Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005601.1 Hibiscus syriacus cultivar Beakdansim tig00013029_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: 92345
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4408 original size:128 final size:129
Alignment explanation
Indices: 4206--4451 Score: 395
Period size: 128 Copynumber: 1.9 Consensus size: 129
4196 TAATTTCTTC
*
4206 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGGGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGGGTTAACACATGTCAGAT
** *
4271 CCTGGTTAAATAATTAATTTATT-AATTTTATTTAATTTAGGACCAAATTGATAGCATATATAA
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAA
* * * * *
4334 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGTTAACACATGTCATAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGGGTTAACACATGTCAGAT
*
4399 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
4452 TATATAAATA
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 79 0.74
129 28 0.26
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (129 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGGGTTAACACATGTCAGAT
CCTAATTAAATAATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAA
Found at i:4886 original size:35 final size:35
Alignment explanation
Indices: 4836--4911 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
4826 AATCTGACAT
* *
4836 AATTGAATTATTTTGGAATTTAAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
**
4871 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
4906 AATTGA
1 AATTGA
4912 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAAGGTTTAGAATGA
Found at i:14250 original size:29 final size:29
Alignment explanation
Indices: 14217--14272 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
14207 TCTTTTTTCA
*
14217 AGTTTAGTATCTAATGTTT-ATTTCGTTTT
1 AGTTTAGTAT-TAATGTTTCATTCCGTTTT
* *
14246 AGTTTTGTGTTAATGTTTCATTCCGTT
1 AGTTTAGTATTAATGTTTCATTCCGTT
14273 ACTCAAACGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (29 bp):
AGTTTAGTATTAATGTTTCATTCCGTTTT
Found at i:19236 original size:2 final size:2
Alignment explanation
Indices: 19229--19265 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19219 TAGATGGACT
19229 TA TA TA TA 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 TA TA TA TA T
19266 CCATTCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20046 original size:31 final size:31
Alignment explanation
Indices: 20010--20068 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
20000 AACTTAAAAG
* *
20010 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
20041 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
20069 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:20119 original size:22 final size:22
Alignment explanation
Indices: 20093--20135 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20083 TAATAAATTA
20093 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
20115 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20136 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20144 original size:22 final size:22
Alignment explanation
Indices: 20095--20143 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
20085 ATAAATTATT
**
20095 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
20117 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20140 TAAA
1 TAAA
20144 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20147 original size:54 final size:54
Alignment explanation
Indices: 20083--20541 Score: 453
Period size: 54 Copynumber: 8.5 Consensus size: 54
20073 ACAACTACAA
20083 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
20137 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * * *
20197 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAATCTATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
20249 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** ** * ** * **
20297 AAATAAATTATTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** *
20352 -AATCCA-TATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
20405 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
20459 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
20513 TAATAAATTATTTAAAATAAATCAATCCA
1 TAATAAATTATTTAAAATAAATCAATCCA
