment explanation
Indices: 71675--71758 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
71665 ATAAATGACT
*
71675 TAAAA-AAATAAATAAAAAAGA
1 TAAAATAAACAAATAAAAAA-A
* *
71696 TAAAACAAACAAA-AATAAAA
1 TAAAATAAACAAATAAAAAAA
* *
71716 TAAAATAAGA-TAATAAACAAA
1 TAAAATAA-ACAAATAAAAAAA
*
71737 TAAAATAAACAAATAAACAAA
1 TAAAATAAACAAATAAAAAAA
71758 T
1 T
71759 TAGAAAAACC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 11 0.21
21 35 0.67
22 6 0.12
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.15
Consensus pattern (21 bp):
TAAAATAAACAAATAAAAAAA
Found at i:71699 original size:30 final size:30
Alignment explanation
Indices: 71678--71745 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
71668 AATGACTTAA
71678 AAAAAT-AAATAAAA-AAGATAAAACAAAC
1 AAAAATAAAATAAAATAAGATAAAACAAAC
71706 AAAAATAAAATAAAATAAGATAATAAACAAA-
1 AAAAATAAAATAAAATAAGAT-A-AAACAAAC
*
71737 TAAAATAAA
1 AAAAATAAA
71746 CAAATAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
30 5 0.14
31 9 0.26
32 7 0.20
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (30 bp):
AAAAATAAAATAAAATAAGATAAAACAAAC
Found at i:71709 original size:28 final size:30
Alignment explanation
Indices: 71676--71745 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
71666 TAAATGACTT
71676 AAAAAAATAAATAAAA-AAGAT-A-AAACA
1 AAAAAAATAAATAAAATAAGATAATAAACA
71703 AACAAAAATAAAATAAAATAAGATAATAAACA
1 AA-AAAAAT-AAATAAAATAAGATAATAAACA
*
71735 AATAAAATAAA
1 AAAAAAATAAA
71746 CAAATAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 2 0.05
28 6 0.16
29 8 0.22
30 8 0.22
31 6 0.16
32 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.03, T:0.14
Consensus pattern (30 bp):
AAAAAAATAAATAAAATAAGATAATAAACA
Found at i:71717 original size:5 final size:5
Alignment explanation
Indices: 71679--71745 Score: 52
Period size: 5 Copynumber: 13.6 Consensus size: 5
71669 ATGACTTAAA
* * *
71679 AAAAT -AAAT AAAA- AAGAT AAAAC AAACA- AAAAT AAAAT AAAAT AAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT
71727 AATAA- ACAAAT AAAAT AAA
1 AA-AAT A-AAAT AAAAT AAA
71746 CAAATAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 8 0.16
5 38 0.76
6 4 0.08
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:71728 original size:15 final size:14
Alignment explanation
Indices: 71675--71745 Score: 62
Period size: 15 Copynumber: 5.3 Consensus size: 14
71665 ATAAATGACT
71675 TAAAAAA-AT-AAA
1 TAAAAAAGATAAAA
71687 TAAAAAAGATAAAA
1 TAAAAAAGATAAAA
* *
71701 CAAACAAAAATAAAA
1 TAAA-AAAGATAAAA
71716 TAAAATAAGAT--AA
1 TAAAA-AAGATAAAA
*
71729 TAAACAA-ATAAAA
1 TAAAAAAGATAAAA
71742 TAAA
1 TAAA
71746 CAAATAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.04
12 9 0.19
13 14 0.29
14 7 0.15
15 16 0.33
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.15
Consensus pattern (14 bp):
TAAAAAAGATAAAA
Found at i:71746 original size:13 final size:13
Alignment explanation
Indices: 71675--71753 Score: 63
Period size: 13 Copynumber: 5.9 Consensus size: 13
71665 ATAAATGACT
*
71675 TAAAAAAAT-AAA
1 TAAACAAATAAAA
*
71687 TAAAAAAGATAAAA
1 TAAACAA-ATAAAA
*
71701 CAAACAAAAATAAAA
1 TAAAC--AAATAAAA
* *
71716 TAAA-ATAAGATAA
1 TAAACA-AATAAAA
71729 TAAACAAATAAAA
1 TAAACAAATAAAA
71742 TAAACAAATAAA
1 TAAACAAATAAA
71754 CAAATTAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 8 0.15
13 28 0.52
14 7 0.13
15 9 0.17
16 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAACAAATAAAA
Found at i:71767 original size:21 final size:22
Alignment explanation
Indices: 71727--71772 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
71717 AAAATAAGAT
71727 AATAAACAAATAAAATAAA-CA
1 AATAAACAAATAAAATAAACCA
*
71748 AATAAACAAATTAGAA-AAACCA
1 AATAAACAAA-TAAAATAAACCA
71770 AAT
1 AAT
71773 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AATAAACAAATAAAATAAACCA
Found at i:72240 original size:18 final size:18
Alignment explanation
Indices: 72218--72267 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
72208 AAAAAATAGT
*
72218 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
72236 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
72254 AATAATAAAAATAA
1 AATAATAAAAATAA
72268 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:72367 original size:26 final size:25
Alignment explanation
Indices: 72300--72355 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
72290 GAAATAAGTA
72300 AATATATACATATATATATATATATAAT
1 AATA-ATA-ATATA-ATATATATATAAT
*
72328 AATAATAACAATAATATATATATAAT
1 AATAATAA-TATAATATATATATAAT
72354 AA
1 AA
72356 AACGTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 16 0.62
27 6 0.23
28 4 0.15
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAATAATATAATATATATATAAT
Found at i:73375 original size:3 final size:3
Alignment explanation
Indices: 73367--73391 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
73357 TATGTTAGTT
73367 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
73392 TGTACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:82666 original size:55 final size:55
Alignment explanation
Indices: 82590--82698 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
82580 CCCCCTGCAC
** * * * *
82590 CGCGCTATACGATGATTTGGCGTCACGTGGGGTATATCG-TGCCCCTGCACTGCGG
1 CGCGCTATACGATGAACTGGCGCCACGT-GGGTATAGCGCAGCCCCTGCAATGCGG
* *
82645 CGCGCTATACGGTGAACTGGCGCCATGTGGGTATAGCGCAGCCCCTGCAATGCG
1 CGCGCTATACGATGAACTGGCGCCACGTGGGTATAGCGCAGCCCCTGCAATGCG
82699 CTATACGCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
54 9 0.20
55 36 0.80
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (55 bp):
CGCGCTATACGATGAACTGGCGCCACGTGGGTATAGCGCAGCCCCTGCAATGCGG
Found at i:86991 original size:17 final size:18
Alignment explanation
Indices: 86969--87007 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
86959 AAAGGCGATG
*
86969 GCGGCATCATA-ATGGTT
1 GCGGCATCATATATGGCT
86986 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
87004 GCGG
1 GCGG
87008 TGGCTGCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:88711 original size:110 final size:111
Alignment explanation
Indices: 88512--88734 Score: 367
Period size: 110 Copynumber: 2.0 Consensus size: 111
88502 TAATTACAAA
* * * *
88512 ATTTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAAT
1 ATTTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAAT
* *
88577 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGAT
66 TAAATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGAT
*
88623 ATTTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAAT
1 ATTTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAAT
*
88687 TAAATTAAAATGTTAAAATATTACCGTATCAGCAAAGTGTAGAGAT
66 TAAATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGAT
88733 AT
1 AT
88735 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.66
111 35 0.34
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (111 bp):
ATTTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAAT
TAAATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGAT
Found at i:88872 original size:12 final size:10
Alignment explanation
Indices: 88858--88898 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
88848 ACCTTAAAAA
*
88858 GAGAGTATTT
1 GAGAGAATTT
88868 GAGAGAAATTT
1 GAGAG-AATTT
88879 -AGAGAATTT
1 GAGAGAATTT
88888 GAGAGAATTT
1 GAGAGAATTT
88898 G
1 G
88899 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:89110 original size:51 final size:49
Alignment explanation
Indices: 89019--89145 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 49
89009 AGATATATAT
* * **
89019 GTATAGCGCGCTGCAGGGGCCGCACTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCG-TGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
89069 GTATAGCGCAGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCATC
1 GTATAGCGC-GTGCAGGGGGCGCGCTATA-CCCACGTGGCGCCAAATCACC
*
89120 GTATAGCGCGGTGCAGGGGGTGCGCT
1 GTATAGCGC-GTGCAGGGGGCGCGCT
89146 TTACTACTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 25 0.37
51 43 0.63
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:89664 original size:130 final size:130
Alignment explanation
Indices: 89495--89885 Score: 732
Period size: 130 Copynumber: 3.0 Consensus size: 130
89485 TAACTGTTCT
89495 TCTGTTGTTCCGTTGACACACAC--GTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
1 TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
*
89558 ATTTGTTATTGTGTAGTTACTGGATTTATCTTGATTATGATATGGTATCATACCATTAACATGTA
66 ATTTGTTATTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
89623 TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
1 TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
* *
89688 ATTTGCTGTTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
66 ATTTGTTATTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
*
89753 TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGATT
1 TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
89818 ATTTGTTATTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
66 ATTTGTTATTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
89883 TCT
1 TCT
89886 CTTGAATGGT
Statistics
Matches: 255, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
128 23 0.09
130 232 0.91
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (130 bp):
TCTGTTGTTCCGTTGACACACACATGTTGAAAGGTAGCATTCCATGTCTGTCATGAGTTTGGGTT
