Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002130.1 Hibiscus syriacus cultivar Beakdansim tig00004359_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: 74800
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:4065 original size:2 final size:2
Alignment explanation
Indices: 3939--4047 Score: 195
Period size: 2 Copynumber: 55.0 Consensus size: 2
3929 TAGTAGTATC
3939 AT AT GAT AT AT AT AT AT AT -T 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
3981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4022 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
4048 CTAATTCATG
Statistics
Matches: 104, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 100 0.96
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5011 original size:17 final size:18
Alignment explanation
Indices: 4989--5057 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
4979 GATGAATTAT
4989 CAGTGGTCCTTC-GAAAA
1 CAGTGGTCCTTCGGAAAA
* * *
5006 CAGTGGTCATTCGGGACA
1 CAGTGGTCCTTCGGAAAA
* *
5024 TAGTGGTTCTTCGGAACAA
1 CAGTGGTCCTTCGGAA-AA
5043 TCAGTGGTCCTTCGG
1 -CAGTGGTCCTTCGG
5058 GACATAGTGG
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.28
18 15 0.38
19 1 0.03
20 12 0.31
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (18 bp):
CAGTGGTCCTTCGGAAAA
Found at i:5030 original size:18 final size:18
Alignment explanation
Indices: 5007--5074 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
4997 CTTCGAAAAC
5007 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
5025 AGTGGTTC-TTCGGAACAAT
1 AGTGG-TCATTCGGGAC-AT
*
5044 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCATTCGGGACAT
5063 AGTGGTCATTCG
1 AGTGGTCATTCG
5075 AGATAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 23 0.53
19 8 0.19
20 12 0.28
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:5057 original size:38 final size:35
Alignment explanation
Indices: 4990--5075 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 35
4980 ATGAATTATC
4990 AGTGGTCCTTCGAAAACAGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGAAAACAGTGGTCATTCGGGACAT
* *
5025 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTC-GAA-AA-CAGTGGTCATTCGGGACAT
*
5063 AGTGGTCATTCGA
1 AGTGGTCCTTCGA
5076 GATAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 10 0.23
36 3 0.07
37 4 0.09
38 27 0.61
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (35 bp):
AGTGGTCCTTCGAAAACAGTGGTCATTCGGGACAT
Found at i:8580 original size:31 final size:31
Alignment explanation
Indices: 8537--8596 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
8527 AACTTAAAAG
*
8537 AGTTTTGAAATACTGAGATTTAAATAATTTT
1 AGTTTTGAAATACTGAAATTTAAATAATTTT
8568 AGTTTT-ACAATACTGAAATTTAAATAATT
1 AGTTTTGA-AATACTGAAATTTAAATAATT
8597 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTGAAATACTGAAATTTAAATAATTTT
Found at i:9089 original size:20 final size:19
Alignment explanation
Indices: 9041--9089 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
9031 TATTTAAATC
*
9041 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
9061 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
9079 AAAATAATTTA
1 AAAATAATTTA
9090 TATGATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:9117 original size:20 final size:20
Alignment explanation
Indices: 9075--9126 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9065 TTTTAATAAT
* * *
9075 ATATAAAAT-AATTTATATG
1 ATATAAATTAAATATATATA
9094 ATATAAATTAAATATATATA
1 ATATAAATTAAATATATATA
9114 ATATAATATTAAA
1 ATATAA-ATTAAA
9127 AATTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAAATTAAATATATATA
Found at i:9166 original size:64 final size:62
Alignment explanation
Indices: 9098--9252 Score: 226