20542 CACAACTACA
Statistics
Matches: 331, Mismatches: 46, Indels: 56
0.76 0.11 0.13
Matches are distributed among these distances:
43 2 0.01
44 6 0.02
47 3 0.01
48 24 0.07
49 4 0.01
50 4 0.01
52 6 0.02
53 11 0.03
54 210 0.63
55 14 0.04
56 6 0.02
57 4 0.01
58 16 0.05
59 1 0.00
60 1 0.00
62 13 0.04
63 6 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:20188 original size:80 final size:83
Alignment explanation
Indices: 20083--20485 Score: 509
Period size: 80 Copynumber: 4.9 Consensus size: 83
20073 ACAACTACAA
20083 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
20148 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
* *
20169 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
20230 AAAATAAATCAATCTATAC
65 AAAATAAATCAATCCATAC
* *
20249 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
**
20310 AAAATAAATCAATATATAC
65 AAAATAAATCAATCCATAC
20329 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT---T-C--AT--A-T-T
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
20384 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
*
20405 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
20470 TTAAAATAAATCAATC
63 TTAAAATAAATCAATC
20486 AATATTTTAA
Statistics
Matches: 289, Mismatches: 10, Indels: 36
0.86 0.03 0.11
Matches are distributed among these distances:
76 67 0.23
77 1 0.00
78 1 0.00
79 1 0.00
80 152 0.53
81 2 0.01
82 5 0.02
83 1 0.00
84 3 0.01
85 3 0.01
86 53 0.18
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (83 bp):
TAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
AAATAAATCAATCCATAC
Found at i:20314 original size:14 final size:14
Alignment explanation
Indices: 20297--20350 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
20287 CAATCCATAC
20297 AAATAAATTATTTA
1 AAATAAATTATTTA
*
20311 AAATAAATCAATATATA
1 AAATAAAT---TATTTA
*
20328 CTAATAAATTATTTA
1 -AAATAAATTATTTA
20343 AAATAAAT
1 AAATAAAT
20351 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:20405 original size:76 final size:76
Alignment explanation
Indices: 20307--20457 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 76
20297 AAATAAATTA
*
20307 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
20372 TCAATTCATAT
66 TCAATCCATAT
* *
20383 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
20448 TCAATCCATA
66 TCAATCCATA
20458 CTAATAAATT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (76 bp):
TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATAT
Found at i:20412 original size:22 final size:22
Alignment explanation
Indices: 20339--20403 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
20329 TAATAAATTA
20339 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
20361 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
20383 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20404 CTAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20414 original size:108 final size:107
Alignment explanation
Indices: 20195--20677 Score: 418
Period size: 108 Copynumber: 4.5 Consensus size: 107
20185 CAATCCATAT
* * **
20195 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAA
1 TTTAAAATAAATCAATT-ATACTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AA
* *
20260 TAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
61 TAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA
20307 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAAT-TATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
20372 TCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA
65 TCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA
** * ** * ** **
20415 TTTAAAATAAATCAATTCATA-TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAAT
1 TTTAAAATAAATCAATT-ATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAAT
20477 AAATCAA-TCAATATTTTAAAATAAATCAATCCATACTAATAAATTA
62 AAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTA
* * *
20523 TTTAAAATAAATCAATCCACAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAAT-TATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
* * ** * ** * ** **
20581 ATTAATACATACTAATAAATTATGTAAAATAAAT-C-AATCTA-TA
64 ATCAATTCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA
* *