ATTTGTTATTGTGTAGTTACTGGATTTATCTTAATTATGATATGGTATCATACCATTAACATGTA
Found at i:91575 original size:19 final size:20
Alignment explanation
Indices: 91551--91601 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
91541 AATGACCAAT
91551 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
91570 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
91590 AAAATCGCAACG
1 AAAATCGCAACG
91602 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:91595 original size:20 final size:20
Alignment explanation
Indices: 91551--91888 Score: 214
Period size: 20 Copynumber: 16.6 Consensus size: 20
91541 AATGACCAAT
* *
91551 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
91570 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
91590 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
91610 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
91630 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
91651 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
91674 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
91694 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
91714 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
91734 AGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
91757 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
91777 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
91797 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
91817 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
91837 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
91857 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
91877 AAAATCGCAACG
1 AAAATCGCAACG
91889 TTAAAAAGAA
Statistics
Matches: 262, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.06
20 202 0.77
21 14 0.05
23 29 0.11
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:91729 original size:40 final size:40
Alignment explanation
Indices: 91655--91886 Score: 293
Period size: 40 Copynumber: 5.7 Consensus size: 40
91645 GCTTCCAAGT
*
91655 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
91698 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAT
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
91738 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * * * *
91781 TCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
91821 TCGCAACGCGATTGAGAGAATCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
91861 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
91887 CGTTAAAAAG
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
40 112 0.68
41 2 0.01
42 4 0.02
43 47 0.28
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:91764 original size:83 final size:83
Alignment explanation
Indices: 91654--91886 Score: 337
Period size: 83 Copynumber: 2.8 Consensus size: 83
91644 AGCTTCCAAG
* *
91654 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
91719 CGCAATGCGATTGAGAGA
66 CGCAATGCGATTGAGAGA
* * *
91737 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
* *
91802 CGCAATGCGATTTATAGA
66 CGCAATGCGATTGAGAGA
* * * * *
91820 ATCGCAACGCGA-TT-G-AGAGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
91882 CGCAA
66 CGCAA
91887 CGTTAAAAAG
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 45 0.33
81 1 0.01
82 2 0.01
83 87 0.64
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
CGCAATGCGATTGAGAGA
Found at i:91887 original size:40 final size:40
Alignment explanation
Indices: 91551--91888 Score: 265
Period size: 40 Copynumber: 8.3 Consensus size: 40
91541 AATGACCAAT
*
91551 AAAATCGCAACGCGATATCA-A-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TGAGAGAATCGCAACGCGATTTAG
** *** * **
91590 AAAATCGCAACGTTAAAAAGAAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGAT--TTAG
* *
91630 AAAATCGCAACGCGAGCTTCCA-AG-TTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA--TT-GAGAGAATCGCAACGCGATTT---AG
* * * *
91674 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * *
91714 AGAATCGCAATGCGATTGAGAGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTT---AG
* * * * *
91757 AAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * * * *
91797 AGAATCGCAATGCGATTTATAGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
*
91837 AGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
91877 AAAATCGCAACG
1 AAAATCGCAACG
91889 TTAAAAAGAA
Statistics
Matches: 239, Mismatches: 43, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.01
39 15 0.06
40 143 0.60
41 9 0.04
42 6 0.03
43 48 0.20
44 16 0.07
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
Found at i:91898 original size:20 final size:20
Alignment explanation
Indices: 91875--91918 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