Period size: 64 Copynumber: 2.5 Consensus size: 62
9088 TATATGATAT
*
9098 AAATTAAATATATATAATATAATATTAAAAATTAATATTTAATTTATTTAGAAAATTATTATTA
1 AAATTAAATATATATAATATAATATTAAAAATTAATATTTAATTTATTTA-AAAAATA-TATTA
*
9162 AAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATATATTA
1 AAATTAAATATATATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATATATTA
9224 AAATTAAA-ATCAATATAATATAA-ATTAAA
1 AAATTAAATAT--ATATAATATAATATTAAA
9253 TATCTATAAT
Statistics
Matches: 84, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
62 15 0.18
63 30 0.36
64 39 0.46
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (62 bp):
AAATTAAATATATATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATATATTA
Found at i:9217 original size:24 final size:28
Alignment explanation
Indices: 9161--9318 Score: 110
Period size: 23 Copynumber: 5.9 Consensus size: 28
9151 AATTATTATT
9161 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
9189 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
* *
9213 AAAA-T-ATAT-TAAAATTAAAATCAATATAA
1 AAAATTAATATCTATAA-TATAAT--AT-TAA
9242 TATAAATTAAATATCTATAATATAATATTAA
1 -A-AAATT-AATATCTATAATATAATATTAA
*
9273 AAAATTAATAT-T-TAAT-T--TATTTA
1 AAAATTAATATCTATAATATAATATTAA
*
9296 AAAATTAATAT-TAAAAT-TAATAT
1 AAAATTAATATCTATAATATAATAT
9319 CTATAATATA
Statistics
Matches: 106, Mismatches: 8, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
22 5 0.05
23 20 0.19
24 13 0.12
25 6 0.06
26 11 0.10
27 2 0.02
28 17 0.16
29 8 0.08
30 2 0.02
31 6 0.06
32 3 0.03
34 9 0.08
35 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:9238 original size:20 final size:20
Alignment explanation
Indices: 9215--9274 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
9205 TTATTTAAAA
9215 AATATATTAAAATTAAAATC
1 AATATATTAAAATTAAAATC
*
9235 AATATAATATAAATTAAATATC
1 AATATATTA-AAATTAAA-ATC
* *
9257 TATA-ATATAATATTAAAA
1 AATATAT-TAAAATTAAAA
9275 AATTAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.27
21 16 0.48
22 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATATTAAAATTAAAATC
Found at i:9255 original size:84 final size:85
Alignment explanation
Indices: 9160--9365 Score: 295
Period size: 84 Copynumber: 2.5 Consensus size: 85
9150 AAATTATTAT
9160 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAT-ATATT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATAATATT
9223 AAAATTAAAATC-AATATAA
66 AAAATTAAAATCTAATATAA
*
9242 TATAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TA-AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATAATAT
*
9307 TAAAATTAATATCTATAATATAA
65 TAAAATTAAAATC--TAATATAA
*
9330 TAAAA--AAATAT-T-TAAT-TTAT-TTAAAAAATTAATATT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATT
9366 AAAATTAATA
Statistics
Matches: 115, Mismatches: 3, Indels: 13
0.88 0.02 0.10
Matches are distributed among these distances:
81 16 0.14
82 5 0.04
83 9 0.08
84 51 0.44
85 22 0.19
87 3 0.03
88 9 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (85 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATAATATT
AAAATTAAAATCTAATATAA
Found at i:9265 original size:147 final size:142
Alignment explanation
Indices: 9089--9427 Score: 467
Period size: 147 Copynumber: 2.3 Consensus size: 142
9079 AAAATAATTT
*
9089 ATATGATATAAATTAAATATATATAATATAATATT-AAAAATTAATATTTAATTTATTTAGAAAA
1 ATATAATATAAATTAAATATATATAATATAATATTAAAAAATTAATATTTAATTTATTTA-AAAA
*
9153 TTATTATTAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAA-
65 TTAATATTAAAATTAATATCTATAATAT-A-A-T-AAAAA--AATATTTAATTTATTTAAAAAAT
9217 T-ATATTAAAATTAAAATC
124 TAATATTAAAATTAAAATC
*
9235 AATATAATATAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAA
1 -ATATAATATAAATTAAATATATATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAA
9300 TTAATATTAAAATTAATATCTATAATATAATAAAAAAATATTTAATTTATTTAAAAAATTAATAT
65 TTAATATTAAAATTAATATCTATAATATAATAAAAAAATATTTAATTTATTTAAAAAATTAATAT
*
9365 TAAAATTAATATC
130 TAAAATTAAAATC
*
9378 -TATAATATAATATTAAA-A-AT-TAATATTTAATTTATTTAAAAATTAATATT
1 ATATAATATAA-ATTAAATATATATAATA--TAA--TATTAAAAAATTAATATT
9428 AAAATTAAAA
Statistics
Matches: 178, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
139 5 0.03
140 1 0.01
141 36 0.20
142 7 0.04
143 38 0.21
144 1 0.01
145 1 0.01
146 1 0.01
147 64 0.36
148 24 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (142 bp):
ATATAATATAAATTAAATATATATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAT
TAATATTAAAATTAATATCTATAATATAATAAAAAAATATTTAATTTATTTAAAAAATTAATATT
AAAATTAAAATC
Found at i:9325 original size:63 final size:61
Alignment explanation
Indices: 9245--9460 Score: 327
Period size: 58 Copynumber: 3.5 Consensus size: 61
9235 AATATAATAT
9245 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
1 AAATT-AATATCTATAATATAATA-T-AAAAATTAATATTTAATTTATTTAAAAATTAATATTA
9309 AAATTAATATCTATAATAT-A-ATAAAAA--AATATTTAATTTATTTAAAAAATTAATATTA
1 AAATTAATATCTATAATATAATATAAAAATTAATATTTAATTTATTT-AAAAATTAATATTA
9367 AAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
1 AAATTAATATCTATAATATAATA-TAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
*
9429 AAATTAAAATC-A-AATATAATATATAAAATTAA
1 AAATTAATATCTATAATATAATATA-AAAATTAA
9461 ATATAAAACC
Statistics
Matches: 144, Mismatches: 1, Indels: 18
0.88 0.01 0.11
Matches are distributed among these distances:
57 16 0.11
58 33 0.23
59 8 0.06
60 19 0.13
61 8 0.06
62 25 0.17
63 30 0.21
64 5 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (61 bp):
AAATTAATATCTATAATATAATATAAAAATTAATATTTAATTTATTTAAAAATTAATATTA
Found at i:9466 original size:12 final size:12
Alignment explanation
Indices: 9416--9468 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
9406 AATTTATTTA
9416 AAAATT-AATATT
1 AAAATTAAATA-T
9428 AAAATTAAA-AT
1 AAAATTAAATAT
*
9439 CAAATATAATATAT
1 AAAAT-TAA-ATAT
9453 AAAATTAAATAT
1 AAAATTAAATAT
9465 AAAA
1 AAAA
9469 CCTCTTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 5 0.14
12 18 0.51
13 6 0.17
14 6 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:9889 original size:32 final size:32
Alignment explanation
Indices: 9832--9892 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
9822 CCTATGTAAC
* *
9832 TGTCCATATGTTCCGAAGAATATAGGTAATCA
1 TGTCCATATGTCCCGAAGAACATAGGTAATCA
9864 TGTCCATATGTCCCGAA-AGACATAGGTAA
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA
9893 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAGAACATAGGTAATCA
Found at i:10989 original size:64 final size:63
Alignment explanation
Indices: 10876--11037 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 63
10866 CCCTTAACAT
* * *
10876 GTGCATCGATGCACTACTCATGCATCGATACACAAATCACCTTCAATGTTTTAATCT-TAAGGGG
1 GTGCATCGATGCACTACTTATGCATCGATACACAAATCACATTCAATGTTTCAAT-TATAA-GGG
* * * * ** * *
10940 GTGCATCGATGCACTCCTTATGCATCGATGCGCTAATTGCATTCGATGTTTCCATTAATAAGGG
1 GTGCATCGATGCACTACTTATGCATCGATACACAAATCACATTCAATGTTTCAATT-ATAAGGG
* * *
11004 ATGCATCGATGCACTTCATATGCATCGATACACA
1 GTGCATCGATGCACTACTTATGCATCGATACACA
11038 CTGAACAATT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
63 1 0.01
64 75 0.95
65 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTATGCATCGATACACAAATCACATTCAATGTTTCAATTATAAGGG
Found at i:21686 original size:15 final size:17
Alignment explanation
Indices: 21658--21690 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
21648 AGAGTTTGGA
21658 TAAAAAATATTAAGTTT
1 TAAAAAATATTAAGTTT
21675 TAAAAAA-A-TAAGTTT
1 TAAAAAATATTAAGTTT
21690 T