20624 TCTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA
1 T-TTAAAATAAATCAAT-TATACTAATAAATTATTTAAAATAAATCAATCCATA
20678 CTAATAAATT
Statistics
Matches: 310, Mismatches: 40, Indels: 46
0.78 0.10 0.12
Matches are distributed among these distances:
101 3 0.01
102 49 0.16
103 14 0.05
104 11 0.04
105 1 0.00
106 6 0.02
107 14 0.05
108 155 0.50
109 7 0.02
112 49 0.16
113 1 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (107 bp):
TTTAAAATAAATCAATTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
CAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:20441 original size:22 final size:22
Alignment explanation
Indices: 20415--20457 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20405 TAATAAATTA
*
20415 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
20437 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20458 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20466 original size:22 final size:22
Alignment explanation
Indices: 20417--20465 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20407 ATAAATTATT
* **
20417 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
20439 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20462 TAAA
1 TAAA
20466 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20520 original size:22 final size:22
Alignment explanation
Indices: 20471--20519 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20461 ATAAATTATT
**
20471 TAAAATAAATCAATCAATATTT
1 TAAAATAAATCAATCAATATAA
*
20493 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCAATA-TAA
20516 TAAA
1 TAAA
20520 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:20632 original size:188 final size:188
Alignment explanation
Indices: 20083--20672 Score: 827
Period size: 188 Copynumber: 3.1 Consensus size: 188
20073 ACAACTACAA
*
20083 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
20148 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATAC
* *
20213 ATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATA-
131 ATACTAATAAATTATTTAAAATAAATCAATCTAT--ATCT-TAA-AATAAATCAATCCATAC
** * ** * ** * **
20274 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATATATACTAATAAAT
1 TAATAAATTATTTAAAATAAAT-C-AATCAATAT-TTTAAAATAAATCAATCCATACTAATAAAT
* * ** *
20337 TATTTAAAATAAATCAAT-C-CA-TATTTTAA-AATAAATCAATTCATATTTTAAAATAAATCAA
63 TATTTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
* *
20398 TCCATACTAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAATCCATAC
128 TACATACTAATAAATTATTTAAAATAAATCAATCT-ATATCTTAAAATAAATCAATCCATAC
20459 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
20524 TTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATTAATAC
66 TTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATAC
*
20589 ATACTAATAAATTATGTAAAATAAATCAATCTATATCTTAAAATAAATCAATCCATAC
131 ATACTAATAAATTATTTAAAATAAATCAATCTATATCTTAAAATAAATCAATCCATAC
20647 TAATAAATTATTTAAAATAAATCAAT
1 TAATAAATTATTTAAAATAAATCAAT
20673 TCATACTAAT
Statistics
Matches: 345, Mismatches: 42, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
184 68 0.20
185 13 0.04
186 9 0.03
187 5 0.01
188 177 0.51
189 5 0.01
190 6 0.02
191 11 0.03
192 51 0.15
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (188 bp):
TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATAC
ATACTAATAAATTATTTAAAATAAATCAATCTATATCTTAAAATAAATCAATCCATAC
Found at i:20636 original size:54 final size:54
Alignment explanation
Indices: 20554--20677 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
20544 CAACTACAAT
* *
20554 AATAAATCAATCCATATTTTAAAATAAATTAATACATACTAATAAATTATGTAA
1 AATAAATCAATCCATATCTTAAAATAAATCAATACATACTAATAAATTATGTAA
* * *
20608 AATAAATCAATCTATATCTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATCTTAAAATAAATCAATACATACTAATAAATTATGTAA
*
20662 AATAAATCAATTCATA
1 AATAAATCAATCCATA
20678 CTAATAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATCTTAAAATAAATCAATACATACTAATAAATTATGTAA
Found at i:20654 original size:22 final size:22
Alignment explanation
Indices: 20606--20654 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
20596 TAAATTATGT
* *
20606 AAAATAAATCAATCTATATCTT
1 AAAATAAATCAATCCATATCTA
20628 AAAATAAATCAATCCATA-CTA
1 AAAATAAATCAATCCATATCTA
20649 ATAAAT