91865 AACGCGATTT
*
91875 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
91895 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
91915 AGAA
1 AGAA
91919 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:91908 original size:60 final size:60
Alignment explanation
Indices: 91655--91888 Score: 243
Period size: 60 Copynumber: 3.8 Consensus size: 60
91645 GCTTCCAAGT
* * * * * * * * *
91655 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAACGCGAATGAGAGAA
* * * *
91718 TCGCAATGCGATTGAGAGATTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTGAGAGAATCGCAACGCGATTT---AGAAAATCGCAACGCGAATGAGAGAA
* * * * * *
91781 TCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGCGAATGAGAGAA
91841 TCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACG
1 TCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACG
91889 TTAAAAAGAA
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
60 81 0.55
61 1 0.01
62 2 0.01
63 62 0.42
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (60 bp):
TCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGCGAATGAGAGAA
Found at i:92007 original size:6 final size:6
Alignment explanation
Indices: 91996--92068 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
91986 GACACGTATT
91996 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
92044 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
92069 GACGAGACGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:92760 original size:6 final size:6
Alignment explanation
Indices: 92751--92825 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
92741 CGCCGTCTCG
92751 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
92799 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
92826 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:92927 original size:20 final size:20
Alignment explanation
Indices: 92902--92941 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
92892 TTTTTAACTA
*
92902 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
92922 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
92942 ATCTAAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:92955 original size:20 final size:20
Alignment explanation
Indices: 92932--93165 Score: 279
Period size: 20 Copynumber: 11.4 Consensus size: 20
92922 TTCTTTTTAA
* *
92932 CGTTGCGATTATCTAAATCG
1 CGTTGCGATTCTCTCAATCG
92952 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
* * *
92972 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTCAATCG
92992 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
93012 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
*
93032 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTCAATCG
* *
93052 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTCAATCG
*
93075 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
93095 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
93115 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
93135 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTCAATCG
93158 CGTTGCGA
1 CGTTGCGA
93166 ACTTGGAAGC
Statistics
Matches: 187, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
20 151 0.81
21 2 0.01
22 6 0.03
23 28 0.15
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTCAATCG
Found at i:92978 original size:40 final size:40
Alignment explanation
Indices: 92934--93165 Score: 320
Period size: 40 Copynumber: 5.7 Consensus size: 40
92924 CTTTTTAACG
*
92934 TTGCGATTATCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
92974 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCG
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
93014 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
93054 TTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
1 TTGCGA--TTC-TCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
93097 TTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
93137 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCGTTGCGA
93166 ACTTGGAAGC
Statistics
Matches: 168, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
40 111 0.66
41 3 0.02
42 6 0.04
43 48 0.29
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:93103 original size:83 final size:83
Alignment explanation
Indices: 92934--93166 Score: 364
Period size: 83 Copynumber: 2.8 Consensus size: 83
92924 CTTTTTAACG
* * *
92934 TTGCGATTATCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGA--TTC-TATAAATCGCGTT
1 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
* *
92996 GCGATTCTCTCAATCGCG
66 GCGAATCTCTCAATCGCA
*
93014 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
93079 GCGAATCTCTCAATCGCA