1 T
21691 TGATAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TAAAAAATATTAAGTTT
Found at i:23135 original size:22 final size:23
Alignment explanation
Indices: 23110--23154 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
23100 TACATGCGGG
* *
23110 CAAGTATTTTTATATAA-TCCAT
1 CAAGTATTTATATAAAATTCCAT
*
23132 CAAGTGTTTATATAAAATTCCAT
1 CAAGTATTTATATAAAATTCCAT
23155 ATCTTTGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
CAAGTATTTATATAAAATTCCAT
Found at i:26394 original size:12 final size:12
Alignment explanation
Indices: 26349--26396 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
26339 TTCTTATTTT
*
26349 ATTTTCATTTTCC
1 ATTTTCATATT-C
26362 ATTTTCATATTC
1 ATTTTCATATTC
**
26374 ATTCACATATTC
1 ATTTTCATATTC
26386 ATTTTCATATT
1 ATTTTCATATT
26397 TAAAGTTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTCATATTC
Found at i:26470 original size:19 final size:19
Alignment explanation
Indices: 26448--26545 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
26438 TCTGAATCAG
* *
26448 AACTTATTTCCATATTCAT
1 AACTTATTTTCAAATTCAT
*** *
26467 AACTTATTTTCAGGCTCGT
1 AACTTATTTTCAAATTCAT
* * *
26486 AGCTTATTATCAGATTCAT
1 AACTTATTTTCAAATTCAT
*
26505 AGCTTATTTTCAAATTCAT
1 AACTTATTTTCAAATTCAT
*
26524 AGCTTATTTTCAAATTCAT
1 AACTTATTTTCAAATTCAT
26543 AAC
1 AAC
26546 CCAATGCATA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (19 bp):
AACTTATTTTCAAATTCAT
Found at i:31910 original size:12 final size:12
Alignment explanation
Indices: 31880--31923 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
31870 CATTTTCCAC
31880 TTTCATATTCAT
1 TTTCATATTCAT
**
31892 TCACATATTCAT
1 TTTCATATTCAT
31904 TTTCATATTCCAT
1 TTTCATATT-CAT
*
31917 ATTCATA
1 TTTCATA
31924 ATAAATACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:32008 original size:19 final size:19
Alignment explanation
Indices: 31985--32042 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
31975 ATATTTATAA
*
31985 CTTATTTTCAAACTCATAG
1 CTTATTTTCAAATTCATAG
* *
32004 TTTATTGTT-AGATTCATAG
1 CTTATT-TTCAAATTCATAG
32023 CTTATTTTCAAATTCATAG
1 CTTATTTTCAAATTCATAG
32042 C
1 C
32043 CCAATGCATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.06
19 28 0.88
20 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (19 bp):
CTTATTTTCAAATTCATAG
Found at i:33207 original size:23 final size:23
Alignment explanation
Indices: 33181--33249 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
33171 CACCACAGCT
*
33181 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
33204 CGTAGAATTGCACCGGAGTGACG
1 CGTAGAATTGCACCGAAGTGCCA
*
33227 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
33250 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:33436 original size:103 final size:103
Alignment explanation
Indices: 33265--33576 Score: 588
Period size: 103 Copynumber: 3.0 Consensus size: 103
33255 TAATGTCCAT
* * *
33265 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
33330 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33368 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
33433 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33471 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
33536 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33574 AAG
1 AAG
33577 AACCGCGTAG
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:37653 original size:64 final size:64
Alignment explanation
Indices: 37537--37742 Score: 199
Period size: 64 Copynumber: 3.2 Consensus size: 64
37527 ATTCAAGGTG
* * * *
37537 ATGCACCGATGCATCAA-ATCATGCATCGATGCACCTATGAT-TTAATT-GAACATCGAATGCAT
1 ATGCATCGATGCA-CAAGA-CATGCATCGATGCACC-AGGATATT-TTTCAAACATCGAATGCAT
37599 TTC
62 TTC