1 A-AAAT
20655 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAAATCAATCCATATCTA
Found at i:20683 original size:18 final size:18
Alignment explanation
Indices: 20630--20686 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
20620 TATATCTTAA
*
20630 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
20648 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
20662 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
20680 AATAAAT
1 AATAAAT
20687 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:20696 original size:28 final size:29
Alignment explanation
Indices: 20631--20701 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 29
20621 ATATCTTAAA
*
20631 ATAAATCAATCCATACTAATAAATTATTT
1 ATAAATCAATTCATACTAATAAATTATTT
20660 AAAATAAATCAATTCATACTAATAAATTATTT
1 ---ATAAATCAATTCATACTAATAAATTATTT
*
20692 -TAAATAAATT
1 ATAAATCAATT
20702 ATTTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 9 0.24
32 28 0.76
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAATCAATTCATACTAATAAATTATTT
Found at i:20713 original size:15 final size:15
Alignment explanation
Indices: 20648--20797 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
20638 AATCCATACT
20648 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
20662 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
20680 AATAAATTATTTT-A
1 AATAAATTATTTTAA
20694 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
20709 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
20731 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
20746 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
20761 AATAAATTATTTTAA
1 AATAAATTATTTTAA
20776 AATAAATTATTTTAA
1 AATAAATTATTTTAA
20791 AATAAAT
1 AATAAAT
20798 AACCTTATTA
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
14 20 0.18
15 59 0.54
16 2 0.02
17 6 0.05
18 9 0.08
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:27723 original size:20 final size:20
Alignment explanation
Indices: 27687--27725 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27677 TGTTTGAATC
*
27687 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
27707 AAATTAATT-GTAAATTATT
1 AAATTAATTAG-AAATTATT
27726 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:42427 original size:2 final size:2
Alignment explanation
Indices: 42422--42448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42412 TTTTTTTATT
42422 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 T
42449 TCGTCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42493 original size:16 final size:16
Alignment explanation
Indices: 42472--42506 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42462 ATCTTACATA
*
42472 ATTATAATATTTATAT
1 ATTATAATAATTATAT
*
42488 ATTATATTAATTATAT
1 ATTATAATAATTATAT
42504 ATT
1 ATT
42507 TATTACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATAATAATTATAT
Found at i:42522 original size:16 final size:16
Alignment explanation
Indices: 42480--42523 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42470 TAATTATAAT
42480 ATTTATATATTATATTA
1 ATTTATATATT-TATTA
42497 A-TTATATATTTATTA
1 ATTTATATATTTATTA
42512 CATTTAT-TATTT
1 -ATTTATATATTT
42524 GTTTACAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATATATTTATTA
Found at i:43524 original size:14 final size:16
Alignment explanation
Indices: 43505--43540 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43495 TTTGATTTTT
*
43505 ATTTTTT-TATTTAAC
1 ATTTTTTATATATAAC
43520 ATTTTTTATATATAAC
1 ATTTTTTATATATAAC
43536 ATTTT
1 ATTTT
43541 ATCCTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTATATATAAC
Found at i:47323 original size:16 final size:17
Alignment explanation
Indices: 47302--47336 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47292 TTACAAATTA
47302 AAAATATAAT-TATAAT
1 AAAATATAATGTATAAT
*
47318 AAAATATATTGTATAAT
1 AAAATATAATGTATAAT
47335 AA
1 AA
47337 CTCACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAATATAATGTATAAT
Found at i:53645 original size:71 final size:71
Alignment explanation
Indices: 53529--53668 Score: 280
Period size: 71 Copynumber: 2.0 Consensus size: 71
53519 TTTATTGTCA
53529 AATAATTTTATTAATCTCAAATAAAATAATTAAATAAGCTTAGTATAAAGATAAAAGGTTGATCT