66 GCGAATCTCTCAATCGCA
* * *
93097 TTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
93162 GCGAA
66 GCGAA
93167 CTTGGAAGCT
Statistics
Matches: 140, Mismatches: 10, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
80 43 0.31
82 3 0.02
83 94 0.67
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
GCGAATCTCTCAATCGCA
Found at i:93204 original size:20 final size:20
Alignment explanation
Indices: 93179--93252 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
93169 TGGAAGCTCG
93179 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
93199 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
*
93219 CGTTGCGATTTTCTTTTTTA-
1 CGTTGCGATTTTC-TTTTGAC
93239 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
93253 AAATCGCAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 1 0.02
20 46 0.88
21 5 0.10
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAC
Found at i:93379 original size:2 final size:2
Alignment explanation
Indices: 93372--93414 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
93362 CGATTTTCTC
93372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93414 A
1 A
93415 GTTATTCGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94407 original size:2 final size:2
Alignment explanation
Indices: 94400--94431 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
94390 GACATTAGAC
94400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94432 TGATTTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94799 original size:17 final size:17
Alignment explanation
Indices: 94777--94813 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
94767 TCATTTAGCT
94777 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
94794 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
94811 TTC
1 TTC
94814 TGTTGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCACATTAATCTATAC
Found at i:95974 original size:10 final size:10
Alignment explanation
Indices: 95941--95974 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
95931 AACGAAAGTT
95941 TTTTATTCGA
1 TTTTATTCGA
*
95951 TTTGATTCGA
1 TTTTATTCGA
*
95961 TTTTATTGGA
1 TTTTATTCGA
95971 TTTT
1 TTTT
95975 GTGATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (10 bp):
TTTTATTCGA
Found at i:97656 original size:136 final size:131
Alignment explanation
Indices: 97402--97753 Score: 341
Period size: 136 Copynumber: 2.6 Consensus size: 131
97392 TTCCATTGTC
* * **
97402 CTTTACGCCTTTGCCTTAGATGGGGATTTGATACGTTA-GAACTGTAACAGACTGTAATTTCCCA
1 CTTTACGCCTTTGCCTTAGATGGGGATTTGATATG-GAGGAACTGTAACAGACTAAAATTTCCCA
* * * * *
97466 TGATTTTCAATAATTTGTGAATGCATTATGGCAGACCTCTGAAGTAGGATTTATCGGTTTC-ATG
65 TGATTTTCAATAATTTGTGAAGGCACTATGGCAGACATCTGAAGTAGGAATTATCAG-TTCGATG
97530 TTG
129 TTG
* *
97533 CTTTATGCCTTTGCCTTAGATGGGGATTTGATATGGAGGAACTGCCCCGTAATAGACTAAAATTT
1 CTTTACGCCTTTGCCTTAGATGGGGATTTGATATGGAGGAACT-----GTAACAGACTAAAATTT
* * * * *
97598 CCCTTGATTTTCAATGATTTGTGAAGGCACTATGGCAGACATTTTAAGTTGGAATTATCAGTTCG
61 CCCATGATTTTCAATAATTTGTGAAGGCACTATGGCAGACATCTGAAGTAGGAATTATCAGTTCG
* *
97663 GTTTTG
126 ATGTTG
* * * * * * * ** *
97669 CTTTACACCTTTGCCTTAAATGGGGATTTAAT-TGGGAGGAACTCTAATAAACTATAGGTTCCTA
1 CTTTACGCCTTTGCCTTAGATGGGGATTTGATAT-GGAGGAACTGTAACAGACTAAAATTTCCCA
* *
97733 TGCTTTTTAATAATTTGTGAA
65 TGATTTTCAATAATTTGTGAA
97754 TGCCCTGTGG
Statistics
Matches: 181, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
130 1 0.01
131 70 0.39
135 4 0.02
136 106 0.59
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (131 bp):
CTTTACGCCTTTGCCTTAGATGGGGATTTGATATGGAGGAACTGTAACAGACTAAAATTTCCCAT
GATTTTCAATAATTTGTGAAGGCACTATGGCAGACATCTGAAGTAGGAATTATCAGTTCGATGTT
G
Found at i:109755 original size:2 final size:2
Alignment explanation
Indices: 109748--109778 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
109738 TTCTTCAGAA
*
109748 AT AT AT AT AT AT GT 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 A
109779 GATAGATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122785 original size:6 final size:6
Alignment explanation
Indices: 122776--122803 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
122766 CAAAGTTTTC
122776 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
122804 AAGATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:134538 original size:9 final size:9
Alignment explanation
Indices: 134516--134550 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
134506 AACCATAAAA
*
134516 GAAAAAAAT
1 GAAAAAATT
*
134525 AAAAAAATT
1 GAAAAAATT
134534 GAAAAAATT
1 GAAAAAATT
134543 GAAAAAAT
1 GAAAAAAT
134551 GGGTGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (9 bp):
GAAAAAATT
Done.