****
37602 ATGCA-CTGATGCACTCTCCATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCATT
1 ATGCATC-GATGCACAAGACATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCGAATGCATT
*
37664 TG
63 TC
* * *
37666 ATGCATCGATGCACAAGACATGCATCGATGCACCAGGCTATTTTTTAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGACATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
37730 ATGCATCGATGCA
1 ATGCATCGATGCA
37743 TCCTTAGTGC
Statistics
Matches: 118, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
63 6 0.05
64 97 0.82
65 15 0.13
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACAAGACATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
Found at i:43576 original size:24 final size:22
Alignment explanation
Indices: 43548--43628 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 22
43538 CACTTAACAA
43548 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
43572 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
* *
43592 ATGCACCGATGCATGCCTTGAATA
1 -TGCATCGATGCAT-CCTTGAATG
43616 TGCATCGATGCAT
1 TGCATCGATGCAT
43629 AAGACCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 14 0.29
24 16 0.33
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:46357 original size:64 final size:64
Alignment explanation
Indices: 46289--46446 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
46279 GATTTAATTG
* **** *
46289 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTC-GGA-ATATTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGAAGCAC-CAGGATAT-TTTTC
46352 A
64 A
* *
46353 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGAAGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGAAGCACCAGGATATTTTTCA
* *
46417 AACATCGAATGCATTTTATGTATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
46447 TCGTTAGTGC
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.96
65 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGAAGCACCAGGATATTTTTCA
Found at i:48389 original size:23 final size:23
Alignment explanation
Indices: 48363--48431 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
48353 CACCACAGCT
*
48363 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
48386 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
48409 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
48432 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:48620 original size:103 final size:103
Alignment explanation
Indices: 48447--48644 Score: 333
Period size: 103 Copynumber: 1.9 Consensus size: 103
48437 TAATGTCCAT
* * *
48447 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCA
48512 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
48550 AAGGACCACATATCATTCCTTAAGAATTATATACATACGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCA
* *
48615 GACTTCACATATGTTCCAAAGAATACATAT
66 AACTTCACACATGTTCCAAAGAATACATAT
48645 GTAACACCCC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:49419 original size:63 final size:63
Alignment explanation
Indices: 49334--49499 Score: 262
Period size: 63 Copynumber: 2.7 Consensus size: 63
49324 CCGAAGAACC
* * *
49334 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCTATATATCTCAAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACA
* * *
49396 TAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACA
*
49459 TAGGTAATTCTGTCCATATGTTTCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
49500 CCTCGACTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 7 0.07
63 88 0.93
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACA
Found at i:49477 original size:32 final size:32
Alignment explanation
Indices: 49325--49496 Score: 151
Period size: 31 Copynumber: 5.5 Consensus size: 32
49315 CTATAGGTTC
*
49325 CGAAGAACCTAGGTAA-ACTGTCCATATGT-T