1 AATAATTTTATTAATCTCAAATAAAATAATTAAATAAGCTTAGTATAAAGATAAAAGGTTGATCT
53594 GCAGAC
66 GCAGAC
53600 AATAATTTTATTAATCTCAAATAAAATAATTAAATAAGCTTAGTATAAAGATAAAAGGTTGATCT
1 AATAATTTTATTAATCTCAAATAAAATAATTAAATAAGCTTAGTATAAAGATAAAAGGTTGATCT
53665 GCAG
66 GCAG
53669 GGATTTTGGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (71 bp):
AATAATTTTATTAATCTCAAATAAAATAATTAAATAAGCTTAGTATAAAGATAAAAGGTTGATCT
GCAGAC
Found at i:58442 original size:20 final size:20
Alignment explanation
Indices: 58393--58446 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
58383 TACTTTTTAC
58393 TATTATTATTATTTATTTATT
1 TATTATTA-TATTTATTTATT
58414 TATGCTATTATATTATATTT-TT
1 TAT--TATTATATT-TATTTATT
58436 TATTATTATAT
1 TATTATTATAT
58447 ACGTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 9 0.30
23 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATATTTATTTATT
Found at i:58447 original size:17 final size:18
Alignment explanation
Indices: 58395--58447 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
58385 CTTTTTACTA
*
58395 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
58413 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
58435 TTATTATTATATA
1 TTATTATTATATA
58448 CGTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:58522 original size:2 final size:2
Alignment explanation
Indices: 58517--58552 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
58507 TATACTCTAC
58517 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
58553 TATTTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59767 original size:10 final size:10
Alignment explanation
Indices: 59752--59785 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
59742 TTCATTTACC
59752 ATTTATTTTT
1 ATTTATTTTT
59762 ATTTATTTTT
1 ATTTATTTTT
* *
59772 ATCTATTTCT
1 ATTTATTTTT
59782 ATTT
1 ATTT
59786 TACTAACCTT
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:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:69243 original size:48 final size:50
Alignment explanation
Indices: 69172--69266 Score: 131
Period size: 48 Copynumber: 1.9 Consensus size: 50
69162 AATACTTTGC
* * * *
69172 TTAGGATGAAAATCCGAGAGGGCGTCCTAAGTT-AAAAAA-AAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAACGT
*
69220 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAA
69267 GAGGAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 28 0.70
49 6 0.15
50 6 0.15
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (50 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAACGT
Found at i:70196 original size:105 final size:105
Alignment explanation
Indices: 70010--70677 Score: 1266
Period size: 105 Copynumber: 6.4 Consensus size: 105
70000 GGTTTTAGCT
70010 AGAG-CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
70074 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
70114 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
70179 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
70219 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
70284 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
70324 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
70389 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCTAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
*
70429 AGAGCCATTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
70494 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
70534 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
70599 CGAAGGGACCGCTGGTTGTCAACAAACATGTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
*
70639 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
70678 GGAACAATAC
Statistics
Matches: 554, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
104 4 0.01
105 550 0.99
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
Found at i:72831 original size:20 final size:20
Alignment explanation
Indices: 72782--72835 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
72772 TACTTTTTAC
72782 TATTATTATTATTTATTTATT
1 TATTATTA-TATTTATTTATT
72803 TATGCTATTATATTATATTT-TT
1 TAT--TATTATATT-TATTTATT
72825 TATTATTATAT
1 TATTATTATAT
72836 ACGTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 9 0.30
23 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATATTTATTTATT
Found at i:72836 original size:17 final size:18
Alignment explanation
Indices: 72784--72836 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
72774 CTTTTTACTA
*
72784 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
72802 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
72824 TTATTATTATATA
1 TTATTATTATATA
72837 CGTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:72869 original size:12 final size:13
Alignment explanation
Indices: 72847--72872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72837 CGTATATGTA
72847 TTACTTTTTTTTT
1 TTACTTTTTTTTT
72860 TTACTTTTTTTTT
1 TTACTTTTTTTTT
72873 ATATATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (13 bp):
TTACTTTTTTTTT
Found at i:73641 original size:12 final size:12
Alignment explanation
Indices: 73624--73648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73614 ATAATAAACT
73624 AAAAAAATTGAA
1 AAAAAAATTGAA
73636 AAAAAAATTGAA
1 AAAAAAATTGAA
73648 A
1 A
73649 TAATAATAAG
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:74906 original size:19 final size:18
Alignment explanation
Indices: 74884--74919 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
74874 TATATATATA
74884 TATATATATTAATCTTAAT
1 TATATATATTAAT-TTAAT
*
74903 TATATATTTTAATTTAA
1 TATATATATTAATTTAA
74920 GTACAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATTAATTTAAT
Found at i:77419 original size:47 final size:44
Alignment explanation
Indices: 77322--77433 Score: 134
Period size: 47 Copynumber: 2.5 Consensus size: 44
77312 GTAACCATGC
* *
77322 AAATAAGCTTATGAGCTTACGGAATAATGGCAACTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAACTATATAGGAA
* * * * *
77366 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAACTATATAGGAA
77413 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
77434 AGATAAATGG
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 22 0.38
46 1 0.02
47 35 0.60
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAACTATATAGGAA
Found at i:77936 original size:7 final size:7
Alignment explanation
Indices: 77924--77948 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
77914 TCGATTCCCC
77924 CACTGTT
1 CACTGTT
77931 CACTGTT
1 CACTGTT
77938 CACTGTT
1 CACTGTT
77945 CACT
1 CACT
77949 ATTCGGGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.12, T:0.40
Consensus pattern (7 bp):
CACTGTT
Found at i:81298 original size:70 final size:70
Alignment explanation
Indices: 81185--81324 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
81175 CATTTATAAT
81185 CTTTTGAATAAATTTTATCCGGAGGATTTCACGGAAGTTGAAAAGAATGGTTTACGAACAAAATA
1 CTTTTGAATAAATTTTATCCGGAGGATTTCACGGAAGTTGAAAAGAATGGTTTACGAACAAAATA
81250 ACGTC
66 ACGTC
81255 CTTTTGAATAAATTTTATCCGGAGGATTTCACGGAAGTTGAAAAGAATGGTTTACGAACAAAATA
1 CTTTTGAATAAATTTTATCCGGAGGATTTCACGGAAGTTGAAAAGAATGGTTTACGAACAAAATA
81320 ACGTC
66 ACGTC
81325 ATTATGAGGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (70 bp):
CTTTTGAATAAATTTTATCCGGAGGATTTCACGGAAGTTGAAAAGAATGGTTTACGAACAAAATA
ACGTC
Found at i:82942 original size:27 final size:27
Alignment explanation
Indices: 82900--82955 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
82890 ACGGTTGAAA
* *
82900 GATTCATCATCCGATGGATTTAAGATC
1 GATTCATCATCAGATGGATATAAGATC
*
82927 GATTCATCATCAGATGGATATGAGATC
1 GATTCATCATCAGATGGATATAAGATC
82954 GA
1 GA
82956 CTCTAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (27 bp):
GATTCATCATCAGATGGATATAAGATC
Found at i:83043 original size:135 final size:133
Alignment explanation
Indices: 82797--83475 Score: 683
Period size: 135 Copynumber: 5.0 Consensus size: 133
82787 ACTGTTAAAA
* * * *
82797 GATTCATCATCAGATGGATTTGAGATTGTCTCTAACTACATTTAG-TTG-CA-TGTAGTGTGGAA
1 GATTCATCATCAGATGAATTTGAGATCGACTCTAACTACATTTAGCTTGACACTGTAGTGTGGAC
** ** * * *
82859 TGCTGTGTGATTTTCACTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAG
66 TGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGGATTTAAG
82924 ATC
131 ATC
* * *
82927 GATTCATCATCAGATGGATATGAGATCGACTCTAACTTCATTTAGCTTGCACACGTGTAGTGTGG
1 GATTCATCATCAGATGAATTTGAGATCGACTCTAACTACATTTAGCTTG-ACAC-TGTAGTGTGG
* ** *
82992 ACTGCAACGCAATTTTCATTAATAGCATAGTTGAAAGTTCAAAGATCCATCATCTGATGGATTTA
64 ACTGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGGATTTA
83057 AGATC
129 AGATC
* *
83062 GATTCATCATCAGAT-ATATTTGAGATCGACTCTAACTACATTTATCTGTTAGAGCCACATGTAA
1 GATTCATCATCAGATGA-ATTTGAGATCGACTCTAACTACATTTAGC--TT-GA--CAC-TGTAG
* ** * * * *
83126 TGTGGACTTCGGTGCAATTTTCATTAATAGCATAGTTGGCGCTTGAAAGATTCATCATCCGATGG
59 TGTGGACTGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGG
83191 ATTTAAGATC
124 ATTTAAGATC
* *
83201 GATTCATCATCAAATGAATTTTGAGATCGAAC-CTAACTACATTTAGCTTGCACTACTCTAGTGT
1 GATTCATCATCAGATGAA-TTTGAGATCG-ACTCTAACTACATTTAGCTTG-AC-ACTGTAGTGT
* * * * * *
83265 GGACTGCAAGGCATTTTTCATTATTAGCATAGTTTACGGTTCAAGGATCCATCATTCGATGGATT
62 GGACTGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGGATT
83330 TAAGATC
127 TAAGATC
* * * * * * *
83337 GATTCATGATCAGATAAATTTGAGATCGACTCTAACTATATTTATCTGTTAGTGTCACGCGTAAT
1 GATTCATCATCAGATGAATTTGAGATCGACTCTAACTACATTTA---GCT--TGACAC-TGTAGT
* * * * * *
83402 GTGGACTTCAGTGCAA----CATTAATAGCATATTTGACGGTTGAAAGATTCATCATCCAATGGA
60 GTGGACTGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGGA
*
83463 TTTATGATC
125 TTTAAGATC
83472 GATT
1 GATT
83476 ATAGTTGTTT
Statistics
Matches: 454, Mismatches: 72, Indels: 41
0.80 0.13 0.07
Matches are distributed among these distances:
130 41 0.09
131 3 0.01
133 2 0.00
134 2 0.00
135 180 0.40
136 81 0.18
137 6 0.01
138 8 0.02
139 102 0.22
140 27 0.06
141 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (133 bp):
GATTCATCATCAGATGAATTTGAGATCGACTCTAACTACATTTAGCTTGACACTGTAGTGTGGAC
TGCAATGCAATTTTCATTAATAGCATAGTTGACGGTTCAAAGATCCATCATCCGATGGATTTAAG
ATC
Found at i:83221 original size:27 final size:28
Alignment explanation
Indices: 83174--83230 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
83164 GCGCTTGAAA
** *
83174 GATTCATCATCCGATGGA-TTTAAGATC
1 GATTCATCATCAAATGAATTTTAAGATC
*
83201 GATTCATCATCAAATGAATTTTGAGATC
1 GATTCATCATCAAATGAATTTTAAGATC
83229 GA
1 GA
83231 ACCTAACTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (28 bp):
GATTCATCATCAAATGAATTTTAAGATC
Found at i:83318 original size:275 final size:274
Alignment explanation
Indices: 82868--83475 Score: 897
Period size: 275 Copynumber: 2.2 Consensus size: 274
82858 ATGCTGTGTG
*
82868 ATTTTCACTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAGATCGATTCA
1 ATTTTCATTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAGATCGATTCA
* * * *
82933 TCATCAGATGGATATGAGATCGACTCTAACTTCATTTAGCTTGCACACGTGTAGTGTGGACTGCA
66 TCATCAAATGAATATGAGATCGACTCTAACTACATTTAGCTTGCACACGTCTAGTGTGGACTGCA
82998 ACGCAATTTTCATTAATAGCATAGTTGAAAGTTCAAAGATCCATCA-TCTGATGGATTTAAGATC
131 ACGCAATTTTCATTAATAGCATAGTTGAAAGTTCAAAGATCCATCATTC-GATGGATTTAAGATC
* *
83062 GATTCATCATCAGATATATTTGAGATCGACTCTAACTACATTTATCTGTTAGAGCCACATGTAAT
195 GATTCATCATCAGATAAATTTGAGATCGACTCTAACTACATTTATCTGTTAGAGCCACACGTAAT
*
83127 GTGGACTTCGGTGCA
260 GTGGACTTCAGTGCA
* *
83142 ATTTTCATTAATAGCATAGTTGGCGCTTGAAAGATTCATCATCCGATGGATTTAAGATCGATTCA
1 ATTTTCATTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAGATCGATTCA
*
83207 TCATCAAATGAATTTTGAGATCGAAC-CTAACTACATTTAGCTTGCACTAC-TCTAGTGTGGACT
66 TCATCAAATGAA-TATGAGATCG-ACTCTAACTACATTTAGCTTGCAC-ACGTCTAGTGTGGACT
* * * * ** *
83270 GCAAGGCATTTTTCATTATTAGCATAGTTTACGGTTCAAGGATCCATCATTCGATGGATTTAAGA
128 GCAACGCAATTTTCATTAATAGCATAGTTGAAAGTTCAAAGATCCATCATTCGATGGATTTAAGA
* * * * *
83335 TCGATTCATGATCAGATAAATTTGAGATCGACTCTAACTATATTTATCTGTTAGTGTCACGCGTA
193 TCGATTCATCATCAGATAAATTTGAGATCGACTCTAACTACATTTATCTGTTAGAGCCACACGTA
83400 ATGTGGACTTCAGTGCA
258 ATGTGGACTTCAGTGCA
* * *
83417 A----CATTAATAGCATATTTGACGGTTGAAAGATTCATCATCCAATGGATTTATGATCGATT
1 ATTTTCATTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAGATCGATT
83476 ATAGTTGTTT
Statistics
Matches: 302, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
271 53 0.18
274 72 0.24
275 171 0.57
276 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (274 bp):
ATTTTCATTAATAGCATAGTTGACGGTTGAAAGATTCATCATCCGATGGATTTAAGATCGATTCA
TCATCAAATGAATATGAGATCGACTCTAACTACATTTAGCTTGCACACGTCTAGTGTGGACTGCA
ACGCAATTTTCATTAATAGCATAGTTGAAAGTTCAAAGATCCATCATTCGATGGATTTAAGATCG
ATTCATCATCAGATAAATTTGAGATCGACTCTAACTACATTTATCTGTTAGAGCCACACGTAATG
TGGACTTCAGTGCA
Found at i:83701 original size:60 final size:60
Alignment explanation