1 CGAAGAACATAGGTAATACTGTCCATATGTCT
** * *
49355 CCTTAGAACATAGGT-ATACTGTCTATATATCT
1 -CGAAGAACATAGGTAATACTGTCCATATGTCT
* **
49387 C-AAAAGACATAGGTAATTTTGTCCATATGT-T
1 CGAAGA-ACATAGGTAATACTGTCCATATGTCT
*
49418 CCGTAGAACATAGGT-ATACTGTCCATATGTCT
1 -CGAAGAACATAGGTAATACTGTCCATATGTCT
* *
49450 CGAA-AGACATAGGTAATTCTGTCCATATGTTT
1 CGAAGA-ACATAGGTAATACTGTCCATATGTCT
*
49482 CGTAGAACATAGGTA
1 CGAAGAACATAGGTA
49497 TACCCTCGAC
Statistics
Matches: 112, Mismatches: 19, Indels: 19
0.75 0.13 0.13
Matches are distributed among these distances:
30 4 0.04
31 56 0.50
32 49 0.44
33 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
CGAAGAACATAGGTAATACTGTCCATATGTCT
Found at i:53881 original size:32 final size:31
Alignment explanation
Indices: 53828--53945 Score: 139
Period size: 32 Copynumber: 3.7 Consensus size: 31
53818 GTTCCTTAGA
*
53828 ACATAGGTATACTGTCTATATGTCTCAAAAG
1 ACATAGGTATACTGTCCATATGTCTCAAAAG
* ***
53859 ACATAGGTAATCCTGTCCATATGT-TCCGTAG
1 ACATAGGT-ATACTGTCCATATGTCTCAAAAG
*
53890 AACATAGGTATACTGTCCATATGTCTCGAAAG
1 -ACATAGGTATACTGTCCATATGTCTCAAAAG
*
53922 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
53946 TCCGTAGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 34 0.47
32 39 0.53
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCAAAAG
Found at i:53883 original size:63 final size:63
Alignment explanation
Indices: 53809--53965 Score: 269
Period size: 63 Copynumber: 2.5 Consensus size: 63
53799 CTAGGTAAAA
* *
53809 TGTCCATATGTTCCTTAGAACATAGGTATACTGTCTATATGTCTCAAAAGACATAGGTAATCC
1 TGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATCC
* *
53872 TGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTC
1 TGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATCC
*
53935 TGTCCATATGTTCCGTAGAACATAGATATAC
1 TGTCCATATGTTCCGTAGAACATAGGTATAC
53966 CCTCGACTCT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 89 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAGACATAGGTAATCC
Found at i:53958 original size:32 final size:31
Alignment explanation
Indices: 53772--53965 Score: 171
Period size: 31 Copynumber: 6.2 Consensus size: 31
53762 AAAGATCCTC
* * ** *
53772 GGTA-ACTGTCTATAGGTTCCAAAGAACCTA
1 GGTATACTGTCCATATGTTCCGTAGAACATA
* * *
53802 GGTAAAATGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCGTAGAACATA
* ***
53833 GGTATACTGTCTATATGTCTCAAAAG-ACATA
1 GGTATACTGTCCATATGT-TCCGTAGAACATA
*
53864 GGTAATCCTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCGTAGAACATA
*
53896 GGTATACTGTCCATATG-TCTCG-AAAGACATA
1 GGTATACTGTCCATATGTTC-CGTAGA-ACATA
*
53927 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCGTAGAACATA
*
53959 GATATAC
1 GGTATAC
53966 CCTCGACTCT
Statistics
Matches: 132, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
30 8 0.06
31 73 0.55
32 47 0.36
33 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCGTAGAACATA
Found at i:55035 original size:64 final size:64
Alignment explanation
Indices: 54883--55039 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
54873 CAATGAAAGT
* * * ** *
54883 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * *
54947 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
55010 AG
63 AG
55012 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
55040 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 60 0.79
65 15 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:60348 original size:20 final size:19
Alignment explanation
Indices: 60321--60359 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
60311 TCGATATTGA
60321 ACCTTTGGTATCGATACCC
1 ACCTTTGGTATCGATACCC
60340 ACCTATTGGTATCGATACCC
1 ACCT-TTGGTATCGATACCC
60360 TTGACTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
ACCTTTGGTATCGATACCC
Found at i:63237 original size:16 final size:18
Alignment explanation
Indices: 63218--63257 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
63208 AATGTTGAAA
*
63218 ATTAAAAATTA-AAAA-T
1 ATTAAAAATAACAAAATT
63234 ATTAAAAATAACAAAATT
1 ATTAAAAATAACAAAATT
63252 ATTAAA
1 ATTAAA
63258 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTAAAAATAACAAAATT
Found at i:63790 original size:29 final size:29
Alignment explanation
Indices: 63749--63832 Score: 116
Period size: 28 Copynumber: 2.9 Consensus size: 29
63739 TTGGTTCTAG
* *
63749 GTTTAGTGTCTAACGTTTATTTCGTTCCA
1 GTTTGGTGCCTAACGTTTATTTCGTTCCA
*
63778 GTTTGGTGCCTAACG-TTATTTCGTTCTA
1 GTTTGGTGCCTAACGTTTATTTCGTTCCA
*
63806 GTTTGGTGCCTAACGTTTCATTCCGTT
1 GTTTGGTGCCTAACGTTT-ATTTCGTT
63833 ACTCATTTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 27 0.55
29 15 0.31
30 7 0.14
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (29 bp):
GTTTGGTGCCTAACGTTTATTTCGTTCCA
Found at i:63808 original size:28 final size:28
Alignment explanation
Indices: 63742--63822 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 28
63732 TTTGTCTTTG
* *
63742 GTTCTAGGTTTAGTGTCTAACGTTTATTTC
1 GTTCTA-GTTTGGTGCCTAACG-TTATTTC
*
63772 GTTCCAGTTTGGTGCCTAACGTTATTTC
1 GTTCTAGTTTGGTGCCTAACGTTATTTC
63800 GTTCTAGTTTGGTGCCTAACGTT
1 GTTCTAGTTTGGTGCCTAACGTT
63823 TCATTCCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 29 0.62
29 13 0.28
30 5 0.11
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (28 bp):
GTTCTAGTTTGGTGCCTAACGTTATTTC
Found at i:64327 original size:2 final size:2
Alignment explanation
Indices: 64316--64356 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
64306 TTTCTTTTTA
64316 AT AT AT -T AT AT AT AT AT AT AT AT AT -T 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
64356 A
1 A
64357 GTTTTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:64340 original size:19 final size:19
Alignment explanation
Indices: 64316--64356 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
64306 TTTCTTTTTA
64316 ATATATTATATATATATAT
1 ATATATTATATATATATAT
64335 ATATATTATATATATATAT
1 ATATATTATATATATATAT
64354 ATA
1 ATA
64357 GTTTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTATATATATATAT
Found at i:64488 original size:2 final size:2
Alignment explanation
Indices: 64481--64519 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
64471 GTTTTCTTTT
64481 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64520 GTTTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64517 original size:167 final size:161
Alignment explanation
Indices: 64242--64563 Score: 540
Period size: 167 Copynumber: 2.0 Consensus size: 161
64232 AAAAGTGATG
*
64242 ATCAGTATGGGTTAGGAGTTGAAATGGAAGTTTTCGGATTTTTGGTTGATTTCAAAATTTGTGTT
1 ATCAGTATGGGTTAGGAGTTGAAATGGAAGTTTTCGGAATTTTGGTTGATTTCAAAATTTGTGTT
64307 TTCTTTTTAATATATTATATATATATATATATATTATATATATATATATAGTTTTATTTTTTAAA
66 TTC-TTTT-ATATATTATA-ATAT-TATATATATTATATATATATATATAGTTTTA-TTTTTAAA
64372 AATTTAAATAAAATTTTTAAAATTATCAAGATGACA
126 AATTTAAATAAAATTTTTAAAATTATCAAGATGACA
64408 ATCAGTATGGGTTTAGGAGTTGAAATGGAAGTTTTCGGAATTTTGGTTGATTTCAAAATTTGTGT
1 ATCAGTATGGG-TTAGGAGTTGAAATGGAAGTTTTCGGAATTTTGGTTGATTTCAAAATTTGTGT
*
64473 TTTCTTTT-TATATATATATATATTATATATA-TATATATATATATATAGTTTTATTTTTAAAAT
65 TTTCTTTTATATAT-TATA-ATATTATATATATTATATATATATATATAGTTTTATTTTTAAAAA
64536 TTTAAATAAAATTTTTAAAATTATCAAG
128 TTTAAATAAAATTTTTAAAATTATCAAG
64564 TTATGACACG
Statistics
Matches: 152, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
162 37 0.24
163 22 0.14
164 13 0.09
165 9 0.06
166 15 0.10
167 56 0.37
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (161 bp):