Indices: 83608--83722 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
83598 AACCCCGTCA
* *
83608 AAGGTATCTTATTCCGATATTGTCTGCACGAAAGTGCCCCGTATATTATAGATGTGTTGT
1 AAGGTATCTTATTCAGATATTGTCTGCACGAAAGTGCCCCGTATATCATAGATGTGTTGT
* *
83668 AAGGTATCTTATTCAGATATTGTCTGCACGAAAGTGCCCTGTCTATCATAGATGT
1 AAGGTATCTTATTCAGATATTGTCTGCACGAAAGTGCCCCGTATATCATAGATGT
83723 CTGGTAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (60 bp):
AAGGTATCTTATTCAGATATTGTCTGCACGAAAGTGCCCCGTATATCATAGATGTGTTGT
Found at i:86734 original size:75 final size:75
Alignment explanation
Indices: 86648--86797 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
86638 AAAATCTTAA
86648 ATCATATTTTTTAACAAAAACATATAAA-CATTTGTCCCTTTAATCAACCAACAACACATTATAA
1 ATCATATTTTTTAACAAAAACATA-AAATCATTTGTCCCTTTAATCAACCAACAACACATTATAA
86712 TACAAATATTT
65 TACAAATATTT
* *
86723 ATCATATTTTTTAACAAAAACATAAAATCATTTGTCTCTTTAATCAACCAACAACACCTTATAAT
1 ATCATATTTTTTAACAAAAACATAAAATCATTTGTCCCTTTAATCAACCAACAACACATTATAAT
86788 ACAAATATTT
66 ACAAATATTT
86798 GAGTTATAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 3 0.04
75 69 0.96
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (75 bp):
ATCATATTTTTTAACAAAAACATAAAATCATTTGTCCCTTTAATCAACCAACAACACATTATAAT
ACAAATATTT
Found at i:87157 original size:30 final size:31
Alignment explanation
Indices: 87109--87191 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
87099 AAAAATGATG
* *
87109 ACATGT-CTAAGTTAACAAAA-AAGATCACCA
1 ACATGTCCCAAGTTTACAAAAGAAGA-CACCA
* *
87139 ACATGTCCCAA-TTTACAAAAGATGACATCA
1 ACATGTCCCAAGTTTACAAAAGAAGACACCA
*
87169 ACATGTCCCAAGTTTACGAAAGA
1 ACATGTCCCAAGTTTACAAAAGA
87192 TGACCGTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 29 0.64
31 16 0.36
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.22
Consensus pattern (31 bp):
ACATGTCCCAAGTTTACAAAAGAAGACACCA
Found at i:87191 original size:31 final size:30
Alignment explanation
Indices: 87137--87195 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
87127 AAAAGATCAC
87137 CAACATGTCCCAATTTACAAAAGATGACAT
1 CAACATGTCCCAATTTACAAAAGATGACAT
*
87167 CAACATGTCCCAAGTTTACGAAAGATGAC
1 CAACATGTCCCAA-TTTACAAAAGATGAC
87196 CGTATGTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (30 bp):
CAACATGTCCCAATTTACAAAAGATGACAT
Found at i:89600 original size:23 final size:24
Alignment explanation
Indices: 89574--89632 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
89564 CACCACAGCT
*
89574 CATATAAA-TGCACCGAAGTGCCA
1 CATAGAAATTGCACCGAAGTGCCA
* *
89597 CATAGAAATTGCACCGTAGTGCCG
1 CATAGAAATTGCACCGAAGTGCCA
*
89621 CGTAG-AATTGCA
1 CATAGAAATTGCA
89633 TCGTAGTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CATAGAAATTGCACCGAAGTGCCA
Found at i:89617 original size:24 final size:24
Alignment explanation
Indices: 89574--89639 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
89564 CACCACAGCT
* *
89574 CATATAAA-TGCACCGAAGTGCCA
1 CATAGAAATTGCACCGTAGTGCCA
*
89597 CATAGAAATTGCACCGTAGTGCCG
1 CATAGAAATTGCACCGTAGTGCCA
* *
89621 CGTAG-AATTGCATCGTAGT
1 CATAGAAATTGCACCGTAGT
89640 ACCATATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CATAGAAATTGCACCGTAGTGCCA
Found at i:89838 original size:103 final size:103
Alignment explanation
Indices: 89659--89979 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
89649 TAATGTCCAT
* * *
89659 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
89724 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
89762 AAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
89827 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
89865 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
89930 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
89968 AAGGACCACATA
1 AAGGACCACATA
89980 GATCCTCGAC
Statistics
Matches: 206, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:91197 original size:21 final size:21
Alignment explanation
Indices: 91157--91197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
91147 ATTTTATTCG
* *
91157 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
91178 CTTGAATGGGTACCGATTCC
1 CTTGAAGGGGTACCGATTCC
91198 TCTAGCCCAG
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:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Done.