ATCAGTATGGGTTAGGAGTTGAAATGGAAGTTTTCGGAATTTTGGTTGATTTCAAAATTTGTGTT
TTCTTTTATATATTATAATATTATATATATTATATATATATATATAGTTTTATTTTTAAAAATTT
AAATAAAATTTTTAAAATTATCAAGATGACA
Found at i:73705 original size:38 final size:38
Alignment explanation
Indices: 73663--73785 Score: 115
Period size: 38 Copynumber: 3.2 Consensus size: 38
73653 AGTATATTTT
73663 TATTTAATTATTTAAAGTATATTTTTAATCAAAATAAG
1 TATTTAATTATTTAAAGTATATTTTTAATCAAAATAAG
* * * * * * ***
73701 TATTTGATTATATAATAAA-TAAATACTTAAAGC-ATATTTT
1 TATTTAATTAT-T--TAAAGTATAT-TTTTAATCAAAATAAG
73741 TATTTAATTATTTAAAGTATATTTTTAATCAAAATAAG
1 TATTTAATTATTTAAAGTATATTTTTAATCAAAATAAG
73779 TATTTAA
1 TATTTAA
73786 AATTATTTTG
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
37 9 0.15
38 24 0.39
39 2 0.03
40 17 0.28
41 9 0.15
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (38 bp):
TATTTAATTATTTAAAGTATATTTTTAATCAAAATAAG
Found at i:73726 original size:78 final size:78
Alignment explanation
Indices: 73628--73783 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
73618 TAAATTTAAG
*
73628 GATTATATAATAAATAAATACTTAAAGTATATTTTTATTTAATTATTTAAAGTATATTTTTAATC
1 GATTATATAATAAATAAATACTTAAAGCATATTTTTATTTAATTATTTAAAGTATATTTTTAATC
73693 AAAATAAGTATTT
66 AAAATAAGTATTT
73706 GATTATATAATAAATAAATACTTAAAGCATATTTTTATTTAATTATTTAAAGTATATTTTTAATC
1 GATTATATAATAAATAAATACTTAAAGCATATTTTTATTTAATTATTTAAAGTATATTTTTAATC
73771 AAAATAAGTATTT
66 AAAATAAGTATTT
73784 AAAATTATTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (78 bp):
GATTATATAATAAATAAATACTTAAAGCATATTTTTATTTAATTATTTAAAGTATATTTTTAATC
AAAATAAGTATTT
Found at i:73745 original size:40 final size:40
Alignment explanation
Indices: 73629--73751 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
73619 AAATTTAAGG
*
73629 ATTATATAATAAATAAATACTTAAAGTATATTTTTATTTA
1 ATTATATAATAAATAAATACTTAAAGCATATTTTTATTTA
* * * * * *** *
73669 ATTAT-T--TAAAGTATAT-TTTTAATCAAAATAAGTATTTG
1 ATTATATAATAAA-TAAATACTTAAAGC-ATATTTTTATTTA
73707 ATTATATAATAAATAAATACTTAAAGCATATTTTTATTTA
1 ATTATATAATAAATAAATACTTAAAGCATATTTTTATTTA
73747 ATTAT
1 ATTAT
73752 TTAAAGTATA
Statistics
Matches: 58, Mismatches: 19, Indels: 12
0.65 0.21 0.13
Matches are distributed among these distances:
37 8 0.14
38 17 0.29
39 2 0.03
40 22 0.38
41 9 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (40 bp):
ATTATATAATAAATAAATACTTAAAGCATATTTTTATTTA
Found at i:74026 original size:28 final size:28
Alignment explanation
Indices: 73939--74033 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 28
73929 AATAAATTAG
* * *
73939 GTACCTATTTTGACATAAAATACTTTATA
1 GTACTTATTTTGACAAAAAATATTTTA-A
73968 -TACTTATTTTGACAAAAAATGATAACTTTAA
1 GTACTTATTTTGACAAAAAAT-AT---TTTAA
73999 GTA-TTATTTTGACCAAAAAATATTTTAA
1 GTACTTATTTTGA-CAAAAAATATTTTAA
74027 GTACTTA
1 GTACTTA
74034 AATGAAAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
28 26 0.46
29 4 0.07
31 12 0.21
32 14 0.25
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (28 bp):
GTACTTATTTTGACAAAAAATATTTTAA
Found at i:74066 original size:60 final size:60
Alignment explanation
Indices: 73935--74067 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 60
73925 TTTGAATAAA
* * **
73935 TTAGGTACCTATTTTGACATAAAATACTTTATATACTTATTTTGACAAAAAATGATAACT
1 TTAGGTACTTATTTTGACAAAAAATACTTTATATACTTATAATGACAAAAAATGATAACT
* *
73995 TTAAGTA-TTATTTTGACCAAAAAATATTTTA-AGTACTTA-AATGA-AAAAGAAT-ATACACT
1 TTAGGTACTTATTTTGA-CAAAAAATACTTTATA-TACTTATAATGACAAAA-AATGATA-ACT
74054 TTAGGTACTTATTT
1 TTAGGTACTTATTT
74068 ACGATATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
58 7 0.11
59 24 0.39
60 30 0.49
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (60 bp):
TTAGGTACTTATTTTGACAAAAAATACTTTATATACTTATAATGACAAAAAATGATAACT
Done.